0:00:00.000052 INFO: Output directory: /home/robbe/ProteoBench_diaPASEF/run_output/alphadia_1.10.4_Again_good_now, cwd: /home/robbe/ProteoBench_diaPASEF.
0:00:00.000157 INFO: User provided config file: config_alphadia110_default.yaml.
0:00:00.000192 INFO: User provided config dict: {}.
0:00:00.013385 PROGRESS:           _      _         ___ ___   _   
0:00:00.013459 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.013489 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.013511 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.013536 PROGRESS:            |_|                           
0:00:00.013560 PROGRESS: 
0:00:00.013580 PROGRESS: version: 1.10.4-dev0
0:00:00.013606 INFO: hostname: thestral
0:00:00.013651 INFO: date: 2025-07-13 20:03:24
0:00:00.013672 INFO: ================ AlphaX Environment ===============
0:00:00.013692 INFO: alphatims       : 1.0.8
0:00:00.013710 INFO: alpharaw        : 0.4.5
0:00:00.013729 INFO: alphabase       : 1.5.0
0:00:00.013746 INFO: alphapeptdeep   : 1.3.0
0:00:00.013764 INFO: directlfq       : 0.2.19
0:00:00.013781 INFO: ===================================================
0:00:00.013800 INFO: ================= Pip Environment =================
0:00:00.070908 INFO: alphatims==1.0.8 click==8.1.8 partd==1.4.2 wget==3.2 torchmetrics==1.4.0.post0 uri-template==1.3.0 directlfq==0.2.19 nvidia-nvjitlink-cu12==12.4.127 lxml==5.3.1 fsspec==2025.3.0 fqdn==1.5.1 jsonref==1.1.0 simplejson==3.20.1 tornado==6.4.2 s3transfer==0.11.4 pythonnet==3.0.3 tqdm==4.67.1 psutil==7.0.0 urllib3==2.3.0 fonttools==4.56.0 arrow==1.3.0 dask==2024.11.2 numpy==1.26.4 tzdata==2025.1 gitdb==4.0.12 contextlib2==21.6.0 future==1.0.0 toolz==1.0.0 monotonic==1.6 argparse==1.4.0 nvidia-cuda-cupti-cu12==12.4.127 numba==0.59.1 importlib_resources==6.5.2 packaging==24.2 SQLAlchemy==2.0.39 typing_extensions==4.12.2 pyarrow==19.0.1 joblib==1.4.2 requests-oauthlib==2.0.0 rdkit==2024.3.3 webcolors==24.11.1 cffi==1.17.1 nvidia-cuda-nvrtc-cu12==12.4.127 protobuf==5.29.3 pyteomics==4.7.5 mpmath==1.3.0 pytz==2025.1 multiprocess==0.70.17 MarkupSafe==3.0.2 pyzstd==0.16.2 six==1.17.0 cycler==0.12.1 charset-normalizer==3.4.1 pyparsing==3.2.1 tenacity==9.0.0 llvmlite==0.42.0 attrs==25.2.0 pip==23.0.1 requests==2.32.3 triton==3.2.0 h5py==3.13.0 oauthlib==3.2.2 zstandard==0.22.0 pyahocorasick==2.1.0 swagger-spec-validator==3.0.4 blinker==1.9.0 pycparser==2.22 alpharaw==0.4.5 regex==2024.11.6 streamlit-aggrid==1.1.1 streamlit==1.43.2 tokenizers==0.19.1 websocket-client==1.8.0 certifi==2025.1.31 narwhals==1.30.0 isoduration==20.11.0 python-dateutil==2.9.0.post0 peptdeep==1.3.0 botocore==1.37.11 locket==1.0.0 referencing==0.36.2 torch==2.6.0 nvidia-cusparse-cu12==12.3.1.170 rocket-fft==0.2.5 lightning-utilities==0.14.0 neptune==1.10.4 importlib_metadata==8.6.1 cloudpickle==3.1.1 clr_loader==0.2.7.post0 setuptools==66.1.1 pandas==2.2.3 dill==0.3.9 jsonschema-specifications==2024.10.1 networkx==3.4.2 transformers==4.40.2 biopython==1.85 filelock==3.17.0 types-python-dateutil==2.9.0.20241206 seaborn==0.13.2 toml==0.10.2 zipp==3.21.0 rfc3339-validator==0.1.4 altair==5.5.0 greenlet==3.1.1 scipy==1.12.0 matplotlib==3.10.1 contourpy==1.3.1 pydeck==0.9.1 threadpoolctl==3.5.0 Jinja2==3.1.6 bravado-core==6.1.1 msgpack==1.1.0 nvidia-nvtx-cu12==12.4.127 nvidia-cusolver-cu12==11.6.1.9 xxhash==3.4.1 safetensors==0.5.3 idna==3.10 cachetools==5.5.2 huggingface-hub==0.29.3 jsonpointer==3.0.0 rpds-py==0.23.1 nvidia-cufft-cu12==11.2.1.3 jsonschema==4.23.0 watchdog==6.0.0 python-decouple==3.8 sympy==1.13.1 boto3==1.37.11 dask-expr==1.1.19 pillow==11.1.0 plotly==6.0.0 nvidia-cublas-cu12==12.4.5.8 nvidia-cudnn-cu12==9.1.0.70 smmap==5.0.2 nvidia-curand-cu12==10.3.5.147 GitPython==3.1.44 progressbar==2.5 PyJWT==2.10.1 kiwisolver==1.4.8 nvidia-cuda-runtime-cu12==12.4.127 scikit-learn==1.6.1 nvidia-nccl-cu12==2.21.5 jmespath==1.0.1 rfc3986-validator==0.1.1 bravado==11.1.0 nvidia-cusparselt-cu12==0.6.2 alphabase==1.5.0 alphadia==1.10.4.dev0 PyYAML==6.0.2
0:00:00.070998 INFO: ===================================================
0:00:00.071038 INFO: Running step 'library'
0:00:00.071164 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:00:00.081591 INFO: loading additional config provided via CLI
0:00:00.081653 INFO: loading additional config provided via CLI parameters
0:00:00.081889 INFO: Updating config with 'user defined'
0:00:00.081973 INFO: Updating config with 'user defined (cli)'
0:00:00.081996 INFO: Updating config with 'multistep search'
0:00:00.082031 INFO: ├──version: 1
0:00:00.082058 INFO: ├──workflow_name: None
0:00:00.082082 INFO: [32;20m├──output_directory: run_output/alphadia_1.10.4_Again_good_now/library [multistep search, default: None][0m
0:00:00.082104 INFO: ├──library_path: None
0:00:00.082124 INFO: ├──raw_paths:
0:00:00.082145 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d [user defined (cli), default: None][0m
0:00:00.082166 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d [user defined (cli), default: None][0m
0:00:00.082184 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d [user defined (cli), default: None][0m
0:00:00.082207 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d [user defined (cli), default: None][0m
0:00:00.082227 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d [user defined (cli), default: None][0m
0:00:00.082245 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d [user defined (cli), default: None][0m
0:00:00.082264 INFO: ├──fasta_paths:
0:00:00.082284 INFO: │   [32;20m- ./ProteoBenchFASTA_DDAQuantification.fasta [user defined (cli), default: None][0m
0:00:00.082304 INFO: ├──quant_directory: None
0:00:00.082322 INFO: ├──general
0:00:00.082342 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
0:00:00.082361 INFO: │   ├──transfer_step_enabled: False
0:00:00.082381 INFO: │   ├──mbr_step_enabled: True
0:00:00.082400 INFO: │   ├──reuse_calibration: False
0:00:00.082418 INFO: │   ├──reuse_quant: False
0:00:00.082436 INFO: │   ├──astral_ms1: False
0:00:00.082454 INFO: │   ├──log_level: INFO
0:00:00.082474 INFO: │   ├──mmap_detector_events: False
0:00:00.082492 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
0:00:00.082510 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.082530 INFO: │   ├──save_mbr_library: True
0:00:00.082548 INFO: │   └──save_figures: True
0:00:00.082566 INFO: ├──library_loading
0:00:00.082588 INFO: │   └──rt_heuristic: 180
0:00:00.082607 INFO: ├──library_prediction
0:00:00.082626 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.082646 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.082664 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.082682 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
0:00:00.082701 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.082720 INFO: │   ├──missed_cleavages: 1
0:00:00.082738 INFO: │   ├──precursor_len:
0:00:00.082757 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.082776 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.082794 INFO: │   ├──precursor_charge:
0:00:00.082812 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.082831 INFO: │   │   [32;20m- 4[0m
0:00:00.082850 INFO: │   ├──precursor_mz:
0:00:00.082868 INFO: │   │   [32;20m- 400[0m
0:00:00.082888 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
0:00:00.082906 INFO: │   ├──fragment_mz:
0:00:00.082923 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
0:00:00.082949 INFO: │   │   [32;20m- 2000[0m
0:00:00.082968 INFO: │   ├──nce: 25
0:00:00.082985 INFO: │   ├──fragment_types:
0:00:00.083003 INFO: │   │   [32;20m- b[0m
0:00:00.083031 INFO: │   │   [32;20m- y[0m
0:00:00.083056 INFO: │   ├──max_fragment_charge: 2
0:00:00.083082 INFO: │   [32;20m├──instrument: timsTOF [user defined, default: Lumos][0m
0:00:00.083106 INFO: │   ├──peptdeep_model_path: None
0:00:00.083129 INFO: │   └──peptdeep_model_type: generic
0:00:00.083153 INFO: ├──custom_modifications:
0:00:00.083172 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.083190 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.083210 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.083228 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.083245 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.083264 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.083282 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.083299 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.083319 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.083336 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.083354 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.083371 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.083391 INFO: │   ├──name: Label:13C(12)@K
0:00:00.083408 INFO: │   └──composition: C(12)
0:00:00.083425 INFO: ├──search
0:00:00.083445 INFO: │   [32;20m├──target_ms1_tolerance: 0 [user defined, default: 5][0m
0:00:00.083463 INFO: │   [32;20m├──target_ms2_tolerance: 0 [user defined, default: 10][0m
0:00:00.083482 INFO: │   ├──target_rt_tolerance: 0
0:00:00.083501 INFO: │   ├──target_mobility_tolerance: 0
0:00:00.083519 INFO: │   ├──quant_window: 3
0:00:00.083537 INFO: │   [32;20m├──target_num_candidates: 2 [user defined, default: 3][0m
0:00:00.083555 INFO: │   ├──channel_filter: 
0:00:00.083573 INFO: │   ├──exclude_shared_ions: True
0:00:00.083590 INFO: │   ├──compete_for_fragments: True
0:00:00.083608 INFO: │   ├──quant_all: True
0:00:00.083627 INFO: │   ├──top_k_fragments: 12
0:00:00.083644 INFO: │   ├──experimental_xic: True
0:00:00.083662 INFO: │   └──optimized_peak_group_score: False
0:00:00.083680 INFO: ├──calibration
0:00:00.083699 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 8000][0m
0:00:00.083717 INFO: │   ├──optimization_lock_target: 200
0:00:00.083735 INFO: │   ├──max_steps: 20
0:00:00.083753 INFO: │   ├──min_steps: 2
0:00:00.083770 INFO: │   ├──max_skips: 1
0:00:00.083789 INFO: │   ├──norm_rt_mode: linear
0:00:00.083807 INFO: │   ├──max_fragments: 5000
0:00:00.083828 INFO: │   └──min_correlation: 0.7
0:00:00.083846 INFO: ├──search_initial
0:00:00.083864 INFO: │   ├──initial_num_candidates: 1
0:00:00.083882 INFO: │   ├──initial_ms1_tolerance: 30
0:00:00.083900 INFO: │   ├──initial_ms2_tolerance: 30
0:00:00.083919 INFO: │   ├──initial_mobility_tolerance: 0.1
0:00:00.083938 INFO: │   └──initial_rt_tolerance: 0.5
0:00:00.083956 INFO: ├──selection_config
0:00:00.083976 INFO: │   ├──peak_len_rt: 10.0
0:00:00.083994 INFO: │   ├──sigma_scale_rt: 0.5
0:00:00.084012 INFO: │   ├──peak_len_mobility: 0.01
0:00:00.084031 INFO: │   ├──sigma_scale_mobility: 1.0
0:00:00.084049 INFO: │   ├──top_k_precursors: 3
0:00:00.084067 INFO: │   ├──kernel_size: 30
0:00:00.084086 INFO: │   ├──f_mobility: 1.0
0:00:00.084105 INFO: │   ├──f_rt: 0.99
0:00:00.084124 INFO: │   ├──center_fraction: 0.5
0:00:00.084142 INFO: │   ├──min_size_mobility: 8
0:00:00.084161 INFO: │   ├──min_size_rt: 3
0:00:00.084179 INFO: │   ├──max_size_mobility: 20
0:00:00.084198 INFO: │   ├──max_size_rt: 15
0:00:00.084223 INFO: │   ├──group_channels: False
0:00:00.084241 INFO: │   ├──use_weighted_score: True
0:00:00.084259 INFO: │   ├──join_close_candidates: False
0:00:00.084278 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
0:00:00.084297 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
0:00:00.084314 INFO: ├──scoring_config
0:00:00.084332 INFO: │   ├──score_grouped: False
0:00:00.084350 INFO: │   ├──top_k_isotopes: 3
0:00:00.084367 INFO: │   ├──reference_channel: -1
0:00:00.084385 INFO: │   ├──precursor_mz_tolerance: 10
0:00:00.084403 INFO: │   └──fragment_mz_tolerance: 15
0:00:00.084420 INFO: ├──library_multiplexing
0:00:00.084438 INFO: │   ├──enabled: False
0:00:00.084456 INFO: │   ├──input_channel: 0
0:00:00.084474 INFO: │   └──multiplex_mapping:
0:00:00.084491 INFO: ├──multiplexing
0:00:00.084510 INFO: │   ├──enabled: False
0:00:00.084527 INFO: │   ├──target_channels: 4,8
0:00:00.084544 INFO: │   ├──decoy_channel: 12
0:00:00.084562 INFO: │   ├──reference_channel: 0
0:00:00.084580 INFO: │   └──competetive_scoring: True
0:00:00.084600 INFO: ├──fdr
0:00:00.084621 INFO: │   ├──fdr: 0.01
0:00:00.084639 INFO: │   ├──group_level: proteins
0:00:00.084657 INFO: │   ├──inference_strategy: heuristic
0:00:00.084675 INFO: │   ├──competetive_scoring: True
0:00:00.084693 INFO: │   ├──keep_decoys: False
0:00:00.084710 INFO: │   ├──channel_wise_fdr: False
0:00:00.084728 INFO: │   ├──enable_two_step_classifier: False
0:00:00.084748 INFO: │   ├──two_step_classifier_max_iterations: 5
0:00:00.084765 INFO: │   └──enable_nn_hyperparameter_tuning: False
0:00:00.084783 INFO: ├──search_output
0:00:00.084801 INFO: │   ├──file_format: tsv
0:00:00.084819 INFO: │   ├──peptide_level_lfq: False
0:00:00.084837 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
0:00:00.084855 INFO: │   ├──min_k_fragments: 12
0:00:00.084876 INFO: │   ├──min_correlation: 0.9
0:00:00.084894 INFO: │   ├──num_samples_quadratic: 50
0:00:00.084911 INFO: │   ├──min_nonnan: 3
0:00:00.084929 INFO: │   ├──normalize_lfq: True
0:00:00.084947 INFO: │   └──save_fragment_quant_matrix: False
0:00:00.084964 INFO: ├──optimization
0:00:00.084982 INFO: │   ├──order_of_optimization: None
0:00:00.085001 INFO: │   ├──ms2_error
0:00:00.085019 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.085037 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.085055 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.085073 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.085091 INFO: │   │   ├──try_narrower_values: True
0:00:00.085109 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.085127 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.085146 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.085165 INFO: │   ├──ms1_error
0:00:00.085183 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.085201 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.085219 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.085238 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.085256 INFO: │   │   ├──try_narrower_values: False
0:00:00.085275 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.085294 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.085312 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.085329 INFO: │   ├──mobility_error
0:00:00.085350 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.085368 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.085386 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.085405 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.085428 INFO: │   │   ├──try_narrower_values: False
0:00:00.085446 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.085466 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.085484 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.085502 INFO: │   └──rt_error
0:00:00.085521 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.085540 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.085558 INFO: │       ├──automatic_update_percentile_range: 0.99
0:00:00.085577 INFO: │       ├──automatic_update_factor: 1.1
0:00:00.085595 INFO: │       ├──try_narrower_values: True
0:00:00.085613 INFO: │       ├──maximal_decrease: 0.2
0:00:00.085630 INFO: │       ├──favour_narrower_optimum: True
0:00:00.085649 INFO: │       └──maximum_decrease_from_maximum: 0.1
0:00:00.085666 INFO: ├──optimization_manager
0:00:00.085685 INFO: │   ├──fwhm_rt: 5
0:00:00.085703 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.085721 INFO: │   └──score_cutoff: 0
0:00:00.085737 INFO: ├──transfer_library
0:00:00.085756 INFO: │   ├──enabled: False
0:00:00.085773 INFO: │   ├──fragment_types:
0:00:00.085790 INFO: │   │   [32;20m- b[0m
0:00:00.085807 INFO: │   │   [32;20m- y[0m
0:00:00.085825 INFO: │   ├──max_charge: 2
0:00:00.085843 INFO: │   ├──top_k_samples: 3
0:00:00.085860 INFO: │   ├──norm_delta_max: True
0:00:00.085878 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.085896 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.085913 INFO: └──transfer_learning
0:00:00.085932 INFO:     ├──enabled: False
0:00:00.085950 INFO:     ├──batch_size: 2000
0:00:00.085968 INFO:     ├──max_lr: 0.0001
0:00:00.085985 INFO:     ├──train_fraction: 0.7
0:00:00.086005 INFO:     ├──validation_fraction: 0.2
0:00:00.086023 INFO:     ├──test_fraction: 0.1
0:00:00.086044 INFO:     ├──test_interval: 1
0:00:00.086063 INFO:     ├──lr_patience: 3
0:00:00.086080 INFO:     ├──epochs: 51
0:00:00.086097 INFO:     ├──warmup_epochs: 5
0:00:00.086116 INFO:     ├──nce: 25
0:00:00.086134 INFO:     [32;20m└──instrument: timsTOF [user defined, default: Lumos][0m
0:00:00.090808 INFO: Registering 7 custom modifications
0:00:00.119691 PROGRESS: No library provided. Building library from fasta files.
0:00:00.119773 INFO: Running FastaDigest
0:00:00.979730 INFO: Digesting fasta file
0:00:07.425940 INFO: Adding modifications
0:01:39.153311 INFO: Removing non-canonical amino acids
0:01:44.779927 INFO: Fasta library contains 5,215,079 precursors
0:01:44.780161 PROGRESS: Predicting library properties.
0:01:44.780234 INFO: Running PeptDeepPrediction
0:01:44.780317 INFO: Device set to cpu
0:01:45.691228 INFO: Loading PeptDeep models of type generic
0:01:46.460897 INFO: Predicting RT, MS2 and mobility
0:01:46.461100 INFO: Using multiprocessing with 100 processes ...
0:01:46.835736 INFO: Predicting rt,ms2,mobility ...
0:08:07.945069 INFO: Adding fragment mz information
0:08:08.224587 INFO: Adding fragment intensity information
0:08:08.544902 INFO: Adding precursor information
0:08:08.987109 INFO: Running PrecursorInitializer
0:08:09.016104 INFO: Running AnnotateFasta
0:08:09.186069 INFO: Dropping decoys from input library before annotation
0:08:41.084914 INFO: Running IsotopeGenerator
0:09:02.088087 INFO: Running RTNormalization
0:09:02.088778 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:09:02.088880 INFO: Saving library to run_output/alphadia_1.10.4_Again_good_now/library/speclib.hdf
0:09:36.899697 INFO: Running DecoyGenerator
0:11:54.274807 INFO: Running FlattenLibrary
0:12:25.780668 INFO: Running InitFlatColumns
0:12:26.032921 INFO: Running LogFlatLibraryStats
0:12:26.033089 INFO: ============ Library Stats ============
0:12:26.033144 INFO: Number of precursors: 10,400,392
0:12:27.483696 INFO: 	thereof targets:5,215,079
0:12:27.483878 INFO: 	thereof decoys: 5,185,313
0:12:27.562488 INFO: Number of elution groups: 5,215,079
0:12:27.562638 INFO: 	average size: 1.99
0:12:27.902148 INFO: Number of proteins: 117,993
0:12:27.927414 INFO: Number of channels: 1 ([0])
0:12:27.927602 INFO: Isotopes Distribution for 4 isotopes
0:12:27.927636 INFO: =======================================
0:12:27.936634 INFO: Searching 6 files:
0:12:27.936762 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:12:27.936792 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
0:12:27.936815 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
0:12:27.936838 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
0:12:27.936859 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
0:12:27.936882 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
0:12:27.936905 INFO: Using 1 fasta files:
0:12:27.936931 INFO:   ./ProteoBenchFASTA_DDAQuantification.fasta
0:12:27.936960 INFO: Using library: None
0:12:27.936984 INFO: Saving output to: run_output/alphadia_1.10.4_Again_good_now/library
0:12:27.937024 PROGRESS: Starting Search Workflows
0:12:27.937144 PROGRESS: Loading raw file 1/6: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
0:12:27.937232 INFO: Quantification results path: run_output/alphadia_1.10.4_Again_good_now/library/quant
0:12:27.937311 INFO: Creating folder run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/figures
0:12:27.937971 INFO: Initializing RawFileManager
0:12:27.938113 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:12:27.938176 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:12:27.938228 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:12:28.160660 INFO: Reading 39,128 frames with 2,835,410,867 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:12:35.898010 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d...
0:12:35.903904 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:12:35.916403 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:12:35.916875 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:12:35.917319 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:12:35.920372 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:12:35.942081 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:12:35.942552 INFO: Indexing quadrupole dimension
0:12:36.568810 INFO: Transposing detector events
0:12:50.499125 INFO: Finished transposing data
0:12:50.540745 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:12:50.543263 INFO: RT (min)            : 0.0 - 70.0
0:12:50.543349 INFO: RT duration (sec)   : 4199.9
0:12:50.543388 INFO: RT duration (min)   : 70.0
0:12:50.543423 INFO: Cycle len (scans)   : 9
0:12:50.543456 INFO: Cycle len (sec)     : 0.97
0:12:50.543486 INFO: Number of cycles    : 4347
0:12:50.543519 INFO: MS2 range (m/z)     : 400.0 - 1000.0
0:12:51.884623 INFO: Initializing CalibrationManager
0:12:51.885097 INFO: Loading calibration config
0:12:51.885223 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6'}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6'}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed']}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed']}], 'name': 'precursor'}]
0:12:51.885309 INFO: Calibration group :fragment, found 1 estimator(s)
0:12:51.885442 INFO: Calibration group :precursor, found 3 estimator(s)
0:12:51.885683 INFO: Initializing OptimizationManager
0:12:51.885788 INFO: initial parameter: ms1_error = 30
0:12:51.885841 INFO: initial parameter: ms2_error = 30
0:12:51.885903 INFO: initial parameter: rt_error = 2099.928159
0:12:51.885957 INFO: initial parameter: mobility_error = 0.1
0:12:51.886000 INFO: initial parameter: column_type = library
0:12:51.886041 INFO: initial parameter: num_candidates = 1
0:12:51.886081 INFO: initial parameter: classifier_version = -1
0:12:51.886124 INFO: initial parameter: fwhm_rt = 5
0:12:51.886168 INFO: initial parameter: fwhm_mobility = 0.01
0:12:51.886209 INFO: initial parameter: score_cutoff = 0
0:12:51.886280 INFO: Initializing TimingManager
0:12:51.886351 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
0:12:51.886495 INFO: FDRManager not loaded from disk.
0:12:51.886521 INFO: Initializing FDRManager
0:12:51.886570 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:12:53.222919 PROGRESS: 5,215,079 target precursors potentially observable (0 removed)
0:12:55.833155 PROGRESS: Starting initial search for precursors.
0:12:57.336488 INFO: Starting optimization step 0.
0:12:57.336861 PROGRESS: === Extracting elution groups 0 to 200 ===
0:12:57.336973 PROGRESS: Extracting batch of 398 precursors
0:13:00.225579 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:13:00.225713 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:13:00.225749 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:13:00.225771 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:13:03.744146 INFO: Starting candidate selection
0:14:42.865446 INFO: Starting candidate scoring
0:22:29.581613 INFO: Finished candidate processing
0:22:29.581885 INFO: Collecting candidate features
0:22:30.171050 INFO: Collecting fragment features
0:22:31.995265 INFO: Finished candidate scoring
0:22:31.998125 PROGRESS: === Extracted 335 precursors and 3444 fragments ===
0:22:31.998557 INFO: performing precursor FDR with 47 features
0:22:31.998595 INFO: Decoy channel: -1
0:22:31.998617 INFO: Competetive: True
0:22:31.999851 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:32.557958 INFO: Test AUC: 0.459
0:22:32.558058 INFO: Train AUC: 0.471
0:22:32.558088 INFO: AUC difference: 2.53%
0:22:32.788625 INFO: Resetting torch num_threads to 128
0:22:32.789328 INFO: === FDR correction performed with classifier version -1 ===
0:22:32.789915 PROGRESS: ============================= Precursor FDR =============================
0:22:32.790005 PROGRESS: Total precursors accumulated: 173
0:22:32.790064 PROGRESS: Target precursors: 78 (45.09%)
0:22:32.790115 PROGRESS: Decoy precursors: 95 (54.91%)
0:22:32.790161 PROGRESS: 
0:22:32.790204 PROGRESS: Precursor Summary:
0:22:32.791070 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:22:32.791160 PROGRESS: 
0:22:32.791213 PROGRESS: Protein Summary:
0:22:32.792151 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:22:32.792237 PROGRESS: =========================================================================
0:22:32.854201 INFO: Starting optimization step 1.
0:22:32.854393 PROGRESS: === Extracting elution groups 200 to 600 ===
0:22:32.854464 PROGRESS: Extracting batch of 786 precursors
0:22:32.855536 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:22:32.855583 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:22:32.855618 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:22:32.855649 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:22:32.856660 INFO: Starting candidate selection
0:22:38.564449 INFO: Starting candidate scoring
0:22:38.671108 INFO: Finished candidate processing
0:22:38.671221 INFO: Collecting candidate features
0:22:38.681598 INFO: Collecting fragment features
0:22:38.683946 INFO: Finished candidate scoring
0:22:38.686046 PROGRESS: === Extracted 1049 precursors and 10734 fragments ===
0:22:38.688260 INFO: performing precursor FDR with 47 features
0:22:38.688312 INFO: Decoy channel: -1
0:22:38.688337 INFO: Competetive: True
0:22:38.691458 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:38.703420 INFO: Test AUC: 0.503
0:22:38.703507 INFO: Train AUC: 0.475
0:22:38.703537 INFO: AUC difference: 5.85%
0:22:38.703559 WARNING: AUC difference > 5%. This may indicate overfitting.
0:22:38.887043 INFO: Resetting torch num_threads to 128
0:22:38.887794 INFO: === FDR correction performed with classifier version -1 ===
0:22:38.888467 PROGRESS: ============================= Precursor FDR =============================
0:22:38.888568 PROGRESS: Total precursors accumulated: 538
0:22:38.888648 PROGRESS: Target precursors: 263 (48.88%)
0:22:38.888722 PROGRESS: Decoy precursors: 275 (51.12%)
0:22:38.888789 PROGRESS: 
0:22:38.888853 PROGRESS: Precursor Summary:
0:22:38.889746 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
0:22:38.889845 PROGRESS: 
0:22:38.889919 PROGRESS: Protein Summary:
0:22:38.890913 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
0:22:38.891010 PROGRESS: =========================================================================
0:22:38.957466 INFO: Starting optimization step 2.
0:22:38.957735 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:22:38.957825 PROGRESS: Extracting batch of 1566 precursors
0:22:38.958848 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:22:38.958899 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:22:38.958943 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:22:38.958973 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:22:38.961942 INFO: Starting candidate selection
0:22:48.077545 INFO: Starting candidate scoring
0:22:48.233474 INFO: Finished candidate processing
0:22:48.233578 INFO: Collecting candidate features
0:22:48.241038 WARNING: intensity_correlation has 1 NaNs ( 0.07 % out of 1378)
0:22:48.244014 INFO: Collecting fragment features
0:22:48.246528 INFO: Finished candidate scoring
0:22:48.249035 PROGRESS: === Extracted 2427 precursors and 24383 fragments ===
0:22:48.249902 INFO: performing precursor FDR with 47 features
0:22:48.249943 INFO: Decoy channel: -1
0:22:48.249967 INFO: Competetive: True
0:22:48.252882 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:48.254145 WARNING: dropped 1 target PSMs due to missing features
0:22:48.270585 INFO: Test AUC: 0.513
0:22:48.270649 INFO: Train AUC: 0.478
0:22:48.270678 INFO: AUC difference: 7.47%
0:22:48.270700 WARNING: AUC difference > 5%. This may indicate overfitting.
0:22:48.451504 INFO: Resetting torch num_threads to 128
0:22:48.452286 INFO: === FDR correction performed with classifier version -1 ===
0:22:48.452989 PROGRESS: ============================= Precursor FDR =============================
0:22:48.453078 PROGRESS: Total precursors accumulated: 1,250
0:22:48.453136 PROGRESS: Target precursors: 609 (48.72%)
0:22:48.453187 PROGRESS: Decoy precursors: 641 (51.28%)
0:22:48.453232 PROGRESS: 
0:22:48.453274 PROGRESS: Precursor Summary:
0:22:48.454144 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
0:22:48.454235 PROGRESS: 
0:22:48.454291 PROGRESS: Protein Summary:
0:22:48.455257 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
0:22:48.455346 PROGRESS: =========================================================================
0:22:48.524765 INFO: Starting optimization step 3.
0:22:48.524991 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:22:48.525074 PROGRESS: Extracting batch of 3160 precursors
0:22:48.526224 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:22:48.526271 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:22:48.526300 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:22:48.526323 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:22:48.527291 INFO: Starting candidate selection
0:23:08.820853 INFO: Starting candidate scoring
0:23:09.064740 INFO: Finished candidate processing
0:23:09.064864 INFO: Collecting candidate features
0:23:09.084792 INFO: Collecting fragment features
0:23:09.090338 INFO: Finished candidate scoring
0:23:09.104022 PROGRESS: === Extracted 5188 precursors and 52001 fragments ===
0:23:09.105363 INFO: performing precursor FDR with 47 features
0:23:09.105411 INFO: Decoy channel: -1
0:23:09.105440 INFO: Competetive: True
0:23:09.109966 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:09.111763 WARNING: dropped 1 target PSMs due to missing features
0:23:09.141681 INFO: Test AUC: 0.499
0:23:09.141816 INFO: Train AUC: 0.491
0:23:09.141852 INFO: AUC difference: 1.62%
0:23:09.332624 INFO: Resetting torch num_threads to 128
0:23:09.333757 INFO: === FDR correction performed with classifier version -1 ===
0:23:09.334677 PROGRESS: ============================= Precursor FDR =============================
0:23:09.334769 PROGRESS: Total precursors accumulated: 2,661
0:23:09.334828 PROGRESS: Target precursors: 1,319 (49.57%)
0:23:09.334877 PROGRESS: Decoy precursors: 1,342 (50.43%)
0:23:09.334922 PROGRESS: 
0:23:09.334967 PROGRESS: Precursor Summary:
0:23:09.335844 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:23:09.335937 PROGRESS: 
0:23:09.335996 PROGRESS: Protein Summary:
0:23:09.336924 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:23:09.337008 PROGRESS: =========================================================================
0:23:09.421383 INFO: Starting optimization step 4.
0:23:09.421608 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:23:09.421685 PROGRESS: Extracting batch of 6310 precursors
0:23:09.423410 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:23:09.423456 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:23:09.423489 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:23:09.423510 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:23:09.424404 INFO: Starting candidate selection
0:23:42.161240 INFO: Starting candidate scoring
0:23:42.525642 INFO: Finished candidate processing
0:23:42.525793 INFO: Collecting candidate features
0:23:42.542155 INFO: Collecting fragment features
0:23:42.546939 INFO: Finished candidate scoring
0:23:42.553505 PROGRESS: === Extracted 10688 precursors and 107652 fragments ===
0:23:42.555817 INFO: performing precursor FDR with 47 features
0:23:42.555877 INFO: Decoy channel: -1
0:23:42.555908 INFO: Competetive: True
0:23:42.561398 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:42.563663 WARNING: dropped 1 target PSMs due to missing features
0:23:42.614354 INFO: Test AUC: 0.490
0:23:42.614467 INFO: Train AUC: 0.495
0:23:42.614504 INFO: AUC difference: 1.08%
0:23:42.804665 INFO: Resetting torch num_threads to 128
0:23:42.806067 INFO: === FDR correction performed with classifier version -1 ===
0:23:42.807326 PROGRESS: ============================= Precursor FDR =============================
0:23:42.807433 PROGRESS: Total precursors accumulated: 5,481
0:23:42.807507 PROGRESS: Target precursors: 2,761 (50.37%)
0:23:42.807572 PROGRESS: Decoy precursors: 2,720 (49.63%)
0:23:42.807633 PROGRESS: 
0:23:42.807693 PROGRESS: Precursor Summary:
0:23:42.808589 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:23:42.808684 PROGRESS: 
0:23:42.808752 PROGRESS: Protein Summary:
0:23:42.809708 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:23:42.809802 PROGRESS: =========================================================================
0:23:42.909576 INFO: Starting optimization step 5.
0:23:42.909840 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:23:42.909927 PROGRESS: Extracting batch of 12602 precursors
0:23:42.912434 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:23:42.912486 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:23:42.912523 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:23:42.912551 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:23:42.913399 INFO: Starting candidate selection
0:24:52.483764 INFO: Starting candidate scoring
0:24:53.112008 INFO: Finished candidate processing
0:24:53.112129 INFO: Collecting candidate features
0:24:53.143013 WARNING: intensity_correlation has 1 NaNs ( 0.01 % out of 10994)
0:24:53.146816 INFO: Collecting fragment features
0:24:53.155157 INFO: Finished candidate scoring
0:24:53.187800 PROGRESS: === Extracted 21682 precursors and 217690 fragments ===
0:24:53.191540 INFO: performing precursor FDR with 47 features
0:24:53.191623 INFO: Decoy channel: -1
0:24:53.191648 INFO: Competetive: True
0:24:53.201664 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:53.205677 WARNING: dropped 2 target PSMs due to missing features
0:24:53.484878 INFO: Test AUC: 0.516
0:24:53.485000 INFO: Train AUC: 0.526
0:24:53.485030 INFO: AUC difference: 1.97%
0:24:53.685814 INFO: Resetting torch num_threads to 128
0:24:53.687803 INFO: === FDR correction performed with classifier version -1 ===
0:24:53.689631 PROGRESS: ============================= Precursor FDR =============================
0:24:53.689731 PROGRESS: Total precursors accumulated: 11,115
0:24:53.689791 PROGRESS: Target precursors: 6,030 (54.25%)
0:24:53.689847 PROGRESS: Decoy precursors: 5,085 (45.75%)
0:24:53.689895 PROGRESS: 
0:24:53.689941 PROGRESS: Precursor Summary:
0:24:53.690871 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
0:24:53.690959 PROGRESS: 
0:24:53.691015 PROGRESS: Protein Summary:
0:24:53.692026 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
0:24:53.692116 PROGRESS: =========================================================================
0:24:53.822830 INFO: Starting optimization step 6.
0:24:53.823105 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:24:53.823191 PROGRESS: Extracting batch of 25176 precursors
0:24:53.828735 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:24:53.828794 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:24:53.828827 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:24:53.828851 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:24:53.829769 INFO: Starting candidate selection
0:27:03.455534 INFO: Starting candidate scoring
0:27:04.645510 INFO: Finished candidate processing
0:27:04.645617 INFO: Collecting candidate features
0:27:04.683900 WARNING: intensity_correlation has 4 NaNs ( 0.02 % out of 21920)
0:27:04.684158 WARNING: height_correlation has 2 NaNs ( 0.01 % out of 21920)
0:27:04.687819 INFO: Collecting fragment features
0:27:04.702311 INFO: Finished candidate scoring
0:27:04.752928 PROGRESS: === Extracted 43602 precursors and 436258 fragments ===
0:27:04.760052 INFO: performing precursor FDR with 47 features
0:27:04.760149 INFO: Decoy channel: -1
0:27:04.760174 INFO: Competetive: True
0:27:04.778545 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:04.787177 WARNING: dropped 5 target PSMs due to missing features
0:27:04.787299 WARNING: dropped 2 decoy PSMs due to missing features
0:27:05.454000 INFO: Test AUC: 0.558
0:27:05.454126 INFO: Train AUC: 0.562
0:27:05.454155 INFO: AUC difference: 0.66%
0:27:05.646716 INFO: Resetting torch num_threads to 128
0:27:05.649645 INFO: === FDR correction performed with classifier version -1 ===
0:27:05.653068 PROGRESS: ============================= Precursor FDR =============================
0:27:05.653202 PROGRESS: Total precursors accumulated: 22,365
0:27:05.653261 PROGRESS: Target precursors: 13,025 (58.24%)
0:27:05.653313 PROGRESS: Decoy precursors: 9,340 (41.76%)
0:27:05.653364 PROGRESS: 
0:27:05.653408 PROGRESS: Precursor Summary:
0:27:05.654475 PROGRESS: Channel   0:	 0.05 FDR:    72; 0.01 FDR:    58; 0.001 FDR:    58
0:27:05.654563 PROGRESS: 
0:27:05.654617 PROGRESS: Protein Summary:
0:27:05.655710 PROGRESS: Channel   0:	 0.05 FDR:    72; 0.01 FDR:    58; 0.001 FDR:    58
0:27:05.655799 PROGRESS: =========================================================================
0:27:05.826885 INFO: Starting optimization step 7.
0:27:05.827175 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:27:05.827263 PROGRESS: Extracting batch of 50417 precursors
0:27:05.842148 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:27:05.842271 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:27:05.842325 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:27:05.842350 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:27:05.843179 INFO: Starting candidate selection
0:31:26.090503 INFO: Starting candidate scoring
0:31:28.443402 INFO: Finished candidate processing
0:31:28.443542 INFO: Collecting candidate features
0:31:28.582392 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 44028)
0:31:28.582736 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 44028)
0:31:28.587808 INFO: Collecting fragment features
0:31:28.621177 INFO: Finished candidate scoring
0:31:28.758095 PROGRESS: === Extracted 87630 precursors and 876680 fragments ===
0:31:28.774578 INFO: performing precursor FDR with 47 features
0:31:28.774732 INFO: Decoy channel: -1
0:31:28.774759 INFO: Competetive: True
0:31:28.831156 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:28.857386 WARNING: dropped 6 target PSMs due to missing features
0:31:28.857540 WARNING: dropped 5 decoy PSMs due to missing features
0:31:31.088450 INFO: Test AUC: 0.563
0:31:31.088683 INFO: Train AUC: 0.578
0:31:31.088716 INFO: AUC difference: 2.67%
0:31:31.327204 INFO: Resetting torch num_threads to 128
0:31:31.335509 INFO: === FDR correction performed with classifier version -1 ===
0:31:31.350631 PROGRESS: ============================= Precursor FDR =============================
0:31:31.350905 PROGRESS: Total precursors accumulated: 44,925
0:31:31.350973 PROGRESS: Target precursors: 26,975 (60.04%)
0:31:31.351030 PROGRESS: Decoy precursors: 17,950 (39.96%)
0:31:31.351079 PROGRESS: 
0:31:31.351123 PROGRESS: Precursor Summary:
0:31:31.352504 PROGRESS: Channel   0:	 0.05 FDR:   345; 0.01 FDR:   243; 0.001 FDR:   192
0:31:31.352598 PROGRESS: 
0:31:31.352652 PROGRESS: Protein Summary:
0:31:31.354024 PROGRESS: Channel   0:	 0.05 FDR:   331; 0.01 FDR:   234; 0.001 FDR:   187
0:31:31.354112 PROGRESS: =========================================================================
0:31:31.435558 INFO: fragments_df: keeping 2245 of 876680 [sum(precursor_idx_mask)=2688 sum(mass_error_mask)=876679 stop_rank=2245
0:31:31.686353 INFO: calibration group: precursor, fitting mz estimator 
0:31:31.792721 INFO: calibration group: precursor, fitting rt estimator 
0:31:31.898710 INFO: calibration group: precursor, fitting mobility estimator 
0:31:31.996725 INFO: calibration group: fragment, fitting mz estimator 
0:31:32.251886 INFO: Using score_cutoff 58.24667220611572 (fac=0.99, q=1)
0:31:32.252638 INFO: calibration group: precursor, predicting mz
0:31:32.266979 INFO: calibration group: precursor, predicting rt
0:31:32.330044 INFO: calibration group: precursor, predicting mobility
0:31:32.345542 INFO: calibration group: fragment, predicting mz
0:31:32.467164 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:31:32.467499 INFO: Starting optimization step 8.
0:31:32.467583 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:31:32.467671 PROGRESS: Extracting batch of 100415 precursors
0:31:32.517937 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:31:32.518108 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:31:32.518190 INFO: FWHM in RT is 3.33 seconds, sigma is 0.73
0:31:32.518220 INFO: FWHM in mobility is 0.012 1/K_0, sigma is 5.36
0:31:32.525284 INFO: Starting candidate selection
0:40:20.265557 INFO: Starting candidate scoring
0:40:29.820505 INFO: Finished candidate processing
0:40:29.820883 INFO: Collecting candidate features
0:40:30.370850 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 172734)
0:40:30.371271 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 172734)
0:40:30.380539 INFO: Collecting fragment features
0:40:30.536411 INFO: Finished candidate scoring
0:40:30.699825 PROGRESS: === Extracted 172734 precursors and 1758344 fragments ===
0:40:30.700501 INFO: performing precursor FDR with 47 features
0:40:30.700542 INFO: Decoy channel: -1
0:40:30.700568 INFO: Competetive: True
0:40:30.760354 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:30.794195 WARNING: dropped 1 target PSMs due to missing features
0:40:30.794340 WARNING: dropped 4 decoy PSMs due to missing features
0:40:34.184628 INFO: Test AUC: 0.563
0:40:34.184755 INFO: Train AUC: 0.593
0:40:34.184787 INFO: AUC difference: 5.06%
0:40:34.184811 WARNING: AUC difference > 5%. This may indicate overfitting.
0:40:35.103819 INFO: Resetting torch num_threads to 128
0:40:35.110050 INFO: === FDR correction performed with classifier version 7 ===
0:40:35.119189 PROGRESS: ============================= Precursor FDR =============================
0:40:35.119459 PROGRESS: Total precursors accumulated: 45,881
0:40:35.119526 PROGRESS: Target precursors: 28,933 (63.06%)
0:40:35.119580 PROGRESS: Decoy precursors: 16,948 (36.94%)
0:40:35.119627 PROGRESS: 
0:40:35.119674 PROGRESS: Precursor Summary:
0:40:35.121022 PROGRESS: Channel   0:	 0.05 FDR:   431; 0.01 FDR:   315; 0.001 FDR:   282
0:40:35.121119 PROGRESS: 
0:40:35.121175 PROGRESS: Protein Summary:
0:40:35.122547 PROGRESS: Channel   0:	 0.05 FDR:   411; 0.01 FDR:   303; 0.001 FDR:   270
0:40:35.122637 PROGRESS: =========================================================================
0:40:35.242831 INFO: fragments_df: keeping 3973 of 1758344 [sum(precursor_idx_mask)=6789 sum(mass_error_mask)=1758344 stop_rank=3973
0:40:35.465178 INFO: calibration group: precursor, fitting mz estimator 
0:40:35.599309 INFO: calibration group: precursor, fitting rt estimator 
0:40:35.718552 INFO: calibration group: precursor, fitting mobility estimator 
0:40:35.842204 INFO: calibration group: fragment, fitting mz estimator 
0:40:36.358737 INFO: Using score_cutoff 56.674933305358884 (fac=0.99, q=1)
0:40:36.359187 INFO: calibration group: precursor, predicting mz
0:40:36.372610 INFO: calibration group: precursor, predicting rt
0:40:36.438019 INFO: calibration group: precursor, predicting mobility
0:40:36.457457 INFO: calibration group: fragment, predicting mz
0:40:36.588069 INFO: === checking if optimization conditions were reached ===
0:40:36.588397 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:40:36.591115 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 17.6894.
0:40:36.591177 INFO: ==============================================
0:40:36.591273 INFO: Starting optimization step 9.
0:40:36.591346 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:40:36.591413 PROGRESS: Extracting batch of 100415 precursors
0:40:36.626672 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:40:36.626837 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:40:36.626896 INFO: FWHM in RT is 3.36 seconds, sigma is 0.74
0:40:36.626922 INFO: FWHM in mobility is 0.012 1/K_0, sigma is 5.35
0:40:36.628923 INFO: Starting candidate selection
0:48:52.090951 INFO: Starting candidate scoring
0:48:58.835534 INFO: Finished candidate processing
0:48:58.835682 INFO: Collecting candidate features
0:48:59.177402 WARNING: intensity_correlation has 13 NaNs ( 0.01 % out of 172663)
0:48:59.187793 INFO: Collecting fragment features
0:48:59.295405 INFO: Finished candidate scoring
0:48:59.423984 PROGRESS: === Extracted 172663 precursors and 1713311 fragments ===
0:48:59.424592 INFO: performing precursor FDR with 47 features
0:48:59.424635 INFO: Decoy channel: -1
0:48:59.424665 INFO: Competetive: True
0:48:59.502205 INFO: Setting torch num_threads to 2 for FDR classification task
0:48:59.546304 WARNING: dropped 4 target PSMs due to missing features
0:48:59.546472 WARNING: dropped 9 decoy PSMs due to missing features
0:49:03.336893 INFO: Test AUC: 0.565
0:49:03.337049 INFO: Train AUC: 0.589
0:49:03.337082 INFO: AUC difference: 4.02%
0:49:03.579300 INFO: Resetting torch num_threads to 128
0:49:03.705870 INFO: === FDR correction performed with classifier version 7 ===
0:49:03.718642 PROGRESS: ============================= Precursor FDR =============================
0:49:03.718906 PROGRESS: Total precursors accumulated: 45,836
0:49:03.718976 PROGRESS: Target precursors: 28,656 (62.52%)
0:49:03.719040 PROGRESS: Decoy precursors: 17,180 (37.48%)
0:49:03.719088 PROGRESS: 
0:49:03.719132 PROGRESS: Precursor Summary:
0:49:03.720603 PROGRESS: Channel   0:	 0.05 FDR:   558; 0.01 FDR:   449; 0.001 FDR:   302
0:49:03.720696 PROGRESS: 
0:49:03.720750 PROGRESS: Protein Summary:
0:49:03.722246 PROGRESS: Channel   0:	 0.05 FDR:   526; 0.01 FDR:   426; 0.001 FDR:   291
0:49:03.722348 PROGRESS: =========================================================================
0:49:03.845722 INFO: fragments_df: keeping 5000 of 1713311 [sum(precursor_idx_mask)=9618 sum(mass_error_mask)=1713311 stop_rank=5000
0:49:04.164671 INFO: calibration group: precursor, fitting mz estimator 
0:49:04.291661 INFO: calibration group: precursor, fitting rt estimator 
0:49:04.406890 INFO: calibration group: precursor, fitting mobility estimator 
0:49:04.523008 INFO: calibration group: fragment, fitting mz estimator 
0:49:05.138315 INFO: Using score_cutoff 48.75700255279541 (fac=0.99, q=1)
0:49:05.138965 INFO: calibration group: precursor, predicting mz
0:49:05.146890 INFO: calibration group: precursor, predicting rt
0:49:05.176767 INFO: calibration group: precursor, predicting mobility
0:49:05.183747 INFO: calibration group: fragment, predicting mz
0:49:05.244833 INFO: === checking if optimization conditions were reached ===
0:49:05.245120 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:49:05.247991 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 10.0349.
0:49:05.248049 INFO: ==============================================
0:49:05.248156 INFO: Starting optimization step 10.
0:49:05.248243 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:49:05.248331 PROGRESS: Extracting batch of 49998 precursors
0:49:05.265635 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:49:05.265749 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:49:05.265801 INFO: FWHM in RT is 3.02 seconds, sigma is 0.66
0:49:05.265827 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.67
0:49:05.274756 INFO: Starting candidate selection
0:53:10.816889 INFO: Starting candidate scoring
0:53:13.632802 INFO: Finished candidate processing
0:53:13.632974 INFO: Collecting candidate features
0:53:13.797333 WARNING: intensity_correlation has 8 NaNs ( 0.01 % out of 85886)
0:53:13.803782 INFO: Collecting fragment features
0:53:13.860609 INFO: Finished candidate scoring
0:53:13.913972 PROGRESS: === Extracted 85886 precursors and 819997 fragments ===
0:53:13.914528 INFO: performing precursor FDR with 47 features
0:53:13.914569 INFO: Decoy channel: -1
0:53:13.914594 INFO: Competetive: True
0:53:13.947534 INFO: Setting torch num_threads to 2 for FDR classification task
0:53:13.967357 WARNING: dropped 4 target PSMs due to missing features
0:53:13.967493 WARNING: dropped 4 decoy PSMs due to missing features
0:53:15.430492 INFO: Test AUC: 0.558
0:53:15.430610 INFO: Train AUC: 0.591
0:53:15.430641 INFO: AUC difference: 5.68%
0:53:15.430663 WARNING: AUC difference > 5%. This may indicate overfitting.
0:53:15.637390 INFO: Resetting torch num_threads to 128
0:53:15.641199 INFO: === FDR correction performed with classifier version 7 ===
0:53:15.645506 PROGRESS: ============================= Precursor FDR =============================
0:53:15.645643 PROGRESS: Total precursors accumulated: 22,803
0:53:15.645715 PROGRESS: Target precursors: 14,181 (62.19%)
0:53:15.645767 PROGRESS: Decoy precursors: 8,622 (37.81%)
0:53:15.645813 PROGRESS: 
0:53:15.645856 PROGRESS: Precursor Summary:
0:53:15.646944 PROGRESS: Channel   0:	 0.05 FDR:   249; 0.01 FDR:   116; 0.001 FDR:   116
0:53:15.647043 PROGRESS: 
0:53:15.647099 PROGRESS: Protein Summary:
0:53:15.648248 PROGRESS: Channel   0:	 0.05 FDR:   245; 0.01 FDR:   114; 0.001 FDR:   114
0:53:15.648335 PROGRESS: =========================================================================
0:53:15.836975 INFO: calibration group: precursor, predicting mz
0:53:15.844805 INFO: calibration group: precursor, predicting rt
0:53:15.875015 INFO: calibration group: precursor, predicting mobility
0:53:15.882227 INFO: calibration group: fragment, predicting mz
0:53:15.937630 INFO: === skipping optimization until target number of precursors are found ===
0:53:15.937925 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:53:15.938002 INFO: Starting optimization step 11.
0:53:15.938071 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:53:15.938146 PROGRESS: Extracting batch of 50417 precursors
0:53:15.954289 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:53:15.954406 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:53:15.954460 INFO: FWHM in RT is 3.02 seconds, sigma is 0.66
0:53:15.954486 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.67
0:53:15.957139 INFO: Starting candidate selection
0:57:21.019090 INFO: Starting candidate scoring
0:57:23.555319 INFO: Finished candidate processing
0:57:23.555423 INFO: Collecting candidate features
0:57:23.688467 WARNING: intensity_correlation has 7 NaNs ( 0.01 % out of 86665)
0:57:23.695008 INFO: Collecting fragment features
0:57:23.751763 INFO: Finished candidate scoring
0:57:23.889175 PROGRESS: === Extracted 172551 precursors and 1647152 fragments ===
0:57:23.910532 INFO: performing precursor FDR with 47 features
0:57:23.910665 INFO: Decoy channel: -1
0:57:23.910691 INFO: Competetive: True
0:57:23.985384 INFO: Setting torch num_threads to 2 for FDR classification task
0:57:24.019725 WARNING: dropped 7 target PSMs due to missing features
0:57:24.019854 WARNING: dropped 8 decoy PSMs due to missing features
0:57:26.896333 INFO: Test AUC: 0.563
0:57:26.896465 INFO: Train AUC: 0.588
0:57:26.896494 INFO: AUC difference: 4.21%
0:57:27.133775 INFO: Resetting torch num_threads to 128
0:57:27.141724 INFO: === FDR correction performed with classifier version 7 ===
0:57:27.150396 PROGRESS: ============================= Precursor FDR =============================
0:57:27.150622 PROGRESS: Total precursors accumulated: 45,769
0:57:27.150692 PROGRESS: Target precursors: 28,428 (62.11%)
0:57:27.150741 PROGRESS: Decoy precursors: 17,341 (37.89%)
0:57:27.150786 PROGRESS: 
0:57:27.150829 PROGRESS: Precursor Summary:
0:57:27.152293 PROGRESS: Channel   0:	 0.05 FDR:   645; 0.01 FDR:   501; 0.001 FDR:   356
0:57:27.152398 PROGRESS: 
0:57:27.152453 PROGRESS: Protein Summary:
0:57:27.153977 PROGRESS: Channel   0:	 0.05 FDR:   605; 0.01 FDR:   473; 0.001 FDR:   338
0:57:27.154084 PROGRESS: =========================================================================
0:57:27.271579 INFO: fragments_df: keeping 5000 of 1647152 [sum(precursor_idx_mask)=10563 sum(mass_error_mask)=1647152 stop_rank=5000
0:57:27.428183 INFO: calibration group: precursor, fitting mz estimator 
0:57:27.564058 INFO: calibration group: precursor, fitting rt estimator 
0:57:27.696583 INFO: calibration group: precursor, fitting mobility estimator 
0:57:27.830769 INFO: calibration group: fragment, fitting mz estimator 
0:57:28.491191 INFO: Using score_cutoff 44.861301040649415 (fac=0.99, q=1)
0:57:28.491640 INFO: calibration group: precursor, predicting mz
0:57:28.498989 INFO: calibration group: precursor, predicting rt
0:57:28.528980 INFO: calibration group: precursor, predicting mobility
0:57:28.535643 INFO: calibration group: fragment, predicting mz
0:57:28.594333 INFO: === checking if optimization conditions were reached ===
0:57:28.594611 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
0:57:28.597144 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 6.1473.
0:57:28.597202 INFO: ==============================================
0:57:28.597296 INFO: Starting optimization step 12.
0:57:28.597364 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:57:28.597436 PROGRESS: Extracting batch of 49998 precursors
0:57:28.610417 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:57:28.610525 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:57:28.610573 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
0:57:28.610597 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.84
0:57:28.619501 INFO: Starting candidate selection
1:01:25.166498 INFO: Starting candidate scoring
1:01:27.639114 INFO: Finished candidate processing
1:01:27.639279 INFO: Collecting candidate features
1:01:27.795376 WARNING: intensity_correlation has 13 NaNs ( 0.02 % out of 85711)
1:01:27.795698 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 85711)
1:01:27.801920 INFO: Collecting fragment features
1:01:27.859225 INFO: Finished candidate scoring
1:01:27.922436 PROGRESS: === Extracted 85711 precursors and 773133 fragments ===
1:01:27.922922 INFO: performing precursor FDR with 47 features
1:01:27.922963 INFO: Decoy channel: -1
1:01:27.922987 INFO: Competetive: True
1:01:27.952154 INFO: Setting torch num_threads to 2 for FDR classification task
1:01:27.971432 WARNING: dropped 2 target PSMs due to missing features
1:01:27.971574 WARNING: dropped 12 decoy PSMs due to missing features
1:01:29.421597 INFO: Test AUC: 0.548
1:01:29.421731 INFO: Train AUC: 0.595
1:01:29.421762 INFO: AUC difference: 7.78%
1:01:29.421786 WARNING: AUC difference > 5%. This may indicate overfitting.
1:01:29.629585 INFO: Resetting torch num_threads to 128
1:01:29.632936 INFO: === FDR correction performed with classifier version 7 ===
1:01:29.636987 PROGRESS: ============================= Precursor FDR =============================
1:01:29.637127 PROGRESS: Total precursors accumulated: 22,771
1:01:29.637187 PROGRESS: Target precursors: 14,190 (62.32%)
1:01:29.637238 PROGRESS: Decoy precursors: 8,581 (37.68%)
1:01:29.637287 PROGRESS: 
1:01:29.637333 PROGRESS: Precursor Summary:
1:01:29.638397 PROGRESS: Channel   0:	 0.05 FDR:   250; 0.01 FDR:    90; 0.001 FDR:    90
1:01:29.638485 PROGRESS: 
1:01:29.638539 PROGRESS: Protein Summary:
1:01:29.639682 PROGRESS: Channel   0:	 0.05 FDR:   243; 0.01 FDR:    88; 0.001 FDR:    88
1:01:29.639773 PROGRESS: =========================================================================
1:01:29.814501 INFO: calibration group: precursor, predicting mz
1:01:29.822268 INFO: calibration group: precursor, predicting rt
1:01:29.852247 INFO: calibration group: precursor, predicting mobility
1:01:29.858884 INFO: calibration group: fragment, predicting mz
1:01:29.914158 INFO: === skipping optimization until target number of precursors are found ===
1:01:29.915124 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
1:01:29.915210 INFO: Starting optimization step 13.
1:01:29.915290 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1:01:29.915373 PROGRESS: Extracting batch of 50417 precursors
1:01:29.934725 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:01:29.934868 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:01:29.934927 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1:01:29.934955 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.84
1:01:29.956131 INFO: Starting candidate selection
1:05:22.182717 INFO: Starting candidate scoring
1:05:24.204313 INFO: Finished candidate processing
1:05:24.204421 INFO: Collecting candidate features
1:05:24.336371 WARNING: intensity_correlation has 13 NaNs ( 0.02 % out of 86385)
1:05:24.342787 INFO: Collecting fragment features
1:05:24.396697 INFO: Finished candidate scoring
1:05:24.544045 PROGRESS: === Extracted 172096 precursors and 1552381 fragments ===
1:05:24.565582 INFO: performing precursor FDR with 47 features
1:05:24.565734 INFO: Decoy channel: -1
1:05:24.565761 INFO: Competetive: True
1:05:24.636132 INFO: Setting torch num_threads to 2 for FDR classification task
1:05:24.669083 WARNING: dropped 9 target PSMs due to missing features
1:05:24.669229 WARNING: dropped 18 decoy PSMs due to missing features
1:05:27.907254 INFO: Test AUC: 0.557
1:05:27.907387 INFO: Train AUC: 0.587
1:05:27.907418 INFO: AUC difference: 5.24%
1:05:27.907440 WARNING: AUC difference > 5%. This may indicate overfitting.
1:05:28.133434 INFO: Resetting torch num_threads to 128
1:05:28.141264 INFO: === FDR correction performed with classifier version 7 ===
1:05:28.148948 PROGRESS: ============================= Precursor FDR =============================
1:05:28.149135 PROGRESS: Total precursors accumulated: 45,703
1:05:28.149203 PROGRESS: Target precursors: 28,268 (61.85%)
1:05:28.149252 PROGRESS: Decoy precursors: 17,435 (38.15%)
1:05:28.149298 PROGRESS: 
1:05:28.149341 PROGRESS: Precursor Summary:
1:05:28.150753 PROGRESS: Channel   0:	 0.05 FDR:   549; 0.01 FDR:   387; 0.001 FDR:   237
1:05:28.150862 PROGRESS: 
1:05:28.150919 PROGRESS: Protein Summary:
1:05:28.152396 PROGRESS: Channel   0:	 0.05 FDR:   517; 0.01 FDR:   363; 0.001 FDR:   225
1:05:28.152503 PROGRESS: =========================================================================
1:05:28.273885 INFO: fragments_df: keeping 4193 of 1552381 [sum(precursor_idx_mask)=8151 sum(mass_error_mask)=1552381 stop_rank=4193
1:05:28.490706 INFO: calibration group: precursor, fitting mz estimator 
1:05:28.613463 INFO: calibration group: precursor, fitting rt estimator 
1:05:28.744929 INFO: calibration group: precursor, fitting mobility estimator 
1:05:28.855534 INFO: calibration group: fragment, fitting mz estimator 
1:05:29.347624 INFO: Using score_cutoff 42.68052633361817 (fac=0.99, q=1)
1:05:29.348056 INFO: calibration group: precursor, predicting mz
1:05:29.361064 INFO: calibration group: precursor, predicting rt
1:05:29.421145 INFO: calibration group: precursor, predicting mobility
1:05:29.437551 INFO: calibration group: fragment, predicting mz
1:05:29.567453 INFO: === checking if optimization conditions were reached ===
1:05:29.567779 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
1:05:29.570741 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 4.6112.
1:05:29.570805 INFO: ==============================================
1:05:29.570914 INFO: Starting optimization step 14.
1:05:29.570988 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:05:29.571078 PROGRESS: Extracting batch of 100415 precursors
1:05:29.608541 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:05:29.608700 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:05:29.608765 INFO: FWHM in RT is 2.56 seconds, sigma is 0.56
1:05:29.608794 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.07
1:05:29.617600 INFO: Starting candidate selection
1:13:11.049100 INFO: Starting candidate scoring
1:13:14.487250 INFO: Finished candidate processing
1:13:14.487372 INFO: Collecting candidate features
1:13:14.745919 WARNING: intensity_correlation has 86 NaNs ( 0.05 % out of 170782)
1:13:14.756174 INFO: Collecting fragment features
1:13:14.854383 INFO: Finished candidate scoring
1:13:14.959036 PROGRESS: === Extracted 170782 precursors and 1419300 fragments ===
1:13:14.959531 INFO: performing precursor FDR with 47 features
1:13:14.959571 INFO: Decoy channel: -1
1:13:14.959594 INFO: Competetive: True
1:13:15.013662 INFO: Setting torch num_threads to 2 for FDR classification task
1:13:15.048096 WARNING: dropped 37 target PSMs due to missing features
1:13:15.048243 WARNING: dropped 49 decoy PSMs due to missing features
1:13:18.003332 INFO: Test AUC: 0.562
1:13:18.003466 INFO: Train AUC: 0.585
1:13:18.003497 INFO: AUC difference: 3.98%
1:13:18.227291 INFO: Resetting torch num_threads to 128
1:13:18.233033 INFO: === FDR correction performed with classifier version 7 ===
1:13:18.242063 PROGRESS: ============================= Precursor FDR =============================
1:13:18.242307 PROGRESS: Total precursors accumulated: 45,559
1:13:18.242371 PROGRESS: Target precursors: 28,055 (61.58%)
1:13:18.242419 PROGRESS: Decoy precursors: 17,504 (38.42%)
1:13:18.242465 PROGRESS: 
1:13:18.242508 PROGRESS: Precursor Summary:
1:13:18.243865 PROGRESS: Channel   0:	 0.05 FDR:   546; 0.01 FDR:   284; 0.001 FDR:   213
1:13:18.243958 PROGRESS: 
1:13:18.244014 PROGRESS: Protein Summary:
1:13:18.245378 PROGRESS: Channel   0:	 0.05 FDR:   512; 0.01 FDR:   269; 0.001 FDR:   201
1:13:18.245464 PROGRESS: =========================================================================
1:13:18.343686 INFO: fragments_df: keeping 2933 of 1419300 [sum(precursor_idx_mask)=5718 sum(mass_error_mask)=1419300 stop_rank=2933
1:13:18.550273 INFO: calibration group: precursor, fitting mz estimator 
1:13:18.794178 INFO: calibration group: precursor, fitting rt estimator 
1:13:20.285238 INFO: calibration group: precursor, fitting mobility estimator 
1:13:20.399420 INFO: calibration group: fragment, fitting mz estimator 
1:13:20.730219 INFO: Using score_cutoff 46.831459728240965 (fac=0.99, q=1)
1:13:20.730707 INFO: calibration group: precursor, predicting mz
1:13:20.745243 INFO: calibration group: precursor, predicting rt
1:13:20.811898 INFO: calibration group: precursor, predicting mobility
1:13:20.831621 INFO: calibration group: fragment, predicting mz
1:13:20.959913 INFO: === checking if optimization conditions were reached ===
1:13:20.960213 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
1:13:20.962794 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 4.1235.
1:13:20.962853 INFO: ==============================================
1:13:20.962942 INFO: Starting optimization step 15.
1:13:20.963009 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:13:20.963086 PROGRESS: Extracting batch of 100415 precursors
1:13:20.993812 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:13:20.993969 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:13:20.994020 INFO: FWHM in RT is 2.43 seconds, sigma is 0.53
1:13:20.994045 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.75
1:13:21.003066 INFO: Starting candidate selection
1:26:27.642495 INFO: Starting candidate scoring
1:26:31.138154 INFO: Finished candidate processing
1:26:31.138342 INFO: Collecting candidate features
1:26:31.479388 WARNING: intensity_correlation has 70 NaNs ( 0.04 % out of 170874)
1:26:31.479857 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 170874)
1:26:31.489726 INFO: Collecting fragment features
1:26:31.594461 INFO: Finished candidate scoring
1:26:31.701069 PROGRESS: === Extracted 170874 precursors and 1410842 fragments ===
1:26:31.701979 INFO: performing precursor FDR with 47 features
1:26:31.702023 INFO: Decoy channel: -1
1:26:31.702052 INFO: Competetive: True
1:26:31.756789 INFO: Setting torch num_threads to 2 for FDR classification task
1:26:31.790013 WARNING: dropped 32 target PSMs due to missing features
1:26:31.790162 WARNING: dropped 39 decoy PSMs due to missing features
1:26:35.230085 INFO: Test AUC: 0.559
1:26:35.230210 INFO: Train AUC: 0.586
1:26:35.230242 INFO: AUC difference: 4.65%
1:26:35.466755 INFO: Resetting torch num_threads to 128
1:26:35.472388 INFO: === FDR correction performed with classifier version 7 ===
1:26:35.480782 PROGRESS: ============================= Precursor FDR =============================
1:26:35.481026 PROGRESS: Total precursors accumulated: 45,597
1:26:35.481090 PROGRESS: Target precursors: 28,042 (61.50%)
1:26:35.481159 PROGRESS: Decoy precursors: 17,555 (38.50%)
1:26:35.481211 PROGRESS: 
1:26:35.481258 PROGRESS: Precursor Summary:
1:26:35.482674 PROGRESS: Channel   0:	 0.05 FDR:   543; 0.01 FDR:   348; 0.001 FDR:   204
1:26:35.482774 PROGRESS: 
1:26:35.482830 PROGRESS: Protein Summary:
1:26:35.484241 PROGRESS: Channel   0:	 0.05 FDR:   514; 0.01 FDR:   331; 0.001 FDR:   194
1:26:35.484334 PROGRESS: =========================================================================
1:26:35.583888 INFO: fragments_df: keeping 3567 of 1410842 [sum(precursor_idx_mask)=7028 sum(mass_error_mask)=1410842 stop_rank=3567
1:26:35.794039 INFO: calibration group: precursor, fitting mz estimator 
1:26:35.922298 INFO: calibration group: precursor, fitting rt estimator 
1:26:36.053860 INFO: calibration group: precursor, fitting mobility estimator 
1:26:36.182477 INFO: calibration group: fragment, fitting mz estimator 
1:26:36.653511 INFO: Using score_cutoff 43.57569024467468 (fac=0.99, q=1)
1:26:36.653928 INFO: calibration group: precursor, predicting mz
1:26:36.666909 INFO: calibration group: precursor, predicting rt
1:26:36.729547 INFO: calibration group: precursor, predicting mobility
1:26:36.746049 INFO: calibration group: fragment, predicting mz
1:26:36.868767 INFO: === checking if optimization conditions were reached ===
1:26:36.869042 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
1:26:36.871437 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 4.1253.
1:26:36.871495 INFO: ==============================================
1:26:36.871594 INFO: Starting optimization step 16.
1:26:36.871686 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:26:36.871760 PROGRESS: Extracting batch of 100415 precursors
1:26:36.897508 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:26:36.897638 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:26:36.897693 INFO: FWHM in RT is 2.35 seconds, sigma is 0.52
1:26:36.897717 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.56
1:26:36.906603 INFO: Starting candidate selection
1:34:34.531873 INFO: Starting candidate scoring
1:34:38.531393 INFO: Finished candidate processing
1:34:38.533336 INFO: Collecting candidate features
1:34:38.925598 WARNING: intensity_correlation has 72 NaNs ( 0.04 % out of 170479)
1:34:38.936235 INFO: Collecting fragment features
1:34:39.054824 INFO: Finished candidate scoring
1:34:39.182239 PROGRESS: === Extracted 170479 precursors and 1401474 fragments ===
1:34:39.182913 INFO: performing precursor FDR with 47 features
1:34:39.182957 INFO: Decoy channel: -1
1:34:39.182984 INFO: Competetive: True
1:34:39.252363 INFO: Setting torch num_threads to 2 for FDR classification task
1:34:39.286188 WARNING: dropped 31 target PSMs due to missing features
1:34:39.286338 WARNING: dropped 41 decoy PSMs due to missing features
1:34:41.384609 INFO: Test AUC: 0.555
1:34:41.384737 INFO: Train AUC: 0.590
1:34:41.384766 INFO: AUC difference: 5.78%
1:34:41.384788 WARNING: AUC difference > 5%. This may indicate overfitting.
1:34:41.619653 INFO: Resetting torch num_threads to 128
1:34:41.625381 INFO: === FDR correction performed with classifier version 7 ===
1:34:41.633961 PROGRESS: ============================= Precursor FDR =============================
1:34:41.634204 PROGRESS: Total precursors accumulated: 45,533
1:34:41.634267 PROGRESS: Target precursors: 28,270 (62.09%)
1:34:41.634316 PROGRESS: Decoy precursors: 17,263 (37.91%)
1:34:41.634361 PROGRESS: 
1:34:41.634403 PROGRESS: Precursor Summary:
1:34:41.635760 PROGRESS: Channel   0:	 0.05 FDR:   583; 0.01 FDR:   270; 0.001 FDR:   243
1:34:41.635854 PROGRESS: 
1:34:41.635908 PROGRESS: Protein Summary:
1:34:41.637291 PROGRESS: Channel   0:	 0.05 FDR:   547; 0.01 FDR:   256; 0.001 FDR:   231
1:34:41.637382 PROGRESS: =========================================================================
1:34:41.733140 INFO: fragments_df: keeping 2921 of 1401474 [sum(precursor_idx_mask)=5451 sum(mass_error_mask)=1401474 stop_rank=2921
1:34:41.948104 INFO: calibration group: precursor, fitting mz estimator 
1:34:42.088740 INFO: calibration group: precursor, fitting rt estimator 
1:34:42.205548 INFO: calibration group: precursor, fitting mobility estimator 
1:34:42.337636 INFO: calibration group: fragment, fitting mz estimator 
1:34:42.736004 INFO: Using score_cutoff 47.429478733062744 (fac=0.99, q=1)
1:34:42.736490 INFO: calibration group: precursor, predicting mz
1:34:42.751031 INFO: calibration group: precursor, predicting rt
1:34:42.864288 INFO: calibration group: precursor, predicting mobility
1:34:42.883037 INFO: calibration group: fragment, predicting mz
1:34:43.017844 INFO: === checking if optimization conditions were reached ===
1:34:43.018260 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
1:34:43.019874 PROGRESS: ✅ ms2_error      : optimization complete. Optimal parameter 10.0349 found after 7 searches.
1:34:43.019939 INFO: ==============================================
1:34:43.020072 PROGRESS: Optimization finished for ms2_error.
1:34:43.233973 INFO: calibration group: precursor, predicting mz
1:34:43.242398 INFO: calibration group: precursor, predicting rt
1:34:43.274429 INFO: calibration group: precursor, predicting mobility
1:34:43.281957 INFO: calibration group: fragment, predicting mz
1:34:43.374742 INFO: Starting optimization step 0.
1:34:43.375055 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:34:43.375164 PROGRESS: Extracting batch of 49998 precursors
1:34:43.399116 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:34:43.399273 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:34:43.399349 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1:34:43.399380 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.84
1:34:43.408386 INFO: Starting candidate selection
1:38:43.152305 INFO: Starting candidate scoring
1:38:45.791318 INFO: Finished candidate processing
1:38:45.791452 INFO: Collecting candidate features
1:38:45.941665 WARNING: intensity_correlation has 7 NaNs ( 0.01 % out of 85908)
1:38:45.942016 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 85908)
1:38:45.948399 INFO: Collecting fragment features
1:38:46.011900 INFO: Finished candidate scoring
1:38:46.073496 PROGRESS: === Extracted 85908 precursors and 817384 fragments ===
1:38:46.074120 INFO: performing precursor FDR with 47 features
1:38:46.074162 INFO: Decoy channel: -1
1:38:46.074187 INFO: Competetive: True
1:38:46.110491 INFO: Setting torch num_threads to 2 for FDR classification task
1:38:46.131629 WARNING: dropped 4 target PSMs due to missing features
1:38:46.131788 WARNING: dropped 3 decoy PSMs due to missing features
1:38:47.763890 INFO: Test AUC: 0.576
1:38:47.764045 INFO: Train AUC: 0.609
1:38:47.764078 INFO: AUC difference: 5.45%
1:38:47.764100 WARNING: AUC difference > 5%. This may indicate overfitting.
1:38:47.977996 INFO: Resetting torch num_threads to 128
1:38:47.981688 INFO: === FDR correction performed with classifier version 11 ===
1:38:47.986104 PROGRESS: ============================= Precursor FDR =============================
1:38:47.986246 PROGRESS: Total precursors accumulated: 22,810
1:38:47.986309 PROGRESS: Target precursors: 14,602 (64.02%)
1:38:47.986360 PROGRESS: Decoy precursors: 8,208 (35.98%)
1:38:47.986406 PROGRESS: 
1:38:47.986449 PROGRESS: Precursor Summary:
1:38:47.987612 PROGRESS: Channel   0:	 0.05 FDR:   330; 0.01 FDR:   204; 0.001 FDR:   158
1:38:47.987706 PROGRESS: 
1:38:47.987760 PROGRESS: Protein Summary:
1:38:47.988979 PROGRESS: Channel   0:	 0.05 FDR:   321; 0.01 FDR:   201; 0.001 FDR:   155
1:38:47.989072 PROGRESS: =========================================================================
1:38:48.077414 INFO: fragments_df: keeping 2379 of 817384 [sum(precursor_idx_mask)=4294 sum(mass_error_mask)=817384 stop_rank=2379
1:38:48.341939 INFO: calibration group: precursor, fitting mz estimator 
1:38:48.460371 INFO: calibration group: precursor, fitting rt estimator 
1:38:48.571274 INFO: calibration group: precursor, fitting mobility estimator 
1:38:48.685660 INFO: calibration group: fragment, fitting mz estimator 
1:38:49.001428 INFO: Using score_cutoff 46.31573213195801 (fac=0.99, q=1)
1:38:49.001904 INFO: calibration group: precursor, predicting mz
1:38:49.009602 INFO: calibration group: precursor, predicting rt
1:38:49.040315 INFO: calibration group: precursor, predicting mobility
1:38:49.047658 INFO: calibration group: fragment, predicting mz
1:38:49.107689 INFO: === checking if optimization conditions were reached ===
1:38:49.108095 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:38:49.110542 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 450.7985.
1:38:49.110610 INFO: ==============================================
1:38:49.110720 INFO: Starting optimization step 1.
1:38:49.110798 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:38:49.110882 PROGRESS: Extracting batch of 49998 precursors
1:38:49.133926 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:38:49.134072 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:38:49.134134 INFO: FWHM in RT is 2.78 seconds, sigma is 0.61
1:38:49.134165 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.87
1:38:49.136599 INFO: Starting candidate selection
1:39:47.093477 INFO: Starting candidate scoring
1:39:49.549378 INFO: Finished candidate processing
1:39:49.550476 INFO: Collecting candidate features
1:39:49.720710 WARNING: intensity_correlation has 53 NaNs ( 0.06 % out of 82648)
1:39:49.721018 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 82648)
1:39:49.726987 INFO: Collecting fragment features
1:39:49.803549 INFO: Finished candidate scoring
1:39:49.849432 PROGRESS: === Extracted 82648 precursors and 771558 fragments ===
1:39:49.849934 INFO: performing precursor FDR with 47 features
1:39:49.849975 INFO: Decoy channel: -1
1:39:49.850000 INFO: Competetive: True
1:39:49.881553 INFO: Setting torch num_threads to 2 for FDR classification task
1:39:49.898102 WARNING: dropped 31 target PSMs due to missing features
1:39:49.898237 WARNING: dropped 22 decoy PSMs due to missing features
1:39:51.205345 INFO: Test AUC: 0.565
1:39:51.205475 INFO: Train AUC: 0.597
1:39:51.205507 INFO: AUC difference: 5.36%
1:39:51.205529 WARNING: AUC difference > 5%. This may indicate overfitting.
1:39:51.420553 INFO: Resetting torch num_threads to 128
1:39:51.423803 INFO: === FDR correction performed with classifier version 11 ===
1:39:51.427522 PROGRESS: ============================= Precursor FDR =============================
1:39:51.427668 PROGRESS: Total precursors accumulated: 22,239
1:39:51.427731 PROGRESS: Target precursors: 13,981 (62.87%)
1:39:51.427781 PROGRESS: Decoy precursors: 8,258 (37.13%)
1:39:51.427826 PROGRESS: 
1:39:51.427875 PROGRESS: Precursor Summary:
1:39:51.428994 PROGRESS: Channel   0:	 0.05 FDR:   345; 0.01 FDR:   248; 0.001 FDR:   184
1:39:51.429080 PROGRESS: 
1:39:51.429163 PROGRESS: Protein Summary:
1:39:51.430379 PROGRESS: Channel   0:	 0.05 FDR:   336; 0.01 FDR:   242; 0.001 FDR:   181
1:39:51.430469 PROGRESS: =========================================================================
1:39:51.482878 INFO: fragments_df: keeping 2789 of 771558 [sum(precursor_idx_mask)=5191 sum(mass_error_mask)=771558 stop_rank=2789
1:39:51.636849 INFO: calibration group: precursor, fitting mz estimator 
1:39:51.754361 INFO: calibration group: precursor, fitting rt estimator 
1:39:51.871280 INFO: calibration group: precursor, fitting mobility estimator 
1:39:51.987252 INFO: calibration group: fragment, fitting mz estimator 
1:39:52.361683 INFO: Using score_cutoff 42.76357505378723 (fac=0.99, q=1)
1:39:52.362148 INFO: calibration group: precursor, predicting mz
1:39:52.369533 INFO: calibration group: precursor, predicting rt
1:39:52.399467 INFO: calibration group: precursor, predicting mobility
1:39:52.406615 INFO: calibration group: fragment, predicting mz
1:39:52.466442 INFO: === checking if optimization conditions were reached ===
1:39:52.466762 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:39:52.469079 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 394.2282.
1:39:52.469143 INFO: ==============================================
1:39:52.469267 INFO: Starting optimization step 2.
1:39:52.469346 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:39:52.469454 PROGRESS: Extracting batch of 49998 precursors
1:39:52.488771 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:39:52.488907 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:39:52.488979 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
1:39:52.489009 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.72
1:39:52.493237 INFO: Starting candidate selection
1:40:38.472994 INFO: Starting candidate scoring
1:40:40.911382 INFO: Finished candidate processing
1:40:40.911576 INFO: Collecting candidate features
1:40:41.114016 WARNING: intensity_correlation has 52 NaNs ( 0.06 % out of 82437)
1:40:41.114373 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 82437)
1:40:41.121510 INFO: Collecting fragment features
1:40:41.199869 INFO: Finished candidate scoring
1:40:41.260082 PROGRESS: === Extracted 82437 precursors and 766642 fragments ===
1:40:41.260739 INFO: performing precursor FDR with 47 features
1:40:41.260784 INFO: Decoy channel: -1
1:40:41.260808 INFO: Competetive: True
1:40:41.303174 INFO: Setting torch num_threads to 2 for FDR classification task
1:40:41.324189 WARNING: dropped 31 target PSMs due to missing features
1:40:41.324345 WARNING: dropped 21 decoy PSMs due to missing features
1:40:43.298790 INFO: Test AUC: 0.560
1:40:43.299045 INFO: Train AUC: 0.597
1:40:43.299084 INFO: AUC difference: 6.10%
1:40:43.299111 WARNING: AUC difference > 5%. This may indicate overfitting.
1:40:43.549862 INFO: Resetting torch num_threads to 128
1:40:43.582456 INFO: === FDR correction performed with classifier version 11 ===
1:40:43.590374 PROGRESS: ============================= Precursor FDR =============================
1:40:43.590596 PROGRESS: Total precursors accumulated: 22,207
1:40:43.590665 PROGRESS: Target precursors: 13,854 (62.39%)
1:40:43.590730 PROGRESS: Decoy precursors: 8,353 (37.61%)
1:40:43.590784 PROGRESS: 
1:40:43.590830 PROGRESS: Precursor Summary:
1:40:43.592313 PROGRESS: Channel   0:	 0.05 FDR:   339; 0.01 FDR:   244; 0.001 FDR:   180
1:40:43.592418 PROGRESS: 
1:40:43.592476 PROGRESS: Protein Summary:
1:40:43.593852 PROGRESS: Channel   0:	 0.05 FDR:   329; 0.01 FDR:   238; 0.001 FDR:   176
1:40:43.593950 PROGRESS: =========================================================================
1:40:43.659600 INFO: fragments_df: keeping 2758 of 766642 [sum(precursor_idx_mask)=5104 sum(mass_error_mask)=766642 stop_rank=2758
1:40:44.035373 INFO: calibration group: precursor, fitting mz estimator 
1:40:44.158135 INFO: calibration group: precursor, fitting rt estimator 
1:40:44.280222 INFO: calibration group: precursor, fitting mobility estimator 
1:40:44.395781 INFO: calibration group: fragment, fitting mz estimator 
1:40:44.761649 INFO: Using score_cutoff 44.724367254638665 (fac=0.99, q=1)
1:40:44.762131 INFO: calibration group: precursor, predicting mz
1:40:44.769694 INFO: calibration group: precursor, predicting rt
1:40:44.799756 INFO: calibration group: precursor, predicting mobility
1:40:44.806956 INFO: calibration group: fragment, predicting mz
1:40:44.867480 INFO: === checking if optimization conditions were reached ===
1:40:44.867832 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:40:44.870433 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 221.1077.
1:40:44.870496 INFO: ==============================================
1:40:44.870621 INFO: Starting optimization step 3.
1:40:44.870700 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:40:44.870794 PROGRESS: Extracting batch of 49998 precursors
1:40:44.893782 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:40:44.893919 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:40:44.893987 INFO: FWHM in RT is 2.83 seconds, sigma is 0.62
1:40:44.894014 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.77
1:40:44.902999 INFO: Starting candidate selection
1:41:12.703337 INFO: Starting candidate scoring
1:41:15.158534 INFO: Finished candidate processing
1:41:15.158645 INFO: Collecting candidate features
1:41:15.303134 WARNING: intensity_correlation has 54 NaNs ( 0.07 % out of 81990)
1:41:15.303462 WARNING: height_correlation has 8 NaNs ( 0.01 % out of 81990)
1:41:15.309469 INFO: Collecting fragment features
1:41:15.367867 INFO: Finished candidate scoring
1:41:15.416737 PROGRESS: === Extracted 81990 precursors and 753877 fragments ===
1:41:15.417207 INFO: performing precursor FDR with 47 features
1:41:15.417247 INFO: Decoy channel: -1
1:41:15.417271 INFO: Competetive: True
1:41:15.450511 INFO: Setting torch num_threads to 2 for FDR classification task
1:41:15.468602 WARNING: dropped 33 target PSMs due to missing features
1:41:15.468750 WARNING: dropped 28 decoy PSMs due to missing features
1:41:16.927431 INFO: Test AUC: 0.548
1:41:16.927579 INFO: Train AUC: 0.593
1:41:16.927610 INFO: AUC difference: 7.52%
1:41:16.927631 WARNING: AUC difference > 5%. This may indicate overfitting.
1:41:17.149328 INFO: Resetting torch num_threads to 128
1:41:17.192738 INFO: === FDR correction performed with classifier version 11 ===
1:41:17.198327 PROGRESS: ============================= Precursor FDR =============================
1:41:17.198508 PROGRESS: Total precursors accumulated: 22,149
1:41:17.198584 PROGRESS: Target precursors: 13,653 (61.64%)
1:41:17.198637 PROGRESS: Decoy precursors: 8,496 (38.36%)
1:41:17.198684 PROGRESS: 
1:41:17.198727 PROGRESS: Precursor Summary:
1:41:17.199874 PROGRESS: Channel   0:	 0.05 FDR:   337; 0.01 FDR:   259; 0.001 FDR:   173
1:41:17.199965 PROGRESS: 
1:41:17.200020 PROGRESS: Protein Summary:
1:41:17.201229 PROGRESS: Channel   0:	 0.05 FDR:   327; 0.01 FDR:   252; 0.001 FDR:   170
1:41:17.201317 PROGRESS: =========================================================================
1:41:17.253313 INFO: fragments_df: keeping 2830 of 753877 [sum(precursor_idx_mask)=5433 sum(mass_error_mask)=753877 stop_rank=2830
1:41:17.440042 INFO: calibration group: precursor, fitting mz estimator 
1:41:17.564759 INFO: calibration group: precursor, fitting rt estimator 
1:41:17.690580 INFO: calibration group: precursor, fitting mobility estimator 
1:41:17.807967 INFO: calibration group: fragment, fitting mz estimator 
1:41:18.210211 INFO: Using score_cutoff 43.810363002777095 (fac=0.99, q=1)
1:41:18.211055 INFO: calibration group: precursor, predicting mz
1:41:18.220209 INFO: calibration group: precursor, predicting rt
1:41:18.255012 INFO: calibration group: precursor, predicting mobility
1:41:18.264890 INFO: calibration group: fragment, predicting mz
1:41:18.409823 INFO: === checking if optimization conditions were reached ===
1:41:18.410232 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:41:18.413457 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 149.8637.
1:41:18.413528 INFO: ==============================================
1:41:18.413647 INFO: Starting optimization step 4.
1:41:18.413745 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:41:18.413854 PROGRESS: Extracting batch of 49998 precursors
1:41:18.440441 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:41:18.440604 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:41:18.440664 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
1:41:18.440693 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.76
1:41:18.444254 INFO: Starting candidate selection
1:41:37.472539 INFO: Starting candidate scoring
1:41:39.988959 INFO: Finished candidate processing
1:41:39.989120 INFO: Collecting candidate features
1:41:40.157784 WARNING: intensity_correlation has 74 NaNs ( 0.09 % out of 81454)
1:41:40.158114 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 81454)
1:41:40.164172 INFO: Collecting fragment features
1:41:40.223772 INFO: Finished candidate scoring
1:41:40.274636 PROGRESS: === Extracted 81454 precursors and 744005 fragments ===
1:41:40.275138 INFO: performing precursor FDR with 47 features
1:41:40.275180 INFO: Decoy channel: -1
1:41:40.275204 INFO: Competetive: True
1:41:40.310917 INFO: Setting torch num_threads to 2 for FDR classification task
1:41:40.329651 WARNING: dropped 39 target PSMs due to missing features
1:41:40.329792 WARNING: dropped 37 decoy PSMs due to missing features
1:41:41.671412 INFO: Test AUC: 0.549
1:41:41.671533 INFO: Train AUC: 0.596
1:41:41.671564 INFO: AUC difference: 7.88%
1:41:41.671587 WARNING: AUC difference > 5%. This may indicate overfitting.
1:41:43.196999 INFO: Resetting torch num_threads to 128
1:41:43.200537 INFO: === FDR correction performed with classifier version 11 ===
1:41:43.204395 PROGRESS: ============================= Precursor FDR =============================
1:41:43.204541 PROGRESS: Total precursors accumulated: 22,032
1:41:43.204601 PROGRESS: Target precursors: 13,726 (62.30%)
1:41:43.204650 PROGRESS: Decoy precursors: 8,306 (37.70%)
1:41:43.204694 PROGRESS: 
1:41:43.204739 PROGRESS: Precursor Summary:
1:41:43.205878 PROGRESS: Channel   0:	 0.05 FDR:   372; 0.01 FDR:   279; 0.001 FDR:   189
1:41:43.205965 PROGRESS: 
1:41:43.206020 PROGRESS: Protein Summary:
1:41:43.207265 PROGRESS: Channel   0:	 0.05 FDR:   360; 0.01 FDR:   272; 0.001 FDR:   185
1:41:43.207356 PROGRESS: =========================================================================
1:41:43.258492 INFO: fragments_df: keeping 2956 of 744005 [sum(precursor_idx_mask)=5846 sum(mass_error_mask)=744005 stop_rank=2956
1:41:43.389971 INFO: calibration group: precursor, fitting mz estimator 
1:41:43.489600 INFO: calibration group: precursor, fitting rt estimator 
1:41:43.593860 INFO: calibration group: precursor, fitting mobility estimator 
1:41:43.691710 INFO: calibration group: fragment, fitting mz estimator 
1:41:44.018796 INFO: Using score_cutoff 41.71251220092773 (fac=0.99, q=1)
1:41:44.019219 INFO: calibration group: precursor, predicting mz
1:41:44.026697 INFO: calibration group: precursor, predicting rt
1:41:44.057011 INFO: calibration group: precursor, predicting mobility
1:41:44.064374 INFO: calibration group: fragment, predicting mz
1:41:44.121491 INFO: === checking if optimization conditions were reached ===
1:41:44.121757 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1:41:44.123800 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 144.4238.
1:41:44.123863 INFO: ==============================================
1:41:44.123955 INFO: Starting optimization step 5.
1:41:44.124027 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:41:44.124092 PROGRESS: Extracting batch of 49998 precursors
1:41:44.138369 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:41:44.138488 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:41:44.138535 INFO: FWHM in RT is 2.83 seconds, sigma is 0.62
1:41:44.138563 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.69
1:41:44.147242 INFO: Starting candidate selection
1:42:01.894298 INFO: Starting candidate scoring
1:42:04.506021 INFO: Finished candidate processing
1:42:04.506551 INFO: Collecting candidate features
1:42:04.652631 WARNING: intensity_correlation has 77 NaNs ( 0.09 % out of 81271)
1:42:04.652953 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 81271)
1:42:04.658957 INFO: Collecting fragment features
1:42:04.727979 INFO: Finished candidate scoring
1:42:04.779106 PROGRESS: === Extracted 81271 precursors and 740982 fragments ===
1:42:04.779646 INFO: performing precursor FDR with 47 features
1:42:04.779686 INFO: Decoy channel: -1
1:42:04.779712 INFO: Competetive: True
1:42:04.808897 INFO: Setting torch num_threads to 2 for FDR classification task
1:42:04.826766 WARNING: dropped 42 target PSMs due to missing features
1:42:04.826897 WARNING: dropped 38 decoy PSMs due to missing features
1:42:06.035416 INFO: Test AUC: 0.556
1:42:06.035545 INFO: Train AUC: 0.585
1:42:06.035576 INFO: AUC difference: 5.01%
1:42:06.035598 WARNING: AUC difference > 5%. This may indicate overfitting.
1:42:06.243446 INFO: Resetting torch num_threads to 128
1:42:06.246709 INFO: === FDR correction performed with classifier version 11 ===
1:42:06.250450 PROGRESS: ============================= Precursor FDR =============================
1:42:06.250581 PROGRESS: Total precursors accumulated: 21,995
1:42:06.250661 PROGRESS: Target precursors: 13,433 (61.07%)
1:42:06.250714 PROGRESS: Decoy precursors: 8,562 (38.93%)
1:42:06.250759 PROGRESS: 
1:42:06.250803 PROGRESS: Precursor Summary:
1:42:06.251933 PROGRESS: Channel   0:	 0.05 FDR:   373; 0.01 FDR:   251; 0.001 FDR:   209
1:42:06.252032 PROGRESS: 
1:42:06.252089 PROGRESS: Protein Summary:
1:42:06.253310 PROGRESS: Channel   0:	 0.05 FDR:   361; 0.01 FDR:   246; 0.001 FDR:   206
1:42:06.253398 PROGRESS: =========================================================================
1:42:06.304243 INFO: fragments_df: keeping 2732 of 740982 [sum(precursor_idx_mask)=5265 sum(mass_error_mask)=740982 stop_rank=2732
1:42:06.446119 INFO: calibration group: precursor, fitting mz estimator 
1:42:06.566588 INFO: calibration group: precursor, fitting rt estimator 
1:42:06.684991 INFO: calibration group: precursor, fitting mobility estimator 
1:42:06.801090 INFO: calibration group: fragment, fitting mz estimator 
1:42:07.162009 INFO: Using score_cutoff 43.67595331192017 (fac=0.99, q=1)
1:42:07.162418 INFO: calibration group: precursor, predicting mz
1:42:07.169601 INFO: calibration group: precursor, predicting rt
1:42:07.199514 INFO: calibration group: precursor, predicting mobility
1:42:07.206474 INFO: calibration group: fragment, predicting mz
1:42:07.264392 INFO: === checking if optimization conditions were reached ===
1:42:07.264659 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1:42:07.265930 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 144.4238 found after 6 searches.
1:42:07.265982 INFO: ==============================================
1:42:07.266078 PROGRESS: Optimization finished for rt_error.
1:42:07.384726 INFO: calibration group: precursor, predicting mz
1:42:07.392121 INFO: calibration group: precursor, predicting rt
1:42:07.422107 INFO: calibration group: precursor, predicting mobility
1:42:07.429189 INFO: calibration group: fragment, predicting mz
1:42:07.510116 INFO: Starting optimization step 0.
1:42:07.510324 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:42:07.510409 PROGRESS: Extracting batch of 49998 precursors
1:42:07.524094 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:42:07.524219 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:42:07.524269 INFO: FWHM in RT is 2.83 seconds, sigma is 0.62
1:42:07.524295 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.67
1:42:07.533075 INFO: Starting candidate selection
1:42:25.275217 INFO: Starting candidate scoring
1:42:28.835710 INFO: Finished candidate processing
1:42:28.835936 INFO: Collecting candidate features
1:42:29.077081 WARNING: intensity_correlation has 78 NaNs ( 0.10 % out of 81375)
1:42:29.077554 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 81375)
1:42:29.085301 INFO: Collecting fragment features
1:42:29.192279 INFO: Finished candidate scoring
1:42:29.438180 PROGRESS: === Extracted 81375 precursors and 742307 fragments ===
1:42:29.438935 INFO: performing precursor FDR with 47 features
1:42:29.438982 INFO: Decoy channel: -1
1:42:29.439010 INFO: Competetive: True
1:42:29.533428 INFO: Setting torch num_threads to 2 for FDR classification task
1:42:29.583281 WARNING: dropped 45 target PSMs due to missing features
1:42:29.583532 WARNING: dropped 36 decoy PSMs due to missing features
1:42:31.116369 INFO: Test AUC: 0.565
1:42:31.116498 INFO: Train AUC: 0.607
1:42:31.116528 INFO: AUC difference: 7.04%
1:42:31.116550 WARNING: AUC difference > 5%. This may indicate overfitting.
1:42:31.325900 INFO: Resetting torch num_threads to 128
1:42:31.329250 INFO: === FDR correction performed with classifier version 22 ===
1:42:31.332984 PROGRESS: ============================= Precursor FDR =============================
1:42:31.333121 PROGRESS: Total precursors accumulated: 22,011
1:42:31.333180 PROGRESS: Target precursors: 13,987 (63.55%)
1:42:31.333232 PROGRESS: Decoy precursors: 8,024 (36.45%)
1:42:31.333278 PROGRESS: 
1:42:31.333321 PROGRESS: Precursor Summary:
1:42:31.334465 PROGRESS: Channel   0:	 0.05 FDR:   380; 0.01 FDR:   302; 0.001 FDR:   213
1:42:31.334555 PROGRESS: 
1:42:31.334608 PROGRESS: Protein Summary:
1:42:31.335868 PROGRESS: Channel   0:	 0.05 FDR:   369; 0.01 FDR:   293; 0.001 FDR:   209
1:42:31.335958 PROGRESS: =========================================================================
1:42:31.388021 INFO: fragments_df: keeping 3082 of 742307 [sum(precursor_idx_mask)=6183 sum(mass_error_mask)=742307 stop_rank=3082
1:42:31.522424 INFO: calibration group: precursor, fitting mz estimator 
1:42:31.699056 INFO: calibration group: precursor, fitting rt estimator 
1:42:31.819617 INFO: calibration group: precursor, fitting mobility estimator 
1:42:31.938776 INFO: calibration group: fragment, fitting mz estimator 
1:42:32.343092 INFO: Using score_cutoff 35.138888219833376 (fac=0.99, q=1)
1:42:32.343510 INFO: calibration group: precursor, predicting mz
1:42:32.350826 INFO: calibration group: precursor, predicting rt
1:42:32.381184 INFO: calibration group: precursor, predicting mobility
1:42:32.388415 INFO: calibration group: fragment, predicting mz
1:42:32.452901 INFO: === checking if optimization conditions were reached ===
1:42:32.453288 PROGRESS: === Optimization of ms1_error has been performed 1 time(s); minimum number is 2 ===
1:42:32.455498 PROGRESS: ❌ ms1_error      : optimization incomplete after 1 search(es). Will search with parameter 12.2562.
1:42:32.455565 INFO: ==============================================
1:42:32.455675 INFO: Starting optimization step 1.
1:42:32.455752 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:42:32.455838 PROGRESS: Extracting batch of 49998 precursors
1:42:32.475793 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:42:32.475942 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:42:32.476000 INFO: FWHM in RT is 2.78 seconds, sigma is 0.61
1:42:32.476028 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.66
1:42:32.486090 INFO: Starting candidate selection
1:42:49.380616 INFO: Starting candidate scoring
1:42:51.400696 INFO: Finished candidate processing
1:42:51.400888 INFO: Collecting candidate features
1:42:51.530611 WARNING: intensity_correlation has 71 NaNs ( 0.09 % out of 81068)
1:42:51.530925 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 81068)
1:42:51.536846 INFO: Collecting fragment features
1:42:51.593577 INFO: Finished candidate scoring
1:42:51.641762 PROGRESS: === Extracted 81068 precursors and 733568 fragments ===
1:42:51.642237 INFO: performing precursor FDR with 47 features
1:42:51.642277 INFO: Decoy channel: -1
1:42:51.642300 INFO: Competetive: True
1:42:51.676570 INFO: Setting torch num_threads to 2 for FDR classification task
1:42:51.693694 WARNING: dropped 40 target PSMs due to missing features
1:42:51.693831 WARNING: dropped 34 decoy PSMs due to missing features
1:42:52.904522 INFO: Test AUC: 0.550
1:42:52.904652 INFO: Train AUC: 0.587
1:42:52.904682 INFO: AUC difference: 6.27%
1:42:52.904703 WARNING: AUC difference > 5%. This may indicate overfitting.
1:42:53.107038 INFO: Resetting torch num_threads to 128
1:42:53.110179 INFO: === FDR correction performed with classifier version 22 ===
1:42:53.113834 PROGRESS: ============================= Precursor FDR =============================
1:42:53.113962 PROGRESS: Total precursors accumulated: 21,977
1:42:53.114023 PROGRESS: Target precursors: 13,376 (60.86%)
1:42:53.114075 PROGRESS: Decoy precursors: 8,601 (39.14%)
1:42:53.114123 PROGRESS: 
1:42:53.114169 PROGRESS: Precursor Summary:
1:42:53.115308 PROGRESS: Channel   0:	 0.05 FDR:   465; 0.01 FDR:   330; 0.001 FDR:   166
1:42:53.115400 PROGRESS: 
1:42:53.115455 PROGRESS: Protein Summary:
1:42:53.116695 PROGRESS: Channel   0:	 0.05 FDR:   451; 0.01 FDR:   319; 0.001 FDR:   164
1:42:53.116784 PROGRESS: =========================================================================
1:42:53.167740 INFO: fragments_df: keeping 3203 of 733568 [sum(precursor_idx_mask)=6825 sum(mass_error_mask)=733567 stop_rank=3203
1:42:53.300148 INFO: calibration group: precursor, fitting mz estimator 
1:42:53.427446 INFO: calibration group: precursor, fitting rt estimator 
1:42:53.551861 INFO: calibration group: precursor, fitting mobility estimator 
1:42:53.676103 INFO: calibration group: fragment, fitting mz estimator 
1:42:54.097915 INFO: Using score_cutoff 35.90058752174377 (fac=0.99, q=1)
1:42:54.098330 INFO: calibration group: precursor, predicting mz
1:42:54.105650 INFO: calibration group: precursor, predicting rt
1:42:54.136020 INFO: calibration group: precursor, predicting mobility
1:42:54.143119 INFO: calibration group: fragment, predicting mz
1:42:54.202135 INFO: === checking if optimization conditions were reached ===
1:42:54.202444 PROGRESS: === Optimization of ms1_error has been performed 2 time(s); minimum number is 2 ===
1:42:54.204805 PROGRESS: ❌ ms1_error      : optimization incomplete after 2 search(es). Will search with parameter 5.1282.
1:42:54.204871 INFO: ==============================================
1:42:54.204979 INFO: Starting optimization step 2.
1:42:54.205051 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:42:54.205130 PROGRESS: Extracting batch of 49998 precursors
1:42:54.223312 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:42:54.223433 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:42:54.223489 INFO: FWHM in RT is 2.74 seconds, sigma is 0.60
1:42:54.223517 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.48
1:42:54.232502 INFO: Starting candidate selection
1:43:10.725305 INFO: Starting candidate scoring
1:43:12.549735 INFO: Finished candidate processing
1:43:12.549895 INFO: Collecting candidate features
1:43:12.666690 WARNING: intensity_correlation has 68 NaNs ( 0.08 % out of 81430)
1:43:12.666986 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 81430)
1:43:12.672903 INFO: Collecting fragment features
1:43:12.721187 INFO: Finished candidate scoring
1:43:12.770661 PROGRESS: === Extracted 81430 precursors and 729742 fragments ===
1:43:12.771053 INFO: performing precursor FDR with 47 features
1:43:12.771093 INFO: Decoy channel: -1
1:43:12.771117 INFO: Competetive: True
1:43:12.797962 INFO: Setting torch num_threads to 2 for FDR classification task
1:43:12.813861 WARNING: dropped 42 target PSMs due to missing features
1:43:12.813997 WARNING: dropped 29 decoy PSMs due to missing features
1:43:14.089851 INFO: Test AUC: 0.546
1:43:14.089981 INFO: Train AUC: 0.584
1:43:14.090011 INFO: AUC difference: 6.49%
1:43:14.090035 WARNING: AUC difference > 5%. This may indicate overfitting.
1:43:14.289470 INFO: Resetting torch num_threads to 128
1:43:14.292621 INFO: === FDR correction performed with classifier version 22 ===
1:43:14.296332 PROGRESS: ============================= Precursor FDR =============================
1:43:14.296469 PROGRESS: Total precursors accumulated: 22,088
1:43:14.297174 PROGRESS: Target precursors: 13,289 (60.16%)
1:43:14.297236 PROGRESS: Decoy precursors: 8,799 (39.84%)
1:43:14.297284 PROGRESS: 
1:43:14.297328 PROGRESS: Precursor Summary:
1:43:14.298455 PROGRESS: Channel   0:	 0.05 FDR:   431; 0.01 FDR:   322; 0.001 FDR:   142
1:43:14.298542 PROGRESS: 
1:43:14.298597 PROGRESS: Protein Summary:
1:43:14.301254 PROGRESS: Channel   0:	 0.05 FDR:   415; 0.01 FDR:   309; 0.001 FDR:   140
1:43:14.301351 PROGRESS: =========================================================================
1:43:14.351081 INFO: fragments_df: keeping 3300 of 729742 [sum(precursor_idx_mask)=6605 sum(mass_error_mask)=729737 stop_rank=3300
1:43:14.477635 INFO: calibration group: precursor, fitting mz estimator 
1:43:14.595570 INFO: calibration group: precursor, fitting rt estimator 
1:43:14.699663 INFO: calibration group: precursor, fitting mobility estimator 
1:43:14.803693 INFO: calibration group: fragment, fitting mz estimator 
1:43:15.183542 INFO: Using score_cutoff 25.00637502536774 (fac=0.99, q=1)
1:43:15.183946 INFO: calibration group: precursor, predicting mz
1:43:15.191157 INFO: calibration group: precursor, predicting rt
1:43:15.221302 INFO: calibration group: precursor, predicting mobility
1:43:15.228362 INFO: calibration group: fragment, predicting mz
1:43:15.284805 INFO: === checking if optimization conditions were reached ===
1:43:15.285062 PROGRESS: === Optimization of ms1_error has been performed 3 time(s); minimum number is 2 ===
1:43:15.286099 PROGRESS: ✅ ms1_error      : optimization complete. Optimal parameter 12.2562 found after 3 searches.
1:43:15.286151 INFO: ==============================================
1:43:15.286247 PROGRESS: Optimization finished for ms1_error.
1:43:15.405130 INFO: calibration group: precursor, predicting mz
1:43:15.412611 INFO: calibration group: precursor, predicting rt
1:43:15.443105 INFO: calibration group: precursor, predicting mobility
1:43:15.450210 INFO: calibration group: fragment, predicting mz
1:43:15.531715 INFO: Starting optimization step 0.
1:43:15.531924 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:43:15.531995 PROGRESS: Extracting batch of 49998 precursors
1:43:15.545759 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:43:15.545883 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:43:15.545924 INFO: FWHM in RT is 2.74 seconds, sigma is 0.60
1:43:15.545948 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.48
1:43:15.554669 INFO: Starting candidate selection
1:43:32.341250 INFO: Starting candidate scoring
1:43:34.910296 INFO: Finished candidate processing
1:43:34.910528 INFO: Collecting candidate features
1:43:35.068582 WARNING: intensity_correlation has 72 NaNs ( 0.09 % out of 81295)
1:43:35.068886 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 81295)
1:43:35.074862 INFO: Collecting fragment features
1:43:35.139067 INFO: Finished candidate scoring
1:43:35.188580 PROGRESS: === Extracted 81295 precursors and 734703 fragments ===
1:43:35.189062 INFO: performing precursor FDR with 47 features
1:43:35.189101 INFO: Decoy channel: -1
1:43:35.189125 INFO: Competetive: True
1:43:35.220351 INFO: Setting torch num_threads to 2 for FDR classification task
1:43:35.236480 WARNING: dropped 43 target PSMs due to missing features
1:43:35.236611 WARNING: dropped 31 decoy PSMs due to missing features
1:43:36.509943 INFO: Test AUC: 0.554
1:43:36.510078 INFO: Train AUC: 0.611
1:43:36.510108 INFO: AUC difference: 9.43%
1:43:36.510128 WARNING: AUC difference > 5%. This may indicate overfitting.
1:43:36.717049 INFO: Resetting torch num_threads to 128
1:43:36.720424 INFO: === FDR correction performed with classifier version 24 ===
1:43:36.724236 PROGRESS: ============================= Precursor FDR =============================
1:43:36.724371 PROGRESS: Total precursors accumulated: 22,037
1:43:36.724430 PROGRESS: Target precursors: 13,700 (62.17%)
1:43:36.724482 PROGRESS: Decoy precursors: 8,337 (37.83%)
1:43:36.724538 PROGRESS: 
1:43:36.724582 PROGRESS: Precursor Summary:
1:43:36.725689 PROGRESS: Channel   0:	 0.05 FDR:   446; 0.01 FDR:   312; 0.001 FDR:     0
1:43:36.725779 PROGRESS: 
1:43:36.725833 PROGRESS: Protein Summary:
1:43:36.727037 PROGRESS: Channel   0:	 0.05 FDR:   431; 0.01 FDR:   302; 0.001 FDR:     0
1:43:36.727124 PROGRESS: =========================================================================
1:43:36.779096 INFO: fragments_df: keeping 3121 of 734703 [sum(precursor_idx_mask)=6411 sum(mass_error_mask)=734702 stop_rank=3121
1:43:36.922589 INFO: calibration group: precursor, fitting mz estimator 
1:43:37.051256 INFO: calibration group: precursor, fitting rt estimator 
1:43:37.177609 INFO: calibration group: precursor, fitting mobility estimator 
1:43:37.283801 INFO: calibration group: fragment, fitting mz estimator 
1:43:37.698858 INFO: Using score_cutoff 41.180938086318974 (fac=0.99, q=1)
1:43:37.699614 INFO: calibration group: precursor, predicting mz
1:43:37.708714 INFO: calibration group: precursor, predicting rt
1:43:37.742509 INFO: calibration group: precursor, predicting mobility
1:43:37.751501 INFO: calibration group: fragment, predicting mz
1:43:37.846324 INFO: === checking if optimization conditions were reached ===
1:43:37.846971 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1:43:37.850437 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0747.
1:43:37.850556 INFO: ==============================================
1:43:37.850686 INFO: Starting optimization step 1.
1:43:37.850769 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:43:37.850881 PROGRESS: Extracting batch of 49998 precursors
1:43:37.892236 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:43:37.892512 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:43:37.892593 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1:43:37.892627 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.57
1:43:37.908529 INFO: Starting candidate selection
1:43:51.988492 INFO: Starting candidate scoring
1:43:54.043290 INFO: Finished candidate processing
1:43:54.043480 INFO: Collecting candidate features
1:43:54.229778 WARNING: intensity_correlation has 68 NaNs ( 0.09 % out of 79635)
1:43:54.230098 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 79635)
1:43:54.236488 INFO: Collecting fragment features
1:43:54.312851 INFO: Finished candidate scoring
1:43:54.371988 PROGRESS: === Extracted 79635 precursors and 716049 fragments ===
1:43:54.372547 INFO: performing precursor FDR with 47 features
1:43:54.372590 INFO: Decoy channel: -1
1:43:54.372616 INFO: Competetive: True
1:43:54.430036 INFO: Setting torch num_threads to 2 for FDR classification task
1:43:54.449626 WARNING: dropped 44 target PSMs due to missing features
1:43:54.449785 WARNING: dropped 28 decoy PSMs due to missing features
1:43:55.985687 INFO: Test AUC: 0.567
1:43:55.985841 INFO: Train AUC: 0.603
1:43:55.985874 INFO: AUC difference: 5.97%
1:43:55.985896 WARNING: AUC difference > 5%. This may indicate overfitting.
1:43:56.199144 INFO: Resetting torch num_threads to 128
1:43:56.202601 INFO: === FDR correction performed with classifier version 24 ===
1:43:56.206962 PROGRESS: ============================= Precursor FDR =============================
1:43:56.207124 PROGRESS: Total precursors accumulated: 21,615
1:43:56.207185 PROGRESS: Target precursors: 13,444 (62.20%)
1:43:56.207237 PROGRESS: Decoy precursors: 8,171 (37.80%)
1:43:56.207282 PROGRESS: 
1:43:56.207326 PROGRESS: Precursor Summary:
1:43:56.208505 PROGRESS: Channel   0:	 0.05 FDR:   442; 0.01 FDR:   311; 0.001 FDR:   284
1:43:56.208594 PROGRESS: 
1:43:56.208647 PROGRESS: Protein Summary:
1:43:56.209959 PROGRESS: Channel   0:	 0.05 FDR:   428; 0.01 FDR:   303; 0.001 FDR:   278
1:43:56.210050 PROGRESS: =========================================================================
1:43:56.261977 INFO: fragments_df: keeping 3072 of 716049 [sum(precursor_idx_mask)=6397 sum(mass_error_mask)=716048 stop_rank=3072
1:43:56.421954 INFO: calibration group: precursor, fitting mz estimator 
1:43:56.539428 INFO: calibration group: precursor, fitting rt estimator 
1:43:56.648390 INFO: calibration group: precursor, fitting mobility estimator 
1:43:56.756286 INFO: calibration group: fragment, fitting mz estimator 
1:43:57.103400 INFO: Using score_cutoff 39.10218760299683 (fac=0.99, q=1)
1:43:57.103900 INFO: calibration group: precursor, predicting mz
1:43:57.111364 INFO: calibration group: precursor, predicting rt
1:43:57.141666 INFO: calibration group: precursor, predicting mobility
1:43:57.148746 INFO: calibration group: fragment, predicting mz
1:43:57.211089 INFO: === checking if optimization conditions were reached ===
1:43:57.211473 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1:43:57.214030 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0604.
1:43:57.214109 INFO: ==============================================
1:43:57.214226 INFO: Starting optimization step 2.
1:43:57.214304 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:43:57.214390 PROGRESS: Extracting batch of 49998 precursors
1:43:57.237856 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:43:57.238011 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:43:57.238082 INFO: FWHM in RT is 2.83 seconds, sigma is 0.62
1:43:57.238722 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.61
1:43:57.247588 INFO: Starting candidate selection
1:44:08.052453 INFO: Starting candidate scoring
1:44:10.010788 INFO: Finished candidate processing
1:44:10.010914 INFO: Collecting candidate features
1:44:10.145996 WARNING: intensity_correlation has 75 NaNs ( 0.10 % out of 78334)
1:44:10.146288 WARNING: height_correlation has 10 NaNs ( 0.01 % out of 78334)
1:44:10.153155 INFO: Collecting fragment features
1:44:10.202538 INFO: Finished candidate scoring
1:44:10.250130 PROGRESS: === Extracted 78334 precursors and 699998 fragments ===
1:44:10.250508 INFO: performing precursor FDR with 47 features
1:44:10.250563 INFO: Decoy channel: -1
1:44:10.250587 INFO: Competetive: True
1:44:10.274188 INFO: Setting torch num_threads to 2 for FDR classification task
1:44:10.289374 WARNING: dropped 48 target PSMs due to missing features
1:44:10.289503 WARNING: dropped 34 decoy PSMs due to missing features
1:44:11.521261 INFO: Test AUC: 0.554
1:44:11.521388 INFO: Train AUC: 0.603
1:44:11.521419 INFO: AUC difference: 8.05%
1:44:11.521440 WARNING: AUC difference > 5%. This may indicate overfitting.
1:44:11.725445 INFO: Resetting torch num_threads to 128
1:44:11.728538 INFO: === FDR correction performed with classifier version 24 ===
1:44:11.732104 PROGRESS: ============================= Precursor FDR =============================
1:44:11.732239 PROGRESS: Total precursors accumulated: 21,281
1:44:11.732299 PROGRESS: Target precursors: 13,171 (61.89%)
1:44:11.732350 PROGRESS: Decoy precursors: 8,110 (38.11%)
1:44:11.732395 PROGRESS: 
1:44:11.732436 PROGRESS: Precursor Summary:
1:44:11.733559 PROGRESS: Channel   0:	 0.05 FDR:   462; 0.01 FDR:   311; 0.001 FDR:   142
1:44:11.733648 PROGRESS: 
1:44:11.733702 PROGRESS: Protein Summary:
1:44:11.734939 PROGRESS: Channel   0:	 0.05 FDR:   448; 0.01 FDR:   302; 0.001 FDR:   140
1:44:11.735038 PROGRESS: =========================================================================
1:44:11.783529 INFO: fragments_df: keeping 3015 of 699998 [sum(precursor_idx_mask)=6353 sum(mass_error_mask)=699997 stop_rank=3015
1:44:11.908166 INFO: calibration group: precursor, fitting mz estimator 
1:44:12.009174 INFO: calibration group: precursor, fitting rt estimator 
1:44:12.110563 INFO: calibration group: precursor, fitting mobility estimator 
1:44:12.209773 INFO: calibration group: fragment, fitting mz estimator 
1:44:12.541222 INFO: Using score_cutoff 39.87164952850342 (fac=0.99, q=1)
1:44:12.541621 INFO: calibration group: precursor, predicting mz
1:44:12.548960 INFO: calibration group: precursor, predicting rt
1:44:12.579363 INFO: calibration group: precursor, predicting mobility
1:44:12.586394 INFO: calibration group: fragment, predicting mz
1:44:12.642945 INFO: === checking if optimization conditions were reached ===
1:44:12.643262 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1:44:12.644355 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.0604 found after 3 searches.
1:44:12.644412 INFO: ==============================================
1:44:12.644510 PROGRESS: Optimization finished for mobility_error.
1:44:12.774188 INFO: calibration group: precursor, predicting mz
1:44:12.781850 INFO: calibration group: precursor, predicting rt
1:44:12.812335 INFO: calibration group: precursor, predicting mobility
1:44:12.819494 INFO: calibration group: fragment, predicting mz
1:44:12.904493 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:44:12.904695 PROGRESS: ==============================================
1:44:12.904768 PROGRESS: ms2_error      : 10.0349
1:44:12.904831 PROGRESS: rt_error       : 144.4238
1:44:12.904885 PROGRESS: ms1_error      : 12.2562
1:44:12.904932 PROGRESS: mobility_error : 0.0604
1:44:12.904973 PROGRESS: ==============================================
1:44:12.907745 INFO: calibration group: precursor, predicting mz
1:44:14.345716 INFO: calibration group: precursor, predicting rt
1:44:20.886908 INFO: calibration group: precursor, predicting mobility
1:44:22.351692 INFO: calibration group: fragment, predicting mz
1:44:35.457387 PROGRESS: Extracting batch of 10272670 precursors
1:44:38.560258 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:44:38.560400 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:44:38.560453 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
1:44:38.560479 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.64
1:44:38.593159 INFO: Starting candidate selection
2:17:11.034012 INFO: Applying score cutoff of 39.87164952850342
2:17:11.250063 INFO: Removed 11554478 precursors with score below cutoff
2:17:13.794432 INFO: Starting candidate scoring
2:19:46.875783 INFO: Finished candidate processing
2:19:46.876311 INFO: Collecting candidate features
2:19:59.392632 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 5764163)
2:19:59.725445 INFO: Collecting fragment features
2:20:04.962174 INFO: Finished candidate scoring
2:20:10.821227 INFO: === FDR correction performed with classifier version 28 ===
2:20:10.823573 INFO: performing precursor FDR with 47 features
2:20:10.823650 INFO: Decoy channel: -1
2:20:10.823680 INFO: Competetive: True
2:20:12.475597 INFO: Setting torch num_threads to 2 for FDR classification task
2:20:13.360013 WARNING: dropped 2 decoy PSMs due to missing features
2:22:04.190034 INFO: Test AUC: 0.567
2:22:04.190297 INFO: Train AUC: 0.570
2:22:04.190335 INFO: AUC difference: 0.61%
2:22:05.902247 INFO: Resetting torch num_threads to 128
2:22:06.085920 INFO: Removing fragments below FDR threshold
2:22:08.201460 PROGRESS: ============================= Precursor FDR =============================
2:22:08.201744 PROGRESS: Total precursors accumulated: 74,079
2:22:08.201809 PROGRESS: Target precursors: 73,346 (99.01%)
2:22:08.201865 PROGRESS: Decoy precursors: 733 (0.99%)
2:22:08.201915 PROGRESS: 
2:22:08.201961 PROGRESS: Precursor Summary:
2:22:08.233717 PROGRESS: Channel   0:	 0.05 FDR: 73,346; 0.01 FDR: 73,346; 0.001 FDR: 54,433
2:22:08.233982 PROGRESS: 
2:22:08.234046 PROGRESS: Protein Summary:
2:22:08.276736 PROGRESS: Channel   0:	 0.05 FDR: 11,529; 0.01 FDR: 11,529; 0.001 FDR: 9,318
2:22:08.276976 PROGRESS: =========================================================================
2:22:09.068560 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
2:22:10.037415 PROGRESS: Loading raw file 2/6: ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
2:22:10.037677 INFO: Quantification results path: run_output/alphadia_1.10.4_Again_good_now/library/quant
2:22:10.037771 INFO: Creating folder run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/figures
2:22:10.039234 INFO: Initializing RawFileManager
2:22:10.039392 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:22:10.039453 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:22:10.039498 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:22:10.267862 INFO: Reading 39,128 frames with 2,860,596,893 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:22:18.169726 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d...
2:22:18.170958 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:22:18.175262 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:22:18.175519 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:22:18.175906 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:22:18.177330 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:22:18.199218 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:22:18.199794 INFO: Indexing quadrupole dimension
2:22:18.778801 INFO: Transposing detector events
2:22:27.783608 INFO: Finished transposing data
2:22:27.823968 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
2:22:27.825904 INFO: RT (min)            : 0.0 - 70.0
2:22:27.826018 INFO: RT duration (sec)   : 4199.8
2:22:27.826078 INFO: RT duration (min)   : 70.0
2:22:27.826132 INFO: Cycle len (scans)   : 9
2:22:27.826181 INFO: Cycle len (sec)     : 0.97
2:22:27.826229 INFO: Number of cycles    : 4347
2:22:27.826278 INFO: MS2 range (m/z)     : 400.0 - 1000.0
2:22:29.111146 INFO: Initializing CalibrationManager
2:22:29.111461 INFO: Loading calibration config
2:22:29.112842 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed'], 'function': LOESSRegression()}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed'], 'function': LOESSRegression(n_kernels=2)}], 'name': 'precursor'}]
2:22:29.112940 INFO: Calibration group :fragment, found 1 estimator(s)
2:22:29.113048 INFO: Calibration group :precursor, found 3 estimator(s)
2:22:29.113235 INFO: Initializing OptimizationManager
2:22:29.113344 INFO: initial parameter: ms1_error = 30
2:22:29.113396 INFO: initial parameter: ms2_error = 30
2:22:29.113457 INFO: initial parameter: rt_error = 2099.894844
2:22:29.113507 INFO: initial parameter: mobility_error = 0.1
2:22:29.113555 INFO: initial parameter: column_type = library
2:22:29.113598 INFO: initial parameter: num_candidates = 1
2:22:29.113639 INFO: initial parameter: classifier_version = -1
2:22:29.113678 INFO: initial parameter: fwhm_rt = 5
2:22:29.113719 INFO: initial parameter: fwhm_mobility = 0.01
2:22:29.113760 INFO: initial parameter: score_cutoff = 0
2:22:29.113828 INFO: Initializing TimingManager
2:22:29.113895 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
2:22:29.114023 INFO: FDRManager not loaded from disk.
2:22:29.114048 INFO: Initializing FDRManager
2:22:29.114084 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
2:22:30.443881 PROGRESS: 5,215,079 target precursors potentially observable (0 removed)
2:22:32.366076 PROGRESS: Starting initial search for precursors.
2:22:32.584045 INFO: Starting optimization step 0.
2:22:32.584287 PROGRESS: === Extracting elution groups 0 to 200 ===
2:22:32.584363 PROGRESS: Extracting batch of 398 precursors
2:22:32.585372 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:22:32.585419 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:22:32.585453 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
2:22:32.585475 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
2:22:32.618747 INFO: Starting candidate selection
2:22:37.515858 INFO: Starting candidate scoring
2:22:37.595011 INFO: Finished candidate processing
2:22:37.595186 INFO: Collecting candidate features
2:22:37.606174 INFO: Collecting fragment features
2:22:37.608608 INFO: Finished candidate scoring
2:22:37.610122 PROGRESS: === Extracted 338 precursors and 3478 fragments ===
2:22:37.610544 INFO: performing precursor FDR with 47 features
2:22:37.610584 INFO: Decoy channel: -1
2:22:37.610609 INFO: Competetive: True
2:22:37.611883 INFO: Setting torch num_threads to 2 for FDR classification task
2:22:37.625224 INFO: Test AUC: 0.591
2:22:37.625299 INFO: Train AUC: 0.532
2:22:37.625330 INFO: AUC difference: 11.04%
2:22:37.625353 WARNING: AUC difference > 5%. This may indicate overfitting.
2:22:37.803523 INFO: Resetting torch num_threads to 100
2:22:37.804068 INFO: === FDR correction performed with classifier version -1 ===
2:22:37.804653 PROGRESS: ============================= Precursor FDR =============================
2:22:37.804744 PROGRESS: Total precursors accumulated: 175
2:22:37.804802 PROGRESS: Target precursors: 86 (49.14%)
2:22:37.804852 PROGRESS: Decoy precursors: 89 (50.86%)
2:22:37.804898 PROGRESS: 
2:22:37.804943 PROGRESS: Precursor Summary:
2:22:37.805781 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:22:37.805868 PROGRESS: 
2:22:37.805923 PROGRESS: Protein Summary:
2:22:37.806837 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:22:37.806925 PROGRESS: =========================================================================
2:22:37.862748 INFO: Starting optimization step 1.
2:22:37.862999 PROGRESS: === Extracting elution groups 200 to 600 ===
2:22:37.863081 PROGRESS: Extracting batch of 786 precursors
2:22:37.863920 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:22:37.863966 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:22:37.863994 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
2:22:37.864017 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
2:22:37.864741 INFO: Starting candidate selection
2:22:44.316332 INFO: Starting candidate scoring
2:22:44.424807 INFO: Finished candidate processing
2:22:44.424932 INFO: Collecting candidate features
2:22:44.436052 INFO: Collecting fragment features
2:22:44.439102 INFO: Finished candidate scoring
2:22:44.441782 PROGRESS: === Extracted 1052 precursors and 10772 fragments ===
2:22:44.442576 INFO: performing precursor FDR with 47 features
2:22:44.442620 INFO: Decoy channel: -1
2:22:44.442644 INFO: Competetive: True
2:22:44.445541 INFO: Setting torch num_threads to 2 for FDR classification task
2:22:44.457942 INFO: Test AUC: 0.553
2:22:44.458017 INFO: Train AUC: 0.523
2:22:44.458048 INFO: AUC difference: 5.63%
2:22:44.458073 WARNING: AUC difference > 5%. This may indicate overfitting.
2:22:44.639403 INFO: Resetting torch num_threads to 100
2:22:44.640128 INFO: === FDR correction performed with classifier version -1 ===
2:22:44.640818 PROGRESS: ============================= Precursor FDR =============================
2:22:44.640912 PROGRESS: Total precursors accumulated: 540
2:22:44.640974 PROGRESS: Target precursors: 291 (53.89%)
2:22:44.641026 PROGRESS: Decoy precursors: 249 (46.11%)
2:22:44.641073 PROGRESS: 
2:22:44.641118 PROGRESS: Precursor Summary:
2:22:44.641965 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:22:44.642057 PROGRESS: 
2:22:44.642115 PROGRESS: Protein Summary:
2:22:44.643004 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:22:44.643117 PROGRESS: =========================================================================
2:22:44.972347 INFO: Starting optimization step 2.
2:22:44.972648 PROGRESS: === Extracting elution groups 600 to 1400 ===
2:22:44.972724 PROGRESS: Extracting batch of 1566 precursors
2:22:44.974360 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:22:44.974411 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:22:44.974441 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
2:22:44.974467 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
2:22:44.975343 INFO: Starting candidate selection
2:22:54.036951 INFO: Starting candidate scoring
2:22:54.186917 INFO: Finished candidate processing
2:22:54.187091 INFO: Collecting candidate features
2:22:54.209955 INFO: Collecting fragment features
2:22:54.217387 INFO: Finished candidate scoring
2:22:54.222146 PROGRESS: === Extracted 2432 precursors and 24465 fragments ===
2:22:54.224067 INFO: performing precursor FDR with 47 features
2:22:54.224150 INFO: Decoy channel: -1
2:22:54.224191 INFO: Competetive: True
2:22:54.228943 INFO: Setting torch num_threads to 2 for FDR classification task
2:22:54.248136 INFO: Test AUC: 0.518
2:22:54.248204 INFO: Train AUC: 0.533
2:22:54.248233 INFO: AUC difference: 2.91%
2:22:54.431642 INFO: Resetting torch num_threads to 100
2:22:54.432475 INFO: === FDR correction performed with classifier version -1 ===
2:22:54.433192 PROGRESS: ============================= Precursor FDR =============================
2:22:54.433286 PROGRESS: Total precursors accumulated: 1,254
2:22:54.433348 PROGRESS: Target precursors: 680 (54.23%)
2:22:54.433398 PROGRESS: Decoy precursors: 574 (45.77%)
2:22:54.433444 PROGRESS: 
2:22:54.433488 PROGRESS: Precursor Summary:
2:22:54.434331 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:22:54.434418 PROGRESS: 
2:22:54.434474 PROGRESS: Protein Summary:
2:22:54.435374 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:22:54.435462 PROGRESS: =========================================================================
2:22:54.498279 INFO: Starting optimization step 3.
2:22:54.498487 PROGRESS: === Extracting elution groups 1400 to 3000 ===
2:22:54.498555 PROGRESS: Extracting batch of 3160 precursors
2:22:54.500051 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:22:54.500102 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:22:54.500131 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
2:22:54.500153 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
2:22:54.500884 INFO: Starting candidate selection
2:23:12.014424 INFO: Starting candidate scoring
2:23:12.252429 INFO: Finished candidate processing
2:23:12.252586 INFO: Collecting candidate features
2:23:12.281778 INFO: Collecting fragment features
2:23:12.291818 INFO: Finished candidate scoring
2:23:12.307438 PROGRESS: === Extracted 5193 precursors and 52172 fragments ===
2:23:12.309369 INFO: performing precursor FDR with 47 features
2:23:12.309441 INFO: Decoy channel: -1
2:23:12.309480 INFO: Competetive: True
2:23:12.316232 INFO: Setting torch num_threads to 2 for FDR classification task
2:23:12.339785 INFO: Test AUC: 0.541
2:23:12.339870 INFO: Train AUC: 0.512
2:23:12.339900 INFO: AUC difference: 5.68%
2:23:12.339921 WARNING: AUC difference > 5%. This may indicate overfitting.
2:23:12.517674 INFO: Resetting torch num_threads to 100
2:23:12.518773 INFO: === FDR correction performed with classifier version -1 ===
2:23:12.519694 PROGRESS: ============================= Precursor FDR =============================
2:23:12.519787 PROGRESS: Total precursors accumulated: 2,665
2:23:12.519848 PROGRESS: Target precursors: 1,413 (53.02%)
2:23:12.519899 PROGRESS: Decoy precursors: 1,252 (46.98%)
2:23:12.519944 PROGRESS: 
2:23:12.519993 PROGRESS: Precursor Summary:
2:23:12.520834 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:23:12.520920 PROGRESS: 
2:23:12.520975 PROGRESS: Protein Summary:
2:23:12.521873 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:23:12.521958 PROGRESS: =========================================================================
2:23:12.604279 INFO: Starting optimization step 4.
2:23:12.604517 PROGRESS: === Extracting elution groups 3000 to 6200 ===
2:23:12.604601 PROGRESS: Extracting batch of 6310 precursors
2:23:12.606370 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:23:12.606416 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:23:12.606450 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
2:23:12.606472 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
2:23:12.607220 INFO: Starting candidate selection
2:23:47.279846 INFO: Starting candidate scoring
2:23:47.713209 INFO: Finished candidate processing
2:23:47.713319 INFO: Collecting candidate features
2:23:47.727771 WARNING: intensity_correlation has 1 NaNs ( 0.02 % out of 5498)
2:23:47.730812 INFO: Collecting fragment features
2:23:47.735868 INFO: Finished candidate scoring
2:23:47.743201 PROGRESS: === Extracted 10691 precursors and 107833 fragments ===
2:23:47.744856 INFO: performing precursor FDR with 47 features
2:23:47.744906 INFO: Decoy channel: -1
2:23:47.744931 INFO: Competetive: True
2:23:47.750365 INFO: Setting torch num_threads to 2 for FDR classification task
2:23:47.752522 WARNING: dropped 1 target PSMs due to missing features
2:23:47.791181 INFO: Test AUC: 0.529
2:23:47.791292 INFO: Train AUC: 0.505
2:23:47.791321 INFO: AUC difference: 4.85%
2:23:47.973347 INFO: Resetting torch num_threads to 100
2:23:47.974737 INFO: === FDR correction performed with classifier version -1 ===
2:23:47.975981 PROGRESS: ============================= Precursor FDR =============================
2:23:47.976082 PROGRESS: Total precursors accumulated: 5,487
2:23:47.976142 PROGRESS: Target precursors: 2,879 (52.47%)
2:23:47.976192 PROGRESS: Decoy precursors: 2,608 (47.53%)
2:23:47.976238 PROGRESS: 
2:23:47.976284 PROGRESS: Precursor Summary:
2:23:47.977191 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:23:47.977283 PROGRESS: 
2:23:47.977340 PROGRESS: Protein Summary:
2:23:47.978296 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:23:47.978382 PROGRESS: =========================================================================
2:23:48.085123 INFO: Starting optimization step 5.
2:23:48.085364 PROGRESS: === Extracting elution groups 6200 to 12600 ===
2:23:48.085432 PROGRESS: Extracting batch of 12602 precursors
2:23:48.089407 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:23:48.089463 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:23:48.089490 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
2:23:48.089512 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
2:23:48.090224 INFO: Starting candidate selection
2:24:55.213638 INFO: Starting candidate scoring
2:24:55.866214 INFO: Finished candidate processing
2:24:55.866372 INFO: Collecting candidate features
2:24:55.920030 WARNING: intensity_correlation has 1 NaNs ( 0.01 % out of 10999)
2:24:55.928021 INFO: Collecting fragment features
2:24:55.940068 INFO: Finished candidate scoring
2:24:55.973324 PROGRESS: === Extracted 21690 precursors and 217891 fragments ===
2:24:55.976358 INFO: performing precursor FDR with 47 features
2:24:55.976429 INFO: Decoy channel: -1
2:24:55.976456 INFO: Competetive: True
2:24:55.986819 INFO: Setting torch num_threads to 2 for FDR classification task
2:24:55.991405 WARNING: dropped 1 target PSMs due to missing features
2:24:55.991504 WARNING: dropped 1 decoy PSMs due to missing features
2:24:56.335489 INFO: Test AUC: 0.541
2:24:56.335631 INFO: Train AUC: 0.564
2:24:56.335660 INFO: AUC difference: 3.98%
2:24:56.535400 INFO: Resetting torch num_threads to 100
2:24:56.537460 INFO: === FDR correction performed with classifier version -1 ===
2:24:56.539591 PROGRESS: ============================= Precursor FDR =============================
2:24:56.539715 PROGRESS: Total precursors accumulated: 11,121
2:24:56.539777 PROGRESS: Target precursors: 6,540 (58.81%)
2:24:56.539831 PROGRESS: Decoy precursors: 4,581 (41.19%)
2:24:56.539891 PROGRESS: 
2:24:56.539942 PROGRESS: Precursor Summary:
2:24:56.540887 PROGRESS: Channel   0:	 0.05 FDR:     5; 0.01 FDR:     5; 0.001 FDR:     5
2:24:56.540980 PROGRESS: 
2:24:56.541036 PROGRESS: Protein Summary:
2:24:56.542054 PROGRESS: Channel   0:	 0.05 FDR:     5; 0.01 FDR:     5; 0.001 FDR:     5
2:24:56.542144 PROGRESS: =========================================================================
2:24:56.726791 INFO: Starting optimization step 6.
2:24:56.727097 PROGRESS: === Extracting elution groups 12600 to 25400 ===
2:24:56.727210 PROGRESS: Extracting batch of 25176 precursors
2:24:56.734360 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:24:56.734435 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:24:56.734488 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
2:24:56.734509 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
2:24:56.735589 INFO: Starting candidate selection
2:27:03.409469 INFO: Starting candidate scoring
2:27:04.829348 INFO: Finished candidate processing
2:27:04.830488 INFO: Collecting candidate features
2:27:04.902960 WARNING: intensity_correlation has 7 NaNs ( 0.03 % out of 21928)
2:27:04.903247 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 21928)
2:27:04.907027 INFO: Collecting fragment features
2:27:04.922948 INFO: Finished candidate scoring
2:27:04.979277 PROGRESS: === Extracted 43618 precursors and 436583 fragments ===
2:27:04.987828 INFO: performing precursor FDR with 47 features
2:27:04.987934 INFO: Decoy channel: -1
2:27:04.987961 INFO: Competetive: True
2:27:05.013007 INFO: Setting torch num_threads to 2 for FDR classification task
2:27:05.026052 WARNING: dropped 4 target PSMs due to missing features
2:27:05.026201 WARNING: dropped 5 decoy PSMs due to missing features
2:27:05.721381 INFO: Test AUC: 0.569
2:27:05.721514 INFO: Train AUC: 0.579
2:27:05.721545 INFO: AUC difference: 1.64%
2:27:05.916719 INFO: Resetting torch num_threads to 100
2:27:05.919742 INFO: === FDR correction performed with classifier version -1 ===
2:27:05.923537 PROGRESS: ============================= Precursor FDR =============================
2:27:05.923701 PROGRESS: Total precursors accumulated: 22,377
2:27:05.923765 PROGRESS: Target precursors: 13,603 (60.79%)
2:27:05.923818 PROGRESS: Decoy precursors: 8,774 (39.21%)
2:27:05.923863 PROGRESS: 
2:27:05.923906 PROGRESS: Precursor Summary:
2:27:05.925016 PROGRESS: Channel   0:	 0.05 FDR:   121; 0.01 FDR:    45; 0.001 FDR:    45
2:27:05.925108 PROGRESS: 
2:27:05.925164 PROGRESS: Protein Summary:
2:27:05.926303 PROGRESS: Channel   0:	 0.05 FDR:   119; 0.01 FDR:    45; 0.001 FDR:    45
2:27:05.926394 PROGRESS: =========================================================================
2:27:06.291743 INFO: Starting optimization step 7.
2:27:06.292032 PROGRESS: === Extracting elution groups 25400 to 51000 ===
2:27:06.292119 PROGRESS: Extracting batch of 50417 precursors
2:27:06.304896 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:27:06.305016 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:27:06.305054 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
2:27:06.305077 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
2:27:06.312535 INFO: Starting candidate selection
2:31:20.673923 INFO: Starting candidate scoring
2:31:22.988307 INFO: Finished candidate processing
2:31:22.988482 INFO: Collecting candidate features
2:31:23.093526 WARNING: intensity_correlation has 10 NaNs ( 0.02 % out of 44023)
2:31:23.098411 INFO: Collecting fragment features
2:31:23.128458 INFO: Finished candidate scoring
2:31:23.254431 PROGRESS: === Extracted 87641 precursors and 877587 fragments ===
2:31:23.268359 INFO: performing precursor FDR with 47 features
2:31:23.268452 INFO: Decoy channel: -1
2:31:23.268479 INFO: Competetive: True
2:31:23.312591 INFO: Setting torch num_threads to 2 for FDR classification task
2:31:23.332986 WARNING: dropped 11 target PSMs due to missing features
2:31:23.333132 WARNING: dropped 8 decoy PSMs due to missing features
2:31:24.899960 INFO: Test AUC: 0.560
2:31:24.900125 INFO: Train AUC: 0.594
2:31:24.900160 INFO: AUC difference: 5.67%
2:31:24.900184 WARNING: AUC difference > 5%. This may indicate overfitting.
2:31:25.107274 INFO: Resetting torch num_threads to 100
2:31:25.112056 INFO: === FDR correction performed with classifier version -1 ===
2:31:25.120263 PROGRESS: ============================= Precursor FDR =============================
2:31:25.120546 PROGRESS: Total precursors accumulated: 44,950
2:31:25.120613 PROGRESS: Target precursors: 27,714 (61.66%)
2:31:25.120664 PROGRESS: Decoy precursors: 17,236 (38.34%)
2:31:25.120715 PROGRESS: 
2:31:25.120760 PROGRESS: Precursor Summary:
2:31:25.122138 PROGRESS: Channel   0:	 0.05 FDR:   433; 0.01 FDR:   310; 0.001 FDR:    37
2:31:25.122235 PROGRESS: 
2:31:25.122293 PROGRESS: Protein Summary:
2:31:25.123652 PROGRESS: Channel   0:	 0.05 FDR:   409; 0.01 FDR:   297; 0.001 FDR:    37
2:31:25.123753 PROGRESS: =========================================================================
2:31:25.191352 INFO: fragments_df: keeping 2759 of 877587 [sum(precursor_idx_mask)=3438 sum(mass_error_mask)=877587 stop_rank=2759
2:31:25.419425 INFO: calibration group: precursor, fitting mz estimator 
2:31:25.531325 INFO: calibration group: precursor, fitting rt estimator 
2:31:25.636138 INFO: calibration group: precursor, fitting mobility estimator 
2:31:25.745688 INFO: calibration group: fragment, fitting mz estimator 
2:31:26.042824 INFO: Using score_cutoff 54.58001510810852 (fac=0.99, q=1)
2:31:26.043337 INFO: calibration group: precursor, predicting mz
2:31:26.056576 INFO: calibration group: precursor, predicting rt
2:31:26.117644 INFO: calibration group: precursor, predicting mobility
2:31:26.132616 INFO: calibration group: fragment, predicting mz
2:31:26.258260 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:31:26.258565 INFO: Starting optimization step 8.
2:31:26.258638 PROGRESS: === Extracting elution groups 0 to 51000 ===
2:31:26.258711 PROGRESS: Extracting batch of 100415 precursors
2:31:26.288164 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:31:26.288304 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:31:26.288357 INFO: FWHM in RT is 3.35 seconds, sigma is 0.74
2:31:26.288382 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.14
2:31:26.312577 INFO: Starting candidate selection
2:40:03.877104 INFO: Starting candidate scoring
2:40:13.250795 INFO: Finished candidate processing
2:40:13.253618 INFO: Collecting candidate features
2:40:13.813615 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 172519)
2:40:13.824074 INFO: Collecting fragment features
2:40:13.954412 INFO: Finished candidate scoring
2:40:14.090027 PROGRESS: === Extracted 172519 precursors and 1756967 fragments ===
2:40:14.090597 INFO: performing precursor FDR with 47 features
2:40:14.090638 INFO: Decoy channel: -1
2:40:14.090664 INFO: Competetive: True
2:40:14.162484 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:14.195305 WARNING: dropped 2 decoy PSMs due to missing features
2:40:17.913883 INFO: Test AUC: 0.568
2:40:17.914031 INFO: Train AUC: 0.595
2:40:17.914063 INFO: AUC difference: 4.51%
2:40:18.147593 INFO: Resetting torch num_threads to 100
2:40:18.153135 INFO: === FDR correction performed with classifier version 7 ===
2:40:18.162591 PROGRESS: ============================= Precursor FDR =============================
2:40:18.162858 PROGRESS: Total precursors accumulated: 45,832
2:40:18.162924 PROGRESS: Target precursors: 29,054 (63.39%)
2:40:18.162975 PROGRESS: Decoy precursors: 16,778 (36.61%)
2:40:18.163033 PROGRESS: 
2:40:18.163081 PROGRESS: Precursor Summary:
2:40:18.164500 PROGRESS: Channel   0:	 0.05 FDR:   463; 0.01 FDR:   361; 0.001 FDR:   281
2:40:18.164605 PROGRESS: 
2:40:18.164662 PROGRESS: Protein Summary:
2:40:18.166074 PROGRESS: Channel   0:	 0.05 FDR:   436; 0.01 FDR:   344; 0.001 FDR:   271
2:40:18.166168 PROGRESS: =========================================================================
2:40:18.286480 INFO: fragments_df: keeping 4404 of 1756967 [sum(precursor_idx_mask)=7660 sum(mass_error_mask)=1756967 stop_rank=4404
2:40:18.503582 INFO: calibration group: precursor, fitting mz estimator 
2:40:18.631464 INFO: calibration group: precursor, fitting rt estimator 
2:40:18.759104 INFO: calibration group: precursor, fitting mobility estimator 
2:40:18.888691 INFO: calibration group: fragment, fitting mz estimator 
2:40:19.464754 INFO: Using score_cutoff 50.47043444824219 (fac=0.99, q=1)
2:40:19.465209 INFO: calibration group: precursor, predicting mz
2:40:19.478322 INFO: calibration group: precursor, predicting rt
2:40:19.540096 INFO: calibration group: precursor, predicting mobility
2:40:19.553292 INFO: calibration group: fragment, predicting mz
2:40:19.675802 INFO: === checking if optimization conditions were reached ===
2:40:19.676123 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
2:40:19.678618 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 18.2300.
2:40:19.679354 INFO: ==============================================
2:40:19.679463 INFO: Starting optimization step 9.
2:40:19.679530 PROGRESS: === Extracting elution groups 0 to 51000 ===
2:40:19.679605 PROGRESS: Extracting batch of 100415 precursors
2:40:19.707840 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:40:19.707989 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:40:19.708040 INFO: FWHM in RT is 3.26 seconds, sigma is 0.72
2:40:19.708063 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.07
2:40:19.717111 INFO: Starting candidate selection
2:50:45.701039 INFO: Starting candidate scoring
2:50:53.273839 INFO: Finished candidate processing
2:50:53.274033 INFO: Collecting candidate features
2:50:53.604801 WARNING: intensity_correlation has 6 NaNs ( 0.00 % out of 172427)
2:50:53.616713 INFO: Collecting fragment features
2:50:53.724063 INFO: Finished candidate scoring
2:50:53.831123 PROGRESS: === Extracted 172427 precursors and 1716314 fragments ===
2:50:53.831636 INFO: performing precursor FDR with 47 features
2:50:53.831678 INFO: Decoy channel: -1
2:50:53.831701 INFO: Competetive: True
2:50:53.897208 INFO: Setting torch num_threads to 2 for FDR classification task
2:50:53.931718 WARNING: dropped 6 decoy PSMs due to missing features
2:50:57.109460 INFO: Test AUC: 0.561
2:50:57.109615 INFO: Train AUC: 0.595
2:50:57.109645 INFO: AUC difference: 5.65%
2:50:57.109666 WARNING: AUC difference > 5%. This may indicate overfitting.
2:50:57.345204 INFO: Resetting torch num_threads to 100
2:50:57.351436 INFO: === FDR correction performed with classifier version 7 ===
2:50:57.360067 PROGRESS: ============================= Precursor FDR =============================
2:50:57.360232 PROGRESS: Total precursors accumulated: 45,812
2:50:57.360294 PROGRESS: Target precursors: 28,750 (62.76%)
2:50:57.360345 PROGRESS: Decoy precursors: 17,062 (37.24%)
2:50:57.360388 PROGRESS: 
2:50:57.360434 PROGRESS: Precursor Summary:
2:50:57.361846 PROGRESS: Channel   0:	 0.05 FDR:   579; 0.01 FDR:   476; 0.001 FDR:   414
2:50:57.361945 PROGRESS: 
2:50:57.362010 PROGRESS: Protein Summary:
2:50:57.363567 PROGRESS: Channel   0:	 0.05 FDR:   546; 0.01 FDR:   449; 0.001 FDR:   392
2:50:57.363668 PROGRESS: =========================================================================
2:50:57.485022 INFO: fragments_df: keeping 5000 of 1716314 [sum(precursor_idx_mask)=10003 sum(mass_error_mask)=1716314 stop_rank=5000
2:50:57.627779 INFO: calibration group: precursor, fitting mz estimator 
2:50:57.763981 INFO: calibration group: precursor, fitting rt estimator 
2:50:57.901900 INFO: calibration group: precursor, fitting mobility estimator 
2:50:58.018676 INFO: calibration group: fragment, fitting mz estimator 
2:50:58.632197 INFO: Using score_cutoff 45.79270503044128 (fac=0.99, q=1)
2:50:58.632671 INFO: calibration group: precursor, predicting mz
2:50:58.639983 INFO: calibration group: precursor, predicting rt
2:50:58.669513 INFO: calibration group: precursor, predicting mobility
2:50:58.676031 INFO: calibration group: fragment, predicting mz
2:50:58.729828 INFO: === checking if optimization conditions were reached ===
2:50:58.730131 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
2:50:58.732804 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 9.1707.
2:50:58.732864 INFO: ==============================================
2:50:58.732965 INFO: Starting optimization step 10.
2:50:58.733032 PROGRESS: === Extracting elution groups 0 to 25400 ===
2:50:58.733101 PROGRESS: Extracting batch of 49998 precursors
2:50:58.749585 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:50:58.749711 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:50:58.749763 INFO: FWHM in RT is 3.02 seconds, sigma is 0.66
2:50:58.749787 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.59
2:50:58.758634 INFO: Starting candidate selection
2:56:42.308184 INFO: Starting candidate scoring
2:56:45.255663 INFO: Finished candidate processing
2:56:45.255805 INFO: Collecting candidate features
2:56:45.405313 WARNING: intensity_correlation has 7 NaNs ( 0.01 % out of 85986)
2:56:45.411767 INFO: Collecting fragment features
2:56:45.478150 INFO: Finished candidate scoring
2:56:45.610928 PROGRESS: === Extracted 85986 precursors and 813824 fragments ===
2:56:45.611440 INFO: performing precursor FDR with 47 features
2:56:45.611479 INFO: Decoy channel: -1
2:56:45.611501 INFO: Competetive: True
2:56:45.649476 INFO: Setting torch num_threads to 2 for FDR classification task
2:56:45.672364 WARNING: dropped 3 target PSMs due to missing features
2:56:45.672519 WARNING: dropped 4 decoy PSMs due to missing features
2:56:47.076891 INFO: Test AUC: 0.554
2:56:47.077041 INFO: Train AUC: 0.595
2:56:47.077072 INFO: AUC difference: 7.01%
2:56:47.077093 WARNING: AUC difference > 5%. This may indicate overfitting.
2:56:47.287241 INFO: Resetting torch num_threads to 100
2:56:47.290557 INFO: === FDR correction performed with classifier version 7 ===
2:56:47.294940 PROGRESS: ============================= Precursor FDR =============================
2:56:47.295094 PROGRESS: Total precursors accumulated: 22,814
2:56:47.295163 PROGRESS: Target precursors: 14,228 (62.37%)
2:56:47.295214 PROGRESS: Decoy precursors: 8,586 (37.63%)
2:56:47.295261 PROGRESS: 
2:56:47.295303 PROGRESS: Precursor Summary:
2:56:47.296423 PROGRESS: Channel   0:	 0.05 FDR:   271; 0.01 FDR:   212; 0.001 FDR:   159
2:56:47.296514 PROGRESS: 
2:56:47.296568 PROGRESS: Protein Summary:
2:56:47.297767 PROGRESS: Channel   0:	 0.05 FDR:   265; 0.01 FDR:   207; 0.001 FDR:   155
2:56:47.297857 PROGRESS: =========================================================================
2:56:47.377979 INFO: fragments_df: keeping 2352 of 813824 [sum(precursor_idx_mask)=4450 sum(mass_error_mask)=813824 stop_rank=2352
2:56:47.511937 INFO: calibration group: precursor, fitting mz estimator 
2:56:47.608539 INFO: calibration group: precursor, fitting rt estimator 
2:56:47.705594 INFO: calibration group: precursor, fitting mobility estimator 
2:56:47.799575 INFO: calibration group: fragment, fitting mz estimator 
2:56:48.057105 INFO: Using score_cutoff 44.81842235298157 (fac=0.99, q=1)
2:56:48.057561 INFO: calibration group: precursor, predicting mz
2:56:48.065228 INFO: calibration group: precursor, predicting rt
2:56:48.095513 INFO: calibration group: precursor, predicting mobility
2:56:48.103105 INFO: calibration group: fragment, predicting mz
2:56:48.159783 INFO: === checking if optimization conditions were reached ===
2:56:48.160066 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
2:56:48.162573 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 5.5799.
2:56:48.162634 INFO: ==============================================
2:56:48.162731 INFO: Starting optimization step 11.
2:56:48.162797 PROGRESS: === Extracting elution groups 0 to 25400 ===
2:56:48.162868 PROGRESS: Extracting batch of 49998 precursors
2:56:48.177862 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:56:48.177993 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:56:48.178044 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
2:56:48.178067 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.76
2:56:48.186816 INFO: Starting candidate selection
3:00:39.401992 INFO: Starting candidate scoring
3:00:41.440378 INFO: Finished candidate processing
3:00:41.440629 INFO: Collecting candidate features
3:00:41.755013 WARNING: intensity_correlation has 29 NaNs ( 0.03 % out of 85521)
3:00:41.755399 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 85521)
3:00:41.763505 INFO: Collecting fragment features
3:00:41.849118 INFO: Finished candidate scoring
3:00:41.930048 PROGRESS: === Extracted 85521 precursors and 753481 fragments ===
3:00:41.930633 INFO: performing precursor FDR with 47 features
3:00:41.930674 INFO: Decoy channel: -1
3:00:41.930699 INFO: Competetive: True
3:00:41.974068 INFO: Setting torch num_threads to 2 for FDR classification task
3:00:41.996305 WARNING: dropped 12 target PSMs due to missing features
3:00:41.996476 WARNING: dropped 18 decoy PSMs due to missing features
3:00:43.959063 INFO: Test AUC: 0.558
3:00:43.959744 INFO: Train AUC: 0.594
3:00:43.959833 INFO: AUC difference: 6.05%
3:00:43.959867 WARNING: AUC difference > 5%. This may indicate overfitting.
3:00:44.229867 INFO: Resetting torch num_threads to 100
3:00:44.234786 INFO: === FDR correction performed with classifier version 7 ===
3:00:44.241001 PROGRESS: ============================= Precursor FDR =============================
3:00:44.241180 PROGRESS: Total precursors accumulated: 22,754
3:00:44.241250 PROGRESS: Target precursors: 14,136 (62.13%)
3:00:44.241304 PROGRESS: Decoy precursors: 8,618 (37.87%)
3:00:44.241351 PROGRESS: 
3:00:44.241394 PROGRESS: Precursor Summary:
3:00:44.242532 PROGRESS: Channel   0:	 0.05 FDR:   252; 0.01 FDR:   130; 0.001 FDR:    70
3:00:44.242625 PROGRESS: 
3:00:44.242681 PROGRESS: Protein Summary:
3:00:44.243856 PROGRESS: Channel   0:	 0.05 FDR:   246; 0.01 FDR:   127; 0.001 FDR:    69
3:00:44.243952 PROGRESS: =========================================================================
3:00:44.478151 INFO: calibration group: precursor, predicting mz
3:00:44.486300 INFO: calibration group: precursor, predicting rt
3:00:44.517241 INFO: calibration group: precursor, predicting mobility
3:00:44.524911 INFO: calibration group: fragment, predicting mz
3:00:44.585008 INFO: === skipping optimization until target number of precursors are found ===
3:00:44.585313 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
3:00:44.585382 INFO: Starting optimization step 12.
3:00:44.585454 PROGRESS: === Extracting elution groups 25400 to 51000 ===
3:00:44.585530 PROGRESS: Extracting batch of 50417 precursors
3:00:44.601479 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:00:44.601597 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:00:44.601649 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
3:00:44.601674 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.76
3:00:44.610739 INFO: Starting candidate selection
3:04:51.081702 INFO: Starting candidate scoring
3:04:53.259667 INFO: Finished candidate processing
3:04:53.259786 INFO: Collecting candidate features
3:04:53.408691 WARNING: intensity_correlation has 23 NaNs ( 0.03 % out of 86225)
3:04:53.409065 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 86225)
3:04:53.415695 INFO: Collecting fragment features
3:04:53.478874 INFO: Finished candidate scoring
3:04:53.616230 PROGRESS: === Extracted 171746 precursors and 1512813 fragments ===
3:04:53.640869 INFO: performing precursor FDR with 47 features
3:04:53.641002 INFO: Decoy channel: -1
3:04:53.641027 INFO: Competetive: True
3:04:53.721644 INFO: Setting torch num_threads to 2 for FDR classification task
3:04:53.761236 WARNING: dropped 24 target PSMs due to missing features
3:04:53.761367 WARNING: dropped 30 decoy PSMs due to missing features
3:04:57.286750 INFO: Test AUC: 0.562
3:04:57.286885 INFO: Train AUC: 0.587
3:04:57.286916 INFO: AUC difference: 4.20%
3:04:57.521462 INFO: Resetting torch num_threads to 100
3:04:57.529310 INFO: === FDR correction performed with classifier version 7 ===
3:04:57.538479 PROGRESS: ============================= Precursor FDR =============================
3:04:57.538737 PROGRESS: Total precursors accumulated: 45,676
3:04:57.538801 PROGRESS: Target precursors: 28,151 (61.63%)
3:04:57.538852 PROGRESS: Decoy precursors: 17,525 (38.37%)
3:04:57.538900 PROGRESS: 
3:04:57.538944 PROGRESS: Precursor Summary:
3:04:57.540294 PROGRESS: Channel   0:	 0.05 FDR:   563; 0.01 FDR:   401; 0.001 FDR:   238
3:04:57.540393 PROGRESS: 
3:04:57.540451 PROGRESS: Protein Summary:
3:04:57.541855 PROGRESS: Channel   0:	 0.05 FDR:   527; 0.01 FDR:   375; 0.001 FDR:   227
3:04:57.541950 PROGRESS: =========================================================================
3:04:57.654829 INFO: fragments_df: keeping 4193 of 1512813 [sum(precursor_idx_mask)=8077 sum(mass_error_mask)=1512813 stop_rank=4193
3:04:57.863954 INFO: calibration group: precursor, fitting mz estimator 
3:04:57.974645 INFO: calibration group: precursor, fitting rt estimator 
3:04:58.080121 INFO: calibration group: precursor, fitting mobility estimator 
3:04:58.191547 INFO: calibration group: fragment, fitting mz estimator 
3:04:58.674509 INFO: Using score_cutoff 40.02559833526611 (fac=0.99, q=1)
3:04:58.674931 INFO: calibration group: precursor, predicting mz
3:04:58.687719 INFO: calibration group: precursor, predicting rt
3:04:58.749379 INFO: calibration group: precursor, predicting mobility
3:04:58.764691 INFO: calibration group: fragment, predicting mz
3:04:58.896175 INFO: === checking if optimization conditions were reached ===
3:04:58.896482 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
3:04:58.899442 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 4.7428.
3:04:58.899507 INFO: ==============================================
3:04:58.899620 INFO: Starting optimization step 13.
3:04:58.899693 PROGRESS: === Extracting elution groups 0 to 51000 ===
3:04:58.899776 PROGRESS: Extracting batch of 100415 precursors
3:04:58.938691 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:04:58.938848 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:04:58.938907 INFO: FWHM in RT is 2.53 seconds, sigma is 0.56
3:04:58.938937 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.97
3:04:58.947896 INFO: Starting candidate selection
3:12:56.177526 INFO: Starting candidate scoring
3:12:59.830795 INFO: Finished candidate processing
3:12:59.830971 INFO: Collecting candidate features
3:13:00.181444 WARNING: intensity_correlation has 79 NaNs ( 0.05 % out of 170932)
3:13:00.181848 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 170932)
3:13:00.191151 INFO: Collecting fragment features
3:13:00.299662 INFO: Finished candidate scoring
3:13:00.422840 PROGRESS: === Extracted 170932 precursors and 1419337 fragments ===
3:13:00.423292 INFO: performing precursor FDR with 47 features
3:13:00.423334 INFO: Decoy channel: -1
3:13:00.423360 INFO: Competetive: True
3:13:00.505448 INFO: Setting torch num_threads to 2 for FDR classification task
3:13:00.547348 WARNING: dropped 39 target PSMs due to missing features
3:13:00.547499 WARNING: dropped 42 decoy PSMs due to missing features
3:13:04.479574 INFO: Test AUC: 0.557
3:13:04.479715 INFO: Train AUC: 0.592
3:13:04.479748 INFO: AUC difference: 5.94%
3:13:04.479769 WARNING: AUC difference > 5%. This may indicate overfitting.
3:13:04.708416 INFO: Resetting torch num_threads to 100
3:13:04.713443 INFO: === FDR correction performed with classifier version 7 ===
3:13:04.721928 PROGRESS: ============================= Precursor FDR =============================
3:13:04.722249 PROGRESS: Total precursors accumulated: 45,608
3:13:04.722314 PROGRESS: Target precursors: 28,223 (61.88%)
3:13:04.722368 PROGRESS: Decoy precursors: 17,385 (38.12%)
3:13:04.722416 PROGRESS: 
3:13:04.722462 PROGRESS: Precursor Summary:
3:13:04.723820 PROGRESS: Channel   0:	 0.05 FDR:   466; 0.01 FDR:   330; 0.001 FDR:   230
3:13:04.723916 PROGRESS: 
3:13:04.723973 PROGRESS: Protein Summary:
3:13:04.725358 PROGRESS: Channel   0:	 0.05 FDR:   437; 0.01 FDR:   313; 0.001 FDR:   220
3:13:04.725452 PROGRESS: =========================================================================
3:13:04.822494 INFO: fragments_df: keeping 3521 of 1419337 [sum(precursor_idx_mask)=6479 sum(mass_error_mask)=1419337 stop_rank=3521
3:13:05.031987 INFO: calibration group: precursor, fitting mz estimator 
3:13:05.172704 INFO: calibration group: precursor, fitting rt estimator 
3:13:05.301803 INFO: calibration group: precursor, fitting mobility estimator 
3:13:05.435185 INFO: calibration group: fragment, fitting mz estimator 
3:13:05.918447 INFO: Using score_cutoff 40.4415825553894 (fac=0.99, q=1)
3:13:05.919109 INFO: calibration group: precursor, predicting mz
3:13:05.934058 INFO: calibration group: precursor, predicting rt
3:13:06.012503 INFO: calibration group: precursor, predicting mobility
3:13:06.040623 INFO: calibration group: fragment, predicting mz
3:13:06.167433 INFO: === checking if optimization conditions were reached ===
3:13:06.167812 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
3:13:06.170855 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 4.0807.
3:13:06.170923 INFO: ==============================================
3:13:06.171059 INFO: Starting optimization step 14.
3:13:06.171154 PROGRESS: === Extracting elution groups 0 to 51000 ===
3:13:06.171245 PROGRESS: Extracting batch of 100415 precursors
3:13:06.223445 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:13:06.223663 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:13:06.223735 INFO: FWHM in RT is 2.34 seconds, sigma is 0.52
3:13:06.223777 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.78
3:13:06.226509 INFO: Starting candidate selection
3:20:45.361769 INFO: Starting candidate scoring
3:20:48.996574 INFO: Finished candidate processing
3:20:48.996773 INFO: Collecting candidate features
3:20:49.342321 WARNING: intensity_correlation has 63 NaNs ( 0.04 % out of 170808)
3:20:49.342755 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 170808)
3:20:49.352946 INFO: Collecting fragment features
3:20:49.468520 INFO: Finished candidate scoring
3:20:49.560306 PROGRESS: === Extracted 170808 precursors and 1408870 fragments ===
3:20:49.561007 INFO: performing precursor FDR with 47 features
3:20:49.561053 INFO: Decoy channel: -1
3:20:49.561080 INFO: Competetive: True
3:20:49.633336 INFO: Setting torch num_threads to 2 for FDR classification task
3:20:49.674891 WARNING: dropped 27 target PSMs due to missing features
3:20:49.675061 WARNING: dropped 38 decoy PSMs due to missing features
3:20:53.430993 INFO: Test AUC: 0.563
3:20:53.431139 INFO: Train AUC: 0.590
3:20:53.431171 INFO: AUC difference: 4.68%
3:20:53.658113 INFO: Resetting torch num_threads to 100
3:20:53.665500 INFO: === FDR correction performed with classifier version 7 ===
3:20:53.676286 PROGRESS: ============================= Precursor FDR =============================
3:20:53.676554 PROGRESS: Total precursors accumulated: 45,571
3:20:53.676623 PROGRESS: Target precursors: 28,047 (61.55%)
3:20:53.676673 PROGRESS: Decoy precursors: 17,524 (38.45%)
3:20:53.676720 PROGRESS: 
3:20:53.676766 PROGRESS: Precursor Summary:
3:20:53.678183 PROGRESS: Channel   0:	 0.05 FDR:   466; 0.01 FDR:   351; 0.001 FDR:   250
3:20:53.678280 PROGRESS: 
3:20:53.678335 PROGRESS: Protein Summary:
3:20:53.679767 PROGRESS: Channel   0:	 0.05 FDR:   440; 0.01 FDR:   329; 0.001 FDR:   238
3:20:53.679865 PROGRESS: =========================================================================
3:20:53.778250 INFO: fragments_df: keeping 3620 of 1408870 [sum(precursor_idx_mask)=6813 sum(mass_error_mask)=1408870 stop_rank=3620
3:20:54.232898 INFO: calibration group: precursor, fitting mz estimator 
3:20:54.340682 INFO: calibration group: precursor, fitting rt estimator 
3:20:54.446868 INFO: calibration group: precursor, fitting mobility estimator 
3:20:54.561202 INFO: calibration group: fragment, fitting mz estimator 
3:20:54.985028 INFO: Using score_cutoff 40.27160848617554 (fac=0.99, q=1)
3:20:54.985506 INFO: calibration group: precursor, predicting mz
3:20:54.998445 INFO: calibration group: precursor, predicting rt
3:20:55.064661 INFO: calibration group: precursor, predicting mobility
3:20:55.081585 INFO: calibration group: fragment, predicting mz
3:20:55.210247 INFO: === checking if optimization conditions were reached ===
3:20:55.210564 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
3:20:55.213491 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 4.0602.
3:20:55.213555 INFO: ==============================================
3:20:55.213668 INFO: Starting optimization step 15.
3:20:55.213742 PROGRESS: === Extracting elution groups 0 to 51000 ===
3:20:55.213821 PROGRESS: Extracting batch of 100415 precursors
3:20:55.253020 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:20:55.253171 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:20:55.253233 INFO: FWHM in RT is 2.32 seconds, sigma is 0.51
3:20:55.253261 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.74
3:20:55.262016 INFO: Starting candidate selection
3:28:45.022404 INFO: Starting candidate scoring
3:28:48.564107 INFO: Finished candidate processing
3:28:48.564236 INFO: Collecting candidate features
3:28:48.869061 WARNING: intensity_correlation has 63 NaNs ( 0.04 % out of 170463)
3:28:48.869469 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 170463)
3:28:48.878627 INFO: Collecting fragment features
3:28:48.985621 INFO: Finished candidate scoring
3:28:49.072848 PROGRESS: === Extracted 170463 precursors and 1404297 fragments ===
3:28:49.073347 INFO: performing precursor FDR with 47 features
3:28:49.073388 INFO: Decoy channel: -1
3:28:49.073419 INFO: Competetive: True
3:28:49.148648 INFO: Setting torch num_threads to 2 for FDR classification task
3:28:49.186315 WARNING: dropped 27 target PSMs due to missing features
3:28:49.186476 WARNING: dropped 38 decoy PSMs due to missing features
3:28:52.580679 INFO: Test AUC: 0.565
3:28:52.580817 INFO: Train AUC: 0.590
3:28:52.580849 INFO: AUC difference: 4.35%
3:28:52.818637 INFO: Resetting torch num_threads to 100
3:28:52.825652 INFO: === FDR correction performed with classifier version 7 ===
3:28:52.835872 PROGRESS: ============================= Precursor FDR =============================
3:28:52.836133 PROGRESS: Total precursors accumulated: 45,496
3:28:52.836197 PROGRESS: Target precursors: 28,069 (61.70%)
3:28:52.836247 PROGRESS: Decoy precursors: 17,427 (38.30%)
3:28:52.836291 PROGRESS: 
3:28:52.836334 PROGRESS: Precursor Summary:
3:28:52.837773 PROGRESS: Channel   0:	 0.05 FDR:   501; 0.01 FDR:   391; 0.001 FDR:   339
3:28:52.837863 PROGRESS: 
3:28:52.837919 PROGRESS: Protein Summary:
3:28:52.839368 PROGRESS: Channel   0:	 0.05 FDR:   473; 0.01 FDR:   367; 0.001 FDR:   321
3:28:52.839462 PROGRESS: =========================================================================
3:28:52.943743 INFO: fragments_df: keeping 3992 of 1404297 [sum(precursor_idx_mask)=7680 sum(mass_error_mask)=1404297 stop_rank=3992
3:28:53.256248 INFO: calibration group: precursor, fitting mz estimator 
3:28:53.367126 INFO: calibration group: precursor, fitting rt estimator 
3:28:53.471411 INFO: calibration group: precursor, fitting mobility estimator 
3:28:53.592402 INFO: calibration group: fragment, fitting mz estimator 
3:28:54.058800 INFO: Using score_cutoff 38.88650164031983 (fac=0.99, q=1)
3:28:54.059273 INFO: calibration group: precursor, predicting mz
3:28:54.072039 INFO: calibration group: precursor, predicting rt
3:28:54.131712 INFO: calibration group: precursor, predicting mobility
3:28:54.148832 INFO: calibration group: fragment, predicting mz
3:28:54.264536 INFO: === checking if optimization conditions were reached ===
3:28:54.264836 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
3:28:54.265960 PROGRESS: ✅ ms2_error      : optimization complete. Optimal parameter 18.2300 found after 7 searches.
3:28:54.266014 INFO: ==============================================
3:28:54.266112 PROGRESS: Optimization finished for ms2_error.
3:28:54.411055 INFO: calibration group: precursor, predicting mz
3:28:54.418533 INFO: calibration group: precursor, predicting rt
3:28:54.448300 INFO: calibration group: precursor, predicting mobility
3:28:54.455084 INFO: calibration group: fragment, predicting mz
3:28:54.532465 INFO: Starting optimization step 0.
3:28:54.532715 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:28:54.532796 PROGRESS: Extracting batch of 49998 precursors
3:28:54.546746 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:28:54.546865 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:28:54.546915 INFO: FWHM in RT is 3.02 seconds, sigma is 0.66
3:28:54.546941 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.59
3:28:54.555845 INFO: Starting candidate selection
3:33:05.007311 INFO: Starting candidate scoring
3:33:08.631562 INFO: Finished candidate processing
3:33:08.631773 INFO: Collecting candidate features
3:33:08.788177 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 85827)
3:33:08.796683 INFO: Collecting fragment features
3:33:08.861158 INFO: Finished candidate scoring
3:33:08.907191 PROGRESS: === Extracted 85827 precursors and 853514 fragments ===
3:33:08.907713 INFO: performing precursor FDR with 47 features
3:33:08.907753 INFO: Decoy channel: -1
3:33:08.907778 INFO: Competetive: True
3:33:08.944688 INFO: Setting torch num_threads to 2 for FDR classification task
3:33:08.962036 WARNING: dropped 4 decoy PSMs due to missing features
3:33:10.380990 INFO: Test AUC: 0.565
3:33:10.381127 INFO: Train AUC: 0.622
3:33:10.381158 INFO: AUC difference: 9.17%
3:33:10.381179 WARNING: AUC difference > 5%. This may indicate overfitting.
3:33:10.589564 INFO: Resetting torch num_threads to 100
3:33:10.592894 INFO: === FDR correction performed with classifier version 9 ===
3:33:10.596845 PROGRESS: ============================= Precursor FDR =============================
3:33:10.597002 PROGRESS: Total precursors accumulated: 22,809
3:33:10.597065 PROGRESS: Target precursors: 14,772 (64.76%)
3:33:10.597125 PROGRESS: Decoy precursors: 8,037 (35.24%)
3:33:10.597177 PROGRESS: 
3:33:10.597223 PROGRESS: Precursor Summary:
3:33:10.598331 PROGRESS: Channel   0:	 0.05 FDR:   317; 0.01 FDR:   227; 0.001 FDR:   220
3:33:10.598425 PROGRESS: 
3:33:10.598482 PROGRESS: Protein Summary:
3:33:10.599690 PROGRESS: Channel   0:	 0.05 FDR:   307; 0.01 FDR:   222; 0.001 FDR:   215
3:33:10.599789 PROGRESS: =========================================================================
3:33:10.728817 INFO: fragments_df: keeping 2634 of 853514 [sum(precursor_idx_mask)=4724 sum(mass_error_mask)=853514 stop_rank=2634
3:33:10.862921 INFO: calibration group: precursor, fitting mz estimator 
3:33:10.980789 INFO: calibration group: precursor, fitting rt estimator 
3:33:11.095600 INFO: calibration group: precursor, fitting mobility estimator 
3:33:11.211068 INFO: calibration group: fragment, fitting mz estimator 
3:33:11.558313 INFO: Using score_cutoff 44.250200896453855 (fac=0.99, q=1)
3:33:11.558787 INFO: calibration group: precursor, predicting mz
3:33:11.566077 INFO: calibration group: precursor, predicting rt
3:33:11.595948 INFO: calibration group: precursor, predicting mobility
3:33:11.602723 INFO: calibration group: fragment, predicting mz
3:33:11.660761 INFO: === checking if optimization conditions were reached ===
3:33:11.661103 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3:33:11.663379 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 727.7950.
3:33:11.663444 INFO: ==============================================
3:33:11.663559 INFO: Starting optimization step 1.
3:33:11.663634 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:33:11.663723 PROGRESS: Extracting batch of 49998 precursors
3:33:11.682908 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:33:11.683055 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:33:11.683125 INFO: FWHM in RT is 3.03 seconds, sigma is 0.67
3:33:11.683156 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.63
3:33:11.692808 INFO: Starting candidate selection
3:34:42.817300 INFO: Starting candidate scoring
3:34:46.865129 INFO: Finished candidate processing
3:34:46.865302 INFO: Collecting candidate features
3:34:47.057557 WARNING: intensity_correlation has 15 NaNs ( 0.02 % out of 85001)
3:34:47.065814 INFO: Collecting fragment features
3:34:47.137580 INFO: Finished candidate scoring
3:34:47.180359 PROGRESS: === Extracted 85001 precursors and 835609 fragments ===
3:34:47.180862 INFO: performing precursor FDR with 47 features
3:34:47.180902 INFO: Decoy channel: -1
3:34:47.180929 INFO: Competetive: True
3:34:47.220324 INFO: Setting torch num_threads to 2 for FDR classification task
3:34:47.244396 WARNING: dropped 8 target PSMs due to missing features
3:34:47.245274 WARNING: dropped 7 decoy PSMs due to missing features
3:34:48.864206 INFO: Test AUC: 0.564
3:34:48.864339 INFO: Train AUC: 0.611
3:34:48.864369 INFO: AUC difference: 7.77%
3:34:48.864392 WARNING: AUC difference > 5%. This may indicate overfitting.
3:34:49.070023 INFO: Resetting torch num_threads to 100
3:34:49.073406 INFO: === FDR correction performed with classifier version 9 ===
3:34:49.077434 PROGRESS: ============================= Precursor FDR =============================
3:34:49.077587 PROGRESS: Total precursors accumulated: 22,725
3:34:49.077648 PROGRESS: Target precursors: 14,534 (63.96%)
3:34:49.077697 PROGRESS: Decoy precursors: 8,191 (36.04%)
3:34:49.077752 PROGRESS: 
3:34:49.077797 PROGRESS: Precursor Summary:
3:34:49.078881 PROGRESS: Channel   0:	 0.05 FDR:   288; 0.01 FDR:   220; 0.001 FDR:   216
3:34:49.078976 PROGRESS: 
3:34:49.079038 PROGRESS: Protein Summary:
3:34:49.080225 PROGRESS: Channel   0:	 0.05 FDR:   281; 0.01 FDR:   215; 0.001 FDR:   211
3:34:49.080314 PROGRESS: =========================================================================
3:34:49.136285 INFO: fragments_df: keeping 2541 of 835609 [sum(precursor_idx_mask)=4624 sum(mass_error_mask)=835609 stop_rank=2541
3:34:49.269938 INFO: calibration group: precursor, fitting mz estimator 
3:34:49.478787 INFO: calibration group: precursor, fitting rt estimator 
3:34:49.597239 INFO: calibration group: precursor, fitting mobility estimator 
3:34:49.717131 INFO: calibration group: fragment, fitting mz estimator 
3:34:50.051539 INFO: Using score_cutoff 49.430879159545896 (fac=0.99, q=1)
3:34:50.052030 INFO: calibration group: precursor, predicting mz
3:34:50.059626 INFO: calibration group: precursor, predicting rt
3:34:50.089924 INFO: calibration group: precursor, predicting mobility
3:34:50.097219 INFO: calibration group: fragment, predicting mz
3:34:50.188174 INFO: === checking if optimization conditions were reached ===
3:34:50.188568 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3:34:50.191265 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 399.7161.
3:34:50.191338 INFO: ==============================================
3:34:50.191472 INFO: Starting optimization step 2.
3:34:50.191590 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:34:50.191677 PROGRESS: Extracting batch of 49998 precursors
3:34:50.232489 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:34:50.232641 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:34:50.232698 INFO: FWHM in RT is 3.05 seconds, sigma is 0.67
3:34:50.232723 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
3:34:50.238897 INFO: Starting candidate selection
3:35:38.062314 INFO: Starting candidate scoring
3:35:41.244796 INFO: Finished candidate processing
3:35:41.244969 INFO: Collecting candidate features
3:35:41.414751 WARNING: intensity_correlation has 28 NaNs ( 0.03 % out of 83192)
3:35:41.415113 WARNING: height_correlation has 9 NaNs ( 0.01 % out of 83192)
3:35:41.422863 INFO: Collecting fragment features
3:35:41.498116 INFO: Finished candidate scoring
3:35:41.538993 PROGRESS: === Extracted 83192 precursors and 811000 fragments ===
3:35:41.539482 INFO: performing precursor FDR with 47 features
3:35:41.539521 INFO: Decoy channel: -1
3:35:41.539545 INFO: Competetive: True
3:35:41.571319 INFO: Setting torch num_threads to 2 for FDR classification task
3:35:41.590986 WARNING: dropped 19 target PSMs due to missing features
3:35:41.591132 WARNING: dropped 14 decoy PSMs due to missing features
3:35:42.992721 INFO: Test AUC: 0.562
3:35:42.992851 INFO: Train AUC: 0.609
3:35:42.992882 INFO: AUC difference: 7.72%
3:35:42.992904 WARNING: AUC difference > 5%. This may indicate overfitting.
3:35:43.200172 INFO: Resetting torch num_threads to 100
3:35:43.203475 INFO: === FDR correction performed with classifier version 9 ===
3:35:43.207312 PROGRESS: ============================= Precursor FDR =============================
3:35:43.207458 PROGRESS: Total precursors accumulated: 22,368
3:35:43.207520 PROGRESS: Target precursors: 14,243 (63.68%)
3:35:43.207569 PROGRESS: Decoy precursors: 8,125 (36.32%)
3:35:43.207613 PROGRESS: 
3:35:43.207655 PROGRESS: Precursor Summary:
3:35:43.208747 PROGRESS: Channel   0:	 0.05 FDR:   342; 0.01 FDR:   223; 0.001 FDR:   211
3:35:43.208843 PROGRESS: 
3:35:43.208905 PROGRESS: Protein Summary:
3:35:43.210101 PROGRESS: Channel   0:	 0.05 FDR:   333; 0.01 FDR:   218; 0.001 FDR:   206
3:35:43.210192 PROGRESS: =========================================================================
3:35:43.266762 INFO: fragments_df: keeping 2522 of 811000 [sum(precursor_idx_mask)=4595 sum(mass_error_mask)=811000 stop_rank=2522
3:35:43.399103 INFO: calibration group: precursor, fitting mz estimator 
3:35:43.518912 INFO: calibration group: precursor, fitting rt estimator 
3:35:43.638914 INFO: calibration group: precursor, fitting mobility estimator 
3:35:43.761231 INFO: calibration group: fragment, fitting mz estimator 
3:35:44.094451 INFO: Using score_cutoff 45.12711043624878 (fac=0.99, q=1)
3:35:44.094867 INFO: calibration group: precursor, predicting mz
3:35:44.102170 INFO: calibration group: precursor, predicting rt
3:35:44.132450 INFO: calibration group: precursor, predicting mobility
3:35:44.139739 INFO: calibration group: fragment, predicting mz
3:35:44.198219 INFO: === checking if optimization conditions were reached ===
3:35:44.198500 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3:35:44.200524 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 289.9723.
3:35:44.200580 INFO: ==============================================
3:35:44.200691 INFO: Starting optimization step 3.
3:35:44.200759 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:35:44.200866 PROGRESS: Extracting batch of 49998 precursors
3:35:44.214401 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:35:44.214519 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:35:44.214597 INFO: FWHM in RT is 3.18 seconds, sigma is 0.70
3:35:44.214622 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.61
3:35:44.223560 INFO: Starting candidate selection
3:36:22.349311 INFO: Starting candidate scoring
3:36:25.599006 INFO: Finished candidate processing
3:36:25.599500 INFO: Collecting candidate features
3:36:25.821804 WARNING: intensity_correlation has 33 NaNs ( 0.04 % out of 82801)
3:36:25.822225 WARNING: height_correlation has 9 NaNs ( 0.01 % out of 82801)
3:36:25.831733 INFO: Collecting fragment features
3:36:25.907001 INFO: Finished candidate scoring
3:36:25.963147 PROGRESS: === Extracted 82801 precursors and 803535 fragments ===
3:36:25.963678 INFO: performing precursor FDR with 47 features
3:36:25.963717 INFO: Decoy channel: -1
3:36:25.963743 INFO: Competetive: True
3:36:25.996000 INFO: Setting torch num_threads to 2 for FDR classification task
3:36:26.014050 WARNING: dropped 19 target PSMs due to missing features
3:36:26.014184 WARNING: dropped 20 decoy PSMs due to missing features
3:36:27.423923 INFO: Test AUC: 0.555
3:36:27.424042 INFO: Train AUC: 0.606
3:36:27.424072 INFO: AUC difference: 8.42%
3:36:27.424093 WARNING: AUC difference > 5%. This may indicate overfitting.
3:36:27.633209 INFO: Resetting torch num_threads to 100
3:36:27.636453 INFO: === FDR correction performed with classifier version 9 ===
3:36:27.640206 PROGRESS: ============================= Precursor FDR =============================
3:36:27.640348 PROGRESS: Total precursors accumulated: 22,288
3:36:27.640410 PROGRESS: Target precursors: 14,051 (63.04%)
3:36:27.640459 PROGRESS: Decoy precursors: 8,237 (36.96%)
3:36:27.640508 PROGRESS: 
3:36:27.640550 PROGRESS: Precursor Summary:
3:36:27.641667 PROGRESS: Channel   0:	 0.05 FDR:   311; 0.01 FDR:   234; 0.001 FDR:   183
3:36:27.641754 PROGRESS: 
3:36:27.641808 PROGRESS: Protein Summary:
3:36:27.643037 PROGRESS: Channel   0:	 0.05 FDR:   301; 0.01 FDR:   229; 0.001 FDR:   180
3:36:27.643127 PROGRESS: =========================================================================
3:36:27.697403 INFO: fragments_df: keeping 2618 of 803535 [sum(precursor_idx_mask)=4816 sum(mass_error_mask)=803535 stop_rank=2618
3:36:27.830282 INFO: calibration group: precursor, fitting mz estimator 
3:36:27.952892 INFO: calibration group: precursor, fitting rt estimator 
3:36:28.072795 INFO: calibration group: precursor, fitting mobility estimator 
3:36:28.191363 INFO: calibration group: fragment, fitting mz estimator 
3:36:28.535165 INFO: Using score_cutoff 42.374125744628905 (fac=0.99, q=1)
3:36:28.535606 INFO: calibration group: precursor, predicting mz
3:36:28.542782 INFO: calibration group: precursor, predicting rt
3:36:28.572390 INFO: calibration group: precursor, predicting mobility
3:36:28.579514 INFO: calibration group: fragment, predicting mz
3:36:28.637242 INFO: === checking if optimization conditions were reached ===
3:36:28.637500 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3:36:28.639503 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 254.7996.
3:36:28.639557 INFO: ==============================================
3:36:28.639663 INFO: Starting optimization step 4.
3:36:28.639730 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:36:28.639802 PROGRESS: Extracting batch of 49998 precursors
3:36:28.653477 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:36:28.653585 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:36:28.653634 INFO: FWHM in RT is 3.14 seconds, sigma is 0.69
3:36:28.653657 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.61
3:36:28.662629 INFO: Starting candidate selection
3:37:01.063901 INFO: Starting candidate scoring
3:37:04.425076 INFO: Finished candidate processing
3:37:04.426214 INFO: Collecting candidate features
3:37:04.604582 WARNING: intensity_correlation has 39 NaNs ( 0.05 % out of 82527)
3:37:04.605244 WARNING: height_correlation has 8 NaNs ( 0.01 % out of 82527)
3:37:04.623806 INFO: Collecting fragment features
3:37:04.691920 INFO: Finished candidate scoring
3:37:04.745779 PROGRESS: === Extracted 82527 precursors and 798949 fragments ===
3:37:04.746238 INFO: performing precursor FDR with 47 features
3:37:04.746278 INFO: Decoy channel: -1
3:37:04.746305 INFO: Competetive: True
3:37:04.778872 INFO: Setting torch num_threads to 2 for FDR classification task
3:37:04.798864 WARNING: dropped 24 target PSMs due to missing features
3:37:04.799035 WARNING: dropped 19 decoy PSMs due to missing features
3:37:06.564889 INFO: Test AUC: 0.555
3:37:06.565045 INFO: Train AUC: 0.603
3:37:06.565078 INFO: AUC difference: 7.91%
3:37:06.565102 WARNING: AUC difference > 5%. This may indicate overfitting.
3:37:06.787628 INFO: Resetting torch num_threads to 100
3:37:06.791919 INFO: === FDR correction performed with classifier version 9 ===
3:37:06.797463 PROGRESS: ============================= Precursor FDR =============================
3:37:06.797676 PROGRESS: Total precursors accumulated: 22,227
3:37:06.797740 PROGRESS: Target precursors: 14,064 (63.27%)
3:37:06.797790 PROGRESS: Decoy precursors: 8,163 (36.73%)
3:37:06.797838 PROGRESS: 
3:37:06.797897 PROGRESS: Precursor Summary:
3:37:06.799190 PROGRESS: Channel   0:	 0.05 FDR:   313; 0.01 FDR:   220; 0.001 FDR:   151
3:37:06.799305 PROGRESS: 
3:37:06.799362 PROGRESS: Protein Summary:
3:37:06.800595 PROGRESS: Channel   0:	 0.05 FDR:   304; 0.01 FDR:   215; 0.001 FDR:   149
3:37:06.800687 PROGRESS: =========================================================================
3:37:06.856718 INFO: fragments_df: keeping 2461 of 798949 [sum(precursor_idx_mask)=4505 sum(mass_error_mask)=798949 stop_rank=2461
3:37:07.017090 INFO: calibration group: precursor, fitting mz estimator 
3:37:07.135577 INFO: calibration group: precursor, fitting rt estimator 
3:37:07.254762 INFO: calibration group: precursor, fitting mobility estimator 
3:37:07.382352 INFO: calibration group: fragment, fitting mz estimator 
3:37:07.733087 INFO: Using score_cutoff 44.005781617355346 (fac=0.99, q=1)
3:37:07.733675 INFO: calibration group: precursor, predicting mz
3:37:07.742288 INFO: calibration group: precursor, predicting rt
3:37:07.774743 INFO: calibration group: precursor, predicting mobility
3:37:07.784045 INFO: calibration group: fragment, predicting mz
3:37:07.878115 INFO: === checking if optimization conditions were reached ===
3:37:07.878694 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3:37:07.882102 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 189.6069.
3:37:07.882200 INFO: ==============================================
3:37:07.882377 INFO: Starting optimization step 5.
3:37:07.882467 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:37:07.884037 PROGRESS: Extracting batch of 49998 precursors
3:37:07.917399 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:37:07.917675 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:37:07.917746 INFO: FWHM in RT is 3.20 seconds, sigma is 0.70
3:37:07.917778 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.65
3:37:07.928711 INFO: Starting candidate selection
3:37:32.757050 INFO: Starting candidate scoring
3:37:36.146284 INFO: Finished candidate processing
3:37:36.146817 INFO: Collecting candidate features
3:37:36.275992 WARNING: intensity_correlation has 36 NaNs ( 0.04 % out of 82253)
3:37:36.276302 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 82253)
3:37:36.282213 INFO: Collecting fragment features
3:37:36.346567 INFO: Finished candidate scoring
3:37:36.399079 PROGRESS: === Extracted 82253 precursors and 793320 fragments ===
3:37:36.399551 INFO: performing precursor FDR with 47 features
3:37:36.399591 INFO: Decoy channel: -1
3:37:36.399615 INFO: Competetive: True
3:37:36.430579 INFO: Setting torch num_threads to 2 for FDR classification task
3:37:36.446342 WARNING: dropped 16 target PSMs due to missing features
3:37:36.446481 WARNING: dropped 21 decoy PSMs due to missing features
3:37:37.798188 INFO: Test AUC: 0.559
3:37:37.798316 INFO: Train AUC: 0.607
3:37:37.798345 INFO: AUC difference: 7.84%
3:37:37.798366 WARNING: AUC difference > 5%. This may indicate overfitting.
3:37:38.005686 INFO: Resetting torch num_threads to 100
3:37:38.008911 INFO: === FDR correction performed with classifier version 9 ===
3:37:38.012536 PROGRESS: ============================= Precursor FDR =============================
3:37:38.012674 PROGRESS: Total precursors accumulated: 22,170
3:37:38.012734 PROGRESS: Target precursors: 13,924 (62.81%)
3:37:38.012784 PROGRESS: Decoy precursors: 8,246 (37.19%)
3:37:38.012829 PROGRESS: 
3:37:38.012880 PROGRESS: Precursor Summary:
3:37:38.014007 PROGRESS: Channel   0:	 0.05 FDR:   347; 0.01 FDR:   246; 0.001 FDR:   216
3:37:38.014101 PROGRESS: 
3:37:38.014156 PROGRESS: Protein Summary:
3:37:38.015410 PROGRESS: Channel   0:	 0.05 FDR:   336; 0.01 FDR:   241; 0.001 FDR:   212
3:37:38.015505 PROGRESS: =========================================================================
3:37:38.069405 INFO: fragments_df: keeping 2744 of 793320 [sum(precursor_idx_mask)=5023 sum(mass_error_mask)=793320 stop_rank=2744
3:37:38.200899 INFO: calibration group: precursor, fitting mz estimator 
3:37:38.299727 INFO: calibration group: precursor, fitting rt estimator 
3:37:38.403573 INFO: calibration group: precursor, fitting mobility estimator 
3:37:38.499295 INFO: calibration group: fragment, fitting mz estimator 
3:37:38.795591 INFO: Using score_cutoff 42.527167877197265 (fac=0.99, q=1)
3:37:38.796003 INFO: calibration group: precursor, predicting mz
3:37:38.803052 INFO: calibration group: precursor, predicting rt
3:37:38.832756 INFO: calibration group: precursor, predicting mobility
3:37:38.839682 INFO: calibration group: fragment, predicting mz
3:37:38.897530 INFO: === checking if optimization conditions were reached ===
3:37:38.897793 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3:37:38.899768 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 164.9221.
3:37:38.899835 INFO: ==============================================
3:37:38.899933 INFO: Starting optimization step 6.
3:37:38.899999 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:37:38.900071 PROGRESS: Extracting batch of 49998 precursors
3:37:38.912768 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:37:38.912881 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:37:38.912930 INFO: FWHM in RT is 3.13 seconds, sigma is 0.69
3:37:38.912954 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.61
3:37:38.921816 INFO: Starting candidate selection
3:38:00.825387 INFO: Starting candidate scoring
3:38:04.435527 INFO: Finished candidate processing
3:38:04.435689 INFO: Collecting candidate features
3:38:04.590218 WARNING: intensity_correlation has 44 NaNs ( 0.05 % out of 82362)
3:38:04.590561 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 82362)
3:38:04.598243 INFO: Collecting fragment features
3:38:04.657209 INFO: Finished candidate scoring
3:38:04.704536 PROGRESS: === Extracted 82362 precursors and 792738 fragments ===
3:38:04.705828 INFO: performing precursor FDR with 47 features
3:38:04.705872 INFO: Decoy channel: -1
3:38:04.705895 INFO: Competetive: True
3:38:04.737012 INFO: Setting torch num_threads to 2 for FDR classification task
3:38:04.755443 WARNING: dropped 21 target PSMs due to missing features
3:38:04.755581 WARNING: dropped 24 decoy PSMs due to missing features
3:38:06.138314 INFO: Test AUC: 0.550
3:38:06.138442 INFO: Train AUC: 0.606
3:38:06.138472 INFO: AUC difference: 9.34%
3:38:06.138495 WARNING: AUC difference > 5%. This may indicate overfitting.
3:38:06.343435 INFO: Resetting torch num_threads to 100
3:38:06.346607 INFO: === FDR correction performed with classifier version 9 ===
3:38:06.350191 PROGRESS: ============================= Precursor FDR =============================
3:38:06.350327 PROGRESS: Total precursors accumulated: 22,200
3:38:06.350392 PROGRESS: Target precursors: 13,995 (63.04%)
3:38:06.350444 PROGRESS: Decoy precursors: 8,205 (36.96%)
3:38:06.350489 PROGRESS: 
3:38:06.350534 PROGRESS: Precursor Summary:
3:38:06.351612 PROGRESS: Channel   0:	 0.05 FDR:   295; 0.01 FDR:   219; 0.001 FDR:   198
3:38:06.351706 PROGRESS: 
3:38:06.351762 PROGRESS: Protein Summary:
3:38:06.352923 PROGRESS: Channel   0:	 0.05 FDR:   287; 0.01 FDR:   215; 0.001 FDR:   194
3:38:06.353012 PROGRESS: =========================================================================
3:38:06.408417 INFO: fragments_df: keeping 2503 of 792738 [sum(precursor_idx_mask)=4447 sum(mass_error_mask)=792738 stop_rank=2503
3:38:06.530744 INFO: calibration group: precursor, fitting mz estimator 
3:38:06.650015 INFO: calibration group: precursor, fitting rt estimator 
3:38:06.770266 INFO: calibration group: precursor, fitting mobility estimator 
3:38:06.884422 INFO: calibration group: fragment, fitting mz estimator 
3:38:07.215695 INFO: Using score_cutoff 50.442876809692386 (fac=0.99, q=1)
3:38:07.216148 INFO: calibration group: precursor, predicting mz
3:38:07.224240 INFO: calibration group: precursor, predicting rt
3:38:07.255482 INFO: calibration group: precursor, predicting mobility
3:38:07.263196 INFO: calibration group: fragment, predicting mz
3:38:07.329189 INFO: === checking if optimization conditions were reached ===
3:38:07.330458 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
3:38:07.332947 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 155.2950.
3:38:07.333022 INFO: ==============================================
3:38:07.333148 INFO: Starting optimization step 7.
3:38:07.333229 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:38:07.333317 PROGRESS: Extracting batch of 49998 precursors
3:38:07.352909 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:38:07.353077 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:38:07.353139 INFO: FWHM in RT is 3.18 seconds, sigma is 0.70
3:38:07.353172 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.71
3:38:07.379747 INFO: Starting candidate selection
3:38:29.206818 INFO: Starting candidate scoring
3:38:33.165769 INFO: Finished candidate processing
3:38:33.165879 INFO: Collecting candidate features
3:38:33.316905 WARNING: intensity_correlation has 39 NaNs ( 0.05 % out of 82333)
3:38:33.317266 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 82333)
3:38:33.325048 INFO: Collecting fragment features
3:38:33.381878 INFO: Finished candidate scoring
3:38:33.420351 PROGRESS: === Extracted 82333 precursors and 792233 fragments ===
3:38:33.420751 INFO: performing precursor FDR with 47 features
3:38:33.420788 INFO: Decoy channel: -1
3:38:33.420812 INFO: Competetive: True
3:38:33.445987 INFO: Setting torch num_threads to 2 for FDR classification task
3:38:33.461890 WARNING: dropped 17 target PSMs due to missing features
3:38:33.462021 WARNING: dropped 23 decoy PSMs due to missing features
3:38:34.847960 INFO: Test AUC: 0.557
3:38:34.848089 INFO: Train AUC: 0.604
3:38:34.848119 INFO: AUC difference: 7.86%
3:38:34.848140 WARNING: AUC difference > 5%. This may indicate overfitting.
3:38:35.054631 INFO: Resetting torch num_threads to 100
3:38:35.057842 INFO: === FDR correction performed with classifier version 9 ===
3:38:35.061412 PROGRESS: ============================= Precursor FDR =============================
3:38:35.061547 PROGRESS: Total precursors accumulated: 22,181
3:38:35.061607 PROGRESS: Target precursors: 13,921 (62.76%)
3:38:35.061657 PROGRESS: Decoy precursors: 8,260 (37.24%)
3:38:35.061703 PROGRESS: 
3:38:35.061748 PROGRESS: Precursor Summary:
3:38:35.062856 PROGRESS: Channel   0:	 0.05 FDR:   333; 0.01 FDR:   222; 0.001 FDR:   208
3:38:35.062950 PROGRESS: 
3:38:35.063013 PROGRESS: Protein Summary:
3:38:35.064211 PROGRESS: Channel   0:	 0.05 FDR:   324; 0.01 FDR:   218; 0.001 FDR:   204
3:38:35.064301 PROGRESS: =========================================================================
3:38:35.117141 INFO: fragments_df: keeping 2520 of 792233 [sum(precursor_idx_mask)=4569 sum(mass_error_mask)=792233 stop_rank=2520
3:38:35.246901 INFO: calibration group: precursor, fitting mz estimator 
3:38:35.343669 INFO: calibration group: precursor, fitting rt estimator 
3:38:35.443209 INFO: calibration group: precursor, fitting mobility estimator 
3:38:35.536665 INFO: calibration group: fragment, fitting mz estimator 
3:38:35.812510 INFO: Using score_cutoff 51.10686119613647 (fac=0.99, q=1)
3:38:35.812907 INFO: calibration group: precursor, predicting mz
3:38:35.820056 INFO: calibration group: precursor, predicting rt
3:38:35.849790 INFO: calibration group: precursor, predicting mobility
3:38:35.856747 INFO: calibration group: fragment, predicting mz
3:38:35.912100 INFO: === checking if optimization conditions were reached ===
3:38:35.912395 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
3:38:35.914672 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 146.6432.
3:38:35.914733 INFO: ==============================================
3:38:35.914833 INFO: Starting optimization step 8.
3:38:35.914906 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:38:35.914978 PROGRESS: Extracting batch of 49998 precursors
3:38:35.933698 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:38:35.933836 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:38:35.933887 INFO: FWHM in RT is 3.13 seconds, sigma is 0.69
3:38:35.933915 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.60
3:38:35.959000 INFO: Starting candidate selection
3:38:55.376197 INFO: Starting candidate scoring
3:38:58.808140 INFO: Finished candidate processing
3:38:58.808336 INFO: Collecting candidate features
3:38:58.979456 WARNING: intensity_correlation has 35 NaNs ( 0.04 % out of 82207)
3:38:58.979791 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 82207)
3:38:58.985831 INFO: Collecting fragment features
3:38:59.046796 INFO: Finished candidate scoring
3:38:59.090611 PROGRESS: === Extracted 82207 precursors and 789494 fragments ===
3:38:59.091156 INFO: performing precursor FDR with 47 features
3:38:59.091199 INFO: Decoy channel: -1
3:38:59.091225 INFO: Competetive: True
3:38:59.126650 INFO: Setting torch num_threads to 2 for FDR classification task
3:38:59.147937 WARNING: dropped 18 target PSMs due to missing features
3:38:59.148094 WARNING: dropped 19 decoy PSMs due to missing features
3:39:00.681249 INFO: Test AUC: 0.555
3:39:00.681404 INFO: Train AUC: 0.602
3:39:00.681436 INFO: AUC difference: 7.91%
3:39:00.681459 WARNING: AUC difference > 5%. This may indicate overfitting.
3:39:00.891764 INFO: Resetting torch num_threads to 100
3:39:00.895943 INFO: === FDR correction performed with classifier version 9 ===
3:39:00.900121 PROGRESS: ============================= Precursor FDR =============================
3:39:00.900267 PROGRESS: Total precursors accumulated: 22,149
3:39:00.900349 PROGRESS: Target precursors: 13,885 (62.69%)
3:39:00.900404 PROGRESS: Decoy precursors: 8,264 (37.31%)
3:39:00.900450 PROGRESS: 
3:39:00.900494 PROGRESS: Precursor Summary:
3:39:00.901643 PROGRESS: Channel   0:	 0.05 FDR:   333; 0.01 FDR:   237; 0.001 FDR:   232
3:39:00.901738 PROGRESS: 
3:39:00.901794 PROGRESS: Protein Summary:
3:39:00.903052 PROGRESS: Channel   0:	 0.05 FDR:   324; 0.01 FDR:   233; 0.001 FDR:   228
3:39:00.903154 PROGRESS: =========================================================================
3:39:00.956407 INFO: fragments_df: keeping 2690 of 789494 [sum(precursor_idx_mask)=4850 sum(mass_error_mask)=789494 stop_rank=2690
3:39:01.087119 INFO: calibration group: precursor, fitting mz estimator 
3:39:01.206991 INFO: calibration group: precursor, fitting rt estimator 
3:39:01.326146 INFO: calibration group: precursor, fitting mobility estimator 
3:39:01.451520 INFO: calibration group: fragment, fitting mz estimator 
3:39:01.818278 INFO: Using score_cutoff 45.669241557312006 (fac=0.99, q=1)
3:39:01.818848 INFO: calibration group: precursor, predicting mz
3:39:01.826622 INFO: calibration group: precursor, predicting rt
3:39:01.858047 INFO: calibration group: precursor, predicting mobility
3:39:01.865663 INFO: calibration group: fragment, predicting mz
3:39:01.970119 INFO: === checking if optimization conditions were reached ===
3:39:01.970735 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
3:39:01.973660 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 126.9083.
3:39:01.973795 INFO: ==============================================
3:39:01.974085 INFO: Starting optimization step 9.
3:39:01.974331 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:39:01.974588 PROGRESS: Extracting batch of 49998 precursors
3:39:02.007385 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:39:02.007578 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:39:02.007642 INFO: FWHM in RT is 3.14 seconds, sigma is 0.69
3:39:02.007669 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.57
3:39:02.009994 INFO: Starting candidate selection
3:39:19.957147 INFO: Starting candidate scoring
3:39:23.313248 INFO: Finished candidate processing
3:39:23.313410 INFO: Collecting candidate features
3:39:23.482010 WARNING: intensity_correlation has 45 NaNs ( 0.05 % out of 82082)
3:39:23.482300 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 82082)
3:39:23.488376 INFO: Collecting fragment features
3:39:23.562954 INFO: Finished candidate scoring
3:39:23.609677 PROGRESS: === Extracted 82082 precursors and 786894 fragments ===
3:39:23.610106 INFO: performing precursor FDR with 47 features
3:39:23.610147 INFO: Decoy channel: -1
3:39:23.610170 INFO: Competetive: True
3:39:23.638583 INFO: Setting torch num_threads to 2 for FDR classification task
3:39:23.654790 WARNING: dropped 17 target PSMs due to missing features
3:39:23.654935 WARNING: dropped 28 decoy PSMs due to missing features
3:39:25.328303 INFO: Test AUC: 0.556
3:39:25.328434 INFO: Train AUC: 0.607
3:39:25.328464 INFO: AUC difference: 8.37%
3:39:25.328485 WARNING: AUC difference > 5%. This may indicate overfitting.
3:39:28.058165 INFO: Resetting torch num_threads to 100
3:39:28.066002 INFO: === FDR correction performed with classifier version 9 ===
3:39:28.072915 PROGRESS: ============================= Precursor FDR =============================
3:39:28.073120 PROGRESS: Total precursors accumulated: 22,153
3:39:28.073191 PROGRESS: Target precursors: 13,920 (62.84%)
3:39:28.073243 PROGRESS: Decoy precursors: 8,233 (37.16%)
3:39:28.073290 PROGRESS: 
3:39:28.073335 PROGRESS: Precursor Summary:
3:39:28.074569 PROGRESS: Channel   0:	 0.05 FDR:   313; 0.01 FDR:   242; 0.001 FDR:   189
3:39:28.074675 PROGRESS: 
3:39:28.074733 PROGRESS: Protein Summary:
3:39:28.076037 PROGRESS: Channel   0:	 0.05 FDR:   306; 0.01 FDR:   237; 0.001 FDR:   185
3:39:28.076134 PROGRESS: =========================================================================
3:39:28.133198 INFO: fragments_df: keeping 2697 of 786894 [sum(precursor_idx_mask)=4936 sum(mass_error_mask)=786894 stop_rank=2697
3:39:28.282139 INFO: calibration group: precursor, fitting mz estimator 
3:39:28.402918 INFO: calibration group: precursor, fitting rt estimator 
3:39:28.523775 INFO: calibration group: precursor, fitting mobility estimator 
3:39:28.652248 INFO: calibration group: fragment, fitting mz estimator 
3:39:29.012520 INFO: Using score_cutoff 43.13978846054077 (fac=0.99, q=1)
3:39:29.013030 INFO: calibration group: precursor, predicting mz
3:39:29.021148 INFO: calibration group: precursor, predicting rt
3:39:29.051480 INFO: calibration group: precursor, predicting mobility
3:39:29.058628 INFO: calibration group: fragment, predicting mz
3:39:29.115990 INFO: === checking if optimization conditions were reached ===
3:39:29.116457 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
3:39:29.119717 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 124.2534.
3:39:29.119853 INFO: ==============================================
3:39:29.120026 INFO: Starting optimization step 10.
3:39:29.120108 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:39:29.120185 PROGRESS: Extracting batch of 49998 precursors
3:39:29.159250 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:39:29.159662 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:39:29.159791 INFO: FWHM in RT is 3.18 seconds, sigma is 0.70
3:39:29.159877 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.54
3:39:29.187645 INFO: Starting candidate selection
3:39:47.649177 INFO: Starting candidate scoring
3:39:50.921442 INFO: Finished candidate processing
3:39:50.921566 INFO: Collecting candidate features
3:39:51.077165 WARNING: intensity_correlation has 44 NaNs ( 0.05 % out of 82130)
3:39:51.077543 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 82130)
3:39:51.085693 INFO: Collecting fragment features
3:39:51.145794 INFO: Finished candidate scoring
3:39:51.184253 PROGRESS: === Extracted 82130 precursors and 787378 fragments ===
3:39:51.184760 INFO: performing precursor FDR with 47 features
3:39:51.184800 INFO: Decoy channel: -1
3:39:51.184824 INFO: Competetive: True
3:39:51.222910 INFO: Setting torch num_threads to 2 for FDR classification task
3:39:51.243034 WARNING: dropped 23 target PSMs due to missing features
3:39:51.243184 WARNING: dropped 23 decoy PSMs due to missing features
3:39:52.669410 INFO: Test AUC: 0.558
3:39:52.669571 INFO: Train AUC: 0.599
3:39:52.669604 INFO: AUC difference: 6.91%
3:39:52.669628 WARNING: AUC difference > 5%. This may indicate overfitting.
3:39:52.880481 INFO: Resetting torch num_threads to 100
3:39:52.884433 INFO: === FDR correction performed with classifier version 9 ===
3:39:52.888462 PROGRESS: ============================= Precursor FDR =============================
3:39:52.888602 PROGRESS: Total precursors accumulated: 22,159
3:39:52.888664 PROGRESS: Target precursors: 13,886 (62.67%)
3:39:52.888717 PROGRESS: Decoy precursors: 8,273 (37.33%)
3:39:52.888764 PROGRESS: 
3:39:52.888811 PROGRESS: Precursor Summary:
3:39:52.889978 PROGRESS: Channel   0:	 0.05 FDR:   325; 0.01 FDR:   252; 0.001 FDR:   139
3:39:52.890079 PROGRESS: 
3:39:52.890133 PROGRESS: Protein Summary:
3:39:52.891368 PROGRESS: Channel   0:	 0.05 FDR:   316; 0.01 FDR:   247; 0.001 FDR:   136
3:39:52.891463 PROGRESS: =========================================================================
3:39:52.945103 INFO: fragments_df: keeping 2757 of 787378 [sum(precursor_idx_mask)=5067 sum(mass_error_mask)=787378 stop_rank=2757
3:39:53.074235 INFO: calibration group: precursor, fitting mz estimator 
3:39:53.173054 INFO: calibration group: precursor, fitting rt estimator 
3:39:53.273634 INFO: calibration group: precursor, fitting mobility estimator 
3:39:53.370765 INFO: calibration group: fragment, fitting mz estimator 
3:39:53.672575 INFO: Using score_cutoff 39.5581853553772 (fac=0.99, q=1)
3:39:53.673048 INFO: calibration group: precursor, predicting mz
3:39:53.680563 INFO: calibration group: precursor, predicting rt
3:39:53.710894 INFO: calibration group: precursor, predicting mobility
3:39:53.718117 INFO: calibration group: fragment, predicting mz
3:39:53.776019 INFO: === checking if optimization conditions were reached ===
3:39:53.776312 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 2 ===
3:39:53.777747 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 124.2534 found after 11 searches.
3:39:53.777802 INFO: ==============================================
3:39:53.777905 PROGRESS: Optimization finished for rt_error.
3:39:53.904445 INFO: calibration group: precursor, predicting mz
3:39:53.912288 INFO: calibration group: precursor, predicting rt
3:39:53.942767 INFO: calibration group: precursor, predicting mobility
3:39:53.949945 INFO: calibration group: fragment, predicting mz
3:39:54.032150 INFO: Starting optimization step 0.
3:39:54.032385 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:39:54.032467 PROGRESS: Extracting batch of 49998 precursors
3:39:54.049385 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:39:54.049522 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:39:54.049574 INFO: FWHM in RT is 3.15 seconds, sigma is 0.69
3:39:54.049598 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.58
3:39:54.058547 INFO: Starting candidate selection
3:40:12.080097 INFO: Starting candidate scoring
3:40:15.561536 INFO: Finished candidate processing
3:40:15.561697 INFO: Collecting candidate features
3:40:15.730250 WARNING: intensity_correlation has 40 NaNs ( 0.05 % out of 82062)
3:40:15.730616 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 82062)
3:40:15.738541 INFO: Collecting fragment features
3:40:15.793166 INFO: Finished candidate scoring
3:40:15.830953 PROGRESS: === Extracted 82062 precursors and 786623 fragments ===
3:40:15.831386 INFO: performing precursor FDR with 47 features
3:40:15.831427 INFO: Decoy channel: -1
3:40:15.831450 INFO: Competetive: True
3:40:15.863068 INFO: Setting torch num_threads to 2 for FDR classification task
3:40:15.882744 WARNING: dropped 18 target PSMs due to missing features
3:40:15.882895 WARNING: dropped 24 decoy PSMs due to missing features
3:40:17.273124 INFO: Test AUC: 0.574
3:40:17.273277 INFO: Train AUC: 0.620
3:40:17.273309 INFO: AUC difference: 7.41%
3:40:17.273331 WARNING: AUC difference > 5%. This may indicate overfitting.
3:40:17.480115 INFO: Resetting torch num_threads to 100
3:40:17.484019 INFO: === FDR correction performed with classifier version 26 ===
3:40:17.488214 PROGRESS: ============================= Precursor FDR =============================
3:40:17.488350 PROGRESS: Total precursors accumulated: 22,150
3:40:17.488413 PROGRESS: Target precursors: 14,264 (64.40%)
3:40:17.488465 PROGRESS: Decoy precursors: 7,886 (35.60%)
3:40:17.488510 PROGRESS: 
3:40:17.488554 PROGRESS: Precursor Summary:
3:40:17.489677 PROGRESS: Channel   0:	 0.05 FDR:   330; 0.01 FDR:   261; 0.001 FDR:   136
3:40:17.489769 PROGRESS: 
3:40:17.489825 PROGRESS: Protein Summary:
3:40:17.491067 PROGRESS: Channel   0:	 0.05 FDR:   321; 0.01 FDR:   255; 0.001 FDR:   133
3:40:17.491170 PROGRESS: =========================================================================
3:40:17.546170 INFO: fragments_df: keeping 2855 of 786623 [sum(precursor_idx_mask)=5278 sum(mass_error_mask)=786623 stop_rank=2855
3:40:17.679522 INFO: calibration group: precursor, fitting mz estimator 
3:40:17.788869 INFO: calibration group: precursor, fitting rt estimator 
3:40:17.889950 INFO: calibration group: precursor, fitting mobility estimator 
3:40:17.987436 INFO: calibration group: fragment, fitting mz estimator 
3:40:18.299440 INFO: Using score_cutoff 40.51549470520019 (fac=0.99, q=1)
3:40:18.299887 INFO: calibration group: precursor, predicting mz
3:40:18.307558 INFO: calibration group: precursor, predicting rt
3:40:18.338123 INFO: calibration group: precursor, predicting mobility
3:40:18.345378 INFO: calibration group: fragment, predicting mz
3:40:18.403096 INFO: === checking if optimization conditions were reached ===
3:40:18.403444 PROGRESS: === Optimization of ms1_error has been performed 1 time(s); minimum number is 2 ===
3:40:18.405821 PROGRESS: ❌ ms1_error      : optimization incomplete after 1 search(es). Will search with parameter 9.0907.
3:40:18.405885 INFO: ==============================================
3:40:18.405989 INFO: Starting optimization step 1.
3:40:18.406062 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:40:18.406132 PROGRESS: Extracting batch of 49998 precursors
3:40:18.429855 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:40:18.430009 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:40:18.430062 INFO: FWHM in RT is 3.15 seconds, sigma is 0.69
3:40:18.430091 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.58
3:40:18.439006 INFO: Starting candidate selection
3:40:34.894218 INFO: Starting candidate scoring
3:40:38.052559 INFO: Finished candidate processing
3:40:38.053897 INFO: Collecting candidate features
3:40:38.206834 WARNING: intensity_correlation has 38 NaNs ( 0.05 % out of 82102)
3:40:38.207318 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 82102)
3:40:38.219297 INFO: Collecting fragment features
3:40:38.278490 INFO: Finished candidate scoring
3:40:38.377275 PROGRESS: === Extracted 82102 precursors and 782600 fragments ===
3:40:38.377742 INFO: performing precursor FDR with 47 features
3:40:38.377784 INFO: Decoy channel: -1
3:40:38.377812 INFO: Competetive: True
3:40:38.423251 INFO: Setting torch num_threads to 2 for FDR classification task
3:40:38.444909 WARNING: dropped 18 target PSMs due to missing features
3:40:38.445084 WARNING: dropped 20 decoy PSMs due to missing features
3:40:40.245479 INFO: Test AUC: 0.545
3:40:40.245618 INFO: Train AUC: 0.598
3:40:40.245651 INFO: AUC difference: 8.93%
3:40:40.245672 WARNING: AUC difference > 5%. This may indicate overfitting.
3:40:40.444270 INFO: Resetting torch num_threads to 100
3:40:40.447048 INFO: === FDR correction performed with classifier version 26 ===
3:40:40.451055 PROGRESS: ============================= Precursor FDR =============================
3:40:40.451206 PROGRESS: Total precursors accumulated: 22,208
3:40:40.451269 PROGRESS: Target precursors: 13,605 (61.26%)
3:40:40.451321 PROGRESS: Decoy precursors: 8,603 (38.74%)
3:40:40.451372 PROGRESS: 
3:40:40.451416 PROGRESS: Precursor Summary:
3:40:40.452555 PROGRESS: Channel   0:	 0.05 FDR:   394; 0.01 FDR:   292; 0.001 FDR:   235
3:40:40.452646 PROGRESS: 
3:40:40.452700 PROGRESS: Protein Summary:
3:40:40.453958 PROGRESS: Channel   0:	 0.05 FDR:   379; 0.01 FDR:   281; 0.001 FDR:   229
3:40:40.454051 PROGRESS: =========================================================================
3:40:40.506248 INFO: fragments_df: keeping 3075 of 782600 [sum(precursor_idx_mask)=6008 sum(mass_error_mask)=782593 stop_rank=3075
3:40:40.810435 INFO: calibration group: precursor, fitting mz estimator 
3:40:40.915833 INFO: calibration group: precursor, fitting rt estimator 
3:40:41.017064 INFO: calibration group: precursor, fitting mobility estimator 
3:40:41.124621 INFO: calibration group: fragment, fitting mz estimator 
3:40:41.461437 INFO: Using score_cutoff 37.65441879959106 (fac=0.99, q=1)
3:40:41.461859 INFO: calibration group: precursor, predicting mz
3:40:41.469182 INFO: calibration group: precursor, predicting rt
3:40:41.498864 INFO: calibration group: precursor, predicting mobility
3:40:41.505957 INFO: calibration group: fragment, predicting mz
3:40:41.562056 INFO: === checking if optimization conditions were reached ===
3:40:41.562364 PROGRESS: === Optimization of ms1_error has been performed 2 time(s); minimum number is 2 ===
3:40:41.564755 PROGRESS: ❌ ms1_error      : optimization incomplete after 2 search(es). Will search with parameter 2.9607.
3:40:41.564821 INFO: ==============================================
3:40:41.564928 INFO: Starting optimization step 2.
3:40:41.565005 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:40:41.565075 PROGRESS: Extracting batch of 49998 precursors
3:40:41.582196 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:40:41.582323 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:40:41.582373 INFO: FWHM in RT is 2.97 seconds, sigma is 0.65
3:40:41.582403 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.32
3:40:41.591323 INFO: Starting candidate selection
3:41:00.094224 INFO: Starting candidate scoring
3:41:02.756199 INFO: Finished candidate processing
3:41:02.756498 INFO: Collecting candidate features
3:41:02.929799 WARNING: intensity_correlation has 33 NaNs ( 0.04 % out of 82722)
3:41:02.930164 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 82722)
3:41:02.937967 INFO: Collecting fragment features
3:41:02.998997 INFO: Finished candidate scoring
3:41:03.038766 PROGRESS: === Extracted 82722 precursors and 781525 fragments ===
3:41:03.039284 INFO: performing precursor FDR with 47 features
3:41:03.039326 INFO: Decoy channel: -1
3:41:03.039356 INFO: Competetive: True
3:41:03.074159 INFO: Setting torch num_threads to 2 for FDR classification task
3:41:03.091611 WARNING: dropped 19 target PSMs due to missing features
3:41:03.091761 WARNING: dropped 17 decoy PSMs due to missing features
3:41:04.484993 INFO: Test AUC: 0.540
3:41:04.485262 INFO: Train AUC: 0.587
3:41:04.485301 INFO: AUC difference: 7.95%
3:41:04.485322 WARNING: AUC difference > 5%. This may indicate overfitting.
3:41:04.702421 INFO: Resetting torch num_threads to 100
3:41:04.705687 INFO: === FDR correction performed with classifier version 26 ===
3:41:04.709277 PROGRESS: ============================= Precursor FDR =============================
3:41:04.709432 PROGRESS: Total precursors accumulated: 22,343
3:41:04.709498 PROGRESS: Target precursors: 13,552 (60.65%)
3:41:04.709550 PROGRESS: Decoy precursors: 8,791 (39.35%)
3:41:04.709596 PROGRESS: 
3:41:04.709644 PROGRESS: Precursor Summary:
3:41:04.710764 PROGRESS: Channel   0:	 0.05 FDR:   378; 0.01 FDR:   310; 0.001 FDR:   218
3:41:04.710855 PROGRESS: 
3:41:04.710912 PROGRESS: Protein Summary:
3:41:04.712154 PROGRESS: Channel   0:	 0.05 FDR:   361; 0.01 FDR:   296; 0.001 FDR:   212
3:41:04.712247 PROGRESS: =========================================================================
3:41:04.765988 INFO: fragments_df: keeping 3313 of 781525 [sum(precursor_idx_mask)=6367 sum(mass_error_mask)=781522 stop_rank=3313
3:41:04.908250 INFO: calibration group: precursor, fitting mz estimator 
3:41:05.015540 INFO: calibration group: precursor, fitting rt estimator 
3:41:05.119610 INFO: calibration group: precursor, fitting mobility estimator 
3:41:05.231940 INFO: calibration group: fragment, fitting mz estimator 
3:41:05.663155 INFO: Using score_cutoff 29.16893641834259 (fac=0.99, q=1)
3:41:05.663615 INFO: calibration group: precursor, predicting mz
3:41:05.670700 INFO: calibration group: precursor, predicting rt
3:41:05.700305 INFO: calibration group: precursor, predicting mobility
3:41:05.707337 INFO: calibration group: fragment, predicting mz
3:41:05.764299 INFO: === checking if optimization conditions were reached ===
3:41:05.764638 PROGRESS: === Optimization of ms1_error has been performed 3 time(s); minimum number is 2 ===
3:41:05.766110 PROGRESS: ✅ ms1_error      : optimization complete. Optimal parameter 9.0907 found after 3 searches.
3:41:05.766183 INFO: ==============================================
3:41:05.766303 PROGRESS: Optimization finished for ms1_error.
3:41:05.914537 INFO: calibration group: precursor, predicting mz
3:41:05.922043 INFO: calibration group: precursor, predicting rt
3:41:05.951672 INFO: calibration group: precursor, predicting mobility
3:41:05.958730 INFO: calibration group: fragment, predicting mz
3:41:06.056766 INFO: Starting optimization step 0.
3:41:06.057767 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:41:06.057868 PROGRESS: Extracting batch of 49998 precursors
3:41:06.073514 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:41:06.073644 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:41:06.073694 INFO: FWHM in RT is 2.97 seconds, sigma is 0.65
3:41:06.073719 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.32
3:41:06.082940 INFO: Starting candidate selection
3:41:22.358687 INFO: Starting candidate scoring
3:41:25.278969 INFO: Finished candidate processing
3:41:25.279103 INFO: Collecting candidate features
3:41:25.424948 WARNING: intensity_correlation has 39 NaNs ( 0.05 % out of 82449)
3:41:25.425326 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 82449)
3:41:25.434031 INFO: Collecting fragment features
3:41:25.489650 INFO: Finished candidate scoring
3:41:25.536833 PROGRESS: === Extracted 82449 precursors and 785016 fragments ===
3:41:25.537268 INFO: performing precursor FDR with 47 features
3:41:25.537308 INFO: Decoy channel: -1
3:41:25.537331 INFO: Competetive: True
3:41:25.576588 INFO: Setting torch num_threads to 2 for FDR classification task
3:41:25.597443 WARNING: dropped 19 target PSMs due to missing features
3:41:25.597605 WARNING: dropped 21 decoy PSMs due to missing features
3:41:27.156889 INFO: Test AUC: 0.556
3:41:27.157027 INFO: Train AUC: 0.609
3:41:27.157058 INFO: AUC difference: 8.69%
3:41:27.157079 WARNING: AUC difference > 5%. This may indicate overfitting.
3:41:27.359802 INFO: Resetting torch num_threads to 100
3:41:27.363368 INFO: === FDR correction performed with classifier version 28 ===
3:41:27.367540 PROGRESS: ============================= Precursor FDR =============================
3:41:27.367704 PROGRESS: Total precursors accumulated: 22,289
3:41:27.367770 PROGRESS: Target precursors: 14,055 (63.06%)
3:41:27.367821 PROGRESS: Decoy precursors: 8,234 (36.94%)
3:41:27.367878 PROGRESS: 
3:41:27.367924 PROGRESS: Precursor Summary:
3:41:27.369051 PROGRESS: Channel   0:	 0.05 FDR:   405; 0.01 FDR:   268; 0.001 FDR:   247
3:41:27.369143 PROGRESS: 
3:41:27.369197 PROGRESS: Protein Summary:
3:41:27.370435 PROGRESS: Channel   0:	 0.05 FDR:   389; 0.01 FDR:   259; 0.001 FDR:   239
3:41:27.370527 PROGRESS: =========================================================================
3:41:27.423227 INFO: fragments_df: keeping 2946 of 785016 [sum(precursor_idx_mask)=5485 sum(mass_error_mask)=785014 stop_rank=2946
3:41:27.565546 INFO: calibration group: precursor, fitting mz estimator 
3:41:27.729469 INFO: calibration group: precursor, fitting rt estimator 
3:41:27.857729 INFO: calibration group: precursor, fitting mobility estimator 
3:41:27.984889 INFO: calibration group: fragment, fitting mz estimator 
3:41:28.377426 INFO: Using score_cutoff 34.932547821807866 (fac=0.99, q=1)
3:41:28.377834 INFO: calibration group: precursor, predicting mz
3:41:28.385070 INFO: calibration group: precursor, predicting rt
3:41:28.415033 INFO: calibration group: precursor, predicting mobility
3:41:28.422207 INFO: calibration group: fragment, predicting mz
3:41:28.478269 INFO: === checking if optimization conditions were reached ===
3:41:28.478538 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
3:41:28.480207 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0689.
3:41:28.480263 INFO: ==============================================
3:41:28.480352 INFO: Starting optimization step 1.
3:41:28.480428 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:41:28.480498 PROGRESS: Extracting batch of 49998 precursors
3:41:28.493180 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:41:28.493292 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:41:28.493335 INFO: FWHM in RT is 3.06 seconds, sigma is 0.67
3:41:28.493359 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.36
3:41:28.518222 INFO: Starting candidate selection
3:41:40.097498 INFO: Starting candidate scoring
3:41:43.003643 INFO: Finished candidate processing
3:41:43.003837 INFO: Collecting candidate features
3:41:43.172481 WARNING: intensity_correlation has 41 NaNs ( 0.05 % out of 80154)
3:41:43.172860 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 80154)
3:41:43.181114 INFO: Collecting fragment features
3:41:43.238638 INFO: Finished candidate scoring
3:41:43.284927 PROGRESS: === Extracted 80154 precursors and 759718 fragments ===
3:41:43.285373 INFO: performing precursor FDR with 47 features
3:41:43.285413 INFO: Decoy channel: -1
3:41:43.285437 INFO: Competetive: True
3:41:43.316380 INFO: Setting torch num_threads to 2 for FDR classification task
3:41:43.335434 WARNING: dropped 26 target PSMs due to missing features
3:41:43.335586 WARNING: dropped 17 decoy PSMs due to missing features
3:41:44.936866 INFO: Test AUC: 0.559
3:41:44.937027 INFO: Train AUC: 0.603
3:41:44.937058 INFO: AUC difference: 7.24%
3:41:44.937081 WARNING: AUC difference > 5%. This may indicate overfitting.
3:41:45.141669 INFO: Resetting torch num_threads to 100
3:41:45.145133 INFO: === FDR correction performed with classifier version 28 ===
3:41:45.149345 PROGRESS: ============================= Precursor FDR =============================
3:41:45.149490 PROGRESS: Total precursors accumulated: 21,746
3:41:45.149552 PROGRESS: Target precursors: 13,579 (62.44%)
3:41:45.149604 PROGRESS: Decoy precursors: 8,167 (37.56%)
3:41:45.149649 PROGRESS: 
3:41:45.149697 PROGRESS: Precursor Summary:
3:41:45.150812 PROGRESS: Channel   0:	 0.05 FDR:   413; 0.01 FDR:   276; 0.001 FDR:     0
3:41:45.150905 PROGRESS: 
3:41:45.150961 PROGRESS: Protein Summary:
3:41:45.152173 PROGRESS: Channel   0:	 0.05 FDR:   399; 0.01 FDR:   267; 0.001 FDR:     0
3:41:45.152267 PROGRESS: =========================================================================
3:41:45.205183 INFO: fragments_df: keeping 2932 of 759718 [sum(precursor_idx_mask)=5648 sum(mass_error_mask)=759712 stop_rank=2932
3:41:45.549015 INFO: calibration group: precursor, fitting mz estimator 
3:41:45.651126 INFO: calibration group: precursor, fitting rt estimator 
3:41:45.753964 INFO: calibration group: precursor, fitting mobility estimator 
3:41:45.857561 INFO: calibration group: fragment, fitting mz estimator 
3:41:46.192588 INFO: Using score_cutoff 27.22188576221466 (fac=0.99, q=1)
3:41:46.193050 INFO: calibration group: precursor, predicting mz
3:41:46.200830 INFO: calibration group: precursor, predicting rt
3:41:46.231300 INFO: calibration group: precursor, predicting mobility
3:41:46.238713 INFO: calibration group: fragment, predicting mz
3:41:46.296918 INFO: === checking if optimization conditions were reached ===
3:41:46.297278 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
3:41:46.299704 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0541.
3:41:46.299773 INFO: ==============================================
3:41:46.299885 INFO: Starting optimization step 2.
3:41:46.299961 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:41:46.300030 PROGRESS: Extracting batch of 49998 precursors
3:41:46.322500 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:41:46.322641 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:41:46.322695 INFO: FWHM in RT is 3.09 seconds, sigma is 0.68
3:41:46.322724 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.34
3:41:46.331587 INFO: Starting candidate selection
3:41:56.948048 INFO: Starting candidate scoring
3:42:00.005023 INFO: Finished candidate processing
3:42:00.005145 INFO: Collecting candidate features
3:42:00.159262 WARNING: intensity_correlation has 45 NaNs ( 0.06 % out of 78690)
3:42:00.159646 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 78690)
3:42:00.168056 INFO: Collecting fragment features
3:42:00.228051 INFO: Finished candidate scoring
3:42:00.274568 PROGRESS: === Extracted 78690 precursors and 740591 fragments ===
3:42:00.275012 INFO: performing precursor FDR with 47 features
3:42:00.275060 INFO: Decoy channel: -1
3:42:00.275084 INFO: Competetive: True
3:42:00.316233 INFO: Setting torch num_threads to 2 for FDR classification task
3:42:00.337107 WARNING: dropped 23 target PSMs due to missing features
3:42:00.337236 WARNING: dropped 23 decoy PSMs due to missing features
3:42:01.690250 INFO: Test AUC: 0.553
3:42:01.690417 INFO: Train AUC: 0.612
3:42:01.690448 INFO: AUC difference: 9.55%
3:42:01.690471 WARNING: AUC difference > 5%. This may indicate overfitting.
3:42:01.894308 INFO: Resetting torch num_threads to 100
3:42:01.898001 INFO: === FDR correction performed with classifier version 28 ===
3:42:01.901925 PROGRESS: ============================= Precursor FDR =============================
3:42:01.902076 PROGRESS: Total precursors accumulated: 21,371
3:42:01.902146 PROGRESS: Target precursors: 13,464 (63.00%)
3:42:01.902199 PROGRESS: Decoy precursors: 7,907 (37.00%)
3:42:01.902246 PROGRESS: 
3:42:01.902292 PROGRESS: Precursor Summary:
3:42:01.903438 PROGRESS: Channel   0:	 0.05 FDR:   432; 0.01 FDR:   313; 0.001 FDR:   248
3:42:01.903542 PROGRESS: 
3:42:01.903601 PROGRESS: Protein Summary:
3:42:01.904841 PROGRESS: Channel   0:	 0.05 FDR:   417; 0.01 FDR:   300; 0.001 FDR:   239
3:42:01.904933 PROGRESS: =========================================================================
3:42:01.959457 INFO: fragments_df: keeping 3224 of 740591 [sum(precursor_idx_mask)=6438 sum(mass_error_mask)=740587 stop_rank=3224
3:42:02.124780 INFO: calibration group: precursor, fitting mz estimator 
3:42:02.268911 INFO: calibration group: precursor, fitting rt estimator 
3:42:02.396814 INFO: calibration group: precursor, fitting mobility estimator 
3:42:02.517756 INFO: calibration group: fragment, fitting mz estimator 
3:42:02.943244 INFO: Using score_cutoff 37.58376007232666 (fac=0.99, q=1)
3:42:02.943759 INFO: calibration group: precursor, predicting mz
3:42:02.951604 INFO: calibration group: precursor, predicting rt
3:42:02.981980 INFO: calibration group: precursor, predicting mobility
3:42:02.989142 INFO: calibration group: fragment, predicting mz
3:42:03.047997 INFO: === checking if optimization conditions were reached ===
3:42:03.048470 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
3:42:03.051096 PROGRESS: ❌ mobility_error : optimization incomplete after 3 search(es). Will search with parameter 0.0459.
3:42:03.051151 INFO: ==============================================
3:42:03.051275 INFO: Starting optimization step 3.
3:42:03.051359 PROGRESS: === Extracting elution groups 0 to 25400 ===
3:42:03.051456 PROGRESS: Extracting batch of 49998 precursors
3:42:03.067631 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:42:03.067742 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:42:03.067800 INFO: FWHM in RT is 3.12 seconds, sigma is 0.69
3:42:03.067829 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.34
3:42:03.076728 INFO: Starting candidate selection
3:42:11.362175 INFO: Starting candidate scoring
3:42:14.135233 INFO: Finished candidate processing
3:42:14.135355 INFO: Collecting candidate features
3:42:14.272680 WARNING: intensity_correlation has 50 NaNs ( 0.06 % out of 77922)
3:42:14.273059 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 77922)
3:42:14.281019 INFO: Collecting fragment features
3:42:14.333371 INFO: Finished candidate scoring
3:42:14.374601 PROGRESS: === Extracted 77922 precursors and 730225 fragments ===
3:42:14.375145 INFO: performing precursor FDR with 47 features
3:42:14.375188 INFO: Decoy channel: -1
3:42:14.375213 INFO: Competetive: True
3:42:14.405289 INFO: Setting torch num_threads to 2 for FDR classification task
3:42:14.423615 WARNING: dropped 26 target PSMs due to missing features
3:42:14.423773 WARNING: dropped 25 decoy PSMs due to missing features
3:42:15.979054 INFO: Test AUC: 0.568
3:42:15.979214 INFO: Train AUC: 0.604
3:42:15.979249 INFO: AUC difference: 5.94%
3:42:15.979273 WARNING: AUC difference > 5%. This may indicate overfitting.
3:42:16.181656 INFO: Resetting torch num_threads to 100
3:42:16.185024 INFO: === FDR correction performed with classifier version 28 ===
3:42:16.188993 PROGRESS: ============================= Precursor FDR =============================
3:42:16.189134 PROGRESS: Total precursors accumulated: 21,170
3:42:16.189198 PROGRESS: Target precursors: 13,271 (62.69%)
3:42:16.189250 PROGRESS: Decoy precursors: 7,899 (37.31%)
3:42:16.189309 PROGRESS: 
3:42:16.189359 PROGRESS: Precursor Summary:
3:42:16.190504 PROGRESS: Channel   0:	 0.05 FDR:   426; 0.01 FDR:   275; 0.001 FDR:   235
3:42:16.190597 PROGRESS: 
3:42:16.190653 PROGRESS: Protein Summary:
3:42:16.191901 PROGRESS: Channel   0:	 0.05 FDR:   412; 0.01 FDR:   264; 0.001 FDR:   224
3:42:16.191995 PROGRESS: =========================================================================
3:42:16.242730 INFO: fragments_df: keeping 2864 of 730225 [sum(precursor_idx_mask)=5700 sum(mass_error_mask)=730222 stop_rank=2864
3:42:16.371835 INFO: calibration group: precursor, fitting mz estimator 
3:42:16.493654 INFO: calibration group: precursor, fitting rt estimator 
3:42:16.615474 INFO: calibration group: precursor, fitting mobility estimator 
3:42:16.736496 INFO: calibration group: fragment, fitting mz estimator 
3:42:17.049459 INFO: Using score_cutoff 34.64351804237366 (fac=0.99, q=1)
3:42:17.049952 INFO: calibration group: precursor, predicting mz
3:42:17.057742 INFO: calibration group: precursor, predicting rt
3:42:17.088268 INFO: calibration group: precursor, predicting mobility
3:42:17.095689 INFO: calibration group: fragment, predicting mz
3:42:17.154595 INFO: === checking if optimization conditions were reached ===
3:42:17.154947 PROGRESS: === Optimization of mobility_error has been performed 4 time(s); minimum number is 2 ===
3:42:17.156182 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.0541 found after 4 searches.
3:42:17.156246 INFO: ==============================================
3:42:17.156354 PROGRESS: Optimization finished for mobility_error.
3:42:17.297543 INFO: calibration group: precursor, predicting mz
3:42:17.305651 INFO: calibration group: precursor, predicting rt
3:42:17.336293 INFO: calibration group: precursor, predicting mobility
3:42:17.343749 INFO: calibration group: fragment, predicting mz
3:42:17.434847 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:42:17.435146 PROGRESS: ==============================================
3:42:17.435235 PROGRESS: ms2_error      : 18.2300
3:42:17.435312 PROGRESS: rt_error       : 124.2534
3:42:17.435380 PROGRESS: ms1_error      : 9.0907
3:42:17.435438 PROGRESS: mobility_error : 0.0541
3:42:17.435491 PROGRESS: ==============================================
3:42:17.440646 INFO: calibration group: precursor, predicting mz
3:42:18.900252 INFO: calibration group: precursor, predicting rt
3:42:25.435814 INFO: calibration group: precursor, predicting mobility
3:42:26.936108 INFO: calibration group: fragment, predicting mz
3:42:39.973387 PROGRESS: Extracting batch of 10272670 precursors
3:42:42.562729 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:42:42.562880 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:42:42.562929 INFO: FWHM in RT is 3.12 seconds, sigma is 0.69
3:42:42.562953 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.34
3:42:42.563867 INFO: Starting candidate selection
4:12:13.771215 INFO: Applying score cutoff of 37.58376007232666
4:12:14.159272 INFO: Removed 7702928 precursors with score below cutoff
4:12:16.979865 INFO: Starting candidate scoring
4:18:10.326335 INFO: Finished candidate processing
4:18:10.326916 INFO: Collecting candidate features
4:18:27.240279 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 9470106)
4:18:27.560770 INFO: Collecting fragment features
4:18:34.843760 INFO: Finished candidate scoring
4:18:42.921232 INFO: === FDR correction performed with classifier version 32 ===
4:18:42.924828 INFO: performing precursor FDR with 47 features
4:18:42.924905 INFO: Decoy channel: -1
4:18:42.924934 INFO: Competetive: True
4:18:45.501464 INFO: Setting torch num_threads to 2 for FDR classification task
4:18:47.121166 WARNING: dropped 2 target PSMs due to missing features
4:18:47.121326 WARNING: dropped 1 decoy PSMs due to missing features
4:21:50.829816 INFO: Test AUC: 0.519
4:21:50.829988 INFO: Train AUC: 0.568
4:21:50.830027 INFO: AUC difference: 8.71%
4:21:50.830050 WARNING: AUC difference > 5%. This may indicate overfitting.
4:21:53.262179 INFO: Resetting torch num_threads to 100
4:21:53.513238 INFO: Removing fragments below FDR threshold
4:21:54.235606 PROGRESS: ============================= Precursor FDR =============================
4:21:54.235883 PROGRESS: Total precursors accumulated: 72,410
4:21:54.235969 PROGRESS: Target precursors: 71,694 (99.01%)
4:21:54.236023 PROGRESS: Decoy precursors: 716 (0.99%)
4:21:54.236071 PROGRESS: 
4:21:54.236122 PROGRESS: Precursor Summary:
4:21:54.265195 PROGRESS: Channel   0:	 0.05 FDR: 71,694; 0.01 FDR: 71,694; 0.001 FDR: 52,106
4:21:54.265470 PROGRESS: 
4:21:54.265535 PROGRESS: Protein Summary:
4:21:54.307514 PROGRESS: Channel   0:	 0.05 FDR: 11,387; 0.01 FDR: 11,387; 0.001 FDR: 9,115
4:21:54.307766 PROGRESS: =========================================================================
4:21:55.052897 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
4:21:55.523290 PROGRESS: Loading raw file 3/6: ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
4:21:55.523472 INFO: Quantification results path: run_output/alphadia_1.10.4_Again_good_now/library/quant
4:21:55.523558 INFO: Creating folder run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/figures
4:21:55.524604 INFO: Initializing RawFileManager
4:21:55.524750 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:21:55.524808 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:21:55.524852 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:21:55.744071 INFO: Reading 39,128 frames with 2,897,842,446 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:22:04.105830 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d...
4:22:04.107846 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:22:04.120960 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:22:04.121349 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:22:04.121932 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:22:04.125592 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:22:04.144487 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:22:04.144922 INFO: Indexing quadrupole dimension
4:22:04.676643 INFO: Transposing detector events
4:22:13.350199 INFO: Finished transposing data
4:22:13.389335 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
4:22:13.390203 INFO: RT (min)            : 0.0 - 70.0
4:22:13.390292 INFO: RT duration (sec)   : 4199.8
4:22:13.390347 INFO: RT duration (min)   : 70.0
4:22:13.390395 INFO: Cycle len (scans)   : 9
4:22:13.390441 INFO: Cycle len (sec)     : 0.97
4:22:13.390485 INFO: Number of cycles    : 4347
4:22:13.390528 INFO: MS2 range (m/z)     : 400.0 - 1000.0
4:22:14.439873 INFO: Initializing CalibrationManager
4:22:14.440188 INFO: Loading calibration config
4:22:14.440764 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed'], 'function': LOESSRegression()}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed'], 'function': LOESSRegression(n_kernels=2)}], 'name': 'precursor'}]
4:22:14.440852 INFO: Calibration group :fragment, found 1 estimator(s)
4:22:14.440954 INFO: Calibration group :precursor, found 3 estimator(s)
4:22:14.441118 INFO: Initializing OptimizationManager
4:22:14.441224 INFO: initial parameter: ms1_error = 30
4:22:14.441281 INFO: initial parameter: ms2_error = 30
4:22:14.441336 INFO: initial parameter: rt_error = 2099.8992935
4:22:14.441383 INFO: initial parameter: mobility_error = 0.1
4:22:14.441427 INFO: initial parameter: column_type = library
4:22:14.441469 INFO: initial parameter: num_candidates = 1
4:22:14.441510 INFO: initial parameter: classifier_version = -1
4:22:14.441555 INFO: initial parameter: fwhm_rt = 5
4:22:14.441599 INFO: initial parameter: fwhm_mobility = 0.01
4:22:14.441643 INFO: initial parameter: score_cutoff = 0
4:22:14.441707 INFO: Initializing TimingManager
4:22:14.441773 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
4:22:14.441885 INFO: FDRManager not loaded from disk.
4:22:14.441910 INFO: Initializing FDRManager
4:22:14.441949 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
4:22:15.755194 PROGRESS: 5,215,079 target precursors potentially observable (0 removed)
4:22:17.619946 PROGRESS: Starting initial search for precursors.
4:22:17.839257 INFO: Starting optimization step 0.
4:22:17.839512 PROGRESS: === Extracting elution groups 0 to 200 ===
4:22:17.839587 PROGRESS: Extracting batch of 398 precursors
4:22:17.840553 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:22:17.840600 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:22:17.840634 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
4:22:17.840657 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
4:22:17.847046 INFO: Starting candidate selection
4:22:20.574455 INFO: Starting candidate scoring
4:22:20.630877 INFO: Finished candidate processing
4:22:20.630976 INFO: Collecting candidate features
4:22:20.640115 INFO: Collecting fragment features
4:22:20.642185 INFO: Finished candidate scoring
4:22:20.643211 PROGRESS: === Extracted 336 precursors and 3471 fragments ===
4:22:20.643500 INFO: performing precursor FDR with 47 features
4:22:20.643538 INFO: Decoy channel: -1
4:22:20.643560 INFO: Competetive: True
4:22:20.644570 INFO: Setting torch num_threads to 2 for FDR classification task
4:22:20.654058 INFO: Test AUC: 0.369
4:22:20.654117 INFO: Train AUC: 0.491
4:22:20.654146 INFO: AUC difference: 24.93%
4:22:20.654168 WARNING: AUC difference > 5%. This may indicate overfitting.
4:22:20.835155 INFO: Resetting torch num_threads to 100
4:22:20.835716 INFO: === FDR correction performed with classifier version -1 ===
4:22:20.836301 PROGRESS: ============================= Precursor FDR =============================
4:22:20.836392 PROGRESS: Total precursors accumulated: 173
4:22:20.836452 PROGRESS: Target precursors: 80 (46.24%)
4:22:20.836502 PROGRESS: Decoy precursors: 93 (53.76%)
4:22:20.836547 PROGRESS: 
4:22:20.836601 PROGRESS: Precursor Summary:
4:22:20.837430 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
4:22:20.837518 PROGRESS: 
4:22:20.837573 PROGRESS: Protein Summary:
4:22:20.838451 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
4:22:20.838538 PROGRESS: =========================================================================
4:22:20.895373 INFO: Starting optimization step 1.
4:22:20.895583 PROGRESS: === Extracting elution groups 200 to 600 ===
4:22:20.895650 PROGRESS: Extracting batch of 786 precursors
4:22:20.896469 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:22:20.896515 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:22:20.896543 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
4:22:20.896564 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
4:22:20.897331 INFO: Starting candidate selection
4:22:25.834655 INFO: Starting candidate scoring
4:22:25.938099 INFO: Finished candidate processing
4:22:25.938219 INFO: Collecting candidate features
4:22:25.948055 INFO: Collecting fragment features
4:22:25.950433 INFO: Finished candidate scoring
4:22:25.952767 PROGRESS: === Extracted 1053 precursors and 10798 fragments ===
4:22:25.953571 INFO: performing precursor FDR with 47 features
4:22:25.953616 INFO: Decoy channel: -1
4:22:25.953640 INFO: Competetive: True
4:22:25.956728 INFO: Setting torch num_threads to 2 for FDR classification task
4:22:25.967466 INFO: Test AUC: 0.378
4:22:25.967536 INFO: Train AUC: 0.489
4:22:25.967567 INFO: AUC difference: 22.65%
4:22:25.967590 WARNING: AUC difference > 5%. This may indicate overfitting.
4:22:26.155743 INFO: Resetting torch num_threads to 100
4:22:26.156890 INFO: === FDR correction performed with classifier version -1 ===
4:22:26.157608 PROGRESS: ============================= Precursor FDR =============================
4:22:26.157702 PROGRESS: Total precursors accumulated: 540
4:22:26.157765 PROGRESS: Target precursors: 255 (47.22%)
4:22:26.157815 PROGRESS: Decoy precursors: 285 (52.78%)
4:22:26.157862 PROGRESS: 
4:22:26.157907 PROGRESS: Precursor Summary:
4:22:26.158758 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
4:22:26.158845 PROGRESS: 
4:22:26.158899 PROGRESS: Protein Summary:
4:22:26.159828 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
4:22:26.159920 PROGRESS: =========================================================================
4:22:26.219985 INFO: Starting optimization step 2.
4:22:26.220223 PROGRESS: === Extracting elution groups 600 to 1400 ===
4:22:26.220294 PROGRESS: Extracting batch of 1566 precursors
4:22:26.221464 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:22:26.221514 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:22:26.221546 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
4:22:26.221570 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
4:22:26.222330 INFO: Starting candidate selection
4:22:35.636662 INFO: Starting candidate scoring
4:22:35.780060 INFO: Finished candidate processing
4:22:35.780163 INFO: Collecting candidate features
4:22:35.788701 WARNING: intensity_correlation has 1 NaNs ( 0.07 % out of 1377)
4:22:35.791667 INFO: Collecting fragment features
4:22:35.795192 INFO: Finished candidate scoring
4:22:35.801006 PROGRESS: === Extracted 2430 precursors and 24471 fragments ===
4:22:35.802119 INFO: performing precursor FDR with 47 features
4:22:35.802163 INFO: Decoy channel: -1
4:22:35.802188 INFO: Competetive: True
4:22:35.807917 INFO: Setting torch num_threads to 2 for FDR classification task
4:22:35.809299 WARNING: dropped 1 target PSMs due to missing features
4:22:35.824515 INFO: Test AUC: 0.473
4:22:35.824582 INFO: Train AUC: 0.496
4:22:35.824611 INFO: AUC difference: 4.60%
4:22:36.000687 INFO: Resetting torch num_threads to 100
4:22:36.001573 INFO: === FDR correction performed with classifier version -1 ===
4:22:36.002350 PROGRESS: ============================= Precursor FDR =============================
4:22:36.002445 PROGRESS: Total precursors accumulated: 1,255
4:22:36.002512 PROGRESS: Target precursors: 624 (49.72%)
4:22:36.002570 PROGRESS: Decoy precursors: 631 (50.28%)
4:22:36.002617 PROGRESS: 
4:22:36.002663 PROGRESS: Precursor Summary:
4:22:36.003529 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
4:22:36.003622 PROGRESS: 
4:22:36.003678 PROGRESS: Protein Summary:
4:22:36.004569 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
4:22:36.004656 PROGRESS: =========================================================================
4:22:36.072263 INFO: Starting optimization step 3.
4:22:36.072478 PROGRESS: === Extracting elution groups 1400 to 3000 ===
4:22:36.072557 PROGRESS: Extracting batch of 3160 precursors
4:22:36.073955 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:22:36.074003 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:22:36.074037 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
4:22:36.074059 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
4:22:36.075052 INFO: Starting candidate selection
4:22:53.609975 INFO: Starting candidate scoring
4:22:53.866846 INFO: Finished candidate processing
4:22:53.867282 INFO: Collecting candidate features
4:22:53.881546 INFO: Collecting fragment features
4:22:53.886710 INFO: Finished candidate scoring
4:22:53.891553 PROGRESS: === Extracted 5193 precursors and 52145 fragments ===
4:22:53.892847 INFO: performing precursor FDR with 47 features
4:22:53.892895 INFO: Decoy channel: -1
4:22:53.892919 INFO: Competetive: True
4:22:53.896996 INFO: Setting torch num_threads to 2 for FDR classification task
4:22:53.898582 WARNING: dropped 1 target PSMs due to missing features
4:22:53.923024 INFO: Test AUC: 0.478
4:22:53.923118 INFO: Train AUC: 0.500
4:22:53.923149 INFO: AUC difference: 4.41%
4:22:54.100410 INFO: Resetting torch num_threads to 100
4:22:54.101558 INFO: === FDR correction performed with classifier version -1 ===
4:22:54.102542 PROGRESS: ============================= Precursor FDR =============================
4:22:54.102638 PROGRESS: Total precursors accumulated: 2,667
4:22:54.102697 PROGRESS: Target precursors: 1,329 (49.83%)
4:22:54.102748 PROGRESS: Decoy precursors: 1,338 (50.17%)
4:22:54.102792 PROGRESS: 
4:22:54.102835 PROGRESS: Precursor Summary:
4:22:54.103732 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
4:22:54.103823 PROGRESS: 
4:22:54.103878 PROGRESS: Protein Summary:
4:22:54.104785 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
4:22:54.104873 PROGRESS: =========================================================================
4:22:54.186271 INFO: Starting optimization step 4.
4:22:54.186553 PROGRESS: === Extracting elution groups 3000 to 6200 ===
4:22:54.186625 PROGRESS: Extracting batch of 6310 precursors
4:22:54.188555 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:22:54.188607 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:22:54.188637 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
4:22:54.188660 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
4:22:54.189477 INFO: Starting candidate selection
4:23:29.994786 INFO: Starting candidate scoring
4:23:30.360007 INFO: Finished candidate processing
4:23:30.360130 INFO: Collecting candidate features
4:23:30.375962 WARNING: intensity_correlation has 1 NaNs ( 0.02 % out of 5483)
4:23:30.379211 INFO: Collecting fragment features
4:23:30.384918 INFO: Finished candidate scoring
4:23:30.393636 PROGRESS: === Extracted 10676 precursors and 107716 fragments ===
4:23:30.395446 INFO: performing precursor FDR with 47 features
4:23:30.395504 INFO: Decoy channel: -1
4:23:30.395529 INFO: Competetive: True
4:23:30.402919 INFO: Setting torch num_threads to 2 for FDR classification task
4:23:30.405114 WARNING: dropped 2 target PSMs due to missing features
4:23:30.441002 INFO: Test AUC: 0.506
4:23:30.441126 INFO: Train AUC: 0.485
4:23:30.441157 INFO: AUC difference: 4.17%
4:23:30.621709 INFO: Resetting torch num_threads to 100
4:23:30.623122 INFO: === FDR correction performed with classifier version -1 ===
4:23:30.624342 PROGRESS: ============================= Precursor FDR =============================
4:23:30.624451 PROGRESS: Total precursors accumulated: 5,480
4:23:30.624513 PROGRESS: Target precursors: 2,685 (49.00%)
4:23:30.624566 PROGRESS: Decoy precursors: 2,795 (51.00%)
4:23:30.624611 PROGRESS: 
4:23:30.624655 PROGRESS: Precursor Summary:
4:23:30.625511 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
4:23:30.625601 PROGRESS: 
4:23:30.625659 PROGRESS: Protein Summary:
4:23:30.626566 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
4:23:30.626654 PROGRESS: =========================================================================
4:23:30.728207 INFO: Starting optimization step 5.
4:23:30.728459 PROGRESS: === Extracting elution groups 6200 to 12600 ===
4:23:30.728529 PROGRESS: Extracting batch of 12602 precursors
4:23:30.731121 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:23:30.731171 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:23:30.731202 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
4:23:30.731224 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
4:23:30.732024 INFO: Starting candidate selection
4:24:41.159853 INFO: Starting candidate scoring
4:24:41.808725 INFO: Finished candidate processing
4:24:41.808902 INFO: Collecting candidate features
4:24:41.872194 WARNING: intensity_correlation has 3 NaNs ( 0.03 % out of 11009)
4:24:41.877049 INFO: Collecting fragment features
4:24:41.892850 INFO: Finished candidate scoring
4:24:41.930872 PROGRESS: === Extracted 21685 precursors and 217833 fragments ===
4:24:41.934059 INFO: performing precursor FDR with 47 features
4:24:41.934124 INFO: Decoy channel: -1
4:24:41.934150 INFO: Competetive: True
4:24:41.945692 INFO: Setting torch num_threads to 2 for FDR classification task
4:24:41.949332 WARNING: dropped 5 target PSMs due to missing features
4:24:42.272025 INFO: Test AUC: 0.505
4:24:42.272172 INFO: Train AUC: 0.523
4:24:42.272203 INFO: AUC difference: 3.51%
4:24:42.466322 INFO: Resetting torch num_threads to 100
4:24:42.468329 INFO: === FDR correction performed with classifier version -1 ===
4:24:42.470267 PROGRESS: ============================= Precursor FDR =============================
4:24:42.470381 PROGRESS: Total precursors accumulated: 11,123
4:24:42.470441 PROGRESS: Target precursors: 5,898 (53.03%)
4:24:42.470492 PROGRESS: Decoy precursors: 5,225 (46.97%)
4:24:42.470539 PROGRESS: 
4:24:42.470583 PROGRESS: Precursor Summary:
4:24:42.471508 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
4:24:42.471600 PROGRESS: 
4:24:42.471656 PROGRESS: Protein Summary:
4:24:42.472645 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
4:24:42.472732 PROGRESS: =========================================================================
4:24:42.949560 INFO: Starting optimization step 6.
4:24:42.949881 PROGRESS: === Extracting elution groups 12600 to 25400 ===
4:24:42.949978 PROGRESS: Extracting batch of 25176 precursors
4:24:42.962973 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:24:42.963129 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:24:42.963168 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
4:24:42.963192 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
4:24:42.964107 INFO: Starting candidate selection
4:26:52.710816 INFO: Starting candidate scoring
4:26:53.924627 INFO: Finished candidate processing
4:26:53.925594 INFO: Collecting candidate features
4:26:53.983972 WARNING: intensity_correlation has 2 NaNs ( 0.01 % out of 21923)
4:26:53.984255 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 21923)
4:26:53.988125 INFO: Collecting fragment features
4:26:54.004800 INFO: Finished candidate scoring
4:26:54.086843 PROGRESS: === Extracted 43608 precursors and 436839 fragments ===
4:26:54.094235 INFO: performing precursor FDR with 47 features
4:26:54.094355 INFO: Decoy channel: -1
4:26:54.094381 INFO: Competetive: True
4:26:54.116878 INFO: Setting torch num_threads to 2 for FDR classification task
4:26:54.126908 WARNING: dropped 5 target PSMs due to missing features
4:26:54.127059 WARNING: dropped 2 decoy PSMs due to missing features
4:26:54.872096 INFO: Test AUC: 0.552
4:26:54.872245 INFO: Train AUC: 0.556
4:26:54.872276 INFO: AUC difference: 0.77%
4:26:55.073575 INFO: Resetting torch num_threads to 100
4:26:55.077027 INFO: === FDR correction performed with classifier version -1 ===
4:26:55.080897 PROGRESS: ============================= Precursor FDR =============================
4:26:55.081074 PROGRESS: Total precursors accumulated: 22,379
4:26:55.081135 PROGRESS: Target precursors: 13,087 (58.48%)
4:26:55.081189 PROGRESS: Decoy precursors: 9,292 (41.52%)
4:26:55.081235 PROGRESS: 
4:26:55.081282 PROGRESS: Precursor Summary:
4:26:55.082339 PROGRESS: Channel   0:	 0.05 FDR:    22; 0.01 FDR:    11; 0.001 FDR:    11
4:26:55.082430 PROGRESS: 
4:26:55.082485 PROGRESS: Protein Summary:
4:26:55.083588 PROGRESS: Channel   0:	 0.05 FDR:    22; 0.01 FDR:    11; 0.001 FDR:    11
4:26:55.083683 PROGRESS: =========================================================================
4:26:55.361818 INFO: Starting optimization step 7.
4:26:55.362123 PROGRESS: === Extracting elution groups 25400 to 51000 ===
4:26:55.362233 PROGRESS: Extracting batch of 50417 precursors
4:26:55.378760 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:26:55.378909 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:26:55.378950 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
4:26:55.378973 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
4:26:55.379956 INFO: Starting candidate selection
4:31:11.426094 INFO: Starting candidate scoring
4:31:13.736250 INFO: Finished candidate processing
4:31:13.736413 INFO: Collecting candidate features
4:31:13.840999 WARNING: intensity_correlation has 9 NaNs ( 0.02 % out of 44040)
4:31:13.841280 WARNING: height_correlation has 4 NaNs ( 0.01 % out of 44040)
4:31:13.845692 INFO: Collecting fragment features
4:31:13.876429 INFO: Finished candidate scoring
4:31:14.045682 PROGRESS: === Extracted 87648 precursors and 877919 fragments ===
4:31:14.058714 INFO: performing precursor FDR with 47 features
4:31:14.058838 INFO: Decoy channel: -1
4:31:14.058864 INFO: Competetive: True
4:31:14.105207 INFO: Setting torch num_threads to 2 for FDR classification task
4:31:14.126442 WARNING: dropped 10 target PSMs due to missing features
4:31:14.126591 WARNING: dropped 9 decoy PSMs due to missing features
4:31:15.913296 INFO: Test AUC: 0.563
4:31:15.913426 INFO: Train AUC: 0.571
4:31:15.913456 INFO: AUC difference: 1.39%
4:31:16.125296 INFO: Resetting torch num_threads to 100
4:31:16.130740 INFO: === FDR correction performed with classifier version -1 ===
4:31:16.139266 PROGRESS: ============================= Precursor FDR =============================
4:31:16.139537 PROGRESS: Total precursors accumulated: 44,953
4:31:16.139600 PROGRESS: Target precursors: 26,896 (59.83%)
4:31:16.139655 PROGRESS: Decoy precursors: 18,057 (40.17%)
4:31:16.139708 PROGRESS: 
4:31:16.139754 PROGRESS: Precursor Summary:
4:31:16.141054 PROGRESS: Channel   0:	 0.05 FDR:   343; 0.01 FDR:   221; 0.001 FDR:   167
4:31:16.141154 PROGRESS: 
4:31:16.141210 PROGRESS: Protein Summary:
4:31:16.142521 PROGRESS: Channel   0:	 0.05 FDR:   329; 0.01 FDR:   214; 0.001 FDR:   162
4:31:16.142613 PROGRESS: =========================================================================
4:31:16.208062 INFO: fragments_df: keeping 2117 of 877919 [sum(precursor_idx_mask)=2457 sum(mass_error_mask)=877919 stop_rank=2117
4:31:16.491595 INFO: calibration group: precursor, fitting mz estimator 
4:31:16.594083 INFO: calibration group: precursor, fitting rt estimator 
4:31:16.699920 INFO: calibration group: precursor, fitting mobility estimator 
4:31:16.793639 INFO: calibration group: fragment, fitting mz estimator 
4:31:17.033380 INFO: Using score_cutoff 58.83417004394531 (fac=0.99, q=1)
4:31:17.033847 INFO: calibration group: precursor, predicting mz
4:31:17.048723 INFO: calibration group: precursor, predicting rt
4:31:17.109789 INFO: calibration group: precursor, predicting mobility
4:31:17.127046 INFO: calibration group: fragment, predicting mz
4:31:17.256486 PROGRESS: Required number of precursors found. Starting search parameter optimization.
4:31:17.256863 INFO: Starting optimization step 8.
4:31:17.256949 PROGRESS: === Extracting elution groups 0 to 51000 ===
4:31:17.257040 PROGRESS: Extracting batch of 100415 precursors
4:31:17.304073 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:31:17.304245 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:31:17.304309 INFO: FWHM in RT is 3.39 seconds, sigma is 0.74
4:31:17.304339 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.22
4:31:17.311353 INFO: Starting candidate selection
4:39:56.309960 INFO: Starting candidate scoring
4:40:05.627611 INFO: Finished candidate processing
4:40:05.627868 INFO: Collecting candidate features
4:40:06.050810 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 172535)
4:40:06.060886 INFO: Collecting fragment features
4:40:06.187335 INFO: Finished candidate scoring
4:40:06.373223 PROGRESS: === Extracted 172535 precursors and 1758151 fragments ===
4:40:06.373726 INFO: performing precursor FDR with 47 features
4:40:06.373765 INFO: Decoy channel: -1
4:40:06.373792 INFO: Competetive: True
4:40:06.438333 INFO: Setting torch num_threads to 2 for FDR classification task
4:40:06.468017 WARNING: dropped 1 target PSMs due to missing features
4:40:09.885363 INFO: Test AUC: 0.560
4:40:09.885507 INFO: Train AUC: 0.581
4:40:09.885538 INFO: AUC difference: 3.48%
4:40:10.117333 INFO: Resetting torch num_threads to 100
4:40:10.124824 INFO: === FDR correction performed with classifier version 7 ===
4:40:10.136267 PROGRESS: ============================= Precursor FDR =============================
4:40:10.136568 PROGRESS: Total precursors accumulated: 45,838
4:40:10.136634 PROGRESS: Target precursors: 28,497 (62.17%)
4:40:10.136689 PROGRESS: Decoy precursors: 17,341 (37.83%)
4:40:10.136736 PROGRESS: 
4:40:10.136781 PROGRESS: Precursor Summary:
4:40:10.138422 PROGRESS: Channel   0:	 0.05 FDR:   433; 0.01 FDR:   315; 0.001 FDR:   238
4:40:10.138526 PROGRESS: 
4:40:10.138583 PROGRESS: Protein Summary:
4:40:10.140016 PROGRESS: Channel   0:	 0.05 FDR:   414; 0.01 FDR:   303; 0.001 FDR:   231
4:40:10.140115 PROGRESS: =========================================================================
4:40:10.256422 INFO: fragments_df: keeping 4014 of 1758151 [sum(precursor_idx_mask)=6858 sum(mass_error_mask)=1758151 stop_rank=4014
4:40:10.566691 INFO: calibration group: precursor, fitting mz estimator 
4:40:10.692586 INFO: calibration group: precursor, fitting rt estimator 
4:40:10.800245 INFO: calibration group: precursor, fitting mobility estimator 
4:40:10.909596 INFO: calibration group: fragment, fitting mz estimator 
4:40:11.370737 INFO: Using score_cutoff 49.520490202331544 (fac=0.99, q=1)
4:40:11.371263 INFO: calibration group: precursor, predicting mz
4:40:11.385218 INFO: calibration group: precursor, predicting rt
4:40:11.444844 INFO: calibration group: precursor, predicting mobility
4:40:11.461776 INFO: calibration group: fragment, predicting mz
4:40:11.589103 INFO: === checking if optimization conditions were reached ===
4:40:11.589479 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
4:40:11.592458 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 17.9949.
4:40:11.592524 INFO: ==============================================
4:40:11.592683 INFO: Starting optimization step 9.
4:40:11.592772 PROGRESS: === Extracting elution groups 0 to 51000 ===
4:40:11.592892 PROGRESS: Extracting batch of 100415 precursors
4:40:11.649938 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:40:11.650089 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:40:11.650142 INFO: FWHM in RT is 3.25 seconds, sigma is 0.72
4:40:11.650167 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.06
4:40:11.650991 INFO: Starting candidate selection
4:48:29.417449 INFO: Starting candidate scoring
4:48:36.102176 INFO: Finished candidate processing
4:48:36.102365 INFO: Collecting candidate features
4:48:36.485985 WARNING: intensity_correlation has 6 NaNs ( 0.00 % out of 172506)
4:48:36.499064 INFO: Collecting fragment features
4:48:36.634799 INFO: Finished candidate scoring
4:48:36.739223 PROGRESS: === Extracted 172506 precursors and 1713469 fragments ===
4:48:36.739725 INFO: performing precursor FDR with 47 features
4:48:36.739766 INFO: Decoy channel: -1
4:48:36.739806 INFO: Competetive: True
4:48:36.793961 INFO: Setting torch num_threads to 2 for FDR classification task
4:48:36.827388 WARNING: dropped 1 target PSMs due to missing features
4:48:36.827528 WARNING: dropped 5 decoy PSMs due to missing features
4:48:39.951933 INFO: Test AUC: 0.562
4:48:39.952106 INFO: Train AUC: 0.581
4:48:39.952142 INFO: AUC difference: 3.17%
4:48:40.206239 INFO: Resetting torch num_threads to 100
4:48:40.221226 INFO: === FDR correction performed with classifier version 7 ===
4:48:40.244333 PROGRESS: ============================= Precursor FDR =============================
4:48:40.244695 PROGRESS: Total precursors accumulated: 45,771
4:48:40.244781 PROGRESS: Target precursors: 28,314 (61.86%)
4:48:40.244840 PROGRESS: Decoy precursors: 17,457 (38.14%)
4:48:40.244887 PROGRESS: 
4:48:40.244930 PROGRESS: Precursor Summary:
4:48:40.247563 PROGRESS: Channel   0:	 0.05 FDR:   547; 0.01 FDR:   363; 0.001 FDR:   273
4:48:40.247780 PROGRESS: 
4:48:40.247843 PROGRESS: Protein Summary:
4:48:40.250479 PROGRESS: Channel   0:	 0.05 FDR:   517; 0.01 FDR:   346; 0.001 FDR:   261
4:48:40.250652 PROGRESS: =========================================================================
4:48:40.376593 INFO: fragments_df: keeping 4341 of 1713469 [sum(precursor_idx_mask)=7864 sum(mass_error_mask)=1713469 stop_rank=4341
4:48:40.819284 INFO: calibration group: precursor, fitting mz estimator 
4:48:40.977861 INFO: calibration group: precursor, fitting rt estimator 
4:48:41.145981 INFO: calibration group: precursor, fitting mobility estimator 
4:48:41.308463 INFO: calibration group: fragment, fitting mz estimator 
4:48:41.932159 INFO: Using score_cutoff 50.53171396179199 (fac=0.99, q=1)
4:48:41.932863 INFO: calibration group: precursor, predicting mz
4:48:41.948987 INFO: calibration group: precursor, predicting rt
4:48:42.038628 INFO: calibration group: precursor, predicting mobility
4:48:42.058768 INFO: calibration group: fragment, predicting mz
4:48:42.211318 INFO: === checking if optimization conditions were reached ===
4:48:42.211717 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
4:48:42.214962 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 8.8746.
4:48:42.215092 INFO: ==============================================
4:48:42.215290 INFO: Starting optimization step 10.
4:48:42.215374 PROGRESS: === Extracting elution groups 0 to 51000 ===
4:48:42.215471 PROGRESS: Extracting batch of 100415 precursors
4:48:42.263677 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:48:42.263848 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:48:42.263936 INFO: FWHM in RT is 3.06 seconds, sigma is 0.67
4:48:42.263969 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
4:48:42.267568 INFO: Starting candidate selection
4:56:39.140486 INFO: Starting candidate scoring
4:56:43.810052 INFO: Finished candidate processing
4:56:43.810184 INFO: Collecting candidate features
4:56:44.112139 WARNING: intensity_correlation has 31 NaNs ( 0.02 % out of 172406)
4:56:44.112562 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 172406)
4:56:44.121960 INFO: Collecting fragment features
4:56:44.233991 INFO: Finished candidate scoring
4:56:44.340278 PROGRESS: === Extracted 172406 precursors and 1614937 fragments ===
4:56:44.340852 INFO: performing precursor FDR with 47 features
4:56:44.340894 INFO: Decoy channel: -1
4:56:44.340920 INFO: Competetive: True
4:56:44.412750 INFO: Setting torch num_threads to 2 for FDR classification task
4:56:44.455893 WARNING: dropped 14 target PSMs due to missing features
4:56:44.456060 WARNING: dropped 18 decoy PSMs due to missing features
4:56:48.198730 INFO: Test AUC: 0.559
4:56:48.198877 INFO: Train AUC: 0.578
4:56:48.198908 INFO: AUC difference: 3.20%
4:56:48.433120 INFO: Resetting torch num_threads to 100
4:56:48.440879 INFO: === FDR correction performed with classifier version 7 ===
4:56:48.451600 PROGRESS: ============================= Precursor FDR =============================
4:56:48.451885 PROGRESS: Total precursors accumulated: 45,740
4:56:48.451958 PROGRESS: Target precursors: 28,152 (61.55%)
4:56:48.452014 PROGRESS: Decoy precursors: 17,588 (38.45%)
4:56:48.452062 PROGRESS: 
4:56:48.452108 PROGRESS: Precursor Summary:
4:56:48.453559 PROGRESS: Channel   0:	 0.05 FDR:   623; 0.01 FDR:   432; 0.001 FDR:   342
4:56:48.453654 PROGRESS: 
4:56:48.453713 PROGRESS: Protein Summary:
4:56:48.455224 PROGRESS: Channel   0:	 0.05 FDR:   582; 0.01 FDR:   403; 0.001 FDR:   323
4:56:48.455321 PROGRESS: =========================================================================
4:56:48.564853 INFO: fragments_df: keeping 4821 of 1614937 [sum(precursor_idx_mask)=9058 sum(mass_error_mask)=1614937 stop_rank=4821
4:56:49.021089 INFO: calibration group: precursor, fitting mz estimator 
4:56:49.134266 INFO: calibration group: precursor, fitting rt estimator 
4:56:49.242053 INFO: calibration group: precursor, fitting mobility estimator 
4:56:49.351029 INFO: calibration group: fragment, fitting mz estimator 
4:56:49.937791 INFO: Using score_cutoff 44.483840616989134 (fac=0.99, q=1)
4:56:49.938304 INFO: calibration group: precursor, predicting mz
4:56:49.945791 INFO: calibration group: precursor, predicting rt
4:56:49.975580 INFO: calibration group: precursor, predicting mobility
4:56:49.982607 INFO: calibration group: fragment, predicting mz
4:56:50.037310 INFO: === checking if optimization conditions were reached ===
4:56:50.037691 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
4:56:50.040953 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 5.2239.
4:56:50.041025 INFO: ==============================================
4:56:50.041143 INFO: Starting optimization step 11.
4:56:50.041221 PROGRESS: === Extracting elution groups 0 to 25400 ===
4:56:50.041306 PROGRESS: Extracting batch of 49998 precursors
4:56:50.066544 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:56:50.066714 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:56:50.066783 INFO: FWHM in RT is 2.66 seconds, sigma is 0.58
4:56:50.066813 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.61
4:56:50.075842 INFO: Starting candidate selection
5:00:42.350194 INFO: Starting candidate scoring
5:00:44.390427 INFO: Finished candidate processing
5:00:44.390619 INFO: Collecting candidate features
5:00:44.557532 WARNING: intensity_correlation has 23 NaNs ( 0.03 % out of 85292)
5:00:44.564403 INFO: Collecting fragment features
5:00:44.617342 INFO: Finished candidate scoring
5:00:44.662020 PROGRESS: === Extracted 85292 precursors and 748055 fragments ===
5:00:44.662550 INFO: performing precursor FDR with 47 features
5:00:44.662596 INFO: Decoy channel: -1
5:00:44.662631 INFO: Competetive: True
5:00:44.698717 INFO: Setting torch num_threads to 2 for FDR classification task
5:00:44.718837 WARNING: dropped 12 target PSMs due to missing features
5:00:44.718997 WARNING: dropped 11 decoy PSMs due to missing features
5:00:46.674333 INFO: Test AUC: 0.554
5:00:46.674496 INFO: Train AUC: 0.574
5:00:46.674528 INFO: AUC difference: 3.59%
5:00:46.893709 INFO: Resetting torch num_threads to 100
5:00:46.897754 INFO: === FDR correction performed with classifier version 7 ===
5:00:46.903395 PROGRESS: ============================= Precursor FDR =============================
5:00:46.903719 PROGRESS: Total precursors accumulated: 22,718
5:00:46.903786 PROGRESS: Target precursors: 13,720 (60.39%)
5:00:46.903837 PROGRESS: Decoy precursors: 8,998 (39.61%)
5:00:46.903887 PROGRESS: 
5:00:46.903937 PROGRESS: Precursor Summary:
5:00:46.905126 PROGRESS: Channel   0:	 0.05 FDR:   177; 0.01 FDR:    13; 0.001 FDR:    13
5:00:46.905223 PROGRESS: 
5:00:46.905280 PROGRESS: Protein Summary:
5:00:46.906387 PROGRESS: Channel   0:	 0.05 FDR:   176; 0.01 FDR:    13; 0.001 FDR:    13
5:00:46.906476 PROGRESS: =========================================================================
5:00:47.134652 INFO: calibration group: precursor, predicting mz
5:00:47.142778 INFO: calibration group: precursor, predicting rt
5:00:47.172980 INFO: calibration group: precursor, predicting mobility
5:00:47.179808 INFO: calibration group: fragment, predicting mz
5:00:47.238572 INFO: === skipping optimization until target number of precursors are found ===
5:00:47.238878 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
5:00:47.238949 INFO: Starting optimization step 12.
5:00:47.239034 PROGRESS: === Extracting elution groups 25400 to 51000 ===
5:00:47.239112 PROGRESS: Extracting batch of 50417 precursors
5:00:47.255784 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:00:47.255918 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:00:47.255984 INFO: FWHM in RT is 2.66 seconds, sigma is 0.58
5:00:47.256008 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.61
5:00:47.259925 INFO: Starting candidate selection
5:04:50.766469 INFO: Starting candidate scoring
5:04:52.818849 INFO: Finished candidate processing
5:04:52.819051 INFO: Collecting candidate features
5:04:53.007556 WARNING: intensity_correlation has 32 NaNs ( 0.04 % out of 85951)
5:04:53.008579 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 85951)
5:04:53.022271 INFO: Collecting fragment features
5:04:53.080527 INFO: Finished candidate scoring
5:04:53.228767 PROGRESS: === Extracted 171243 precursors and 1501947 fragments ===
5:04:53.251594 INFO: performing precursor FDR with 47 features
5:04:53.251739 INFO: Decoy channel: -1
5:04:53.251766 INFO: Competetive: True
5:04:53.333153 INFO: Setting torch num_threads to 2 for FDR classification task
5:04:53.370812 WARNING: dropped 29 target PSMs due to missing features
5:04:53.370956 WARNING: dropped 28 decoy PSMs due to missing features
5:04:56.516752 INFO: Test AUC: 0.558
5:04:56.516883 INFO: Train AUC: 0.576
5:04:56.516915 INFO: AUC difference: 3.02%
5:04:56.743479 INFO: Resetting torch num_threads to 100
5:04:56.751555 INFO: === FDR correction performed with classifier version 7 ===
5:04:56.760762 PROGRESS: ============================= Precursor FDR =============================
5:04:56.761022 PROGRESS: Total precursors accumulated: 45,611
5:04:56.761088 PROGRESS: Target precursors: 27,599 (60.51%)
5:04:56.761139 PROGRESS: Decoy precursors: 18,012 (39.49%)
5:04:56.761187 PROGRESS: 
5:04:56.761231 PROGRESS: Precursor Summary:
5:04:56.762568 PROGRESS: Channel   0:	 0.05 FDR:   526; 0.01 FDR:   328; 0.001 FDR:   201
5:04:56.762670 PROGRESS: 
5:04:56.762727 PROGRESS: Protein Summary:
5:04:56.764127 PROGRESS: Channel   0:	 0.05 FDR:   492; 0.01 FDR:   312; 0.001 FDR:   191
5:04:56.764224 PROGRESS: =========================================================================
5:04:56.877241 INFO: fragments_df: keeping 3660 of 1501947 [sum(precursor_idx_mask)=6692 sum(mass_error_mask)=1501947 stop_rank=3660
5:04:57.118490 INFO: calibration group: precursor, fitting mz estimator 
5:04:57.222711 INFO: calibration group: precursor, fitting rt estimator 
5:04:57.327829 INFO: calibration group: precursor, fitting mobility estimator 
5:04:57.429637 INFO: calibration group: fragment, fitting mz estimator 
5:04:57.848729 INFO: Using score_cutoff 44.618767317581174 (fac=0.99, q=1)
5:04:57.849740 INFO: calibration group: precursor, predicting mz
5:04:57.866944 INFO: calibration group: precursor, predicting rt
5:04:57.938970 INFO: calibration group: precursor, predicting mobility
5:04:57.975846 INFO: calibration group: fragment, predicting mz
5:04:58.117360 INFO: === checking if optimization conditions were reached ===
5:04:58.117729 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
5:04:58.121197 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 4.5862.
5:04:58.121266 INFO: ==============================================
5:04:58.121380 INFO: Starting optimization step 13.
5:04:58.121462 PROGRESS: === Extracting elution groups 0 to 51000 ===
5:04:58.121545 PROGRESS: Extracting batch of 100415 precursors
5:04:58.166800 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:04:58.166968 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:04:58.167050 INFO: FWHM in RT is 2.57 seconds, sigma is 0.56
5:04:58.167082 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.00
5:04:58.174662 INFO: Starting candidate selection
5:12:39.341983 INFO: Starting candidate scoring
5:12:42.938650 INFO: Finished candidate processing
5:12:42.939558 INFO: Collecting candidate features
5:12:43.231183 WARNING: intensity_correlation has 98 NaNs ( 0.06 % out of 170581)
5:12:43.231727 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 170581)
5:12:43.244349 INFO: Collecting fragment features
5:12:43.342528 INFO: Finished candidate scoring
5:12:43.446986 PROGRESS: === Extracted 170581 precursors and 1419775 fragments ===
5:12:43.447493 INFO: performing precursor FDR with 47 features
5:12:43.447534 INFO: Decoy channel: -1
5:12:43.447559 INFO: Competetive: True
5:12:43.506886 INFO: Setting torch num_threads to 2 for FDR classification task
5:12:43.541909 WARNING: dropped 57 target PSMs due to missing features
5:12:43.542061 WARNING: dropped 43 decoy PSMs due to missing features
5:12:46.906585 INFO: Test AUC: 0.558
5:12:46.906716 INFO: Train AUC: 0.580
5:12:46.906747 INFO: AUC difference: 3.89%
5:12:47.137453 INFO: Resetting torch num_threads to 100
5:12:47.142917 INFO: === FDR correction performed with classifier version 7 ===
5:12:47.151687 PROGRESS: ============================= Precursor FDR =============================
5:12:47.152000 PROGRESS: Total precursors accumulated: 45,536
5:12:47.152069 PROGRESS: Target precursors: 27,921 (61.32%)
5:12:47.152118 PROGRESS: Decoy precursors: 17,615 (38.68%)
5:12:47.152164 PROGRESS: 
5:12:47.152206 PROGRESS: Precursor Summary:
5:12:47.153578 PROGRESS: Channel   0:	 0.05 FDR:   561; 0.01 FDR:   341; 0.001 FDR:   217
5:12:47.153672 PROGRESS: 
5:12:47.153726 PROGRESS: Protein Summary:
5:12:47.155157 PROGRESS: Channel   0:	 0.05 FDR:   531; 0.01 FDR:   324; 0.001 FDR:   205
5:12:47.155251 PROGRESS: =========================================================================
5:12:47.252760 INFO: fragments_df: keeping 3467 of 1419775 [sum(precursor_idx_mask)=6606 sum(mass_error_mask)=1419775 stop_rank=3467
5:12:47.453258 INFO: calibration group: precursor, fitting mz estimator 
5:12:47.579431 INFO: calibration group: precursor, fitting rt estimator 
5:12:47.698696 INFO: calibration group: precursor, fitting mobility estimator 
5:12:47.822547 INFO: calibration group: fragment, fitting mz estimator 
5:12:48.282922 INFO: Using score_cutoff 37.90310078430176 (fac=0.99, q=1)
5:12:48.283361 INFO: calibration group: precursor, predicting mz
5:12:48.296877 INFO: calibration group: precursor, predicting rt
5:12:48.357057 INFO: calibration group: precursor, predicting mobility
5:12:48.371284 INFO: calibration group: fragment, predicting mz
5:12:48.492913 INFO: === checking if optimization conditions were reached ===
5:12:48.493253 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
5:12:48.495695 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 4.0951.
5:12:48.495758 INFO: ==============================================
5:12:48.495871 INFO: Starting optimization step 14.
5:12:48.495967 PROGRESS: === Extracting elution groups 0 to 51000 ===
5:12:48.496058 PROGRESS: Extracting batch of 100415 precursors
5:12:48.523436 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:12:48.523587 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:12:48.523648 INFO: FWHM in RT is 2.39 seconds, sigma is 0.53
5:12:48.523694 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.64
5:12:48.524739 INFO: Starting candidate selection
5:20:37.004897 INFO: Starting candidate scoring
5:20:40.544251 INFO: Finished candidate processing
5:20:40.544370 INFO: Collecting candidate features
5:20:40.845336 WARNING: intensity_correlation has 78 NaNs ( 0.05 % out of 170867)
5:20:40.845774 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 170867)
5:20:40.855164 INFO: Collecting fragment features
5:20:40.957994 INFO: Finished candidate scoring
5:20:41.051131 PROGRESS: === Extracted 170867 precursors and 1410724 fragments ===
5:20:41.051668 INFO: performing precursor FDR with 47 features
5:20:41.051709 INFO: Decoy channel: -1
5:20:41.051734 INFO: Competetive: True
5:20:41.118738 INFO: Setting torch num_threads to 2 for FDR classification task
5:20:41.158520 WARNING: dropped 43 target PSMs due to missing features
5:20:41.158654 WARNING: dropped 38 decoy PSMs due to missing features
5:20:44.759980 INFO: Test AUC: 0.558
5:20:44.760136 INFO: Train AUC: 0.576
5:20:44.760170 INFO: AUC difference: 3.09%
5:20:45.011535 INFO: Resetting torch num_threads to 100
5:20:45.019803 INFO: === FDR correction performed with classifier version 7 ===
5:20:45.031757 PROGRESS: ============================= Precursor FDR =============================
5:20:45.032103 PROGRESS: Total precursors accumulated: 45,575
5:20:45.032170 PROGRESS: Target precursors: 27,863 (61.14%)
5:20:45.032221 PROGRESS: Decoy precursors: 17,712 (38.86%)
5:20:45.032270 PROGRESS: 
5:20:45.032315 PROGRESS: Precursor Summary:
5:20:45.033828 PROGRESS: Channel   0:	 0.05 FDR:   542; 0.01 FDR:   391; 0.001 FDR:   193
5:20:45.033924 PROGRESS: 
5:20:45.033979 PROGRESS: Protein Summary:
5:20:45.035717 PROGRESS: Channel   0:	 0.05 FDR:   509; 0.01 FDR:   371; 0.001 FDR:   183
5:20:45.035815 PROGRESS: =========================================================================
5:20:45.137927 INFO: fragments_df: keeping 3982 of 1410724 [sum(precursor_idx_mask)=7612 sum(mass_error_mask)=1410724 stop_rank=3982
5:20:45.444054 INFO: calibration group: precursor, fitting mz estimator 
5:20:45.590066 INFO: calibration group: precursor, fitting rt estimator 
5:20:45.715061 INFO: calibration group: precursor, fitting mobility estimator 
5:20:45.825095 INFO: calibration group: fragment, fitting mz estimator 
5:20:46.292360 INFO: Using score_cutoff 38.86557577514649 (fac=0.99, q=1)
5:20:46.292799 INFO: calibration group: precursor, predicting mz
5:20:46.305774 INFO: calibration group: precursor, predicting rt
5:20:46.365694 INFO: calibration group: precursor, predicting mobility
5:20:46.381379 INFO: calibration group: fragment, predicting mz
5:20:46.501486 INFO: === checking if optimization conditions were reached ===
5:20:46.501792 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
5:20:46.504258 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 4.2363.
5:20:46.504317 INFO: ==============================================
5:20:46.504415 INFO: Starting optimization step 15.
5:20:46.504483 PROGRESS: === Extracting elution groups 0 to 51000 ===
5:20:46.504555 PROGRESS: Extracting batch of 100415 precursors
5:20:46.530900 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:20:46.531055 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:20:46.531110 INFO: FWHM in RT is 2.38 seconds, sigma is 0.52
5:20:46.531137 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.53
5:20:46.540849 INFO: Starting candidate selection
5:28:35.738941 INFO: Starting candidate scoring
5:28:39.404653 INFO: Finished candidate processing
5:28:39.404817 INFO: Collecting candidate features
5:28:39.931365 WARNING: intensity_correlation has 84 NaNs ( 0.05 % out of 170808)
5:28:39.932048 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 170808)
5:28:39.946480 INFO: Collecting fragment features
5:28:40.201594 INFO: Finished candidate scoring
5:28:40.728048 PROGRESS: === Extracted 170808 precursors and 1408303 fragments ===
5:28:40.728599 INFO: performing precursor FDR with 47 features
5:28:40.728639 INFO: Decoy channel: -1
5:28:40.728664 INFO: Competetive: True
5:28:40.863550 INFO: Setting torch num_threads to 2 for FDR classification task
5:28:40.972133 WARNING: dropped 46 target PSMs due to missing features
5:28:40.972608 WARNING: dropped 41 decoy PSMs due to missing features
5:28:44.592796 INFO: Test AUC: 0.560
5:28:44.592921 INFO: Train AUC: 0.573
5:28:44.592952 INFO: AUC difference: 2.18%
5:28:44.823209 INFO: Resetting torch num_threads to 100
5:28:44.829096 INFO: === FDR correction performed with classifier version 7 ===
5:28:44.837690 PROGRESS: ============================= Precursor FDR =============================
5:28:44.837936 PROGRESS: Total precursors accumulated: 45,580
5:28:44.837998 PROGRESS: Target precursors: 27,626 (60.61%)
5:28:44.838048 PROGRESS: Decoy precursors: 17,954 (39.39%)
5:28:44.838096 PROGRESS: 
5:28:44.838139 PROGRESS: Precursor Summary:
5:28:44.839481 PROGRESS: Channel   0:	 0.05 FDR:   492; 0.01 FDR:   183; 0.001 FDR:   148
5:28:44.839578 PROGRESS: 
5:28:44.839635 PROGRESS: Protein Summary:
5:28:44.840968 PROGRESS: Channel   0:	 0.05 FDR:   463; 0.01 FDR:   176; 0.001 FDR:   142
5:28:44.841058 PROGRESS: =========================================================================
5:28:45.077182 INFO: calibration group: precursor, predicting mz
5:28:45.091293 INFO: calibration group: precursor, predicting rt
5:28:45.152398 INFO: calibration group: precursor, predicting mobility
5:28:45.166595 INFO: calibration group: fragment, predicting mz
5:28:45.289451 INFO: === skipping optimization until target number of precursors are found ===
5:28:45.289766 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
5:28:45.289835 INFO: Starting optimization step 16.
5:28:45.289903 PROGRESS: === Extracting elution groups 51000 to 102200 ===
5:28:45.289976 PROGRESS: Extracting batch of 100803 precursors
5:28:45.317409 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:28:45.317538 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:28:45.317590 INFO: FWHM in RT is 2.38 seconds, sigma is 0.52
5:28:45.317614 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.53
5:28:45.318807 INFO: Starting candidate selection
5:36:44.974550 INFO: Starting candidate scoring
5:36:48.601684 INFO: Finished candidate processing
5:36:48.601870 INFO: Collecting candidate features
5:36:48.931731 WARNING: intensity_correlation has 62 NaNs ( 0.04 % out of 171649)
5:36:48.932306 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 171649)
5:36:48.946851 INFO: Collecting fragment features
5:36:49.049021 INFO: Finished candidate scoring
5:36:49.411040 PROGRESS: === Extracted 342457 precursors and 2827168 fragments ===
5:36:49.456178 INFO: performing precursor FDR with 47 features
5:36:49.456335 INFO: Decoy channel: -1
5:36:49.456363 INFO: Competetive: True
5:36:49.655690 INFO: Setting torch num_threads to 2 for FDR classification task
5:36:49.737304 WARNING: dropped 71 target PSMs due to missing features
5:36:49.737466 WARNING: dropped 80 decoy PSMs due to missing features
5:36:57.238511 INFO: Test AUC: 0.558
5:36:57.239363 INFO: Train AUC: 0.577
5:36:57.239405 INFO: AUC difference: 3.21%
5:36:57.533909 INFO: Resetting torch num_threads to 100
5:36:57.554859 INFO: === FDR correction performed with classifier version 7 ===
5:36:57.576402 PROGRESS: ============================= Precursor FDR =============================
5:36:57.576741 PROGRESS: Total precursors accumulated: 91,395
5:36:57.576805 PROGRESS: Target precursors: 55,391 (60.61%)
5:36:57.576855 PROGRESS: Decoy precursors: 36,004 (39.39%)
5:36:57.576903 PROGRESS: 
5:36:57.576945 PROGRESS: Precursor Summary:
5:36:57.578879 PROGRESS: Channel   0:	 0.05 FDR: 1,049; 0.01 FDR:   748; 0.001 FDR:   452
5:36:57.578976 PROGRESS: 
5:36:57.579042 PROGRESS: Protein Summary:
5:36:57.580893 PROGRESS: Channel   0:	 0.05 FDR:   927; 0.01 FDR:   674; 0.001 FDR:   416
5:36:57.581000 PROGRESS: =========================================================================
5:36:57.800311 INFO: fragments_df: keeping 5000 of 2827168 [sum(precursor_idx_mask)=14722 sum(mass_error_mask)=2827168 stop_rank=5000
5:36:58.367543 INFO: calibration group: precursor, fitting mz estimator 
5:36:58.510912 INFO: calibration group: precursor, fitting rt estimator 
5:36:58.646273 INFO: calibration group: precursor, fitting mobility estimator 
5:36:58.776618 INFO: calibration group: fragment, fitting mz estimator 
5:36:59.413054 INFO: Using score_cutoff 41.30337562179565 (fac=0.99, q=1)
5:36:59.413747 INFO: calibration group: precursor, predicting mz
5:36:59.429096 INFO: calibration group: precursor, predicting rt
5:36:59.511337 INFO: calibration group: precursor, predicting mobility
5:36:59.530724 INFO: calibration group: fragment, predicting mz
5:36:59.697500 INFO: === checking if optimization conditions were reached ===
5:36:59.697976 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
5:36:59.699692 PROGRESS: ✅ ms2_error      : optimization complete. Optimal parameter 8.8746 found after 7 searches.
5:36:59.699758 INFO: ==============================================
5:36:59.699907 PROGRESS: Optimization finished for ms2_error.
5:36:59.860683 INFO: calibration group: precursor, predicting mz
5:36:59.868420 INFO: calibration group: precursor, predicting rt
5:36:59.898126 INFO: calibration group: precursor, predicting mobility
5:36:59.904696 INFO: calibration group: fragment, predicting mz
5:37:00.002314 INFO: Starting optimization step 0.
5:37:00.002733 PROGRESS: === Extracting elution groups 0 to 25400 ===
5:37:00.002909 PROGRESS: Extracting batch of 49998 precursors
5:37:00.033354 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:37:00.033561 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:37:00.033629 INFO: FWHM in RT is 2.66 seconds, sigma is 0.58
5:37:00.033653 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.61
5:37:00.039945 INFO: Starting candidate selection
5:40:52.369022 INFO: Starting candidate scoring
5:40:54.756358 INFO: Finished candidate processing
5:40:54.756526 INFO: Collecting candidate features
5:40:54.915994 WARNING: intensity_correlation has 14 NaNs ( 0.02 % out of 85767)
5:40:54.927475 INFO: Collecting fragment features
5:40:54.986406 INFO: Finished candidate scoring
5:40:55.073796 PROGRESS: === Extracted 85767 precursors and 798642 fragments ===
5:40:55.074275 INFO: performing precursor FDR with 47 features
5:40:55.074316 INFO: Decoy channel: -1
5:40:55.074340 INFO: Competetive: True
5:40:55.103598 INFO: Setting torch num_threads to 2 for FDR classification task
5:40:55.120069 WARNING: dropped 4 target PSMs due to missing features
5:40:55.120208 WARNING: dropped 10 decoy PSMs due to missing features
5:40:56.491122 INFO: Test AUC: 0.568
5:40:56.491254 INFO: Train AUC: 0.592
5:40:56.491285 INFO: AUC difference: 3.94%
5:40:56.700148 INFO: Resetting torch num_threads to 100
5:40:56.702886 INFO: === FDR correction performed with classifier version 10 ===
5:40:56.706625 PROGRESS: ============================= Precursor FDR =============================
5:40:56.706766 PROGRESS: Total precursors accumulated: 22,789
5:40:56.706828 PROGRESS: Target precursors: 14,300 (62.75%)
5:40:56.706880 PROGRESS: Decoy precursors: 8,489 (37.25%)
5:40:56.706926 PROGRESS: 
5:40:56.706988 PROGRESS: Precursor Summary:
5:40:56.708098 PROGRESS: Channel   0:	 0.05 FDR:   303; 0.01 FDR:   202; 0.001 FDR:   167
5:40:56.708191 PROGRESS: 
5:40:56.708248 PROGRESS: Protein Summary:
5:40:56.709406 PROGRESS: Channel   0:	 0.05 FDR:   293; 0.01 FDR:   195; 0.001 FDR:   165
5:40:56.709501 PROGRESS: =========================================================================
5:40:56.925497 INFO: fragments_df: keeping 2295 of 798642 [sum(precursor_idx_mask)=4213 sum(mass_error_mask)=798642 stop_rank=2295
5:40:57.056308 INFO: calibration group: precursor, fitting mz estimator 
5:40:57.172829 INFO: calibration group: precursor, fitting rt estimator 
5:40:57.291779 INFO: calibration group: precursor, fitting mobility estimator 
5:40:57.407865 INFO: calibration group: fragment, fitting mz estimator 
5:40:57.705850 INFO: Using score_cutoff 42.5903722984314 (fac=0.99, q=1)
5:40:57.706281 INFO: calibration group: precursor, predicting mz
5:40:57.713753 INFO: calibration group: precursor, predicting rt
5:40:57.744174 INFO: calibration group: precursor, predicting mobility
5:40:57.752869 INFO: calibration group: fragment, predicting mz
5:40:57.811218 INFO: === checking if optimization conditions were reached ===
5:40:57.811493 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
5:40:57.813560 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 733.4560.
5:40:57.813615 INFO: ==============================================
5:40:57.813716 INFO: Starting optimization step 1.
5:40:57.813786 PROGRESS: === Extracting elution groups 0 to 25400 ===
5:40:57.813856 PROGRESS: Extracting batch of 49998 precursors
5:40:57.826982 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:40:57.827112 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:40:57.827181 INFO: FWHM in RT is 2.65 seconds, sigma is 0.58
5:40:57.827205 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.56
5:40:57.836241 INFO: Starting candidate selection
5:42:23.733235 INFO: Starting candidate scoring
5:42:26.090886 INFO: Finished candidate processing
5:42:26.091027 INFO: Collecting candidate features
5:42:26.238563 WARNING: intensity_correlation has 39 NaNs ( 0.05 % out of 84234)
5:42:26.238930 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 84234)
5:42:26.247095 INFO: Collecting fragment features
5:42:26.308813 INFO: Finished candidate scoring
5:42:26.365859 PROGRESS: === Extracted 84234 precursors and 773539 fragments ===
5:42:26.366334 INFO: performing precursor FDR with 47 features
5:42:26.366374 INFO: Decoy channel: -1
5:42:26.366397 INFO: Competetive: True
5:42:26.403955 INFO: Setting torch num_threads to 2 for FDR classification task
5:42:26.421187 WARNING: dropped 21 target PSMs due to missing features
5:42:26.421319 WARNING: dropped 19 decoy PSMs due to missing features
5:42:27.805598 INFO: Test AUC: 0.558
5:42:27.805729 INFO: Train AUC: 0.586
5:42:27.805759 INFO: AUC difference: 4.77%
5:42:28.012913 INFO: Resetting torch num_threads to 100
5:42:28.015699 INFO: === FDR correction performed with classifier version 10 ===
5:42:28.019490 PROGRESS: ============================= Precursor FDR =============================
5:42:28.019626 PROGRESS: Total precursors accumulated: 22,543
5:42:28.019688 PROGRESS: Target precursors: 13,965 (61.95%)
5:42:28.019744 PROGRESS: Decoy precursors: 8,578 (38.05%)
5:42:28.019789 PROGRESS: 
5:42:28.019834 PROGRESS: Precursor Summary:
5:42:28.020958 PROGRESS: Channel   0:	 0.05 FDR:   292; 0.01 FDR:   221; 0.001 FDR:   166
5:42:28.021050 PROGRESS: 
5:42:28.021111 PROGRESS: Protein Summary:
5:42:28.022321 PROGRESS: Channel   0:	 0.05 FDR:   282; 0.01 FDR:   214; 0.001 FDR:   162
5:42:28.022415 PROGRESS: =========================================================================
5:42:28.075403 INFO: fragments_df: keeping 2533 of 773539 [sum(precursor_idx_mask)=4592 sum(mass_error_mask)=773539 stop_rank=2533
5:42:28.204503 INFO: calibration group: precursor, fitting mz estimator 
5:42:28.321270 INFO: calibration group: precursor, fitting rt estimator 
5:42:28.434589 INFO: calibration group: precursor, fitting mobility estimator 
5:42:28.529733 INFO: calibration group: fragment, fitting mz estimator 
5:42:28.806880 INFO: Using score_cutoff 43.97794402313232 (fac=0.99, q=1)
5:42:28.807300 INFO: calibration group: precursor, predicting mz
5:42:28.814449 INFO: calibration group: precursor, predicting rt
5:42:28.844273 INFO: calibration group: precursor, predicting mobility
5:42:28.851199 INFO: calibration group: fragment, predicting mz
5:42:28.905971 INFO: === checking if optimization conditions were reached ===
5:42:28.906275 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
5:42:28.908581 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 410.7846.
5:42:28.908673 INFO: ==============================================
5:42:28.908807 INFO: Starting optimization step 2.
5:42:28.908886 PROGRESS: === Extracting elution groups 0 to 25400 ===
5:42:28.908968 PROGRESS: Extracting batch of 49998 precursors
5:42:28.928107 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:42:28.928240 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:42:28.928305 INFO: FWHM in RT is 2.62 seconds, sigma is 0.58
5:42:28.928336 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.50
5:42:28.937411 INFO: Starting candidate selection
5:43:16.867442 INFO: Starting candidate scoring
5:43:19.165938 INFO: Finished candidate processing
5:43:19.166093 INFO: Collecting candidate features
5:43:19.332337 WARNING: intensity_correlation has 55 NaNs ( 0.07 % out of 82043)
5:43:19.332680 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 82043)
5:43:19.340643 INFO: Collecting fragment features
5:43:19.406587 INFO: Finished candidate scoring
5:43:19.450419 PROGRESS: === Extracted 82043 precursors and 747414 fragments ===
5:43:19.450886 INFO: performing precursor FDR with 47 features
5:43:19.450925 INFO: Decoy channel: -1
5:43:19.450948 INFO: Competetive: True
5:43:19.481700 INFO: Setting torch num_threads to 2 for FDR classification task
5:43:19.497009 WARNING: dropped 31 target PSMs due to missing features
5:43:19.497141 WARNING: dropped 25 decoy PSMs due to missing features
5:43:20.865193 INFO: Test AUC: 0.554
5:43:20.865326 INFO: Train AUC: 0.580
5:43:20.865357 INFO: AUC difference: 4.54%
5:43:21.068652 INFO: Resetting torch num_threads to 100
5:43:21.071314 INFO: === FDR correction performed with classifier version 10 ===
5:43:21.074904 PROGRESS: ============================= Precursor FDR =============================
5:43:21.075041 PROGRESS: Total precursors accumulated: 22,131
5:43:21.075112 PROGRESS: Target precursors: 13,321 (60.19%)
5:43:21.075164 PROGRESS: Decoy precursors: 8,810 (39.81%)
5:43:21.075212 PROGRESS: 
5:43:21.075268 PROGRESS: Precursor Summary:
5:43:21.076304 PROGRESS: Channel   0:	 0.05 FDR:   290; 0.01 FDR:   208; 0.001 FDR:     0
5:43:21.076406 PROGRESS: 
5:43:21.076467 PROGRESS: Protein Summary:
5:43:21.077604 PROGRESS: Channel   0:	 0.05 FDR:   278; 0.01 FDR:   200; 0.001 FDR:     0
5:43:21.077697 PROGRESS: =========================================================================
5:43:21.128550 INFO: fragments_df: keeping 2433 of 747414 [sum(precursor_idx_mask)=4350 sum(mass_error_mask)=747413 stop_rank=2433
5:43:21.256080 INFO: calibration group: precursor, fitting mz estimator 
5:43:21.351047 INFO: calibration group: precursor, fitting rt estimator 
5:43:21.448003 INFO: calibration group: precursor, fitting mobility estimator 
5:43:21.541559 INFO: calibration group: fragment, fitting mz estimator 
5:43:21.838266 INFO: Using score_cutoff 44.4256957157135 (fac=0.99, q=1)
5:43:21.838678 INFO: calibration group: precursor, predicting mz
5:43:21.846060 INFO: calibration group: precursor, predicting rt
5:43:21.876009 INFO: calibration group: precursor, predicting mobility
5:43:21.883115 INFO: calibration group: fragment, predicting mz
5:43:21.938721 INFO: === checking if optimization conditions were reached ===
5:43:21.938988 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
5:43:21.940929 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 182.0868.
5:43:21.940981 INFO: ==============================================
5:43:21.941079 INFO: Starting optimization step 3.
5:43:21.941144 PROGRESS: === Extracting elution groups 0 to 25400 ===
5:43:21.941228 PROGRESS: Extracting batch of 49998 precursors
5:43:21.953800 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:43:21.953913 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:43:21.953963 INFO: FWHM in RT is 2.65 seconds, sigma is 0.58
5:43:21.953985 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.51
5:43:21.962905 INFO: Starting candidate selection
5:43:43.003634 INFO: Starting candidate scoring
5:43:45.319169 INFO: Finished candidate processing
5:43:45.320442 INFO: Collecting candidate features
5:43:45.448413 WARNING: intensity_correlation has 86 NaNs ( 0.11 % out of 81046)
5:43:45.448850 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 81046)
5:43:45.458912 INFO: Collecting fragment features
5:43:45.515482 INFO: Finished candidate scoring
5:43:45.558492 PROGRESS: === Extracted 81046 precursors and 725716 fragments ===
5:43:45.558968 INFO: performing precursor FDR with 47 features
5:43:45.559028 INFO: Decoy channel: -1
5:43:45.559056 INFO: Competetive: True
5:43:45.589275 INFO: Setting torch num_threads to 2 for FDR classification task
5:43:45.613460 WARNING: dropped 48 target PSMs due to missing features
5:43:45.613598 WARNING: dropped 39 decoy PSMs due to missing features
5:43:46.868381 INFO: Test AUC: 0.547
5:43:46.868514 INFO: Train AUC: 0.571
5:43:46.868544 INFO: AUC difference: 4.30%
5:43:47.070839 INFO: Resetting torch num_threads to 100
5:43:47.073553 INFO: === FDR correction performed with classifier version 10 ===
5:43:47.076922 PROGRESS: ============================= Precursor FDR =============================
5:43:47.077048 PROGRESS: Total precursors accumulated: 21,926
5:43:47.077108 PROGRESS: Target precursors: 13,113 (59.81%)
5:43:47.077174 PROGRESS: Decoy precursors: 8,813 (40.19%)
5:43:47.077220 PROGRESS: 
5:43:47.077264 PROGRESS: Precursor Summary:
5:43:47.078357 PROGRESS: Channel   0:	 0.05 FDR:   328; 0.01 FDR:   226; 0.001 FDR:   197
5:43:47.078445 PROGRESS: 
5:43:47.078499 PROGRESS: Protein Summary:
5:43:47.079717 PROGRESS: Channel   0:	 0.05 FDR:   316; 0.01 FDR:   217; 0.001 FDR:   191
5:43:47.079811 PROGRESS: =========================================================================
5:43:47.127849 INFO: fragments_df: keeping 2525 of 725716 [sum(precursor_idx_mask)=4677 sum(mass_error_mask)=725716 stop_rank=2525
5:43:47.257670 INFO: calibration group: precursor, fitting mz estimator 
5:43:47.373741 INFO: calibration group: precursor, fitting rt estimator 
5:43:47.494725 INFO: calibration group: precursor, fitting mobility estimator 
5:43:47.609790 INFO: calibration group: fragment, fitting mz estimator 
5:43:47.943940 INFO: Using score_cutoff 43.73004389762878 (fac=0.99, q=1)
5:43:47.944386 INFO: calibration group: precursor, predicting mz
5:43:47.951751 INFO: calibration group: precursor, predicting rt
5:43:47.981888 INFO: calibration group: precursor, predicting mobility
5:43:47.988969 INFO: calibration group: fragment, predicting mz
5:43:48.044906 INFO: === checking if optimization conditions were reached ===
5:43:48.045217 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
5:43:48.047597 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 154.5434.
5:43:48.047661 INFO: ==============================================
5:43:48.047772 INFO: Starting optimization step 4.
5:43:48.047847 PROGRESS: === Extracting elution groups 0 to 25400 ===
5:43:48.047930 PROGRESS: Extracting batch of 49998 precursors
5:43:48.066045 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:43:48.066182 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:43:48.066239 INFO: FWHM in RT is 2.67 seconds, sigma is 0.59
5:43:48.066270 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.51
5:43:48.075048 INFO: Starting candidate selection
5:44:06.748715 INFO: Starting candidate scoring
5:44:08.915850 INFO: Finished candidate processing
5:44:08.915984 INFO: Collecting candidate features
5:44:09.066631 WARNING: intensity_correlation has 101 NaNs ( 0.13 % out of 80779)
5:44:09.066978 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 80779)
5:44:09.075777 INFO: Collecting fragment features
5:44:09.128526 INFO: Finished candidate scoring
5:44:09.204335 PROGRESS: === Extracted 80779 precursors and 721121 fragments ===
5:44:09.204736 INFO: performing precursor FDR with 47 features
5:44:09.204774 INFO: Decoy channel: -1
5:44:09.204803 INFO: Competetive: True
5:44:09.228896 INFO: Setting torch num_threads to 2 for FDR classification task
5:44:09.243911 WARNING: dropped 66 target PSMs due to missing features
5:44:09.244047 WARNING: dropped 39 decoy PSMs due to missing features
5:44:10.513173 INFO: Test AUC: 0.546
5:44:10.513303 INFO: Train AUC: 0.573
5:44:10.513332 INFO: AUC difference: 4.71%
5:44:10.717783 INFO: Resetting torch num_threads to 100
5:44:10.720408 INFO: === FDR correction performed with classifier version 10 ===
5:44:10.723974 PROGRESS: ============================= Precursor FDR =============================
5:44:10.724102 PROGRESS: Total precursors accumulated: 21,878
5:44:10.724163 PROGRESS: Target precursors: 13,170 (60.20%)
5:44:10.724212 PROGRESS: Decoy precursors: 8,708 (39.80%)
5:44:10.724256 PROGRESS: 
5:44:10.724301 PROGRESS: Precursor Summary:
5:44:10.725439 PROGRESS: Channel   0:	 0.05 FDR:   346; 0.01 FDR:   220; 0.001 FDR:   214
5:44:10.725531 PROGRESS: 
5:44:10.725586 PROGRESS: Protein Summary:
5:44:10.727061 PROGRESS: Channel   0:	 0.05 FDR:   332; 0.01 FDR:   211; 0.001 FDR:   206
5:44:10.727167 PROGRESS: =========================================================================
5:44:10.774952 INFO: fragments_df: keeping 2444 of 721121 [sum(precursor_idx_mask)=4546 sum(mass_error_mask)=721121 stop_rank=2444
5:44:10.901380 INFO: calibration group: precursor, fitting mz estimator 
5:44:10.996546 INFO: calibration group: precursor, fitting rt estimator 
5:44:11.095587 INFO: calibration group: precursor, fitting mobility estimator 
5:44:11.188970 INFO: calibration group: fragment, fitting mz estimator 
5:44:11.455167 INFO: Using score_cutoff 43.93346218986511 (fac=0.99, q=1)
5:44:11.455561 INFO: calibration group: precursor, predicting mz
5:44:11.462896 INFO: calibration group: precursor, predicting rt
5:44:11.492909 INFO: calibration group: precursor, predicting mobility
5:44:11.500101 INFO: calibration group: fragment, predicting mz
5:44:11.555220 INFO: === checking if optimization conditions were reached ===
5:44:11.555513 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
5:44:11.557793 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 155.5825.
5:44:11.557853 INFO: ==============================================
5:44:11.557955 INFO: Starting optimization step 5.
5:44:11.558027 PROGRESS: === Extracting elution groups 0 to 25400 ===
5:44:11.558093 PROGRESS: Extracting batch of 49998 precursors
5:44:11.573930 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:44:11.574047 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:44:11.574089 INFO: FWHM in RT is 2.66 seconds, sigma is 0.58
5:44:11.574112 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.51
5:44:11.582839 INFO: Starting candidate selection
5:44:30.488885 INFO: Starting candidate scoring
5:44:32.726814 INFO: Finished candidate processing
5:44:32.728384 INFO: Collecting candidate features
5:44:32.896322 WARNING: intensity_correlation has 92 NaNs ( 0.11 % out of 80831)
5:44:32.896646 WARNING: height_correlation has 9 NaNs ( 0.01 % out of 80831)
5:44:32.902856 INFO: Collecting fragment features
5:44:32.972052 INFO: Finished candidate scoring
5:44:33.014204 PROGRESS: === Extracted 80831 precursors and 721876 fragments ===
5:44:33.014789 INFO: performing precursor FDR with 47 features
5:44:33.014832 INFO: Decoy channel: -1
5:44:33.014866 INFO: Competetive: True
5:44:33.054592 INFO: Setting torch num_threads to 2 for FDR classification task
5:44:33.076595 WARNING: dropped 55 target PSMs due to missing features
5:44:33.076745 WARNING: dropped 40 decoy PSMs due to missing features
5:44:34.511077 INFO: Test AUC: 0.549
5:44:34.511216 INFO: Train AUC: 0.571
5:44:34.511247 INFO: AUC difference: 3.99%
5:44:34.715459 INFO: Resetting torch num_threads to 100
5:44:34.718086 INFO: === FDR correction performed with classifier version 10 ===
5:44:34.721460 PROGRESS: ============================= Precursor FDR =============================
5:44:34.721602 PROGRESS: Total precursors accumulated: 21,874
5:44:34.721663 PROGRESS: Target precursors: 13,173 (60.22%)
5:44:34.721716 PROGRESS: Decoy precursors: 8,701 (39.78%)
5:44:34.721762 PROGRESS: 
5:44:34.721813 PROGRESS: Precursor Summary:
5:44:34.722909 PROGRESS: Channel   0:	 0.05 FDR:   309; 0.01 FDR:   216; 0.001 FDR:   209
5:44:34.723004 PROGRESS: 
5:44:34.723073 PROGRESS: Protein Summary:
5:44:34.724266 PROGRESS: Channel   0:	 0.05 FDR:   298; 0.01 FDR:   208; 0.001 FDR:   202
5:44:34.724360 PROGRESS: =========================================================================
5:44:34.773669 INFO: fragments_df: keeping 2411 of 721876 [sum(precursor_idx_mask)=4449 sum(mass_error_mask)=721876 stop_rank=2411
5:44:34.892864 INFO: calibration group: precursor, fitting mz estimator 
5:44:34.988356 INFO: calibration group: precursor, fitting rt estimator 
5:44:35.105489 INFO: calibration group: precursor, fitting mobility estimator 
5:44:35.205892 INFO: calibration group: fragment, fitting mz estimator 
5:44:35.471942 INFO: Using score_cutoff 45.83639650726318 (fac=0.99, q=1)
5:44:35.472345 INFO: calibration group: precursor, predicting mz
5:44:35.479683 INFO: calibration group: precursor, predicting rt
5:44:35.510112 INFO: calibration group: precursor, predicting mobility
5:44:35.517398 INFO: calibration group: fragment, predicting mz
5:44:35.573788 INFO: === checking if optimization conditions were reached ===
5:44:35.574083 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
5:44:35.575510 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 154.5434 found after 6 searches.
5:44:35.575573 INFO: ==============================================
5:44:35.575683 PROGRESS: Optimization finished for rt_error.
5:44:35.702193 INFO: calibration group: precursor, predicting mz
5:44:35.709863 INFO: calibration group: precursor, predicting rt
5:44:35.740893 INFO: calibration group: precursor, predicting mobility
5:44:35.748284 INFO: calibration group: fragment, predicting mz
5:44:35.832644 INFO: Starting optimization step 0.
5:44:35.832885 PROGRESS: === Extracting elution groups 0 to 25400 ===
5:44:35.832998 PROGRESS: Extracting batch of 49998 precursors
5:44:35.846800 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:44:35.846925 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:44:35.846980 INFO: FWHM in RT is 2.66 seconds, sigma is 0.58
5:44:35.847007 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.51
5:44:35.855932 INFO: Starting candidate selection
5:44:54.259069 INFO: Starting candidate scoring
5:44:56.488292 INFO: Finished candidate processing
5:44:56.488589 INFO: Collecting candidate features
5:44:56.634840 WARNING: intensity_correlation has 95 NaNs ( 0.12 % out of 80676)
5:44:56.635668 WARNING: height_correlation has 8 NaNs ( 0.01 % out of 80676)
5:44:56.653504 INFO: Collecting fragment features
5:44:56.705391 INFO: Finished candidate scoring
5:44:56.752661 PROGRESS: === Extracted 80676 precursors and 720468 fragments ===
5:44:56.753064 INFO: performing precursor FDR with 47 features
5:44:56.753102 INFO: Decoy channel: -1
5:44:56.753126 INFO: Competetive: True
5:44:56.780019 INFO: Setting torch num_threads to 2 for FDR classification task
5:44:56.795268 WARNING: dropped 59 target PSMs due to missing features
5:44:56.795377 WARNING: dropped 40 decoy PSMs due to missing features
5:44:58.230231 INFO: Test AUC: 0.557
5:44:58.230363 INFO: Train AUC: 0.589
5:44:58.230393 INFO: AUC difference: 5.45%
5:44:58.230414 WARNING: AUC difference > 5%. This may indicate overfitting.
5:44:58.433167 INFO: Resetting torch num_threads to 100
5:44:58.445114 INFO: === FDR correction performed with classifier version 21 ===
5:44:58.448801 PROGRESS: ============================= Precursor FDR =============================
5:44:58.448937 PROGRESS: Total precursors accumulated: 21,853
5:44:58.448997 PROGRESS: Target precursors: 13,401 (61.32%)
5:44:58.449048 PROGRESS: Decoy precursors: 8,452 (38.68%)
5:44:58.449093 PROGRESS: 
5:44:58.449139 PROGRESS: Precursor Summary:
5:44:58.450246 PROGRESS: Channel   0:	 0.05 FDR:   353; 0.01 FDR:   223; 0.001 FDR:   198
5:44:58.450337 PROGRESS: 
5:44:58.450398 PROGRESS: Protein Summary:
5:44:58.451609 PROGRESS: Channel   0:	 0.05 FDR:   338; 0.01 FDR:   214; 0.001 FDR:   190
5:44:58.451701 PROGRESS: =========================================================================
5:44:58.498831 INFO: fragments_df: keeping 2456 of 720468 [sum(precursor_idx_mask)=4603 sum(mass_error_mask)=720468 stop_rank=2456
5:44:58.639395 INFO: calibration group: precursor, fitting mz estimator 
5:44:58.755190 INFO: calibration group: precursor, fitting rt estimator 
5:44:58.875555 INFO: calibration group: precursor, fitting mobility estimator 
5:44:58.990246 INFO: calibration group: fragment, fitting mz estimator 
5:44:59.312464 INFO: Using score_cutoff 43.977531472778324 (fac=0.99, q=1)
5:44:59.312866 INFO: calibration group: precursor, predicting mz
5:44:59.320055 INFO: calibration group: precursor, predicting rt
5:44:59.350717 INFO: calibration group: precursor, predicting mobility
5:44:59.357737 INFO: calibration group: fragment, predicting mz
5:44:59.414272 INFO: === checking if optimization conditions were reached ===
5:44:59.414534 PROGRESS: === Optimization of ms1_error has been performed 1 time(s); minimum number is 2 ===
5:44:59.416358 PROGRESS: ❌ ms1_error      : optimization incomplete after 1 search(es). Will search with parameter 10.1276.
5:44:59.416413 INFO: ==============================================
5:44:59.416509 INFO: Starting optimization step 1.
5:44:59.416576 PROGRESS: === Extracting elution groups 0 to 25400 ===
5:44:59.416635 PROGRESS: Extracting batch of 49998 precursors
5:44:59.429682 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:44:59.429806 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:44:59.429851 INFO: FWHM in RT is 2.64 seconds, sigma is 0.58
5:44:59.429875 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.50
5:44:59.464291 INFO: Starting candidate selection
5:45:17.056084 INFO: Starting candidate scoring
5:45:18.893147 INFO: Finished candidate processing
5:45:18.893275 INFO: Collecting candidate features
5:45:19.049358 WARNING: intensity_correlation has 93 NaNs ( 0.12 % out of 80680)
5:45:19.049748 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 80680)
5:45:19.057660 INFO: Collecting fragment features
5:45:19.115672 INFO: Finished candidate scoring
5:45:19.161670 PROGRESS: === Extracted 80680 precursors and 711711 fragments ===
5:45:19.162351 INFO: performing precursor FDR with 47 features
5:45:19.162393 INFO: Decoy channel: -1
5:45:19.162417 INFO: Competetive: True
5:45:19.202408 INFO: Setting torch num_threads to 2 for FDR classification task
5:45:19.222937 WARNING: dropped 52 target PSMs due to missing features
5:45:19.223094 WARNING: dropped 45 decoy PSMs due to missing features
5:45:20.782499 INFO: Test AUC: 0.539
5:45:20.782649 INFO: Train AUC: 0.580
5:45:20.782681 INFO: AUC difference: 7.12%
5:45:20.782701 WARNING: AUC difference > 5%. This may indicate overfitting.
5:45:20.992066 INFO: Resetting torch num_threads to 100
5:45:20.996599 INFO: === FDR correction performed with classifier version 21 ===
5:45:21.001681 PROGRESS: ============================= Precursor FDR =============================
5:45:21.001850 PROGRESS: Total precursors accumulated: 21,904
5:45:21.001911 PROGRESS: Target precursors: 12,986 (59.29%)
5:45:21.001961 PROGRESS: Decoy precursors: 8,918 (40.71%)
5:45:21.002006 PROGRESS: 
5:45:21.002048 PROGRESS: Precursor Summary:
5:45:21.003247 PROGRESS: Channel   0:	 0.05 FDR:   363; 0.01 FDR:   240; 0.001 FDR:   189
5:45:21.003342 PROGRESS: 
5:45:21.003398 PROGRESS: Protein Summary:
5:45:21.004637 PROGRESS: Channel   0:	 0.05 FDR:   347; 0.01 FDR:   233; 0.001 FDR:   184
5:45:21.004725 PROGRESS: =========================================================================
5:45:21.053690 INFO: fragments_df: keeping 2563 of 711711 [sum(precursor_idx_mask)=4909 sum(mass_error_mask)=711705 stop_rank=2563
5:45:21.208625 INFO: calibration group: precursor, fitting mz estimator 
5:45:21.313493 INFO: calibration group: precursor, fitting rt estimator 
5:45:21.416295 INFO: calibration group: precursor, fitting mobility estimator 
5:45:21.512335 INFO: calibration group: fragment, fitting mz estimator 
5:45:21.792939 INFO: Using score_cutoff 41.086950286102294 (fac=0.99, q=1)
5:45:21.793405 INFO: calibration group: precursor, predicting mz
5:45:21.800653 INFO: calibration group: precursor, predicting rt
5:45:21.831491 INFO: calibration group: precursor, predicting mobility
5:45:21.838493 INFO: calibration group: fragment, predicting mz
5:45:21.892462 INFO: === checking if optimization conditions were reached ===
5:45:21.892825 PROGRESS: === Optimization of ms1_error has been performed 2 time(s); minimum number is 2 ===
5:45:21.895367 PROGRESS: ❌ ms1_error      : optimization incomplete after 2 search(es). Will search with parameter 2.8278.
5:45:21.895437 INFO: ==============================================
5:45:21.895552 INFO: Starting optimization step 2.
5:45:21.895631 PROGRESS: === Extracting elution groups 0 to 25400 ===
5:45:21.895715 PROGRESS: Extracting batch of 49998 precursors
5:45:21.919939 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:45:21.920094 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:45:21.920155 INFO: FWHM in RT is 2.61 seconds, sigma is 0.57
5:45:21.920184 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.28
5:45:21.921291 INFO: Starting candidate selection
5:45:37.647881 INFO: Starting candidate scoring
5:45:39.217394 INFO: Finished candidate processing
5:45:39.217516 INFO: Collecting candidate features
5:45:39.351899 WARNING: intensity_correlation has 54 NaNs ( 0.07 % out of 80996)
5:45:39.352304 WARNING: height_correlation has 10 NaNs ( 0.01 % out of 80996)
5:45:39.363491 INFO: Collecting fragment features
5:45:39.418895 INFO: Finished candidate scoring
5:45:39.460722 PROGRESS: === Extracted 80996 precursors and 704623 fragments ===
5:45:39.461156 INFO: performing precursor FDR with 47 features
5:45:39.461195 INFO: Decoy channel: -1
5:45:39.461220 INFO: Competetive: True
5:45:39.493211 INFO: Setting torch num_threads to 2 for FDR classification task
5:45:39.512590 WARNING: dropped 33 target PSMs due to missing features
5:45:39.512747 WARNING: dropped 27 decoy PSMs due to missing features
5:45:41.045184 INFO: Test AUC: 0.545
5:45:41.045319 INFO: Train AUC: 0.568
5:45:41.045350 INFO: AUC difference: 4.06%
5:45:41.252838 INFO: Resetting torch num_threads to 100
5:45:41.255615 INFO: === FDR correction performed with classifier version 21 ===
5:45:41.259411 PROGRESS: ============================= Precursor FDR =============================
5:45:41.259570 PROGRESS: Total precursors accumulated: 21,996
5:45:41.259636 PROGRESS: Target precursors: 12,978 (59.00%)
5:45:41.259687 PROGRESS: Decoy precursors: 9,018 (41.00%)
5:45:41.259734 PROGRESS: 
5:45:41.259778 PROGRESS: Precursor Summary:
5:45:41.261008 PROGRESS: Channel   0:	 0.05 FDR:   324; 0.01 FDR:   234; 0.001 FDR:   192
5:45:41.261105 PROGRESS: 
5:45:41.261163 PROGRESS: Protein Summary:
5:45:41.262414 PROGRESS: Channel   0:	 0.05 FDR:   311; 0.01 FDR:   225; 0.001 FDR:   185
5:45:41.262518 PROGRESS: =========================================================================
5:45:41.311438 INFO: fragments_df: keeping 2510 of 704623 [sum(precursor_idx_mask)=4782 sum(mass_error_mask)=704620 stop_rank=2510
5:45:41.434548 INFO: calibration group: precursor, fitting mz estimator 
5:45:41.542275 INFO: calibration group: precursor, fitting rt estimator 
5:45:41.662959 INFO: calibration group: precursor, fitting mobility estimator 
5:45:41.782763 INFO: calibration group: fragment, fitting mz estimator 
5:45:42.114408 INFO: Using score_cutoff 27.479327568626402 (fac=0.99, q=1)
5:45:42.114863 INFO: calibration group: precursor, predicting mz
5:45:42.122301 INFO: calibration group: precursor, predicting rt
5:45:42.153153 INFO: calibration group: precursor, predicting mobility
5:45:42.160716 INFO: calibration group: fragment, predicting mz
5:45:42.242845 INFO: === checking if optimization conditions were reached ===
5:45:42.243197 PROGRESS: === Optimization of ms1_error has been performed 3 time(s); minimum number is 2 ===
5:45:42.244564 PROGRESS: ✅ ms1_error      : optimization complete. Optimal parameter 10.1276 found after 3 searches.
5:45:42.244626 INFO: ==============================================
5:45:42.244731 PROGRESS: Optimization finished for ms1_error.
5:45:42.377953 INFO: calibration group: precursor, predicting mz
5:45:42.385605 INFO: calibration group: precursor, predicting rt
5:45:42.415854 INFO: calibration group: precursor, predicting mobility
5:45:42.423050 INFO: calibration group: fragment, predicting mz
5:45:42.515660 INFO: Starting optimization step 0.
5:45:42.515940 PROGRESS: === Extracting elution groups 0 to 25400 ===
5:45:42.516020 PROGRESS: Extracting batch of 49998 precursors
5:45:42.535788 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:45:42.535954 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:45:42.536009 INFO: FWHM in RT is 2.61 seconds, sigma is 0.57
5:45:42.536038 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.28
5:45:42.550339 INFO: Starting candidate selection
5:45:58.949951 INFO: Starting candidate scoring
5:46:00.763660 INFO: Finished candidate processing
5:46:00.763812 INFO: Collecting candidate features
5:46:00.918350 WARNING: intensity_correlation has 87 NaNs ( 0.11 % out of 80586)
5:46:00.918804 WARNING: height_correlation has 6 NaNs ( 0.01 % out of 80586)
5:46:00.930446 INFO: Collecting fragment features
5:46:00.987200 INFO: Finished candidate scoring
5:46:01.026416 PROGRESS: === Extracted 80586 precursors and 709709 fragments ===
5:46:01.026936 INFO: performing precursor FDR with 47 features
5:46:01.026977 INFO: Decoy channel: -1
5:46:01.027002 INFO: Competetive: True
5:46:01.053282 INFO: Setting torch num_threads to 2 for FDR classification task
5:46:01.068213 WARNING: dropped 45 target PSMs due to missing features
5:46:01.068333 WARNING: dropped 44 decoy PSMs due to missing features
5:46:02.470709 INFO: Test AUC: 0.548
5:46:02.470842 INFO: Train AUC: 0.587
5:46:02.470871 INFO: AUC difference: 6.70%
5:46:02.470892 WARNING: AUC difference > 5%. This may indicate overfitting.
5:46:02.668556 INFO: Resetting torch num_threads to 100
5:46:02.671245 INFO: === FDR correction performed with classifier version 24 ===
5:46:02.674828 PROGRESS: ============================= Precursor FDR =============================
5:46:02.674968 PROGRESS: Total precursors accumulated: 21,878
5:46:02.675053 PROGRESS: Target precursors: 13,327 (60.92%)
5:46:02.675125 PROGRESS: Decoy precursors: 8,551 (39.08%)
5:46:02.675177 PROGRESS: 
5:46:02.675223 PROGRESS: Precursor Summary:
5:46:02.676374 PROGRESS: Channel   0:	 0.05 FDR:   406; 0.01 FDR:   234; 0.001 FDR:   204
5:46:02.676472 PROGRESS: 
5:46:02.676527 PROGRESS: Protein Summary:
5:46:02.677749 PROGRESS: Channel   0:	 0.05 FDR:   388; 0.01 FDR:   227; 0.001 FDR:   198
5:46:02.677841 PROGRESS: =========================================================================
5:46:02.726142 INFO: fragments_df: keeping 2533 of 709709 [sum(precursor_idx_mask)=4865 sum(mass_error_mask)=709703 stop_rank=2533
5:46:02.847804 INFO: calibration group: precursor, fitting mz estimator 
5:46:02.943400 INFO: calibration group: precursor, fitting rt estimator 
5:46:03.045115 INFO: calibration group: precursor, fitting mobility estimator 
5:46:03.141318 INFO: calibration group: fragment, fitting mz estimator 
5:46:03.419101 INFO: Using score_cutoff 42.06518704948425 (fac=0.99, q=1)
5:46:03.419522 INFO: calibration group: precursor, predicting mz
5:46:03.426969 INFO: calibration group: precursor, predicting rt
5:46:03.457493 INFO: calibration group: precursor, predicting mobility
5:46:03.464607 INFO: calibration group: fragment, predicting mz
5:46:03.521240 INFO: === checking if optimization conditions were reached ===
5:46:03.521563 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
5:46:03.523776 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0709.
5:46:03.523863 INFO: ==============================================
5:46:03.523982 INFO: Starting optimization step 1.
5:46:03.524063 PROGRESS: === Extracting elution groups 0 to 25400 ===
5:46:03.524148 PROGRESS: Extracting batch of 49998 precursors
5:46:03.541933 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:46:03.542076 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:46:03.542138 INFO: FWHM in RT is 2.59 seconds, sigma is 0.57
5:46:03.542169 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.25
5:46:03.551035 INFO: Starting candidate selection
5:46:20.413534 INFO: Starting candidate scoring
5:46:22.213231 INFO: Finished candidate processing
5:46:22.213354 INFO: Collecting candidate features
5:46:22.363288 WARNING: intensity_correlation has 84 NaNs ( 0.11 % out of 78779)
5:46:22.363598 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 78779)
5:46:22.369585 INFO: Collecting fragment features
5:46:22.415815 INFO: Finished candidate scoring
5:46:22.459771 PROGRESS: === Extracted 78779 precursors and 687949 fragments ===
5:46:22.460204 INFO: performing precursor FDR with 47 features
5:46:22.460246 INFO: Decoy channel: -1
5:46:22.460275 INFO: Competetive: True
5:46:22.492214 INFO: Setting torch num_threads to 2 for FDR classification task
5:46:22.511397 WARNING: dropped 44 target PSMs due to missing features
5:46:22.511551 WARNING: dropped 44 decoy PSMs due to missing features
5:46:23.980770 INFO: Test AUC: 0.551
5:46:23.980913 INFO: Train AUC: 0.593
5:46:23.980946 INFO: AUC difference: 7.04%
5:46:23.980969 WARNING: AUC difference > 5%. This may indicate overfitting.
5:46:24.185085 INFO: Resetting torch num_threads to 100
5:46:24.188909 INFO: === FDR correction performed with classifier version 24 ===
5:46:24.193212 PROGRESS: ============================= Precursor FDR =============================
5:46:24.193361 PROGRESS: Total precursors accumulated: 21,412
5:46:24.193423 PROGRESS: Target precursors: 13,279 (62.02%)
5:46:24.193475 PROGRESS: Decoy precursors: 8,133 (37.98%)
5:46:24.193521 PROGRESS: 
5:46:24.193567 PROGRESS: Precursor Summary:
5:46:24.194689 PROGRESS: Channel   0:	 0.05 FDR:   371; 0.01 FDR:   215; 0.001 FDR:   188
5:46:24.194784 PROGRESS: 
5:46:24.194839 PROGRESS: Protein Summary:
5:46:24.196062 PROGRESS: Channel   0:	 0.05 FDR:   355; 0.01 FDR:   208; 0.001 FDR:   182
5:46:24.196153 PROGRESS: =========================================================================
5:46:24.243189 INFO: fragments_df: keeping 2357 of 687949 [sum(precursor_idx_mask)=4452 sum(mass_error_mask)=687949 stop_rank=2357
5:46:24.477727 INFO: calibration group: precursor, fitting mz estimator 
5:46:24.578172 INFO: calibration group: precursor, fitting rt estimator 
5:46:24.678522 INFO: calibration group: precursor, fitting mobility estimator 
5:46:24.776551 INFO: calibration group: fragment, fitting mz estimator 
5:46:25.034522 INFO: Using score_cutoff 45.60037095108032 (fac=0.99, q=1)
5:46:25.034953 INFO: calibration group: precursor, predicting mz
5:46:25.042408 INFO: calibration group: precursor, predicting rt
5:46:25.073035 INFO: calibration group: precursor, predicting mobility
5:46:25.080330 INFO: calibration group: fragment, predicting mz
5:46:25.137609 INFO: === checking if optimization conditions were reached ===
5:46:25.137929 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
5:46:25.140199 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0558.
5:46:25.140265 INFO: ==============================================
5:46:25.140369 INFO: Starting optimization step 2.
5:46:25.140442 PROGRESS: === Extracting elution groups 0 to 25400 ===
5:46:25.140511 PROGRESS: Extracting batch of 49998 precursors
5:46:25.160285 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:46:25.160426 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:46:25.160480 INFO: FWHM in RT is 2.68 seconds, sigma is 0.59
5:46:25.160510 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.47
5:46:25.169524 INFO: Starting candidate selection
5:46:34.692203 INFO: Starting candidate scoring
5:46:36.375761 INFO: Finished candidate processing
5:46:36.375928 INFO: Collecting candidate features
5:46:36.523181 WARNING: intensity_correlation has 104 NaNs ( 0.13 % out of 77304)
5:46:36.523483 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 77304)
5:46:36.529642 INFO: Collecting fragment features
5:46:36.577931 INFO: Finished candidate scoring
5:46:36.623845 PROGRESS: === Extracted 77304 precursors and 668163 fragments ===
5:46:36.624256 INFO: performing precursor FDR with 47 features
5:46:36.624295 INFO: Decoy channel: -1
5:46:36.624319 INFO: Competetive: True
5:46:36.652289 INFO: Setting torch num_threads to 2 for FDR classification task
5:46:36.667614 WARNING: dropped 52 target PSMs due to missing features
5:46:36.667751 WARNING: dropped 55 decoy PSMs due to missing features
5:46:37.912094 INFO: Test AUC: 0.558
5:46:37.912237 INFO: Train AUC: 0.586
5:46:37.912270 INFO: AUC difference: 4.78%
5:46:38.116097 INFO: Resetting torch num_threads to 100
5:46:38.118651 INFO: === FDR correction performed with classifier version 24 ===
5:46:38.121929 PROGRESS: ============================= Precursor FDR =============================
5:46:38.122064 PROGRESS: Total precursors accumulated: 21,043
5:46:38.122126 PROGRESS: Target precursors: 12,964 (61.61%)
5:46:38.122176 PROGRESS: Decoy precursors: 8,079 (38.39%)
5:46:38.122222 PROGRESS: 
5:46:38.122268 PROGRESS: Precursor Summary:
5:46:38.123368 PROGRESS: Channel   0:	 0.05 FDR:   373; 0.01 FDR:   229; 0.001 FDR:   198
5:46:38.123463 PROGRESS: 
5:46:38.123519 PROGRESS: Protein Summary:
5:46:38.124732 PROGRESS: Channel   0:	 0.05 FDR:   356; 0.01 FDR:   223; 0.001 FDR:   192
5:46:38.124827 PROGRESS: =========================================================================
5:46:38.171291 INFO: fragments_df: keeping 2408 of 668163 [sum(precursor_idx_mask)=4733 sum(mass_error_mask)=668162 stop_rank=2408
5:46:38.299424 INFO: calibration group: precursor, fitting mz estimator 
5:46:38.444679 INFO: calibration group: precursor, fitting rt estimator 
5:46:38.565406 INFO: calibration group: precursor, fitting mobility estimator 
5:46:38.678131 INFO: calibration group: fragment, fitting mz estimator 
5:46:38.990863 INFO: Using score_cutoff 41.40901819610596 (fac=0.99, q=1)
5:46:38.991307 INFO: calibration group: precursor, predicting mz
5:46:38.998884 INFO: calibration group: precursor, predicting rt
5:46:39.031557 INFO: calibration group: precursor, predicting mobility
5:46:39.039572 INFO: calibration group: fragment, predicting mz
5:46:39.110849 INFO: === checking if optimization conditions were reached ===
5:46:39.111167 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
5:46:39.112364 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.0558 found after 3 searches.
5:46:39.112425 INFO: ==============================================
5:46:39.112530 PROGRESS: Optimization finished for mobility_error.
5:46:39.265144 INFO: calibration group: precursor, predicting mz
5:46:39.273664 INFO: calibration group: precursor, predicting rt
5:46:39.306500 INFO: calibration group: precursor, predicting mobility
5:46:39.314966 INFO: calibration group: fragment, predicting mz
5:46:39.403552 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
5:46:39.403863 PROGRESS: ==============================================
5:46:39.403959 PROGRESS: ms2_error      : 8.8746
5:46:39.404038 PROGRESS: rt_error       : 154.5434
5:46:39.404116 PROGRESS: ms1_error      : 10.1276
5:46:39.404186 PROGRESS: mobility_error : 0.0558
5:46:39.404254 PROGRESS: ==============================================
5:46:39.406900 INFO: calibration group: precursor, predicting mz
5:46:40.868768 INFO: calibration group: precursor, predicting rt
5:46:47.474320 INFO: calibration group: precursor, predicting mobility
5:46:48.940006 INFO: calibration group: fragment, predicting mz
5:47:01.733572 PROGRESS: Extracting batch of 10272670 precursors
5:47:04.602039 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:47:04.602197 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:47:04.602253 INFO: FWHM in RT is 2.69 seconds, sigma is 0.59
5:47:04.602280 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.30
5:47:04.633565 INFO: Starting candidate selection
6:15:33.494574 INFO: Applying score cutoff of 41.40901819610596
6:15:33.675029 INFO: Removed 13683804 precursors with score below cutoff
6:15:36.336493 INFO: Starting candidate scoring
6:17:00.098865 INFO: Finished candidate processing
6:17:00.100481 INFO: Collecting candidate features
6:17:09.741411 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 3563923)
6:17:09.870967 INFO: Collecting fragment features
6:17:13.692414 INFO: Finished candidate scoring
6:17:19.157225 INFO: === FDR correction performed with classifier version 28 ===
6:17:19.160672 INFO: performing precursor FDR with 47 features
6:17:19.160732 INFO: Decoy channel: -1
6:17:19.160774 INFO: Competetive: True
6:17:20.381621 INFO: Setting torch num_threads to 2 for FDR classification task
6:17:21.025045 WARNING: dropped 1 target PSMs due to missing features
6:17:21.025293 WARNING: FDR calculation for 1898280 target and 1665642 decoy PSMs
6:17:21.025326 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
6:18:32.863919 INFO: Test AUC: 0.575
6:18:32.864083 INFO: Train AUC: 0.580
6:18:32.864120 INFO: AUC difference: 0.96%
6:18:34.023106 INFO: Resetting torch num_threads to 100
6:18:34.194753 INFO: Removing fragments below FDR threshold
6:18:34.531847 PROGRESS: ============================= Precursor FDR =============================
6:18:34.532139 PROGRESS: Total precursors accumulated: 74,732
6:18:34.532223 PROGRESS: Target precursors: 73,993 (99.01%)
6:18:34.532276 PROGRESS: Decoy precursors: 739 (0.99%)
6:18:34.532324 PROGRESS: 
6:18:34.532368 PROGRESS: Precursor Summary:
6:18:34.567560 PROGRESS: Channel   0:	 0.05 FDR: 73,993; 0.01 FDR: 73,993; 0.001 FDR: 56,144
6:18:34.567858 PROGRESS: 
6:18:34.567924 PROGRESS: Protein Summary:
6:18:34.618432 PROGRESS: Channel   0:	 0.05 FDR: 11,505; 0.01 FDR: 11,505; 0.001 FDR: 9,429
6:18:34.618723 PROGRESS: =========================================================================
6:18:35.270694 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
6:18:35.846018 PROGRESS: Loading raw file 4/6: ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
6:18:35.846235 INFO: Quantification results path: run_output/alphadia_1.10.4_Again_good_now/library/quant
6:18:35.846325 INFO: Creating folder run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/figures
6:18:35.847393 INFO: Initializing RawFileManager
6:18:35.847532 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
6:18:35.847593 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
6:18:35.847640 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
6:18:36.067970 INFO: Reading 39,128 frames with 2,751,035,867 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
6:18:42.697530 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d...
6:18:42.704653 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
6:18:42.710198 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
6:18:42.710552 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
6:18:42.711141 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
6:18:42.713637 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
6:18:42.733252 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
6:18:42.733554 INFO: Indexing quadrupole dimension
6:18:43.219697 INFO: Transposing detector events
6:18:53.164813 INFO: Finished transposing data
6:18:53.195723 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
6:18:53.196635 INFO: RT (min)            : 0.0 - 70.0
6:18:53.196679 INFO: RT duration (sec)   : 4199.8
6:18:53.196704 INFO: RT duration (min)   : 70.0
6:18:53.196727 INFO: Cycle len (scans)   : 9
6:18:53.196746 INFO: Cycle len (sec)     : 0.97
6:18:53.196764 INFO: Number of cycles    : 4347
6:18:53.196783 INFO: MS2 range (m/z)     : 400.0 - 1000.0
6:18:54.900492 INFO: Initializing CalibrationManager
6:18:54.900829 INFO: Loading calibration config
6:18:54.901792 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed'], 'function': LOESSRegression()}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed'], 'function': LOESSRegression(n_kernels=2)}], 'name': 'precursor'}]
6:18:54.901881 INFO: Calibration group :fragment, found 1 estimator(s)
6:18:54.901989 INFO: Calibration group :precursor, found 3 estimator(s)
6:18:54.902158 INFO: Initializing OptimizationManager
6:18:54.902255 INFO: initial parameter: ms1_error = 30
6:18:54.902321 INFO: initial parameter: ms2_error = 30
6:18:54.902380 INFO: initial parameter: rt_error = 2099.891532
6:18:54.902424 INFO: initial parameter: mobility_error = 0.1
6:18:54.902466 INFO: initial parameter: column_type = library
6:18:54.902506 INFO: initial parameter: num_candidates = 1
6:18:54.902545 INFO: initial parameter: classifier_version = -1
6:18:54.902584 INFO: initial parameter: fwhm_rt = 5
6:18:54.902624 INFO: initial parameter: fwhm_mobility = 0.01
6:18:54.902664 INFO: initial parameter: score_cutoff = 0
6:18:54.902752 INFO: Initializing TimingManager
6:18:54.902825 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
6:18:54.902988 INFO: FDRManager not loaded from disk.
6:18:54.903015 INFO: Initializing FDRManager
6:18:54.903068 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
6:18:56.192997 PROGRESS: 5,215,079 target precursors potentially observable (0 removed)
6:18:58.064504 PROGRESS: Starting initial search for precursors.
6:18:58.279637 INFO: Starting optimization step 0.
6:18:58.279902 PROGRESS: === Extracting elution groups 0 to 200 ===
6:18:58.279992 PROGRESS: Extracting batch of 398 precursors
6:18:58.281297 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
6:18:58.281346 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
6:18:58.281397 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
6:18:58.281420 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
6:18:58.312264 INFO: Starting candidate selection
6:19:01.046849 INFO: Starting candidate scoring
6:19:01.126168 INFO: Finished candidate processing
6:19:01.126272 INFO: Collecting candidate features
6:19:01.136452 INFO: Collecting fragment features
6:19:01.138786 INFO: Finished candidate scoring
6:19:01.139767 PROGRESS: === Extracted 339 precursors and 3443 fragments ===
6:19:01.140074 INFO: performing precursor FDR with 47 features
6:19:01.140119 INFO: Decoy channel: -1
6:19:01.140142 INFO: Competetive: True
6:19:01.141237 INFO: Setting torch num_threads to 2 for FDR classification task
6:19:01.154561 INFO: Test AUC: 0.449
6:19:01.154626 INFO: Train AUC: 0.451
6:19:01.154656 INFO: AUC difference: 0.29%
6:19:01.373142 INFO: Resetting torch num_threads to 100
6:19:01.373774 INFO: === FDR correction performed with classifier version -1 ===
6:19:01.374437 PROGRESS: ============================= Precursor FDR =============================
6:19:01.374531 PROGRESS: Total precursors accumulated: 174
6:19:01.374593 PROGRESS: Target precursors: 75 (43.10%)
6:19:01.374645 PROGRESS: Decoy precursors: 99 (56.90%)
6:19:01.374692 PROGRESS: 
6:19:01.374737 PROGRESS: Precursor Summary:
6:19:01.375599 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
6:19:01.375691 PROGRESS: 
6:19:01.375749 PROGRESS: Protein Summary:
6:19:01.376687 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
6:19:01.376779 PROGRESS: =========================================================================
6:19:01.433278 INFO: Starting optimization step 1.
6:19:01.433505 PROGRESS: === Extracting elution groups 200 to 600 ===
6:19:01.433576 PROGRESS: Extracting batch of 786 precursors
6:19:01.434451 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
6:19:01.434499 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
6:19:01.434529 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
6:19:01.434553 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
6:19:01.435401 INFO: Starting candidate selection
6:19:06.417074 INFO: Starting candidate scoring
6:19:06.544996 INFO: Finished candidate processing
6:19:06.545099 INFO: Collecting candidate features
6:19:06.555170 INFO: Collecting fragment features
6:19:06.557911 INFO: Finished candidate scoring
6:19:06.559872 PROGRESS: === Extracted 1052 precursors and 10736 fragments ===
6:19:06.560590 INFO: performing precursor FDR with 47 features
6:19:06.560634 INFO: Decoy channel: -1
6:19:06.560658 INFO: Competetive: True
6:19:06.563549 INFO: Setting torch num_threads to 2 for FDR classification task
6:19:06.575538 INFO: Test AUC: 0.412
6:19:06.575599 INFO: Train AUC: 0.489
6:19:06.575628 INFO: AUC difference: 15.69%
6:19:06.575649 WARNING: AUC difference > 5%. This may indicate overfitting.
6:19:06.754960 INFO: Resetting torch num_threads to 100
6:19:06.755719 INFO: === FDR correction performed with classifier version -1 ===
6:19:06.756421 PROGRESS: ============================= Precursor FDR =============================
6:19:06.756514 PROGRESS: Total precursors accumulated: 541
6:19:06.756572 PROGRESS: Target precursors: 247 (45.66%)
6:19:06.756621 PROGRESS: Decoy precursors: 294 (54.34%)
6:19:06.756670 PROGRESS: 
6:19:06.756715 PROGRESS: Precursor Summary:
6:19:06.757550 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
6:19:06.757635 PROGRESS: 
6:19:06.757690 PROGRESS: Protein Summary:
6:19:06.758577 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
6:19:06.758663 PROGRESS: =========================================================================
6:19:06.818133 INFO: Starting optimization step 2.
6:19:06.818359 PROGRESS: === Extracting elution groups 600 to 1400 ===
6:19:06.818428 PROGRESS: Extracting batch of 1566 precursors
6:19:06.819538 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
6:19:06.819589 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
6:19:06.819621 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
6:19:06.819643 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
6:19:06.820603 INFO: Starting candidate selection
6:19:15.866807 INFO: Starting candidate scoring
6:19:16.052770 INFO: Finished candidate processing
6:19:16.052926 INFO: Collecting candidate features
6:19:16.065612 WARNING: intensity_correlation has 1 NaNs ( 0.07 % out of 1375)
6:19:16.070677 INFO: Collecting fragment features
6:19:16.075907 INFO: Finished candidate scoring
6:19:16.080024 PROGRESS: === Extracted 2427 precursors and 24322 fragments ===
6:19:16.081637 INFO: performing precursor FDR with 47 features
6:19:16.081720 INFO: Decoy channel: -1
6:19:16.081783 INFO: Competetive: True
6:19:16.086723 INFO: Setting torch num_threads to 2 for FDR classification task
6:19:16.088908 WARNING: dropped 1 decoy PSMs due to missing features
6:19:16.105636 INFO: Test AUC: 0.512
6:19:16.105716 INFO: Train AUC: 0.471
6:19:16.105756 INFO: AUC difference: 8.82%
6:19:16.105788 WARNING: AUC difference > 5%. This may indicate overfitting.
6:19:16.281629 INFO: Resetting torch num_threads to 100
6:19:16.282513 INFO: === FDR correction performed with classifier version -1 ===
6:19:16.283333 PROGRESS: ============================= Precursor FDR =============================
6:19:16.283430 PROGRESS: Total precursors accumulated: 1,253
6:19:16.283489 PROGRESS: Target precursors: 593 (47.33%)
6:19:16.283538 PROGRESS: Decoy precursors: 660 (52.67%)
6:19:16.283583 PROGRESS: 
6:19:16.283628 PROGRESS: Precursor Summary:
6:19:16.284495 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
6:19:16.284585 PROGRESS: 
6:19:16.284645 PROGRESS: Protein Summary:
6:19:16.285599 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
6:19:16.285686 PROGRESS: =========================================================================
6:19:16.346104 INFO: Starting optimization step 3.
6:19:16.346326 PROGRESS: === Extracting elution groups 1400 to 3000 ===
6:19:16.346393 PROGRESS: Extracting batch of 3160 precursors
6:19:16.347732 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
6:19:16.347781 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
6:19:16.347810 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
6:19:16.347831 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
6:19:16.348668 INFO: Starting candidate selection
6:19:34.371747 INFO: Starting candidate scoring
6:19:34.596596 INFO: Finished candidate processing
6:19:34.596707 INFO: Collecting candidate features
6:19:34.609146 WARNING: intensity_correlation has 2 NaNs ( 0.07 % out of 2760)
6:19:34.612270 INFO: Collecting fragment features
6:19:34.616951 INFO: Finished candidate scoring
6:19:34.621946 PROGRESS: === Extracted 5187 precursors and 51916 fragments ===
6:19:34.623196 INFO: performing precursor FDR with 47 features
6:19:34.623243 INFO: Decoy channel: -1
6:19:34.623268 INFO: Competetive: True
6:19:34.628065 INFO: Setting torch num_threads to 2 for FDR classification task
6:19:34.629877 WARNING: dropped 1 target PSMs due to missing features
6:19:34.629929 WARNING: dropped 2 decoy PSMs due to missing features
6:19:34.655962 INFO: Test AUC: 0.495
6:19:34.656065 INFO: Train AUC: 0.496
6:19:34.656095 INFO: AUC difference: 0.31%
6:19:34.836404 INFO: Resetting torch num_threads to 100
6:19:34.837466 INFO: === FDR correction performed with classifier version -1 ===
6:19:34.838403 PROGRESS: ============================= Precursor FDR =============================
6:19:34.838498 PROGRESS: Total precursors accumulated: 2,663
6:19:34.838561 PROGRESS: Target precursors: 1,327 (49.83%)
6:19:34.838612 PROGRESS: Decoy precursors: 1,336 (50.17%)
6:19:34.838658 PROGRESS: 
6:19:34.838701 PROGRESS: Precursor Summary:
6:19:34.839559 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
6:19:34.839647 PROGRESS: 
6:19:34.839702 PROGRESS: Protein Summary:
6:19:34.840597 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
6:19:34.840688 PROGRESS: =========================================================================
6:19:35.230587 INFO: Starting optimization step 4.
6:19:35.230870 PROGRESS: === Extracting elution groups 3000 to 6200 ===
6:19:35.230943 PROGRESS: Extracting batch of 6310 precursors
6:19:35.233442 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
6:19:35.233497 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
6:19:35.233527 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
6:19:35.233549 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
6:19:35.234344 INFO: Starting candidate selection
6:20:11.134181 INFO: Starting candidate scoring
6:20:11.541935 INFO: Finished candidate processing
6:20:11.542077 INFO: Collecting candidate features
6:20:11.573931 INFO: Collecting fragment features
6:20:11.581221 INFO: Finished candidate scoring
6:20:11.601974 PROGRESS: === Extracted 10666 precursors and 107391 fragments ===
6:20:11.604041 INFO: performing precursor FDR with 47 features
6:20:11.604104 INFO: Decoy channel: -1
6:20:11.604130 INFO: Competetive: True
6:20:11.615095 INFO: Setting torch num_threads to 2 for FDR classification task
6:20:11.618021 WARNING: dropped 1 target PSMs due to missing features
6:20:11.618095 WARNING: dropped 2 decoy PSMs due to missing features
6:20:11.668355 INFO: Test AUC: 0.484
6:20:11.668490 INFO: Train AUC: 0.487
6:20:11.668522 INFO: AUC difference: 0.52%
6:20:11.851773 INFO: Resetting torch num_threads to 100
6:20:11.853324 INFO: === FDR correction performed with classifier version -1 ===
6:20:11.854732 PROGRESS: ============================= Precursor FDR =============================
6:20:11.854842 PROGRESS: Total precursors accumulated: 5,476
6:20:11.854906 PROGRESS: Target precursors: 2,691 (49.14%)
6:20:11.854957 PROGRESS: Decoy precursors: 2,785 (50.86%)
6:20:11.855003 PROGRESS: 
6:20:11.855059 PROGRESS: Precursor Summary:
6:20:11.855936 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
6:20:11.856028 PROGRESS: 
6:20:11.856086 PROGRESS: Protein Summary:
6:20:11.857018 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
6:20:11.857107 PROGRESS: =========================================================================
6:20:11.978565 INFO: Starting optimization step 5.
6:20:11.978849 PROGRESS: === Extracting elution groups 6200 to 12600 ===
6:20:11.978933 PROGRESS: Extracting batch of 12602 precursors
6:20:11.981993 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
6:20:11.982049 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
6:20:11.982086 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
6:20:11.982110 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
6:20:12.088778 INFO: Starting candidate selection
6:21:17.556484 INFO: Starting candidate scoring
6:21:18.182471 INFO: Finished candidate processing
6:21:18.182584 INFO: Collecting candidate features
6:21:18.206939 WARNING: intensity_correlation has 1 NaNs ( 0.01 % out of 10969)
6:21:18.210416 INFO: Collecting fragment features
6:21:18.222974 INFO: Finished candidate scoring
6:21:18.258690 PROGRESS: === Extracted 21635 precursors and 217048 fragments ===
6:21:18.262693 INFO: performing precursor FDR with 47 features
6:21:18.262783 INFO: Decoy channel: -1
6:21:18.262809 INFO: Competetive: True
6:21:18.273231 INFO: Setting torch num_threads to 2 for FDR classification task
6:21:18.278141 WARNING: dropped 1 target PSMs due to missing features
6:21:18.278240 WARNING: dropped 3 decoy PSMs due to missing features
6:21:18.590343 INFO: Test AUC: 0.534
6:21:18.590464 INFO: Train AUC: 0.551
6:21:18.590493 INFO: AUC difference: 3.09%
6:21:18.781768 INFO: Resetting torch num_threads to 100
6:21:18.784126 INFO: === FDR correction performed with classifier version -1 ===
6:21:18.786082 PROGRESS: ============================= Precursor FDR =============================
6:21:18.786194 PROGRESS: Total precursors accumulated: 11,106
6:21:18.786255 PROGRESS: Target precursors: 6,378 (57.43%)
6:21:18.786308 PROGRESS: Decoy precursors: 4,728 (42.57%)
6:21:18.786351 PROGRESS: 
6:21:18.786396 PROGRESS: Precursor Summary:
6:21:18.787349 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
6:21:18.787442 PROGRESS: 
6:21:18.787496 PROGRESS: Protein Summary:
6:21:18.788500 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
6:21:18.788587 PROGRESS: =========================================================================
6:21:18.929576 INFO: Starting optimization step 6.
6:21:18.929891 PROGRESS: === Extracting elution groups 12600 to 25400 ===
6:21:18.929986 PROGRESS: Extracting batch of 25176 precursors
6:21:18.939934 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
6:21:18.940049 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
6:21:18.940094 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
6:21:18.940117 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
6:21:18.941489 INFO: Starting candidate selection
6:23:29.232519 INFO: Starting candidate scoring
6:23:30.395920 INFO: Finished candidate processing
6:23:30.396080 INFO: Collecting candidate features
6:23:30.472821 WARNING: intensity_correlation has 5 NaNs ( 0.02 % out of 21904)
6:23:30.473089 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 21904)
6:23:30.476703 INFO: Collecting fragment features
6:23:30.492928 INFO: Finished candidate scoring
6:23:30.568474 PROGRESS: === Extracted 43539 precursors and 435323 fragments ===
6:23:30.574942 INFO: performing precursor FDR with 47 features
6:23:30.575041 INFO: Decoy channel: -1
6:23:30.575071 INFO: Competetive: True
6:23:30.607810 INFO: Setting torch num_threads to 2 for FDR classification task
6:23:30.628165 WARNING: dropped 4 target PSMs due to missing features
6:23:30.628302 WARNING: dropped 5 decoy PSMs due to missing features
6:23:31.375849 INFO: Test AUC: 0.553
6:23:31.375988 INFO: Train AUC: 0.576
6:23:31.376020 INFO: AUC difference: 4.12%
6:23:31.598321 INFO: Resetting torch num_threads to 100
6:23:31.602153 INFO: === FDR correction performed with classifier version -1 ===
6:23:31.607539 PROGRESS: ============================= Precursor FDR =============================
6:23:31.607805 PROGRESS: Total precursors accumulated: 22,356
6:23:31.607869 PROGRESS: Target precursors: 12,996 (58.13%)
6:23:31.607920 PROGRESS: Decoy precursors: 9,360 (41.87%)
6:23:31.607966 PROGRESS: 
6:23:31.608009 PROGRESS: Precursor Summary:
6:23:31.609113 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
6:23:31.609205 PROGRESS: 
6:23:31.609261 PROGRESS: Protein Summary:
6:23:31.610328 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
6:23:31.610416 PROGRESS: =========================================================================
6:23:32.177353 INFO: Starting optimization step 7.
6:23:32.177696 PROGRESS: === Extracting elution groups 25400 to 51000 ===
6:23:32.177805 PROGRESS: Extracting batch of 50417 precursors
6:23:32.192113 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
6:23:32.192252 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
6:23:32.192290 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
6:23:32.192314 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
6:23:32.194453 INFO: Starting candidate selection
6:27:51.333065 INFO: Starting candidate scoring
6:27:53.701571 INFO: Finished candidate processing
6:27:53.701827 INFO: Collecting candidate features
6:27:53.937634 WARNING: intensity_correlation has 10 NaNs ( 0.02 % out of 43983)
6:27:53.937960 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 43983)
6:27:53.942917 INFO: Collecting fragment features
6:27:53.983634 INFO: Finished candidate scoring
6:27:54.102463 PROGRESS: === Extracted 87522 precursors and 875082 fragments ===
6:27:54.126075 INFO: performing precursor FDR with 47 features
6:27:54.126239 INFO: Decoy channel: -1
6:27:54.126268 INFO: Competetive: True
6:27:54.207677 INFO: Setting torch num_threads to 2 for FDR classification task
6:27:54.249387 WARNING: dropped 13 target PSMs due to missing features
6:27:54.249626 WARNING: dropped 7 decoy PSMs due to missing features
6:27:55.778063 INFO: Test AUC: 0.556
6:27:55.778208 INFO: Train AUC: 0.588
6:27:55.778240 INFO: AUC difference: 5.35%
6:27:55.778265 WARNING: AUC difference > 5%. This may indicate overfitting.
6:27:55.982728 INFO: Resetting torch num_threads to 100
6:27:55.988423 INFO: === FDR correction performed with classifier version -1 ===
6:27:55.997426 PROGRESS: ============================= Precursor FDR =============================
6:27:55.997722 PROGRESS: Total precursors accumulated: 44,899
6:27:55.997809 PROGRESS: Target precursors: 26,891 (59.89%)
6:27:55.997865 PROGRESS: Decoy precursors: 18,008 (40.11%)
6:27:55.997928 PROGRESS: 
6:27:55.997978 PROGRESS: Precursor Summary:
6:27:55.999219 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
6:27:55.999331 PROGRESS: 
6:27:55.999390 PROGRESS: Protein Summary:
6:27:56.000520 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
6:27:56.000612 PROGRESS: =========================================================================
6:27:56.242508 INFO: Starting optimization step 8.
6:27:56.242834 PROGRESS: === Extracting elution groups 51000 to 102200 ===
6:27:56.242935 PROGRESS: Extracting batch of 100803 precursors
6:27:56.270754 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
6:27:56.270901 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
6:27:56.270941 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
6:27:56.270964 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
6:27:56.272088 INFO: Starting candidate selection
6:36:28.275071 INFO: Starting candidate scoring
6:36:32.295748 INFO: Finished candidate processing
6:36:32.295980 INFO: Collecting candidate features
6:36:32.667037 WARNING: intensity_correlation has 15 NaNs ( 0.02 % out of 87973)
6:36:32.667831 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 87973)
6:36:32.675801 INFO: Collecting fragment features
6:36:32.737214 INFO: Finished candidate scoring
6:36:32.936457 PROGRESS: === Extracted 175495 precursors and 1756503 fragments ===
6:36:32.961676 INFO: performing precursor FDR with 47 features
6:36:32.961822 INFO: Decoy channel: -1
6:36:32.961855 INFO: Competetive: True
6:36:33.052711 INFO: Setting torch num_threads to 2 for FDR classification task
6:36:33.091708 WARNING: dropped 18 target PSMs due to missing features
6:36:33.091858 WARNING: dropped 18 decoy PSMs due to missing features
6:36:36.272642 INFO: Test AUC: 0.562
6:36:36.272778 INFO: Train AUC: 0.598
6:36:36.272810 INFO: AUC difference: 6.06%
6:36:36.272831 WARNING: AUC difference > 5%. This may indicate overfitting.
6:36:36.498736 INFO: Resetting torch num_threads to 100
6:36:36.509592 INFO: === FDR correction performed with classifier version -1 ===
6:36:36.530251 PROGRESS: ============================= Precursor FDR =============================
6:36:36.530547 PROGRESS: Total precursors accumulated: 90,033
6:36:36.530619 PROGRESS: Target precursors: 55,875 (62.06%)
6:36:36.530669 PROGRESS: Decoy precursors: 34,158 (37.94%)
6:36:36.530719 PROGRESS: 
6:36:36.530763 PROGRESS: Precursor Summary:
6:36:36.532376 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
6:36:36.532500 PROGRESS: 
6:36:36.532557 PROGRESS: Protein Summary:
6:36:36.534021 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
6:36:36.534123 PROGRESS: =========================================================================
6:36:36.894754 INFO: Starting optimization step 9.
6:36:36.895092 PROGRESS: === Extracting elution groups 102200 to 204600 ===
6:36:36.895183 PROGRESS: Extracting batch of 201717 precursors
6:36:36.947512 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
6:36:36.947655 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
6:36:36.947694 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
6:36:36.947716 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
6:36:36.948829 INFO: Starting candidate selection
6:53:39.790879 INFO: Starting candidate scoring
6:53:48.407953 INFO: Finished candidate processing
6:53:48.408057 INFO: Collecting candidate features
6:53:48.778926 WARNING: intensity_correlation has 47 NaNs ( 0.03 % out of 175810)
6:53:48.779349 WARNING: height_correlation has 5 NaNs ( 0.00 % out of 175810)
6:53:48.788054 INFO: Collecting fragment features
6:53:48.920200 INFO: Finished candidate scoring
6:53:49.181508 PROGRESS: === Extracted 351305 precursors and 3512361 fragments ===
6:53:49.231094 INFO: performing precursor FDR with 47 features
6:53:49.231237 INFO: Decoy channel: -1
6:53:49.231262 INFO: Competetive: True
6:53:49.419917 INFO: Setting torch num_threads to 2 for FDR classification task
6:53:49.501997 WARNING: dropped 49 target PSMs due to missing features
6:53:49.502156 WARNING: dropped 36 decoy PSMs due to missing features
6:53:56.254004 INFO: Test AUC: 0.566
6:53:56.254228 INFO: Train AUC: 0.597
6:53:56.254260 INFO: AUC difference: 5.28%
6:53:56.254280 WARNING: AUC difference > 5%. This may indicate overfitting.
6:53:56.531228 INFO: Resetting torch num_threads to 100
6:53:56.553470 INFO: === FDR correction performed with classifier version -1 ===
6:53:56.587448 PROGRESS: ============================= Precursor FDR =============================
6:53:56.587766 PROGRESS: Total precursors accumulated: 180,211
6:53:56.587837 PROGRESS: Target precursors: 111,525 (61.89%)
6:53:56.587889 PROGRESS: Decoy precursors: 68,686 (38.11%)
6:53:56.587936 PROGRESS: 
6:53:56.587981 PROGRESS: Precursor Summary:
6:53:56.589936 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
6:53:56.590034 PROGRESS: 
6:53:56.590090 PROGRESS: Protein Summary:
6:53:56.591869 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
6:53:56.591964 PROGRESS: =========================================================================
6:53:57.187478 INFO: Starting optimization step 10.
6:53:57.187796 PROGRESS: === Extracting elution groups 204600 to 409400 ===
6:53:57.187890 PROGRESS: Extracting batch of 403498 precursors
6:53:57.282929 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
6:53:57.283072 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
6:53:57.283111 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
6:53:57.283134 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
6:53:57.284105 INFO: Starting candidate selection
7:28:12.088463 INFO: Starting candidate scoring
7:28:28.355462 INFO: Finished candidate processing
7:28:28.355657 INFO: Collecting candidate features
7:28:29.340703 WARNING: intensity_correlation has 66 NaNs ( 0.02 % out of 352007)
7:28:29.341312 WARNING: height_correlation has 5 NaNs ( 0.00 % out of 352007)
7:28:29.360411 INFO: Collecting fragment features
7:28:29.603912 INFO: Finished candidate scoring
7:28:30.269897 PROGRESS: === Extracted 703312 precursors and 7033147 fragments ===
7:28:30.375073 INFO: performing precursor FDR with 47 features
7:28:30.375216 INFO: Decoy channel: -1
7:28:30.375243 INFO: Competetive: True
7:28:30.761442 INFO: Setting torch num_threads to 2 for FDR classification task
7:28:30.930868 WARNING: dropped 83 target PSMs due to missing features
7:28:30.931040 WARNING: dropped 72 decoy PSMs due to missing features
7:28:46.313911 INFO: Test AUC: 0.566
7:28:46.314175 INFO: Train AUC: 0.591
7:28:46.314209 INFO: AUC difference: 4.19%
7:28:46.724966 INFO: Resetting torch num_threads to 100
7:28:46.784921 INFO: === FDR correction performed with classifier version -1 ===
7:28:46.876162 PROGRESS: ============================= Precursor FDR =============================
7:28:46.876539 PROGRESS: Total precursors accumulated: 360,686
7:28:46.876619 PROGRESS: Target precursors: 221,943 (61.53%)
7:28:46.876672 PROGRESS: Decoy precursors: 138,743 (38.47%)
7:28:46.876719 PROGRESS: 
7:28:46.876768 PROGRESS: Precursor Summary:
7:28:46.881218 PROGRESS: Channel   0:	 0.05 FDR: 3,332; 0.01 FDR:   147; 0.001 FDR:   124
7:28:46.881366 PROGRESS: 
7:28:46.881423 PROGRESS: Protein Summary:
7:28:46.885095 PROGRESS: Channel   0:	 0.05 FDR: 2,299; 0.01 FDR:   141; 0.001 FDR:   119
7:28:46.885213 PROGRESS: =========================================================================
7:28:47.920830 INFO: Starting optimization step 11.
7:28:47.921184 PROGRESS: === Extracting elution groups 409400 to 819000 ===
7:28:47.921287 PROGRESS: Extracting batch of 806744 precursors
7:28:48.152416 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
7:28:48.152580 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
7:28:48.152618 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
7:28:48.152644 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
7:28:48.153681 INFO: Starting candidate selection
8:36:49.165804 INFO: Starting candidate scoring
8:37:26.401695 INFO: Finished candidate processing
8:37:26.402002 INFO: Collecting candidate features
8:37:28.182550 WARNING: intensity_correlation has 139 NaNs ( 0.02 % out of 702898)
8:37:28.183409 WARNING: height_correlation has 13 NaNs ( 0.00 % out of 702898)
8:37:28.207417 INFO: Collecting fragment features
8:37:28.701405 INFO: Finished candidate scoring
8:37:29.886394 PROGRESS: === Extracted 1406210 precursors and 14061813 fragments ===
8:37:30.053941 INFO: performing precursor FDR with 47 features
8:37:30.054087 INFO: Decoy channel: -1
8:37:30.054120 INFO: Competetive: True
8:37:30.735141 INFO: Setting torch num_threads to 2 for FDR classification task
8:37:31.023940 WARNING: dropped 154 target PSMs due to missing features
8:37:31.024098 WARNING: dropped 147 decoy PSMs due to missing features
8:38:02.455212 INFO: Test AUC: 0.570
8:38:02.455378 INFO: Train AUC: 0.586
8:38:02.455411 INFO: AUC difference: 2.69%
8:38:03.044573 INFO: Resetting torch num_threads to 100
8:38:03.182788 INFO: === FDR correction performed with classifier version -1 ===
8:38:03.386568 PROGRESS: ============================= Precursor FDR =============================
8:38:03.386983 PROGRESS: Total precursors accumulated: 721,184
8:38:03.387066 PROGRESS: Target precursors: 441,576 (61.23%)
8:38:03.387123 PROGRESS: Decoy precursors: 279,608 (38.77%)
8:38:03.387171 PROGRESS: 
8:38:03.387217 PROGRESS: Precursor Summary:
8:38:03.396033 PROGRESS: Channel   0:	 0.05 FDR: 8,449; 0.01 FDR: 6,305; 0.001 FDR:    11
8:38:03.396315 PROGRESS: 
8:38:03.396374 PROGRESS: Protein Summary:
8:38:03.404083 PROGRESS: Channel   0:	 0.05 FDR: 4,499; 0.01 FDR: 3,391; 0.001 FDR:    11
8:38:03.404332 PROGRESS: =========================================================================
8:38:04.877021 INFO: fragments_df: keeping 5000 of 14061813 [sum(precursor_idx_mask)=71223 sum(mass_error_mask)=14061811 stop_rank=5000
8:38:05.270083 INFO: calibration group: precursor, fitting mz estimator 
8:38:06.148010 INFO: calibration group: precursor, fitting rt estimator 
8:38:07.036379 INFO: calibration group: precursor, fitting mobility estimator 
8:38:07.902663 INFO: calibration group: fragment, fitting mz estimator 
8:38:08.526823 INFO: Using score_cutoff 52.233686595153806 (fac=0.99, q=1)
8:38:08.527477 INFO: calibration group: precursor, predicting mz
8:38:08.540215 INFO: calibration group: precursor, predicting rt
8:38:08.599663 INFO: calibration group: precursor, predicting mobility
8:38:08.614571 INFO: calibration group: fragment, predicting mz
8:38:08.740010 PROGRESS: Required number of precursors found. Starting search parameter optimization.
8:38:08.740377 INFO: Starting optimization step 12.
8:38:08.740457 PROGRESS: === Extracting elution groups 0 to 51000 ===
8:38:08.740565 PROGRESS: Extracting batch of 100415 precursors
8:38:08.774875 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
8:38:08.775040 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
8:38:08.775111 INFO: FWHM in RT is 3.26 seconds, sigma is 0.72
8:38:08.775138 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.03
8:38:08.784081 INFO: Starting candidate selection
8:47:04.278468 INFO: Starting candidate scoring
8:47:12.950233 INFO: Finished candidate processing
8:47:12.950739 INFO: Collecting candidate features
8:47:13.311697 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 172316)
8:47:13.321898 INFO: Collecting fragment features
8:47:13.438196 INFO: Finished candidate scoring
8:47:13.542956 PROGRESS: === Extracted 172316 precursors and 1752226 fragments ===
8:47:13.543526 INFO: performing precursor FDR with 47 features
8:47:13.543566 INFO: Decoy channel: -1
8:47:13.543593 INFO: Competetive: True
8:47:13.609917 INFO: Setting torch num_threads to 2 for FDR classification task
8:47:13.639544 WARNING: dropped 1 decoy PSMs due to missing features
8:47:16.658851 INFO: Test AUC: 0.565
8:47:16.658972 INFO: Train AUC: 0.605
8:47:16.659002 INFO: AUC difference: 6.63%
8:47:16.659029 WARNING: AUC difference > 5%. This may indicate overfitting.
8:47:16.887983 INFO: Resetting torch num_threads to 100
8:47:16.893646 INFO: === FDR correction performed with classifier version 11 ===
8:47:16.902084 PROGRESS: ============================= Precursor FDR =============================
8:47:16.902359 PROGRESS: Total precursors accumulated: 45,813
8:47:16.902420 PROGRESS: Target precursors: 28,660 (62.56%)
8:47:16.902469 PROGRESS: Decoy precursors: 17,153 (37.44%)
8:47:16.902517 PROGRESS: 
8:47:16.902560 PROGRESS: Precursor Summary:
8:47:16.903868 PROGRESS: Channel   0:	 0.05 FDR:   529; 0.01 FDR:    27; 0.001 FDR:    27
8:47:16.903966 PROGRESS: 
8:47:16.904021 PROGRESS: Protein Summary:
8:47:16.905327 PROGRESS: Channel   0:	 0.05 FDR:   499; 0.01 FDR:    27; 0.001 FDR:    27
8:47:16.905420 PROGRESS: =========================================================================
8:47:17.194783 INFO: calibration group: precursor, predicting mz
8:47:17.208698 INFO: calibration group: precursor, predicting rt
8:47:17.269241 INFO: calibration group: precursor, predicting mobility
8:47:17.284733 INFO: calibration group: fragment, predicting mz
8:47:17.408087 INFO: === skipping optimization until target number of precursors are found ===
8:47:17.408449 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
8:47:17.408530 INFO: Starting optimization step 13.
8:47:17.408622 PROGRESS: === Extracting elution groups 51000 to 102200 ===
8:47:17.408709 PROGRESS: Extracting batch of 100803 precursors
8:47:17.445796 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
8:47:17.445943 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
8:47:17.446004 INFO: FWHM in RT is 3.26 seconds, sigma is 0.72
8:47:17.446034 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.03
8:47:17.447279 INFO: Starting candidate selection
8:56:14.273929 INFO: Starting candidate scoring
8:56:23.259598 INFO: Finished candidate processing
8:56:23.259753 INFO: Collecting candidate features
8:56:23.619193 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 173248)
8:56:23.629189 INFO: Collecting fragment features
8:56:23.736750 INFO: Finished candidate scoring
8:56:24.115090 PROGRESS: === Extracted 345564 precursors and 3517812 fragments ===
8:56:24.210866 INFO: performing precursor FDR with 47 features
8:56:24.211030 INFO: Decoy channel: -1
8:56:24.211059 INFO: Competetive: True
8:56:24.460550 INFO: Setting torch num_threads to 2 for FDR classification task
8:56:24.540766 WARNING: dropped 2 decoy PSMs due to missing features
8:56:32.223034 INFO: Test AUC: 0.569
8:56:32.223294 INFO: Train AUC: 0.591
8:56:32.223329 INFO: AUC difference: 3.76%
8:56:32.506130 INFO: Resetting torch num_threads to 100
8:56:32.527048 INFO: === FDR correction performed with classifier version 11 ===
8:56:32.550405 PROGRESS: ============================= Precursor FDR =============================
8:56:32.550738 PROGRESS: Total precursors accumulated: 91,838
8:56:32.550810 PROGRESS: Target precursors: 57,110 (62.19%)
8:56:32.550863 PROGRESS: Decoy precursors: 34,728 (37.81%)
8:56:32.550909 PROGRESS: 
8:56:32.550954 PROGRESS: Precursor Summary:
8:56:32.552716 PROGRESS: Channel   0:	 0.05 FDR: 1,019; 0.01 FDR:     4; 0.001 FDR:     4
8:56:32.552817 PROGRESS: 
8:56:32.552880 PROGRESS: Protein Summary:
8:56:32.554490 PROGRESS: Channel   0:	 0.05 FDR:   911; 0.01 FDR:     4; 0.001 FDR:     4
8:56:32.554588 PROGRESS: =========================================================================
8:56:32.951010 INFO: calibration group: precursor, predicting mz
8:56:32.977662 INFO: calibration group: precursor, predicting rt
8:56:33.098090 INFO: calibration group: precursor, predicting mobility
8:56:33.124946 INFO: calibration group: fragment, predicting mz
8:56:33.393545 INFO: === skipping optimization until target number of precursors are found ===
8:56:33.393924 PROGRESS: === Optimization of ms2_error has been skipped 2 time(s); maximum number is 1 ===
8:56:33.394017 INFO: Starting optimization step 14.
8:56:33.394089 PROGRESS: === Extracting elution groups 102200 to 204600 ===
8:56:33.394188 PROGRESS: Extracting batch of 201717 precursors
8:56:33.453676 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
8:56:33.453819 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
8:56:33.453881 INFO: FWHM in RT is 3.26 seconds, sigma is 0.72
8:56:33.453905 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.03
8:56:33.455839 INFO: Starting candidate selection
9:14:10.125340 INFO: Starting candidate scoring
9:14:27.817301 INFO: Finished candidate processing
9:14:27.817545 INFO: Collecting candidate features
9:14:28.807084 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 346575)
9:14:28.826573 INFO: Collecting fragment features
9:14:29.074381 INFO: Finished candidate scoring
9:14:29.652276 PROGRESS: === Extracted 692139 precursors and 7040042 fragments ===
9:14:29.735888 INFO: performing precursor FDR with 47 features
9:14:29.736039 INFO: Decoy channel: -1
9:14:29.736074 INFO: Competetive: True
9:14:30.071643 INFO: Setting torch num_threads to 2 for FDR classification task
9:14:30.210468 WARNING: dropped 1 target PSMs due to missing features
9:14:30.210623 WARNING: dropped 4 decoy PSMs due to missing features
9:14:43.593504 INFO: Test AUC: 0.560
9:14:43.593669 INFO: Train AUC: 0.587
9:14:43.593704 INFO: AUC difference: 4.72%
9:14:43.968603 INFO: Resetting torch num_threads to 100
9:14:44.019218 INFO: === FDR correction performed with classifier version 11 ===
9:14:44.063782 PROGRESS: ============================= Precursor FDR =============================
9:14:44.064104 PROGRESS: Total precursors accumulated: 183,876
9:14:44.064171 PROGRESS: Target precursors: 114,459 (62.25%)
9:14:44.064232 PROGRESS: Decoy precursors: 69,417 (37.75%)
9:14:44.064284 PROGRESS: 
9:14:44.064342 PROGRESS: Precursor Summary:
9:14:44.066904 PROGRESS: Channel   0:	 0.05 FDR: 2,069; 0.01 FDR:    30; 0.001 FDR:    30
9:14:44.067005 PROGRESS: 
9:14:44.067077 PROGRESS: Protein Summary:
9:14:44.069356 PROGRESS: Channel   0:	 0.05 FDR: 1,638; 0.01 FDR:    30; 0.001 FDR:    30
9:14:44.069453 PROGRESS: =========================================================================
9:14:44.700929 INFO: calibration group: precursor, predicting mz
9:14:44.760640 INFO: calibration group: precursor, predicting rt
9:14:45.024042 INFO: calibration group: precursor, predicting mobility
9:14:45.078651 INFO: calibration group: fragment, predicting mz
9:14:45.612647 INFO: === skipping optimization until target number of precursors are found ===
9:14:45.612987 PROGRESS: === Optimization of ms2_error has been skipped 3 time(s); maximum number is 1 ===
9:14:45.613068 INFO: Starting optimization step 15.
9:14:45.613139 PROGRESS: === Extracting elution groups 204600 to 409400 ===
9:14:45.613229 PROGRESS: Extracting batch of 403498 precursors
9:14:45.744251 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
9:14:45.744393 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
9:14:45.744447 INFO: FWHM in RT is 3.26 seconds, sigma is 0.72
9:14:45.744469 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.03
9:14:45.745439 INFO: Starting candidate selection
9:49:00.279688 INFO: Starting candidate scoring
9:49:35.343787 INFO: Finished candidate processing
9:49:35.344553 INFO: Collecting candidate features
9:49:36.698842 WARNING: intensity_correlation has 10 NaNs ( 0.00 % out of 693862)
9:49:36.727070 INFO: Collecting fragment features
9:49:37.175096 INFO: Finished candidate scoring
9:49:38.384435 PROGRESS: === Extracted 1386001 precursors and 14098522 fragments ===
9:49:38.572897 INFO: performing precursor FDR with 47 features
9:49:38.573054 INFO: Decoy channel: -1
9:49:38.573083 INFO: Competetive: True
9:49:39.348100 INFO: Setting torch num_threads to 2 for FDR classification task
9:49:39.690684 WARNING: dropped 7 target PSMs due to missing features
9:49:39.690859 WARNING: dropped 8 decoy PSMs due to missing features
9:50:06.739146 INFO: Test AUC: 0.511
9:50:06.739306 INFO: Train AUC: 0.589
9:50:06.739341 INFO: AUC difference: 13.20%
9:50:06.739363 WARNING: AUC difference > 5%. This may indicate overfitting.
9:50:07.303285 INFO: Resetting torch num_threads to 100
9:50:07.400833 INFO: === FDR correction performed with classifier version 11 ===
9:50:07.499358 PROGRESS: ============================= Precursor FDR =============================
9:50:07.499706 PROGRESS: Total precursors accumulated: 367,987
9:50:07.499783 PROGRESS: Target precursors: 231,179 (62.82%)
9:50:07.499833 PROGRESS: Decoy precursors: 136,808 (37.18%)
9:50:07.499879 PROGRESS: 
9:50:07.499927 PROGRESS: Precursor Summary:
9:50:07.505186 PROGRESS: Channel   0:	 0.05 FDR: 4,374; 0.01 FDR: 3,411; 0.001 FDR:   102
9:50:07.505342 PROGRESS: 
9:50:07.505403 PROGRESS: Protein Summary:
9:50:07.509691 PROGRESS: Channel   0:	 0.05 FDR: 2,911; 0.01 FDR: 2,263; 0.001 FDR:   100
9:50:07.509798 PROGRESS: =========================================================================
9:50:08.546311 INFO: fragments_df: keeping 5000 of 14098522 [sum(precursor_idx_mask)=74218 sum(mass_error_mask)=14098520 stop_rank=5000
9:50:08.764084 INFO: calibration group: precursor, fitting mz estimator 
9:50:09.154564 INFO: calibration group: precursor, fitting rt estimator 
9:50:09.549308 INFO: calibration group: precursor, fitting mobility estimator 
9:50:09.933475 INFO: calibration group: fragment, fitting mz estimator 
9:50:10.551751 INFO: Using score_cutoff 51.7135471572876 (fac=0.99, q=1)
9:50:10.552446 INFO: calibration group: precursor, predicting mz
9:50:10.560267 INFO: calibration group: precursor, predicting rt
9:50:10.591490 INFO: calibration group: precursor, predicting mobility
9:50:10.598240 INFO: calibration group: fragment, predicting mz
9:50:10.662589 INFO: === checking if optimization conditions were reached ===
9:50:10.663055 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
9:50:10.666446 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 10.0599.
9:50:10.666517 INFO: ==============================================
9:50:10.666640 INFO: Starting optimization step 16.
9:50:10.666721 PROGRESS: === Extracting elution groups 0 to 25400 ===
9:50:10.666811 PROGRESS: Extracting batch of 49998 precursors
9:50:10.707493 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
9:50:10.707777 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
9:50:10.707857 INFO: FWHM in RT is 3.23 seconds, sigma is 0.71
9:50:10.707891 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.01
9:50:10.720068 INFO: Starting candidate selection
9:54:20.961570 INFO: Starting candidate scoring
9:54:23.895886 INFO: Finished candidate processing
9:54:23.896014 INFO: Collecting candidate features
9:54:24.037443 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 85822)
9:54:24.047831 INFO: Collecting fragment features
9:54:24.105818 INFO: Finished candidate scoring
9:54:24.149843 PROGRESS: === Extracted 85822 precursors and 819678 fragments ===
9:54:24.150456 INFO: performing precursor FDR with 47 features
9:54:24.150496 INFO: Decoy channel: -1
9:54:24.150520 INFO: Competetive: True
9:54:24.193642 INFO: Setting torch num_threads to 2 for FDR classification task
9:54:24.216053 WARNING: dropped 2 target PSMs due to missing features
9:54:24.216205 WARNING: dropped 1 decoy PSMs due to missing features
9:54:25.785733 INFO: Test AUC: 0.566
9:54:25.785881 INFO: Train AUC: 0.598
9:54:25.785911 INFO: AUC difference: 5.24%
9:54:25.785934 WARNING: AUC difference > 5%. This may indicate overfitting.
9:54:25.999036 INFO: Resetting torch num_threads to 100
9:54:26.003420 INFO: === FDR correction performed with classifier version 11 ===
9:54:26.008020 PROGRESS: ============================= Precursor FDR =============================
9:54:26.008183 PROGRESS: Total precursors accumulated: 22,766
9:54:26.008245 PROGRESS: Target precursors: 14,410 (63.30%)
9:54:26.008295 PROGRESS: Decoy precursors: 8,356 (36.70%)
9:54:26.008343 PROGRESS: 
9:54:26.008388 PROGRESS: Precursor Summary:
9:54:26.009860 PROGRESS: Channel   0:	 0.05 FDR:   376; 0.01 FDR:   307; 0.001 FDR:   253
9:54:26.009953 PROGRESS: 
9:54:26.010009 PROGRESS: Protein Summary:
9:54:26.011297 PROGRESS: Channel   0:	 0.05 FDR:   363; 0.01 FDR:   300; 0.001 FDR:   249
9:54:26.011398 PROGRESS: =========================================================================
9:54:26.231031 INFO: fragments_df: keeping 3081 of 819678 [sum(precursor_idx_mask)=6292 sum(mass_error_mask)=819678 stop_rank=3081
9:54:26.368512 INFO: calibration group: precursor, fitting mz estimator 
9:54:26.488215 INFO: calibration group: precursor, fitting rt estimator 
9:54:26.592314 INFO: calibration group: precursor, fitting mobility estimator 
9:54:26.698330 INFO: calibration group: fragment, fitting mz estimator 
9:54:27.039977 INFO: Using score_cutoff 37.13940988082886 (fac=0.99, q=1)
9:54:27.040437 INFO: calibration group: precursor, predicting mz
9:54:27.047842 INFO: calibration group: precursor, predicting rt
9:54:27.077859 INFO: calibration group: precursor, predicting mobility
9:54:27.084562 INFO: calibration group: fragment, predicting mz
9:54:27.221101 INFO: === checking if optimization conditions were reached ===
9:54:27.221489 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
9:54:27.224250 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 6.9379.
9:54:27.224330 INFO: ==============================================
9:54:27.224484 INFO: Starting optimization step 17.
9:54:27.224571 PROGRESS: === Extracting elution groups 0 to 25400 ===
9:54:27.224662 PROGRESS: Extracting batch of 49998 precursors
9:54:27.243622 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
9:54:27.243744 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
9:54:27.243801 INFO: FWHM in RT is 2.69 seconds, sigma is 0.59
9:54:27.243825 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.57
9:54:27.244741 INFO: Starting candidate selection
9:58:23.666411 INFO: Starting candidate scoring
9:58:25.749011 INFO: Finished candidate processing
9:58:25.749135 INFO: Collecting candidate features
9:58:25.882460 WARNING: intensity_correlation has 24 NaNs ( 0.03 % out of 85481)
9:58:25.882837 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 85481)
9:58:25.891617 INFO: Collecting fragment features
9:58:25.949716 INFO: Finished candidate scoring
9:58:25.991490 PROGRESS: === Extracted 85481 precursors and 768540 fragments ===
9:58:25.992009 INFO: performing precursor FDR with 47 features
9:58:25.992048 INFO: Decoy channel: -1
9:58:25.992071 INFO: Competetive: True
9:58:26.025648 INFO: Setting torch num_threads to 2 for FDR classification task
9:58:26.045294 WARNING: dropped 13 target PSMs due to missing features
9:58:26.045439 WARNING: dropped 11 decoy PSMs due to missing features
9:58:27.792405 INFO: Test AUC: 0.564
9:58:27.792562 INFO: Train AUC: 0.594
9:58:27.792593 INFO: AUC difference: 5.16%
9:58:27.792614 WARNING: AUC difference > 5%. This may indicate overfitting.
9:58:28.065041 INFO: Resetting torch num_threads to 100
9:58:28.080325 INFO: === FDR correction performed with classifier version 11 ===
9:58:28.097363 PROGRESS: ============================= Precursor FDR =============================
9:58:28.097809 PROGRESS: Total precursors accumulated: 22,768
9:58:28.097882 PROGRESS: Target precursors: 14,228 (62.49%)
9:58:28.097934 PROGRESS: Decoy precursors: 8,540 (37.51%)
9:58:28.097981 PROGRESS: 
9:58:28.098041 PROGRESS: Precursor Summary:
9:58:28.099954 PROGRESS: Channel   0:	 0.05 FDR:   304; 0.01 FDR:   165; 0.001 FDR:   138
9:58:28.100148 PROGRESS: 
9:58:28.100211 PROGRESS: Protein Summary:
9:58:28.101511 PROGRESS: Channel   0:	 0.05 FDR:   296; 0.01 FDR:   163; 0.001 FDR:   138
9:58:28.101610 PROGRESS: =========================================================================
9:58:28.377182 INFO: calibration group: precursor, predicting mz
9:58:28.385380 INFO: calibration group: precursor, predicting rt
9:58:28.416291 INFO: calibration group: precursor, predicting mobility
9:58:28.423226 INFO: calibration group: fragment, predicting mz
9:58:28.482273 INFO: === skipping optimization until target number of precursors are found ===
9:58:28.482570 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
9:58:28.482651 INFO: Starting optimization step 18.
9:58:28.482725 PROGRESS: === Extracting elution groups 25400 to 51000 ===
9:58:28.482800 PROGRESS: Extracting batch of 50417 precursors
9:58:28.498058 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
9:58:28.498182 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
9:58:28.498238 INFO: FWHM in RT is 2.69 seconds, sigma is 0.59
9:58:28.498262 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.57
9:58:28.499496 INFO: Starting candidate selection
10:02:38.307723 INFO: Starting candidate scoring
10:02:40.402356 INFO: Finished candidate processing
10:02:40.403623 INFO: Collecting candidate features
10:02:40.629804 WARNING: intensity_correlation has 28 NaNs ( 0.03 % out of 86404)
10:02:40.641592 INFO: Collecting fragment features
10:02:40.704431 INFO: Finished candidate scoring
10:02:40.863054 PROGRESS: === Extracted 171885 precursors and 1545388 fragments ===
10:02:40.901999 INFO: performing precursor FDR with 47 features
10:02:40.902196 INFO: Decoy channel: -1
10:02:40.902224 INFO: Competetive: True
10:02:41.151620 INFO: Setting torch num_threads to 2 for FDR classification task
10:02:41.252249 WARNING: dropped 31 target PSMs due to missing features
10:02:41.252499 WARNING: dropped 21 decoy PSMs due to missing features
10:02:45.275304 INFO: Test AUC: 0.561
10:02:45.275648 INFO: Train AUC: 0.596
10:02:45.275685 INFO: AUC difference: 5.83%
10:02:45.275711 WARNING: AUC difference > 5%. This may indicate overfitting.
10:02:45.506794 INFO: Resetting torch num_threads to 100
10:02:45.515372 INFO: === FDR correction performed with classifier version 11 ===
10:02:45.523860 PROGRESS: ============================= Precursor FDR =============================
10:02:45.524132 PROGRESS: Total precursors accumulated: 45,696
10:02:45.524195 PROGRESS: Target precursors: 28,681 (62.76%)
10:02:45.524245 PROGRESS: Decoy precursors: 17,015 (37.24%)
10:02:45.524291 PROGRESS: 
10:02:45.524335 PROGRESS: Precursor Summary:
10:02:45.525659 PROGRESS: Channel   0:	 0.05 FDR:   642; 0.01 FDR:   124; 0.001 FDR:   100
10:02:45.525766 PROGRESS: 
10:02:45.525824 PROGRESS: Protein Summary:
10:02:45.527167 PROGRESS: Channel   0:	 0.05 FDR:   605; 0.01 FDR:   124; 0.001 FDR:   100
10:02:45.527265 PROGRESS: =========================================================================
10:02:45.887292 INFO: calibration group: precursor, predicting mz
10:02:45.901895 INFO: calibration group: precursor, predicting rt
10:02:45.962503 INFO: calibration group: precursor, predicting mobility
10:02:45.978721 INFO: calibration group: fragment, predicting mz
10:02:46.104717 INFO: === skipping optimization until target number of precursors are found ===
10:02:46.105061 PROGRESS: === Optimization of ms2_error has been skipped 2 time(s); maximum number is 1 ===
10:02:46.105478 PROGRESS: ✅ ms2_error      : optimization complete. Optimal parameter 10.0599 found after 2 searches.
10:02:46.105555 PROGRESS: Optimization finished for ms2_error.
10:02:46.252496 INFO: calibration group: precursor, predicting mz
10:02:46.260489 INFO: calibration group: precursor, predicting rt
10:02:46.290680 INFO: calibration group: precursor, predicting mobility
10:02:46.297652 INFO: calibration group: fragment, predicting mz
10:02:46.384760 INFO: Starting optimization step 0.
10:02:46.385092 PROGRESS: === Extracting elution groups 0 to 25400 ===
10:02:46.385189 PROGRESS: Extracting batch of 49998 precursors
10:02:46.400562 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:02:46.400682 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:02:46.400737 INFO: FWHM in RT is 2.69 seconds, sigma is 0.59
10:02:46.400762 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.57
10:02:46.412230 INFO: Starting candidate selection
10:07:01.200299 INFO: Starting candidate scoring
10:07:04.170490 INFO: Finished candidate processing
10:07:04.170633 INFO: Collecting candidate features
10:07:04.351811 WARNING: intensity_correlation has 7 NaNs ( 0.01 % out of 85802)
10:07:04.352219 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 85802)
10:07:04.360754 INFO: Collecting fragment features
10:07:04.421935 INFO: Finished candidate scoring
10:07:04.467311 PROGRESS: === Extracted 85802 precursors and 813802 fragments ===
10:07:04.467822 INFO: performing precursor FDR with 47 features
10:07:04.467862 INFO: Decoy channel: -1
10:07:04.467886 INFO: Competetive: True
10:07:04.501417 INFO: Setting torch num_threads to 2 for FDR classification task
10:07:04.520438 WARNING: dropped 5 target PSMs due to missing features
10:07:04.520576 WARNING: dropped 2 decoy PSMs due to missing features
10:07:05.909157 INFO: Test AUC: 0.568
10:07:05.909284 INFO: Train AUC: 0.626
10:07:05.909314 INFO: AUC difference: 9.35%
10:07:05.909334 WARNING: AUC difference > 5%. This may indicate overfitting.
10:07:06.114952 INFO: Resetting torch num_threads to 100
10:07:06.118526 INFO: === FDR correction performed with classifier version 16 ===
10:07:06.122577 PROGRESS: ============================= Precursor FDR =============================
10:07:06.122733 PROGRESS: Total precursors accumulated: 22,802
10:07:06.122797 PROGRESS: Target precursors: 14,836 (65.06%)
10:07:06.122848 PROGRESS: Decoy precursors: 7,966 (34.94%)
10:07:06.122894 PROGRESS: 
10:07:06.122938 PROGRESS: Precursor Summary:
10:07:06.124048 PROGRESS: Channel   0:	 0.05 FDR:   328; 0.01 FDR:   126; 0.001 FDR:    73
10:07:06.124141 PROGRESS: 
10:07:06.124202 PROGRESS: Protein Summary:
10:07:06.125338 PROGRESS: Channel   0:	 0.05 FDR:   319; 0.01 FDR:   126; 0.001 FDR:    73
10:07:06.125430 PROGRESS: =========================================================================
10:07:06.293674 INFO: calibration group: precursor, predicting mz
10:07:06.301734 INFO: calibration group: precursor, predicting rt
10:07:06.331816 INFO: calibration group: precursor, predicting mobility
10:07:06.338845 INFO: calibration group: fragment, predicting mz
10:07:06.413298 INFO: === skipping optimization until target number of precursors are found ===
10:07:06.413650 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
10:07:06.413726 INFO: Starting optimization step 1.
10:07:06.413806 PROGRESS: === Extracting elution groups 25400 to 51000 ===
10:07:06.413888 PROGRESS: Extracting batch of 50417 precursors
10:07:06.434847 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:07:06.434991 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:07:06.435058 INFO: FWHM in RT is 2.69 seconds, sigma is 0.59
10:07:06.435090 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.57
10:07:06.515312 INFO: Starting candidate selection
10:11:46.417241 INFO: Starting candidate scoring
10:11:49.535445 INFO: Finished candidate processing
10:11:49.535746 INFO: Collecting candidate features
10:11:49.802551 WARNING: intensity_correlation has 9 NaNs ( 0.01 % out of 86570)
10:11:49.809641 INFO: Collecting fragment features
10:11:49.881394 INFO: Finished candidate scoring
10:11:50.071049 PROGRESS: === Extracted 172372 precursors and 1635330 fragments ===
10:11:50.102059 INFO: performing precursor FDR with 47 features
10:11:50.102206 INFO: Decoy channel: -1
10:11:50.102232 INFO: Competetive: True
10:11:50.211839 INFO: Setting torch num_threads to 2 for FDR classification task
10:11:50.256180 WARNING: dropped 10 target PSMs due to missing features
10:11:50.256353 WARNING: dropped 6 decoy PSMs due to missing features
10:11:53.457723 INFO: Test AUC: 0.566
10:11:53.457861 INFO: Train AUC: 0.614
10:11:53.457893 INFO: AUC difference: 7.90%
10:11:53.457915 WARNING: AUC difference > 5%. This may indicate overfitting.
10:11:53.686951 INFO: Resetting torch num_threads to 100
10:11:53.695041 INFO: === FDR correction performed with classifier version 16 ===
10:11:53.703765 PROGRESS: ============================= Precursor FDR =============================
10:11:53.704045 PROGRESS: Total precursors accumulated: 45,766
10:11:53.704109 PROGRESS: Target precursors: 29,352 (64.13%)
10:11:53.704161 PROGRESS: Decoy precursors: 16,414 (35.87%)
10:11:53.704209 PROGRESS: 
10:11:53.704268 PROGRESS: Precursor Summary:
10:11:53.705658 PROGRESS: Channel   0:	 0.05 FDR:   710; 0.01 FDR:    13; 0.001 FDR:    13
10:11:53.705757 PROGRESS: 
10:11:53.705815 PROGRESS: Protein Summary:
10:11:53.707149 PROGRESS: Channel   0:	 0.05 FDR:   662; 0.01 FDR:    13; 0.001 FDR:    13
10:11:53.707250 PROGRESS: =========================================================================
10:11:53.978240 INFO: calibration group: precursor, predicting mz
10:11:53.992308 INFO: calibration group: precursor, predicting rt
10:11:54.053767 INFO: calibration group: precursor, predicting mobility
10:11:54.069418 INFO: calibration group: fragment, predicting mz
10:11:54.197020 INFO: === skipping optimization until target number of precursors are found ===
10:11:54.197392 PROGRESS: === Optimization of rt_error has been skipped 2 time(s); maximum number is 1 ===
10:11:54.197473 INFO: Starting optimization step 2.
10:11:54.197552 PROGRESS: === Extracting elution groups 51000 to 102200 ===
10:11:54.197639 PROGRESS: Extracting batch of 100803 precursors
10:11:54.235088 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:11:54.235261 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:11:54.235330 INFO: FWHM in RT is 2.69 seconds, sigma is 0.59
10:11:54.235370 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.57
10:11:54.282449 INFO: Starting candidate selection
10:21:02.532944 INFO: Starting candidate scoring
10:21:07.548339 INFO: Finished candidate processing
10:21:07.548471 INFO: Collecting candidate features
10:21:07.856986 WARNING: intensity_correlation has 13 NaNs ( 0.01 % out of 173329)
10:21:07.866737 INFO: Collecting fragment features
10:21:07.984586 INFO: Finished candidate scoring
10:21:08.273046 PROGRESS: === Extracted 345701 precursors and 3284052 fragments ===
10:21:08.319429 INFO: performing precursor FDR with 47 features
10:21:08.319599 INFO: Decoy channel: -1
10:21:08.319625 INFO: Competetive: True
10:21:08.529008 INFO: Setting torch num_threads to 2 for FDR classification task
10:21:08.611916 WARNING: dropped 14 target PSMs due to missing features
10:21:08.612080 WARNING: dropped 15 decoy PSMs due to missing features
10:21:16.049991 INFO: Test AUC: 0.567
10:21:16.050682 INFO: Train AUC: 0.602
10:21:16.050725 INFO: AUC difference: 5.87%
10:21:16.050749 WARNING: AUC difference > 5%. This may indicate overfitting.
10:21:16.340073 INFO: Resetting torch num_threads to 100
10:21:16.364280 INFO: === FDR correction performed with classifier version 16 ===
10:21:16.386664 PROGRESS: ============================= Precursor FDR =============================
10:21:16.386999 PROGRESS: Total precursors accumulated: 91,750
10:21:16.387080 PROGRESS: Target precursors: 58,027 (63.24%)
10:21:16.387151 PROGRESS: Decoy precursors: 33,723 (36.76%)
10:21:16.387207 PROGRESS: 
10:21:16.387253 PROGRESS: Precursor Summary:
10:21:16.389180 PROGRESS: Channel   0:	 0.05 FDR: 1,289; 0.01 FDR:    47; 0.001 FDR:    47
10:21:16.389304 PROGRESS: 
10:21:16.389365 PROGRESS: Protein Summary:
10:21:16.391131 PROGRESS: Channel   0:	 0.05 FDR: 1,124; 0.01 FDR:    47; 0.001 FDR:    47
10:21:16.391244 PROGRESS: =========================================================================
10:21:17.066990 INFO: calibration group: precursor, predicting mz
10:21:17.094193 INFO: calibration group: precursor, predicting rt
10:21:17.216949 INFO: calibration group: precursor, predicting mobility
10:21:17.249018 INFO: calibration group: fragment, predicting mz
10:21:17.497224 INFO: === skipping optimization until target number of precursors are found ===
10:21:17.497619 PROGRESS: === Optimization of rt_error has been skipped 3 time(s); maximum number is 1 ===
10:21:17.497714 INFO: Starting optimization step 3.
10:21:17.497789 PROGRESS: === Extracting elution groups 102200 to 204600 ===
10:21:17.497900 PROGRESS: Extracting batch of 201717 precursors
10:21:17.560481 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:21:17.560639 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:21:17.560711 INFO: FWHM in RT is 2.69 seconds, sigma is 0.59
10:21:17.560750 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.57
10:21:17.561774 INFO: Starting candidate selection
10:37:48.557393 INFO: Starting candidate scoring
10:37:59.418523 INFO: Finished candidate processing
10:37:59.418645 INFO: Collecting candidate features
10:38:00.124110 WARNING: intensity_correlation has 19 NaNs ( 0.01 % out of 346614)
10:38:00.124688 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 346614)
10:38:00.139726 INFO: Collecting fragment features
10:38:00.378896 INFO: Finished candidate scoring
10:38:00.982589 PROGRESS: === Extracted 692315 precursors and 6569265 fragments ===
10:38:01.120557 INFO: performing precursor FDR with 47 features
10:38:01.120759 INFO: Decoy channel: -1
10:38:01.120806 INFO: Competetive: True
10:38:01.617819 INFO: Setting torch num_threads to 2 for FDR classification task
10:38:01.811009 WARNING: dropped 25 target PSMs due to missing features
10:38:01.811192 WARNING: dropped 23 decoy PSMs due to missing features
10:38:15.834934 INFO: Test AUC: 0.570
10:38:15.835095 INFO: Train AUC: 0.593
10:38:15.835128 INFO: AUC difference: 4.04%
10:38:16.203204 INFO: Resetting torch num_threads to 100
10:38:16.238287 INFO: === FDR correction performed with classifier version 16 ===
10:38:16.273742 PROGRESS: ============================= Precursor FDR =============================
10:38:16.274058 PROGRESS: Total precursors accumulated: 183,706
10:38:16.274127 PROGRESS: Target precursors: 115,455 (62.85%)
10:38:16.274179 PROGRESS: Decoy precursors: 68,251 (37.15%)
10:38:16.274227 PROGRESS: 
10:38:16.274272 PROGRESS: Precursor Summary:
10:38:16.277045 PROGRESS: Channel   0:	 0.05 FDR: 2,630; 0.01 FDR:   503; 0.001 FDR:    81
10:38:16.277189 PROGRESS: 
10:38:16.277248 PROGRESS: Protein Summary:
10:38:16.279778 PROGRESS: Channel   0:	 0.05 FDR: 2,058; 0.01 FDR:   467; 0.001 FDR:    78
10:38:16.279881 PROGRESS: =========================================================================
10:38:16.748735 INFO: fragments_df: keeping 5000 of 6569265 [sum(precursor_idx_mask)=10709 sum(mass_error_mask)=6569265 stop_rank=5000
10:38:17.179784 INFO: calibration group: precursor, fitting mz estimator 
10:38:17.320304 INFO: calibration group: precursor, fitting rt estimator 
10:38:17.456773 INFO: calibration group: precursor, fitting mobility estimator 
10:38:17.594368 INFO: calibration group: fragment, fitting mz estimator 
10:38:18.255490 INFO: Using score_cutoff 45.18904638977051 (fac=0.99, q=1)
10:38:18.255917 INFO: calibration group: precursor, predicting mz
10:38:18.282173 INFO: calibration group: precursor, predicting rt
10:38:18.401327 INFO: calibration group: precursor, predicting mobility
10:38:18.427990 INFO: calibration group: fragment, predicting mz
10:38:18.669062 INFO: === checking if optimization conditions were reached ===
10:38:18.669388 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
10:38:18.671464 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 488.8174.
10:38:18.671520 INFO: ==============================================
10:38:18.671620 INFO: Starting optimization step 4.
10:38:18.671688 PROGRESS: === Extracting elution groups 0 to 102200 ===
10:38:18.671764 PROGRESS: Extracting batch of 201218 precursors
10:38:18.723926 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:38:18.724065 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:38:18.724117 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
10:38:18.724140 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.66
10:38:18.724968 INFO: Starting candidate selection
10:42:04.277892 INFO: Starting candidate scoring
10:42:13.625621 INFO: Finished candidate processing
10:42:13.626626 INFO: Collecting candidate features
10:42:14.327096 WARNING: intensity_correlation has 168 NaNs ( 0.05 % out of 334540)
10:42:14.327631 WARNING: height_correlation has 10 NaNs ( 0.00 % out of 334540)
10:42:14.341795 INFO: Collecting fragment features
10:42:14.568349 INFO: Finished candidate scoring
10:42:14.779460 PROGRESS: === Extracted 334540 precursors and 3115634 fragments ===
10:42:14.779960 INFO: performing precursor FDR with 47 features
10:42:14.780001 INFO: Decoy channel: -1
10:42:14.780025 INFO: Competetive: True
10:42:14.906052 INFO: Setting torch num_threads to 2 for FDR classification task
10:42:14.983669 WARNING: dropped 75 target PSMs due to missing features
10:42:14.983819 WARNING: dropped 98 decoy PSMs due to missing features
10:42:22.243174 INFO: Test AUC: 0.563
10:42:22.243312 INFO: Train AUC: 0.591
10:42:22.243343 INFO: AUC difference: 4.78%
10:42:22.526058 INFO: Resetting torch num_threads to 100
10:42:22.538866 INFO: === FDR correction performed with classifier version 16 ===
10:42:22.558938 PROGRESS: ============================= Precursor FDR =============================
10:42:22.559282 PROGRESS: Total precursors accumulated: 89,957
10:42:22.559349 PROGRESS: Target precursors: 55,550 (61.75%)
10:42:22.559398 PROGRESS: Decoy precursors: 34,407 (38.25%)
10:42:22.559457 PROGRESS: 
10:42:22.559502 PROGRESS: Precursor Summary:
10:42:22.561356 PROGRESS: Channel   0:	 0.05 FDR: 1,416; 0.01 FDR:   107; 0.001 FDR:    81
10:42:22.561451 PROGRESS: 
10:42:22.561510 PROGRESS: Protein Summary:
10:42:22.563231 PROGRESS: Channel   0:	 0.05 FDR: 1,236; 0.01 FDR:   106; 0.001 FDR:    80
10:42:22.563329 PROGRESS: =========================================================================
10:42:23.254657 INFO: calibration group: precursor, predicting mz
10:42:23.281241 INFO: calibration group: precursor, predicting rt
10:42:23.402716 INFO: calibration group: precursor, predicting mobility
10:42:23.430585 INFO: calibration group: fragment, predicting mz
10:42:23.686085 INFO: === skipping optimization until target number of precursors are found ===
10:42:23.686462 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
10:42:23.686551 INFO: Starting optimization step 5.
10:42:23.686625 PROGRESS: === Extracting elution groups 102200 to 204600 ===
10:42:23.686723 PROGRESS: Extracting batch of 201717 precursors
10:42:23.745586 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:42:23.745729 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:42:23.745797 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
10:42:23.745822 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.66
10:42:23.760435 INFO: Starting candidate selection
10:46:10.865705 INFO: Starting candidate scoring
10:46:23.114921 INFO: Finished candidate processing
10:46:23.115143 INFO: Collecting candidate features
10:46:23.900087 WARNING: intensity_correlation has 166 NaNs ( 0.05 % out of 335038)
10:46:23.900662 WARNING: height_correlation has 11 NaNs ( 0.00 % out of 335038)
10:46:23.915028 INFO: Collecting fragment features
10:46:24.144656 INFO: Finished candidate scoring
10:46:24.560515 PROGRESS: === Extracted 669578 precursors and 6228869 fragments ===
10:46:24.632331 INFO: performing precursor FDR with 47 features
10:46:24.632473 INFO: Decoy channel: -1
10:46:24.632513 INFO: Competetive: True
10:46:24.933915 INFO: Setting torch num_threads to 2 for FDR classification task
10:46:25.066606 WARNING: dropped 161 target PSMs due to missing features
10:46:25.066754 WARNING: dropped 185 decoy PSMs due to missing features
10:46:36.608206 INFO: Test AUC: 0.556
10:46:36.608365 INFO: Train AUC: 0.585
10:46:36.608400 INFO: AUC difference: 5.00%
10:46:36.608421 WARNING: AUC difference > 5%. This may indicate overfitting.
10:46:36.983144 INFO: Resetting torch num_threads to 100
10:46:37.015291 INFO: === FDR correction performed with classifier version 16 ===
10:46:37.046862 PROGRESS: ============================= Precursor FDR =============================
10:46:37.047173 PROGRESS: Total precursors accumulated: 180,196
10:46:37.047244 PROGRESS: Target precursors: 110,728 (61.45%)
10:46:37.047324 PROGRESS: Decoy precursors: 69,468 (38.55%)
10:46:37.047374 PROGRESS: 
10:46:37.047423 PROGRESS: Precursor Summary:
10:46:37.049957 PROGRESS: Channel   0:	 0.05 FDR: 2,814; 0.01 FDR:    14; 0.001 FDR:    14
10:46:37.050110 PROGRESS: 
10:46:37.050173 PROGRESS: Protein Summary:
10:46:37.052628 PROGRESS: Channel   0:	 0.05 FDR: 2,185; 0.01 FDR:    14; 0.001 FDR:    14
10:46:37.052729 PROGRESS: =========================================================================
10:46:37.760750 INFO: calibration group: precursor, predicting mz
10:46:37.810525 INFO: calibration group: precursor, predicting rt
10:46:38.060374 INFO: calibration group: precursor, predicting mobility
10:46:38.119939 INFO: calibration group: fragment, predicting mz
10:46:38.578966 INFO: === skipping optimization until target number of precursors are found ===
10:46:38.579390 PROGRESS: === Optimization of rt_error has been skipped 2 time(s); maximum number is 1 ===
10:46:38.579503 INFO: Starting optimization step 6.
10:46:38.579586 PROGRESS: === Extracting elution groups 204600 to 409400 ===
10:46:38.579691 PROGRESS: Extracting batch of 403498 precursors
10:46:38.674241 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:46:38.674388 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:46:38.674453 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
10:46:38.674478 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.66
10:46:38.675612 INFO: Starting candidate selection
10:54:10.808122 INFO: Starting candidate scoring
10:54:31.151822 INFO: Finished candidate processing
10:54:31.153617 INFO: Collecting candidate features
10:54:33.192558 WARNING: intensity_correlation has 332 NaNs ( 0.05 % out of 671091)
10:54:33.193403 WARNING: height_correlation has 24 NaNs ( 0.00 % out of 671091)
10:54:33.218782 INFO: Collecting fragment features
10:54:33.662883 INFO: Finished candidate scoring
10:54:35.715094 PROGRESS: === Extracted 1340669 precursors and 12470653 fragments ===
10:54:35.895783 INFO: performing precursor FDR with 47 features
10:54:35.895950 INFO: Decoy channel: -1
10:54:35.895982 INFO: Competetive: True
10:54:36.644863 INFO: Setting torch num_threads to 2 for FDR classification task
10:54:36.969112 WARNING: dropped 328 target PSMs due to missing features
10:54:36.969275 WARNING: dropped 362 decoy PSMs due to missing features
10:55:04.075463 INFO: Test AUC: 0.514
10:55:04.075705 INFO: Train AUC: 0.582
10:55:04.075740 INFO: AUC difference: 11.58%
10:55:04.075773 WARNING: AUC difference > 5%. This may indicate overfitting.
10:55:04.649616 INFO: Resetting torch num_threads to 100
10:55:04.736669 INFO: === FDR correction performed with classifier version 16 ===
10:55:04.815192 PROGRESS: ============================= Precursor FDR =============================
10:55:04.815553 PROGRESS: Total precursors accumulated: 360,637
10:55:04.815630 PROGRESS: Target precursors: 221,506 (61.42%)
10:55:04.815683 PROGRESS: Decoy precursors: 139,131 (38.58%)
10:55:04.815728 PROGRESS: 
10:55:04.815774 PROGRESS: Precursor Summary:
10:55:04.819979 PROGRESS: Channel   0:	 0.05 FDR: 5,709; 0.01 FDR:    32; 0.001 FDR:    32
10:55:04.820137 PROGRESS: 
10:55:04.820195 PROGRESS: Protein Summary:
10:55:04.824186 PROGRESS: Channel   0:	 0.05 FDR: 3,629; 0.01 FDR:    31; 0.001 FDR:    31
10:55:04.824300 PROGRESS: =========================================================================
10:55:05.818445 INFO: calibration group: precursor, predicting mz
10:55:05.921891 INFO: calibration group: precursor, predicting rt
10:55:06.428829 INFO: calibration group: precursor, predicting mobility
10:55:06.551935 INFO: calibration group: fragment, predicting mz
10:55:07.616069 INFO: === skipping optimization until target number of precursors are found ===
10:55:07.616488 PROGRESS: === Optimization of rt_error has been skipped 3 time(s); maximum number is 1 ===
10:55:07.616608 INFO: Starting optimization step 7.
10:55:07.616728 PROGRESS: === Extracting elution groups 409400 to 819000 ===
10:55:07.616824 PROGRESS: Extracting batch of 806744 precursors
10:55:08.121639 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:55:08.121931 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:55:08.122011 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
10:55:08.122044 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.66
10:55:08.124327 INFO: Starting candidate selection
11:10:13.518580 INFO: Starting candidate scoring
11:10:48.633877 INFO: Finished candidate processing
11:10:48.634315 INFO: Collecting candidate features
11:10:51.557070 WARNING: intensity_correlation has 661 NaNs ( 0.05 % out of 1339167)
11:10:51.558499 WARNING: height_correlation has 39 NaNs ( 0.00 % out of 1339167)
11:10:51.603567 INFO: Collecting fragment features
11:10:52.493838 INFO: Finished candidate scoring
11:10:54.431614 PROGRESS: === Extracted 2679836 precursors and 24931813 fragments ===
11:10:54.733817 INFO: performing precursor FDR with 47 features
11:10:54.733972 INFO: Decoy channel: -1
11:10:54.734009 INFO: Competetive: True
11:10:55.953460 INFO: Setting torch num_threads to 2 for FDR classification task
11:10:56.478181 WARNING: dropped 692 target PSMs due to missing features
11:10:56.478339 WARNING: dropped 680 decoy PSMs due to missing features
11:11:54.749309 INFO: Test AUC: 0.569
11:11:54.749857 INFO: Train AUC: 0.578
11:11:54.749898 INFO: AUC difference: 1.47%
11:11:55.673798 INFO: Resetting torch num_threads to 100
11:11:55.911571 INFO: === FDR correction performed with classifier version 16 ===
11:11:56.105514 PROGRESS: ============================= Precursor FDR =============================
11:11:56.105869 PROGRESS: Total precursors accumulated: 720,984
11:11:56.105935 PROGRESS: Target precursors: 440,753 (61.13%)
11:11:56.105985 PROGRESS: Decoy precursors: 280,231 (38.87%)
11:11:56.106030 PROGRESS: 
11:11:56.106095 PROGRESS: Precursor Summary:
11:11:56.113996 PROGRESS: Channel   0:	 0.05 FDR: 11,894; 0.01 FDR: 3,549; 0.001 FDR:    88
11:11:56.114129 PROGRESS: 
11:11:56.114187 PROGRESS: Protein Summary:
11:11:56.121706 PROGRESS: Channel   0:	 0.05 FDR: 5,788; 0.01 FDR: 2,448; 0.001 FDR:    80
11:11:56.121829 PROGRESS: =========================================================================
11:11:57.899789 INFO: fragments_df: keeping 5000 of 24931813 [sum(precursor_idx_mask)=74529 sum(mass_error_mask)=24931810 stop_rank=5000
11:11:58.421766 INFO: calibration group: precursor, fitting mz estimator 
11:11:58.891953 INFO: calibration group: precursor, fitting rt estimator 
11:11:59.396360 INFO: calibration group: precursor, fitting mobility estimator 
11:11:59.872549 INFO: calibration group: fragment, fitting mz estimator 
11:12:00.563229 INFO: Using score_cutoff 42.08357624359131 (fac=0.99, q=1)
11:12:00.563828 INFO: calibration group: precursor, predicting mz
11:12:00.577590 INFO: calibration group: precursor, predicting rt
11:12:00.642090 INFO: calibration group: precursor, predicting mobility
11:12:00.657620 INFO: calibration group: fragment, predicting mz
11:12:00.785507 INFO: === checking if optimization conditions were reached ===
11:12:00.786119 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
11:12:00.791816 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 211.9020.
11:12:00.792022 INFO: ==============================================
11:12:00.792382 INFO: Starting optimization step 8.
11:12:00.792640 PROGRESS: === Extracting elution groups 0 to 51000 ===
11:12:00.792910 PROGRESS: Extracting batch of 100415 precursors
11:12:00.846168 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:12:00.846448 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:12:00.846546 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
11:12:00.846610 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.56
11:12:00.879300 INFO: Starting candidate selection
11:12:53.171267 INFO: Starting candidate scoring
11:12:58.439506 INFO: Finished candidate processing
11:12:58.439649 INFO: Collecting candidate features
11:12:58.875397 WARNING: intensity_correlation has 120 NaNs ( 0.07 % out of 163886)
11:12:58.875802 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 163886)
11:12:58.885065 INFO: Collecting fragment features
11:12:58.985052 INFO: Finished candidate scoring
11:12:59.094443 PROGRESS: === Extracted 163886 precursors and 1499099 fragments ===
11:12:59.095012 INFO: performing precursor FDR with 47 features
11:12:59.095065 INFO: Decoy channel: -1
11:12:59.095090 INFO: Competetive: True
11:12:59.162546 INFO: Setting torch num_threads to 2 for FDR classification task
11:12:59.201471 WARNING: dropped 60 target PSMs due to missing features
11:12:59.201621 WARNING: dropped 62 decoy PSMs due to missing features
11:13:02.373139 INFO: Test AUC: 0.559
11:13:02.373313 INFO: Train AUC: 0.607
11:13:02.373345 INFO: AUC difference: 7.91%
11:13:02.373367 WARNING: AUC difference > 5%. This may indicate overfitting.
11:13:02.608404 INFO: Resetting torch num_threads to 100
11:13:02.623229 INFO: === FDR correction performed with classifier version 16 ===
11:13:02.638588 PROGRESS: ============================= Precursor FDR =============================
11:13:02.638942 PROGRESS: Total precursors accumulated: 44,309
11:13:02.639014 PROGRESS: Target precursors: 27,891 (62.95%)
11:13:02.639090 PROGRESS: Decoy precursors: 16,418 (37.05%)
11:13:02.639145 PROGRESS: 
11:13:02.639199 PROGRESS: Precursor Summary:
11:13:02.640721 PROGRESS: Channel   0:	 0.05 FDR:   714; 0.01 FDR:    58; 0.001 FDR:    58
11:13:02.640823 PROGRESS: 
11:13:02.640887 PROGRESS: Protein Summary:
11:13:02.642289 PROGRESS: Channel   0:	 0.05 FDR:   664; 0.01 FDR:    57; 0.001 FDR:    57
11:13:02.642388 PROGRESS: =========================================================================
11:13:03.021450 INFO: calibration group: precursor, predicting mz
11:13:03.035981 INFO: calibration group: precursor, predicting rt
11:13:03.101272 INFO: calibration group: precursor, predicting mobility
11:13:03.118707 INFO: calibration group: fragment, predicting mz
11:13:03.242481 INFO: === skipping optimization until target number of precursors are found ===
11:13:03.242976 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
11:13:03.243102 INFO: Starting optimization step 9.
11:13:03.243191 PROGRESS: === Extracting elution groups 51000 to 102200 ===
11:13:03.243329 PROGRESS: Extracting batch of 100803 precursors
11:13:03.321452 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:13:03.321750 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:13:03.321853 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
11:13:03.321882 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.56
11:13:03.334610 INFO: Starting candidate selection
11:13:53.516352 INFO: Starting candidate scoring
11:13:58.373340 INFO: Finished candidate processing
11:13:58.373455 INFO: Collecting candidate features
11:13:58.671195 WARNING: intensity_correlation has 143 NaNs ( 0.09 % out of 164790)
11:13:58.671609 WARNING: height_correlation has 11 NaNs ( 0.01 % out of 164790)
11:13:58.680831 INFO: Collecting fragment features
11:13:58.797087 INFO: Finished candidate scoring
11:13:59.089102 PROGRESS: === Extracted 328676 precursors and 3012133 fragments ===
11:13:59.149904 INFO: performing precursor FDR with 47 features
11:13:59.150101 INFO: Decoy channel: -1
11:13:59.150132 INFO: Competetive: True
11:13:59.326655 INFO: Setting torch num_threads to 2 for FDR classification task
11:13:59.402121 WARNING: dropped 132 target PSMs due to missing features
11:13:59.402282 WARNING: dropped 138 decoy PSMs due to missing features
11:14:06.372130 INFO: Test AUC: 0.555
11:14:06.372593 INFO: Train AUC: 0.597
11:14:06.372631 INFO: AUC difference: 7.04%
11:14:06.372653 WARNING: AUC difference > 5%. This may indicate overfitting.
11:14:06.743145 INFO: Resetting torch num_threads to 100
11:14:06.814337 INFO: === FDR correction performed with classifier version 16 ===
11:14:06.881033 PROGRESS: ============================= Precursor FDR =============================
11:14:06.881843 PROGRESS: Total precursors accumulated: 88,856
11:14:06.881953 PROGRESS: Target precursors: 55,052 (61.96%)
11:14:06.882028 PROGRESS: Decoy precursors: 33,804 (38.04%)
11:14:06.882089 PROGRESS: 
11:14:06.882149 PROGRESS: Precursor Summary:
11:14:06.888348 PROGRESS: Channel   0:	 0.05 FDR: 1,551; 0.01 FDR:    39; 0.001 FDR:    39
11:14:06.890224 PROGRESS: 
11:14:06.890357 PROGRESS: Protein Summary:
11:14:06.894002 PROGRESS: Channel   0:	 0.05 FDR: 1,358; 0.01 FDR:    39; 0.001 FDR:    39
11:14:06.894217 PROGRESS: =========================================================================
11:14:07.677563 INFO: calibration group: precursor, predicting mz
11:14:07.711277 INFO: calibration group: precursor, predicting rt
11:14:07.869250 INFO: calibration group: precursor, predicting mobility
11:14:07.902483 INFO: calibration group: fragment, predicting mz
11:14:08.228332 INFO: === skipping optimization until target number of precursors are found ===
11:14:08.229010 PROGRESS: === Optimization of rt_error has been skipped 2 time(s); maximum number is 1 ===
11:14:08.230322 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 488.8174 found after 2 searches.
11:14:08.230430 PROGRESS: Optimization finished for rt_error.
11:14:08.588840 INFO: calibration group: precursor, predicting mz
11:14:08.604741 INFO: calibration group: precursor, predicting rt
11:14:08.675621 INFO: calibration group: precursor, predicting mobility
11:14:08.694228 INFO: calibration group: fragment, predicting mz
11:14:08.898161 INFO: Starting optimization step 0.
11:14:08.898868 PROGRESS: === Extracting elution groups 0 to 51000 ===
11:14:08.899058 PROGRESS: Extracting batch of 100415 precursors
11:14:08.973742 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:14:08.974034 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:14:08.974120 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
11:14:08.974144 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.56
11:14:09.019696 INFO: Starting candidate selection
11:16:07.079860 INFO: Starting candidate scoring
11:16:11.801551 INFO: Finished candidate processing
11:16:11.801682 INFO: Collecting candidate features
11:16:12.208210 WARNING: intensity_correlation has 93 NaNs ( 0.06 % out of 167226)
11:16:12.208676 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 167226)
11:16:12.218283 INFO: Collecting fragment features
11:16:12.339092 INFO: Finished candidate scoring
11:16:12.474045 PROGRESS: === Extracted 167226 precursors and 1552533 fragments ===
11:16:12.474798 INFO: performing precursor FDR with 47 features
11:16:12.474840 INFO: Decoy channel: -1
11:16:12.474865 INFO: Competetive: True
11:16:12.552542 INFO: Setting torch num_threads to 2 for FDR classification task
11:16:12.592528 WARNING: dropped 56 target PSMs due to missing features
11:16:12.592696 WARNING: dropped 38 decoy PSMs due to missing features
11:16:16.243097 INFO: Test AUC: 0.566
11:16:16.243252 INFO: Train AUC: 0.603
11:16:16.243283 INFO: AUC difference: 6.04%
11:16:16.243306 WARNING: AUC difference > 5%. This may indicate overfitting.
11:16:16.480180 INFO: Resetting torch num_threads to 100
11:16:16.487082 INFO: === FDR correction performed with classifier version 26 ===
11:16:16.497262 PROGRESS: ============================= Precursor FDR =============================
11:16:16.497561 PROGRESS: Total precursors accumulated: 44,968
11:16:16.497635 PROGRESS: Target precursors: 28,422 (63.20%)
11:16:16.497689 PROGRESS: Decoy precursors: 16,546 (36.80%)
11:16:16.497735 PROGRESS: 
11:16:16.497779 PROGRESS: Precursor Summary:
11:16:16.499489 PROGRESS: Channel   0:	 0.05 FDR:   812; 0.01 FDR:   222; 0.001 FDR:   184
11:16:16.499592 PROGRESS: 
11:16:16.499650 PROGRESS: Protein Summary:
11:16:16.501124 PROGRESS: Channel   0:	 0.05 FDR:   754; 0.01 FDR:   216; 0.001 FDR:   179
11:16:16.501221 PROGRESS: =========================================================================
11:16:16.688952 INFO: fragments_df: keeping 2262 of 1552533 [sum(precursor_idx_mask)=4674 sum(mass_error_mask)=1552532 stop_rank=2262
11:16:17.263389 INFO: calibration group: precursor, fitting mz estimator 
11:16:17.369155 INFO: calibration group: precursor, fitting rt estimator 
11:16:22.525188 INFO: calibration group: precursor, fitting mobility estimator 
11:16:22.654311 INFO: calibration group: fragment, fitting mz estimator 
11:16:22.955522 INFO: Using score_cutoff 39.31815952606201 (fac=0.99, q=1)
11:16:22.955959 INFO: calibration group: precursor, predicting mz
11:16:22.971694 INFO: calibration group: precursor, predicting rt
11:16:23.079580 INFO: calibration group: precursor, predicting mobility
11:16:23.114263 INFO: calibration group: fragment, predicting mz
11:16:23.242805 INFO: === checking if optimization conditions were reached ===
11:16:23.243167 PROGRESS: === Optimization of ms1_error has been performed 1 time(s); minimum number is 2 ===
11:16:23.245572 PROGRESS: ❌ ms1_error      : optimization incomplete after 1 search(es). Will search with parameter 11.0039.
11:16:23.245636 INFO: ==============================================
11:16:23.245742 INFO: Starting optimization step 1.
11:16:23.245818 PROGRESS: === Extracting elution groups 0 to 51000 ===
11:16:23.245892 PROGRESS: Extracting batch of 100415 precursors
11:16:23.294583 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:16:23.294764 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:16:23.294826 INFO: FWHM in RT is 2.61 seconds, sigma is 0.57
11:16:23.294855 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.40
11:16:23.296355 INFO: Starting candidate selection
11:18:04.716748 INFO: Starting candidate scoring
11:18:08.598626 INFO: Finished candidate processing
11:18:08.598792 INFO: Collecting candidate features
11:18:08.887712 WARNING: intensity_correlation has 72 NaNs ( 0.04 % out of 167122)
11:18:08.888106 WARNING: height_correlation has 9 NaNs ( 0.01 % out of 167122)
11:18:08.897384 INFO: Collecting fragment features
11:18:09.006644 INFO: Finished candidate scoring
11:18:09.108877 PROGRESS: === Extracted 167122 precursors and 1538730 fragments ===
11:18:09.109350 INFO: performing precursor FDR with 47 features
11:18:09.109391 INFO: Decoy channel: -1
11:18:09.109415 INFO: Competetive: True
11:18:09.166492 INFO: Setting torch num_threads to 2 for FDR classification task
11:18:09.197032 WARNING: dropped 47 target PSMs due to missing features
11:18:09.197155 WARNING: dropped 28 decoy PSMs due to missing features
11:18:12.608057 INFO: Test AUC: 0.562
11:18:12.608189 INFO: Train AUC: 0.593
11:18:12.608218 INFO: AUC difference: 5.25%
11:18:12.608239 WARNING: AUC difference > 5%. This may indicate overfitting.
11:18:12.848331 INFO: Resetting torch num_threads to 100
11:18:12.852907 INFO: === FDR correction performed with classifier version 26 ===
11:18:12.860831 PROGRESS: ============================= Precursor FDR =============================
11:18:12.861083 PROGRESS: Total precursors accumulated: 45,029
11:18:12.861163 PROGRESS: Target precursors: 27,836 (61.82%)
11:18:12.861225 PROGRESS: Decoy precursors: 17,193 (38.18%)
11:18:12.861272 PROGRESS: 
11:18:12.861317 PROGRESS: Precursor Summary:
11:18:12.862702 PROGRESS: Channel   0:	 0.05 FDR:   890; 0.01 FDR:   687; 0.001 FDR:    36
11:18:12.862797 PROGRESS: 
11:18:12.862853 PROGRESS: Protein Summary:
11:18:12.864347 PROGRESS: Channel   0:	 0.05 FDR:   827; 0.01 FDR:   635; 0.001 FDR:    36
11:18:12.864464 PROGRESS: =========================================================================
11:18:12.977744 INFO: fragments_df: keeping 5000 of 1538730 [sum(precursor_idx_mask)=14215 sum(mass_error_mask)=1538728 stop_rank=5000
11:18:13.120003 INFO: calibration group: precursor, fitting mz estimator 
11:18:13.246655 INFO: calibration group: precursor, fitting rt estimator 
11:18:13.377623 INFO: calibration group: precursor, fitting mobility estimator 
11:18:13.528261 INFO: calibration group: fragment, fitting mz estimator 
11:18:14.196765 INFO: Using score_cutoff 35.35617608184815 (fac=0.99, q=1)
11:18:14.197191 INFO: calibration group: precursor, predicting mz
11:18:14.204980 INFO: calibration group: precursor, predicting rt
11:18:14.234589 INFO: calibration group: precursor, predicting mobility
11:18:14.241258 INFO: calibration group: fragment, predicting mz
11:18:14.295397 INFO: === checking if optimization conditions were reached ===
11:18:14.295710 PROGRESS: === Optimization of ms1_error has been performed 2 time(s); minimum number is 2 ===
11:18:14.297777 PROGRESS: ❌ ms1_error      : optimization incomplete after 2 search(es). Will search with parameter 3.5009.
11:18:14.297835 INFO: ==============================================
11:18:14.297961 INFO: Starting optimization step 2.
11:18:14.298036 PROGRESS: === Extracting elution groups 0 to 25400 ===
11:18:14.298131 PROGRESS: Extracting batch of 49998 precursors
11:18:14.311825 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:18:14.311934 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:18:14.311998 INFO: FWHM in RT is 2.63 seconds, sigma is 0.58
11:18:14.312023 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.48
11:18:14.321109 INFO: Starting candidate selection
11:19:04.659360 INFO: Starting candidate scoring
11:19:06.972044 INFO: Finished candidate processing
11:19:06.972168 INFO: Collecting candidate features
11:19:07.111308 WARNING: intensity_correlation has 27 NaNs ( 0.03 % out of 83498)
11:19:07.111621 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 83498)
11:19:07.117621 INFO: Collecting fragment features
11:19:07.182406 INFO: Finished candidate scoring
11:19:07.226040 PROGRESS: === Extracted 83498 precursors and 761316 fragments ===
11:19:07.226511 INFO: performing precursor FDR with 47 features
11:19:07.226557 INFO: Decoy channel: -1
11:19:07.226583 INFO: Competetive: True
11:19:07.255586 INFO: Setting torch num_threads to 2 for FDR classification task
11:19:07.271408 WARNING: dropped 13 target PSMs due to missing features
11:19:07.271554 WARNING: dropped 14 decoy PSMs due to missing features
11:19:08.194491 INFO: Test AUC: 0.549
11:19:08.194628 INFO: Train AUC: 0.599
11:19:08.194659 INFO: AUC difference: 8.33%
11:19:08.194680 WARNING: AUC difference > 5%. This may indicate overfitting.
11:19:08.399033 INFO: Resetting torch num_threads to 100
11:19:08.401878 INFO: === FDR correction performed with classifier version 26 ===
11:19:08.405511 PROGRESS: ============================= Precursor FDR =============================
11:19:08.405653 PROGRESS: Total precursors accumulated: 22,474
11:19:08.405712 PROGRESS: Target precursors: 13,907 (61.88%)
11:19:08.405763 PROGRESS: Decoy precursors: 8,567 (38.12%)
11:19:08.405807 PROGRESS: 
11:19:08.405859 PROGRESS: Precursor Summary:
11:19:08.406928 PROGRESS: Channel   0:	 0.05 FDR:   415; 0.01 FDR:    34; 0.001 FDR:    34
11:19:08.407031 PROGRESS: 
11:19:08.407089 PROGRESS: Protein Summary:
11:19:08.408225 PROGRESS: Channel   0:	 0.05 FDR:   397; 0.01 FDR:    34; 0.001 FDR:    34
11:19:08.408328 PROGRESS: =========================================================================
11:19:08.575709 INFO: calibration group: precursor, predicting mz
11:19:08.583258 INFO: calibration group: precursor, predicting rt
11:19:08.613135 INFO: calibration group: precursor, predicting mobility
11:19:08.619786 INFO: calibration group: fragment, predicting mz
11:19:08.713602 INFO: === skipping optimization until target number of precursors are found ===
11:19:08.714067 PROGRESS: === Optimization of ms1_error has been skipped 1 time(s); maximum number is 1 ===
11:19:08.714195 INFO: Starting optimization step 3.
11:19:08.714286 PROGRESS: === Extracting elution groups 25400 to 51000 ===
11:19:08.714379 PROGRESS: Extracting batch of 50417 precursors
11:19:08.732709 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:19:08.732849 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:19:08.732909 INFO: FWHM in RT is 2.63 seconds, sigma is 0.58
11:19:08.732939 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.48
11:19:08.772997 INFO: Starting candidate selection
11:19:59.185569 INFO: Starting candidate scoring
11:20:00.984125 INFO: Finished candidate processing
11:20:00.984303 INFO: Collecting candidate features
11:20:01.174299 WARNING: intensity_correlation has 41 NaNs ( 0.05 % out of 84125)
11:20:01.174607 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 84125)
11:20:01.180787 INFO: Collecting fragment features
11:20:01.234532 INFO: Finished candidate scoring
11:20:01.318532 PROGRESS: === Extracted 167623 precursors and 1529023 fragments ===
11:20:01.338306 INFO: performing precursor FDR with 47 features
11:20:01.338449 INFO: Decoy channel: -1
11:20:01.338476 INFO: Competetive: True
11:20:01.404163 INFO: Setting torch num_threads to 2 for FDR classification task
11:20:01.434410 WARNING: dropped 35 target PSMs due to missing features
11:20:01.434559 WARNING: dropped 35 decoy PSMs due to missing features
11:20:04.316890 INFO: Test AUC: 0.553
11:20:04.317059 INFO: Train AUC: 0.592
11:20:04.317091 INFO: AUC difference: 6.70%
11:20:04.317114 WARNING: AUC difference > 5%. This may indicate overfitting.
11:20:04.545996 INFO: Resetting torch num_threads to 100
11:20:04.553249 INFO: === FDR correction performed with classifier version 26 ===
11:20:04.560922 PROGRESS: ============================= Precursor FDR =============================
11:20:04.561181 PROGRESS: Total precursors accumulated: 45,133
11:20:04.561246 PROGRESS: Target precursors: 27,618 (61.19%)
11:20:04.561487 PROGRESS: Decoy precursors: 17,515 (38.81%)
11:20:04.561542 PROGRESS: 
11:20:04.561589 PROGRESS: Precursor Summary:
11:20:04.562913 PROGRESS: Channel   0:	 0.05 FDR:   873; 0.01 FDR:    50; 0.001 FDR:    50
11:20:04.563009 PROGRESS: 
11:20:04.563076 PROGRESS: Protein Summary:
11:20:04.564445 PROGRESS: Channel   0:	 0.05 FDR:   805; 0.01 FDR:    48; 0.001 FDR:    48
11:20:04.564538 PROGRESS: =========================================================================
11:20:04.834520 INFO: calibration group: precursor, predicting mz
11:20:04.847846 INFO: calibration group: precursor, predicting rt
11:20:04.909034 INFO: calibration group: precursor, predicting mobility
11:20:04.924938 INFO: calibration group: fragment, predicting mz
11:20:05.056592 INFO: === skipping optimization until target number of precursors are found ===
11:20:05.056902 PROGRESS: === Optimization of ms1_error has been skipped 2 time(s); maximum number is 1 ===
11:20:05.057340 PROGRESS: ✅ ms1_error      : optimization complete. Optimal parameter 11.0039 found after 2 searches.
11:20:05.057415 PROGRESS: Optimization finished for ms1_error.
11:20:05.186308 INFO: calibration group: precursor, predicting mz
11:20:05.193673 INFO: calibration group: precursor, predicting rt
11:20:05.223460 INFO: calibration group: precursor, predicting mobility
11:20:05.229984 INFO: calibration group: fragment, predicting mz
11:20:05.311379 INFO: Starting optimization step 0.
11:20:05.311630 PROGRESS: === Extracting elution groups 0 to 25400 ===
11:20:05.311713 PROGRESS: Extracting batch of 49998 precursors
11:20:05.324480 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:20:05.324598 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:20:05.324648 INFO: FWHM in RT is 2.63 seconds, sigma is 0.58
11:20:05.324673 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.48
11:20:05.355352 INFO: Starting candidate selection
11:20:59.683218 INFO: Starting candidate scoring
11:21:01.608632 INFO: Finished candidate processing
11:21:01.608791 INFO: Collecting candidate features
11:21:01.756386 WARNING: intensity_correlation has 32 NaNs ( 0.04 % out of 83253)
11:21:01.756683 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 83253)
11:21:01.762625 INFO: Collecting fragment features
11:21:01.817529 INFO: Finished candidate scoring
11:21:01.859591 PROGRESS: === Extracted 83253 precursors and 766613 fragments ===
11:21:01.860064 INFO: performing precursor FDR with 47 features
11:21:01.860102 INFO: Decoy channel: -1
11:21:01.860126 INFO: Competetive: True
11:21:01.886211 INFO: Setting torch num_threads to 2 for FDR classification task
11:21:01.901897 WARNING: dropped 22 target PSMs due to missing features
11:21:01.902040 WARNING: dropped 11 decoy PSMs due to missing features
11:21:03.227821 INFO: Test AUC: 0.566
11:21:03.227960 INFO: Train AUC: 0.631
11:21:03.227990 INFO: AUC difference: 10.34%
11:21:03.228012 WARNING: AUC difference > 5%. This may indicate overfitting.
11:21:03.434769 INFO: Resetting torch num_threads to 100
11:21:03.438070 INFO: === FDR correction performed with classifier version 30 ===
11:21:03.442108 PROGRESS: ============================= Precursor FDR =============================
11:21:03.442279 PROGRESS: Total precursors accumulated: 22,422
11:21:03.442341 PROGRESS: Target precursors: 14,568 (64.97%)
11:21:03.442391 PROGRESS: Decoy precursors: 7,854 (35.03%)
11:21:03.442440 PROGRESS: 
11:21:03.442483 PROGRESS: Precursor Summary:
11:21:03.443631 PROGRESS: Channel   0:	 0.05 FDR:   467; 0.01 FDR:   106; 0.001 FDR:    47
11:21:03.443726 PROGRESS: 
11:21:03.443781 PROGRESS: Protein Summary:
11:21:03.444951 PROGRESS: Channel   0:	 0.05 FDR:   454; 0.01 FDR:   106; 0.001 FDR:    47
11:21:03.445043 PROGRESS: =========================================================================
11:21:03.619774 INFO: calibration group: precursor, predicting mz
11:21:03.627620 INFO: calibration group: precursor, predicting rt
11:21:03.659048 INFO: calibration group: precursor, predicting mobility
11:21:03.666605 INFO: calibration group: fragment, predicting mz
11:21:03.723205 INFO: === skipping optimization until target number of precursors are found ===
11:21:03.723523 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
11:21:03.723593 INFO: Starting optimization step 1.
11:21:03.723664 PROGRESS: === Extracting elution groups 25400 to 51000 ===
11:21:03.723732 PROGRESS: Extracting batch of 50417 precursors
11:21:03.737809 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:21:03.737929 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:21:03.737980 INFO: FWHM in RT is 2.63 seconds, sigma is 0.58
11:21:03.738004 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.48
11:21:03.754888 INFO: Starting candidate selection
11:21:57.103053 INFO: Starting candidate scoring
11:21:59.086063 INFO: Finished candidate processing
11:21:59.086168 INFO: Collecting candidate features
11:21:59.206742 WARNING: intensity_correlation has 43 NaNs ( 0.05 % out of 83884)
11:21:59.207113 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 83884)
11:21:59.216279 INFO: Collecting fragment features
11:21:59.270015 INFO: Finished candidate scoring
11:21:59.379549 PROGRESS: === Extracted 167137 precursors and 1539386 fragments ===
11:21:59.397920 INFO: performing precursor FDR with 47 features
11:21:59.398056 INFO: Decoy channel: -1
11:21:59.398082 INFO: Competetive: True
11:21:59.460014 INFO: Setting torch num_threads to 2 for FDR classification task
11:21:59.488620 WARNING: dropped 47 target PSMs due to missing features
11:21:59.488762 WARNING: dropped 30 decoy PSMs due to missing features
11:22:02.078058 INFO: Test AUC: 0.570
11:22:02.078190 INFO: Train AUC: 0.607
11:22:02.078220 INFO: AUC difference: 6.14%
11:22:02.078241 WARNING: AUC difference > 5%. This may indicate overfitting.
11:22:02.304241 INFO: Resetting torch num_threads to 100
11:22:02.311093 INFO: === FDR correction performed with classifier version 30 ===
11:22:02.318709 PROGRESS: ============================= Precursor FDR =============================
11:22:02.318988 PROGRESS: Total precursors accumulated: 45,007
11:22:02.319069 PROGRESS: Target precursors: 28,283 (62.84%)
11:22:02.319123 PROGRESS: Decoy precursors: 16,724 (37.16%)
11:22:02.319175 PROGRESS: 
11:22:02.319222 PROGRESS: Precursor Summary:
11:22:02.320585 PROGRESS: Channel   0:	 0.05 FDR:   918; 0.01 FDR:    27; 0.001 FDR:    27
11:22:02.320680 PROGRESS: 
11:22:02.320735 PROGRESS: Protein Summary:
11:22:02.322086 PROGRESS: Channel   0:	 0.05 FDR:   856; 0.01 FDR:    27; 0.001 FDR:    27
11:22:02.322179 PROGRESS: =========================================================================
11:22:02.557793 INFO: calibration group: precursor, predicting mz
11:22:02.571481 INFO: calibration group: precursor, predicting rt
11:22:02.631466 INFO: calibration group: precursor, predicting mobility
11:22:02.645507 INFO: calibration group: fragment, predicting mz
11:22:02.763197 INFO: === skipping optimization until target number of precursors are found ===
11:22:02.763490 PROGRESS: === Optimization of mobility_error has been skipped 2 time(s); maximum number is 1 ===
11:22:02.763577 INFO: Starting optimization step 2.
11:22:02.763643 PROGRESS: === Extracting elution groups 51000 to 102200 ===
11:22:02.763716 PROGRESS: Extracting batch of 100803 precursors
11:22:02.787623 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:22:02.787752 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:22:02.787801 INFO: FWHM in RT is 2.63 seconds, sigma is 0.58
11:22:02.787824 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.48
11:22:02.805209 INFO: Starting candidate selection
11:23:44.558717 INFO: Starting candidate scoring
11:23:48.505039 INFO: Finished candidate processing
11:23:48.505207 INFO: Collecting candidate features
11:23:48.795549 WARNING: intensity_correlation has 69 NaNs ( 0.04 % out of 167873)
11:23:48.795927 WARNING: height_correlation has 9 NaNs ( 0.01 % out of 167873)
11:23:48.804885 INFO: Collecting fragment features
11:23:48.906354 INFO: Finished candidate scoring
11:23:49.117836 PROGRESS: === Extracted 335010 precursors and 3091030 fragments ===
11:23:49.156475 INFO: performing precursor FDR with 47 features
11:23:49.156616 INFO: Decoy channel: -1
11:23:49.156643 INFO: Competetive: True
11:23:49.304211 INFO: Setting torch num_threads to 2 for FDR classification task
11:23:49.369642 WARNING: dropped 80 target PSMs due to missing features
11:23:49.369771 WARNING: dropped 72 decoy PSMs due to missing features
11:23:55.690346 INFO: Test AUC: 0.541
11:23:55.690582 INFO: Train AUC: 0.593
11:23:55.690622 INFO: AUC difference: 8.68%
11:23:55.690648 WARNING: AUC difference > 5%. This may indicate overfitting.
11:23:55.980994 INFO: Resetting torch num_threads to 100
11:23:56.001824 INFO: === FDR correction performed with classifier version 30 ===
11:23:56.019924 PROGRESS: ============================= Precursor FDR =============================
11:23:56.020228 PROGRESS: Total precursors accumulated: 90,224
11:23:56.020329 PROGRESS: Target precursors: 55,633 (61.66%)
11:23:56.020382 PROGRESS: Decoy precursors: 34,591 (38.34%)
11:23:56.020431 PROGRESS: 
11:23:56.020474 PROGRESS: Precursor Summary:
11:23:56.022400 PROGRESS: Channel   0:	 0.05 FDR: 1,851; 0.01 FDR:   134; 0.001 FDR:    13
11:23:56.022504 PROGRESS: 
11:23:56.022563 PROGRESS: Protein Summary:
11:23:56.024357 PROGRESS: Channel   0:	 0.05 FDR: 1,608; 0.01 FDR:   128; 0.001 FDR:    13
11:23:56.024454 PROGRESS: =========================================================================
11:23:56.713973 INFO: calibration group: precursor, predicting mz
11:23:56.741810 INFO: calibration group: precursor, predicting rt
11:23:56.874850 INFO: calibration group: precursor, predicting mobility
11:23:56.907510 INFO: calibration group: fragment, predicting mz
11:23:57.178696 INFO: === skipping optimization until target number of precursors are found ===
11:23:57.179072 PROGRESS: === Optimization of mobility_error has been skipped 3 time(s); maximum number is 1 ===
11:23:57.179163 INFO: Starting optimization step 3.
11:23:57.179243 PROGRESS: === Extracting elution groups 102200 to 204600 ===
11:23:57.179331 PROGRESS: Extracting batch of 201717 precursors
11:23:57.238255 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:23:57.238401 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:23:57.238453 INFO: FWHM in RT is 2.63 seconds, sigma is 0.58
11:23:57.238476 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.48
11:23:57.263804 INFO: Starting candidate selection
11:27:20.611385 INFO: Starting candidate scoring
11:27:28.079620 INFO: Finished candidate processing
11:27:28.079799 INFO: Collecting candidate features
11:27:29.146033 WARNING: intensity_correlation has 177 NaNs ( 0.05 % out of 335538)
11:27:29.146642 WARNING: height_correlation has 13 NaNs ( 0.00 % out of 335538)
11:27:29.163222 INFO: Collecting fragment features
11:27:29.451309 INFO: Finished candidate scoring
11:27:29.930708 PROGRESS: === Extracted 670548 precursors and 6182254 fragments ===
11:27:30.009706 INFO: performing precursor FDR with 47 features
11:27:30.009872 INFO: Decoy channel: -1
11:27:30.009899 INFO: Competetive: True
11:27:30.324348 INFO: Setting torch num_threads to 2 for FDR classification task
11:27:30.464369 WARNING: dropped 178 target PSMs due to missing features
11:27:30.464507 WARNING: dropped 162 decoy PSMs due to missing features
11:27:42.242010 INFO: Test AUC: 0.522
11:27:42.242157 INFO: Train AUC: 0.583
11:27:42.242189 INFO: AUC difference: 10.39%
11:27:42.242212 WARNING: AUC difference > 5%. This may indicate overfitting.
11:27:42.609784 INFO: Resetting torch num_threads to 100
11:27:42.644035 INFO: === FDR correction performed with classifier version 30 ===
11:27:42.678073 PROGRESS: ============================= Precursor FDR =============================
11:27:42.678391 PROGRESS: Total precursors accumulated: 180,685
11:27:42.678455 PROGRESS: Target precursors: 109,542 (60.63%)
11:27:42.678506 PROGRESS: Decoy precursors: 71,143 (39.37%)
11:27:42.678560 PROGRESS: 
11:27:42.678606 PROGRESS: Precursor Summary:
11:27:42.681276 PROGRESS: Channel   0:	 0.05 FDR: 3,224; 0.01 FDR: 1,031; 0.001 FDR:    68
11:27:42.681378 PROGRESS: 
11:27:42.681434 PROGRESS: Protein Summary:
11:27:42.684172 PROGRESS: Channel   0:	 0.05 FDR: 2,446; 0.01 FDR:   907; 0.001 FDR:    67
11:27:42.684277 PROGRESS: =========================================================================
11:27:43.118477 INFO: fragments_df: keeping 5000 of 6182254 [sum(precursor_idx_mask)=21557 sum(mass_error_mask)=6182249 stop_rank=5000
11:27:43.334435 INFO: calibration group: precursor, fitting mz estimator 
11:27:43.508265 INFO: calibration group: precursor, fitting rt estimator 
11:27:43.691415 INFO: calibration group: precursor, fitting mobility estimator 
11:27:43.865016 INFO: calibration group: fragment, fitting mz estimator 
11:27:44.514424 INFO: Using score_cutoff 40.717840759277344 (fac=0.99, q=1)
11:27:44.514857 INFO: calibration group: precursor, predicting mz
11:27:44.527970 INFO: calibration group: precursor, predicting rt
11:27:44.587949 INFO: calibration group: precursor, predicting mobility
11:27:44.602201 INFO: calibration group: fragment, predicting mz
11:27:44.716513 INFO: === checking if optimization conditions were reached ===
11:27:44.716798 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
11:27:44.718638 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0719.
11:27:44.718693 INFO: ==============================================
11:27:44.718790 INFO: Starting optimization step 4.
11:27:44.718858 PROGRESS: === Extracting elution groups 0 to 51000 ===
11:27:44.718928 PROGRESS: Extracting batch of 100415 precursors
11:27:44.744713 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:27:44.744847 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:27:44.744896 INFO: FWHM in RT is 2.63 seconds, sigma is 0.58
11:27:44.744922 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.47
11:27:44.758974 INFO: Starting candidate selection
11:28:53.115492 INFO: Starting candidate scoring
11:28:57.451644 INFO: Finished candidate processing
11:28:57.451752 INFO: Collecting candidate features
11:28:57.712469 WARNING: intensity_correlation has 86 NaNs ( 0.05 % out of 163108)
11:28:57.712846 WARNING: height_correlation has 7 NaNs ( 0.00 % out of 163108)
11:28:57.721641 INFO: Collecting fragment features
11:28:57.819828 INFO: Finished candidate scoring
11:28:57.917135 PROGRESS: === Extracted 163108 precursors and 1491416 fragments ===
11:28:57.917567 INFO: performing precursor FDR with 47 features
11:28:57.917607 INFO: Decoy channel: -1
11:28:57.917631 INFO: Competetive: True
11:28:57.967979 INFO: Setting torch num_threads to 2 for FDR classification task
11:28:57.998847 WARNING: dropped 53 target PSMs due to missing features
11:28:57.998975 WARNING: dropped 37 decoy PSMs due to missing features
11:29:00.583403 INFO: Test AUC: 0.568
11:29:00.583530 INFO: Train AUC: 0.607
11:29:00.583560 INFO: AUC difference: 6.41%
11:29:00.583581 WARNING: AUC difference > 5%. This may indicate overfitting.
11:29:00.809103 INFO: Resetting torch num_threads to 100
11:29:00.814130 INFO: === FDR correction performed with classifier version 30 ===
11:29:00.822240 PROGRESS: ============================= Precursor FDR =============================
11:29:00.822499 PROGRESS: Total precursors accumulated: 44,163
11:29:00.822562 PROGRESS: Target precursors: 27,623 (62.55%)
11:29:00.822612 PROGRESS: Decoy precursors: 16,540 (37.45%)
11:29:00.822664 PROGRESS: 
11:29:00.822707 PROGRESS: Precursor Summary:
11:29:00.824088 PROGRESS: Channel   0:	 0.05 FDR:   885; 0.01 FDR:    60; 0.001 FDR:    60
11:29:00.824212 PROGRESS: 
11:29:00.824270 PROGRESS: Protein Summary:
11:29:00.825631 PROGRESS: Channel   0:	 0.05 FDR:   825; 0.01 FDR:    60; 0.001 FDR:    60
11:29:00.825727 PROGRESS: =========================================================================
11:29:01.072912 INFO: calibration group: precursor, predicting mz
11:29:01.086676 INFO: calibration group: precursor, predicting rt
11:29:01.147220 INFO: calibration group: precursor, predicting mobility
11:29:01.163338 INFO: calibration group: fragment, predicting mz
11:29:01.288478 INFO: === skipping optimization until target number of precursors are found ===
11:29:01.288796 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
11:29:01.288876 INFO: Starting optimization step 5.
11:29:01.288954 PROGRESS: === Extracting elution groups 51000 to 102200 ===
11:29:01.289033 PROGRESS: Extracting batch of 100803 precursors
11:29:01.324303 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:29:01.324434 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:29:01.324491 INFO: FWHM in RT is 2.63 seconds, sigma is 0.58
11:29:01.324520 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.47
11:29:01.331207 INFO: Starting candidate selection
11:30:11.357709 INFO: Starting candidate scoring
11:30:15.107962 INFO: Finished candidate processing
11:30:15.108126 INFO: Collecting candidate features
11:30:15.384328 WARNING: intensity_correlation has 75 NaNs ( 0.05 % out of 163804)
11:30:15.384704 WARNING: height_correlation has 9 NaNs ( 0.01 % out of 163804)
11:30:15.393413 INFO: Collecting fragment features
11:30:15.487547 INFO: Finished candidate scoring
11:30:15.762814 PROGRESS: === Extracted 326912 precursors and 2993421 fragments ===
11:30:15.798174 INFO: performing precursor FDR with 47 features
11:30:15.798313 INFO: Decoy channel: -1
11:30:15.798340 INFO: Competetive: True
11:30:15.947194 INFO: Setting torch num_threads to 2 for FDR classification task
11:30:16.010110 WARNING: dropped 91 target PSMs due to missing features
11:30:16.010249 WARNING: dropped 79 decoy PSMs due to missing features
11:30:22.607942 INFO: Test AUC: 0.559
11:30:22.608093 INFO: Train AUC: 0.593
11:30:22.608124 INFO: AUC difference: 5.71%
11:30:22.608146 WARNING: AUC difference > 5%. This may indicate overfitting.
11:30:22.893286 INFO: Resetting torch num_threads to 100
11:30:22.916737 INFO: === FDR correction performed with classifier version 30 ===
11:30:22.938369 PROGRESS: ============================= Precursor FDR =============================
11:30:22.938712 PROGRESS: Total precursors accumulated: 88,513
11:30:22.938782 PROGRESS: Target precursors: 54,290 (61.34%)
11:30:22.938839 PROGRESS: Decoy precursors: 34,223 (38.66%)
11:30:22.938887 PROGRESS: 
11:30:22.938931 PROGRESS: Precursor Summary:
11:30:22.940878 PROGRESS: Channel   0:	 0.05 FDR: 1,752; 0.01 FDR:     7; 0.001 FDR:     7
11:30:22.940982 PROGRESS: 
11:30:22.941037 PROGRESS: Protein Summary:
11:30:22.942784 PROGRESS: Channel   0:	 0.05 FDR: 1,518; 0.01 FDR:     7; 0.001 FDR:     7
11:30:22.942880 PROGRESS: =========================================================================
11:30:23.534760 INFO: calibration group: precursor, predicting mz
11:30:23.562505 INFO: calibration group: precursor, predicting rt
11:30:23.684530 INFO: calibration group: precursor, predicting mobility
11:30:23.712465 INFO: calibration group: fragment, predicting mz
11:30:23.954944 INFO: === skipping optimization until target number of precursors are found ===
11:30:23.955359 PROGRESS: === Optimization of mobility_error has been skipped 2 time(s); maximum number is 1 ===
11:30:23.955446 INFO: Starting optimization step 6.
11:30:23.955523 PROGRESS: === Extracting elution groups 102200 to 204600 ===
11:30:23.955599 PROGRESS: Extracting batch of 201717 precursors
11:30:24.019477 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:30:24.019635 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:30:24.019692 INFO: FWHM in RT is 2.63 seconds, sigma is 0.58
11:30:24.019715 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.47
11:30:24.020560 INFO: Starting candidate selection
11:32:43.349886 INFO: Starting candidate scoring
11:32:50.291461 INFO: Finished candidate processing
11:32:50.291848 INFO: Collecting candidate features
11:32:51.120133 WARNING: intensity_correlation has 206 NaNs ( 0.06 % out of 326917)
11:32:51.120652 WARNING: height_correlation has 12 NaNs ( 0.00 % out of 326917)
11:32:51.134739 INFO: Collecting fragment features
11:32:51.349327 INFO: Finished candidate scoring
11:32:51.805275 PROGRESS: === Extracted 653829 precursors and 5982110 fragments ===
11:32:51.884795 INFO: performing precursor FDR with 47 features
11:32:51.884934 INFO: Decoy channel: -1
11:32:51.884965 INFO: Competetive: True
11:32:52.247430 INFO: Setting torch num_threads to 2 for FDR classification task
11:32:52.399919 WARNING: dropped 207 target PSMs due to missing features
11:32:52.400089 WARNING: dropped 179 decoy PSMs due to missing features
11:33:06.093837 INFO: Test AUC: 0.563
11:33:06.093983 INFO: Train AUC: 0.583
11:33:06.094017 INFO: AUC difference: 3.29%
11:33:06.470209 INFO: Resetting torch num_threads to 100
11:33:06.514398 INFO: === FDR correction performed with classifier version 30 ===
11:33:06.550476 PROGRESS: ============================= Precursor FDR =============================
11:33:06.550808 PROGRESS: Total precursors accumulated: 177,043
11:33:06.550873 PROGRESS: Target precursors: 107,367 (60.64%)
11:33:06.550924 PROGRESS: Decoy precursors: 69,676 (39.36%)
11:33:06.550972 PROGRESS: 
11:33:06.551016 PROGRESS: Precursor Summary:
11:33:06.553640 PROGRESS: Channel   0:	 0.05 FDR: 3,304; 0.01 FDR:   112; 0.001 FDR:    28
11:33:06.553747 PROGRESS: 
11:33:06.553803 PROGRESS: Protein Summary:
11:33:06.556275 PROGRESS: Channel   0:	 0.05 FDR: 2,512; 0.01 FDR:   110; 0.001 FDR:    28
11:33:06.556377 PROGRESS: =========================================================================
11:33:07.424849 INFO: calibration group: precursor, predicting mz
11:33:07.477118 INFO: calibration group: precursor, predicting rt
11:33:07.720330 INFO: calibration group: precursor, predicting mobility
11:33:07.774591 INFO: calibration group: fragment, predicting mz
11:33:08.232945 INFO: === skipping optimization until target number of precursors are found ===
11:33:08.233347 PROGRESS: === Optimization of mobility_error has been skipped 3 time(s); maximum number is 1 ===
11:33:08.233453 INFO: Starting optimization step 7.
11:33:08.233531 PROGRESS: === Extracting elution groups 204600 to 409400 ===
11:33:08.233634 PROGRESS: Extracting batch of 403498 precursors
11:33:08.341139 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:33:08.341281 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:33:08.341348 INFO: FWHM in RT is 2.63 seconds, sigma is 0.58
11:33:08.341372 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.47
11:33:08.342457 INFO: Starting candidate selection
11:37:43.528396 INFO: Starting candidate scoring
11:37:57.416825 INFO: Finished candidate processing
11:37:57.417457 INFO: Collecting candidate features
11:37:58.895670 WARNING: intensity_correlation has 363 NaNs ( 0.06 % out of 655416)
11:37:58.896484 WARNING: height_correlation has 24 NaNs ( 0.00 % out of 655416)
11:37:58.923629 INFO: Collecting fragment features
11:37:59.385913 INFO: Finished candidate scoring
11:38:00.873258 PROGRESS: === Extracted 1309245 precursors and 11979025 fragments ===
11:38:01.038648 INFO: performing precursor FDR with 47 features
11:38:01.038824 INFO: Decoy channel: -1
11:38:01.038852 INFO: Competetive: True
11:38:01.658748 INFO: Setting torch num_threads to 2 for FDR classification task
11:38:01.925106 WARNING: dropped 404 target PSMs due to missing features
11:38:01.925275 WARNING: dropped 357 decoy PSMs due to missing features
11:38:28.377127 INFO: Test AUC: 0.563
11:38:28.377366 INFO: Train AUC: 0.577
11:38:28.377398 INFO: AUC difference: 2.38%
11:38:28.933167 INFO: Resetting torch num_threads to 100
11:38:29.025762 INFO: === FDR correction performed with classifier version 30 ===
11:38:29.112721 PROGRESS: ============================= Precursor FDR =============================
11:38:29.113091 PROGRESS: Total precursors accumulated: 354,410
11:38:29.113168 PROGRESS: Target precursors: 214,294 (60.46%)
11:38:29.113220 PROGRESS: Decoy precursors: 140,116 (39.54%)
11:38:29.113270 PROGRESS: 
11:38:29.113317 PROGRESS: Precursor Summary:
11:38:29.118000 PROGRESS: Channel   0:	 0.05 FDR: 6,658; 0.01 FDR: 3,524; 0.001 FDR:    10
11:38:29.118121 PROGRESS: 
11:38:29.118176 PROGRESS: Protein Summary:
11:38:29.122963 PROGRESS: Channel   0:	 0.05 FDR: 4,157; 0.01 FDR: 2,452; 0.001 FDR:    10
11:38:29.123085 PROGRESS: =========================================================================
11:38:29.989801 INFO: fragments_df: keeping 5000 of 11979025 [sum(precursor_idx_mask)=74146 sum(mass_error_mask)=11979008 stop_rank=5000
11:38:30.240164 INFO: calibration group: precursor, fitting mz estimator 
11:38:30.709101 INFO: calibration group: precursor, fitting rt estimator 
11:38:31.178944 INFO: calibration group: precursor, fitting mobility estimator 
11:38:31.591498 INFO: calibration group: fragment, fitting mz estimator 
11:38:32.268887 INFO: Using score_cutoff 40.249841960906984 (fac=0.99, q=1)
11:38:32.269432 INFO: calibration group: precursor, predicting mz
11:38:32.276897 INFO: calibration group: precursor, predicting rt
11:38:32.307077 INFO: calibration group: precursor, predicting mobility
11:38:32.314043 INFO: calibration group: fragment, predicting mz
11:38:32.377223 INFO: === checking if optimization conditions were reached ===
11:38:32.377595 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
11:38:32.381064 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0609.
11:38:32.381139 INFO: ==============================================
11:38:32.381259 INFO: Starting optimization step 8.
11:38:32.381336 PROGRESS: === Extracting elution groups 0 to 25400 ===
11:38:32.381423 PROGRESS: Extracting batch of 49998 precursors
11:38:32.459730 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:38:32.459898 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:38:32.459957 INFO: FWHM in RT is 2.72 seconds, sigma is 0.60
11:38:32.459987 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.42
11:38:32.463142 INFO: Starting candidate selection
11:39:04.029437 INFO: Starting candidate scoring
11:39:05.860226 INFO: Finished candidate processing
11:39:05.860331 INFO: Collecting candidate features
11:39:06.004441 WARNING: intensity_correlation has 49 NaNs ( 0.06 % out of 80356)
11:39:06.004844 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 80356)
11:39:06.014871 INFO: Collecting fragment features
11:39:06.074794 INFO: Finished candidate scoring
11:39:06.117067 PROGRESS: === Extracted 80356 precursors and 730336 fragments ===
11:39:06.117520 INFO: performing precursor FDR with 47 features
11:39:06.117560 INFO: Decoy channel: -1
11:39:06.117583 INFO: Competetive: True
11:39:06.152487 INFO: Setting torch num_threads to 2 for FDR classification task
11:39:06.171404 WARNING: dropped 35 target PSMs due to missing features
11:39:06.171543 WARNING: dropped 15 decoy PSMs due to missing features
11:39:07.409815 INFO: Test AUC: 0.568
11:39:07.409950 INFO: Train AUC: 0.614
11:39:07.409981 INFO: AUC difference: 7.45%
11:39:07.410004 WARNING: AUC difference > 5%. This may indicate overfitting.
11:39:07.611704 INFO: Resetting torch num_threads to 100
11:39:07.615607 INFO: === FDR correction performed with classifier version 30 ===
11:39:07.619676 PROGRESS: ============================= Precursor FDR =============================
11:39:07.619806 PROGRESS: Total precursors accumulated: 21,795
11:39:07.619871 PROGRESS: Target precursors: 13,822 (63.42%)
11:39:07.619923 PROGRESS: Decoy precursors: 7,973 (36.58%)
11:39:07.619967 PROGRESS: 
11:39:07.620011 PROGRESS: Precursor Summary:
11:39:07.621357 PROGRESS: Channel   0:	 0.05 FDR:   450; 0.01 FDR:    67; 0.001 FDR:    67
11:39:07.621454 PROGRESS: 
11:39:07.621508 PROGRESS: Protein Summary:
11:39:07.622674 PROGRESS: Channel   0:	 0.05 FDR:   434; 0.01 FDR:    67; 0.001 FDR:    67
11:39:07.622767 PROGRESS: =========================================================================
11:39:07.774796 INFO: calibration group: precursor, predicting mz
11:39:07.782323 INFO: calibration group: precursor, predicting rt
11:39:07.812921 INFO: calibration group: precursor, predicting mobility
11:39:07.819558 INFO: calibration group: fragment, predicting mz
11:39:07.874469 INFO: === skipping optimization until target number of precursors are found ===
11:39:07.874807 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
11:39:07.874880 INFO: Starting optimization step 9.
11:39:07.874955 PROGRESS: === Extracting elution groups 25400 to 51000 ===
11:39:07.875034 PROGRESS: Extracting batch of 50417 precursors
11:39:07.896181 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:39:07.896314 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:39:07.896357 INFO: FWHM in RT is 2.72 seconds, sigma is 0.60
11:39:07.896380 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.42
11:39:07.905506 INFO: Starting candidate selection
11:39:40.614761 INFO: Starting candidate scoring
11:39:42.536125 INFO: Finished candidate processing
11:39:42.536304 INFO: Collecting candidate features
11:39:42.697093 WARNING: intensity_correlation has 45 NaNs ( 0.06 % out of 81024)
11:39:42.697422 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 81024)
11:39:42.703507 INFO: Collecting fragment features
11:39:42.760222 INFO: Finished candidate scoring
11:39:42.886239 PROGRESS: === Extracted 161380 precursors and 1467722 fragments ===
11:39:42.906689 INFO: performing precursor FDR with 47 features
11:39:42.906847 INFO: Decoy channel: -1
11:39:42.906874 INFO: Competetive: True
11:39:42.986496 INFO: Setting torch num_threads to 2 for FDR classification task
11:39:43.022291 WARNING: dropped 57 target PSMs due to missing features
11:39:43.022452 WARNING: dropped 42 decoy PSMs due to missing features
11:39:46.228733 INFO: Test AUC: 0.562
11:39:46.228886 INFO: Train AUC: 0.608
11:39:46.228917 INFO: AUC difference: 7.56%
11:39:46.228939 WARNING: AUC difference > 5%. This may indicate overfitting.
11:39:46.477585 INFO: Resetting torch num_threads to 100
11:39:46.487138 INFO: === FDR correction performed with classifier version 30 ===
11:39:46.496191 PROGRESS: ============================= Precursor FDR =============================
11:39:46.496481 PROGRESS: Total precursors accumulated: 43,728
11:39:46.496562 PROGRESS: Target precursors: 27,342 (62.53%)
11:39:46.496618 PROGRESS: Decoy precursors: 16,386 (37.47%)
11:39:46.496665 PROGRESS: 
11:39:46.496710 PROGRESS: Precursor Summary:
11:39:46.498072 PROGRESS: Channel   0:	 0.05 FDR:   875; 0.01 FDR:    52; 0.001 FDR:    52
11:39:46.498169 PROGRESS: 
11:39:46.498226 PROGRESS: Protein Summary:
11:39:46.499623 PROGRESS: Channel   0:	 0.05 FDR:   813; 0.01 FDR:    52; 0.001 FDR:    52
11:39:46.499719 PROGRESS: =========================================================================
11:39:46.782853 INFO: calibration group: precursor, predicting mz
11:39:46.796739 INFO: calibration group: precursor, predicting rt
11:39:46.857585 INFO: calibration group: precursor, predicting mobility
11:39:46.871690 INFO: calibration group: fragment, predicting mz
11:39:46.989499 INFO: === skipping optimization until target number of precursors are found ===
11:39:46.989864 PROGRESS: === Optimization of mobility_error has been skipped 2 time(s); maximum number is 1 ===
11:39:46.990288 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.0719 found after 2 searches.
11:39:46.990363 PROGRESS: Optimization finished for mobility_error.
11:39:47.149090 INFO: calibration group: precursor, predicting mz
11:39:47.156869 INFO: calibration group: precursor, predicting rt
11:39:47.186858 INFO: calibration group: precursor, predicting mobility
11:39:47.193564 INFO: calibration group: fragment, predicting mz
11:39:47.278408 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
11:39:47.278800 PROGRESS: ==============================================
11:39:47.278923 PROGRESS: ms2_error      : 10.0599
11:39:47.278997 PROGRESS: rt_error       : 488.8174
11:39:47.279080 PROGRESS: ms1_error      : 11.0039
11:39:47.279139 PROGRESS: mobility_error : 0.0719
11:39:47.279191 PROGRESS: ==============================================
11:39:47.288435 INFO: calibration group: precursor, predicting mz
11:39:48.726321 INFO: calibration group: precursor, predicting rt
11:39:55.295149 INFO: calibration group: precursor, predicting mobility
11:39:56.662585 INFO: calibration group: fragment, predicting mz
11:40:08.548695 PROGRESS: Extracting batch of 10272670 precursors
11:40:11.152908 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:40:11.153051 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:40:11.153103 INFO: FWHM in RT is 2.72 seconds, sigma is 0.60
11:40:11.153131 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.42
11:40:11.154346 INFO: Starting candidate selection
13:31:30.469994 INFO: Applying score cutoff of 40.249841960906984
13:31:30.758642 INFO: Removed 9849870 precursors with score below cutoff
13:31:33.291405 INFO: Starting candidate scoring
13:34:34.481796 INFO: Finished candidate processing
13:34:34.482377 INFO: Collecting candidate features
13:34:48.901274 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 7581542)
13:34:49.160918 INFO: Collecting fragment features
13:34:55.056165 INFO: Finished candidate scoring
13:35:06.033134 INFO: === FDR correction performed with classifier version 40 ===
13:35:06.038071 INFO: performing precursor FDR with 47 features
13:35:06.038156 INFO: Decoy channel: -1
13:35:06.038195 INFO: Competetive: True
13:35:08.144011 INFO: Setting torch num_threads to 2 for FDR classification task
13:35:09.497931 WARNING: dropped 1 target PSMs due to missing features
13:35:09.498098 WARNING: dropped 2 decoy PSMs due to missing features
13:37:36.518204 INFO: Test AUC: 0.567
13:37:36.518499 INFO: Train AUC: 0.571
13:37:36.518536 INFO: AUC difference: 0.78%
13:37:38.374403 INFO: Resetting torch num_threads to 100
13:37:38.600108 INFO: Removing fragments below FDR threshold
13:37:39.184503 PROGRESS: ============================= Precursor FDR =============================
13:37:39.185302 PROGRESS: Total precursors accumulated: 70,811
13:37:39.185396 PROGRESS: Target precursors: 70,110 (99.01%)
13:37:39.185448 PROGRESS: Decoy precursors: 701 (0.99%)
13:37:39.185496 PROGRESS: 
13:37:39.185539 PROGRESS: Precursor Summary:
13:37:39.206071 PROGRESS: Channel   0:	 0.05 FDR: 70,110; 0.01 FDR: 70,110; 0.001 FDR:   661
13:37:39.206310 PROGRESS: 
13:37:39.206371 PROGRESS: Protein Summary:
13:37:39.235772 PROGRESS: Channel   0:	 0.05 FDR: 10,835; 0.01 FDR: 10,835; 0.001 FDR:   396
13:37:39.235997 PROGRESS: =========================================================================
13:37:39.947789 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
13:37:40.400489 PROGRESS: Loading raw file 5/6: ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
13:37:40.400667 INFO: Quantification results path: run_output/alphadia_1.10.4_Again_good_now/library/quant
13:37:40.400747 INFO: Creating folder run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/figures
13:37:40.401767 INFO: Initializing RawFileManager
13:37:40.401910 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
13:37:40.401966 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
13:37:40.402009 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
13:37:40.622335 INFO: Reading 39,128 frames with 2,766,418,119 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
13:37:48.412292 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d...
13:37:48.414863 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
13:37:48.417829 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
13:37:48.418324 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
13:37:48.418763 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
13:37:48.421360 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
13:37:48.441007 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
13:37:48.442029 INFO: Indexing quadrupole dimension
13:37:48.926807 INFO: Transposing detector events
13:37:58.448523 INFO: Finished transposing data
13:37:58.486292 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
13:37:58.487455 INFO: RT (min)            : 0.0 - 70.0
13:37:58.487557 INFO: RT duration (sec)   : 4199.9
13:37:58.487632 INFO: RT duration (min)   : 70.0
13:37:58.487698 INFO: Cycle len (scans)   : 9
13:37:58.487760 INFO: Cycle len (sec)     : 0.97
13:37:58.487819 INFO: Number of cycles    : 4347
13:37:58.487878 INFO: MS2 range (m/z)     : 400.0 - 1000.0
13:37:59.761601 INFO: Initializing CalibrationManager
13:37:59.761955 INFO: Loading calibration config
13:37:59.762633 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed'], 'function': LOESSRegression()}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed'], 'function': LOESSRegression(n_kernels=2)}], 'name': 'precursor'}]
13:37:59.762743 INFO: Calibration group :fragment, found 1 estimator(s)
13:37:59.762867 INFO: Calibration group :precursor, found 3 estimator(s)
13:37:59.763084 INFO: Initializing OptimizationManager
13:37:59.763211 INFO: initial parameter: ms1_error = 30
13:37:59.763275 INFO: initial parameter: ms2_error = 30
13:37:59.763351 INFO: initial parameter: rt_error = 2099.9331315
13:37:59.763422 INFO: initial parameter: mobility_error = 0.1
13:37:59.763478 INFO: initial parameter: column_type = library
13:37:59.763530 INFO: initial parameter: num_candidates = 1
13:37:59.763581 INFO: initial parameter: classifier_version = -1
13:37:59.763630 INFO: initial parameter: fwhm_rt = 5
13:37:59.763684 INFO: initial parameter: fwhm_mobility = 0.01
13:37:59.763735 INFO: initial parameter: score_cutoff = 0
13:37:59.763825 INFO: Initializing TimingManager
13:37:59.763902 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
13:37:59.764081 INFO: FDRManager not loaded from disk.
13:37:59.764118 INFO: Initializing FDRManager
13:37:59.764176 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
13:38:01.069061 PROGRESS: 5,215,079 target precursors potentially observable (0 removed)
13:38:02.925827 PROGRESS: Starting initial search for precursors.
13:38:03.139090 INFO: Starting optimization step 0.
13:38:03.139359 PROGRESS: === Extracting elution groups 0 to 200 ===
13:38:03.139467 PROGRESS: Extracting batch of 398 precursors
13:38:03.140558 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:38:03.140606 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:38:03.140649 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
13:38:03.140677 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
13:38:03.141984 INFO: Starting candidate selection
13:38:06.161891 INFO: Starting candidate scoring
13:38:06.220335 INFO: Finished candidate processing
13:38:06.220430 INFO: Collecting candidate features
13:38:06.229738 INFO: Collecting fragment features
13:38:06.231778 INFO: Finished candidate scoring
13:38:06.232694 PROGRESS: === Extracted 336 precursors and 3457 fragments ===
13:38:06.232974 INFO: performing precursor FDR with 47 features
13:38:06.233010 INFO: Decoy channel: -1
13:38:06.233033 INFO: Competetive: True
13:38:06.234020 INFO: Setting torch num_threads to 2 for FDR classification task
13:38:06.244528 INFO: Test AUC: 0.488
13:38:06.244586 INFO: Train AUC: 0.457
13:38:06.244614 INFO: AUC difference: 6.94%
13:38:06.244634 WARNING: AUC difference > 5%. This may indicate overfitting.
13:38:06.420540 INFO: Resetting torch num_threads to 100
13:38:06.421110 INFO: === FDR correction performed with classifier version -1 ===
13:38:06.421697 PROGRESS: ============================= Precursor FDR =============================
13:38:06.421786 PROGRESS: Total precursors accumulated: 174
13:38:06.421845 PROGRESS: Target precursors: 87 (50.00%)
13:38:06.421895 PROGRESS: Decoy precursors: 87 (50.00%)
13:38:06.421947 PROGRESS: 
13:38:06.421993 PROGRESS: Precursor Summary:
13:38:06.422800 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
13:38:06.422887 PROGRESS: 
13:38:06.422941 PROGRESS: Protein Summary:
13:38:06.423818 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
13:38:06.423909 PROGRESS: =========================================================================
13:38:06.479632 INFO: Starting optimization step 1.
13:38:06.479831 PROGRESS: === Extracting elution groups 200 to 600 ===
13:38:06.479899 PROGRESS: Extracting batch of 786 precursors
13:38:06.480740 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:38:06.480788 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:38:06.480817 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
13:38:06.480838 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
13:38:06.481598 INFO: Starting candidate selection
13:38:11.370589 INFO: Starting candidate scoring
13:38:11.460445 INFO: Finished candidate processing
13:38:11.460569 INFO: Collecting candidate features
13:38:11.470688 INFO: Collecting fragment features
13:38:11.473074 INFO: Finished candidate scoring
13:38:11.475380 PROGRESS: === Extracted 1048 precursors and 10749 fragments ===
13:38:11.476106 INFO: performing precursor FDR with 47 features
13:38:11.476148 INFO: Decoy channel: -1
13:38:11.476173 INFO: Competetive: True
13:38:11.478890 INFO: Setting torch num_threads to 2 for FDR classification task
13:38:11.490228 INFO: Test AUC: 0.491
13:38:11.490298 INFO: Train AUC: 0.481
13:38:11.490327 INFO: AUC difference: 2.18%
13:38:11.667874 INFO: Resetting torch num_threads to 100
13:38:11.668656 INFO: === FDR correction performed with classifier version -1 ===
13:38:11.669368 PROGRESS: ============================= Precursor FDR =============================
13:38:11.669459 PROGRESS: Total precursors accumulated: 539
13:38:11.669518 PROGRESS: Target precursors: 278 (51.58%)
13:38:11.669568 PROGRESS: Decoy precursors: 261 (48.42%)
13:38:11.669625 PROGRESS: 
13:38:11.669669 PROGRESS: Precursor Summary:
13:38:11.670507 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
13:38:11.670595 PROGRESS: 
13:38:11.670650 PROGRESS: Protein Summary:
13:38:11.671564 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
13:38:11.671654 PROGRESS: =========================================================================
13:38:11.732138 INFO: Starting optimization step 2.
13:38:11.732394 PROGRESS: === Extracting elution groups 600 to 1400 ===
13:38:11.732466 PROGRESS: Extracting batch of 1566 precursors
13:38:11.733534 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:38:11.733583 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:38:11.733612 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
13:38:11.733634 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
13:38:11.734493 INFO: Starting candidate selection
13:38:20.328784 INFO: Starting candidate scoring
13:38:20.463647 INFO: Finished candidate processing
13:38:20.463760 INFO: Collecting candidate features
13:38:20.475080 INFO: Collecting fragment features
13:38:20.478160 INFO: Finished candidate scoring
13:38:20.481589 PROGRESS: === Extracted 2415 precursors and 24319 fragments ===
13:38:20.482605 INFO: performing precursor FDR with 47 features
13:38:20.482650 INFO: Decoy channel: -1
13:38:20.482676 INFO: Competetive: True
13:38:20.485933 INFO: Setting torch num_threads to 2 for FDR classification task
13:38:20.502952 INFO: Test AUC: 0.489
13:38:20.503230 INFO: Train AUC: 0.485
13:38:20.503266 INFO: AUC difference: 0.77%
13:38:20.690205 INFO: Resetting torch num_threads to 100
13:38:20.691195 INFO: === FDR correction performed with classifier version -1 ===
13:38:20.692059 PROGRESS: ============================= Precursor FDR =============================
13:38:20.692158 PROGRESS: Total precursors accumulated: 1,247
13:38:20.692219 PROGRESS: Target precursors: 630 (50.52%)
13:38:20.692270 PROGRESS: Decoy precursors: 617 (49.48%)
13:38:20.692321 PROGRESS: 
13:38:20.692368 PROGRESS: Precursor Summary:
13:38:20.693229 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
13:38:20.693321 PROGRESS: 
13:38:20.693377 PROGRESS: Protein Summary:
13:38:20.694284 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
13:38:20.694378 PROGRESS: =========================================================================
13:38:20.762673 INFO: Starting optimization step 3.
13:38:20.762947 PROGRESS: === Extracting elution groups 1400 to 3000 ===
13:38:20.763025 PROGRESS: Extracting batch of 3160 precursors
13:38:20.764423 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:38:20.764476 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:38:20.764506 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
13:38:20.764528 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
13:38:20.765377 INFO: Starting candidate selection
13:38:38.501794 INFO: Starting candidate scoring
13:38:38.739150 INFO: Finished candidate processing
13:38:38.739273 INFO: Collecting candidate features
13:38:38.755127 INFO: Collecting fragment features
13:38:38.761784 INFO: Finished candidate scoring
13:38:38.776244 PROGRESS: === Extracted 5169 precursors and 51906 fragments ===
13:38:38.777681 INFO: performing precursor FDR with 47 features
13:38:38.777726 INFO: Decoy channel: -1
13:38:38.777751 INFO: Competetive: True
13:38:38.782643 INFO: Setting torch num_threads to 2 for FDR classification task
13:38:38.812352 INFO: Test AUC: 0.476
13:38:38.812482 INFO: Train AUC: 0.494
13:38:38.812513 INFO: AUC difference: 3.71%
13:38:39.002075 INFO: Resetting torch num_threads to 100
13:38:39.003340 INFO: === FDR correction performed with classifier version -1 ===
13:38:39.004343 PROGRESS: ============================= Precursor FDR =============================
13:38:39.004445 PROGRESS: Total precursors accumulated: 2,655
13:38:39.004506 PROGRESS: Target precursors: 1,351 (50.89%)
13:38:39.004557 PROGRESS: Decoy precursors: 1,304 (49.11%)
13:38:39.004629 PROGRESS: 
13:38:39.004680 PROGRESS: Precursor Summary:
13:38:39.005567 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
13:38:39.005659 PROGRESS: 
13:38:39.005715 PROGRESS: Protein Summary:
13:38:39.006627 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
13:38:39.006717 PROGRESS: =========================================================================
13:38:39.095863 INFO: Starting optimization step 4.
13:38:39.096133 PROGRESS: === Extracting elution groups 3000 to 6200 ===
13:38:39.096221 PROGRESS: Extracting batch of 6310 precursors
13:38:39.098235 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:38:39.098286 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:38:39.098325 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
13:38:39.098346 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
13:38:39.099271 INFO: Starting candidate selection
13:39:14.979110 INFO: Starting candidate scoring
13:39:15.420315 INFO: Finished candidate processing
13:39:15.420419 INFO: Collecting candidate features
13:39:15.434813 WARNING: intensity_correlation has 1 NaNs ( 0.02 % out of 5478)
13:39:15.437997 INFO: Collecting fragment features
13:39:15.446987 INFO: Finished candidate scoring
13:39:15.456455 PROGRESS: === Extracted 10647 precursors and 107301 fragments ===
13:39:15.458123 INFO: performing precursor FDR with 47 features
13:39:15.458175 INFO: Decoy channel: -1
13:39:15.458201 INFO: Competetive: True
13:39:15.464259 INFO: Setting torch num_threads to 2 for FDR classification task
13:39:15.466437 WARNING: dropped 1 target PSMs due to missing features
13:39:15.500889 INFO: Test AUC: 0.480
13:39:15.501013 INFO: Train AUC: 0.494
13:39:15.501042 INFO: AUC difference: 2.91%
13:39:15.688226 INFO: Resetting torch num_threads to 100
13:39:15.689712 INFO: === FDR correction performed with classifier version -1 ===
13:39:15.690975 PROGRESS: ============================= Precursor FDR =============================
13:39:15.691087 PROGRESS: Total precursors accumulated: 5,463
13:39:15.691148 PROGRESS: Target precursors: 2,754 (50.41%)
13:39:15.691199 PROGRESS: Decoy precursors: 2,709 (49.59%)
13:39:15.691244 PROGRESS: 
13:39:15.691289 PROGRESS: Precursor Summary:
13:39:15.692147 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
13:39:15.692234 PROGRESS: 
13:39:15.692293 PROGRESS: Protein Summary:
13:39:15.693217 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
13:39:15.693304 PROGRESS: =========================================================================
13:39:15.793011 INFO: Starting optimization step 5.
13:39:15.793266 PROGRESS: === Extracting elution groups 6200 to 12600 ===
13:39:15.793342 PROGRESS: Extracting batch of 12602 precursors
13:39:15.796485 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:39:15.796536 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:39:15.796566 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
13:39:15.796587 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
13:39:15.845815 INFO: Starting candidate selection
13:40:20.428474 INFO: Starting candidate scoring
13:40:21.034104 INFO: Finished candidate processing
13:40:21.034237 INFO: Collecting candidate features
13:40:21.064654 WARNING: intensity_correlation has 1 NaNs ( 0.01 % out of 10962)
13:40:21.068455 INFO: Collecting fragment features
13:40:21.084304 INFO: Finished candidate scoring
13:40:21.162475 PROGRESS: === Extracted 21609 precursors and 216900 fragments ===
13:40:21.169304 INFO: performing precursor FDR with 47 features
13:40:21.169415 INFO: Decoy channel: -1
13:40:21.169442 INFO: Competetive: True
13:40:21.188163 INFO: Setting torch num_threads to 2 for FDR classification task
13:40:21.193315 WARNING: dropped 2 target PSMs due to missing features
13:40:21.513172 INFO: Test AUC: 0.511
13:40:21.513319 INFO: Train AUC: 0.522
13:40:21.513349 INFO: AUC difference: 2.07%
13:40:21.702333 INFO: Resetting torch num_threads to 100
13:40:21.705045 INFO: === FDR correction performed with classifier version -1 ===
13:40:21.707456 PROGRESS: ============================= Precursor FDR =============================
13:40:21.707591 PROGRESS: Total precursors accumulated: 11,083
13:40:21.707655 PROGRESS: Target precursors: 5,970 (53.87%)
13:40:21.707712 PROGRESS: Decoy precursors: 5,113 (46.13%)
13:40:21.707757 PROGRESS: 
13:40:21.707802 PROGRESS: Precursor Summary:
13:40:21.708771 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
13:40:21.708868 PROGRESS: 
13:40:21.708922 PROGRESS: Protein Summary:
13:40:21.709896 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
13:40:21.709988 PROGRESS: =========================================================================
13:40:21.897893 INFO: Starting optimization step 6.
13:40:21.898196 PROGRESS: === Extracting elution groups 12600 to 25400 ===
13:40:21.898298 PROGRESS: Extracting batch of 25176 precursors
13:40:21.905155 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:40:21.905234 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:40:21.905290 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
13:40:21.905313 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
13:40:21.906373 INFO: Starting candidate selection
13:42:30.991272 INFO: Starting candidate scoring
13:42:32.385742 INFO: Finished candidate processing
13:42:32.387164 INFO: Collecting candidate features
13:42:32.468933 WARNING: intensity_correlation has 7 NaNs ( 0.03 % out of 21872)
13:42:32.469246 WARNING: height_correlation has 2 NaNs ( 0.01 % out of 21872)
13:42:32.473223 INFO: Collecting fragment features
13:42:32.493173 INFO: Finished candidate scoring
13:42:32.578712 PROGRESS: === Extracted 43481 precursors and 434947 fragments ===
13:42:32.586417 INFO: performing precursor FDR with 47 features
13:42:32.586529 INFO: Decoy channel: -1
13:42:32.586555 INFO: Competetive: True
13:42:32.608608 INFO: Setting torch num_threads to 2 for FDR classification task
13:42:32.618176 WARNING: dropped 5 target PSMs due to missing features
13:42:32.618324 WARNING: dropped 5 decoy PSMs due to missing features
13:42:33.340992 INFO: Test AUC: 0.547
13:42:33.341132 INFO: Train AUC: 0.566
13:42:33.341163 INFO: AUC difference: 3.37%
13:42:33.540655 INFO: Resetting torch num_threads to 100
13:42:33.543863 INFO: === FDR correction performed with classifier version -1 ===
13:42:33.547353 PROGRESS: ============================= Precursor FDR =============================
13:42:33.547504 PROGRESS: Total precursors accumulated: 22,307
13:42:33.547564 PROGRESS: Target precursors: 13,302 (59.63%)
13:42:33.547616 PROGRESS: Decoy precursors: 9,005 (40.37%)
13:42:33.547660 PROGRESS: 
13:42:33.547705 PROGRESS: Precursor Summary:
13:42:33.548772 PROGRESS: Channel   0:	 0.05 FDR:    64; 0.01 FDR:    17; 0.001 FDR:    17
13:42:33.548869 PROGRESS: 
13:42:33.548924 PROGRESS: Protein Summary:
13:42:33.550038 PROGRESS: Channel   0:	 0.05 FDR:    64; 0.01 FDR:    17; 0.001 FDR:    17
13:42:33.550130 PROGRESS: =========================================================================
13:42:34.062728 INFO: Starting optimization step 7.
13:42:34.063059 PROGRESS: === Extracting elution groups 25400 to 51000 ===
13:42:34.063143 PROGRESS: Extracting batch of 50417 precursors
13:42:34.085927 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:42:34.086169 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:42:34.086259 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
13:42:34.086315 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
13:42:34.087681 INFO: Starting candidate selection
13:46:55.616988 INFO: Starting candidate scoring
13:46:57.870694 INFO: Finished candidate processing
13:46:57.870887 INFO: Collecting candidate features
13:46:57.978657 WARNING: intensity_correlation has 9 NaNs ( 0.02 % out of 43914)
13:46:57.985026 INFO: Collecting fragment features
13:46:58.020830 INFO: Finished candidate scoring
13:46:58.153038 PROGRESS: === Extracted 87395 precursors and 874459 fragments ===
13:46:58.167623 INFO: performing precursor FDR with 47 features
13:46:58.167735 INFO: Decoy channel: -1
13:46:58.167762 INFO: Competetive: True
13:46:58.212265 INFO: Setting torch num_threads to 2 for FDR classification task
13:46:58.234277 WARNING: dropped 11 target PSMs due to missing features
13:46:58.234414 WARNING: dropped 8 decoy PSMs due to missing features
13:46:59.867747 INFO: Test AUC: 0.553
13:46:59.867903 INFO: Train AUC: 0.587
13:46:59.868010 INFO: AUC difference: 5.77%
13:46:59.868035 WARNING: AUC difference > 5%. This may indicate overfitting.
13:47:00.076792 INFO: Resetting torch num_threads to 100
13:47:00.082465 INFO: === FDR correction performed with classifier version -1 ===
13:47:00.091377 PROGRESS: ============================= Precursor FDR =============================
13:47:00.091650 PROGRESS: Total precursors accumulated: 44,820
13:47:00.091714 PROGRESS: Target precursors: 27,398 (61.13%)
13:47:00.091764 PROGRESS: Decoy precursors: 17,422 (38.87%)
13:47:00.091812 PROGRESS: 
13:47:00.091855 PROGRESS: Precursor Summary:
13:47:00.093258 PROGRESS: Channel   0:	 0.05 FDR:   471; 0.01 FDR:   343; 0.001 FDR:    15
13:47:00.093358 PROGRESS: 
13:47:00.093413 PROGRESS: Protein Summary:
13:47:00.094800 PROGRESS: Channel   0:	 0.05 FDR:   446; 0.01 FDR:   328; 0.001 FDR:    15
13:47:00.094894 PROGRESS: =========================================================================
13:47:00.161115 INFO: fragments_df: keeping 3035 of 874459 [sum(precursor_idx_mask)=3820 sum(mass_error_mask)=874459 stop_rank=3035
13:47:00.408890 INFO: calibration group: precursor, fitting mz estimator 
13:47:00.535569 INFO: calibration group: precursor, fitting rt estimator 
13:47:00.669527 INFO: calibration group: precursor, fitting mobility estimator 
13:47:00.799430 INFO: calibration group: fragment, fitting mz estimator 
13:47:01.201681 INFO: Using score_cutoff 56.61695865097046 (fac=0.99, q=1)
13:47:01.202138 INFO: calibration group: precursor, predicting mz
13:47:01.216664 INFO: calibration group: precursor, predicting rt
13:47:01.277319 INFO: calibration group: precursor, predicting mobility
13:47:01.290383 INFO: calibration group: fragment, predicting mz
13:47:01.412218 PROGRESS: Required number of precursors found. Starting search parameter optimization.
13:47:01.412505 INFO: Starting optimization step 8.
13:47:01.412581 PROGRESS: === Extracting elution groups 0 to 51000 ===
13:47:01.412655 PROGRESS: Extracting batch of 100415 precursors
13:47:01.443640 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:47:01.443771 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:47:01.443824 INFO: FWHM in RT is 3.35 seconds, sigma is 0.74
13:47:01.443847 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.24
13:47:01.468795 INFO: Starting candidate selection
13:55:38.583386 INFO: Starting candidate scoring
13:55:47.731597 INFO: Finished candidate processing
13:55:47.733489 INFO: Collecting candidate features
13:55:48.072230 INFO: Collecting fragment features
13:55:48.186519 INFO: Finished candidate scoring
13:55:48.296418 PROGRESS: === Extracted 172746 precursors and 1757773 fragments ===
13:55:48.296947 INFO: performing precursor FDR with 47 features
13:55:48.296990 INFO: Decoy channel: -1
13:55:48.297019 INFO: Competetive: True
13:55:48.361847 INFO: Setting torch num_threads to 2 for FDR classification task
13:55:51.946948 INFO: Test AUC: 0.567
13:55:51.947100 INFO: Train AUC: 0.594
13:55:51.947131 INFO: AUC difference: 4.40%
13:55:52.178591 INFO: Resetting torch num_threads to 100
13:55:52.185346 INFO: === FDR correction performed with classifier version 7 ===
13:55:52.195396 PROGRESS: ============================= Precursor FDR =============================
13:55:52.195676 PROGRESS: Total precursors accumulated: 45,857
13:55:52.195745 PROGRESS: Target precursors: 28,880 (62.98%)
13:55:52.195797 PROGRESS: Decoy precursors: 16,977 (37.02%)
13:55:52.195843 PROGRESS: 
13:55:52.195893 PROGRESS: Precursor Summary:
13:55:52.197502 PROGRESS: Channel   0:	 0.05 FDR:   481; 0.01 FDR:   361; 0.001 FDR:   211
13:55:52.197599 PROGRESS: 
13:55:52.197671 PROGRESS: Protein Summary:
13:55:52.199089 PROGRESS: Channel   0:	 0.05 FDR:   456; 0.01 FDR:   347; 0.001 FDR:   206
13:55:52.199197 PROGRESS: =========================================================================
13:55:52.317297 INFO: fragments_df: keeping 4408 of 1757773 [sum(precursor_idx_mask)=7755 sum(mass_error_mask)=1757773 stop_rank=4408
13:55:52.528508 INFO: calibration group: precursor, fitting mz estimator 
13:55:52.658967 INFO: calibration group: precursor, fitting rt estimator 
13:55:52.788448 INFO: calibration group: precursor, fitting mobility estimator 
13:55:52.907005 INFO: calibration group: fragment, fitting mz estimator 
13:55:53.424151 INFO: Using score_cutoff 51.54666291046143 (fac=0.99, q=1)
13:55:53.424615 INFO: calibration group: precursor, predicting mz
13:55:53.438402 INFO: calibration group: precursor, predicting rt
13:55:53.499051 INFO: calibration group: precursor, predicting mobility
13:55:53.512383 INFO: calibration group: fragment, predicting mz
13:55:53.629467 INFO: === checking if optimization conditions were reached ===
13:55:53.629807 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
13:55:53.632332 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 16.5683.
13:55:53.632389 INFO: ==============================================
13:55:53.632496 INFO: Starting optimization step 9.
13:55:53.632562 PROGRESS: === Extracting elution groups 0 to 51000 ===
13:55:53.632635 PROGRESS: Extracting batch of 100415 precursors
13:55:53.663637 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:55:53.663781 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:55:53.663835 INFO: FWHM in RT is 3.20 seconds, sigma is 0.70
13:55:53.663859 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.10
13:55:53.688678 INFO: Starting candidate selection
14:03:54.772799 INFO: Starting candidate scoring
14:04:01.462904 INFO: Finished candidate processing
14:04:01.463211 INFO: Collecting candidate features
14:04:01.798454 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 172730)
14:04:01.808093 INFO: Collecting fragment features
14:04:01.928529 INFO: Finished candidate scoring
14:04:02.061324 PROGRESS: === Extracted 172730 precursors and 1706439 fragments ===
14:04:02.061855 INFO: performing precursor FDR with 47 features
14:04:02.061896 INFO: Decoy channel: -1
14:04:02.061920 INFO: Competetive: True
14:04:02.153015 INFO: Setting torch num_threads to 2 for FDR classification task
14:04:02.190476 WARNING: dropped 1 target PSMs due to missing features
14:04:02.190638 WARNING: dropped 2 decoy PSMs due to missing features
14:04:05.700625 INFO: Test AUC: 0.560
14:04:05.700781 INFO: Train AUC: 0.588
14:04:05.700812 INFO: AUC difference: 4.88%
14:04:05.938870 INFO: Resetting torch num_threads to 100
14:04:05.945791 INFO: === FDR correction performed with classifier version 7 ===
14:04:05.955934 PROGRESS: ============================= Precursor FDR =============================
14:04:05.956222 PROGRESS: Total precursors accumulated: 45,825
14:04:05.956287 PROGRESS: Target precursors: 28,409 (61.99%)
14:04:05.956338 PROGRESS: Decoy precursors: 17,416 (38.01%)
14:04:05.956384 PROGRESS: 
14:04:05.956429 PROGRESS: Precursor Summary:
14:04:05.957840 PROGRESS: Channel   0:	 0.05 FDR:   654; 0.01 FDR:   436; 0.001 FDR:   218
14:04:05.957944 PROGRESS: 
14:04:05.958002 PROGRESS: Protein Summary:
14:04:05.959495 PROGRESS: Channel   0:	 0.05 FDR:   611; 0.01 FDR:   413; 0.001 FDR:   210
14:04:05.959598 PROGRESS: =========================================================================
14:04:06.073104 INFO: fragments_df: keeping 5000 of 1706439 [sum(precursor_idx_mask)=9179 sum(mass_error_mask)=1706439 stop_rank=5000
14:04:06.236603 INFO: calibration group: precursor, fitting mz estimator 
14:04:06.349356 INFO: calibration group: precursor, fitting rt estimator 
14:04:06.458939 INFO: calibration group: precursor, fitting mobility estimator 
14:04:06.572885 INFO: calibration group: fragment, fitting mz estimator 
14:04:07.243033 INFO: Using score_cutoff 50.14850619506836 (fac=0.99, q=1)
14:04:07.243575 INFO: calibration group: precursor, predicting mz
14:04:07.251119 INFO: calibration group: precursor, predicting rt
14:04:07.281807 INFO: calibration group: precursor, predicting mobility
14:04:07.288966 INFO: calibration group: fragment, predicting mz
14:04:07.351617 INFO: === checking if optimization conditions were reached ===
14:04:07.351998 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
14:04:07.354857 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 8.4559.
14:04:07.354965 INFO: ==============================================
14:04:07.355163 INFO: Starting optimization step 10.
14:04:07.355247 PROGRESS: === Extracting elution groups 0 to 25400 ===
14:04:07.355331 PROGRESS: Extracting batch of 49998 precursors
14:04:07.378863 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:04:07.379045 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:04:07.379114 INFO: FWHM in RT is 3.01 seconds, sigma is 0.66
14:04:07.379144 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.56
14:04:07.399510 INFO: Starting candidate selection
14:08:02.057673 INFO: Starting candidate scoring
14:08:04.355777 INFO: Finished candidate processing
14:08:04.355958 INFO: Collecting candidate features
14:08:04.561665 WARNING: intensity_correlation has 10 NaNs ( 0.01 % out of 85626)
14:08:04.568700 INFO: Collecting fragment features
14:08:04.625227 INFO: Finished candidate scoring
14:08:04.674556 PROGRESS: === Extracted 85626 precursors and 799046 fragments ===
14:08:04.675095 INFO: performing precursor FDR with 47 features
14:08:04.675136 INFO: Decoy channel: -1
14:08:04.675160 INFO: Competetive: True
14:08:04.714284 INFO: Setting torch num_threads to 2 for FDR classification task
14:08:04.736600 WARNING: dropped 3 target PSMs due to missing features
14:08:04.736750 WARNING: dropped 7 decoy PSMs due to missing features
14:08:06.129840 INFO: Test AUC: 0.558
14:08:06.129989 INFO: Train AUC: 0.588
14:08:06.130022 INFO: AUC difference: 5.10%
14:08:06.130043 WARNING: AUC difference > 5%. This may indicate overfitting.
14:08:06.339505 INFO: Resetting torch num_threads to 100
14:08:06.343246 INFO: === FDR correction performed with classifier version 7 ===
14:08:06.348111 PROGRESS: ============================= Precursor FDR =============================
14:08:06.348268 PROGRESS: Total precursors accumulated: 22,741
14:08:06.348331 PROGRESS: Target precursors: 14,160 (62.27%)
14:08:06.348386 PROGRESS: Decoy precursors: 8,581 (37.73%)
14:08:06.348432 PROGRESS: 
14:08:06.348475 PROGRESS: Precursor Summary:
14:08:06.349984 PROGRESS: Channel   0:	 0.05 FDR:   231; 0.01 FDR:   201; 0.001 FDR:   184
14:08:06.350077 PROGRESS: 
14:08:06.350132 PROGRESS: Protein Summary:
14:08:06.351428 PROGRESS: Channel   0:	 0.05 FDR:   227; 0.01 FDR:   197; 0.001 FDR:   180
14:08:06.351519 PROGRESS: =========================================================================
14:08:06.426236 INFO: fragments_df: keeping 2152 of 799046 [sum(precursor_idx_mask)=4128 sum(mass_error_mask)=799046 stop_rank=2152
14:08:06.560515 INFO: calibration group: precursor, fitting mz estimator 
14:08:06.679525 INFO: calibration group: precursor, fitting rt estimator 
14:08:06.793470 INFO: calibration group: precursor, fitting mobility estimator 
14:08:06.921018 INFO: calibration group: fragment, fitting mz estimator 
14:08:07.209719 INFO: Using score_cutoff 39.28625930786133 (fac=0.99, q=1)
14:08:07.210196 INFO: calibration group: precursor, predicting mz
14:08:07.218062 INFO: calibration group: precursor, predicting rt
14:08:07.248807 INFO: calibration group: precursor, predicting mobility
14:08:07.256000 INFO: calibration group: fragment, predicting mz
14:08:07.313972 INFO: === checking if optimization conditions were reached ===
14:08:07.314281 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
14:08:07.316778 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 5.1536.
14:08:07.316847 INFO: ==============================================
14:08:07.316947 INFO: Starting optimization step 11.
14:08:07.317015 PROGRESS: === Extracting elution groups 0 to 25400 ===
14:08:07.317084 PROGRESS: Extracting batch of 49998 precursors
14:08:07.332942 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:08:07.333076 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:08:07.333130 INFO: FWHM in RT is 2.78 seconds, sigma is 0.61
14:08:07.333154 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.48
14:08:07.342286 INFO: Starting candidate selection
14:12:00.344603 INFO: Starting candidate scoring
14:12:02.606204 INFO: Finished candidate processing
14:12:02.606374 INFO: Collecting candidate features
14:12:02.769770 WARNING: intensity_correlation has 25 NaNs ( 0.03 % out of 85488)
14:12:02.778763 INFO: Collecting fragment features
14:12:02.832992 INFO: Finished candidate scoring
14:12:02.881202 PROGRESS: === Extracted 85488 precursors and 747351 fragments ===
14:12:02.881696 INFO: performing precursor FDR with 47 features
14:12:02.881737 INFO: Decoy channel: -1
14:12:02.881763 INFO: Competetive: True
14:12:02.914402 INFO: Setting torch num_threads to 2 for FDR classification task
14:12:02.932492 WARNING: dropped 14 target PSMs due to missing features
14:12:02.932637 WARNING: dropped 11 decoy PSMs due to missing features
14:12:04.034322 INFO: Test AUC: 0.557
14:12:04.034467 INFO: Train AUC: 0.591
14:12:04.034499 INFO: AUC difference: 5.80%
14:12:04.034521 WARNING: AUC difference > 5%. This may indicate overfitting.
14:12:04.240939 INFO: Resetting torch num_threads to 100
14:12:04.244009 INFO: === FDR correction performed with classifier version 7 ===
14:12:04.247720 PROGRESS: ============================= Precursor FDR =============================
14:12:04.247864 PROGRESS: Total precursors accumulated: 22,741
14:12:04.247929 PROGRESS: Target precursors: 14,013 (61.62%)
14:12:04.247982 PROGRESS: Decoy precursors: 8,728 (38.38%)
14:12:04.248029 PROGRESS: 
14:12:04.248075 PROGRESS: Precursor Summary:
14:12:04.249139 PROGRESS: Channel   0:	 0.05 FDR:   239; 0.01 FDR:    25; 0.001 FDR:    25
14:12:04.249239 PROGRESS: 
14:12:04.249295 PROGRESS: Protein Summary:
14:12:04.250415 PROGRESS: Channel   0:	 0.05 FDR:   234; 0.01 FDR:    25; 0.001 FDR:    25
14:12:04.250506 PROGRESS: =========================================================================
14:12:04.413146 INFO: calibration group: precursor, predicting mz
14:12:04.421275 INFO: calibration group: precursor, predicting rt
14:12:04.451932 INFO: calibration group: precursor, predicting mobility
14:12:04.458957 INFO: calibration group: fragment, predicting mz
14:12:04.515512 INFO: === skipping optimization until target number of precursors are found ===
14:12:04.515850 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
14:12:04.515943 INFO: Starting optimization step 12.
14:12:04.516035 PROGRESS: === Extracting elution groups 25400 to 51000 ===
14:12:04.516118 PROGRESS: Extracting batch of 50417 precursors
14:12:04.533998 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:12:04.534144 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:12:04.534204 INFO: FWHM in RT is 2.78 seconds, sigma is 0.61
14:12:04.534233 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.48
14:12:04.535383 INFO: Starting candidate selection
14:16:35.758358 INFO: Starting candidate scoring
14:16:37.740761 INFO: Finished candidate processing
14:16:37.740943 INFO: Collecting candidate features
14:16:37.937256 WARNING: intensity_correlation has 18 NaNs ( 0.02 % out of 86104)
14:16:37.945568 INFO: Collecting fragment features
14:16:38.003159 INFO: Finished candidate scoring
14:16:38.142667 PROGRESS: === Extracted 171592 precursors and 1500498 fragments ===
14:16:38.167028 INFO: performing precursor FDR with 47 features
14:16:38.167197 INFO: Decoy channel: -1
14:16:38.167227 INFO: Competetive: True
14:16:38.259713 INFO: Setting torch num_threads to 2 for FDR classification task
14:16:38.300468 WARNING: dropped 24 target PSMs due to missing features
14:16:38.300637 WARNING: dropped 19 decoy PSMs due to missing features
14:16:42.415684 INFO: Test AUC: 0.556
14:16:42.415837 INFO: Train AUC: 0.591
14:16:42.415869 INFO: AUC difference: 5.98%
14:16:42.415892 WARNING: AUC difference > 5%. This may indicate overfitting.
14:16:42.660940 INFO: Resetting torch num_threads to 100
14:16:42.671819 INFO: === FDR correction performed with classifier version 7 ===
14:16:42.681837 PROGRESS: ============================= Precursor FDR =============================
14:16:42.682141 PROGRESS: Total precursors accumulated: 45,641
14:16:42.682207 PROGRESS: Target precursors: 28,178 (61.74%)
14:16:42.682259 PROGRESS: Decoy precursors: 17,463 (38.26%)
14:16:42.682304 PROGRESS: 
14:16:42.682347 PROGRESS: Precursor Summary:
14:16:42.683873 PROGRESS: Channel   0:	 0.05 FDR:   588; 0.01 FDR:   436; 0.001 FDR:   237
14:16:42.683973 PROGRESS: 
14:16:42.684033 PROGRESS: Protein Summary:
14:16:42.685508 PROGRESS: Channel   0:	 0.05 FDR:   554; 0.01 FDR:   413; 0.001 FDR:   227
14:16:42.685606 PROGRESS: =========================================================================
14:16:42.796125 INFO: fragments_df: keeping 4471 of 1500498 [sum(precursor_idx_mask)=8774 sum(mass_error_mask)=1500498 stop_rank=4471
14:16:43.736734 INFO: calibration group: precursor, fitting mz estimator 
14:16:43.978914 INFO: calibration group: precursor, fitting rt estimator 
14:16:44.144755 INFO: calibration group: precursor, fitting mobility estimator 
14:16:44.301225 INFO: calibration group: fragment, fitting mz estimator 
14:16:44.932314 INFO: Using score_cutoff 41.17825454521179 (fac=0.99, q=1)
14:16:44.932885 INFO: calibration group: precursor, predicting mz
14:16:44.941265 INFO: calibration group: precursor, predicting rt
14:16:44.976312 INFO: calibration group: precursor, predicting mobility
14:16:44.984690 INFO: calibration group: fragment, predicting mz
14:16:45.062857 INFO: === checking if optimization conditions were reached ===
14:16:45.063305 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
14:16:45.066307 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 4.5486.
14:16:45.066388 INFO: ==============================================
14:16:45.066546 INFO: Starting optimization step 13.
14:16:45.066623 PROGRESS: === Extracting elution groups 0 to 25400 ===
14:16:45.066723 PROGRESS: Extracting batch of 49998 precursors
14:16:45.086800 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:16:45.086975 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:16:45.087064 INFO: FWHM in RT is 2.48 seconds, sigma is 0.55
14:16:45.087091 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.88
14:16:45.103916 INFO: Starting candidate selection
14:20:37.834645 INFO: Starting candidate scoring
14:20:39.575506 INFO: Finished candidate processing
14:20:39.575648 INFO: Collecting candidate features
14:20:39.781375 WARNING: intensity_correlation has 39 NaNs ( 0.05 % out of 85192)
14:20:39.797821 INFO: Collecting fragment features
14:20:39.860039 INFO: Finished candidate scoring
14:20:39.932710 PROGRESS: === Extracted 85192 precursors and 703253 fragments ===
14:20:39.933501 INFO: performing precursor FDR with 47 features
14:20:39.933558 INFO: Decoy channel: -1
14:20:39.933582 INFO: Competetive: True
14:20:39.975707 INFO: Setting torch num_threads to 2 for FDR classification task
14:20:39.996915 WARNING: dropped 19 target PSMs due to missing features
14:20:39.997073 WARNING: dropped 20 decoy PSMs due to missing features
14:20:41.495490 INFO: Test AUC: 0.547
14:20:41.495644 INFO: Train AUC: 0.586
14:20:41.495675 INFO: AUC difference: 6.63%
14:20:41.495696 WARNING: AUC difference > 5%. This may indicate overfitting.
14:20:41.708032 INFO: Resetting torch num_threads to 100
14:20:41.711564 INFO: === FDR correction performed with classifier version 7 ===
14:20:41.716150 PROGRESS: ============================= Precursor FDR =============================
14:20:41.716327 PROGRESS: Total precursors accumulated: 22,723
14:20:41.716390 PROGRESS: Target precursors: 13,773 (60.61%)
14:20:41.716444 PROGRESS: Decoy precursors: 8,950 (39.39%)
14:20:41.716495 PROGRESS: 
14:20:41.716538 PROGRESS: Precursor Summary:
14:20:41.717648 PROGRESS: Channel   0:	 0.05 FDR:   194; 0.01 FDR:   140; 0.001 FDR:   133
14:20:41.717755 PROGRESS: 
14:20:41.717814 PROGRESS: Protein Summary:
14:20:41.718960 PROGRESS: Channel   0:	 0.05 FDR:   189; 0.01 FDR:   139; 0.001 FDR:   133
14:20:41.719061 PROGRESS: =========================================================================
14:20:41.911094 INFO: calibration group: precursor, predicting mz
14:20:41.918950 INFO: calibration group: precursor, predicting rt
14:20:41.949258 INFO: calibration group: precursor, predicting mobility
14:20:41.955803 INFO: calibration group: fragment, predicting mz
14:20:42.013330 INFO: === skipping optimization until target number of precursors are found ===
14:20:42.013661 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
14:20:42.013735 INFO: Starting optimization step 14.
14:20:42.013804 PROGRESS: === Extracting elution groups 25400 to 51000 ===
14:20:42.013875 PROGRESS: Extracting batch of 50417 precursors
14:20:42.028390 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:20:42.028522 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:20:42.028575 INFO: FWHM in RT is 2.48 seconds, sigma is 0.55
14:20:42.028600 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.88
14:20:42.029872 INFO: Starting candidate selection
14:24:41.106507 INFO: Starting candidate scoring
14:24:42.902540 INFO: Finished candidate processing
14:24:42.902647 INFO: Collecting candidate features
14:24:43.044574 WARNING: intensity_correlation has 46 NaNs ( 0.05 % out of 85828)
14:24:43.052872 INFO: Collecting fragment features
14:24:43.104990 INFO: Finished candidate scoring
14:24:43.231714 PROGRESS: === Extracted 171020 precursors and 1412292 fragments ===
14:24:43.253530 INFO: performing precursor FDR with 47 features
14:24:43.253669 INFO: Decoy channel: -1
14:24:43.253696 INFO: Competetive: True
14:24:43.333362 INFO: Setting torch num_threads to 2 for FDR classification task
14:24:43.368324 WARNING: dropped 46 target PSMs due to missing features
14:24:43.368467 WARNING: dropped 39 decoy PSMs due to missing features
14:24:46.419294 INFO: Test AUC: 0.553
14:24:46.419421 INFO: Train AUC: 0.590
14:24:46.419452 INFO: AUC difference: 6.31%
14:24:46.419473 WARNING: AUC difference > 5%. This may indicate overfitting.
14:24:46.648534 INFO: Resetting torch num_threads to 100
14:24:46.657228 INFO: === FDR correction performed with classifier version 7 ===
14:24:46.665992 PROGRESS: ============================= Precursor FDR =============================
14:24:46.666240 PROGRESS: Total precursors accumulated: 45,610
14:24:46.666303 PROGRESS: Target precursors: 28,173 (61.77%)
14:24:46.666357 PROGRESS: Decoy precursors: 17,437 (38.23%)
14:24:46.666404 PROGRESS: 
14:24:46.666448 PROGRESS: Precursor Summary:
14:24:46.668007 PROGRESS: Channel   0:	 0.05 FDR:   524; 0.01 FDR:   366; 0.001 FDR:   319
14:24:46.668107 PROGRESS: 
14:24:46.668161 PROGRESS: Protein Summary:
14:24:46.669599 PROGRESS: Channel   0:	 0.05 FDR:   491; 0.01 FDR:   345; 0.001 FDR:   302
14:24:46.669692 PROGRESS: =========================================================================
14:24:46.776531 INFO: fragments_df: keeping 3797 of 1412292 [sum(precursor_idx_mask)=7290 sum(mass_error_mask)=1412292 stop_rank=3797
14:24:46.989449 INFO: calibration group: precursor, fitting mz estimator 
14:24:47.099777 INFO: calibration group: precursor, fitting rt estimator 
14:24:47.206622 INFO: calibration group: precursor, fitting mobility estimator 
14:24:47.314059 INFO: calibration group: fragment, fitting mz estimator 
14:24:47.751625 INFO: Using score_cutoff 43.19814964485168 (fac=0.99, q=1)
14:24:47.752033 INFO: calibration group: precursor, predicting mz
14:24:47.765519 INFO: calibration group: precursor, predicting rt
14:24:47.827501 INFO: calibration group: precursor, predicting mobility
14:24:47.843701 INFO: calibration group: fragment, predicting mz
14:24:47.962250 INFO: === checking if optimization conditions were reached ===
14:24:47.962559 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
14:24:47.965010 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 4.1394.
14:24:47.965067 INFO: ==============================================
14:24:47.965179 INFO: Starting optimization step 15.
14:24:47.965250 PROGRESS: === Extracting elution groups 0 to 51000 ===
14:24:47.965319 PROGRESS: Extracting batch of 100415 precursors
14:24:47.994149 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:24:47.994280 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:24:47.994331 INFO: FWHM in RT is 2.35 seconds, sigma is 0.52
14:24:47.994354 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.61
14:24:48.003308 INFO: Starting candidate selection
14:32:21.939371 INFO: Starting candidate scoring
14:32:25.221164 INFO: Finished candidate processing
14:32:25.221268 INFO: Collecting candidate features
14:32:25.489298 WARNING: intensity_correlation has 67 NaNs ( 0.04 % out of 170679)
14:32:25.498824 INFO: Collecting fragment features
14:32:25.597318 INFO: Finished candidate scoring
14:32:25.687399 PROGRESS: === Extracted 170679 precursors and 1400562 fragments ===
14:32:25.687898 INFO: performing precursor FDR with 47 features
14:32:25.687939 INFO: Decoy channel: -1
14:32:25.687968 INFO: Competetive: True
14:32:25.749113 INFO: Setting torch num_threads to 2 for FDR classification task
14:32:25.782644 WARNING: dropped 31 target PSMs due to missing features
14:32:25.782785 WARNING: dropped 36 decoy PSMs due to missing features
14:32:29.066882 INFO: Test AUC: 0.559
14:32:29.067015 INFO: Train AUC: 0.589
14:32:29.067054 INFO: AUC difference: 5.02%
14:32:29.067076 WARNING: AUC difference > 5%. This may indicate overfitting.
14:32:29.295911 INFO: Resetting torch num_threads to 100
14:32:29.302651 INFO: === FDR correction performed with classifier version 7 ===
14:32:29.312180 PROGRESS: ============================= Precursor FDR =============================
14:32:29.312442 PROGRESS: Total precursors accumulated: 45,569
14:32:29.312521 PROGRESS: Target precursors: 28,111 (61.69%)
14:32:29.312574 PROGRESS: Decoy precursors: 17,458 (38.31%)
14:32:29.312620 PROGRESS: 
14:32:29.312666 PROGRESS: Precursor Summary:
14:32:29.314013 PROGRESS: Channel   0:	 0.05 FDR:   581; 0.01 FDR:   410; 0.001 FDR:   259
14:32:29.314105 PROGRESS: 
14:32:29.314160 PROGRESS: Protein Summary:
14:32:29.315606 PROGRESS: Channel   0:	 0.05 FDR:   549; 0.01 FDR:   385; 0.001 FDR:   243
14:32:29.315702 PROGRESS: =========================================================================
14:32:29.407506 INFO: fragments_df: keeping 4238 of 1400562 [sum(precursor_idx_mask)=8085 sum(mass_error_mask)=1400562 stop_rank=4238
14:32:29.541722 INFO: calibration group: precursor, fitting mz estimator 
14:32:29.674252 INFO: calibration group: precursor, fitting rt estimator 
14:32:29.804496 INFO: calibration group: precursor, fitting mobility estimator 
14:32:29.925378 INFO: calibration group: fragment, fitting mz estimator 
14:32:30.437492 INFO: Using score_cutoff 40.57087717323303 (fac=0.99, q=1)
14:32:30.437929 INFO: calibration group: precursor, predicting mz
14:32:30.445030 INFO: calibration group: precursor, predicting rt
14:32:30.474723 INFO: calibration group: precursor, predicting mobility
14:32:30.481318 INFO: calibration group: fragment, predicting mz
14:32:30.538206 INFO: === checking if optimization conditions were reached ===
14:32:30.538598 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
14:32:30.541646 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 4.1811.
14:32:30.541716 INFO: ==============================================
14:32:30.541851 INFO: Starting optimization step 16.
14:32:30.541924 PROGRESS: === Extracting elution groups 0 to 25400 ===
14:32:30.542003 PROGRESS: Extracting batch of 49998 precursors
14:32:30.565226 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:32:30.565397 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:32:30.565461 INFO: FWHM in RT is 2.26 seconds, sigma is 0.50
14:32:30.565489 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.52
14:32:30.594128 INFO: Starting candidate selection
14:41:45.542820 INFO: Starting candidate scoring
14:41:47.265907 INFO: Finished candidate processing
14:41:47.266038 INFO: Collecting candidate features
14:41:47.412618 WARNING: intensity_correlation has 30 NaNs ( 0.04 % out of 85029)
14:41:47.421529 INFO: Collecting fragment features
14:41:47.472353 INFO: Finished candidate scoring
14:41:47.519719 PROGRESS: === Extracted 85029 precursors and 696983 fragments ===
14:41:47.520448 INFO: performing precursor FDR with 47 features
14:41:47.520492 INFO: Decoy channel: -1
14:41:47.520518 INFO: Competetive: True
14:41:47.561624 INFO: Setting torch num_threads to 2 for FDR classification task
14:41:47.581561 WARNING: dropped 17 target PSMs due to missing features
14:41:47.581717 WARNING: dropped 13 decoy PSMs due to missing features
14:41:49.220458 INFO: Test AUC: 0.557
14:41:49.220606 INFO: Train AUC: 0.589
14:41:49.220638 INFO: AUC difference: 5.39%
14:41:49.220662 WARNING: AUC difference > 5%. This may indicate overfitting.
14:41:49.435974 INFO: Resetting torch num_threads to 100
14:41:49.439816 INFO: === FDR correction performed with classifier version 7 ===
14:41:49.445146 PROGRESS: ============================= Precursor FDR =============================
14:41:49.445327 PROGRESS: Total precursors accumulated: 22,713
14:41:49.445390 PROGRESS: Target precursors: 13,984 (61.57%)
14:41:49.445441 PROGRESS: Decoy precursors: 8,729 (38.43%)
14:41:49.445490 PROGRESS: 
14:41:49.445539 PROGRESS: Precursor Summary:
14:41:49.446697 PROGRESS: Channel   0:	 0.05 FDR:   248; 0.01 FDR:   169; 0.001 FDR:    94
14:41:49.446793 PROGRESS: 
14:41:49.446849 PROGRESS: Protein Summary:
14:41:49.448074 PROGRESS: Channel   0:	 0.05 FDR:   241; 0.01 FDR:   166; 0.001 FDR:    93
14:41:49.448184 PROGRESS: =========================================================================
14:41:49.962187 INFO: calibration group: precursor, predicting mz
14:41:49.970748 INFO: calibration group: precursor, predicting rt
14:41:50.001246 INFO: calibration group: precursor, predicting mobility
14:41:50.008391 INFO: calibration group: fragment, predicting mz
14:41:50.065433 INFO: === skipping optimization until target number of precursors are found ===
14:41:50.065765 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
14:41:50.065850 INFO: Starting optimization step 17.
14:41:50.065921 PROGRESS: === Extracting elution groups 25400 to 51000 ===
14:41:50.066021 PROGRESS: Extracting batch of 50417 precursors
14:41:50.082167 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:41:50.082299 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:41:50.082371 INFO: FWHM in RT is 2.26 seconds, sigma is 0.50
14:41:50.082398 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.52
14:41:50.083617 INFO: Starting candidate selection
14:45:35.277404 INFO: Starting candidate scoring
14:45:36.967485 INFO: Finished candidate processing
14:45:36.967599 INFO: Collecting candidate features
14:45:37.160066 WARNING: intensity_correlation has 41 NaNs ( 0.05 % out of 85856)
14:45:37.168917 INFO: Collecting fragment features
14:45:37.221739 INFO: Finished candidate scoring
14:45:37.431835 PROGRESS: === Extracted 170885 precursors and 1401308 fragments ===
14:45:37.454609 INFO: performing precursor FDR with 47 features
14:45:37.454772 INFO: Decoy channel: -1
14:45:37.454801 INFO: Competetive: True
14:45:37.544967 INFO: Setting torch num_threads to 2 for FDR classification task
14:45:37.582541 WARNING: dropped 37 target PSMs due to missing features
14:45:37.582704 WARNING: dropped 34 decoy PSMs due to missing features
14:45:41.431399 INFO: Test AUC: 0.557
14:45:41.431636 INFO: Train AUC: 0.592
14:45:41.431674 INFO: AUC difference: 5.88%
14:45:41.431697 WARNING: AUC difference > 5%. This may indicate overfitting.
14:45:41.674706 INFO: Resetting torch num_threads to 100
14:45:41.684814 INFO: === FDR correction performed with classifier version 7 ===
14:45:41.694015 PROGRESS: ============================= Precursor FDR =============================
14:45:41.694289 PROGRESS: Total precursors accumulated: 45,586
14:45:41.694364 PROGRESS: Target precursors: 28,082 (61.60%)
14:45:41.694432 PROGRESS: Decoy precursors: 17,504 (38.40%)
14:45:41.694481 PROGRESS: 
14:45:41.694527 PROGRESS: Precursor Summary:
14:45:41.696053 PROGRESS: Channel   0:	 0.05 FDR:   583; 0.01 FDR:   422; 0.001 FDR:   303
14:45:41.696152 PROGRESS: 
14:45:41.696207 PROGRESS: Protein Summary:
14:45:41.697710 PROGRESS: Channel   0:	 0.05 FDR:   545; 0.01 FDR:   398; 0.001 FDR:   285
14:45:41.697803 PROGRESS: =========================================================================
14:45:41.802995 INFO: fragments_df: keeping 4254 of 1401308 [sum(precursor_idx_mask)=8248 sum(mass_error_mask)=1401308 stop_rank=4254
14:45:42.007542 INFO: calibration group: precursor, fitting mz estimator 
14:45:42.119730 INFO: calibration group: precursor, fitting rt estimator 
14:45:42.227622 INFO: calibration group: precursor, fitting mobility estimator 
14:45:42.342015 INFO: calibration group: fragment, fitting mz estimator 
14:45:42.854136 INFO: Using score_cutoff 40.646381327819824 (fac=0.99, q=1)
14:45:42.854682 INFO: calibration group: precursor, predicting mz
14:45:42.862078 INFO: calibration group: precursor, predicting rt
14:45:42.892280 INFO: calibration group: precursor, predicting mobility
14:45:42.899137 INFO: calibration group: fragment, predicting mz
14:45:42.954591 INFO: === checking if optimization conditions were reached ===
14:45:42.955126 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
14:45:42.956751 PROGRESS: ✅ ms2_error      : optimization complete. Optimal parameter 5.1536 found after 7 searches.
14:45:42.956913 INFO: ==============================================
14:45:42.957234 PROGRESS: Optimization finished for ms2_error.
14:45:43.127400 INFO: calibration group: precursor, predicting mz
14:45:43.135638 INFO: calibration group: precursor, predicting rt
14:45:43.167295 INFO: calibration group: precursor, predicting mobility
14:45:43.174574 INFO: calibration group: fragment, predicting mz
14:45:43.262398 INFO: Starting optimization step 0.
14:45:43.262709 PROGRESS: === Extracting elution groups 0 to 25400 ===
14:45:43.262809 PROGRESS: Extracting batch of 49998 precursors
14:45:43.287493 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:45:43.287643 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:45:43.287706 INFO: FWHM in RT is 2.48 seconds, sigma is 0.55
14:45:43.287737 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.88
14:45:43.302069 INFO: Starting candidate selection
14:49:33.425510 INFO: Starting candidate scoring
14:49:35.434281 INFO: Finished candidate processing
14:49:35.434392 INFO: Collecting candidate features
14:49:35.581063 WARNING: intensity_correlation has 25 NaNs ( 0.03 % out of 85362)
14:49:35.593016 INFO: Collecting fragment features
14:49:35.655993 INFO: Finished candidate scoring
14:49:35.802004 PROGRESS: === Extracted 85362 precursors and 741510 fragments ===
14:49:35.802684 INFO: performing precursor FDR with 47 features
14:49:35.802730 INFO: Decoy channel: -1
14:49:35.802756 INFO: Competetive: True
14:49:35.875198 INFO: Setting torch num_threads to 2 for FDR classification task
14:49:35.905540 WARNING: dropped 13 target PSMs due to missing features
14:49:35.905749 WARNING: dropped 12 decoy PSMs due to missing features
14:49:37.712349 INFO: Test AUC: 0.568
14:49:37.712486 INFO: Train AUC: 0.612
14:49:37.712517 INFO: AUC difference: 7.16%
14:49:37.712538 WARNING: AUC difference > 5%. This may indicate overfitting.
14:49:37.922681 INFO: Resetting torch num_threads to 100
14:49:37.925611 INFO: === FDR correction performed with classifier version 12 ===
14:49:37.929469 PROGRESS: ============================= Precursor FDR =============================
14:49:37.929619 PROGRESS: Total precursors accumulated: 22,731
14:49:37.929697 PROGRESS: Target precursors: 14,410 (63.39%)
14:49:37.929753 PROGRESS: Decoy precursors: 8,321 (36.61%)
14:49:37.929801 PROGRESS: 
14:49:37.929857 PROGRESS: Precursor Summary:
14:49:37.930964 PROGRESS: Channel   0:	 0.05 FDR:   289; 0.01 FDR:   206; 0.001 FDR:   199
14:49:37.931066 PROGRESS: 
14:49:37.931124 PROGRESS: Protein Summary:
14:49:37.932348 PROGRESS: Channel   0:	 0.05 FDR:   281; 0.01 FDR:   202; 0.001 FDR:   195
14:49:37.932465 PROGRESS: =========================================================================
14:49:38.003427 INFO: fragments_df: keeping 2183 of 741510 [sum(precursor_idx_mask)=4194 sum(mass_error_mask)=741510 stop_rank=2183
14:49:38.136902 INFO: calibration group: precursor, fitting mz estimator 
14:49:38.275983 INFO: calibration group: precursor, fitting rt estimator 
14:49:38.381312 INFO: calibration group: precursor, fitting mobility estimator 
14:49:38.483346 INFO: calibration group: fragment, fitting mz estimator 
14:49:38.722073 INFO: Using score_cutoff 36.359069526672364 (fac=0.99, q=1)
14:49:38.722564 INFO: calibration group: precursor, predicting mz
14:49:38.730448 INFO: calibration group: precursor, predicting rt
14:49:38.760822 INFO: calibration group: precursor, predicting mobility
14:49:38.767694 INFO: calibration group: fragment, predicting mz
14:49:38.836044 INFO: === checking if optimization conditions were reached ===
14:49:38.836441 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
14:49:38.838982 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 745.3813.
14:49:38.839061 INFO: ==============================================
14:49:38.839188 INFO: Starting optimization step 1.
14:49:38.839269 PROGRESS: === Extracting elution groups 0 to 25400 ===
14:49:38.839387 PROGRESS: Extracting batch of 49998 precursors
14:49:38.864508 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:49:38.864669 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:49:38.864752 INFO: FWHM in RT is 2.38 seconds, sigma is 0.52
14:49:38.864785 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.69
14:49:38.874434 INFO: Starting candidate selection
14:51:15.775607 INFO: Starting candidate scoring
14:51:17.665019 INFO: Finished candidate processing
14:51:17.665123 INFO: Collecting candidate features
14:51:17.790562 WARNING: intensity_correlation has 51 NaNs ( 0.06 % out of 83326)
14:51:17.790917 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 83326)
14:51:17.799756 INFO: Collecting fragment features
14:51:17.852970 INFO: Finished candidate scoring
14:51:17.895534 PROGRESS: === Extracted 83326 precursors and 712651 fragments ===
14:51:17.896005 INFO: performing precursor FDR with 47 features
14:51:17.896044 INFO: Decoy channel: -1
14:51:17.896069 INFO: Competetive: True
14:51:17.922906 INFO: Setting torch num_threads to 2 for FDR classification task
14:51:17.939064 WARNING: dropped 31 target PSMs due to missing features
14:51:17.939209 WARNING: dropped 21 decoy PSMs due to missing features
14:51:19.201118 INFO: Test AUC: 0.560
14:51:19.201255 INFO: Train AUC: 0.606
14:51:19.201285 INFO: AUC difference: 7.47%
14:51:19.201307 WARNING: AUC difference > 5%. This may indicate overfitting.
14:51:19.407839 INFO: Resetting torch num_threads to 100
14:51:19.410657 INFO: === FDR correction performed with classifier version 12 ===
14:51:19.414410 PROGRESS: ============================= Precursor FDR =============================
14:51:19.414552 PROGRESS: Total precursors accumulated: 22,429
14:51:19.414612 PROGRESS: Target precursors: 14,106 (62.89%)
14:51:19.414663 PROGRESS: Decoy precursors: 8,323 (37.11%)
14:51:19.414710 PROGRESS: 
14:51:19.414770 PROGRESS: Precursor Summary:
14:51:19.415894 PROGRESS: Channel   0:	 0.05 FDR:   303; 0.01 FDR:   222; 0.001 FDR:   198
14:51:19.415989 PROGRESS: 
14:51:19.416051 PROGRESS: Protein Summary:
14:51:19.417487 PROGRESS: Channel   0:	 0.05 FDR:   293; 0.01 FDR:   217; 0.001 FDR:   194
14:51:19.417582 PROGRESS: =========================================================================
14:51:19.466587 INFO: fragments_df: keeping 2283 of 712651 [sum(precursor_idx_mask)=4411 sum(mass_error_mask)=712651 stop_rank=2283
14:51:19.592279 INFO: calibration group: precursor, fitting mz estimator 
14:51:19.709770 INFO: calibration group: precursor, fitting rt estimator 
14:51:19.828772 INFO: calibration group: precursor, fitting mobility estimator 
14:51:19.952652 INFO: calibration group: fragment, fitting mz estimator 
14:51:20.249869 INFO: Using score_cutoff 36.897656581878664 (fac=0.99, q=1)
14:51:20.250288 INFO: calibration group: precursor, predicting mz
14:51:20.257574 INFO: calibration group: precursor, predicting rt
14:51:20.287219 INFO: calibration group: precursor, predicting mobility
14:51:20.293838 INFO: calibration group: fragment, predicting mz
14:51:20.347623 INFO: === checking if optimization conditions were reached ===
14:51:20.347871 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
14:51:20.349796 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 605.3809.
14:51:20.349849 INFO: ==============================================
14:51:20.349949 INFO: Starting optimization step 2.
14:51:20.350015 PROGRESS: === Extracting elution groups 0 to 25400 ===
14:51:20.350079 PROGRESS: Extracting batch of 49998 precursors
14:51:20.362159 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:51:20.362264 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:51:20.362314 INFO: FWHM in RT is 2.38 seconds, sigma is 0.52
14:51:20.362336 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.68
14:51:20.371343 INFO: Starting candidate selection
14:52:37.861972 INFO: Starting candidate scoring
14:52:39.680227 INFO: Finished candidate processing
14:52:39.680374 INFO: Collecting candidate features
14:52:39.864520 WARNING: intensity_correlation has 69 NaNs ( 0.08 % out of 81995)
14:52:39.864967 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 81995)
14:52:39.874036 INFO: Collecting fragment features
14:52:39.948619 INFO: Finished candidate scoring
14:52:39.995788 PROGRESS: === Extracted 81995 precursors and 698328 fragments ===
14:52:39.996478 INFO: performing precursor FDR with 47 features
14:52:39.996525 INFO: Decoy channel: -1
14:52:39.996555 INFO: Competetive: True
14:52:40.032526 INFO: Setting torch num_threads to 2 for FDR classification task
14:52:40.054107 WARNING: dropped 41 target PSMs due to missing features
14:52:40.054271 WARNING: dropped 29 decoy PSMs due to missing features
14:52:41.880601 INFO: Test AUC: 0.558
14:52:41.881435 INFO: Train AUC: 0.603
14:52:41.881473 INFO: AUC difference: 7.44%
14:52:41.881494 WARNING: AUC difference > 5%. This may indicate overfitting.
14:52:42.088928 INFO: Resetting torch num_threads to 100
14:52:42.092648 INFO: === FDR correction performed with classifier version 12 ===
14:52:42.096872 PROGRESS: ============================= Precursor FDR =============================
14:52:42.097045 PROGRESS: Total precursors accumulated: 22,125
14:52:42.097107 PROGRESS: Target precursors: 13,845 (62.58%)
14:52:42.097164 PROGRESS: Decoy precursors: 8,280 (37.42%)
14:52:42.097238 PROGRESS: 
14:52:42.097286 PROGRESS: Precursor Summary:
14:52:42.098429 PROGRESS: Channel   0:	 0.05 FDR:   266; 0.01 FDR:   191; 0.001 FDR:   190
14:52:42.098525 PROGRESS: 
14:52:42.098580 PROGRESS: Protein Summary:
14:52:42.099804 PROGRESS: Channel   0:	 0.05 FDR:   257; 0.01 FDR:   187; 0.001 FDR:   186
14:52:42.099899 PROGRESS: =========================================================================
14:52:42.269631 INFO: calibration group: precursor, predicting mz
14:52:42.278026 INFO: calibration group: precursor, predicting rt
14:52:42.308985 INFO: calibration group: precursor, predicting mobility
14:52:42.316381 INFO: calibration group: fragment, predicting mz
14:52:42.374457 INFO: === skipping optimization until target number of precursors are found ===
14:52:42.374763 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
14:52:42.374837 INFO: Starting optimization step 3.
14:52:42.374908 PROGRESS: === Extracting elution groups 25400 to 51000 ===
14:52:42.374996 PROGRESS: Extracting batch of 50417 precursors
14:52:42.388585 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:52:42.388711 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:52:42.388780 INFO: FWHM in RT is 2.38 seconds, sigma is 0.52
14:52:42.388805 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.68
14:52:42.403688 INFO: Starting candidate selection
14:54:00.268934 INFO: Starting candidate scoring
14:54:02.136777 INFO: Finished candidate processing
14:54:02.136900 INFO: Collecting candidate features
14:54:02.273945 WARNING: intensity_correlation has 71 NaNs ( 0.09 % out of 82615)
14:54:02.280309 INFO: Collecting fragment features
14:54:02.333585 INFO: Finished candidate scoring
14:54:02.448837 PROGRESS: === Extracted 164610 precursors and 1404618 fragments ===
14:54:02.468914 INFO: performing precursor FDR with 47 features
14:54:02.469052 INFO: Decoy channel: -1
14:54:02.469078 INFO: Competetive: True
14:54:02.540016 INFO: Setting torch num_threads to 2 for FDR classification task
14:54:02.570568 WARNING: dropped 78 target PSMs due to missing features
14:54:02.570712 WARNING: dropped 63 decoy PSMs due to missing features
14:54:05.175395 INFO: Test AUC: 0.556
14:54:05.175520 INFO: Train AUC: 0.599
14:54:05.175550 INFO: AUC difference: 7.11%
14:54:05.175571 WARNING: AUC difference > 5%. This may indicate overfitting.
14:54:05.403049 INFO: Resetting torch num_threads to 100
14:54:05.409810 INFO: === FDR correction performed with classifier version 12 ===
14:54:05.417170 PROGRESS: ============================= Precursor FDR =============================
14:54:05.417437 PROGRESS: Total precursors accumulated: 44,403
14:54:05.417502 PROGRESS: Target precursors: 27,555 (62.06%)
14:54:05.417551 PROGRESS: Decoy precursors: 16,848 (37.94%)
14:54:05.417598 PROGRESS: 
14:54:05.417641 PROGRESS: Precursor Summary:
14:54:05.419088 PROGRESS: Channel   0:	 0.05 FDR:   583; 0.01 FDR:   315; 0.001 FDR:   211
14:54:05.419214 PROGRESS: 
14:54:05.419273 PROGRESS: Protein Summary:
14:54:05.420698 PROGRESS: Channel   0:	 0.05 FDR:   547; 0.01 FDR:   299; 0.001 FDR:   202
14:54:05.420792 PROGRESS: =========================================================================
14:54:05.523745 INFO: fragments_df: keeping 3611 of 1404618 [sum(precursor_idx_mask)=6317 sum(mass_error_mask)=1404618 stop_rank=3611
14:54:05.725647 INFO: calibration group: precursor, fitting mz estimator 
14:54:12.411100 INFO: calibration group: precursor, fitting rt estimator 
14:54:12.536415 INFO: calibration group: precursor, fitting mobility estimator 
14:54:12.663316 INFO: calibration group: fragment, fitting mz estimator 
14:54:13.132400 INFO: Using score_cutoff 42.816189083862305 (fac=0.99, q=1)
14:54:13.132811 INFO: calibration group: precursor, predicting mz
14:54:13.145638 INFO: calibration group: precursor, predicting rt
14:54:13.205154 INFO: calibration group: precursor, predicting mobility
14:54:13.220037 INFO: calibration group: fragment, predicting mz
14:54:13.343068 INFO: === checking if optimization conditions were reached ===
14:54:13.343333 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
14:54:13.344511 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 745.3813 found after 3 searches.
14:54:13.344567 INFO: ==============================================
14:54:13.344661 PROGRESS: Optimization finished for rt_error.
14:54:13.464949 INFO: calibration group: precursor, predicting mz
14:54:13.472423 INFO: calibration group: precursor, predicting rt
14:54:13.502449 INFO: calibration group: precursor, predicting mobility
14:54:13.509320 INFO: calibration group: fragment, predicting mz
14:54:13.587990 INFO: Starting optimization step 0.
14:54:13.588222 PROGRESS: === Extracting elution groups 0 to 25400 ===
14:54:13.588294 PROGRESS: Extracting batch of 49998 precursors
14:54:13.600827 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:54:13.600952 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:54:13.600998 INFO: FWHM in RT is 2.38 seconds, sigma is 0.52
14:54:13.601022 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.68
14:54:13.610029 INFO: Starting candidate selection
14:55:53.728385 INFO: Starting candidate scoring
14:55:55.941699 INFO: Finished candidate processing
14:55:55.941904 INFO: Collecting candidate features
14:55:56.195438 WARNING: intensity_correlation has 64 NaNs ( 0.08 % out of 82327)
14:55:56.195825 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 82327)
14:55:56.204691 INFO: Collecting fragment features
14:55:56.277846 INFO: Finished candidate scoring
14:55:56.323339 PROGRESS: === Extracted 82327 precursors and 703283 fragments ===
14:55:56.325160 INFO: performing precursor FDR with 47 features
14:55:56.325202 INFO: Decoy channel: -1
14:55:56.325228 INFO: Competetive: True
14:55:56.354515 INFO: Setting torch num_threads to 2 for FDR classification task
14:55:56.370243 WARNING: dropped 34 target PSMs due to missing features
14:55:56.370386 WARNING: dropped 30 decoy PSMs due to missing features
14:55:57.936255 INFO: Test AUC: 0.574
14:55:57.936421 INFO: Train AUC: 0.624
14:55:57.936476 INFO: AUC difference: 7.90%
14:55:57.936499 WARNING: AUC difference > 5%. This may indicate overfitting.
14:55:58.154655 INFO: Resetting torch num_threads to 100
14:55:58.157792 INFO: === FDR correction performed with classifier version 19 ===
14:55:58.162495 PROGRESS: ============================= Precursor FDR =============================
14:55:58.162785 PROGRESS: Total precursors accumulated: 22,191
14:55:58.162848 PROGRESS: Target precursors: 14,308 (64.48%)
14:55:58.162897 PROGRESS: Decoy precursors: 7,883 (35.52%)
14:55:58.162945 PROGRESS: 
14:55:58.162989 PROGRESS: Precursor Summary:
14:55:58.164259 PROGRESS: Channel   0:	 0.05 FDR:   338; 0.01 FDR:   257; 0.001 FDR:   196
14:55:58.164358 PROGRESS: 
14:55:58.164414 PROGRESS: Protein Summary:
14:55:58.165659 PROGRESS: Channel   0:	 0.05 FDR:   329; 0.01 FDR:   251; 0.001 FDR:   192
14:55:58.165753 PROGRESS: =========================================================================
14:55:58.254813 INFO: fragments_df: keeping 2533 of 703283 [sum(precursor_idx_mask)=5117 sum(mass_error_mask)=703283 stop_rank=2533
14:55:58.396155 INFO: calibration group: precursor, fitting mz estimator 
14:55:58.523009 INFO: calibration group: precursor, fitting rt estimator 
14:55:58.642791 INFO: calibration group: precursor, fitting mobility estimator 
14:55:58.762770 INFO: calibration group: fragment, fitting mz estimator 
14:55:59.101145 INFO: Using score_cutoff 32.305632083129886 (fac=0.99, q=1)
14:55:59.101722 INFO: calibration group: precursor, predicting mz
14:55:59.109602 INFO: calibration group: precursor, predicting rt
14:55:59.139241 INFO: calibration group: precursor, predicting mobility
14:55:59.146512 INFO: calibration group: fragment, predicting mz
14:55:59.205500 INFO: === checking if optimization conditions were reached ===
14:55:59.205907 PROGRESS: === Optimization of ms1_error has been performed 1 time(s); minimum number is 2 ===
14:55:59.208606 PROGRESS: ❌ ms1_error      : optimization incomplete after 1 search(es). Will search with parameter 11.9223.
14:55:59.208675 INFO: ==============================================
14:55:59.208794 INFO: Starting optimization step 1.
14:55:59.208869 PROGRESS: === Extracting elution groups 0 to 25400 ===
14:55:59.208952 PROGRESS: Extracting batch of 49998 precursors
14:55:59.241310 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:55:59.241496 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:55:59.241565 INFO: FWHM in RT is 2.35 seconds, sigma is 0.52
14:55:59.241619 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.62
14:55:59.258744 INFO: Starting candidate selection
14:57:35.665722 INFO: Starting candidate scoring
14:57:37.020812 INFO: Finished candidate processing
14:57:37.020919 INFO: Collecting candidate features
14:57:37.151162 WARNING: intensity_correlation has 58 NaNs ( 0.07 % out of 82456)
14:57:37.151529 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 82456)
14:57:37.159737 INFO: Collecting fragment features
14:57:37.210933 INFO: Finished candidate scoring
14:57:37.253897 PROGRESS: === Extracted 82456 precursors and 694638 fragments ===
14:57:37.254368 INFO: performing precursor FDR with 47 features
14:57:37.254408 INFO: Decoy channel: -1
14:57:37.254431 INFO: Competetive: True
14:57:37.279445 INFO: Setting torch num_threads to 2 for FDR classification task
14:57:37.294951 WARNING: dropped 32 target PSMs due to missing features
14:57:37.295098 WARNING: dropped 28 decoy PSMs due to missing features
14:57:38.695234 INFO: Test AUC: 0.556
14:57:38.695367 INFO: Train AUC: 0.609
14:57:38.695397 INFO: AUC difference: 8.66%
14:57:38.695418 WARNING: AUC difference > 5%. This may indicate overfitting.
14:57:38.899748 INFO: Resetting torch num_threads to 100
14:57:38.902446 INFO: === FDR correction performed with classifier version 19 ===
14:57:38.905954 PROGRESS: ============================= Precursor FDR =============================
14:57:38.906125 PROGRESS: Total precursors accumulated: 22,284
14:57:38.906188 PROGRESS: Target precursors: 13,909 (62.42%)
14:57:38.906239 PROGRESS: Decoy precursors: 8,375 (37.58%)
14:57:38.906288 PROGRESS: 
14:57:38.906331 PROGRESS: Precursor Summary:
14:57:38.907446 PROGRESS: Channel   0:	 0.05 FDR:   290; 0.01 FDR:   242; 0.001 FDR:   181
14:57:38.907541 PROGRESS: 
14:57:38.907600 PROGRESS: Protein Summary:
14:57:38.908864 PROGRESS: Channel   0:	 0.05 FDR:   278; 0.01 FDR:   235; 0.001 FDR:   177
14:57:38.908956 PROGRESS: =========================================================================
14:57:38.956180 INFO: fragments_df: keeping 2443 of 694638 [sum(precursor_idx_mask)=4925 sum(mass_error_mask)=694638 stop_rank=2443
14:57:39.081552 INFO: calibration group: precursor, fitting mz estimator 
14:57:39.200319 INFO: calibration group: precursor, fitting rt estimator 
14:57:39.318049 INFO: calibration group: precursor, fitting mobility estimator 
14:57:39.442779 INFO: calibration group: fragment, fitting mz estimator 
14:57:39.760024 INFO: Using score_cutoff 36.32085786209107 (fac=0.99, q=1)
14:57:39.760433 INFO: calibration group: precursor, predicting mz
14:57:39.767827 INFO: calibration group: precursor, predicting rt
14:57:39.798239 INFO: calibration group: precursor, predicting mobility
14:57:39.805543 INFO: calibration group: fragment, predicting mz
14:57:39.861107 INFO: === checking if optimization conditions were reached ===
14:57:39.861390 PROGRESS: === Optimization of ms1_error has been performed 2 time(s); minimum number is 2 ===
14:57:39.863348 PROGRESS: ❌ ms1_error      : optimization incomplete after 2 search(es). Will search with parameter 2.5773.
14:57:39.863402 INFO: ==============================================
14:57:39.863501 INFO: Starting optimization step 2.
14:57:39.863565 PROGRESS: === Extracting elution groups 0 to 25400 ===
14:57:39.863628 PROGRESS: Extracting batch of 49998 precursors
14:57:39.876749 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:57:39.876870 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:57:39.876920 INFO: FWHM in RT is 2.35 seconds, sigma is 0.52
14:57:39.876943 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.64
14:57:39.901660 INFO: Starting candidate selection
14:59:11.696771 INFO: Starting candidate scoring
14:59:12.875983 INFO: Finished candidate processing
14:59:12.876104 INFO: Collecting candidate features
14:59:13.012048 WARNING: intensity_correlation has 62 NaNs ( 0.07 % out of 82802)
14:59:13.012383 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 82802)
14:59:13.018686 INFO: Collecting fragment features
14:59:13.070615 INFO: Finished candidate scoring
14:59:13.151656 PROGRESS: === Extracted 82802 precursors and 684825 fragments ===
14:59:13.152163 INFO: performing precursor FDR with 47 features
14:59:13.152203 INFO: Decoy channel: -1
14:59:13.152230 INFO: Competetive: True
14:59:13.183783 INFO: Setting torch num_threads to 2 for FDR classification task
14:59:13.204295 WARNING: dropped 32 target PSMs due to missing features
14:59:13.204448 WARNING: dropped 30 decoy PSMs due to missing features
14:59:14.671386 INFO: Test AUC: 0.544
14:59:14.671540 INFO: Train AUC: 0.591
14:59:14.671570 INFO: AUC difference: 8.04%
14:59:14.671592 WARNING: AUC difference > 5%. This may indicate overfitting.
14:59:14.883757 INFO: Resetting torch num_threads to 100
14:59:14.887676 INFO: === FDR correction performed with classifier version 19 ===
14:59:14.892632 PROGRESS: ============================= Precursor FDR =============================
14:59:14.892840 PROGRESS: Total precursors accumulated: 22,331
14:59:14.892911 PROGRESS: Target precursors: 13,541 (60.64%)
14:59:14.892965 PROGRESS: Decoy precursors: 8,790 (39.36%)
14:59:14.893010 PROGRESS: 
14:59:14.893054 PROGRESS: Precursor Summary:
14:59:14.894244 PROGRESS: Channel   0:	 0.05 FDR:   266; 0.01 FDR:   210; 0.001 FDR:    73
14:59:14.894340 PROGRESS: 
14:59:14.894397 PROGRESS: Protein Summary:
14:59:14.895581 PROGRESS: Channel   0:	 0.05 FDR:   258; 0.01 FDR:   204; 0.001 FDR:    73
14:59:14.895673 PROGRESS: =========================================================================
14:59:14.941838 INFO: fragments_df: keeping 2148 of 684825 [sum(precursor_idx_mask)=4236 sum(mass_error_mask)=684820 stop_rank=2148
14:59:15.077437 INFO: calibration group: precursor, fitting mz estimator 
14:59:15.205432 INFO: calibration group: precursor, fitting rt estimator 
14:59:15.297352 INFO: calibration group: precursor, fitting mobility estimator 
14:59:15.396925 INFO: calibration group: fragment, fitting mz estimator 
14:59:15.634304 INFO: Using score_cutoff 33.927899753952026 (fac=0.99, q=1)
14:59:15.634766 INFO: calibration group: precursor, predicting mz
14:59:15.642399 INFO: calibration group: precursor, predicting rt
14:59:15.672726 INFO: calibration group: precursor, predicting mobility
14:59:15.680128 INFO: calibration group: fragment, predicting mz
14:59:15.735795 INFO: === checking if optimization conditions were reached ===
14:59:15.736136 PROGRESS: === Optimization of ms1_error has been performed 3 time(s); minimum number is 2 ===
14:59:15.737542 PROGRESS: ✅ ms1_error      : optimization complete. Optimal parameter 11.9223 found after 3 searches.
14:59:15.737602 INFO: ==============================================
14:59:15.737715 PROGRESS: Optimization finished for ms1_error.
14:59:15.872020 INFO: calibration group: precursor, predicting mz
14:59:15.879954 INFO: calibration group: precursor, predicting rt
14:59:15.910496 INFO: calibration group: precursor, predicting mobility
14:59:15.917911 INFO: calibration group: fragment, predicting mz
14:59:16.005331 INFO: Starting optimization step 0.
14:59:16.005605 PROGRESS: === Extracting elution groups 0 to 25400 ===
14:59:16.005692 PROGRESS: Extracting batch of 49998 precursors
14:59:16.029478 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
14:59:16.029634 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
14:59:16.029696 INFO: FWHM in RT is 2.35 seconds, sigma is 0.52
14:59:16.029724 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.64
14:59:16.038664 INFO: Starting candidate selection
15:00:48.989785 INFO: Starting candidate scoring
15:00:50.361654 INFO: Finished candidate processing
15:00:50.361827 INFO: Collecting candidate features
15:00:50.567300 WARNING: intensity_correlation has 58 NaNs ( 0.07 % out of 82509)
15:00:50.567731 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 82509)
15:00:50.577836 INFO: Collecting fragment features
15:00:50.636949 INFO: Finished candidate scoring
15:00:50.700670 PROGRESS: === Extracted 82509 precursors and 695022 fragments ===
15:00:50.701213 INFO: performing precursor FDR with 47 features
15:00:50.701267 INFO: Decoy channel: -1
15:00:50.701291 INFO: Competetive: True
15:00:50.738763 INFO: Setting torch num_threads to 2 for FDR classification task
15:00:50.759895 WARNING: dropped 33 target PSMs due to missing features
15:00:50.760066 WARNING: dropped 27 decoy PSMs due to missing features
15:00:52.113838 INFO: Test AUC: 0.569
15:00:52.114928 INFO: Train AUC: 0.622
15:00:52.114971 INFO: AUC difference: 8.56%
15:00:52.114994 WARNING: AUC difference > 5%. This may indicate overfitting.
15:00:52.328726 INFO: Resetting torch num_threads to 100
15:00:52.332339 INFO: === FDR correction performed with classifier version 23 ===
15:00:52.336877 PROGRESS: ============================= Precursor FDR =============================
15:00:52.337037 PROGRESS: Total precursors accumulated: 22,311
15:00:52.337105 PROGRESS: Target precursors: 14,351 (64.32%)
15:00:52.337159 PROGRESS: Decoy precursors: 7,960 (35.68%)
15:00:52.337210 PROGRESS: 
15:00:52.337259 PROGRESS: Precursor Summary:
15:00:52.338659 PROGRESS: Channel   0:	 0.05 FDR:   354; 0.01 FDR:   258; 0.001 FDR:   161
15:00:52.338757 PROGRESS: 
15:00:52.338816 PROGRESS: Protein Summary:
15:00:52.340098 PROGRESS: Channel   0:	 0.05 FDR:   343; 0.01 FDR:   251; 0.001 FDR:   158
15:00:52.340195 PROGRESS: =========================================================================
15:00:52.388219 INFO: fragments_df: keeping 2521 of 695022 [sum(precursor_idx_mask)=5227 sum(mass_error_mask)=695022 stop_rank=2521
15:00:52.525927 INFO: calibration group: precursor, fitting mz estimator 
15:00:52.649090 INFO: calibration group: precursor, fitting rt estimator 
15:00:52.768289 INFO: calibration group: precursor, fitting mobility estimator 
15:00:52.890378 INFO: calibration group: fragment, fitting mz estimator 
15:00:53.221154 INFO: Using score_cutoff 34.78844633216858 (fac=0.99, q=1)
15:00:53.221633 INFO: calibration group: precursor, predicting mz
15:00:53.229158 INFO: calibration group: precursor, predicting rt
15:00:53.259516 INFO: calibration group: precursor, predicting mobility
15:00:53.266999 INFO: calibration group: fragment, predicting mz
15:00:53.321428 INFO: === checking if optimization conditions were reached ===
15:00:53.321745 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
15:00:53.323773 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0636.
15:00:53.323832 INFO: ==============================================
15:00:53.323936 INFO: Starting optimization step 1.
15:00:53.324003 PROGRESS: === Extracting elution groups 0 to 25400 ===
15:00:53.324073 PROGRESS: Extracting batch of 49998 precursors
15:00:53.339896 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:00:53.340040 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:00:53.340096 INFO: FWHM in RT is 2.32 seconds, sigma is 0.51
15:00:53.340123 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.50
15:00:53.349075 INFO: Starting candidate selection
15:01:49.027248 INFO: Starting candidate scoring
15:01:50.371624 INFO: Finished candidate processing
15:01:50.372467 INFO: Collecting candidate features
15:01:50.520150 WARNING: intensity_correlation has 88 NaNs ( 0.11 % out of 80175)
15:01:50.520461 WARNING: height_correlation has 6 NaNs ( 0.01 % out of 80175)
15:01:50.526495 INFO: Collecting fragment features
15:01:50.575610 INFO: Finished candidate scoring
15:01:50.622517 PROGRESS: === Extracted 80175 precursors and 663233 fragments ===
15:01:50.623009 INFO: performing precursor FDR with 47 features
15:01:50.623058 INFO: Decoy channel: -1
15:01:50.623083 INFO: Competetive: True
15:01:50.652121 INFO: Setting torch num_threads to 2 for FDR classification task
15:01:50.670781 WARNING: dropped 49 target PSMs due to missing features
15:01:50.670927 WARNING: dropped 44 decoy PSMs due to missing features
15:01:52.039674 INFO: Test AUC: 0.564
15:01:52.039823 INFO: Train AUC: 0.616
15:01:52.039855 INFO: AUC difference: 8.49%
15:01:52.039876 WARNING: AUC difference > 5%. This may indicate overfitting.
15:01:52.247863 INFO: Resetting torch num_threads to 100
15:01:52.251395 INFO: === FDR correction performed with classifier version 23 ===
15:01:52.255471 PROGRESS: ============================= Precursor FDR =============================
15:01:52.255626 PROGRESS: Total precursors accumulated: 21,793
15:01:52.255688 PROGRESS: Target precursors: 13,851 (63.56%)
15:01:52.255742 PROGRESS: Decoy precursors: 7,942 (36.44%)
15:01:52.255789 PROGRESS: 
15:01:52.255837 PROGRESS: Precursor Summary:
15:01:52.256951 PROGRESS: Channel   0:	 0.05 FDR:   364; 0.01 FDR:   216; 0.001 FDR:   184
15:01:52.257044 PROGRESS: 
15:01:52.257100 PROGRESS: Protein Summary:
15:01:52.258312 PROGRESS: Channel   0:	 0.05 FDR:   354; 0.01 FDR:   210; 0.001 FDR:   181
15:01:52.258401 PROGRESS: =========================================================================
15:01:52.304431 INFO: fragments_df: keeping 2271 of 663233 [sum(precursor_idx_mask)=4458 sum(mass_error_mask)=663233 stop_rank=2271
15:01:52.439498 INFO: calibration group: precursor, fitting mz estimator 
15:01:52.534226 INFO: calibration group: precursor, fitting rt estimator 
15:01:52.629071 INFO: calibration group: precursor, fitting mobility estimator 
15:01:52.721767 INFO: calibration group: fragment, fitting mz estimator 
15:01:52.984570 INFO: Using score_cutoff 42.82757130432129 (fac=0.99, q=1)
15:01:52.985054 INFO: calibration group: precursor, predicting mz
15:01:52.992700 INFO: calibration group: precursor, predicting rt
15:01:53.023173 INFO: calibration group: precursor, predicting mobility
15:01:53.030523 INFO: calibration group: fragment, predicting mz
15:01:53.083958 INFO: === checking if optimization conditions were reached ===
15:01:53.084279 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
15:01:53.086653 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0463.
15:01:53.086717 INFO: ==============================================
15:01:53.086837 INFO: Starting optimization step 2.
15:01:53.086913 PROGRESS: === Extracting elution groups 0 to 25400 ===
15:01:53.086993 PROGRESS: Extracting batch of 49998 precursors
15:01:53.107715 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:01:53.107852 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:01:53.107906 INFO: FWHM in RT is 2.40 seconds, sigma is 0.53
15:01:53.107929 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.62
15:01:53.117809 INFO: Starting candidate selection
15:02:36.247871 INFO: Starting candidate scoring
15:02:37.735206 INFO: Finished candidate processing
15:02:37.735316 INFO: Collecting candidate features
15:02:37.859839 WARNING: intensity_correlation has 78 NaNs ( 0.10 % out of 78274)
15:02:37.860204 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 78274)
15:02:37.868716 INFO: Collecting fragment features
15:02:37.917938 INFO: Finished candidate scoring
15:02:37.961872 PROGRESS: === Extracted 78274 precursors and 636000 fragments ===
15:02:37.962386 INFO: performing precursor FDR with 47 features
15:02:37.962432 INFO: Decoy channel: -1
15:02:37.962461 INFO: Competetive: True
15:02:37.985259 INFO: Setting torch num_threads to 2 for FDR classification task
15:02:37.999734 WARNING: dropped 39 target PSMs due to missing features
15:02:37.999883 WARNING: dropped 42 decoy PSMs due to missing features
15:02:38.858577 INFO: Test AUC: 0.568
15:02:38.858712 INFO: Train AUC: 0.614
15:02:38.858742 INFO: AUC difference: 7.53%
15:02:38.858761 WARNING: AUC difference > 5%. This may indicate overfitting.
15:02:39.068153 INFO: Resetting torch num_threads to 100
15:02:39.070747 INFO: === FDR correction performed with classifier version 23 ===
15:02:39.073904 PROGRESS: ============================= Precursor FDR =============================
15:02:39.074040 PROGRESS: Total precursors accumulated: 21,308
15:02:39.074100 PROGRESS: Target precursors: 13,538 (63.53%)
15:02:39.074152 PROGRESS: Decoy precursors: 7,770 (36.47%)
15:02:39.074222 PROGRESS: 
15:02:39.074271 PROGRESS: Precursor Summary:
15:02:39.075356 PROGRESS: Channel   0:	 0.05 FDR:   381; 0.01 FDR:   271; 0.001 FDR:   256
15:02:39.075449 PROGRESS: 
15:02:39.075506 PROGRESS: Protein Summary:
15:02:39.076714 PROGRESS: Channel   0:	 0.05 FDR:   368; 0.01 FDR:   262; 0.001 FDR:   247
15:02:39.076804 PROGRESS: =========================================================================
15:02:39.120071 INFO: fragments_df: keeping 2593 of 636000 [sum(precursor_idx_mask)=5498 sum(mass_error_mask)=636000 stop_rank=2593
15:02:39.248325 INFO: calibration group: precursor, fitting mz estimator 
15:02:39.413600 INFO: calibration group: precursor, fitting rt estimator 
15:02:39.514020 INFO: calibration group: precursor, fitting mobility estimator 
15:02:39.612991 INFO: calibration group: fragment, fitting mz estimator 
15:02:39.903935 INFO: Using score_cutoff 34.32679225158691 (fac=0.99, q=1)
15:02:39.904348 INFO: calibration group: precursor, predicting mz
15:02:39.911993 INFO: calibration group: precursor, predicting rt
15:02:39.942054 INFO: calibration group: precursor, predicting mobility
15:02:39.949414 INFO: calibration group: fragment, predicting mz
15:02:40.003492 INFO: === checking if optimization conditions were reached ===
15:02:40.003763 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
15:02:40.005601 PROGRESS: ❌ mobility_error : optimization incomplete after 3 search(es). Will search with parameter 0.0437.
15:02:40.005655 INFO: ==============================================
15:02:40.005751 INFO: Starting optimization step 3.
15:02:40.005830 PROGRESS: === Extracting elution groups 0 to 25400 ===
15:02:40.005898 PROGRESS: Extracting batch of 49998 precursors
15:02:40.018254 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:02:40.018361 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:02:40.018411 INFO: FWHM in RT is 2.33 seconds, sigma is 0.51
15:02:40.018440 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.50
15:02:40.027342 INFO: Starting candidate selection
15:03:16.669348 INFO: Starting candidate scoring
15:03:17.975631 INFO: Finished candidate processing
15:03:17.975816 INFO: Collecting candidate features
15:03:18.142884 WARNING: intensity_correlation has 79 NaNs ( 0.10 % out of 78083)
15:03:18.143415 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 78083)
15:03:18.155769 INFO: Collecting fragment features
15:03:18.208551 INFO: Finished candidate scoring
15:03:18.249335 PROGRESS: === Extracted 78083 precursors and 629898 fragments ===
15:03:18.249829 INFO: performing precursor FDR with 47 features
15:03:18.249874 INFO: Decoy channel: -1
15:03:18.249910 INFO: Competetive: True
15:03:18.283239 INFO: Setting torch num_threads to 2 for FDR classification task
15:03:18.303235 WARNING: dropped 34 target PSMs due to missing features
15:03:18.303396 WARNING: dropped 48 decoy PSMs due to missing features
15:03:19.911149 INFO: Test AUC: 0.558
15:03:19.911300 INFO: Train AUC: 0.609
15:03:19.911339 INFO: AUC difference: 8.28%
15:03:19.911368 WARNING: AUC difference > 5%. This may indicate overfitting.
15:03:20.126780 INFO: Resetting torch num_threads to 100
15:03:20.130754 INFO: === FDR correction performed with classifier version 23 ===
15:03:20.135147 PROGRESS: ============================= Precursor FDR =============================
15:03:20.135308 PROGRESS: Total precursors accumulated: 21,293
15:03:20.135394 PROGRESS: Target precursors: 13,381 (62.84%)
15:03:20.135458 PROGRESS: Decoy precursors: 7,912 (37.16%)
15:03:20.135516 PROGRESS: 
15:03:20.135573 PROGRESS: Precursor Summary:
15:03:20.136912 PROGRESS: Channel   0:	 0.05 FDR:   335; 0.01 FDR:   237; 0.001 FDR:   225
15:03:20.137013 PROGRESS: 
15:03:20.137088 PROGRESS: Protein Summary:
15:03:20.138629 PROGRESS: Channel   0:	 0.05 FDR:   324; 0.01 FDR:   230; 0.001 FDR:   218
15:03:20.138732 PROGRESS: =========================================================================
15:03:20.185209 INFO: fragments_df: keeping 2398 of 629898 [sum(precursor_idx_mask)=4858 sum(mass_error_mask)=629897 stop_rank=2398
15:03:20.343040 INFO: calibration group: precursor, fitting mz estimator 
15:03:20.453888 INFO: calibration group: precursor, fitting rt estimator 
15:03:20.550862 INFO: calibration group: precursor, fitting mobility estimator 
15:03:20.650923 INFO: calibration group: fragment, fitting mz estimator 
15:03:20.927822 INFO: Using score_cutoff 35.52301274414063 (fac=0.99, q=1)
15:03:20.928300 INFO: calibration group: precursor, predicting mz
15:03:20.935822 INFO: calibration group: precursor, predicting rt
15:03:20.966141 INFO: calibration group: precursor, predicting mobility
15:03:20.973422 INFO: calibration group: fragment, predicting mz
15:03:21.034356 INFO: === checking if optimization conditions were reached ===
15:03:21.034763 PROGRESS: === Optimization of mobility_error has been performed 4 time(s); minimum number is 2 ===
15:03:21.037891 PROGRESS: ❌ mobility_error : optimization incomplete after 4 search(es). Will search with parameter 0.0369.
15:03:21.038007 INFO: ==============================================
15:03:21.038181 INFO: Starting optimization step 4.
15:03:21.038262 PROGRESS: === Extracting elution groups 0 to 25400 ===
15:03:21.038335 PROGRESS: Extracting batch of 49998 precursors
15:03:21.072798 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:03:21.073120 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:03:21.073237 INFO: FWHM in RT is 2.32 seconds, sigma is 0.51
15:03:21.073324 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.61
15:03:21.083471 INFO: Starting candidate selection
15:03:55.807357 INFO: Starting candidate scoring
15:03:57.107363 INFO: Finished candidate processing
15:03:57.107469 INFO: Collecting candidate features
15:03:57.223792 WARNING: intensity_correlation has 101 NaNs ( 0.13 % out of 77449)
15:03:57.224097 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 77449)
15:03:57.229885 INFO: Collecting fragment features
15:03:57.274112 INFO: Finished candidate scoring
15:03:57.314742 PROGRESS: === Extracted 77449 precursors and 619610 fragments ===
15:03:57.315237 INFO: performing precursor FDR with 47 features
15:03:57.315278 INFO: Decoy channel: -1
15:03:57.315302 INFO: Competetive: True
15:03:57.338934 INFO: Setting torch num_threads to 2 for FDR classification task
15:03:57.353225 WARNING: dropped 48 target PSMs due to missing features
15:03:57.353349 WARNING: dropped 56 decoy PSMs due to missing features
15:03:58.653835 INFO: Test AUC: 0.565
15:03:58.654103 INFO: Train AUC: 0.607
15:03:58.654139 INFO: AUC difference: 6.88%
15:03:58.654162 WARNING: AUC difference > 5%. This may indicate overfitting.
15:03:58.864240 INFO: Resetting torch num_threads to 100
15:03:58.866823 INFO: === FDR correction performed with classifier version 23 ===
15:03:58.869990 PROGRESS: ============================= Precursor FDR =============================
15:03:58.870120 PROGRESS: Total precursors accumulated: 21,111
15:03:58.870184 PROGRESS: Target precursors: 13,161 (62.34%)
15:03:58.870237 PROGRESS: Decoy precursors: 7,950 (37.66%)
15:03:58.870288 PROGRESS: 
15:03:58.870342 PROGRESS: Precursor Summary:
15:03:58.871463 PROGRESS: Channel   0:	 0.05 FDR:   345; 0.01 FDR:   240; 0.001 FDR:   117
15:03:58.871558 PROGRESS: 
15:03:58.871615 PROGRESS: Protein Summary:
15:03:58.872816 PROGRESS: Channel   0:	 0.05 FDR:   334; 0.01 FDR:   234; 0.001 FDR:   115
15:03:58.872910 PROGRESS: =========================================================================
15:03:58.915797 INFO: fragments_df: keeping 2374 of 619610 [sum(precursor_idx_mask)=4877 sum(mass_error_mask)=619609 stop_rank=2374
15:03:59.040071 INFO: calibration group: precursor, fitting mz estimator 
15:03:59.160918 INFO: calibration group: precursor, fitting rt estimator 
15:03:59.274760 INFO: calibration group: precursor, fitting mobility estimator 
15:03:59.392136 INFO: calibration group: fragment, fitting mz estimator 
15:03:59.710427 INFO: Using score_cutoff 37.5955245929718 (fac=0.99, q=1)
15:03:59.710840 INFO: calibration group: precursor, predicting mz
15:03:59.718106 INFO: calibration group: precursor, predicting rt
15:03:59.748500 INFO: calibration group: precursor, predicting mobility
15:03:59.755866 INFO: calibration group: fragment, predicting mz
15:03:59.810498 INFO: === checking if optimization conditions were reached ===
15:03:59.810776 PROGRESS: === Optimization of mobility_error has been performed 5 time(s); minimum number is 2 ===
15:03:59.811689 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.0463 found after 5 searches.
15:03:59.811742 INFO: ==============================================
15:03:59.811837 PROGRESS: Optimization finished for mobility_error.
15:03:59.929107 INFO: calibration group: precursor, predicting mz
15:03:59.936720 INFO: calibration group: precursor, predicting rt
15:03:59.967274 INFO: calibration group: precursor, predicting mobility
15:03:59.974602 INFO: calibration group: fragment, predicting mz
15:04:00.055927 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
15:04:00.056146 PROGRESS: ==============================================
15:04:00.056217 PROGRESS: ms2_error      : 5.1536
15:04:00.056277 PROGRESS: rt_error       : 745.3813
15:04:00.056329 PROGRESS: ms1_error      : 11.9223
15:04:00.056375 PROGRESS: mobility_error : 0.0463
15:04:00.056421 PROGRESS: ==============================================
15:04:00.059231 INFO: calibration group: precursor, predicting mz
15:04:01.473506 INFO: calibration group: precursor, predicting rt
15:04:07.998921 INFO: calibration group: precursor, predicting mobility
15:04:09.510008 INFO: calibration group: fragment, predicting mz
15:04:21.876760 PROGRESS: Extracting batch of 10272670 precursors
15:04:24.348033 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:04:24.348177 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:04:24.348230 INFO: FWHM in RT is 2.33 seconds, sigma is 0.51
15:04:24.348252 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.50
15:04:24.349253 INFO: Starting candidate selection
17:20:14.982377 INFO: Applying score cutoff of 34.32679225158691
17:20:15.276395 INFO: Removed 9044330 precursors with score below cutoff
17:20:17.925058 INFO: Starting candidate scoring
17:22:22.819806 INFO: Finished candidate processing
17:22:22.820129 INFO: Collecting candidate features
17:22:37.484811 WARNING: intensity_correlation has 15 NaNs ( 0.00 % out of 8058275)
17:22:37.491924 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 8058275)
17:22:37.756730 INFO: Collecting fragment features
17:22:43.611104 INFO: Finished candidate scoring
17:22:54.501958 INFO: === FDR correction performed with classifier version 27 ===
17:22:54.509008 INFO: performing precursor FDR with 47 features
17:22:54.509093 INFO: Decoy channel: -1
17:22:54.509127 INFO: Competetive: True
17:22:56.687337 INFO: Setting torch num_threads to 2 for FDR classification task
17:22:58.072455 WARNING: dropped 8 target PSMs due to missing features
17:22:58.072870 WARNING: dropped 7 decoy PSMs due to missing features
17:25:54.414995 INFO: Test AUC: 0.574
17:25:54.415163 INFO: Train AUC: 0.576
17:25:54.415198 INFO: AUC difference: 0.39%
17:25:56.487698 INFO: Resetting torch num_threads to 100
17:25:56.717877 INFO: Removing fragments below FDR threshold
17:25:57.249373 PROGRESS: ============================= Precursor FDR =============================
17:25:57.249658 PROGRESS: Total precursors accumulated: 63,391
17:25:57.249727 PROGRESS: Target precursors: 62,764 (99.01%)
17:25:57.249779 PROGRESS: Decoy precursors: 627 (0.99%)
17:25:57.249832 PROGRESS: 
17:25:57.249879 PROGRESS: Precursor Summary:
17:25:57.273363 PROGRESS: Channel   0:	 0.05 FDR: 62,764; 0.01 FDR: 62,764; 0.001 FDR: 42,340
17:25:57.273658 PROGRESS: 
17:25:57.273723 PROGRESS: Protein Summary:
17:25:57.307363 PROGRESS: Channel   0:	 0.05 FDR: 10,306; 0.01 FDR: 10,306; 0.001 FDR: 7,874
17:25:57.307645 PROGRESS: =========================================================================
17:25:57.951203 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
17:25:58.429244 PROGRESS: Loading raw file 6/6: ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
17:25:58.429425 INFO: Quantification results path: run_output/alphadia_1.10.4_Again_good_now/library/quant
17:25:58.429506 INFO: Creating folder run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/figures
17:25:58.430235 INFO: Initializing RawFileManager
17:25:58.430366 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
17:25:58.430430 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
17:25:58.430474 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
17:25:58.648359 INFO: Reading 39,129 frames with 2,804,178,635 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
17:26:06.783622 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d...
17:26:06.784860 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
17:26:06.792955 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
17:26:06.793200 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
17:26:06.793567 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
17:26:06.795241 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
17:26:06.811469 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
17:26:06.811664 INFO: Indexing quadrupole dimension
17:26:07.325289 INFO: Transposing detector events
17:26:16.135321 INFO: Finished transposing data
17:26:16.164303 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
17:26:16.165128 INFO: RT (min)            : 0.0 - 70.0
17:26:16.165170 INFO: RT duration (sec)   : 4199.8
17:26:16.165195 INFO: RT duration (min)   : 70.0
17:26:16.165215 INFO: Cycle len (scans)   : 9
17:26:16.165234 INFO: Cycle len (sec)     : 0.97
17:26:16.165252 INFO: Number of cycles    : 4347
17:26:16.165273 INFO: MS2 range (m/z)     : 400.0 - 1000.0
17:26:17.628904 INFO: Initializing CalibrationManager
17:26:17.629211 INFO: Loading calibration config
17:26:17.629724 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed'], 'function': LOESSRegression()}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed'], 'function': LOESSRegression(n_kernels=2)}], 'name': 'precursor'}]
17:26:17.629809 INFO: Calibration group :fragment, found 1 estimator(s)
17:26:17.629896 INFO: Calibration group :precursor, found 3 estimator(s)
17:26:17.630065 INFO: Initializing OptimizationManager
17:26:17.630168 INFO: initial parameter: ms1_error = 30
17:26:17.630228 INFO: initial parameter: ms2_error = 30
17:26:17.630291 INFO: initial parameter: rt_error = 2099.9231665
17:26:17.630339 INFO: initial parameter: mobility_error = 0.1
17:26:17.630381 INFO: initial parameter: column_type = library
17:26:17.630420 INFO: initial parameter: num_candidates = 1
17:26:17.630461 INFO: initial parameter: classifier_version = -1
17:26:17.630506 INFO: initial parameter: fwhm_rt = 5
17:26:17.630545 INFO: initial parameter: fwhm_mobility = 0.01
17:26:17.630584 INFO: initial parameter: score_cutoff = 0
17:26:17.630644 INFO: Initializing TimingManager
17:26:17.630697 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
17:26:17.630799 INFO: FDRManager not loaded from disk.
17:26:17.630822 INFO: Initializing FDRManager
17:26:17.630854 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
17:26:18.926453 PROGRESS: 5,215,079 target precursors potentially observable (0 removed)
17:26:20.802128 PROGRESS: Starting initial search for precursors.
17:26:21.013560 INFO: Starting optimization step 0.
17:26:21.013783 PROGRESS: === Extracting elution groups 0 to 200 ===
17:26:21.013854 PROGRESS: Extracting batch of 398 precursors
17:26:21.014786 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
17:26:21.014833 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
17:26:21.014866 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
17:26:21.014888 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
17:26:21.015799 INFO: Starting candidate selection
17:26:23.878739 INFO: Starting candidate scoring
17:26:23.934157 INFO: Finished candidate processing
17:26:23.934254 INFO: Collecting candidate features
17:26:23.943208 INFO: Collecting fragment features
17:26:23.945282 INFO: Finished candidate scoring
17:26:23.946068 PROGRESS: === Extracted 334 precursors and 3463 fragments ===
17:26:23.946357 INFO: performing precursor FDR with 47 features
17:26:23.946396 INFO: Decoy channel: -1
17:26:23.946420 INFO: Competetive: True
17:26:23.947440 INFO: Setting torch num_threads to 2 for FDR classification task
17:26:23.956669 INFO: Test AUC: 0.487
17:26:23.956732 INFO: Train AUC: 0.511
17:26:23.956760 INFO: AUC difference: 4.79%
17:26:24.135146 INFO: Resetting torch num_threads to 100
17:26:24.135679 INFO: === FDR correction performed with classifier version -1 ===
17:26:24.136273 PROGRESS: ============================= Precursor FDR =============================
17:26:24.136362 PROGRESS: Total precursors accumulated: 173
17:26:24.136419 PROGRESS: Target precursors: 92 (53.18%)
17:26:24.136468 PROGRESS: Decoy precursors: 81 (46.82%)
17:26:24.136512 PROGRESS: 
17:26:24.136556 PROGRESS: Precursor Summary:
17:26:24.137374 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
17:26:24.137460 PROGRESS: 
17:26:24.137513 PROGRESS: Protein Summary:
17:26:24.138385 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
17:26:24.138472 PROGRESS: =========================================================================
17:26:24.193849 INFO: Starting optimization step 1.
17:26:24.194057 PROGRESS: === Extracting elution groups 200 to 600 ===
17:26:24.194123 PROGRESS: Extracting batch of 786 precursors
17:26:24.194932 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
17:26:24.194978 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
17:26:24.195006 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
17:26:24.195037 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
17:26:24.195726 INFO: Starting candidate selection
17:26:29.274450 INFO: Starting candidate scoring
17:26:29.354551 INFO: Finished candidate processing
17:26:29.354674 INFO: Collecting candidate features
17:26:29.361802 WARNING: intensity_correlation has 1 NaNs ( 0.14 % out of 713)
17:26:29.361961 WARNING: height_correlation has 1 NaNs ( 0.14 % out of 713)
17:26:29.364751 INFO: Collecting fragment features
17:26:29.367249 INFO: Finished candidate scoring
17:26:29.369436 PROGRESS: === Extracted 1047 precursors and 10750 fragments ===
17:26:29.370223 INFO: performing precursor FDR with 47 features
17:26:29.370265 INFO: Decoy channel: -1
17:26:29.370289 INFO: Competetive: True
17:26:29.373164 INFO: Setting torch num_threads to 2 for FDR classification task
17:26:29.374291 WARNING: dropped 1 target PSMs due to missing features
17:26:29.384693 INFO: Test AUC: 0.521
17:26:29.384832 INFO: Train AUC: 0.482
17:26:29.384863 INFO: AUC difference: 8.09%
17:26:29.384886 WARNING: AUC difference > 5%. This may indicate overfitting.
17:26:29.564262 INFO: Resetting torch num_threads to 100
17:26:29.564868 INFO: === FDR correction performed with classifier version -1 ===
17:26:29.565501 PROGRESS: ============================= Precursor FDR =============================
17:26:29.565593 PROGRESS: Total precursors accumulated: 537
17:26:29.565653 PROGRESS: Target precursors: 262 (48.79%)
17:26:29.565703 PROGRESS: Decoy precursors: 275 (51.21%)
17:26:29.565749 PROGRESS: 
17:26:29.565794 PROGRESS: Precursor Summary:
17:26:29.566642 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
17:26:29.566730 PROGRESS: 
17:26:29.566784 PROGRESS: Protein Summary:
17:26:29.567728 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
17:26:29.567819 PROGRESS: =========================================================================
17:26:29.625421 INFO: Starting optimization step 2.
17:26:29.625638 PROGRESS: === Extracting elution groups 600 to 1400 ===
17:26:29.625702 PROGRESS: Extracting batch of 1566 precursors
17:26:29.626611 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
17:26:29.626657 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
17:26:29.626685 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
17:26:29.626706 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
17:26:29.627477 INFO: Starting candidate selection
17:26:38.647465 INFO: Starting candidate scoring
17:26:38.781831 INFO: Finished candidate processing
17:26:38.781934 INFO: Collecting candidate features
17:26:38.792021 INFO: Collecting fragment features
17:26:38.795082 INFO: Finished candidate scoring
17:26:38.798108 PROGRESS: === Extracted 2415 precursors and 24364 fragments ===
17:26:38.799075 INFO: performing precursor FDR with 47 features
17:26:38.799122 INFO: Decoy channel: -1
17:26:38.799146 INFO: Competetive: True
17:26:38.802120 INFO: Setting torch num_threads to 2 for FDR classification task
17:26:38.803340 WARNING: dropped 1 target PSMs due to missing features
17:26:38.814926 INFO: Test AUC: 0.494
17:26:38.814990 INFO: Train AUC: 0.487
17:26:38.815026 INFO: AUC difference: 1.40%
17:26:38.987886 INFO: Resetting torch num_threads to 100
17:26:38.989427 INFO: === FDR correction performed with classifier version -1 ===
17:26:38.990168 PROGRESS: ============================= Precursor FDR =============================
17:26:38.990262 PROGRESS: Total precursors accumulated: 1,249
17:26:38.990321 PROGRESS: Target precursors: 614 (49.16%)
17:26:38.990372 PROGRESS: Decoy precursors: 635 (50.84%)
17:26:38.990418 PROGRESS: 
17:26:38.990461 PROGRESS: Precursor Summary:
17:26:38.991312 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
17:26:38.991399 PROGRESS: 
17:26:38.991458 PROGRESS: Protein Summary:
17:26:38.992349 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
17:26:38.992443 PROGRESS: =========================================================================
17:26:39.054216 INFO: Starting optimization step 3.
17:26:39.054436 PROGRESS: === Extracting elution groups 1400 to 3000 ===
17:26:39.054504 PROGRESS: Extracting batch of 3160 precursors
17:26:39.055793 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
17:26:39.055843 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
17:26:39.055873 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
17:26:39.055894 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
17:26:39.056652 INFO: Starting candidate selection
17:26:55.953715 INFO: Starting candidate scoring
17:26:56.199046 INFO: Finished candidate processing
17:26:56.199151 INFO: Collecting candidate features
17:26:56.208982 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2751)
17:26:56.211997 INFO: Collecting fragment features
17:26:56.216182 INFO: Finished candidate scoring
17:26:56.223322 PROGRESS: === Extracted 5166 precursors and 51971 fragments ===
17:26:56.224539 INFO: performing precursor FDR with 47 features
17:26:56.224583 INFO: Decoy channel: -1
17:26:56.224607 INFO: Competetive: True
17:26:56.228725 INFO: Setting torch num_threads to 2 for FDR classification task
17:26:56.230279 WARNING: dropped 2 target PSMs due to missing features
17:26:56.251217 INFO: Test AUC: 0.486
17:26:56.251305 INFO: Train AUC: 0.483
17:26:56.251334 INFO: AUC difference: 0.66%
17:26:56.426524 INFO: Resetting torch num_threads to 100
17:26:56.427490 INFO: === FDR correction performed with classifier version -1 ===
17:26:56.428378 PROGRESS: ============================= Precursor FDR =============================
17:26:56.428473 PROGRESS: Total precursors accumulated: 2,655
17:26:56.428532 PROGRESS: Target precursors: 1,312 (49.42%)
17:26:56.428582 PROGRESS: Decoy precursors: 1,343 (50.58%)
17:26:56.428626 PROGRESS: 
17:26:56.428670 PROGRESS: Precursor Summary:
17:26:56.429525 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
17:26:56.429613 PROGRESS: 
17:26:56.429669 PROGRESS: Protein Summary:
17:26:56.430579 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
17:26:56.430666 PROGRESS: =========================================================================
17:26:56.505552 INFO: Starting optimization step 4.
17:26:56.505766 PROGRESS: === Extracting elution groups 3000 to 6200 ===
17:26:56.505846 PROGRESS: Extracting batch of 6310 precursors
17:26:56.507758 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
17:26:56.507808 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
17:26:56.507843 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
17:26:56.507868 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
17:26:56.508611 INFO: Starting candidate selection
17:27:29.694188 INFO: Starting candidate scoring
17:27:30.052745 INFO: Finished candidate processing
17:27:30.052849 INFO: Collecting candidate features
17:27:30.082981 INFO: Collecting fragment features
17:27:30.092682 INFO: Finished candidate scoring
17:27:30.102919 PROGRESS: === Extracted 10639 precursors and 107375 fragments ===
17:27:30.105325 INFO: performing precursor FDR with 47 features
17:27:30.105405 INFO: Decoy channel: -1
17:27:30.105445 INFO: Competetive: True
17:27:30.111763 INFO: Setting torch num_threads to 2 for FDR classification task
17:27:30.113889 WARNING: dropped 2 target PSMs due to missing features
17:27:30.148165 INFO: Test AUC: 0.488
17:27:30.148282 INFO: Train AUC: 0.481
17:27:30.148313 INFO: AUC difference: 1.40%
17:27:30.325650 INFO: Resetting torch num_threads to 100
17:27:30.326835 INFO: === FDR correction performed with classifier version -1 ===
17:27:30.328054 PROGRESS: ============================= Precursor FDR =============================
17:27:30.328160 PROGRESS: Total precursors accumulated: 5,463
17:27:30.328219 PROGRESS: Target precursors: 2,695 (49.33%)
17:27:30.328267 PROGRESS: Decoy precursors: 2,768 (50.67%)
17:27:30.328314 PROGRESS: 
17:27:30.328357 PROGRESS: Precursor Summary:
17:27:30.329214 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
17:27:30.329303 PROGRESS: 
17:27:30.329358 PROGRESS: Protein Summary:
17:27:30.330291 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
17:27:30.330379 PROGRESS: =========================================================================
17:27:30.422767 INFO: Starting optimization step 5.
17:27:30.422991 PROGRESS: === Extracting elution groups 6200 to 12600 ===
17:27:30.423068 PROGRESS: Extracting batch of 12602 precursors
17:27:30.425587 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
17:27:30.425642 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
17:27:30.425671 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
17:27:30.425693 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
17:27:30.426416 INFO: Starting candidate selection
17:28:32.894535 INFO: Starting candidate scoring
17:28:33.507326 INFO: Finished candidate processing
17:28:33.507426 INFO: Collecting candidate features
17:28:33.532173 WARNING: intensity_correlation has 3 NaNs ( 0.03 % out of 10968)
17:28:33.535494 INFO: Collecting fragment features
17:28:33.545098 INFO: Finished candidate scoring
17:28:33.576150 PROGRESS: === Extracted 21607 precursors and 217118 fragments ===
17:28:33.579531 INFO: performing precursor FDR with 47 features
17:28:33.579608 INFO: Decoy channel: -1
17:28:33.579633 INFO: Competetive: True
17:28:33.589089 INFO: Setting torch num_threads to 2 for FDR classification task
17:28:33.593275 WARNING: dropped 4 target PSMs due to missing features
17:28:33.593359 WARNING: dropped 1 decoy PSMs due to missing features
17:28:33.840176 INFO: Test AUC: 0.499
17:28:33.840304 INFO: Train AUC: 0.513
17:28:33.840335 INFO: AUC difference: 2.59%
17:28:34.017740 INFO: Resetting torch num_threads to 100
17:28:34.019457 INFO: === FDR correction performed with classifier version -1 ===
17:28:34.021370 PROGRESS: ============================= Precursor FDR =============================
17:28:34.021476 PROGRESS: Total precursors accumulated: 11,084
17:28:34.021542 PROGRESS: Target precursors: 5,716 (51.57%)
17:28:34.021595 PROGRESS: Decoy precursors: 5,368 (48.43%)
17:28:34.021650 PROGRESS: 
17:28:34.021697 PROGRESS: Precursor Summary:
17:28:34.022621 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
17:28:34.022709 PROGRESS: 
17:28:34.022765 PROGRESS: Protein Summary:
17:28:34.023768 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
17:28:34.023860 PROGRESS: =========================================================================
17:28:34.141371 INFO: Starting optimization step 6.
17:28:34.141640 PROGRESS: === Extracting elution groups 12600 to 25400 ===
17:28:34.141719 PROGRESS: Extracting batch of 25176 precursors
17:28:34.147114 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
17:28:34.147181 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
17:28:34.147218 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
17:28:34.147242 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
17:28:34.148286 INFO: Starting candidate selection
17:30:35.239437 INFO: Starting candidate scoring
17:30:36.391320 INFO: Finished candidate processing
17:30:36.391423 INFO: Collecting candidate features
17:30:36.429288 WARNING: intensity_correlation has 9 NaNs ( 0.04 % out of 21878)
17:30:36.429540 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 21878)
17:30:36.433099 INFO: Collecting fragment features
17:30:36.450060 INFO: Finished candidate scoring
17:30:36.495800 PROGRESS: === Extracted 43485 precursors and 435182 fragments ===
17:30:36.502230 INFO: performing precursor FDR with 47 features
17:30:36.502313 INFO: Decoy channel: -1
17:30:36.502339 INFO: Competetive: True
17:30:36.519914 INFO: Setting torch num_threads to 2 for FDR classification task
17:30:36.528739 WARNING: dropped 7 target PSMs due to missing features
17:30:36.528863 WARNING: dropped 7 decoy PSMs due to missing features
17:30:37.128407 INFO: Test AUC: 0.540
17:30:37.128543 INFO: Train AUC: 0.552
17:30:37.128574 INFO: AUC difference: 2.21%
17:30:37.312746 INFO: Resetting torch num_threads to 100
17:30:37.315331 INFO: === FDR correction performed with classifier version -1 ===
17:30:37.318588 PROGRESS: ============================= Precursor FDR =============================
17:30:37.318722 PROGRESS: Total precursors accumulated: 22,325
17:30:37.318782 PROGRESS: Target precursors: 12,916 (57.85%)
17:30:37.318862 PROGRESS: Decoy precursors: 9,409 (42.15%)
17:30:37.318909 PROGRESS: 
17:30:37.318953 PROGRESS: Precursor Summary:
17:30:37.320029 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
17:30:37.320125 PROGRESS: 
17:30:37.320182 PROGRESS: Protein Summary:
17:30:37.321181 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
17:30:37.321271 PROGRESS: =========================================================================
17:30:37.479201 INFO: Starting optimization step 7.
17:30:37.479467 PROGRESS: === Extracting elution groups 25400 to 51000 ===
17:30:37.479564 PROGRESS: Extracting batch of 50417 precursors
17:30:37.491510 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
17:30:37.491623 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
17:30:37.491662 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
17:30:37.491685 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
17:30:37.492520 INFO: Starting candidate selection
17:34:41.049713 INFO: Starting candidate scoring
17:34:43.359558 INFO: Finished candidate processing
17:34:43.360181 INFO: Collecting candidate features
17:34:43.462761 WARNING: intensity_correlation has 9 NaNs ( 0.02 % out of 43900)
17:34:43.463041 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 43900)
17:34:43.468186 INFO: Collecting fragment features
17:34:43.498903 INFO: Finished candidate scoring
17:34:43.575825 PROGRESS: === Extracted 87385 precursors and 874742 fragments ===
17:34:43.587669 INFO: performing precursor FDR with 47 features
17:34:43.587767 INFO: Decoy channel: -1
17:34:43.587793 INFO: Competetive: True
17:34:43.624343 INFO: Setting torch num_threads to 2 for FDR classification task
17:34:43.642715 WARNING: dropped 12 target PSMs due to missing features
17:34:43.642844 WARNING: dropped 13 decoy PSMs due to missing features
17:34:44.996336 INFO: Test AUC: 0.555
17:34:44.996469 INFO: Train AUC: 0.565
17:34:44.996498 INFO: AUC difference: 1.77%
17:34:45.184700 INFO: Resetting torch num_threads to 100
17:34:45.188981 INFO: === FDR correction performed with classifier version -1 ===
17:34:45.196317 PROGRESS: ============================= Precursor FDR =============================
17:34:45.196594 PROGRESS: Total precursors accumulated: 44,824
17:34:45.196663 PROGRESS: Target precursors: 27,441 (61.22%)
17:34:45.196715 PROGRESS: Decoy precursors: 17,383 (38.78%)
17:34:45.196764 PROGRESS: 
17:34:45.196808 PROGRESS: Precursor Summary:
17:34:45.197953 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
17:34:45.198064 PROGRESS: 
17:34:45.198122 PROGRESS: Protein Summary:
17:34:45.199254 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
17:34:45.199359 PROGRESS: =========================================================================
17:34:45.426232 INFO: Starting optimization step 8.
17:34:45.426511 PROGRESS: === Extracting elution groups 51000 to 102200 ===
17:34:45.426610 PROGRESS: Extracting batch of 100803 precursors
17:34:45.450779 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
17:34:45.450908 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
17:34:45.450945 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
17:34:45.450967 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
17:34:45.451894 INFO: Starting candidate selection
17:42:55.379430 INFO: Starting candidate scoring
17:42:59.814620 INFO: Finished candidate processing
17:42:59.814779 INFO: Collecting candidate features
17:42:59.991652 WARNING: intensity_correlation has 22 NaNs ( 0.03 % out of 87763)
17:42:59.991957 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 87763)
17:42:59.997732 INFO: Collecting fragment features
17:43:00.056229 INFO: Finished candidate scoring
17:43:00.219737 PROGRESS: === Extracted 175148 precursors and 1755356 fragments ===
17:43:00.242780 INFO: performing precursor FDR with 47 features
17:43:00.242928 INFO: Decoy channel: -1
17:43:00.242959 INFO: Competetive: True
17:43:00.319158 INFO: Setting torch num_threads to 2 for FDR classification task
17:43:00.353384 WARNING: dropped 24 target PSMs due to missing features
17:43:00.353522 WARNING: dropped 24 decoy PSMs due to missing features
17:43:03.271685 INFO: Test AUC: 0.565
17:43:03.271824 INFO: Train AUC: 0.583
17:43:03.271862 INFO: AUC difference: 3.13%
17:43:03.501481 INFO: Resetting torch num_threads to 100
17:43:03.510544 INFO: === FDR correction performed with classifier version -1 ===
17:43:03.526966 PROGRESS: ============================= Precursor FDR =============================
17:43:03.527279 PROGRESS: Total precursors accumulated: 89,865
17:43:03.527354 PROGRESS: Target precursors: 54,720 (60.89%)
17:43:03.527432 PROGRESS: Decoy precursors: 35,145 (39.11%)
17:43:03.527487 PROGRESS: 
17:43:03.527539 PROGRESS: Precursor Summary:
17:43:03.529350 PROGRESS: Channel   0:	 0.05 FDR:   568; 0.01 FDR:   247; 0.001 FDR:    39
17:43:03.529481 PROGRESS: 
17:43:03.529545 PROGRESS: Protein Summary:
17:43:03.531582 PROGRESS: Channel   0:	 0.05 FDR:   526; 0.01 FDR:   238; 0.001 FDR:    39
17:43:03.531700 PROGRESS: =========================================================================
17:43:03.663889 INFO: fragments_df: keeping 2529 of 1755356 [sum(precursor_idx_mask)=2786 sum(mass_error_mask)=1755356 stop_rank=2529
17:43:03.985157 INFO: calibration group: precursor, fitting mz estimator 
17:43:04.093462 INFO: calibration group: precursor, fitting rt estimator 
17:43:04.195863 INFO: calibration group: precursor, fitting mobility estimator 
17:43:04.291158 INFO: calibration group: fragment, fitting mz estimator 
17:43:04.567176 INFO: Using score_cutoff 57.4142701423645 (fac=0.99, q=1)
17:43:04.567588 INFO: calibration group: precursor, predicting mz
17:43:04.594790 INFO: calibration group: precursor, predicting rt
17:43:04.718177 INFO: calibration group: precursor, predicting mobility
17:43:04.750301 INFO: calibration group: fragment, predicting mz
17:43:05.008046 PROGRESS: Required number of precursors found. Starting search parameter optimization.
17:43:05.008398 INFO: Starting optimization step 9.
17:43:05.008486 PROGRESS: === Extracting elution groups 0 to 102200 ===
17:43:05.008575 PROGRESS: Extracting batch of 201218 precursors
17:43:05.056901 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
17:43:05.057043 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
17:43:05.057106 INFO: FWHM in RT is 3.35 seconds, sigma is 0.74
17:43:05.057136 INFO: FWHM in mobility is 0.012 1/K_0, sigma is 5.53
17:43:05.057915 INFO: Starting candidate selection
17:58:56.216332 INFO: Starting candidate scoring
17:59:13.769565 INFO: Finished candidate processing
17:59:13.769725 INFO: Collecting candidate features
17:59:14.370008 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 344997)
17:59:14.385581 INFO: Collecting fragment features
17:59:14.590193 INFO: Finished candidate scoring
17:59:14.924500 PROGRESS: === Extracted 344997 precursors and 3514053 fragments ===
17:59:14.925000 INFO: performing precursor FDR with 47 features
17:59:14.925051 INFO: Decoy channel: -1
17:59:14.925078 INFO: Competetive: True
17:59:15.035051 INFO: Setting torch num_threads to 2 for FDR classification task
17:59:15.092588 WARNING: dropped 1 decoy PSMs due to missing features
17:59:21.270765 INFO: Test AUC: 0.564
17:59:21.270905 INFO: Train AUC: 0.587
17:59:21.270936 INFO: AUC difference: 3.96%
17:59:21.547872 INFO: Resetting torch num_threads to 100
17:59:21.557455 INFO: === FDR correction performed with classifier version 8 ===
17:59:21.574214 PROGRESS: ============================= Precursor FDR =============================
17:59:21.574518 PROGRESS: Total precursors accumulated: 91,721
17:59:21.574585 PROGRESS: Target precursors: 56,962 (62.10%)
17:59:21.574648 PROGRESS: Decoy precursors: 34,759 (37.90%)
17:59:21.574697 PROGRESS: 
17:59:21.574740 PROGRESS: Precursor Summary:
17:59:21.576610 PROGRESS: Channel   0:	 0.05 FDR:   925; 0.01 FDR:   682; 0.001 FDR:   238
17:59:21.576710 PROGRESS: 
17:59:21.576771 PROGRESS: Protein Summary:
17:59:21.578533 PROGRESS: Channel   0:	 0.05 FDR:   820; 0.01 FDR:   615; 0.001 FDR:   225
17:59:21.578635 PROGRESS: =========================================================================
17:59:21.812232 INFO: fragments_df: keeping 5000 of 3514053 [sum(precursor_idx_mask)=14569 sum(mass_error_mask)=3514053 stop_rank=5000
17:59:22.010266 INFO: calibration group: precursor, fitting mz estimator 
17:59:22.135592 INFO: calibration group: precursor, fitting rt estimator 
17:59:22.256115 INFO: calibration group: precursor, fitting mobility estimator 
17:59:22.383994 INFO: calibration group: fragment, fitting mz estimator 
17:59:22.998931 INFO: Using score_cutoff 51.59204892539978 (fac=0.99, q=1)
17:59:22.999368 INFO: calibration group: precursor, predicting mz
17:59:23.012838 INFO: calibration group: precursor, predicting rt
17:59:23.072369 INFO: calibration group: precursor, predicting mobility
17:59:23.086808 INFO: calibration group: fragment, predicting mz
17:59:23.204999 INFO: === checking if optimization conditions were reached ===
17:59:23.205267 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
17:59:23.207561 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 14.7038.
17:59:23.207615 INFO: ==============================================
17:59:23.207711 INFO: Starting optimization step 10.
17:59:23.207777 PROGRESS: === Extracting elution groups 0 to 51000 ===
17:59:23.207841 PROGRESS: Extracting batch of 100415 precursors
17:59:23.232718 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
17:59:23.232840 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
17:59:23.232889 INFO: FWHM in RT is 3.28 seconds, sigma is 0.72
17:59:23.232912 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.28
17:59:23.241697 INFO: Starting candidate selection
18:06:50.546535 INFO: Starting candidate scoring
18:06:56.266638 INFO: Finished candidate processing
18:06:56.266807 INFO: Collecting candidate features
18:06:56.557494 WARNING: intensity_correlation has 6 NaNs ( 0.00 % out of 172309)
18:06:56.567039 INFO: Collecting fragment features
18:06:56.676085 INFO: Finished candidate scoring
18:06:56.761709 PROGRESS: === Extracted 172309 precursors and 1689739 fragments ===
18:06:56.762187 INFO: performing precursor FDR with 47 features
18:06:56.762226 INFO: Decoy channel: -1
18:06:56.762249 INFO: Competetive: True
18:06:56.821275 INFO: Setting torch num_threads to 2 for FDR classification task
18:06:56.853806 WARNING: dropped 2 target PSMs due to missing features
18:06:56.853953 WARNING: dropped 4 decoy PSMs due to missing features
18:07:00.171800 INFO: Test AUC: 0.564
18:07:00.171938 INFO: Train AUC: 0.587
18:07:00.171970 INFO: AUC difference: 3.97%
18:07:00.398278 INFO: Resetting torch num_threads to 100
18:07:00.402983 INFO: === FDR correction performed with classifier version 8 ===
18:07:00.410856 PROGRESS: ============================= Precursor FDR =============================
18:07:00.411118 PROGRESS: Total precursors accumulated: 45,722
18:07:00.411184 PROGRESS: Target precursors: 28,208 (61.69%)
18:07:00.411240 PROGRESS: Decoy precursors: 17,514 (38.31%)
18:07:00.411288 PROGRESS: 
18:07:00.411333 PROGRESS: Precursor Summary:
18:07:00.413417 PROGRESS: Channel   0:	 0.05 FDR:   483; 0.01 FDR:   227; 0.001 FDR:   152
18:07:00.413520 PROGRESS: 
18:07:00.413579 PROGRESS: Protein Summary:
18:07:00.414918 PROGRESS: Channel   0:	 0.05 FDR:   454; 0.01 FDR:   220; 0.001 FDR:   148
18:07:00.415012 PROGRESS: =========================================================================
18:07:00.546558 INFO: fragments_df: keeping 2898 of 1689739 [sum(precursor_idx_mask)=4750 sum(mass_error_mask)=1689739 stop_rank=2898
18:07:00.736630 INFO: calibration group: precursor, fitting mz estimator 
18:07:00.853126 INFO: calibration group: precursor, fitting rt estimator 
18:07:00.963583 INFO: calibration group: precursor, fitting mobility estimator 
18:07:01.082600 INFO: calibration group: fragment, fitting mz estimator 
18:07:01.462853 INFO: Using score_cutoff 50.8150693611145 (fac=0.99, q=1)
18:07:01.463285 INFO: calibration group: precursor, predicting mz
18:07:01.477038 INFO: calibration group: precursor, predicting rt
18:07:01.537508 INFO: calibration group: precursor, predicting mobility
18:07:01.554055 INFO: calibration group: fragment, predicting mz
18:07:01.677277 INFO: === checking if optimization conditions were reached ===
18:07:01.677558 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
18:07:01.679747 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 6.4087.
18:07:01.679804 INFO: ==============================================
18:07:01.679914 INFO: Starting optimization step 11.
18:07:01.679979 PROGRESS: === Extracting elution groups 0 to 51000 ===
18:07:01.680045 PROGRESS: Extracting batch of 100415 precursors
18:07:01.704636 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
18:07:01.704774 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
18:07:01.704825 INFO: FWHM in RT is 3.19 seconds, sigma is 0.70
18:07:01.704849 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.86
18:07:01.713734 INFO: Starting candidate selection
18:14:13.414105 INFO: Starting candidate scoring
18:14:17.370210 INFO: Finished candidate processing
18:14:17.370370 INFO: Collecting candidate features
18:14:17.656772 WARNING: intensity_correlation has 29 NaNs ( 0.02 % out of 171807)
18:14:17.666329 INFO: Collecting fragment features
18:14:17.763644 INFO: Finished candidate scoring
18:14:17.848830 PROGRESS: === Extracted 171807 precursors and 1559442 fragments ===
18:14:17.849304 INFO: performing precursor FDR with 47 features
18:14:17.849344 INFO: Decoy channel: -1
18:14:17.849370 INFO: Competetive: True
18:14:17.902060 INFO: Setting torch num_threads to 2 for FDR classification task
18:14:17.932509 WARNING: dropped 9 target PSMs due to missing features
18:14:17.932645 WARNING: dropped 20 decoy PSMs due to missing features
18:14:21.166110 INFO: Test AUC: 0.557
18:14:21.166565 INFO: Train AUC: 0.589
18:14:21.166601 INFO: AUC difference: 5.46%
18:14:21.166621 WARNING: AUC difference > 5%. This may indicate overfitting.
18:14:21.394245 INFO: Resetting torch num_threads to 100
18:14:21.398941 INFO: === FDR correction performed with classifier version 8 ===
18:14:21.406634 PROGRESS: ============================= Precursor FDR =============================
18:14:21.406882 PROGRESS: Total precursors accumulated: 45,651
18:14:21.406947 PROGRESS: Target precursors: 28,125 (61.61%)
18:14:21.406999 PROGRESS: Decoy precursors: 17,526 (38.39%)
18:14:21.407063 PROGRESS: 
18:14:21.407110 PROGRESS: Precursor Summary:
18:14:21.408430 PROGRESS: Channel   0:	 0.05 FDR:   535; 0.01 FDR:   281; 0.001 FDR:   268
18:14:21.408527 PROGRESS: 
18:14:21.408584 PROGRESS: Protein Summary:
18:14:21.409951 PROGRESS: Channel   0:	 0.05 FDR:   506; 0.01 FDR:   268; 0.001 FDR:   256
18:14:21.410046 PROGRESS: =========================================================================
18:14:21.514840 INFO: fragments_df: keeping 3154 of 1559442 [sum(precursor_idx_mask)=5742 sum(mass_error_mask)=1559442 stop_rank=3154
18:14:21.704021 INFO: calibration group: precursor, fitting mz estimator 
18:14:21.830578 INFO: calibration group: precursor, fitting rt estimator 
18:14:21.947349 INFO: calibration group: precursor, fitting mobility estimator 
18:14:22.066183 INFO: calibration group: fragment, fitting mz estimator 
18:14:22.480694 INFO: Using score_cutoff 47.22623348236084 (fac=0.99, q=1)
18:14:22.481102 INFO: calibration group: precursor, predicting mz
18:14:22.494992 INFO: calibration group: precursor, predicting rt
18:14:22.555310 INFO: calibration group: precursor, predicting mobility
18:14:22.570269 INFO: calibration group: fragment, predicting mz
18:14:22.690523 INFO: === checking if optimization conditions were reached ===
18:14:22.690791 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
18:14:22.693038 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 4.4793.
18:14:22.693094 INFO: ==============================================
18:14:22.693194 INFO: Starting optimization step 12.
18:14:22.693260 PROGRESS: === Extracting elution groups 0 to 51000 ===
18:14:22.693325 PROGRESS: Extracting batch of 100415 precursors
18:14:22.717877 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
18:14:22.718012 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
18:14:22.718066 INFO: FWHM in RT is 2.62 seconds, sigma is 0.58
18:14:22.718091 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.52
18:14:22.727014 INFO: Starting candidate selection
18:21:45.438196 INFO: Starting candidate scoring
18:21:48.916556 INFO: Finished candidate processing
18:21:48.916725 INFO: Collecting candidate features
18:21:49.197318 WARNING: intensity_correlation has 101 NaNs ( 0.06 % out of 170682)
18:21:49.197718 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 170682)
18:21:49.207809 INFO: Collecting fragment features
18:21:49.312471 INFO: Finished candidate scoring
18:21:49.401472 PROGRESS: === Extracted 170682 precursors and 1410845 fragments ===
18:21:49.401936 INFO: performing precursor FDR with 47 features
18:21:49.401977 INFO: Decoy channel: -1
18:21:49.402001 INFO: Competetive: True
18:21:49.456484 INFO: Setting torch num_threads to 2 for FDR classification task
18:21:49.486671 WARNING: dropped 47 target PSMs due to missing features
18:21:49.486815 WARNING: dropped 55 decoy PSMs due to missing features
18:21:52.537043 INFO: Test AUC: 0.568
18:21:52.537181 INFO: Train AUC: 0.589
18:21:52.537212 INFO: AUC difference: 3.58%
18:21:52.764598 INFO: Resetting torch num_threads to 100
18:21:52.769196 INFO: === FDR correction performed with classifier version 8 ===
18:21:52.776802 PROGRESS: ============================= Precursor FDR =============================
18:21:52.777064 PROGRESS: Total precursors accumulated: 45,566
18:21:52.777128 PROGRESS: Target precursors: 28,279 (62.06%)
18:21:52.777179 PROGRESS: Decoy precursors: 17,287 (37.94%)
18:21:52.777228 PROGRESS: 
18:21:52.777273 PROGRESS: Precursor Summary:
18:21:52.778576 PROGRESS: Channel   0:	 0.05 FDR:   335; 0.01 FDR:   234; 0.001 FDR:   158
18:21:52.778672 PROGRESS: 
18:21:52.778726 PROGRESS: Protein Summary:
18:21:52.780038 PROGRESS: Channel   0:	 0.05 FDR:   317; 0.01 FDR:   221; 0.001 FDR:   154
18:21:52.780132 PROGRESS: =========================================================================
18:21:52.874525 INFO: fragments_df: keeping 2536 of 1410845 [sum(precursor_idx_mask)=4662 sum(mass_error_mask)=1410845 stop_rank=2536
18:21:53.063993 INFO: calibration group: precursor, fitting mz estimator 
18:21:53.168059 INFO: calibration group: precursor, fitting rt estimator 
18:21:53.265540 INFO: calibration group: precursor, fitting mobility estimator 
18:21:53.362132 INFO: calibration group: fragment, fitting mz estimator 
18:21:53.653592 INFO: Using score_cutoff 45.67738334655762 (fac=0.99, q=1)
18:21:53.654087 INFO: calibration group: precursor, predicting mz
18:21:53.667285 INFO: calibration group: precursor, predicting rt
18:21:53.728956 INFO: calibration group: precursor, predicting mobility
18:21:53.745652 INFO: calibration group: fragment, predicting mz
18:21:53.877981 INFO: === checking if optimization conditions were reached ===
18:21:53.878373 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
18:21:53.881487 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 4.1101.
18:21:53.881557 INFO: ==============================================
18:21:53.881688 INFO: Starting optimization step 13.
18:21:53.881770 PROGRESS: === Extracting elution groups 0 to 51000 ===
18:21:53.881850 PROGRESS: Extracting batch of 100415 precursors
18:21:53.931138 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
18:21:53.931288 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
18:21:53.931344 INFO: FWHM in RT is 2.40 seconds, sigma is 0.53
18:21:53.931370 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.91
18:21:53.932224 INFO: Starting candidate selection
18:28:58.377035 INFO: Starting candidate scoring
18:29:01.873551 INFO: Finished candidate processing
18:29:01.873712 INFO: Collecting candidate features
18:29:02.151213 WARNING: intensity_correlation has 77 NaNs ( 0.05 % out of 170745)
18:29:02.151652 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 170745)
18:29:02.163398 INFO: Collecting fragment features
18:29:02.263419 INFO: Finished candidate scoring
18:29:02.351890 PROGRESS: === Extracted 170745 precursors and 1405176 fragments ===
18:29:02.352355 INFO: performing precursor FDR with 47 features
18:29:02.352395 INFO: Decoy channel: -1
18:29:02.352433 INFO: Competetive: True
18:29:02.408215 INFO: Setting torch num_threads to 2 for FDR classification task
18:29:02.439668 WARNING: dropped 45 target PSMs due to missing features
18:29:02.439810 WARNING: dropped 33 decoy PSMs due to missing features
18:29:05.680539 INFO: Test AUC: 0.566
18:29:05.680672 INFO: Train AUC: 0.590
18:29:05.680703 INFO: AUC difference: 4.01%
18:29:05.907513 INFO: Resetting torch num_threads to 100
18:29:05.912204 INFO: === FDR correction performed with classifier version 8 ===
18:29:05.919880 PROGRESS: ============================= Precursor FDR =============================
18:29:05.920130 PROGRESS: Total precursors accumulated: 45,564
18:29:05.920195 PROGRESS: Target precursors: 28,081 (61.63%)
18:29:05.920245 PROGRESS: Decoy precursors: 17,483 (38.37%)
18:29:05.920294 PROGRESS: 
18:29:05.920341 PROGRESS: Precursor Summary:
18:29:05.921879 PROGRESS: Channel   0:	 0.05 FDR:   463; 0.01 FDR:   248; 0.001 FDR:   183
18:29:05.921991 PROGRESS: 
18:29:05.922048 PROGRESS: Protein Summary:
18:29:05.923450 PROGRESS: Channel   0:	 0.05 FDR:   436; 0.01 FDR:   235; 0.001 FDR:   174
18:29:05.923545 PROGRESS: =========================================================================
18:29:06.019477 INFO: fragments_df: keeping 2707 of 1405176 [sum(precursor_idx_mask)=4884 sum(mass_error_mask)=1405176 stop_rank=2707
18:29:06.208927 INFO: calibration group: precursor, fitting mz estimator 
18:29:06.329217 INFO: calibration group: precursor, fitting rt estimator 
18:29:06.441185 INFO: calibration group: precursor, fitting mobility estimator 
18:29:06.562159 INFO: calibration group: fragment, fitting mz estimator 
18:29:06.923857 INFO: Using score_cutoff 45.87387484130859 (fac=0.99, q=1)
18:29:06.924268 INFO: calibration group: precursor, predicting mz
18:29:06.937453 INFO: calibration group: precursor, predicting rt
18:29:06.998744 INFO: calibration group: precursor, predicting mobility
18:29:07.013511 INFO: calibration group: fragment, predicting mz
18:29:07.128924 INFO: === checking if optimization conditions were reached ===
18:29:07.129192 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
18:29:07.131451 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 4.2097.
18:29:07.131506 INFO: ==============================================
18:29:07.131613 INFO: Starting optimization step 14.
18:29:07.131679 PROGRESS: === Extracting elution groups 0 to 51000 ===
18:29:07.131747 PROGRESS: Extracting batch of 100415 precursors
18:29:07.156463 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
18:29:07.156596 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
18:29:07.156648 INFO: FWHM in RT is 2.43 seconds, sigma is 0.53
18:29:07.156671 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.90
18:29:07.165617 INFO: Starting candidate selection
18:36:27.030858 INFO: Starting candidate scoring
18:36:30.421920 INFO: Finished candidate processing
18:36:30.422021 INFO: Collecting candidate features
18:36:30.679292 WARNING: intensity_correlation has 93 NaNs ( 0.05 % out of 170719)
18:36:30.679671 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 170719)
18:36:30.688609 INFO: Collecting fragment features
18:36:30.786008 INFO: Finished candidate scoring
18:36:30.871701 PROGRESS: === Extracted 170719 precursors and 1405561 fragments ===
18:36:30.872163 INFO: performing precursor FDR with 47 features
18:36:30.872203 INFO: Decoy channel: -1
18:36:30.872226 INFO: Competetive: True
18:36:30.923783 INFO: Setting torch num_threads to 2 for FDR classification task
18:36:30.956076 WARNING: dropped 52 target PSMs due to missing features
18:36:30.956209 WARNING: dropped 42 decoy PSMs due to missing features
18:36:33.859557 INFO: Test AUC: 0.566
18:36:33.859692 INFO: Train AUC: 0.593
18:36:33.859723 INFO: AUC difference: 4.52%
18:36:34.088020 INFO: Resetting torch num_threads to 100
18:36:34.092647 INFO: === FDR correction performed with classifier version 8 ===
18:36:34.100572 PROGRESS: ============================= Precursor FDR =============================
18:36:34.100838 PROGRESS: Total precursors accumulated: 45,558
18:36:34.100902 PROGRESS: Target precursors: 28,192 (61.88%)
18:36:34.100952 PROGRESS: Decoy precursors: 17,366 (38.12%)
18:36:34.100999 PROGRESS: 
18:36:34.101050 PROGRESS: Precursor Summary:
18:36:34.102332 PROGRESS: Channel   0:	 0.05 FDR:   405; 0.01 FDR:   248; 0.001 FDR:    18
18:36:34.102429 PROGRESS: 
18:36:34.102484 PROGRESS: Protein Summary:
18:36:34.103788 PROGRESS: Channel   0:	 0.05 FDR:   381; 0.01 FDR:   233; 0.001 FDR:    18
18:36:34.103891 PROGRESS: =========================================================================
18:36:34.195284 INFO: fragments_df: keeping 2626 of 1405561 [sum(precursor_idx_mask)=4819 sum(mass_error_mask)=1405561 stop_rank=2626
18:36:34.385310 INFO: calibration group: precursor, fitting mz estimator 
18:36:34.503943 INFO: calibration group: precursor, fitting rt estimator 
18:36:34.621558 INFO: calibration group: precursor, fitting mobility estimator 
18:36:34.746276 INFO: calibration group: fragment, fitting mz estimator 
18:36:35.102990 INFO: Using score_cutoff 38.22604489173889 (fac=0.99, q=1)
18:36:35.103450 INFO: calibration group: precursor, predicting mz
18:36:35.116868 INFO: calibration group: precursor, predicting rt
18:36:35.177947 INFO: calibration group: precursor, predicting mobility
18:36:35.192235 INFO: calibration group: fragment, predicting mz
18:36:35.308768 INFO: === checking if optimization conditions were reached ===
18:36:35.309071 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
18:36:35.310077 PROGRESS: ✅ ms2_error      : optimization complete. Optimal parameter 30.0000 found after 6 searches.
18:36:35.310127 INFO: ==============================================
18:36:35.310234 PROGRESS: Optimization finished for ms2_error.
18:36:35.489995 INFO: calibration group: precursor, predicting mz
18:36:35.503780 INFO: calibration group: precursor, predicting rt
18:36:35.564871 INFO: calibration group: precursor, predicting mobility
18:36:35.579461 INFO: calibration group: fragment, predicting mz
18:36:35.721849 INFO: Starting optimization step 0.
18:36:35.722028 PROGRESS: === Extracting elution groups 0 to 51000 ===
18:36:35.722103 PROGRESS: Extracting batch of 100415 precursors
18:36:35.746669 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
18:36:35.746789 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
18:36:35.746840 INFO: FWHM in RT is 3.28 seconds, sigma is 0.72
18:36:35.746863 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.28
18:36:35.755577 INFO: Starting candidate selection
18:44:48.550079 INFO: Starting candidate scoring
18:44:57.398935 INFO: Finished candidate processing
18:44:57.399307 INFO: Collecting candidate features
18:44:57.777854 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 172686)
18:44:57.787600 INFO: Collecting fragment features
18:44:57.889417 INFO: Finished candidate scoring
18:44:57.999187 PROGRESS: === Extracted 172686 precursors and 1758053 fragments ===
18:44:57.999696 INFO: performing precursor FDR with 47 features
18:44:57.999735 INFO: Decoy channel: -1
18:44:57.999761 INFO: Competetive: True
18:44:58.052746 INFO: Setting torch num_threads to 2 for FDR classification task
18:44:58.079809 WARNING: dropped 1 decoy PSMs due to missing features
18:45:01.267089 INFO: Test AUC: 0.570
18:45:01.267219 INFO: Train AUC: 0.607
18:45:01.267250 INFO: AUC difference: 5.98%
18:45:01.267272 WARNING: AUC difference > 5%. This may indicate overfitting.
18:45:01.496070 INFO: Resetting torch num_threads to 100
18:45:01.500840 INFO: === FDR correction performed with classifier version 9 ===
18:45:01.508949 PROGRESS: ============================= Precursor FDR =============================
18:45:01.509207 PROGRESS: Total precursors accumulated: 45,893
18:45:01.509272 PROGRESS: Target precursors: 29,335 (63.92%)
18:45:01.509322 PROGRESS: Decoy precursors: 16,558 (36.08%)
18:45:01.509369 PROGRESS: 
18:45:01.509413 PROGRESS: Precursor Summary:
18:45:01.510746 PROGRESS: Channel   0:	 0.05 FDR:   507; 0.01 FDR:   424; 0.001 FDR:    96
18:45:01.510839 PROGRESS: 
18:45:01.510894 PROGRESS: Protein Summary:
18:45:01.512280 PROGRESS: Channel   0:	 0.05 FDR:   476; 0.01 FDR:   394; 0.001 FDR:    95
18:45:01.512374 PROGRESS: =========================================================================
18:45:01.626403 INFO: fragments_df: keeping 4937 of 1758053 [sum(precursor_idx_mask)=9005 sum(mass_error_mask)=1758053 stop_rank=4937
18:45:01.758004 INFO: calibration group: precursor, fitting mz estimator 
18:45:01.887922 INFO: calibration group: precursor, fitting rt estimator 
18:45:02.013431 INFO: calibration group: precursor, fitting mobility estimator 
18:45:02.146041 INFO: calibration group: fragment, fitting mz estimator 
18:45:02.808110 INFO: Using score_cutoff 51.40160508499145 (fac=0.99, q=1)
18:45:02.808536 INFO: calibration group: precursor, predicting mz
18:45:02.816043 INFO: calibration group: precursor, predicting rt
18:45:02.846269 INFO: calibration group: precursor, predicting mobility
18:45:02.853251 INFO: calibration group: fragment, predicting mz
18:45:02.909961 INFO: === checking if optimization conditions were reached ===
18:45:02.910239 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
18:45:02.912139 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 682.7409.
18:45:02.912194 INFO: ==============================================
18:45:02.912292 INFO: Starting optimization step 1.
18:45:02.912357 PROGRESS: === Extracting elution groups 0 to 25400 ===
18:45:02.912422 PROGRESS: Extracting batch of 49998 precursors
18:45:02.925206 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
18:45:02.925323 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
18:45:02.925372 INFO: FWHM in RT is 3.33 seconds, sigma is 0.73
18:45:02.925396 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.22
18:45:02.950243 INFO: Starting candidate selection
18:46:46.065251 INFO: Starting candidate scoring
18:46:50.711684 INFO: Finished candidate processing
18:46:50.711845 INFO: Collecting candidate features
18:46:50.861148 WARNING: intensity_correlation has 8 NaNs ( 0.01 % out of 84769)
18:46:50.861452 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 84769)
18:46:50.867496 INFO: Collecting fragment features
18:46:50.926940 INFO: Finished candidate scoring
18:46:50.968138 PROGRESS: === Extracted 84769 precursors and 853852 fragments ===
18:46:50.968610 INFO: performing precursor FDR with 47 features
18:46:50.968648 INFO: Decoy channel: -1
18:46:50.968672 INFO: Competetive: True
18:46:50.998689 INFO: Setting torch num_threads to 2 for FDR classification task
18:46:51.015239 WARNING: dropped 5 target PSMs due to missing features
18:46:51.015371 WARNING: dropped 4 decoy PSMs due to missing features
18:46:52.507074 INFO: Test AUC: 0.561
18:46:52.507208 INFO: Train AUC: 0.606
18:46:52.507240 INFO: AUC difference: 7.45%
18:46:52.507260 WARNING: AUC difference > 5%. This may indicate overfitting.
18:46:52.710632 INFO: Resetting torch num_threads to 100
18:46:52.713386 INFO: === FDR correction performed with classifier version 9 ===
18:46:52.717146 PROGRESS: ============================= Precursor FDR =============================
18:46:52.717297 PROGRESS: Total precursors accumulated: 22,695
18:46:52.717377 PROGRESS: Target precursors: 14,540 (64.07%)
18:46:52.717437 PROGRESS: Decoy precursors: 8,155 (35.93%)
18:46:52.717494 PROGRESS: 
18:46:52.717547 PROGRESS: Precursor Summary:
18:46:52.718634 PROGRESS: Channel   0:	 0.05 FDR:   199; 0.01 FDR:   178; 0.001 FDR:   138
18:46:52.718736 PROGRESS: 
18:46:52.718799 PROGRESS: Protein Summary:
18:46:52.719975 PROGRESS: Channel   0:	 0.05 FDR:   194; 0.01 FDR:   173; 0.001 FDR:   136
18:46:52.720074 PROGRESS: =========================================================================
18:46:52.878513 INFO: calibration group: precursor, predicting mz
18:46:52.886601 INFO: calibration group: precursor, predicting rt
18:46:52.917967 INFO: calibration group: precursor, predicting mobility
18:46:52.925120 INFO: calibration group: fragment, predicting mz
18:46:52.983976 INFO: === skipping optimization until target number of precursors are found ===
18:46:52.984257 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
18:46:52.984329 INFO: Starting optimization step 2.
18:46:52.984402 PROGRESS: === Extracting elution groups 25400 to 51000 ===
18:46:52.984476 PROGRESS: Extracting batch of 50417 precursors
18:46:52.997360 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
18:46:52.997487 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
18:46:52.997542 INFO: FWHM in RT is 3.33 seconds, sigma is 0.73
18:46:52.997570 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.22
18:46:52.998720 INFO: Starting candidate selection
18:48:37.483389 INFO: Starting candidate scoring
18:48:42.243381 INFO: Finished candidate processing
18:48:42.243550 INFO: Collecting candidate features
18:48:42.402376 WARNING: intensity_correlation has 7 NaNs ( 0.01 % out of 85715)
18:48:42.402766 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 85715)
18:48:42.412320 INFO: Collecting fragment features
18:48:42.470987 INFO: Finished candidate scoring
18:48:42.593593 PROGRESS: === Extracted 170484 precursors and 1717278 fragments ===
18:48:42.615128 INFO: performing precursor FDR with 47 features
18:48:42.615267 INFO: Decoy channel: -1
18:48:42.615294 INFO: Competetive: True
18:48:42.686562 INFO: Setting torch num_threads to 2 for FDR classification task
18:48:42.717113 WARNING: dropped 9 target PSMs due to missing features
18:48:42.717255 WARNING: dropped 8 decoy PSMs due to missing features
18:48:46.195056 INFO: Test AUC: 0.564
18:48:46.195179 INFO: Train AUC: 0.600
18:48:46.195210 INFO: AUC difference: 6.01%
18:48:46.195231 WARNING: AUC difference > 5%. This may indicate overfitting.
18:48:46.422366 INFO: Resetting torch num_threads to 100
18:48:46.429303 INFO: === FDR correction performed with classifier version 9 ===
18:48:46.437285 PROGRESS: ============================= Precursor FDR =============================
18:48:46.437550 PROGRESS: Total precursors accumulated: 45,567
18:48:46.437616 PROGRESS: Target precursors: 28,872 (63.36%)
18:48:46.437666 PROGRESS: Decoy precursors: 16,695 (36.64%)
18:48:46.437714 PROGRESS: 
18:48:46.437759 PROGRESS: Precursor Summary:
18:48:46.439133 PROGRESS: Channel   0:	 0.05 FDR:   511; 0.01 FDR:   373; 0.001 FDR:   124
18:48:46.439230 PROGRESS: 
18:48:46.439286 PROGRESS: Protein Summary:
18:48:46.440653 PROGRESS: Channel   0:	 0.05 FDR:   482; 0.01 FDR:   349; 0.001 FDR:   121
18:48:46.440747 PROGRESS: =========================================================================
18:48:46.567841 INFO: fragments_df: keeping 4459 of 1717278 [sum(precursor_idx_mask)=7878 sum(mass_error_mask)=1717278 stop_rank=4459
18:48:46.765576 INFO: calibration group: precursor, fitting mz estimator 
18:48:46.875927 INFO: calibration group: precursor, fitting rt estimator 
18:48:46.983856 INFO: calibration group: precursor, fitting mobility estimator 
18:48:47.094040 INFO: calibration group: fragment, fitting mz estimator 
18:48:47.614919 INFO: Using score_cutoff 47.048270498657224 (fac=0.99, q=1)
18:48:47.615356 INFO: calibration group: precursor, predicting mz
18:48:47.628572 INFO: calibration group: precursor, predicting rt
18:48:47.689187 INFO: calibration group: precursor, predicting mobility
18:48:47.702832 INFO: calibration group: fragment, predicting mz
18:48:47.825872 INFO: === checking if optimization conditions were reached ===
18:48:47.826161 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
18:48:47.828199 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 587.7539.
18:48:47.828263 INFO: ==============================================
18:48:47.828372 INFO: Starting optimization step 3.
18:48:47.828443 PROGRESS: === Extracting elution groups 0 to 51000 ===
18:48:47.828514 PROGRESS: Extracting batch of 100415 precursors
18:48:47.852961 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
18:48:47.853098 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
18:48:47.853153 INFO: FWHM in RT is 3.35 seconds, sigma is 0.74
18:48:47.853180 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.24
18:48:47.862046 INFO: Starting candidate selection
18:51:21.621535 INFO: Starting candidate scoring
18:51:29.973598 INFO: Finished candidate processing
18:51:29.973779 INFO: Collecting candidate features
18:51:30.262663 WARNING: intensity_correlation has 29 NaNs ( 0.02 % out of 169396)
18:51:30.263077 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 169396)
18:51:30.272175 INFO: Collecting fragment features
18:51:30.371762 INFO: Finished candidate scoring
18:51:30.461892 PROGRESS: === Extracted 169396 precursors and 1700382 fragments ===
18:51:30.462374 INFO: performing precursor FDR with 47 features
18:51:30.462414 INFO: Decoy channel: -1
18:51:30.462438 INFO: Competetive: True
18:51:30.514625 INFO: Setting torch num_threads to 2 for FDR classification task
18:51:30.545387 WARNING: dropped 15 target PSMs due to missing features
18:51:30.545529 WARNING: dropped 16 decoy PSMs due to missing features
18:51:33.844962 INFO: Test AUC: 0.562
18:51:33.845107 INFO: Train AUC: 0.598
18:51:33.845139 INFO: AUC difference: 6.13%
18:51:33.845161 WARNING: AUC difference > 5%. This may indicate overfitting.
18:51:34.077163 INFO: Resetting torch num_threads to 100
18:51:34.081815 INFO: === FDR correction performed with classifier version 9 ===
18:51:34.090039 PROGRESS: ============================= Precursor FDR =============================
18:51:34.090316 PROGRESS: Total precursors accumulated: 45,375
18:51:34.090384 PROGRESS: Target precursors: 28,622 (63.08%)
18:51:34.090457 PROGRESS: Decoy precursors: 16,753 (36.92%)
18:51:34.090510 PROGRESS: 
18:51:34.090562 PROGRESS: Precursor Summary:
18:51:34.092039 PROGRESS: Channel   0:	 0.05 FDR:   525; 0.01 FDR:   366; 0.001 FDR:   153
18:51:34.092155 PROGRESS: 
18:51:34.092212 PROGRESS: Protein Summary:
18:51:34.093680 PROGRESS: Channel   0:	 0.05 FDR:   492; 0.01 FDR:   343; 0.001 FDR:   150
18:51:34.093782 PROGRESS: =========================================================================
18:51:34.210851 INFO: fragments_df: keeping 4455 of 1700382 [sum(precursor_idx_mask)=7752 sum(mass_error_mask)=1700382 stop_rank=4455
18:51:34.406682 INFO: calibration group: precursor, fitting mz estimator 
18:51:34.531966 INFO: calibration group: precursor, fitting rt estimator 
18:51:34.659478 INFO: calibration group: precursor, fitting mobility estimator 
18:51:34.789218 INFO: calibration group: fragment, fitting mz estimator 
18:51:35.377113 INFO: Using score_cutoff 55.07753765487671 (fac=0.99, q=1)
18:51:35.377551 INFO: calibration group: precursor, predicting mz
18:51:35.391042 INFO: calibration group: precursor, predicting rt
18:51:35.451298 INFO: calibration group: precursor, predicting mobility
18:51:35.467692 INFO: calibration group: fragment, predicting mz
18:51:35.596646 INFO: === checking if optimization conditions were reached ===
18:51:35.596975 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
18:51:35.599487 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 496.1112.
18:51:35.599550 INFO: ==============================================
18:51:35.599665 INFO: Starting optimization step 4.
18:51:35.599763 PROGRESS: === Extracting elution groups 0 to 51000 ===
18:51:35.599844 PROGRESS: Extracting batch of 100415 precursors
18:51:35.626551 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
18:51:35.626699 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
18:51:35.626755 INFO: FWHM in RT is 3.35 seconds, sigma is 0.74
18:51:35.626781 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.21
18:51:35.650340 INFO: Starting candidate selection
18:53:42.983753 INFO: Starting candidate scoring
18:53:51.736362 INFO: Finished candidate processing
18:53:51.736490 INFO: Collecting candidate features
18:53:51.984864 WARNING: intensity_correlation has 30 NaNs ( 0.02 % out of 168387)
18:53:51.985251 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 168387)
18:53:51.994322 INFO: Collecting fragment features
18:53:52.090199 INFO: Finished candidate scoring
18:53:52.176970 PROGRESS: === Extracted 168387 precursors and 1687500 fragments ===
18:53:52.177451 INFO: performing precursor FDR with 47 features
18:53:52.177492 INFO: Decoy channel: -1
18:53:52.177516 INFO: Competetive: True
18:53:52.228295 INFO: Setting torch num_threads to 2 for FDR classification task
18:53:52.257923 WARNING: dropped 13 target PSMs due to missing features
18:53:52.258067 WARNING: dropped 19 decoy PSMs due to missing features
18:53:55.357450 INFO: Test AUC: 0.562
18:53:55.357583 INFO: Train AUC: 0.598
18:53:55.357613 INFO: AUC difference: 6.11%
18:53:55.357634 WARNING: AUC difference > 5%. This may indicate overfitting.
18:53:55.585067 INFO: Resetting torch num_threads to 100
18:53:55.589568 INFO: === FDR correction performed with classifier version 9 ===
18:53:55.597331 PROGRESS: ============================= Precursor FDR =============================
18:53:55.597576 PROGRESS: Total precursors accumulated: 45,207
18:53:55.597645 PROGRESS: Target precursors: 28,535 (63.12%)
18:53:55.597695 PROGRESS: Decoy precursors: 16,672 (36.88%)
18:53:55.597745 PROGRESS: 
18:53:55.597788 PROGRESS: Precursor Summary:
18:53:55.599114 PROGRESS: Channel   0:	 0.05 FDR:   542; 0.01 FDR:   361; 0.001 FDR:   172
18:53:55.599211 PROGRESS: 
18:53:55.599264 PROGRESS: Protein Summary:
18:53:55.600646 PROGRESS: Channel   0:	 0.05 FDR:   508; 0.01 FDR:   339; 0.001 FDR:   169
18:53:55.600741 PROGRESS: =========================================================================
18:53:55.714508 INFO: fragments_df: keeping 4385 of 1687500 [sum(precursor_idx_mask)=7654 sum(mass_error_mask)=1687500 stop_rank=4385
18:53:55.907915 INFO: calibration group: precursor, fitting mz estimator 
18:53:56.032007 INFO: calibration group: precursor, fitting rt estimator 
18:53:56.158792 INFO: calibration group: precursor, fitting mobility estimator 
18:53:56.287460 INFO: calibration group: fragment, fitting mz estimator 
18:53:56.863266 INFO: Using score_cutoff 53.41346912384033 (fac=0.99, q=1)
18:53:56.863679 INFO: calibration group: precursor, predicting mz
18:53:56.877033 INFO: calibration group: precursor, predicting rt
18:53:56.937891 INFO: calibration group: precursor, predicting mobility
18:53:56.954308 INFO: calibration group: fragment, predicting mz
18:53:57.082813 INFO: === checking if optimization conditions were reached ===
18:53:57.083139 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
18:53:57.085588 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 432.5558.
18:53:57.085650 INFO: ==============================================
18:53:57.085764 INFO: Starting optimization step 5.
18:53:57.085844 PROGRESS: === Extracting elution groups 0 to 51000 ===
18:53:57.085920 PROGRESS: Extracting batch of 100415 precursors
18:53:57.111787 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
18:53:57.111927 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
18:53:57.111981 INFO: FWHM in RT is 3.33 seconds, sigma is 0.73
18:53:57.112005 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.23
18:53:57.120956 INFO: Starting candidate selection
18:55:49.789334 INFO: Starting candidate scoring
18:55:58.533969 INFO: Finished candidate processing
18:55:58.534151 INFO: Collecting candidate features
18:55:58.811133 WARNING: intensity_correlation has 37 NaNs ( 0.02 % out of 168402)
18:55:58.811508 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 168402)
18:55:58.820341 INFO: Collecting fragment features
18:55:58.915907 INFO: Finished candidate scoring
18:55:59.001058 PROGRESS: === Extracted 168402 precursors and 1683593 fragments ===
18:55:59.001529 INFO: performing precursor FDR with 47 features
18:55:59.001569 INFO: Decoy channel: -1
18:55:59.001605 INFO: Competetive: True
18:55:59.050463 INFO: Setting torch num_threads to 2 for FDR classification task
18:55:59.079772 WARNING: dropped 15 target PSMs due to missing features
18:55:59.079908 WARNING: dropped 23 decoy PSMs due to missing features
18:56:02.433048 INFO: Test AUC: 0.562
18:56:02.433177 INFO: Train AUC: 0.597
18:56:02.433206 INFO: AUC difference: 5.96%
18:56:02.433228 WARNING: AUC difference > 5%. This may indicate overfitting.
18:56:02.659046 INFO: Resetting torch num_threads to 100
18:56:02.663642 INFO: === FDR correction performed with classifier version 9 ===
18:56:02.671137 PROGRESS: ============================= Precursor FDR =============================
18:56:02.671394 PROGRESS: Total precursors accumulated: 45,210
18:56:02.671460 PROGRESS: Target precursors: 28,622 (63.31%)
18:56:02.671510 PROGRESS: Decoy precursors: 16,588 (36.69%)
18:56:02.671566 PROGRESS: 
18:56:02.671611 PROGRESS: Precursor Summary:
18:56:02.673008 PROGRESS: Channel   0:	 0.05 FDR:   541; 0.01 FDR:   345; 0.001 FDR:   163
18:56:02.673118 PROGRESS: 
18:56:02.673179 PROGRESS: Protein Summary:
18:56:02.674598 PROGRESS: Channel   0:	 0.05 FDR:   509; 0.01 FDR:   324; 0.001 FDR:   160
18:56:02.674697 PROGRESS: =========================================================================
18:56:02.793387 INFO: fragments_df: keeping 4234 of 1683593 [sum(precursor_idx_mask)=7343 sum(mass_error_mask)=1683593 stop_rank=4234
18:56:02.985664 INFO: calibration group: precursor, fitting mz estimator 
18:56:03.108165 INFO: calibration group: precursor, fitting rt estimator 
18:56:03.240463 INFO: calibration group: precursor, fitting mobility estimator 
18:56:03.367581 INFO: calibration group: fragment, fitting mz estimator 
18:56:03.920187 INFO: Using score_cutoff 54.9993842880249 (fac=0.99, q=1)
18:56:03.920612 INFO: calibration group: precursor, predicting mz
18:56:03.933789 INFO: calibration group: precursor, predicting rt
18:56:03.994735 INFO: calibration group: precursor, predicting mobility
18:56:04.009386 INFO: calibration group: fragment, predicting mz
18:56:04.124911 INFO: === checking if optimization conditions were reached ===
18:56:04.125182 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
18:56:04.127341 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 216.6747.
18:56:04.127395 INFO: ==============================================
18:56:04.127493 INFO: Starting optimization step 6.
18:56:04.127559 PROGRESS: === Extracting elution groups 0 to 51000 ===
18:56:04.127622 PROGRESS: Extracting batch of 100415 precursors
18:56:04.151660 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
18:56:04.151786 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
18:56:04.151836 INFO: FWHM in RT is 3.36 seconds, sigma is 0.74
18:56:04.151860 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.21
18:56:04.160783 INFO: Starting candidate selection
18:57:04.695288 INFO: Starting candidate scoring
18:57:13.408028 INFO: Finished candidate processing
18:57:13.408145 INFO: Collecting candidate features
18:57:13.660119 WARNING: intensity_correlation has 54 NaNs ( 0.03 % out of 167148)
18:57:13.660503 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 167148)
18:57:13.669273 INFO: Collecting fragment features
18:57:13.766499 INFO: Finished candidate scoring
18:57:13.864791 PROGRESS: === Extracted 167148 precursors and 1657646 fragments ===
18:57:13.865272 INFO: performing precursor FDR with 47 features
18:57:13.865311 INFO: Decoy channel: -1
18:57:13.865336 INFO: Competetive: True
18:57:13.917315 INFO: Setting torch num_threads to 2 for FDR classification task
18:57:13.946508 WARNING: dropped 26 target PSMs due to missing features
18:57:13.946648 WARNING: dropped 33 decoy PSMs due to missing features
18:57:16.640647 INFO: Test AUC: 0.559
18:57:16.640779 INFO: Train AUC: 0.594
18:57:16.640810 INFO: AUC difference: 5.90%
18:57:16.640833 WARNING: AUC difference > 5%. This may indicate overfitting.
18:57:16.869564 INFO: Resetting torch num_threads to 100
18:57:16.874047 INFO: === FDR correction performed with classifier version 9 ===
18:57:16.881876 PROGRESS: ============================= Precursor FDR =============================
18:57:16.882120 PROGRESS: Total precursors accumulated: 44,994
18:57:16.882184 PROGRESS: Target precursors: 28,240 (62.76%)
18:57:16.882234 PROGRESS: Decoy precursors: 16,754 (37.24%)
18:57:16.882299 PROGRESS: 
18:57:16.882346 PROGRESS: Precursor Summary:
18:57:16.883737 PROGRESS: Channel   0:	 0.05 FDR:   581; 0.01 FDR:   428; 0.001 FDR:   294
18:57:16.883836 PROGRESS: 
18:57:16.883894 PROGRESS: Protein Summary:
18:57:16.885302 PROGRESS: Channel   0:	 0.05 FDR:   541; 0.01 FDR:   400; 0.001 FDR:   276
18:57:16.885397 PROGRESS: =========================================================================
18:57:16.994826 INFO: fragments_df: keeping 4962 of 1657646 [sum(precursor_idx_mask)=9094 sum(mass_error_mask)=1657646 stop_rank=4962
18:57:17.122627 INFO: calibration group: precursor, fitting mz estimator 
18:57:17.257102 INFO: calibration group: precursor, fitting rt estimator 
18:57:17.390104 INFO: calibration group: precursor, fitting mobility estimator 
18:57:17.517019 INFO: calibration group: fragment, fitting mz estimator 
18:57:18.186336 INFO: Using score_cutoff 51.40961858482361 (fac=0.99, q=1)
18:57:18.186751 INFO: calibration group: precursor, predicting mz
18:57:18.194035 INFO: calibration group: precursor, predicting rt
18:57:18.224468 INFO: calibration group: precursor, predicting mobility
18:57:18.231269 INFO: calibration group: fragment, predicting mz
18:57:18.285731 INFO: === checking if optimization conditions were reached ===
18:57:18.286004 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
18:57:18.288104 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 181.9990.
18:57:18.288159 INFO: ==============================================
18:57:18.288259 INFO: Starting optimization step 7.
18:57:18.288326 PROGRESS: === Extracting elution groups 0 to 25400 ===
18:57:18.288409 PROGRESS: Extracting batch of 49998 precursors
18:57:18.300704 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
18:57:18.300825 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
18:57:18.300874 INFO: FWHM in RT is 3.32 seconds, sigma is 0.73
18:57:18.300898 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.17
18:57:18.309703 INFO: Starting candidate selection
18:57:55.146199 INFO: Starting candidate scoring
18:57:59.753168 INFO: Finished candidate processing
18:57:59.753276 INFO: Collecting candidate features
18:57:59.872088 WARNING: intensity_correlation has 39 NaNs ( 0.05 % out of 83051)
18:57:59.872423 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 83051)
18:57:59.880079 INFO: Collecting fragment features
18:57:59.925838 INFO: Finished candidate scoring
18:57:59.965438 PROGRESS: === Extracted 83051 precursors and 821225 fragments ===
18:57:59.965919 INFO: performing precursor FDR with 47 features
18:57:59.965958 INFO: Decoy channel: -1
18:57:59.965983 INFO: Competetive: True
18:57:59.990599 INFO: Setting torch num_threads to 2 for FDR classification task
18:58:00.006061 WARNING: dropped 19 target PSMs due to missing features
18:58:00.006201 WARNING: dropped 22 decoy PSMs due to missing features
18:58:01.313571 INFO: Test AUC: 0.556
18:58:01.313703 INFO: Train AUC: 0.603
18:58:01.313733 INFO: AUC difference: 7.79%
18:58:01.313757 WARNING: AUC difference > 5%. This may indicate overfitting.
18:58:01.516518 INFO: Resetting torch num_threads to 100
18:58:01.519212 INFO: === FDR correction performed with classifier version 9 ===
18:58:01.522676 PROGRESS: ============================= Precursor FDR =============================
18:58:01.522812 PROGRESS: Total precursors accumulated: 22,376
18:58:01.522872 PROGRESS: Target precursors: 14,186 (63.40%)
18:58:01.522920 PROGRESS: Decoy precursors: 8,190 (36.60%)
18:58:01.522964 PROGRESS: 
18:58:01.523014 PROGRESS: Precursor Summary:
18:58:01.524132 PROGRESS: Channel   0:	 0.05 FDR:   246; 0.01 FDR:   207; 0.001 FDR:   148
18:58:01.524233 PROGRESS: 
18:58:01.524292 PROGRESS: Protein Summary:
18:58:01.525445 PROGRESS: Channel   0:	 0.05 FDR:   239; 0.01 FDR:   202; 0.001 FDR:   143
18:58:01.525538 PROGRESS: =========================================================================
18:58:01.600042 INFO: fragments_df: keeping 2423 of 821225 [sum(precursor_idx_mask)=4380 sum(mass_error_mask)=821225 stop_rank=2423
18:58:01.725779 INFO: calibration group: precursor, fitting mz estimator 
18:58:01.825147 INFO: calibration group: precursor, fitting rt estimator 
18:58:01.943992 INFO: calibration group: precursor, fitting mobility estimator 
18:58:02.064743 INFO: calibration group: fragment, fitting mz estimator 
18:58:02.379625 INFO: Using score_cutoff 47.369242906951904 (fac=0.99, q=1)
18:58:02.380038 INFO: calibration group: precursor, predicting mz
18:58:02.387408 INFO: calibration group: precursor, predicting rt
18:58:02.417727 INFO: calibration group: precursor, predicting mobility
18:58:02.424916 INFO: calibration group: fragment, predicting mz
18:58:02.481943 INFO: === checking if optimization conditions were reached ===
18:58:02.482249 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
18:58:02.484537 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 135.9007.
18:58:02.484599 INFO: ==============================================
18:58:02.484708 INFO: Starting optimization step 8.
18:58:02.484780 PROGRESS: === Extracting elution groups 0 to 25400 ===
18:58:02.484854 PROGRESS: Extracting batch of 49998 precursors
18:58:02.502966 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
18:58:02.503107 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
18:58:02.503167 INFO: FWHM in RT is 3.41 seconds, sigma is 0.75
18:58:02.503195 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.04
18:58:02.512136 INFO: Starting candidate selection
18:58:22.151954 INFO: Starting candidate scoring
18:58:26.743985 INFO: Finished candidate processing
18:58:26.744144 INFO: Collecting candidate features
18:58:26.886705 WARNING: intensity_correlation has 38 NaNs ( 0.05 % out of 82464)
18:58:26.887068 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 82464)
18:58:26.894860 INFO: Collecting fragment features
18:58:26.940793 INFO: Finished candidate scoring
18:58:26.979586 PROGRESS: === Extracted 82464 precursors and 813206 fragments ===
18:58:26.979991 INFO: performing precursor FDR with 47 features
18:58:26.980030 INFO: Decoy channel: -1
18:58:26.980060 INFO: Competetive: True
18:58:27.004703 INFO: Setting torch num_threads to 2 for FDR classification task
18:58:27.019483 WARNING: dropped 16 target PSMs due to missing features
18:58:27.019626 WARNING: dropped 23 decoy PSMs due to missing features
18:58:28.299764 INFO: Test AUC: 0.556
18:58:28.299903 INFO: Train AUC: 0.601
18:58:28.299933 INFO: AUC difference: 7.44%
18:58:28.299953 WARNING: AUC difference > 5%. This may indicate overfitting.
18:58:28.506752 INFO: Resetting torch num_threads to 100
18:58:28.509437 INFO: === FDR correction performed with classifier version 9 ===
18:58:28.512775 PROGRESS: ============================= Precursor FDR =============================
18:58:28.512909 PROGRESS: Total precursors accumulated: 22,233
18:58:28.512968 PROGRESS: Target precursors: 14,030 (63.10%)
18:58:28.513026 PROGRESS: Decoy precursors: 8,203 (36.90%)
18:58:28.513081 PROGRESS: 
18:58:28.513140 PROGRESS: Precursor Summary:
18:58:28.514234 PROGRESS: Channel   0:	 0.05 FDR:   293; 0.01 FDR:   139; 0.001 FDR:   128
18:58:28.514332 PROGRESS: 
18:58:28.514394 PROGRESS: Protein Summary:
18:58:28.515576 PROGRESS: Channel   0:	 0.05 FDR:   286; 0.01 FDR:   137; 0.001 FDR:   127
18:58:28.515674 PROGRESS: =========================================================================
18:58:28.654700 INFO: calibration group: precursor, predicting mz
18:58:28.662405 INFO: calibration group: precursor, predicting rt
18:58:28.692705 INFO: calibration group: precursor, predicting mobility
18:58:28.699917 INFO: calibration group: fragment, predicting mz
18:58:28.757498 INFO: === skipping optimization until target number of precursors are found ===
18:58:28.757811 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
18:58:28.757880 INFO: Starting optimization step 9.
18:58:28.757957 PROGRESS: === Extracting elution groups 25400 to 51000 ===
18:58:28.758027 PROGRESS: Extracting batch of 50417 precursors
18:58:28.775385 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
18:58:28.775575 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
18:58:28.775670 INFO: FWHM in RT is 3.41 seconds, sigma is 0.75
18:58:28.775727 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.04
18:58:28.776847 INFO: Starting candidate selection
18:58:48.985664 INFO: Starting candidate scoring
18:58:53.360348 INFO: Finished candidate processing
18:58:53.361352 INFO: Collecting candidate features
18:58:53.562991 WARNING: intensity_correlation has 24 NaNs ( 0.03 % out of 83197)
18:58:53.563344 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 83197)
18:58:53.569653 INFO: Collecting fragment features
18:58:53.625286 INFO: Finished candidate scoring
18:58:53.873453 PROGRESS: === Extracted 165661 precursors and 1634429 fragments ===
18:58:53.898221 INFO: performing precursor FDR with 47 features
18:58:53.898379 INFO: Decoy channel: -1
18:58:53.898415 INFO: Competetive: True
18:58:53.990468 INFO: Setting torch num_threads to 2 for FDR classification task
18:58:54.030091 WARNING: dropped 30 target PSMs due to missing features
18:58:54.030247 WARNING: dropped 37 decoy PSMs due to missing features
18:58:57.810120 INFO: Test AUC: 0.559
18:58:57.810268 INFO: Train AUC: 0.593
18:58:57.810300 INFO: AUC difference: 5.75%
18:58:57.810322 WARNING: AUC difference > 5%. This may indicate overfitting.
18:58:58.051529 INFO: Resetting torch num_threads to 100
18:58:58.061795 INFO: === FDR correction performed with classifier version 9 ===
18:58:58.071497 PROGRESS: ============================= Precursor FDR =============================
18:58:58.071789 PROGRESS: Total precursors accumulated: 44,656
18:58:58.071856 PROGRESS: Target precursors: 27,984 (62.67%)
18:58:58.071908 PROGRESS: Decoy precursors: 16,672 (37.33%)
18:58:58.071959 PROGRESS: 
18:58:58.072003 PROGRESS: Precursor Summary:
18:58:58.073430 PROGRESS: Channel   0:	 0.05 FDR:   630; 0.01 FDR:   414; 0.001 FDR:   346
18:58:58.073543 PROGRESS: 
18:58:58.073600 PROGRESS: Protein Summary:
18:58:58.075117 PROGRESS: Channel   0:	 0.05 FDR:   587; 0.01 FDR:   388; 0.001 FDR:   328
18:58:58.075215 PROGRESS: =========================================================================
18:58:58.192682 INFO: fragments_df: keeping 4794 of 1634429 [sum(precursor_idx_mask)=8826 sum(mass_error_mask)=1634429 stop_rank=4794
18:58:58.398377 INFO: calibration group: precursor, fitting mz estimator 
18:58:58.513151 INFO: calibration group: precursor, fitting rt estimator 
18:58:58.628289 INFO: calibration group: precursor, fitting mobility estimator 
18:58:58.741833 INFO: calibration group: fragment, fitting mz estimator 
18:58:59.324071 INFO: Using score_cutoff 50.889992606735234 (fac=0.99, q=1)
18:58:59.324559 INFO: calibration group: precursor, predicting mz
18:58:59.332359 INFO: calibration group: precursor, predicting rt
18:58:59.364319 INFO: calibration group: precursor, predicting mobility
18:58:59.371636 INFO: calibration group: fragment, predicting mz
18:58:59.431204 INFO: === checking if optimization conditions were reached ===
18:58:59.431546 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
18:58:59.434647 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 124.4504.
18:58:59.434715 INFO: ==============================================
18:58:59.434846 INFO: Starting optimization step 10.
18:58:59.434926 PROGRESS: === Extracting elution groups 0 to 25400 ===
18:58:59.435044 PROGRESS: Extracting batch of 49998 precursors
18:58:59.458734 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
18:58:59.458883 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
18:58:59.458964 INFO: FWHM in RT is 3.24 seconds, sigma is 0.71
18:58:59.458994 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.07
18:58:59.467851 INFO: Starting candidate selection
18:59:18.840138 INFO: Starting candidate scoring
18:59:23.463101 INFO: Finished candidate processing
18:59:23.463220 INFO: Collecting candidate features
18:59:23.592345 WARNING: intensity_correlation has 36 NaNs ( 0.04 % out of 82622)
18:59:23.592659 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 82622)
18:59:23.598583 INFO: Collecting fragment features
18:59:23.647132 INFO: Finished candidate scoring
18:59:23.689312 PROGRESS: === Extracted 82622 precursors and 813843 fragments ===
18:59:23.689748 INFO: performing precursor FDR with 47 features
18:59:23.689789 INFO: Decoy channel: -1
18:59:23.689814 INFO: Competetive: True
18:59:23.717281 INFO: Setting torch num_threads to 2 for FDR classification task
18:59:23.734815 WARNING: dropped 14 target PSMs due to missing features
18:59:23.734963 WARNING: dropped 22 decoy PSMs due to missing features
18:59:25.100137 INFO: Test AUC: 0.554
18:59:25.100284 INFO: Train AUC: 0.602
18:59:25.100315 INFO: AUC difference: 7.93%
18:59:25.100338 WARNING: AUC difference > 5%. This may indicate overfitting.
18:59:25.303603 INFO: Resetting torch num_threads to 100
18:59:25.306791 INFO: === FDR correction performed with classifier version 9 ===
18:59:25.310464 PROGRESS: ============================= Precursor FDR =============================
18:59:25.310601 PROGRESS: Total precursors accumulated: 22,273
18:59:25.310662 PROGRESS: Target precursors: 14,071 (63.18%)
18:59:25.310713 PROGRESS: Decoy precursors: 8,202 (36.82%)
18:59:25.310759 PROGRESS: 
18:59:25.310806 PROGRESS: Precursor Summary:
18:59:25.311927 PROGRESS: Channel   0:	 0.05 FDR:   283; 0.01 FDR:   203; 0.001 FDR:   150
18:59:25.312022 PROGRESS: 
18:59:25.312077 PROGRESS: Protein Summary:
18:59:25.313259 PROGRESS: Channel   0:	 0.05 FDR:   273; 0.01 FDR:   197; 0.001 FDR:   146
18:59:25.313351 PROGRESS: =========================================================================
18:59:25.369076 INFO: fragments_df: keeping 2354 of 813843 [sum(precursor_idx_mask)=4344 sum(mass_error_mask)=813843 stop_rank=2354
18:59:25.496091 INFO: calibration group: precursor, fitting mz estimator 
18:59:25.597922 INFO: calibration group: precursor, fitting rt estimator 
18:59:25.694412 INFO: calibration group: precursor, fitting mobility estimator 
18:59:25.787785 INFO: calibration group: fragment, fitting mz estimator 
18:59:26.043458 INFO: Using score_cutoff 49.973454402923586 (fac=0.99, q=1)
18:59:26.043889 INFO: calibration group: precursor, predicting mz
18:59:26.051676 INFO: calibration group: precursor, predicting rt
18:59:26.083452 INFO: calibration group: precursor, predicting mobility
18:59:26.090906 INFO: calibration group: fragment, predicting mz
18:59:26.149264 INFO: === checking if optimization conditions were reached ===
18:59:26.149574 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
18:59:26.152091 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 112.3031.
18:59:26.152154 INFO: ==============================================
18:59:26.152257 INFO: Starting optimization step 11.
18:59:26.152332 PROGRESS: === Extracting elution groups 0 to 25400 ===
18:59:26.152402 PROGRESS: Extracting batch of 49998 precursors
18:59:26.172858 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
18:59:26.173021 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
18:59:26.173076 INFO: FWHM in RT is 3.37 seconds, sigma is 0.74
18:59:26.173105 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.04
18:59:26.181885 INFO: Starting candidate selection
18:59:43.189594 INFO: Starting candidate scoring
18:59:47.708569 INFO: Finished candidate processing
18:59:47.708711 INFO: Collecting candidate features
18:59:47.854883 WARNING: intensity_correlation has 36 NaNs ( 0.04 % out of 82352)
18:59:47.855236 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 82352)
18:59:47.863111 INFO: Collecting fragment features
18:59:47.918700 INFO: Finished candidate scoring
18:59:47.962692 PROGRESS: === Extracted 82352 precursors and 810710 fragments ===
18:59:47.963781 INFO: performing precursor FDR with 47 features
18:59:47.963824 INFO: Decoy channel: -1
18:59:47.963848 INFO: Competetive: True
18:59:47.991122 INFO: Setting torch num_threads to 2 for FDR classification task
18:59:48.008303 WARNING: dropped 16 target PSMs due to missing features
18:59:48.008453 WARNING: dropped 20 decoy PSMs due to missing features
18:59:49.284691 INFO: Test AUC: 0.557
18:59:49.284833 INFO: Train AUC: 0.600
18:59:49.284866 INFO: AUC difference: 7.18%
18:59:49.284889 WARNING: AUC difference > 5%. This may indicate overfitting.
18:59:49.489247 INFO: Resetting torch num_threads to 100
18:59:49.492400 INFO: === FDR correction performed with classifier version 9 ===
18:59:49.495958 PROGRESS: ============================= Precursor FDR =============================
18:59:49.496094 PROGRESS: Total precursors accumulated: 22,213
18:59:49.496154 PROGRESS: Target precursors: 14,027 (63.15%)
18:59:49.496205 PROGRESS: Decoy precursors: 8,186 (36.85%)
18:59:49.496248 PROGRESS: 
18:59:49.496294 PROGRESS: Precursor Summary:
18:59:49.497393 PROGRESS: Channel   0:	 0.05 FDR:   242; 0.01 FDR:   204; 0.001 FDR:   165
18:59:49.497483 PROGRESS: 
18:59:49.497537 PROGRESS: Protein Summary:
18:59:49.498929 PROGRESS: Channel   0:	 0.05 FDR:   235; 0.01 FDR:   198; 0.001 FDR:   161
18:59:49.499031 PROGRESS: =========================================================================
18:59:49.553782 INFO: fragments_df: keeping 2389 of 810710 [sum(precursor_idx_mask)=4405 sum(mass_error_mask)=810710 stop_rank=2389
18:59:49.677676 INFO: calibration group: precursor, fitting mz estimator 
18:59:49.799715 INFO: calibration group: precursor, fitting rt estimator 
18:59:49.916128 INFO: calibration group: precursor, fitting mobility estimator 
18:59:50.029123 INFO: calibration group: fragment, fitting mz estimator 
18:59:50.341535 INFO: Using score_cutoff 50.187589223098755 (fac=0.99, q=1)
18:59:50.341966 INFO: calibration group: precursor, predicting mz
18:59:50.349830 INFO: calibration group: precursor, predicting rt
18:59:50.381597 INFO: calibration group: precursor, predicting mobility
18:59:50.389232 INFO: calibration group: fragment, predicting mz
18:59:50.448661 INFO: === checking if optimization conditions were reached ===
18:59:50.448938 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
18:59:50.451082 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 106.2255.
18:59:50.451141 INFO: ==============================================
18:59:50.451235 INFO: Starting optimization step 12.
18:59:50.451302 PROGRESS: === Extracting elution groups 0 to 25400 ===
18:59:50.451361 PROGRESS: Extracting batch of 49998 precursors
18:59:50.465305 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
18:59:50.465437 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
18:59:50.465483 INFO: FWHM in RT is 3.27 seconds, sigma is 0.72
18:59:50.465507 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.04
18:59:50.474391 INFO: Starting candidate selection
19:00:06.528259 INFO: Starting candidate scoring
19:00:11.056609 INFO: Finished candidate processing
19:00:11.056777 INFO: Collecting candidate features
19:00:11.206790 WARNING: intensity_correlation has 36 NaNs ( 0.04 % out of 82224)
19:00:11.207158 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 82224)
19:00:11.214798 INFO: Collecting fragment features
19:00:11.260426 INFO: Finished candidate scoring
19:00:11.299468 PROGRESS: === Extracted 82224 precursors and 808919 fragments ===
19:00:11.299964 INFO: performing precursor FDR with 47 features
19:00:11.300001 INFO: Decoy channel: -1
19:00:11.300025 INFO: Competetive: True
19:00:11.327840 INFO: Setting torch num_threads to 2 for FDR classification task
19:00:11.345273 WARNING: dropped 18 target PSMs due to missing features
19:00:11.345424 WARNING: dropped 18 decoy PSMs due to missing features
19:00:12.677999 INFO: Test AUC: 0.553
19:00:12.678141 INFO: Train AUC: 0.599
19:00:12.678172 INFO: AUC difference: 7.76%
19:00:12.678193 WARNING: AUC difference > 5%. This may indicate overfitting.
19:00:18.154678 INFO: Resetting torch num_threads to 100
19:00:18.157855 INFO: === FDR correction performed with classifier version 9 ===
19:00:18.161456 PROGRESS: ============================= Precursor FDR =============================
19:00:18.161595 PROGRESS: Total precursors accumulated: 22,203
19:00:18.161657 PROGRESS: Target precursors: 13,965 (62.90%)
19:00:18.161709 PROGRESS: Decoy precursors: 8,238 (37.10%)
19:00:18.161757 PROGRESS: 
19:00:18.161803 PROGRESS: Precursor Summary:
19:00:18.162899 PROGRESS: Channel   0:	 0.05 FDR:   251; 0.01 FDR:   161; 0.001 FDR:   151
19:00:18.162995 PROGRESS: 
19:00:18.163064 PROGRESS: Protein Summary:
19:00:18.164244 PROGRESS: Channel   0:	 0.05 FDR:   244; 0.01 FDR:   156; 0.001 FDR:   146
19:00:18.164338 PROGRESS: =========================================================================
19:00:18.290238 INFO: calibration group: precursor, predicting mz
19:00:18.298495 INFO: calibration group: precursor, predicting rt
19:00:18.330509 INFO: calibration group: precursor, predicting mobility
19:00:18.338251 INFO: calibration group: fragment, predicting mz
19:00:18.397138 INFO: === skipping optimization until target number of precursors are found ===
19:00:18.397466 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
19:00:18.397538 INFO: Starting optimization step 13.
19:00:18.397616 PROGRESS: === Extracting elution groups 25400 to 51000 ===
19:00:18.397683 PROGRESS: Extracting batch of 50417 precursors
19:00:18.416877 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:00:18.417027 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:00:18.417084 INFO: FWHM in RT is 3.27 seconds, sigma is 0.72
19:00:18.417114 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.04
19:00:18.418197 INFO: Starting candidate selection
19:00:34.870677 INFO: Starting candidate scoring
19:00:39.443385 INFO: Finished candidate processing
19:00:39.443548 INFO: Collecting candidate features
19:00:39.563605 WARNING: intensity_correlation has 31 NaNs ( 0.04 % out of 83072)
19:00:39.563956 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 83072)
19:00:39.571756 INFO: Collecting fragment features
19:00:39.620871 INFO: Finished candidate scoring
19:00:39.696269 PROGRESS: === Extracted 165296 precursors and 1626808 fragments ===
19:00:39.715299 INFO: performing precursor FDR with 47 features
19:00:39.715448 INFO: Decoy channel: -1
19:00:39.715476 INFO: Competetive: True
19:00:39.785542 INFO: Setting torch num_threads to 2 for FDR classification task
19:00:39.817415 WARNING: dropped 36 target PSMs due to missing features
19:00:39.817566 WARNING: dropped 35 decoy PSMs due to missing features
19:00:42.620697 INFO: Test AUC: 0.563
19:00:42.620836 INFO: Train AUC: 0.579
19:00:42.620867 INFO: AUC difference: 2.87%
19:00:42.851688 INFO: Resetting torch num_threads to 100
19:00:42.859384 INFO: === FDR correction performed with classifier version 9 ===
19:00:42.867477 PROGRESS: ============================= Precursor FDR =============================
19:00:42.867752 PROGRESS: Total precursors accumulated: 44,585
19:00:42.867815 PROGRESS: Target precursors: 27,148 (60.89%)
19:00:42.867864 PROGRESS: Decoy precursors: 17,437 (39.11%)
19:00:42.867914 PROGRESS: 
19:00:42.867959 PROGRESS: Precursor Summary:
19:00:42.869411 PROGRESS: Channel   0:	 0.05 FDR:   607; 0.01 FDR:   369; 0.001 FDR:   276
19:00:42.869521 PROGRESS: 
19:00:42.869580 PROGRESS: Protein Summary:
19:00:42.871056 PROGRESS: Channel   0:	 0.05 FDR:   569; 0.01 FDR:   346; 0.001 FDR:   261
19:00:42.871154 PROGRESS: =========================================================================
19:00:42.994164 INFO: fragments_df: keeping 4348 of 1626808 [sum(precursor_idx_mask)=7899 sum(mass_error_mask)=1626807 stop_rank=4348
19:00:43.187417 INFO: calibration group: precursor, fitting mz estimator 
19:00:43.317365 INFO: calibration group: precursor, fitting rt estimator 
19:00:43.446218 INFO: calibration group: precursor, fitting mobility estimator 
19:00:43.576500 INFO: calibration group: fragment, fitting mz estimator 
19:00:44.131358 INFO: Using score_cutoff 51.14379170379639 (fac=0.99, q=1)
19:00:44.131792 INFO: calibration group: precursor, predicting mz
19:00:44.145335 INFO: calibration group: precursor, predicting rt
19:00:44.208247 INFO: calibration group: precursor, predicting mobility
19:00:44.223073 INFO: calibration group: fragment, predicting mz
19:00:44.340553 INFO: === checking if optimization conditions were reached ===
19:00:44.340835 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 2 ===
19:00:44.343162 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 106.6468.
19:00:44.343218 INFO: ==============================================
19:00:44.343309 INFO: Starting optimization step 14.
19:00:44.343376 PROGRESS: === Extracting elution groups 0 to 51000 ===
19:00:44.343434 PROGRESS: Extracting batch of 100415 precursors
19:00:44.370590 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:00:44.370725 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:00:44.370772 INFO: FWHM in RT is 3.34 seconds, sigma is 0.73
19:00:44.370796 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.17
19:00:44.380493 INFO: Starting candidate selection
19:01:16.822798 INFO: Starting candidate scoring
19:01:25.502398 INFO: Finished candidate processing
19:01:25.502582 INFO: Collecting candidate features
19:01:25.833894 WARNING: intensity_correlation has 65 NaNs ( 0.04 % out of 165852)
19:01:25.834283 WARNING: height_correlation has 8 NaNs ( 0.00 % out of 165852)
19:01:25.843284 INFO: Collecting fragment features
19:01:25.942156 INFO: Finished candidate scoring
19:01:26.029540 PROGRESS: === Extracted 165852 precursors and 1630628 fragments ===
19:01:26.029984 INFO: performing precursor FDR with 47 features
19:01:26.030026 INFO: Decoy channel: -1
19:01:26.030051 INFO: Competetive: True
19:01:26.085221 INFO: Setting torch num_threads to 2 for FDR classification task
19:01:26.166343 WARNING: dropped 33 target PSMs due to missing features
19:01:26.166483 WARNING: dropped 36 decoy PSMs due to missing features
19:01:29.033428 INFO: Test AUC: 0.559
19:01:29.033591 INFO: Train AUC: 0.592
19:01:29.033622 INFO: AUC difference: 5.64%
19:01:29.033644 WARNING: AUC difference > 5%. This may indicate overfitting.
19:01:29.266807 INFO: Resetting torch num_threads to 100
19:01:29.272409 INFO: === FDR correction performed with classifier version 9 ===
19:01:29.280200 PROGRESS: ============================= Precursor FDR =============================
19:01:29.280500 PROGRESS: Total precursors accumulated: 44,705
19:01:29.280565 PROGRESS: Target precursors: 27,982 (62.59%)
19:01:29.280617 PROGRESS: Decoy precursors: 16,723 (37.41%)
19:01:29.280663 PROGRESS: 
19:01:29.280706 PROGRESS: Precursor Summary:
19:01:29.282088 PROGRESS: Channel   0:	 0.05 FDR:   625; 0.01 FDR:   406; 0.001 FDR:   332
19:01:29.282183 PROGRESS: 
19:01:29.282238 PROGRESS: Protein Summary:
19:01:29.283703 PROGRESS: Channel   0:	 0.05 FDR:   584; 0.01 FDR:   380; 0.001 FDR:   311
19:01:29.283798 PROGRESS: =========================================================================
19:01:29.387456 INFO: fragments_df: keeping 4637 of 1630628 [sum(precursor_idx_mask)=8584 sum(mass_error_mask)=1630628 stop_rank=4637
19:01:29.588118 INFO: calibration group: precursor, fitting mz estimator 
19:01:29.709550 INFO: calibration group: precursor, fitting rt estimator 
19:01:29.817527 INFO: calibration group: precursor, fitting mobility estimator 
19:01:29.925543 INFO: calibration group: fragment, fitting mz estimator 
19:01:30.477818 INFO: Using score_cutoff 50.07672341537475 (fac=0.99, q=1)
19:01:30.478289 INFO: calibration group: precursor, predicting mz
19:01:30.486356 INFO: calibration group: precursor, predicting rt
19:01:30.518893 INFO: calibration group: precursor, predicting mobility
19:01:30.526521 INFO: calibration group: fragment, predicting mz
19:01:30.588088 INFO: === checking if optimization conditions were reached ===
19:01:30.588431 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 2 ===
19:01:30.590094 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 106.6468 found after 12 searches.
19:01:30.590154 INFO: ==============================================
19:01:30.590265 PROGRESS: Optimization finished for rt_error.
19:01:30.724057 INFO: calibration group: precursor, predicting mz
19:01:30.732350 INFO: calibration group: precursor, predicting rt
19:01:30.764426 INFO: calibration group: precursor, predicting mobility
19:01:30.772169 INFO: calibration group: fragment, predicting mz
19:01:30.865206 INFO: Starting optimization step 0.
19:01:30.865465 PROGRESS: === Extracting elution groups 0 to 25400 ===
19:01:30.865573 PROGRESS: Extracting batch of 49998 precursors
19:01:30.884842 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:01:30.884979 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:01:30.885047 INFO: FWHM in RT is 3.33 seconds, sigma is 0.73
19:01:30.885077 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.16
19:01:30.894009 INFO: Starting candidate selection
19:01:46.998399 INFO: Starting candidate scoring
19:01:51.543035 INFO: Finished candidate processing
19:01:51.543149 INFO: Collecting candidate features
19:01:51.662855 WARNING: intensity_correlation has 44 NaNs ( 0.05 % out of 82309)
19:01:51.663215 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 82309)
19:01:51.671567 INFO: Collecting fragment features
19:01:51.719580 INFO: Finished candidate scoring
19:01:51.755274 PROGRESS: === Extracted 82309 precursors and 809503 fragments ===
19:01:51.755856 INFO: performing precursor FDR with 47 features
19:01:51.755895 INFO: Decoy channel: -1
19:01:51.755919 INFO: Competetive: True
19:01:51.785158 INFO: Setting torch num_threads to 2 for FDR classification task
19:01:51.800902 WARNING: dropped 21 target PSMs due to missing features
19:01:51.801037 WARNING: dropped 23 decoy PSMs due to missing features
19:01:53.051610 INFO: Test AUC: 0.571
19:01:53.051744 INFO: Train AUC: 0.622
19:01:53.051777 INFO: AUC difference: 8.31%
19:01:53.051805 WARNING: AUC difference > 5%. This may indicate overfitting.
19:01:53.254946 INFO: Resetting torch num_threads to 100
19:01:53.257613 INFO: === FDR correction performed with classifier version 29 ===
19:01:53.261007 PROGRESS: ============================= Precursor FDR =============================
19:01:53.261146 PROGRESS: Total precursors accumulated: 22,206
19:01:53.261207 PROGRESS: Target precursors: 14,475 (65.19%)
19:01:53.261270 PROGRESS: Decoy precursors: 7,731 (34.81%)
19:01:53.261320 PROGRESS: 
19:01:53.261362 PROGRESS: Precursor Summary:
19:01:53.262442 PROGRESS: Channel   0:	 0.05 FDR:   280; 0.01 FDR:   191; 0.001 FDR:   131
19:01:53.262534 PROGRESS: 
19:01:53.262587 PROGRESS: Protein Summary:
19:01:53.263765 PROGRESS: Channel   0:	 0.05 FDR:   272; 0.01 FDR:   185; 0.001 FDR:   130
19:01:53.263861 PROGRESS: =========================================================================
19:01:53.382144 INFO: calibration group: precursor, predicting mz
19:01:53.389754 INFO: calibration group: precursor, predicting rt
19:01:53.420481 INFO: calibration group: precursor, predicting mobility
19:01:53.427511 INFO: calibration group: fragment, predicting mz
19:01:53.483188 INFO: === skipping optimization until target number of precursors are found ===
19:01:53.483444 PROGRESS: === Optimization of ms1_error has been skipped 1 time(s); maximum number is 1 ===
19:01:53.483503 INFO: Starting optimization step 1.
19:01:53.483584 PROGRESS: === Extracting elution groups 25400 to 51000 ===
19:01:53.483649 PROGRESS: Extracting batch of 50417 precursors
19:01:53.496755 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:01:53.496869 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:01:53.496925 INFO: FWHM in RT is 3.33 seconds, sigma is 0.73
19:01:53.496949 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.16
19:01:53.498029 INFO: Starting candidate selection
19:02:10.296844 INFO: Starting candidate scoring
19:02:14.883759 INFO: Finished candidate processing
19:02:14.884434 INFO: Collecting candidate features
19:02:15.005763 WARNING: intensity_correlation has 27 NaNs ( 0.03 % out of 83039)
19:02:15.006097 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 83039)
19:02:15.013753 INFO: Collecting fragment features
19:02:15.059940 INFO: Finished candidate scoring
19:02:15.133606 PROGRESS: === Extracted 165348 precursors and 1627077 fragments ===
19:02:15.152245 INFO: performing precursor FDR with 47 features
19:02:15.152387 INFO: Decoy channel: -1
19:02:15.152414 INFO: Competetive: True
19:02:15.213218 INFO: Setting torch num_threads to 2 for FDR classification task
19:02:15.241900 WARNING: dropped 36 target PSMs due to missing features
19:02:15.242047 WARNING: dropped 39 decoy PSMs due to missing features
19:02:18.037138 INFO: Test AUC: 0.574
19:02:18.037272 INFO: Train AUC: 0.611
19:02:18.037304 INFO: AUC difference: 6.09%
19:02:18.037327 WARNING: AUC difference > 5%. This may indicate overfitting.
19:02:18.261893 INFO: Resetting torch num_threads to 100
19:02:18.268816 INFO: === FDR correction performed with classifier version 29 ===
19:02:18.276206 PROGRESS: ============================= Precursor FDR =============================
19:02:18.276462 PROGRESS: Total precursors accumulated: 44,575
19:02:18.276526 PROGRESS: Target precursors: 28,702 (64.39%)
19:02:18.276576 PROGRESS: Decoy precursors: 15,873 (35.61%)
19:02:18.276623 PROGRESS: 
19:02:18.276667 PROGRESS: Precursor Summary:
19:02:18.278151 PROGRESS: Channel   0:	 0.05 FDR:   645; 0.01 FDR:   487; 0.001 FDR:   332
19:02:18.278248 PROGRESS: 
19:02:18.278304 PROGRESS: Protein Summary:
19:02:18.279748 PROGRESS: Channel   0:	 0.05 FDR:   604; 0.01 FDR:   455; 0.001 FDR:   314
19:02:18.279843 PROGRESS: =========================================================================
19:02:18.400523 INFO: fragments_df: keeping 5000 of 1627077 [sum(precursor_idx_mask)=10279 sum(mass_error_mask)=1627077 stop_rank=5000
19:02:18.523544 INFO: calibration group: precursor, fitting mz estimator 
19:02:18.662815 INFO: calibration group: precursor, fitting rt estimator 
19:02:18.801177 INFO: calibration group: precursor, fitting mobility estimator 
19:02:18.935614 INFO: calibration group: fragment, fitting mz estimator 
19:02:19.578805 INFO: Using score_cutoff 48.72350711975098 (fac=0.99, q=1)
19:02:19.579255 INFO: calibration group: precursor, predicting mz
19:02:19.586441 INFO: calibration group: precursor, predicting rt
19:02:19.617216 INFO: calibration group: precursor, predicting mobility
19:02:19.624182 INFO: calibration group: fragment, predicting mz
19:02:19.679144 INFO: === checking if optimization conditions were reached ===
19:02:19.679403 PROGRESS: === Optimization of ms1_error has been performed 1 time(s); minimum number is 2 ===
19:02:19.681248 PROGRESS: ❌ ms1_error      : optimization incomplete after 1 search(es). Will search with parameter 8.9249.
19:02:19.681306 INFO: ==============================================
19:02:19.681399 INFO: Starting optimization step 2.
19:02:19.681470 PROGRESS: === Extracting elution groups 0 to 25400 ===
19:02:19.681534 PROGRESS: Extracting batch of 49998 precursors
19:02:19.693637 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:02:19.693753 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:02:19.693801 INFO: FWHM in RT is 3.28 seconds, sigma is 0.72
19:02:19.693828 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.04
19:02:19.694734 INFO: Starting candidate selection
19:02:35.169073 INFO: Starting candidate scoring
19:02:39.207741 INFO: Finished candidate processing
19:02:39.207906 INFO: Collecting candidate features
19:02:39.352087 WARNING: intensity_correlation has 24 NaNs ( 0.03 % out of 82424)
19:02:39.352423 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 82424)
19:02:39.360077 INFO: Collecting fragment features
19:02:39.405488 INFO: Finished candidate scoring
19:02:39.445632 PROGRESS: === Extracted 82424 precursors and 806774 fragments ===
19:02:39.446020 INFO: performing precursor FDR with 47 features
19:02:39.446057 INFO: Decoy channel: -1
19:02:39.446081 INFO: Competetive: True
19:02:39.469877 INFO: Setting torch num_threads to 2 for FDR classification task
19:02:39.485011 WARNING: dropped 14 target PSMs due to missing features
19:02:39.485147 WARNING: dropped 11 decoy PSMs due to missing features
19:02:40.776658 INFO: Test AUC: 0.549
19:02:40.776792 INFO: Train AUC: 0.588
19:02:40.776822 INFO: AUC difference: 6.70%
19:02:40.776844 WARNING: AUC difference > 5%. This may indicate overfitting.
19:02:40.977717 INFO: Resetting torch num_threads to 100
19:02:40.980338 INFO: === FDR correction performed with classifier version 29 ===
19:02:40.983678 PROGRESS: ============================= Precursor FDR =============================
19:02:40.983805 PROGRESS: Total precursors accumulated: 22,257
19:02:40.983865 PROGRESS: Target precursors: 13,624 (61.21%)
19:02:40.983917 PROGRESS: Decoy precursors: 8,633 (38.79%)
19:02:40.983963 PROGRESS: 
19:02:40.984008 PROGRESS: Precursor Summary:
19:02:40.985087 PROGRESS: Channel   0:	 0.05 FDR:   343; 0.01 FDR:   232; 0.001 FDR:   146
19:02:40.985182 PROGRESS: 
19:02:40.985237 PROGRESS: Protein Summary:
19:02:40.986407 PROGRESS: Channel   0:	 0.05 FDR:   332; 0.01 FDR:   224; 0.001 FDR:   144
19:02:40.986499 PROGRESS: =========================================================================
19:02:41.041636 INFO: fragments_df: keeping 2594 of 806774 [sum(precursor_idx_mask)=5006 sum(mass_error_mask)=806767 stop_rank=2594
19:02:41.161650 INFO: calibration group: precursor, fitting mz estimator 
19:02:41.258285 INFO: calibration group: precursor, fitting rt estimator 
19:02:41.359964 INFO: calibration group: precursor, fitting mobility estimator 
19:02:41.459133 INFO: calibration group: fragment, fitting mz estimator 
19:02:41.739733 INFO: Using score_cutoff 48.174584930419925 (fac=0.99, q=1)
19:02:41.740412 INFO: calibration group: precursor, predicting mz
19:02:41.747719 INFO: calibration group: precursor, predicting rt
19:02:41.777966 INFO: calibration group: precursor, predicting mobility
19:02:41.785047 INFO: calibration group: fragment, predicting mz
19:02:41.840552 INFO: === checking if optimization conditions were reached ===
19:02:41.840837 PROGRESS: === Optimization of ms1_error has been performed 2 time(s); minimum number is 2 ===
19:02:41.843067 PROGRESS: ❌ ms1_error      : optimization incomplete after 2 search(es). Will search with parameter 2.4815.
19:02:41.843132 INFO: ==============================================
19:02:41.843238 INFO: Starting optimization step 3.
19:02:41.843314 PROGRESS: === Extracting elution groups 0 to 25400 ===
19:02:41.843381 PROGRESS: Extracting batch of 49998 precursors
19:02:41.858726 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:02:41.858846 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:02:41.858889 INFO: FWHM in RT is 3.37 seconds, sigma is 0.74
19:02:41.858913 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.87
19:02:41.869652 INFO: Starting candidate selection
19:02:57.004139 INFO: Starting candidate scoring
19:03:00.931975 INFO: Finished candidate processing
19:03:00.933878 INFO: Collecting candidate features
19:03:01.125451 WARNING: intensity_correlation has 13 NaNs ( 0.02 % out of 83218)
19:03:01.126053 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 83218)
19:03:01.143116 INFO: Collecting fragment features
19:03:01.203181 INFO: Finished candidate scoring
19:03:01.258819 PROGRESS: === Extracted 83218 precursors and 808533 fragments ===
19:03:01.259444 INFO: performing precursor FDR with 47 features
19:03:01.259486 INFO: Decoy channel: -1
19:03:01.259512 INFO: Competetive: True
19:03:01.296509 INFO: Setting torch num_threads to 2 for FDR classification task
19:03:01.318450 WARNING: dropped 6 target PSMs due to missing features
19:03:01.318606 WARNING: dropped 8 decoy PSMs due to missing features
19:03:02.695387 INFO: Test AUC: 0.541
19:03:02.695564 INFO: Train AUC: 0.586
19:03:02.695593 INFO: AUC difference: 7.67%
19:03:02.695616 WARNING: AUC difference > 5%. This may indicate overfitting.
19:03:02.900069 INFO: Resetting torch num_threads to 100
19:03:02.902756 INFO: === FDR correction performed with classifier version 29 ===
19:03:02.906310 PROGRESS: ============================= Precursor FDR =============================
19:03:02.906453 PROGRESS: Total precursors accumulated: 22,394
19:03:02.906516 PROGRESS: Target precursors: 13,577 (60.63%)
19:03:02.906568 PROGRESS: Decoy precursors: 8,817 (39.37%)
19:03:02.906627 PROGRESS: 
19:03:02.906674 PROGRESS: Precursor Summary:
19:03:02.907782 PROGRESS: Channel   0:	 0.05 FDR:   301; 0.01 FDR:   142; 0.001 FDR:     1
19:03:02.907876 PROGRESS: 
19:03:02.907931 PROGRESS: Protein Summary:
19:03:02.909070 PROGRESS: Channel   0:	 0.05 FDR:   291; 0.01 FDR:   138; 0.001 FDR:     1
19:03:02.909158 PROGRESS: =========================================================================
19:03:03.060392 INFO: calibration group: precursor, predicting mz
19:03:03.068195 INFO: calibration group: precursor, predicting rt
19:03:03.098702 INFO: calibration group: precursor, predicting mobility
19:03:03.105956 INFO: calibration group: fragment, predicting mz
19:03:03.162508 INFO: === skipping optimization until target number of precursors are found ===
19:03:03.162810 PROGRESS: === Optimization of ms1_error has been skipped 1 time(s); maximum number is 1 ===
19:03:03.162880 INFO: Starting optimization step 4.
19:03:03.162947 PROGRESS: === Extracting elution groups 25400 to 51000 ===
19:03:03.163015 PROGRESS: Extracting batch of 50417 precursors
19:03:03.175998 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:03:03.176125 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:03:03.176176 INFO: FWHM in RT is 3.37 seconds, sigma is 0.74
19:03:03.176200 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.87
19:03:03.177259 INFO: Starting candidate selection
19:03:18.168872 INFO: Starting candidate scoring
19:03:22.098684 INFO: Finished candidate processing
19:03:22.098862 INFO: Collecting candidate features
19:03:22.246133 WARNING: intensity_correlation has 16 NaNs ( 0.02 % out of 83825)
19:03:22.246464 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 83825)
19:03:22.254175 INFO: Collecting fragment features
19:03:22.301140 INFO: Finished candidate scoring
19:03:22.376340 PROGRESS: === Extracted 167043 precursors and 1623353 fragments ===
19:03:22.396286 INFO: performing precursor FDR with 47 features
19:03:22.396430 INFO: Decoy channel: -1
19:03:22.396456 INFO: Competetive: True
19:03:22.460926 INFO: Setting torch num_threads to 2 for FDR classification task
19:03:22.491121 WARNING: dropped 14 target PSMs due to missing features
19:03:22.491272 WARNING: dropped 20 decoy PSMs due to missing features
19:03:25.204092 INFO: Test AUC: 0.538
19:03:25.204224 INFO: Train AUC: 0.580
19:03:25.204254 INFO: AUC difference: 7.23%
19:03:25.204276 WARNING: AUC difference > 5%. This may indicate overfitting.
19:03:25.430127 INFO: Resetting torch num_threads to 100
19:03:25.437240 INFO: === FDR correction performed with classifier version 29 ===
19:03:25.444916 PROGRESS: ============================= Precursor FDR =============================
19:03:25.445150 PROGRESS: Total precursors accumulated: 44,968
19:03:25.445211 PROGRESS: Target precursors: 26,952 (59.94%)
19:03:25.445259 PROGRESS: Decoy precursors: 18,016 (40.06%)
19:03:25.445303 PROGRESS: 
19:03:25.445346 PROGRESS: Precursor Summary:
19:03:25.446751 PROGRESS: Channel   0:	 0.05 FDR:   662; 0.01 FDR:   474; 0.001 FDR:   313
19:03:25.446840 PROGRESS: 
19:03:25.446894 PROGRESS: Protein Summary:
19:03:25.448350 PROGRESS: Channel   0:	 0.05 FDR:   616; 0.01 FDR:   443; 0.001 FDR:   297
19:03:25.448457 PROGRESS: =========================================================================
19:03:25.571001 INFO: fragments_df: keeping 5000 of 1623353 [sum(precursor_idx_mask)=9933 sum(mass_error_mask)=1623334 stop_rank=5000
19:03:25.693466 INFO: calibration group: precursor, fitting mz estimator 
19:03:25.831222 INFO: calibration group: precursor, fitting rt estimator 
19:03:25.968806 INFO: calibration group: precursor, fitting mobility estimator 
19:03:26.104093 INFO: calibration group: fragment, fitting mz estimator 
19:03:26.781017 INFO: Using score_cutoff 30.930947968482972 (fac=0.99, q=1)
19:03:26.781442 INFO: calibration group: precursor, predicting mz
19:03:26.788749 INFO: calibration group: precursor, predicting rt
19:03:26.818914 INFO: calibration group: precursor, predicting mobility
19:03:26.825847 INFO: calibration group: fragment, predicting mz
19:03:26.883694 INFO: === checking if optimization conditions were reached ===
19:03:26.883958 PROGRESS: === Optimization of ms1_error has been performed 3 time(s); minimum number is 2 ===
19:03:26.884972 PROGRESS: ✅ ms1_error      : optimization complete. Optimal parameter 8.9249 found after 3 searches.
19:03:26.885022 INFO: ==============================================
19:03:26.885105 PROGRESS: Optimization finished for ms1_error.
19:03:27.005736 INFO: calibration group: precursor, predicting mz
19:03:27.013344 INFO: calibration group: precursor, predicting rt
19:03:27.043578 INFO: calibration group: precursor, predicting mobility
19:03:27.050515 INFO: calibration group: fragment, predicting mz
19:03:27.132625 INFO: Starting optimization step 0.
19:03:27.132853 PROGRESS: === Extracting elution groups 0 to 25400 ===
19:03:27.132921 PROGRESS: Extracting batch of 49998 precursors
19:03:27.145766 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:03:27.145884 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:03:27.145926 INFO: FWHM in RT is 3.37 seconds, sigma is 0.74
19:03:27.145948 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.87
19:03:27.154756 INFO: Starting candidate selection
19:03:42.250935 INFO: Starting candidate scoring
19:03:46.205521 INFO: Finished candidate processing
19:03:46.206567 INFO: Collecting candidate features
19:03:46.352549 WARNING: intensity_correlation has 27 NaNs ( 0.03 % out of 82579)
19:03:46.352839 WARNING: height_correlation has 6 NaNs ( 0.01 % out of 82579)
19:03:46.358672 INFO: Collecting fragment features
19:03:46.405351 INFO: Finished candidate scoring
19:03:46.442088 PROGRESS: === Extracted 82579 precursors and 808094 fragments ===
19:03:46.442482 INFO: performing precursor FDR with 47 features
19:03:46.442518 INFO: Decoy channel: -1
19:03:46.442540 INFO: Competetive: True
19:03:46.467196 INFO: Setting torch num_threads to 2 for FDR classification task
19:03:46.482434 WARNING: dropped 19 target PSMs due to missing features
19:03:46.482570 WARNING: dropped 10 decoy PSMs due to missing features
19:03:47.710288 INFO: Test AUC: 0.557
19:03:47.710424 INFO: Train AUC: 0.601
19:03:47.710454 INFO: AUC difference: 7.38%
19:03:47.710475 WARNING: AUC difference > 5%. This may indicate overfitting.
19:03:47.915423 INFO: Resetting torch num_threads to 100
19:03:47.918036 INFO: === FDR correction performed with classifier version 32 ===
19:03:47.921375 PROGRESS: ============================= Precursor FDR =============================
19:03:47.921527 PROGRESS: Total precursors accumulated: 22,295
19:03:47.921586 PROGRESS: Target precursors: 13,914 (62.41%)
19:03:47.921637 PROGRESS: Decoy precursors: 8,381 (37.59%)
19:03:47.921684 PROGRESS: 
19:03:47.921726 PROGRESS: Precursor Summary:
19:03:47.922812 PROGRESS: Channel   0:	 0.05 FDR:   324; 0.01 FDR:   250; 0.001 FDR:   164
19:03:47.922900 PROGRESS: 
19:03:47.922953 PROGRESS: Protein Summary:
19:03:47.924151 PROGRESS: Channel   0:	 0.05 FDR:   314; 0.01 FDR:   243; 0.001 FDR:   161
19:03:47.924240 PROGRESS: =========================================================================
19:03:47.979302 INFO: fragments_df: keeping 2695 of 808094 [sum(precursor_idx_mask)=5263 sum(mass_error_mask)=808089 stop_rank=2695
19:03:48.098936 INFO: calibration group: precursor, fitting mz estimator 
19:03:48.201976 INFO: calibration group: precursor, fitting rt estimator 
19:03:48.303797 INFO: calibration group: precursor, fitting mobility estimator 
19:03:48.417711 INFO: calibration group: fragment, fitting mz estimator 
19:03:48.767549 INFO: Using score_cutoff 45.08169073448181 (fac=0.99, q=1)
19:03:48.767956 INFO: calibration group: precursor, predicting mz
19:03:48.775261 INFO: calibration group: precursor, predicting rt
19:03:48.805477 INFO: calibration group: precursor, predicting mobility
19:03:48.812508 INFO: calibration group: fragment, predicting mz
19:03:48.869863 INFO: === checking if optimization conditions were reached ===
19:03:48.870127 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
19:03:48.871804 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0674.
19:03:48.871858 INFO: ==============================================
19:03:48.871946 INFO: Starting optimization step 1.
19:03:48.872009 PROGRESS: === Extracting elution groups 0 to 25400 ===
19:03:48.872065 PROGRESS: Extracting batch of 49998 precursors
19:03:48.884188 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:03:48.884303 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:03:48.884344 INFO: FWHM in RT is 3.37 seconds, sigma is 0.74
19:03:48.884367 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.92
19:03:48.885660 INFO: Starting candidate selection
19:04:00.083389 INFO: Starting candidate scoring
19:04:04.034743 INFO: Finished candidate processing
19:04:04.034924 INFO: Collecting candidate features
19:04:04.197133 WARNING: intensity_correlation has 30 NaNs ( 0.04 % out of 80430)
19:04:04.197457 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 80430)
19:04:04.203629 INFO: Collecting fragment features
19:04:04.254447 INFO: Finished candidate scoring
19:04:04.323553 PROGRESS: === Extracted 80430 precursors and 783354 fragments ===
19:04:04.323992 INFO: performing precursor FDR with 47 features
19:04:04.324033 INFO: Decoy channel: -1
19:04:04.324060 INFO: Competetive: True
19:04:04.357375 INFO: Setting torch num_threads to 2 for FDR classification task
19:04:04.377740 WARNING: dropped 12 target PSMs due to missing features
19:04:04.377896 WARNING: dropped 21 decoy PSMs due to missing features
19:04:05.883409 INFO: Test AUC: 0.570
19:04:05.883559 INFO: Train AUC: 0.598
19:04:05.883590 INFO: AUC difference: 4.58%
19:04:06.094869 INFO: Resetting torch num_threads to 100
19:04:06.098709 INFO: === FDR correction performed with classifier version 32 ===
19:04:06.102815 PROGRESS: ============================= Precursor FDR =============================
19:04:06.102969 PROGRESS: Total precursors accumulated: 21,790
19:04:06.103043 PROGRESS: Target precursors: 13,546 (62.17%)
19:04:06.103100 PROGRESS: Decoy precursors: 8,244 (37.83%)
19:04:06.103148 PROGRESS: 
19:04:06.103194 PROGRESS: Precursor Summary:
19:04:06.104577 PROGRESS: Channel   0:	 0.05 FDR:   310; 0.01 FDR:   203; 0.001 FDR:   177
19:04:06.104685 PROGRESS: 
19:04:06.104745 PROGRESS: Protein Summary:
19:04:06.105977 PROGRESS: Channel   0:	 0.05 FDR:   300; 0.01 FDR:   198; 0.001 FDR:   174
19:04:06.106067 PROGRESS: =========================================================================
19:04:06.160287 INFO: fragments_df: keeping 2307 of 783354 [sum(precursor_idx_mask)=4353 sum(mass_error_mask)=783346 stop_rank=2307
19:04:06.482437 INFO: calibration group: precursor, fitting mz estimator 
19:04:06.586460 INFO: calibration group: precursor, fitting rt estimator 
19:04:06.692316 INFO: calibration group: precursor, fitting mobility estimator 
19:04:06.790068 INFO: calibration group: fragment, fitting mz estimator 
19:04:07.040989 INFO: Using score_cutoff 47.361793359375 (fac=0.99, q=1)
19:04:07.041431 INFO: calibration group: precursor, predicting mz
19:04:07.049023 INFO: calibration group: precursor, predicting rt
19:04:07.079677 INFO: calibration group: precursor, predicting mobility
19:04:07.086875 INFO: calibration group: fragment, predicting mz
19:04:07.145955 INFO: === checking if optimization conditions were reached ===
19:04:07.146290 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
19:04:07.148684 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0434.
19:04:07.148750 INFO: ==============================================
19:04:07.148861 INFO: Starting optimization step 2.
19:04:07.148939 PROGRESS: === Extracting elution groups 0 to 25400 ===
19:04:07.149009 PROGRESS: Extracting batch of 49998 precursors
19:04:07.173739 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:04:07.173897 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:04:07.173952 INFO: FWHM in RT is 3.36 seconds, sigma is 0.74
19:04:07.173980 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.98
19:04:07.182708 INFO: Starting candidate selection
19:04:14.833271 INFO: Starting candidate scoring
19:04:18.667612 INFO: Finished candidate processing
19:04:18.667777 INFO: Collecting candidate features
19:04:18.806913 WARNING: intensity_correlation has 44 NaNs ( 0.06 % out of 77830)
19:04:18.807230 WARNING: height_correlation has 8 NaNs ( 0.01 % out of 77830)
19:04:18.813787 INFO: Collecting fragment features
19:04:18.858096 INFO: Finished candidate scoring
19:04:18.895881 PROGRESS: === Extracted 77830 precursors and 748853 fragments ===
19:04:18.896283 INFO: performing precursor FDR with 47 features
19:04:18.896320 INFO: Decoy channel: -1
19:04:18.896342 INFO: Competetive: True
19:04:18.919602 INFO: Setting torch num_threads to 2 for FDR classification task
19:04:18.934062 WARNING: dropped 25 target PSMs due to missing features
19:04:18.934205 WARNING: dropped 22 decoy PSMs due to missing features
19:04:20.168059 INFO: Test AUC: 0.554
19:04:20.168389 INFO: Train AUC: 0.601
19:04:20.168424 INFO: AUC difference: 7.91%
19:04:20.168447 WARNING: AUC difference > 5%. This may indicate overfitting.
19:04:20.374395 INFO: Resetting torch num_threads to 100
19:04:20.376972 INFO: === FDR correction performed with classifier version 32 ===
19:04:20.380154 PROGRESS: ============================= Precursor FDR =============================
19:04:20.380283 PROGRESS: Total precursors accumulated: 21,127
19:04:20.380342 PROGRESS: Target precursors: 13,183 (62.40%)
19:04:20.380392 PROGRESS: Decoy precursors: 7,944 (37.60%)
19:04:20.380439 PROGRESS: 
19:04:20.380484 PROGRESS: Precursor Summary:
19:04:20.381574 PROGRESS: Channel   0:	 0.05 FDR:   323; 0.01 FDR:   237; 0.001 FDR:     2
19:04:20.381663 PROGRESS: 
19:04:20.381717 PROGRESS: Protein Summary:
19:04:20.382884 PROGRESS: Channel   0:	 0.05 FDR:   313; 0.01 FDR:   230; 0.001 FDR:     2
19:04:20.382976 PROGRESS: =========================================================================
19:04:20.434472 INFO: fragments_df: keeping 2503 of 748853 [sum(precursor_idx_mask)=4917 sum(mass_error_mask)=748849 stop_rank=2503
19:04:20.567733 INFO: calibration group: precursor, fitting mz estimator 
19:04:20.687978 INFO: calibration group: precursor, fitting rt estimator 
19:04:20.788581 INFO: calibration group: precursor, fitting mobility estimator 
19:04:20.884920 INFO: calibration group: fragment, fitting mz estimator 
19:04:21.151006 INFO: Using score_cutoff 45.128209487915036 (fac=0.99, q=1)
19:04:21.151429 INFO: calibration group: precursor, predicting mz
19:04:21.158782 INFO: calibration group: precursor, predicting rt
19:04:21.189204 INFO: calibration group: precursor, predicting mobility
19:04:21.196283 INFO: calibration group: fragment, predicting mz
19:04:21.252282 INFO: === checking if optimization conditions were reached ===
19:04:21.252547 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
19:04:21.254320 PROGRESS: ❌ mobility_error : optimization incomplete after 3 search(es). Will search with parameter 0.0338.
19:04:21.254376 INFO: ==============================================
19:04:21.254489 INFO: Starting optimization step 3.
19:04:21.254555 PROGRESS: === Extracting elution groups 0 to 25400 ===
19:04:21.254612 PROGRESS: Extracting batch of 49998 precursors
19:04:21.267013 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:04:21.267145 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:04:21.267187 INFO: FWHM in RT is 3.39 seconds, sigma is 0.74
19:04:21.267210 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.93
19:04:21.274069 INFO: Starting candidate selection
19:04:27.836629 INFO: Starting candidate scoring
19:04:31.586990 INFO: Finished candidate processing
19:04:31.587186 INFO: Collecting candidate features
19:04:31.749454 WARNING: intensity_correlation has 35 NaNs ( 0.05 % out of 76826)
19:04:31.749869 WARNING: height_correlation has 10 NaNs ( 0.01 % out of 76826)
19:04:31.760404 INFO: Collecting fragment features
19:04:31.813213 INFO: Finished candidate scoring
19:04:31.861092 PROGRESS: === Extracted 76826 precursors and 733620 fragments ===
19:04:31.861579 INFO: performing precursor FDR with 47 features
19:04:31.861620 INFO: Decoy channel: -1
19:04:31.861645 INFO: Competetive: True
19:04:31.896081 INFO: Setting torch num_threads to 2 for FDR classification task
19:04:31.916481 WARNING: dropped 25 target PSMs due to missing features
19:04:31.916636 WARNING: dropped 15 decoy PSMs due to missing features
19:04:33.414126 INFO: Test AUC: 0.559
19:04:33.414271 INFO: Train AUC: 0.610
19:04:33.414317 INFO: AUC difference: 8.31%
19:04:33.414339 WARNING: AUC difference > 5%. This may indicate overfitting.
19:04:33.626025 INFO: Resetting torch num_threads to 100
19:04:33.629849 INFO: === FDR correction performed with classifier version 32 ===
19:04:33.634226 PROGRESS: ============================= Precursor FDR =============================
19:04:33.634386 PROGRESS: Total precursors accumulated: 20,895
19:04:33.634450 PROGRESS: Target precursors: 12,843 (61.46%)
19:04:33.634500 PROGRESS: Decoy precursors: 8,052 (38.54%)
19:04:33.634545 PROGRESS: 
19:04:33.634604 PROGRESS: Precursor Summary:
19:04:33.635803 PROGRESS: Channel   0:	 0.05 FDR:   315; 0.01 FDR:   246; 0.001 FDR:   233
19:04:33.635901 PROGRESS: 
19:04:33.635956 PROGRESS: Protein Summary:
19:04:33.637729 PROGRESS: Channel   0:	 0.05 FDR:   304; 0.01 FDR:   238; 0.001 FDR:   227
19:04:33.637829 PROGRESS: =========================================================================
19:04:33.688254 INFO: fragments_df: keeping 2564 of 733620 [sum(precursor_idx_mask)=5112 sum(mass_error_mask)=733619 stop_rank=2564
19:04:33.828076 INFO: calibration group: precursor, fitting mz estimator 
19:04:33.926761 INFO: calibration group: precursor, fitting rt estimator 
19:04:34.033620 INFO: calibration group: precursor, fitting mobility estimator 
19:04:34.131674 INFO: calibration group: fragment, fitting mz estimator 
19:04:34.411031 INFO: Using score_cutoff 45.86691481018067 (fac=0.99, q=1)
19:04:34.411494 INFO: calibration group: precursor, predicting mz
19:04:34.418820 INFO: calibration group: precursor, predicting rt
19:04:34.449327 INFO: calibration group: precursor, predicting mobility
19:04:34.456203 INFO: calibration group: fragment, predicting mz
19:04:34.516208 INFO: === checking if optimization conditions were reached ===
19:04:34.516575 PROGRESS: === Optimization of mobility_error has been performed 4 time(s); minimum number is 2 ===
19:04:34.519064 PROGRESS: ❌ mobility_error : optimization incomplete after 4 search(es). Will search with parameter 0.0297.
19:04:34.519131 INFO: ==============================================
19:04:34.519260 INFO: Starting optimization step 4.
19:04:34.519341 PROGRESS: === Extracting elution groups 0 to 25400 ===
19:04:34.519413 PROGRESS: Extracting batch of 49998 precursors
19:04:34.544290 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:04:34.544443 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:04:34.544496 INFO: FWHM in RT is 3.38 seconds, sigma is 0.74
19:04:34.544526 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.83
19:04:34.553388 INFO: Starting candidate selection
19:04:41.018843 INFO: Starting candidate scoring
19:04:44.734295 INFO: Finished candidate processing
19:04:44.734407 INFO: Collecting candidate features
19:04:44.873967 WARNING: intensity_correlation has 34 NaNs ( 0.04 % out of 76815)
19:04:44.874310 WARNING: height_correlation has 9 NaNs ( 0.01 % out of 76815)
19:04:44.881820 INFO: Collecting fragment features
19:04:44.927036 INFO: Finished candidate scoring
19:04:44.966463 PROGRESS: === Extracted 76815 precursors and 733211 fragments ===
19:04:44.966846 INFO: performing precursor FDR with 47 features
19:04:44.966884 INFO: Decoy channel: -1
19:04:44.966908 INFO: Competetive: True
19:04:44.989500 INFO: Setting torch num_threads to 2 for FDR classification task
19:04:45.003266 WARNING: dropped 21 target PSMs due to missing features
19:04:45.003407 WARNING: dropped 17 decoy PSMs due to missing features
19:04:46.170752 INFO: Test AUC: 0.564
19:04:46.170909 INFO: Train AUC: 0.602
19:04:46.170939 INFO: AUC difference: 6.29%
19:04:46.170959 WARNING: AUC difference > 5%. This may indicate overfitting.
19:04:46.375439 INFO: Resetting torch num_threads to 100
19:04:46.377980 INFO: === FDR correction performed with classifier version 32 ===
19:04:46.381133 PROGRESS: ============================= Precursor FDR =============================
19:04:46.381268 PROGRESS: Total precursors accumulated: 20,906
19:04:46.381330 PROGRESS: Target precursors: 13,029 (62.32%)
19:04:46.381380 PROGRESS: Decoy precursors: 7,877 (37.68%)
19:04:46.381430 PROGRESS: 
19:04:46.381475 PROGRESS: Precursor Summary:
19:04:46.382585 PROGRESS: Channel   0:	 0.05 FDR:   311; 0.01 FDR:   241; 0.001 FDR:   202
19:04:46.382683 PROGRESS: 
19:04:46.382741 PROGRESS: Protein Summary:
19:04:46.383939 PROGRESS: Channel   0:	 0.05 FDR:   301; 0.01 FDR:   235; 0.001 FDR:   197
19:04:46.384030 PROGRESS: =========================================================================
19:04:46.433519 INFO: fragments_df: keeping 2516 of 733211 [sum(precursor_idx_mask)=5016 sum(mass_error_mask)=733208 stop_rank=2516
19:04:46.581599 INFO: calibration group: precursor, fitting mz estimator 
19:04:46.696950 INFO: calibration group: precursor, fitting rt estimator 
19:04:46.816237 INFO: calibration group: precursor, fitting mobility estimator 
19:04:46.928434 INFO: calibration group: fragment, fitting mz estimator 
19:04:47.253551 INFO: Using score_cutoff 46.49606694030762 (fac=0.99, q=1)
19:04:47.253970 INFO: calibration group: precursor, predicting mz
19:04:47.261281 INFO: calibration group: precursor, predicting rt
19:04:47.291994 INFO: calibration group: precursor, predicting mobility
19:04:47.298995 INFO: calibration group: fragment, predicting mz
19:04:47.353984 INFO: === checking if optimization conditions were reached ===
19:04:47.354290 PROGRESS: === Optimization of mobility_error has been performed 5 time(s); minimum number is 2 ===
19:04:47.355350 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.0338 found after 5 searches.
19:04:47.355412 INFO: ==============================================
19:04:47.355521 PROGRESS: Optimization finished for mobility_error.
19:04:47.502625 INFO: calibration group: precursor, predicting mz
19:04:47.510140 INFO: calibration group: precursor, predicting rt
19:04:47.540882 INFO: calibration group: precursor, predicting mobility
19:04:47.547898 INFO: calibration group: fragment, predicting mz
19:04:47.634986 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
19:04:47.635248 PROGRESS: ==============================================
19:04:47.635330 PROGRESS: ms2_error      : 30.0000
19:04:47.635401 PROGRESS: rt_error       : 106.6468
19:04:47.635462 PROGRESS: ms1_error      : 8.9249
19:04:47.635518 PROGRESS: mobility_error : 0.0338
19:04:47.635570 PROGRESS: ==============================================
19:04:47.638904 INFO: calibration group: precursor, predicting mz
19:04:48.998901 INFO: calibration group: precursor, predicting rt
19:04:55.507266 INFO: calibration group: precursor, predicting mobility
19:04:56.929632 INFO: calibration group: fragment, predicting mz
19:05:08.975235 PROGRESS: Extracting batch of 10272670 precursors
19:05:11.218588 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
19:05:11.218728 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
19:05:11.218779 INFO: FWHM in RT is 3.38 seconds, sigma is 0.74
19:05:11.218802 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.83
19:05:11.221221 INFO: Starting candidate selection
19:25:06.022156 INFO: Applying score cutoff of 45.86691481018067
19:25:06.242976 INFO: Removed 10909192 precursors with score below cutoff
19:25:08.818787 INFO: Starting candidate scoring
19:30:17.165059 INFO: Finished candidate processing
19:30:17.165597 INFO: Collecting candidate features
19:30:28.848052 INFO: Collecting fragment features
19:30:33.565401 INFO: Finished candidate scoring
19:30:40.098701 INFO: === FDR correction performed with classifier version 38 ===
19:30:40.105494 INFO: performing precursor FDR with 47 features
19:30:40.105568 INFO: Decoy channel: -1
19:30:40.105597 INFO: Competetive: True
19:30:41.723388 INFO: Setting torch num_threads to 2 for FDR classification task
19:30:42.437702 WARNING: FDR calculation for 3115840 target and 2758197 decoy PSMs
19:30:42.437852 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
19:32:38.461121 INFO: Test AUC: 0.529
19:32:38.461279 INFO: Train AUC: 0.585
19:32:38.461314 INFO: AUC difference: 9.65%
19:32:38.461337 WARNING: AUC difference > 5%. This may indicate overfitting.
19:32:40.192411 INFO: Resetting torch num_threads to 100
19:32:40.362508 INFO: Removing fragments below FDR threshold
19:32:40.826680 PROGRESS: ============================= Precursor FDR =============================
19:32:40.826949 PROGRESS: Total precursors accumulated: 63,183
19:32:40.827012 PROGRESS: Target precursors: 62,558 (99.01%)
19:32:40.827080 PROGRESS: Decoy precursors: 625 (0.99%)
19:32:40.827127 PROGRESS: 
19:32:40.827171 PROGRESS: Precursor Summary:
19:32:40.850959 PROGRESS: Channel   0:	 0.05 FDR: 62,558; 0.01 FDR: 62,558; 0.001 FDR: 44,482
19:32:40.851243 PROGRESS: 
19:32:40.851307 PROGRESS: Protein Summary:
19:32:40.884829 PROGRESS: Channel   0:	 0.05 FDR: 10,688; 0.01 FDR: 10,688; 0.001 FDR: 8,414
19:32:40.885088 PROGRESS: =========================================================================
19:32:41.403347 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
19:33:10.404091 PROGRESS: Processing search outputs
19:33:10.404207 PROGRESS: Performing protein grouping and FDR
19:33:10.404243 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
19:33:10.453973 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
19:33:10.489682 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
19:33:10.523491 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
19:33:10.569184 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
19:33:10.611774 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
19:33:10.661336 INFO: Building combined output
19:33:11.018750 INFO: Performing protein inference
19:33:11.462435 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
19:33:37.947998 INFO: Performing protein FDR
19:33:43.034511 INFO: Normalizing q-values using 14,911 targets and 3,003 decoys
19:33:43.046756 INFO: Test AUC: 0.881
19:33:43.046841 INFO: Train AUC: 0.876
19:33:43.046876 INFO: AUC difference: 0.61%
19:33:43.593181 PROGRESS: ================ Protein FDR =================
19:33:43.593328 PROGRESS: Unique protein groups in output
19:33:43.593358 PROGRESS:   1% protein FDR: 9,663
19:33:43.593380 PROGRESS: 
19:33:43.593399 PROGRESS: Unique precursor in output
19:33:43.593418 PROGRESS:   1% protein FDR: 95,522
19:33:43.593445 PROGRESS: ================================================
19:33:43.655368 PROGRESS: Building search statistics
19:33:43.765446 INFO: Loaded OptimizationManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/optimization_manager.pkl
19:33:43.765643 INFO: Initializing OptimizationManager
19:33:43.765948 INFO: Loaded CalibrationManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/calibration_manager.pkl
19:33:43.766023 INFO: Initializing CalibrationManager
19:33:43.766240 INFO: Loaded RawFileManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/raw_file_manager.pkl
19:33:43.766313 INFO: Initializing RawFileManager
19:33:43.795684 INFO: Loaded OptimizationManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/optimization_manager.pkl
19:33:43.796515 INFO: Initializing OptimizationManager
19:33:43.796810 INFO: Loaded CalibrationManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/calibration_manager.pkl
19:33:43.796889 INFO: Initializing CalibrationManager
19:33:43.797083 INFO: Loaded RawFileManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/raw_file_manager.pkl
19:33:43.797157 INFO: Initializing RawFileManager
19:33:43.827452 INFO: Loaded OptimizationManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/optimization_manager.pkl
19:33:43.827655 INFO: Initializing OptimizationManager
19:33:43.827877 INFO: Loaded CalibrationManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/calibration_manager.pkl
19:33:43.827948 INFO: Initializing CalibrationManager
19:33:43.828134 INFO: Loaded RawFileManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/raw_file_manager.pkl
19:33:43.828205 INFO: Initializing RawFileManager
19:33:43.857628 INFO: Loaded OptimizationManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/optimization_manager.pkl
19:33:43.857821 INFO: Initializing OptimizationManager
19:33:43.858037 INFO: Loaded CalibrationManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/calibration_manager.pkl
19:33:43.858110 INFO: Initializing CalibrationManager
19:33:43.858294 INFO: Loaded RawFileManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/raw_file_manager.pkl
19:33:43.858363 INFO: Initializing RawFileManager
19:33:43.886114 INFO: Loaded OptimizationManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/optimization_manager.pkl
19:33:43.886307 INFO: Initializing OptimizationManager
19:33:43.886523 INFO: Loaded CalibrationManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/calibration_manager.pkl
19:33:43.886593 INFO: Initializing CalibrationManager
19:33:43.886776 INFO: Loaded RawFileManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/raw_file_manager.pkl
19:33:43.886846 INFO: Initializing RawFileManager
19:33:43.914070 INFO: Loaded OptimizationManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/optimization_manager.pkl
19:33:43.914262 INFO: Initializing OptimizationManager
19:33:43.914475 INFO: Loaded CalibrationManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/calibration_manager.pkl
19:33:43.914546 INFO: Initializing CalibrationManager
19:33:43.914749 INFO: Loaded RawFileManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/raw_file_manager.pkl
19:33:43.914833 INFO: Initializing RawFileManager
19:33:43.918216 INFO: Writing stat output to disk
19:33:43.918299 INFO: Saving run_output/alphadia_1.10.4_Again_good_now/library/stat.tsv to disk
19:33:43.926661 PROGRESS: Building internal statistics
19:33:43.926926 INFO: Loaded TimingManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/timing_manager.pkl
19:33:43.926970 INFO: Initializing TimingManager
19:33:43.927270 INFO: Loaded TimingManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/timing_manager.pkl
19:33:43.927315 INFO: Initializing TimingManager
19:33:43.927492 INFO: Loaded TimingManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/timing_manager.pkl
19:33:43.927532 INFO: Initializing TimingManager
19:33:43.927702 INFO: Loaded TimingManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/timing_manager.pkl
19:33:43.927739 INFO: Initializing TimingManager
19:33:43.927892 INFO: Loaded TimingManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/timing_manager.pkl
19:33:43.927928 INFO: Initializing TimingManager
19:33:43.928080 INFO: Loaded TimingManager from run_output/alphadia_1.10.4_Again_good_now/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/timing_manager.pkl
19:33:43.928114 INFO: Initializing TimingManager
19:33:43.928494 INFO: Writing internal output to disk
19:33:43.928540 INFO: Saving run_output/alphadia_1.10.4_Again_good_now/library/internal.tsv to disk
19:33:43.929000 PROGRESS: Performing label free quantification
19:33:44.004235 INFO: Accumulating fragment data
19:33:44.004399 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
19:33:44.268299 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
19:33:45.396331 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
19:33:46.471394 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
19:33:47.632388 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
19:33:48.785042 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
19:33:50.172481 PROGRESS: Performing label free quantification on the precursor level
19:33:50.172619 INFO: Filtering fragments by quality
19:33:50.450235 INFO: Performing label-free quantification using directLFQ
19:33:52.022007 INFO: 95522 lfq-groups total
19:34:48.320205 INFO: using 100 processes
19:34:48.522982 INFO: lfq-object 0
19:34:48.632536 INFO: lfq-object 100
19:34:48.647662 INFO: lfq-object 300
19:34:48.669022 INFO: lfq-object 500
19:34:48.751370 INFO: lfq-object 200
19:34:48.756546 INFO: lfq-object 400
19:34:48.781044 INFO: lfq-object 600
19:34:48.807827 INFO: lfq-object 800
19:34:48.817624 INFO: lfq-object 1000
19:34:48.836105 INFO: lfq-object 1200
19:34:48.890475 INFO: lfq-object 700
19:34:48.914049 INFO: lfq-object 900
19:34:48.922983 INFO: lfq-object 1100
19:34:48.938985 INFO: lfq-object 1300
19:34:48.968667 INFO: lfq-object 1500
19:34:49.017375 INFO: lfq-object 1700
19:34:49.045242 INFO: lfq-object 1400
19:34:49.076237 INFO: lfq-object 1600
19:34:49.122919 INFO: lfq-object 1800
19:34:49.204454 INFO: lfq-object 2000
19:34:49.230808 INFO: lfq-object 1900
19:34:49.276862 INFO: lfq-object 2200
19:34:49.311922 INFO: lfq-object 2100
19:34:49.348080 INFO: lfq-object 2400
19:34:49.382425 INFO: lfq-object 2300
19:34:49.471490 INFO: lfq-object 2500
19:34:49.540538 INFO: lfq-object 2700
19:34:49.578135 INFO: lfq-object 2600
19:34:49.596942 INFO: lfq-object 2900
19:34:49.651253 INFO: lfq-object 2800
19:34:49.705233 INFO: lfq-object 3000
19:34:49.755052 INFO: lfq-object 3200
19:34:49.781384 INFO: lfq-object 3400
19:34:49.813110 INFO: lfq-object 3100
19:34:49.837628 INFO: lfq-object 3600
19:34:49.861074 INFO: lfq-object 3300
19:34:49.883880 INFO: lfq-object 3500
19:34:49.941564 INFO: lfq-object 3700
19:34:49.999351 INFO: lfq-object 3900
19:34:50.033670 INFO: lfq-object 4100
19:34:50.054513 INFO: lfq-object 3800
19:34:50.104994 INFO: lfq-object 4000
19:34:50.138617 INFO: lfq-object 4200
19:34:50.195097 INFO: lfq-object 4400
19:34:50.242647 INFO: lfq-object 4300
19:34:50.254846 INFO: lfq-object 4600
19:34:50.296590 INFO: lfq-object 4800
19:34:50.302682 INFO: lfq-object 4500
19:34:50.359444 INFO: lfq-object 4700
19:34:50.403622 INFO: lfq-object 4900
19:34:50.451636 INFO: lfq-object 5100
19:34:50.509003 INFO: lfq-object 5000
19:34:50.509883 INFO: lfq-object 5300
19:34:50.541066 INFO: lfq-object 5500
19:34:50.554608 INFO: lfq-object 5200
19:34:50.614895 INFO: lfq-object 5400
19:34:50.641268 INFO: lfq-object 5600
19:34:50.703333 INFO: lfq-object 5800
19:34:50.745204 INFO: lfq-object 5700
19:34:50.755279 INFO: lfq-object 6000
19:34:50.821324 INFO: lfq-object 5900
19:34:50.856635 INFO: lfq-object 6100
19:34:50.941957 INFO: lfq-object 6300
19:34:50.963987 INFO: lfq-object 6500
19:34:50.965200 INFO: lfq-object 6200
19:34:51.047474 INFO: lfq-object 6700
19:34:51.049485 INFO: lfq-object 6400
19:34:51.068689 INFO: lfq-object 6600
19:34:51.157035 INFO: lfq-object 6800
19:34:51.266745 INFO: lfq-object 6900
19:34:58.596773 INFO: lfq-object 7000
19:34:58.693161 INFO: lfq-object 7200
19:34:58.702796 INFO: lfq-object 7100
19:34:58.800563 INFO: lfq-object 7300
19:34:58.849338 INFO: lfq-object 7500
19:34:58.892523 INFO: lfq-object 7700
19:34:58.908029 INFO: lfq-object 7400
19:34:58.910940 INFO: lfq-object 7900
19:34:58.955397 INFO: lfq-object 7600
19:34:58.999411 INFO: lfq-object 7800
19:34:59.016844 INFO: lfq-object 8000
19:34:59.076610 INFO: lfq-object 8200
19:34:59.092813 INFO: lfq-object 8400
19:34:59.118305 INFO: lfq-object 8100
19:34:59.182349 INFO: lfq-object 8300
19:34:59.199296 INFO: lfq-object 8500
19:34:59.261652 INFO: lfq-object 8700
19:34:59.306230 INFO: lfq-object 8600
19:34:59.346277 INFO: lfq-object 8900
19:34:59.372721 INFO: lfq-object 8800
19:34:59.419853 INFO: lfq-object 9100
19:34:59.454532 INFO: lfq-object 9000
19:34:59.530991 INFO: lfq-object 9200
19:34:59.602253 INFO: lfq-object 9400
19:34:59.633923 INFO: lfq-object 9300
19:34:59.665692 INFO: lfq-object 9600
19:34:59.691109 INFO: lfq-object 9800
19:34:59.711832 INFO: lfq-object 9500
19:34:59.770944 INFO: lfq-object 9700
19:34:59.810707 INFO: lfq-object 9900
19:34:59.877640 INFO: lfq-object 10100
19:34:59.915843 INFO: lfq-object 10000
19:34:59.920531 INFO: lfq-object 10300
19:34:59.983514 INFO: lfq-object 10200
19:35:00.043803 INFO: lfq-object 10400
19:35:00.108910 INFO: lfq-object 10600
19:35:00.162242 INFO: lfq-object 10500
19:35:00.185947 INFO: lfq-object 10800
19:35:00.204222 INFO: lfq-object 11000
19:35:00.213804 INFO: lfq-object 10700
19:35:00.289396 INFO: lfq-object 10900
19:35:00.308040 INFO: lfq-object 11100
19:35:00.353019 INFO: lfq-object 11300
19:35:00.379292 INFO: lfq-object 11500
19:35:00.413844 INFO: lfq-object 11200
19:35:00.460174 INFO: lfq-object 11400
19:35:00.491491 INFO: lfq-object 11600
19:35:00.520803 INFO: lfq-object 11800
19:35:00.554899 INFO: lfq-object 12000
19:35:00.597655 INFO: lfq-object 11700
19:35:00.600188 INFO: lfq-object 12200
19:35:00.636496 INFO: lfq-object 11900
19:35:00.663185 INFO: lfq-object 12100
19:35:00.710978 INFO: lfq-object 12300
19:35:00.777237 INFO: lfq-object 12500
19:35:00.798676 INFO: lfq-object 12700
19:35:00.819789 INFO: lfq-object 12400
19:35:00.885994 INFO: lfq-object 12600
19:35:00.905534 INFO: lfq-object 12800
19:35:00.940055 INFO: lfq-object 13000
19:35:00.976983 INFO: lfq-object 13200
19:35:01.014325 INFO: lfq-object 12900
19:35:01.025847 INFO: lfq-object 13400
19:35:01.073091 INFO: lfq-object 13100
19:35:01.085944 INFO: lfq-object 13300
19:35:01.129280 INFO: lfq-object 13500
19:35:01.150610 INFO: lfq-object 13700
19:35:01.183666 INFO: lfq-object 13900
19:35:01.241374 INFO: lfq-object 13600
19:35:01.257022 INFO: lfq-object 13800
19:35:01.291443 INFO: lfq-object 14000
19:35:01.316023 INFO: lfq-object 14200
19:35:01.365215 INFO: lfq-object 14400
19:35:01.393879 INFO: lfq-object 14600
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19:35:53.961899 INFO: Writing precursor output to disk
19:35:53.962286 INFO: Saving run_output/alphadia_1.10.4_Again_good_now/library/precursor.matrix.tsv to disk
19:35:54.384884 PROGRESS: Performing label free quantification on the pg level
19:35:54.385007 INFO: Filtering fragments by quality
19:35:54.678352 INFO: Performing label-free quantification using directLFQ
19:35:54.998619 INFO: 9663 lfq-groups total
19:36:36.689736 INFO: using 100 processes
19:36:36.790989 INFO: lfq-object 0
19:36:36.817726 INFO: lfq-object 100
19:36:36.847959 INFO: lfq-object 200
19:36:36.879347 INFO: lfq-object 300
19:36:36.906008 INFO: lfq-object 400
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19:36:37.001196 INFO: lfq-object 700
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19:36:39.166876 INFO: lfq-object 5000
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19:36:39.925104 INFO: lfq-object 6800
19:36:39.973334 INFO: lfq-object 6900
19:36:40.005932 INFO: lfq-object 7000
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19:36:40.102478 INFO: lfq-object 7200
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19:36:40.261161 INFO: lfq-object 7600
19:36:40.286628 INFO: lfq-object 7700
19:36:40.316736 INFO: lfq-object 7800
19:36:40.349154 INFO: lfq-object 7900
19:36:40.390091 INFO: lfq-object 8000
19:36:40.429469 INFO: lfq-object 8100
19:36:40.471912 INFO: lfq-object 8200
19:36:40.508779 INFO: lfq-object 8300
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19:36:40.625458 INFO: lfq-object 8600
19:36:40.656869 INFO: lfq-object 8700
19:36:40.701253 INFO: lfq-object 8800
19:36:40.746603 INFO: lfq-object 8900
19:36:40.791592 INFO: lfq-object 9000
19:36:40.844589 INFO: lfq-object 9100
19:36:40.891227 INFO: lfq-object 9200
19:36:40.935965 INFO: lfq-object 9300
19:36:40.978963 INFO: lfq-object 9400
19:36:41.025434 INFO: lfq-object 9500
19:36:41.064792 INFO: lfq-object 9600
19:36:43.692731 INFO: Writing pg output to disk
19:36:43.692911 INFO: Saving run_output/alphadia_1.10.4_Again_good_now/library/pg.matrix.tsv to disk
19:36:43.934096 INFO: Writing psm output to disk
19:36:43.934247 INFO: Saving run_output/alphadia_1.10.4_Again_good_now/library/precursors.tsv to disk
19:37:06.113741 PROGRESS: Building spectral library
19:37:06.204589 INFO: Building MBR spectral library
19:37:06.204840 INFO: Running MbrLibraryBuilder
19:37:08.037022 INFO: MBR spectral library contains 95,522 precursors, 9,663 proteins
19:37:08.037244 INFO: Writing MBR spectral library to disk
19:37:09.134682 PROGRESS: =================== Search Finished ===================
19:37:10.302126 INFO: Running step 'mbr'
19:37:10.305883 INFO: Extracted extra_config from previous step: defaultdict(<class 'dict'>, {'search': {'target_ms1_tolerance': 10.5657535, 'target_ms2_tolerance': 10.0473985}})
19:37:10.306056 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
19:37:10.317656 INFO: loading additional config provided via CLI
19:37:10.317744 INFO: loading additional config provided via CLI parameters
19:37:10.318036 INFO: Updating config with 'user defined'
19:37:10.318138 INFO: Updating config with 'user defined (cli)'
19:37:10.318162 INFO: Updating config with 'multistep search'
19:37:10.318213 INFO: ├──version: 1
19:37:10.318242 INFO: ├──workflow_name: None
19:37:10.318266 INFO: [32;20m├──output_directory: run_output/alphadia_1.10.4_Again_good_now [multistep search, default: None][0m
19:37:10.318288 INFO: [32;20m├──library_path: run_output/alphadia_1.10.4_Again_good_now/library/speclib.mbr.hdf [multistep search, default: None][0m
19:37:10.318308 INFO: ├──raw_paths:
19:37:10.318330 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d [user defined (cli), default: None][0m
19:37:10.318349 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d [user defined (cli), default: None][0m
19:37:10.318368 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d [user defined (cli), default: None][0m
19:37:10.318388 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d [user defined (cli), default: None][0m
19:37:10.318407 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d [user defined (cli), default: None][0m
19:37:10.318425 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d [user defined (cli), default: None][0m
19:37:10.318445 INFO: ├──fasta_paths:
19:37:10.318465 INFO: ├──quant_directory: None
19:37:10.318483 INFO: ├──general
19:37:10.318506 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
19:37:10.318526 INFO: │   ├──transfer_step_enabled: False
19:37:10.318544 INFO: │   ├──mbr_step_enabled: True
19:37:10.318565 INFO: │   ├──reuse_calibration: False
19:37:10.318586 INFO: │   ├──reuse_quant: False
19:37:10.318604 INFO: │   ├──astral_ms1: False
19:37:10.318624 INFO: │   ├──log_level: INFO
19:37:10.318643 INFO: │   ├──mmap_detector_events: False
19:37:10.318669 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
19:37:10.318694 INFO: │   ├──save_library: True
19:37:10.318713 INFO: │   ├──save_mbr_library: True
19:37:10.318732 INFO: │   └──save_figures: True
19:37:10.318753 INFO: ├──library_loading
19:37:10.318772 INFO: │   └──rt_heuristic: 180
19:37:10.318790 INFO: ├──library_prediction
19:37:10.318810 INFO: │   ├──enabled: False
19:37:10.318828 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
19:37:10.318847 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
19:37:10.318867 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
19:37:10.318887 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
19:37:10.318905 INFO: │   ├──missed_cleavages: 1
19:37:10.318924 INFO: │   ├──precursor_len:
19:37:10.318946 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
19:37:10.318964 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
19:37:10.318985 INFO: │   ├──precursor_charge:
19:37:10.319005 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
19:37:10.319035 INFO: │   │   [32;20m- 4[0m
19:37:10.319053 INFO: │   ├──precursor_mz:
19:37:10.319074 INFO: │   │   [32;20m- 400[0m
19:37:10.319091 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
19:37:10.319108 INFO: │   ├──fragment_mz:
19:37:10.319128 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
19:37:10.319147 INFO: │   │   [32;20m- 2000[0m
19:37:10.319166 INFO: │   ├──nce: 25
19:37:10.319185 INFO: │   ├──fragment_types:
19:37:10.319211 INFO: │   │   [32;20m- b[0m
19:37:10.319230 INFO: │   │   [32;20m- y[0m
19:37:10.319250 INFO: │   ├──max_fragment_charge: 2
19:37:10.319268 INFO: │   [32;20m├──instrument: timsTOF [user defined, default: Lumos][0m
19:37:10.319286 INFO: │   ├──peptdeep_model_path: None
19:37:10.319306 INFO: │   └──peptdeep_model_type: generic
19:37:10.319325 INFO: ├──custom_modifications:
19:37:10.319343 INFO: │   ├──name: Dimethyl:d12@K
19:37:10.319363 INFO: │   └──composition: H(-2)2H(8)13C(2)
19:37:10.319381 INFO: │   ├──name: Dimethyl:d12@Any_N-term
19:37:10.319398 INFO: │   └──composition: H(-2)2H(8)13C(2)
19:37:10.319418 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
19:37:10.319436 INFO: │   └──composition: H(-2)2H(8)13C(2)
19:37:10.319456 INFO: │   ├──name: mTRAQ:d12@K
19:37:10.319476 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
19:37:10.319494 INFO: │   ├──name: mTRAQ:d12@Any_N-term
19:37:10.319511 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
19:37:10.319530 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
19:37:10.319548 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
19:37:10.319566 INFO: │   ├──name: Label:13C(12)@K
19:37:10.319584 INFO: │   └──composition: C(12)
19:37:10.319603 INFO: ├──search
19:37:10.319625 INFO: │   [32;20m├──target_ms1_tolerance: 10.5657535 [multistep search, default: 5][0m
19:37:10.319644 INFO: │   [32;20m├──target_ms2_tolerance: 10.0473985 [multistep search, default: 10][0m
19:37:10.319664 INFO: │   ├──target_rt_tolerance: 0
19:37:10.319684 INFO: │   ├──target_mobility_tolerance: 0
19:37:10.319702 INFO: │   ├──quant_window: 3
19:37:10.319722 INFO: │   [32;20m├──target_num_candidates: 2 [user defined, default: 3][0m
19:37:10.319741 INFO: │   ├──channel_filter: 
19:37:10.319759 INFO: │   ├──exclude_shared_ions: True
19:37:10.319778 INFO: │   ├──compete_for_fragments: True
19:37:10.319795 INFO: │   ├──quant_all: True
19:37:10.319814 INFO: │   ├──top_k_fragments: 12
19:37:10.319834 INFO: │   ├──experimental_xic: True
19:37:10.319853 INFO: │   └──optimized_peak_group_score: False
19:37:10.319870 INFO: ├──calibration
19:37:10.319890 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 8000][0m
19:37:10.319910 INFO: │   ├──optimization_lock_target: 200
19:37:10.319928 INFO: │   ├──max_steps: 20
19:37:10.319948 INFO: │   ├──min_steps: 2
19:37:10.319966 INFO: │   ├──max_skips: 1
19:37:10.319984 INFO: │   ├──norm_rt_mode: linear
19:37:10.320004 INFO: │   ├──max_fragments: 5000
19:37:10.320028 INFO: │   └──min_correlation: 0.7
19:37:10.320047 INFO: ├──search_initial
19:37:10.320068 INFO: │   ├──initial_num_candidates: 1
19:37:10.320086 INFO: │   ├──initial_ms1_tolerance: 30
19:37:10.320103 INFO: │   ├──initial_ms2_tolerance: 30
19:37:10.320121 INFO: │   ├──initial_mobility_tolerance: 0.1
19:37:10.320142 INFO: │   └──initial_rt_tolerance: 0.5
19:37:10.320160 INFO: ├──selection_config
19:37:10.320178 INFO: │   ├──peak_len_rt: 10.0
19:37:10.320199 INFO: │   ├──sigma_scale_rt: 0.5
19:37:10.320217 INFO: │   ├──peak_len_mobility: 0.01
19:37:10.320234 INFO: │   ├──sigma_scale_mobility: 1.0
19:37:10.320253 INFO: │   ├──top_k_precursors: 3
19:37:10.320271 INFO: │   ├──kernel_size: 30
19:37:10.320290 INFO: │   ├──f_mobility: 1.0
19:37:10.320312 INFO: │   ├──f_rt: 0.99
19:37:10.320329 INFO: │   ├──center_fraction: 0.5
19:37:10.320346 INFO: │   ├──min_size_mobility: 8
19:37:10.320365 INFO: │   ├──min_size_rt: 3
19:37:10.320388 INFO: │   ├──max_size_mobility: 20
19:37:10.320406 INFO: │   ├──max_size_rt: 15
19:37:10.320425 INFO: │   ├──group_channels: False
19:37:10.320445 INFO: │   ├──use_weighted_score: True
19:37:10.320469 INFO: │   ├──join_close_candidates: False
19:37:10.320490 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
19:37:10.320508 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
19:37:10.320526 INFO: ├──scoring_config
19:37:10.320546 INFO: │   ├──score_grouped: False
19:37:10.320565 INFO: │   ├──top_k_isotopes: 3
19:37:10.320582 INFO: │   ├──reference_channel: -1
19:37:10.320600 INFO: │   ├──precursor_mz_tolerance: 10
19:37:10.320620 INFO: │   └──fragment_mz_tolerance: 15
19:37:10.320637 INFO: ├──library_multiplexing
19:37:10.320656 INFO: │   ├──enabled: False
19:37:10.320675 INFO: │   ├──input_channel: 0
19:37:10.320693 INFO: │   └──multiplex_mapping:
19:37:10.320710 INFO: ├──multiplexing
19:37:10.320729 INFO: │   ├──enabled: False
19:37:10.320746 INFO: │   ├──target_channels: 4,8
19:37:10.320764 INFO: │   ├──decoy_channel: 12
19:37:10.320783 INFO: │   ├──reference_channel: 0
19:37:10.320801 INFO: │   └──competetive_scoring: True
19:37:10.320818 INFO: ├──fdr
19:37:10.320836 INFO: │   ├──fdr: 0.01
19:37:10.320856 INFO: │   ├──group_level: proteins
19:37:10.320873 INFO: │   [32;20m├──inference_strategy: library [multistep search, default: heuristic][0m
19:37:10.320892 INFO: │   ├──competetive_scoring: True
19:37:10.320911 INFO: │   ├──keep_decoys: False
19:37:10.320929 INFO: │   ├──channel_wise_fdr: False
19:37:10.320946 INFO: │   ├──enable_two_step_classifier: False
19:37:10.320966 INFO: │   ├──two_step_classifier_max_iterations: 5
19:37:10.320984 INFO: │   └──enable_nn_hyperparameter_tuning: False
19:37:10.321001 INFO: ├──search_output
19:37:10.321022 INFO: │   ├──file_format: tsv
19:37:10.321040 INFO: │   ├──peptide_level_lfq: False
19:37:10.321058 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
19:37:10.321077 INFO: │   ├──min_k_fragments: 12
19:37:10.321096 INFO: │   ├──min_correlation: 0.9
19:37:10.321113 INFO: │   ├──num_samples_quadratic: 50
19:37:10.321131 INFO: │   ├──min_nonnan: 3
19:37:10.321149 INFO: │   ├──normalize_lfq: True
19:37:10.321167 INFO: │   └──save_fragment_quant_matrix: False
19:37:10.321184 INFO: ├──optimization
19:37:10.321204 INFO: │   ├──order_of_optimization: None
19:37:10.321222 INFO: │   ├──ms2_error
19:37:10.321239 INFO: │   │   ├──targeted_update_percentile_range: 0.95
19:37:10.321259 INFO: │   │   ├──targeted_update_factor: 1.0
19:37:10.321278 INFO: │   │   ├──automatic_update_percentile_range: 0.99
19:37:10.321296 INFO: │   │   ├──automatic_update_factor: 1.1
19:37:10.321315 INFO: │   │   ├──try_narrower_values: True
19:37:10.321335 INFO: │   │   ├──maximal_decrease: 0.5
19:37:10.321353 INFO: │   │   ├──favour_narrower_optimum: False
19:37:10.321371 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
19:37:10.321391 INFO: │   ├──ms1_error
19:37:10.321409 INFO: │   │   ├──targeted_update_percentile_range: 0.95
19:37:10.321428 INFO: │   │   ├──targeted_update_factor: 1.0
19:37:10.321448 INFO: │   │   ├──automatic_update_percentile_range: 0.99
19:37:10.321467 INFO: │   │   ├──automatic_update_factor: 1.1
19:37:10.321485 INFO: │   │   ├──try_narrower_values: False
19:37:10.321504 INFO: │   │   ├──maximal_decrease: 0.2
19:37:10.321522 INFO: │   │   ├──favour_narrower_optimum: False
19:37:10.321540 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
19:37:10.321559 INFO: │   ├──mobility_error
19:37:10.321579 INFO: │   │   ├──targeted_update_percentile_range: 0.95
19:37:10.321598 INFO: │   │   ├──targeted_update_factor: 1.0
19:37:10.321618 INFO: │   │   ├──automatic_update_percentile_range: 0.99
19:37:10.321641 INFO: │   │   ├──automatic_update_factor: 1.1
19:37:10.321659 INFO: │   │   ├──try_narrower_values: False
19:37:10.321679 INFO: │   │   ├──maximal_decrease: 0.2
19:37:10.321697 INFO: │   │   ├──favour_narrower_optimum: False
19:37:10.321717 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
19:37:10.321736 INFO: │   └──rt_error
19:37:10.321755 INFO: │       ├──targeted_update_percentile_range: 0.95
19:37:10.321773 INFO: │       ├──targeted_update_factor: 1.0
19:37:10.321793 INFO: │       ├──automatic_update_percentile_range: 0.99
19:37:10.321811 INFO: │       ├──automatic_update_factor: 1.1
19:37:10.321829 INFO: │       ├──try_narrower_values: True
19:37:10.321848 INFO: │       ├──maximal_decrease: 0.2
19:37:10.321867 INFO: │       ├──favour_narrower_optimum: True
19:37:10.321885 INFO: │       └──maximum_decrease_from_maximum: 0.1
19:37:10.321903 INFO: ├──optimization_manager
19:37:10.321923 INFO: │   ├──fwhm_rt: 5
19:37:10.321942 INFO: │   ├──fwhm_mobility: 0.01
19:37:10.321960 INFO: │   └──score_cutoff: 0
19:37:10.321979 INFO: ├──transfer_library
19:37:10.321998 INFO: │   ├──enabled: False
19:37:10.322016 INFO: │   ├──fragment_types:
19:37:10.322035 INFO: │   │   [32;20m- b[0m
19:37:10.322053 INFO: │   │   [32;20m- y[0m
19:37:10.322071 INFO: │   ├──max_charge: 2
19:37:10.322090 INFO: │   ├──top_k_samples: 3
19:37:10.322108 INFO: │   ├──norm_delta_max: True
19:37:10.322126 INFO: │   ├──precursor_correlation_cutoff: 0.5
19:37:10.322147 INFO: │   └──fragment_correlation_ratio: 0.75
19:37:10.322165 INFO: └──transfer_learning
19:37:10.322184 INFO:     ├──enabled: False
19:37:10.322203 INFO:     ├──batch_size: 2000
19:37:10.322222 INFO:     ├──max_lr: 0.0001
19:37:10.322240 INFO:     ├──train_fraction: 0.7
19:37:10.322258 INFO:     ├──validation_fraction: 0.2
19:37:10.322278 INFO:     ├──test_fraction: 0.1
19:37:10.322295 INFO:     ├──test_interval: 1
19:37:10.322313 INFO:     ├──lr_patience: 3
19:37:10.322332 INFO:     ├──epochs: 51
19:37:10.322350 INFO:     ├──warmup_epochs: 5
19:37:10.322367 INFO:     ├──nce: 25
19:37:10.322386 INFO:     [32;20m└──instrument: timsTOF [user defined, default: Lumos][0m
19:37:10.328332 INFO: Registering 7 custom modifications
19:37:10.345832 INFO: Running DynamicLoader
19:37:10.345939 INFO: Loading .hdf library from run_output/alphadia_1.10.4_Again_good_now/library/speclib.mbr.hdf
19:37:10.808456 INFO: Running PrecursorInitializer
19:37:10.808646 INFO: Running AnnotateFasta
19:37:10.808950 INFO: Dropping decoys from input library before annotation
19:37:10.827939 INFO: Running IsotopeGenerator
19:37:10.828198 WARNING: Input library already contains isotope information. Skipping isotope generation. 
 Please note that isotope generation outside of alphabase is not supported.
19:37:10.828365 INFO: Running RTNormalization
19:37:10.832695 INFO: Saving library to run_output/alphadia_1.10.4_Again_good_now/speclib.hdf
19:37:11.513532 INFO: Running DecoyGenerator
19:37:24.012995 INFO: Running FlattenLibrary
19:37:24.907358 INFO: Running InitFlatColumns
19:37:24.912309 INFO: Running LogFlatLibraryStats
19:37:24.912426 INFO: ============ Library Stats ============
19:37:24.912454 INFO: Number of precursors: 191,030
19:37:24.953043 INFO: 	thereof targets:95,522
19:37:24.953178 INFO: 	thereof decoys: 95,508
19:37:24.954973 INFO: Number of elution groups: 95,522
19:37:24.955048 INFO: 	average size: 2.00
19:37:24.966542 INFO: Number of proteins: 9,663
19:37:24.967319 INFO: Number of channels: 1 ([0])
19:37:24.967407 INFO: Isotopes Distribution for 4 isotopes
19:37:24.967434 INFO: =======================================
19:37:24.967835 INFO: Searching 6 files:
19:37:24.967872 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
19:37:24.967893 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
19:37:24.967924 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
19:37:24.967944 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
19:37:24.967962 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
19:37:24.967979 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
19:37:24.967996 INFO: Using 0 fasta files:
19:37:24.968017 INFO: Using library: run_output/alphadia_1.10.4_Again_good_now/library/speclib.mbr.hdf
19:37:24.968034 INFO: Saving output to: run_output/alphadia_1.10.4_Again_good_now
19:37:24.968070 PROGRESS: Starting Search Workflows
19:37:24.968122 PROGRESS: Loading raw file 1/6: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
19:37:24.968162 INFO: Quantification results path: run_output/alphadia_1.10.4_Again_good_now/quant
19:37:24.968224 INFO: Creating folder run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/figures
19:37:24.969786 INFO: Initializing RawFileManager
19:37:24.969890 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
19:37:24.969942 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
19:37:24.969972 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
19:37:25.176286 INFO: Reading 39,128 frames with 2,835,410,867 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
20:30:26.042609 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d...
20:30:26.047865 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
20:30:26.053082 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
20:30:26.053445 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
20:30:26.054054 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
20:30:26.058144 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
20:30:26.079745 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
20:30:26.080124 INFO: Indexing quadrupole dimension
20:30:26.650555 INFO: Transposing detector events
20:30:38.004997 INFO: Finished transposing data
20:30:38.038995 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
20:30:38.039927 INFO: RT (min)            : 0.0 - 70.0
20:30:38.039969 INFO: RT duration (sec)   : 4199.9
20:30:38.039992 INFO: RT duration (min)   : 70.0
20:30:38.040013 INFO: Cycle len (scans)   : 9
20:30:38.040032 INFO: Cycle len (sec)     : 0.97
20:30:38.040051 INFO: Number of cycles    : 4347
20:30:38.040068 INFO: MS2 range (m/z)     : 400.0 - 1000.0
20:30:38.079273 INFO: Initializing CalibrationManager
20:30:38.079625 INFO: Loading calibration config
20:30:38.080384 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed'], 'function': LOESSRegression()}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed'], 'function': LOESSRegression(n_kernels=2)}], 'name': 'precursor'}]
20:30:38.080485 INFO: Calibration group :fragment, found 1 estimator(s)
20:30:38.080596 INFO: Calibration group :precursor, found 3 estimator(s)
20:30:38.080773 INFO: Initializing OptimizationManager
20:30:38.080888 INFO: initial parameter: ms1_error = 30
20:30:38.080937 INFO: initial parameter: ms2_error = 30
20:30:38.081992 INFO: initial parameter: rt_error = 2099.928159
20:30:38.082048 INFO: initial parameter: mobility_error = 0.1
20:30:38.082091 INFO: initial parameter: column_type = library
20:30:38.082130 INFO: initial parameter: num_candidates = 1
20:30:38.082169 INFO: initial parameter: classifier_version = -1
20:30:38.082208 INFO: initial parameter: fwhm_rt = 5
20:30:38.082250 INFO: initial parameter: fwhm_mobility = 0.01
20:30:38.082289 INFO: initial parameter: score_cutoff = 0
20:30:38.082364 INFO: Initializing TimingManager
20:30:38.082441 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
20:30:38.082619 INFO: FDRManager not loaded from disk.
20:30:38.082648 INFO: Initializing FDRManager
20:30:38.082692 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
20:30:38.126171 PROGRESS: 95,522 target precursors potentially observable (0 removed)
20:30:38.198106 PROGRESS: Starting initial search for precursors.
20:30:38.206292 INFO: Starting optimization step 0.
20:30:38.206507 PROGRESS: === Extracting elution groups 0 to 200 ===
20:30:38.206594 PROGRESS: Extracting batch of 395 precursors
20:30:38.207831 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:30:38.207886 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:30:38.207924 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:30:38.207947 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:30:38.212922 INFO: Starting candidate selection
20:30:41.540310 INFO: Starting candidate scoring
20:30:41.609549 INFO: Finished candidate processing
20:30:41.609665 INFO: Collecting candidate features
20:30:41.623896 INFO: Collecting fragment features
20:30:41.626864 INFO: Finished candidate scoring
20:30:41.627918 PROGRESS: === Extracted 394 precursors and 4345 fragments ===
20:30:41.629347 INFO: performing precursor FDR with 47 features
20:30:41.629396 INFO: Decoy channel: -1
20:30:41.629426 INFO: Competetive: True
20:30:41.630953 INFO: Setting torch num_threads to 2 for FDR classification task
20:30:41.644851 INFO: Test AUC: 0.497
20:30:41.644928 INFO: Train AUC: 0.514
20:30:41.644964 INFO: AUC difference: 3.31%
20:30:41.855740 INFO: Resetting torch num_threads to 100
20:30:41.856346 INFO: === FDR correction performed with classifier version -1 ===
20:30:41.856995 PROGRESS: ============================= Precursor FDR =============================
20:30:41.857083 PROGRESS: Total precursors accumulated: 200
20:30:41.857144 PROGRESS: Target precursors: 104 (52.00%)
20:30:41.857194 PROGRESS: Decoy precursors: 96 (48.00%)
20:30:41.857239 PROGRESS: 
20:30:41.857283 PROGRESS: Precursor Summary:
20:30:41.858121 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
20:30:41.858205 PROGRESS: 
20:30:41.858260 PROGRESS: Protein Summary:
20:30:41.859184 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
20:30:41.859272 PROGRESS: =========================================================================
20:30:41.862923 INFO: Starting optimization step 1.
20:30:41.863036 PROGRESS: === Extracting elution groups 200 to 600 ===
20:30:41.863102 PROGRESS: Extracting batch of 793 precursors
20:30:41.863903 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:30:41.863948 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:30:41.863975 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:30:41.863995 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:30:41.864915 INFO: Starting candidate selection
20:30:47.540482 INFO: Starting candidate scoring
20:30:47.651624 INFO: Finished candidate processing
20:30:47.651740 INFO: Collecting candidate features
20:30:47.661664 INFO: Collecting fragment features
20:30:47.664219 INFO: Finished candidate scoring
20:30:47.666703 PROGRESS: === Extracted 1187 precursors and 13138 fragments ===
20:30:47.667509 INFO: performing precursor FDR with 47 features
20:30:47.667554 INFO: Decoy channel: -1
20:30:47.667578 INFO: Competetive: True
20:30:47.670696 INFO: Setting torch num_threads to 2 for FDR classification task
20:30:47.683439 INFO: Test AUC: 0.505
20:30:47.683501 INFO: Train AUC: 0.505
20:30:47.683529 INFO: AUC difference: 0.03%
20:30:47.862663 INFO: Resetting torch num_threads to 100
20:30:47.863393 INFO: === FDR correction performed with classifier version -1 ===
20:30:47.864162 PROGRESS: ============================= Precursor FDR =============================
20:30:47.864258 PROGRESS: Total precursors accumulated: 600
20:30:47.864321 PROGRESS: Target precursors: 297 (49.50%)
20:30:47.864373 PROGRESS: Decoy precursors: 303 (50.50%)
20:30:47.864421 PROGRESS: 
20:30:47.864468 PROGRESS: Precursor Summary:
20:30:47.865302 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:30:47.865386 PROGRESS: 
20:30:47.865440 PROGRESS: Protein Summary:
20:30:47.866327 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:30:47.866409 PROGRESS: =========================================================================
20:30:47.872704 INFO: Starting optimization step 2.
20:30:47.872823 PROGRESS: === Extracting elution groups 600 to 1400 ===
20:30:47.872886 PROGRESS: Extracting batch of 1583 precursors
20:30:47.873859 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:30:47.873905 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:30:47.873935 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:30:47.873957 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:30:47.874876 INFO: Starting candidate selection
20:30:58.353741 INFO: Starting candidate scoring
20:30:58.529442 INFO: Finished candidate processing
20:30:58.529557 INFO: Collecting candidate features
20:30:58.541097 INFO: Collecting fragment features
20:30:58.544437 INFO: Finished candidate scoring
20:30:58.547662 PROGRESS: === Extracted 2770 precursors and 30810 fragments ===
20:30:58.548743 INFO: performing precursor FDR with 47 features
20:30:58.548787 INFO: Decoy channel: -1
20:30:58.548811 INFO: Competetive: True
20:30:58.552284 INFO: Setting torch num_threads to 2 for FDR classification task
20:30:58.568111 INFO: Test AUC: 0.530
20:30:58.568206 INFO: Train AUC: 0.515
20:30:58.568237 INFO: AUC difference: 2.90%
20:30:58.742662 INFO: Resetting torch num_threads to 100
20:30:58.746477 INFO: === FDR correction performed with classifier version -1 ===
20:30:58.747338 PROGRESS: ============================= Precursor FDR =============================
20:30:58.747437 PROGRESS: Total precursors accumulated: 1,400
20:30:58.747498 PROGRESS: Target precursors: 718 (51.29%)
20:30:58.747550 PROGRESS: Decoy precursors: 682 (48.71%)
20:30:58.747596 PROGRESS: 
20:30:58.747640 PROGRESS: Precursor Summary:
20:30:58.748521 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
20:30:58.748607 PROGRESS: 
20:30:58.748662 PROGRESS: Protein Summary:
20:30:58.749597 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
20:30:58.749681 PROGRESS: =========================================================================
20:30:58.757054 INFO: Starting optimization step 3.
20:30:58.757172 PROGRESS: === Extracting elution groups 1400 to 3000 ===
20:30:58.757234 PROGRESS: Extracting batch of 3171 precursors
20:30:58.759062 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:30:58.759112 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:30:58.759140 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:30:58.759162 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:30:58.760096 INFO: Starting candidate selection
20:31:18.975530 INFO: Starting candidate scoring
20:31:19.351390 INFO: Finished candidate processing
20:31:19.351568 INFO: Collecting candidate features
20:31:19.382247 INFO: Collecting fragment features
20:31:19.391619 INFO: Finished candidate scoring
20:31:19.405917 PROGRESS: === Extracted 5940 precursors and 65957 fragments ===
20:31:19.408021 INFO: performing precursor FDR with 47 features
20:31:19.408097 INFO: Decoy channel: -1
20:31:19.408140 INFO: Competetive: True
20:31:19.416043 INFO: Setting torch num_threads to 2 for FDR classification task
20:31:19.449868 INFO: Test AUC: 0.510
20:31:19.450003 INFO: Train AUC: 0.505
20:31:19.450033 INFO: AUC difference: 0.93%
20:31:19.640756 INFO: Resetting torch num_threads to 100
20:31:19.654138 INFO: === FDR correction performed with classifier version -1 ===
20:31:19.655370 PROGRESS: ============================= Precursor FDR =============================
20:31:19.655477 PROGRESS: Total precursors accumulated: 3,000
20:31:19.655544 PROGRESS: Target precursors: 1,505 (50.17%)
20:31:19.655594 PROGRESS: Decoy precursors: 1,495 (49.83%)
20:31:19.655638 PROGRESS: 
20:31:19.655682 PROGRESS: Precursor Summary:
20:31:19.656568 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:31:19.656657 PROGRESS: 
20:31:19.656710 PROGRESS: Protein Summary:
20:31:19.657634 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:31:19.657719 PROGRESS: =========================================================================
20:31:19.684631 INFO: Starting optimization step 4.
20:31:19.684802 PROGRESS: === Extracting elution groups 3000 to 6200 ===
20:31:19.684869 PROGRESS: Extracting batch of 6347 precursors
20:31:19.687736 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:31:19.687789 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:31:19.687829 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:31:19.687852 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:31:19.714873 INFO: Starting candidate selection
20:32:03.630956 INFO: Starting candidate scoring
20:32:04.356507 INFO: Finished candidate processing
20:32:04.356662 INFO: Collecting candidate features
20:32:04.385902 INFO: Collecting fragment features
20:32:04.397638 INFO: Finished candidate scoring
20:32:04.412064 PROGRESS: === Extracted 12286 precursors and 136555 fragments ===
20:32:04.415006 INFO: performing precursor FDR with 47 features
20:32:04.415102 INFO: Decoy channel: -1
20:32:04.415129 INFO: Competetive: True
20:32:04.425600 INFO: Setting torch num_threads to 2 for FDR classification task
20:32:04.488041 INFO: Test AUC: 0.517
20:32:04.488178 INFO: Train AUC: 0.504
20:32:04.488209 INFO: AUC difference: 2.59%
20:32:04.684670 INFO: Resetting torch num_threads to 100
20:32:04.686203 INFO: === FDR correction performed with classifier version -1 ===
20:32:04.688788 PROGRESS: ============================= Precursor FDR =============================
20:32:04.688925 PROGRESS: Total precursors accumulated: 6,200
20:32:04.688989 PROGRESS: Target precursors: 3,113 (50.21%)
20:32:04.689040 PROGRESS: Decoy precursors: 3,087 (49.79%)
20:32:04.689085 PROGRESS: 
20:32:04.689129 PROGRESS: Precursor Summary:
20:32:04.690049 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:32:04.690137 PROGRESS: 
20:32:04.690209 PROGRESS: Protein Summary:
20:32:04.691175 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:32:04.691264 PROGRESS: =========================================================================
20:32:04.719690 INFO: Starting optimization step 5.
20:32:04.719980 PROGRESS: === Extracting elution groups 6200 to 12600 ===
20:32:04.720075 PROGRESS: Extracting batch of 12697 precursors
20:32:04.724873 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:32:04.724957 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:32:04.725004 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:32:04.725027 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:32:04.831326 INFO: Starting candidate selection
20:33:22.115119 INFO: Starting candidate scoring
20:33:23.239725 INFO: Finished candidate processing
20:33:23.239880 INFO: Collecting candidate features
20:33:23.287882 INFO: Collecting fragment features
20:33:23.299569 INFO: Finished candidate scoring
20:33:23.318339 PROGRESS: === Extracted 24982 precursors and 277708 fragments ===
20:33:23.322353 INFO: performing precursor FDR with 47 features
20:33:23.322441 INFO: Decoy channel: -1
20:33:23.322467 INFO: Competetive: True
20:33:23.334733 INFO: Setting torch num_threads to 2 for FDR classification task
20:33:23.561730 INFO: Test AUC: 0.810
20:33:23.561868 INFO: Train AUC: 0.805
20:33:23.561899 INFO: AUC difference: 0.62%
20:33:23.765114 INFO: Resetting torch num_threads to 100
20:33:23.766809 INFO: === FDR correction performed with classifier version -1 ===
20:33:23.768825 PROGRESS: ============================= Precursor FDR =============================
20:33:23.768955 PROGRESS: Total precursors accumulated: 12,600
20:33:23.769016 PROGRESS: Target precursors: 10,199 (80.94%)
20:33:23.769071 PROGRESS: Decoy precursors: 2,401 (19.06%)
20:33:23.769118 PROGRESS: 
20:33:23.769162 PROGRESS: Precursor Summary:
20:33:23.771756 PROGRESS: Channel   0:	 0.05 FDR: 7,292; 0.01 FDR: 4,891; 0.001 FDR: 1,393
20:33:23.771862 PROGRESS: 
20:33:23.771921 PROGRESS: Protein Summary:
20:33:23.775235 PROGRESS: Channel   0:	 0.05 FDR: 3,725; 0.01 FDR: 2,740; 0.001 FDR:   993
20:33:23.775333 PROGRESS: =========================================================================
20:33:23.805437 INFO: fragments_df: keeping 5000 of 277708 [sum(precursor_idx_mask)=54610 sum(mass_error_mask)=277708 stop_rank=5000
20:33:23.816515 INFO: calibration group: precursor, fitting mz estimator 
20:33:24.492689 INFO: calibration group: precursor, fitting rt estimator 
20:33:25.178744 INFO: calibration group: precursor, fitting mobility estimator 
20:33:25.854261 INFO: calibration group: fragment, fitting mz estimator 
20:33:26.550437 INFO: Using score_cutoff 52.09450213623047 (fac=0.99, q=1)
20:33:26.551933 INFO: calibration group: precursor, predicting mz
20:33:26.553061 INFO: calibration group: precursor, predicting rt
20:33:26.554404 INFO: calibration group: precursor, predicting mobility
20:33:26.555188 INFO: calibration group: fragment, predicting mz
20:33:26.557149 PROGRESS: Required number of precursors found. Starting search parameter optimization.
20:33:26.557276 INFO: Starting optimization step 6.
20:33:26.557343 PROGRESS: === Extracting elution groups 0 to 600 ===
20:33:26.557406 PROGRESS: Extracting batch of 1188 precursors
20:33:26.558669 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:33:26.558717 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:33:26.558761 INFO: FWHM in RT is 3.28 seconds, sigma is 0.72
20:33:26.558784 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.18
20:33:26.559676 INFO: Starting candidate selection
20:33:35.586983 INFO: Starting candidate scoring
20:33:35.836327 INFO: Finished candidate processing
20:33:35.836448 INFO: Collecting candidate features
20:33:35.853833 INFO: Collecting fragment features
20:33:35.859800 INFO: Finished candidate scoring
20:33:35.862237 PROGRESS: === Extracted 2273 precursors and 25128 fragments ===
20:33:35.862595 INFO: performing precursor FDR with 47 features
20:33:35.862640 INFO: Decoy channel: -1
20:33:35.862669 INFO: Competetive: True
20:33:35.866133 INFO: Setting torch num_threads to 2 for FDR classification task
20:33:35.883561 INFO: Test AUC: 0.753
20:33:35.883653 INFO: Train AUC: 0.705
20:33:35.883689 INFO: AUC difference: 6.82%
20:33:35.883714 WARNING: AUC difference > 5%. This may indicate overfitting.
20:33:36.072146 INFO: Resetting torch num_threads to 100
20:33:36.072790 INFO: === FDR correction performed with classifier version 5 ===
20:33:36.073512 PROGRESS: ============================= Precursor FDR =============================
20:33:36.073602 PROGRESS: Total precursors accumulated: 600
20:33:36.073667 PROGRESS: Target precursors: 502 (83.67%)
20:33:36.073722 PROGRESS: Decoy precursors: 98 (16.33%)
20:33:36.073767 PROGRESS: 
20:33:36.073810 PROGRESS: Precursor Summary:
20:33:36.074861 PROGRESS: Channel   0:	 0.05 FDR:   369; 0.01 FDR:   215; 0.001 FDR:   131
20:33:36.074973 PROGRESS: 
20:33:36.075044 PROGRESS: Protein Summary:
20:33:36.076168 PROGRESS: Channel   0:	 0.05 FDR:   344; 0.01 FDR:   205; 0.001 FDR:   129
20:33:36.076257 PROGRESS: =========================================================================
20:33:36.079877 INFO: fragments_df: keeping 2749 of 25128 [sum(precursor_idx_mask)=4612 sum(mass_error_mask)=25128 stop_rank=2749
20:33:36.084960 INFO: calibration group: precursor, fitting mz estimator 
20:33:36.204611 INFO: calibration group: precursor, fitting rt estimator 
20:33:36.312129 INFO: calibration group: precursor, fitting mobility estimator 
20:33:36.417005 INFO: calibration group: fragment, fitting mz estimator 
20:33:36.732019 INFO: Using score_cutoff 53.67962218551636 (fac=0.99, q=1)
20:33:36.732414 INFO: calibration group: precursor, predicting mz
20:33:36.733527 INFO: calibration group: precursor, predicting rt
20:33:36.735001 INFO: calibration group: precursor, predicting mobility
20:33:36.735794 INFO: calibration group: fragment, predicting mz
20:33:36.737878 INFO: === checking if optimization conditions were reached ===
20:33:36.739227 PROGRESS: ❌ ms2_error      : 10.0474 > 10.0474 or insufficient steps taken.
20:33:36.740125 PROGRESS: ❌ ms1_error      : 10.5658 > 10.5658 or insufficient steps taken.
20:33:36.740174 INFO: ==============================================
20:33:36.740258 INFO: Starting optimization step 7.
20:33:36.740325 PROGRESS: === Extracting elution groups 0 to 600 ===
20:33:36.740381 PROGRESS: Extracting batch of 1188 precursors
20:33:36.741345 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:33:36.741395 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:33:36.741431 INFO: FWHM in RT is 3.31 seconds, sigma is 0.73
20:33:36.741456 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.22
20:33:36.742263 INFO: Starting candidate selection
20:33:44.450070 INFO: Starting candidate scoring
20:33:44.591074 INFO: Finished candidate processing
20:33:44.591180 INFO: Collecting candidate features
20:33:44.604050 INFO: Collecting fragment features
20:33:44.609060 INFO: Finished candidate scoring
20:33:44.610704 PROGRESS: === Extracted 2292 precursors and 24698 fragments ===
20:33:44.611004 INFO: performing precursor FDR with 47 features
20:33:44.611708 INFO: Decoy channel: -1
20:33:44.611732 INFO: Competetive: True
20:33:44.614347 INFO: Setting torch num_threads to 2 for FDR classification task
20:33:44.626926 INFO: Test AUC: 0.788
20:33:44.626997 INFO: Train AUC: 0.746
20:33:44.627033 INFO: AUC difference: 5.70%
20:33:44.627055 WARNING: AUC difference > 5%. This may indicate overfitting.
20:33:44.808752 INFO: Resetting torch num_threads to 100
20:33:44.809361 INFO: === FDR correction performed with classifier version 6 ===
20:33:44.810061 PROGRESS: ============================= Precursor FDR =============================
20:33:44.810149 PROGRESS: Total precursors accumulated: 600
20:33:44.810210 PROGRESS: Target precursors: 537 (89.50%)
20:33:44.810261 PROGRESS: Decoy precursors: 63 (10.50%)
20:33:44.810309 PROGRESS: 
20:33:44.810352 PROGRESS: Precursor Summary:
20:33:44.811382 PROGRESS: Channel   0:	 0.05 FDR:   488; 0.01 FDR:   406; 0.001 FDR:   254
20:33:44.811471 PROGRESS: 
20:33:44.811527 PROGRESS: Protein Summary:
20:33:44.812720 PROGRESS: Channel   0:	 0.05 FDR:   454; 0.01 FDR:   378; 0.001 FDR:   240
20:33:44.812816 PROGRESS: =========================================================================
20:33:44.817270 INFO: fragments_df: keeping 4013 of 24698 [sum(precursor_idx_mask)=8442 sum(mass_error_mask)=24698 stop_rank=4013
20:33:44.824385 INFO: calibration group: precursor, fitting mz estimator 
20:33:44.969054 INFO: calibration group: precursor, fitting rt estimator 
20:33:45.101640 INFO: calibration group: precursor, fitting mobility estimator 
20:33:45.236111 INFO: calibration group: fragment, fitting mz estimator 
20:33:45.772924 INFO: Using score_cutoff 42.44115600013733 (fac=0.99, q=1)
20:33:45.773332 INFO: calibration group: precursor, predicting mz
20:33:45.774647 INFO: calibration group: precursor, predicting rt
20:33:45.776006 INFO: calibration group: precursor, predicting mobility
20:33:45.776790 INFO: calibration group: fragment, predicting mz
20:33:45.778958 INFO: === checking if optimization conditions were reached ===
20:33:45.780412 PROGRESS: ✅ ms2_error      : 10.0474 <= 10.0474
20:33:45.781340 PROGRESS: ✅ ms1_error      : 10.5658 <= 10.5658
20:33:45.781389 INFO: ==============================================
20:33:45.781475 PROGRESS: Optimization finished for ms2_error, ms1_error.
20:33:45.789796 INFO: calibration group: precursor, predicting mz
20:33:45.790910 INFO: calibration group: precursor, predicting rt
20:33:45.792244 INFO: calibration group: precursor, predicting mobility
20:33:45.793011 INFO: calibration group: fragment, predicting mz
20:33:45.795013 INFO: Starting optimization step 0.
20:33:45.795122 PROGRESS: === Extracting elution groups 0 to 600 ===
20:33:45.795199 PROGRESS: Extracting batch of 1188 precursors
20:33:45.796116 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:33:45.796164 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:33:45.796201 INFO: FWHM in RT is 2.74 seconds, sigma is 0.60
20:33:45.796224 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.63
20:33:45.797361 INFO: Starting candidate selection
20:34:01.027270 INFO: Starting candidate scoring
20:34:01.159785 INFO: Finished candidate processing
20:34:01.159889 INFO: Collecting candidate features
20:34:01.173300 INFO: Collecting fragment features
20:34:01.178115 INFO: Finished candidate scoring
20:34:01.179617 PROGRESS: === Extracted 2286 precursors and 24563 fragments ===
20:34:01.179922 INFO: performing precursor FDR with 47 features
20:34:01.179960 INFO: Decoy channel: -1
20:34:01.179984 INFO: Competetive: True
20:34:01.182650 INFO: Setting torch num_threads to 2 for FDR classification task
20:34:01.196031 INFO: Test AUC: 0.781
20:34:01.196090 INFO: Train AUC: 0.769
20:34:01.196119 INFO: AUC difference: 1.57%
20:34:01.376947 INFO: Resetting torch num_threads to 100
20:34:01.377515 INFO: === FDR correction performed with classifier version 7 ===
20:34:01.378199 PROGRESS: ============================= Precursor FDR =============================
20:34:01.378290 PROGRESS: Total precursors accumulated: 600
20:34:01.378347 PROGRESS: Target precursors: 538 (89.67%)
20:34:01.378397 PROGRESS: Decoy precursors: 62 (10.33%)
20:34:01.378441 PROGRESS: 
20:34:01.378484 PROGRESS: Precursor Summary:
20:34:01.379496 PROGRESS: Channel   0:	 0.05 FDR:   485; 0.01 FDR:   338; 0.001 FDR:   212
20:34:01.379586 PROGRESS: 
20:34:01.379640 PROGRESS: Protein Summary:
20:34:01.380787 PROGRESS: Channel   0:	 0.05 FDR:   452; 0.01 FDR:   316; 0.001 FDR:   204
20:34:01.380874 PROGRESS: =========================================================================
20:34:01.384546 INFO: fragments_df: keeping 3690 of 24563 [sum(precursor_idx_mask)=6974 sum(mass_error_mask)=24563 stop_rank=3690
20:34:01.389943 INFO: calibration group: precursor, fitting mz estimator 
20:34:01.502211 INFO: calibration group: precursor, fitting rt estimator 
20:34:01.626324 INFO: calibration group: precursor, fitting mobility estimator 
20:34:01.738040 INFO: calibration group: fragment, fitting mz estimator 
20:34:02.158798 INFO: Using score_cutoff 43.40298497428894 (fac=0.99, q=1)
20:34:02.159209 INFO: calibration group: precursor, predicting mz
20:34:02.160328 INFO: calibration group: precursor, predicting rt
20:34:02.161659 INFO: calibration group: precursor, predicting mobility
20:34:02.162439 INFO: calibration group: fragment, predicting mz
20:34:02.165023 INFO: === checking if optimization conditions were reached ===
20:34:02.165143 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
20:34:02.166647 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 175.2173.
20:34:02.166699 INFO: ==============================================
20:34:02.166783 INFO: Starting optimization step 1.
20:34:02.166850 PROGRESS: === Extracting elution groups 0 to 600 ===
20:34:02.166917 PROGRESS: Extracting batch of 1188 precursors
20:34:02.169685 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:34:02.169736 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:34:02.169778 INFO: FWHM in RT is 2.74 seconds, sigma is 0.60
20:34:02.169802 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.75
20:34:02.170608 INFO: Starting candidate selection
20:34:03.392638 INFO: Starting candidate scoring
20:34:03.513180 INFO: Finished candidate processing
20:34:03.513311 INFO: Collecting candidate features
20:34:03.530459 INFO: Collecting fragment features
20:34:03.537018 INFO: Finished candidate scoring
20:34:03.539383 PROGRESS: === Extracted 2273 precursors and 23974 fragments ===
20:34:03.540038 INFO: performing precursor FDR with 47 features
20:34:03.540084 INFO: Decoy channel: -1
20:34:03.540114 INFO: Competetive: True
20:34:03.546039 INFO: Setting torch num_threads to 2 for FDR classification task
20:34:03.561215 INFO: Test AUC: 0.749
20:34:03.561296 INFO: Train AUC: 0.802
20:34:03.561327 INFO: AUC difference: 6.61%
20:34:03.561349 WARNING: AUC difference > 5%. This may indicate overfitting.
20:34:03.744576 INFO: Resetting torch num_threads to 100
20:34:03.745323 INFO: === FDR correction performed with classifier version 7 ===
20:34:03.745985 PROGRESS: ============================= Precursor FDR =============================
20:34:03.746070 PROGRESS: Total precursors accumulated: 600
20:34:03.746128 PROGRESS: Target precursors: 550 (91.67%)
20:34:03.746177 PROGRESS: Decoy precursors: 50 (8.33%)
20:34:03.746219 PROGRESS: 
20:34:03.746261 PROGRESS: Precursor Summary:
20:34:03.747290 PROGRESS: Channel   0:	 0.05 FDR:   523; 0.01 FDR:   411; 0.001 FDR:   299
20:34:03.747380 PROGRESS: 
20:34:03.747432 PROGRESS: Protein Summary:
20:34:03.748622 PROGRESS: Channel   0:	 0.05 FDR:   489; 0.01 FDR:   383; 0.001 FDR:   280
20:34:03.748707 PROGRESS: =========================================================================
20:34:03.752269 INFO: fragments_df: keeping 4158 of 23974 [sum(precursor_idx_mask)=8471 sum(mass_error_mask)=23974 stop_rank=4158
20:34:03.758583 INFO: calibration group: precursor, fitting mz estimator 
20:34:03.889258 INFO: calibration group: precursor, fitting rt estimator 
20:34:04.003174 INFO: calibration group: precursor, fitting mobility estimator 
20:34:04.114055 INFO: calibration group: fragment, fitting mz estimator 
20:34:04.667984 INFO: Using score_cutoff 41.60116567611694 (fac=0.99, q=1)
20:34:04.668435 INFO: calibration group: precursor, predicting mz
20:34:04.669576 INFO: calibration group: precursor, predicting rt
20:34:04.670902 INFO: calibration group: precursor, predicting mobility
20:34:04.671677 INFO: calibration group: fragment, predicting mz
20:34:04.673675 INFO: === checking if optimization conditions were reached ===
20:34:04.673813 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
20:34:04.675451 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 14.1489.
20:34:04.675503 INFO: ==============================================
20:34:04.675607 INFO: Starting optimization step 2.
20:34:04.675674 PROGRESS: === Extracting elution groups 0 to 600 ===
20:34:04.675745 PROGRESS: Extracting batch of 1188 precursors
20:34:04.676960 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:34:04.677006 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:34:04.677063 INFO: FWHM in RT is 2.69 seconds, sigma is 0.59
20:34:04.677088 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.57
20:34:04.677961 INFO: Starting candidate selection
20:34:05.218695 INFO: Starting candidate scoring
20:34:05.347220 INFO: Finished candidate processing
20:34:05.347327 INFO: Collecting candidate features
20:34:05.356164 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2273)
20:34:05.359349 INFO: Collecting fragment features
20:34:05.363593 INFO: Finished candidate scoring
20:34:05.365662 PROGRESS: === Extracted 2273 precursors and 23404 fragments ===
20:34:05.366095 INFO: performing precursor FDR with 47 features
20:34:05.366155 INFO: Decoy channel: -1
20:34:05.366195 INFO: Competetive: True
20:34:05.370140 INFO: Setting torch num_threads to 2 for FDR classification task
20:34:05.372141 WARNING: dropped 1 decoy PSMs due to missing features
20:34:05.386631 INFO: Test AUC: 0.840
20:34:05.386710 INFO: Train AUC: 0.866
20:34:05.386740 INFO: AUC difference: 2.99%
20:34:05.572851 INFO: Resetting torch num_threads to 100
20:34:05.573430 INFO: === FDR correction performed with classifier version 7 ===
20:34:05.574129 PROGRESS: ============================= Precursor FDR =============================
20:34:05.574216 PROGRESS: Total precursors accumulated: 600
20:34:05.574275 PROGRESS: Target precursors: 573 (95.50%)
20:34:05.574323 PROGRESS: Decoy precursors: 27 (4.50%)
20:34:05.574373 PROGRESS: 
20:34:05.574426 PROGRESS: Precursor Summary:
20:34:05.575477 PROGRESS: Channel   0:	 0.05 FDR:   573; 0.01 FDR:   433; 0.001 FDR:   359
20:34:05.575566 PROGRESS: 
20:34:05.575620 PROGRESS: Protein Summary:
20:34:05.576834 PROGRESS: Channel   0:	 0.05 FDR:   538; 0.01 FDR:   404; 0.001 FDR:   334
20:34:05.576924 PROGRESS: =========================================================================
20:34:05.580234 INFO: fragments_df: keeping 4422 of 23404 [sum(precursor_idx_mask)=8846 sum(mass_error_mask)=23404 stop_rank=4422
20:34:05.584903 INFO: calibration group: precursor, fitting mz estimator 
20:34:05.701567 INFO: calibration group: precursor, fitting rt estimator 
20:34:05.812081 INFO: calibration group: precursor, fitting mobility estimator 
20:34:05.928885 INFO: calibration group: fragment, fitting mz estimator 
20:34:06.472445 INFO: Using score_cutoff 34.58366428985595 (fac=0.99, q=1)
20:34:06.472853 INFO: calibration group: precursor, predicting mz
20:34:06.473979 INFO: calibration group: precursor, predicting rt
20:34:06.475334 INFO: calibration group: precursor, predicting mobility
20:34:06.476109 INFO: calibration group: fragment, predicting mz
20:34:06.478420 INFO: === checking if optimization conditions were reached ===
20:34:06.478515 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
20:34:06.480283 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 11.3657.
20:34:06.480337 INFO: ==============================================
20:34:06.480420 INFO: Starting optimization step 3.
20:34:06.480483 PROGRESS: === Extracting elution groups 0 to 600 ===
20:34:06.480545 PROGRESS: Extracting batch of 1188 precursors
20:34:06.481565 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:34:06.481611 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:34:06.481647 INFO: FWHM in RT is 2.59 seconds, sigma is 0.57
20:34:06.481670 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.42
20:34:06.482456 INFO: Starting candidate selection
20:34:06.998955 INFO: Starting candidate scoring
20:34:07.116242 INFO: Finished candidate processing
20:34:07.116371 INFO: Collecting candidate features
20:34:07.132812 INFO: Collecting fragment features
20:34:07.138259 INFO: Finished candidate scoring
20:34:07.140394 PROGRESS: === Extracted 2262 precursors and 23303 fragments ===
20:34:07.140734 INFO: performing precursor FDR with 47 features
20:34:07.140777 INFO: Decoy channel: -1
20:34:07.140805 INFO: Competetive: True
20:34:07.143884 INFO: Setting torch num_threads to 2 for FDR classification task
20:34:07.155958 INFO: Test AUC: 0.890
20:34:07.156018 INFO: Train AUC: 0.858
20:34:07.156046 INFO: AUC difference: 3.71%
20:34:07.335111 INFO: Resetting torch num_threads to 100
20:34:07.335631 INFO: === FDR correction performed with classifier version 7 ===
20:34:07.336288 PROGRESS: ============================= Precursor FDR =============================
20:34:07.336379 PROGRESS: Total precursors accumulated: 600
20:34:07.336436 PROGRESS: Target precursors: 578 (96.33%)
20:34:07.336484 PROGRESS: Decoy precursors: 22 (3.67%)
20:34:07.336529 PROGRESS: 
20:34:07.336580 PROGRESS: Precursor Summary:
20:34:07.337587 PROGRESS: Channel   0:	 0.05 FDR:   578; 0.01 FDR:   431; 0.001 FDR:   314
20:34:07.337675 PROGRESS: 
20:34:07.337729 PROGRESS: Protein Summary:
20:34:07.338927 PROGRESS: Channel   0:	 0.05 FDR:   543; 0.01 FDR:   404; 0.001 FDR:   295
20:34:07.339024 PROGRESS: =========================================================================
20:34:07.342321 INFO: fragments_df: keeping 4441 of 23303 [sum(precursor_idx_mask)=8826 sum(mass_error_mask)=23303 stop_rank=4441
20:34:07.346870 INFO: calibration group: precursor, fitting mz estimator 
20:34:07.459866 INFO: calibration group: precursor, fitting rt estimator 
20:34:07.571894 INFO: calibration group: precursor, fitting mobility estimator 
20:34:07.686346 INFO: calibration group: fragment, fitting mz estimator 
20:34:08.222452 INFO: Using score_cutoff 35.58621814727783 (fac=0.99, q=1)
20:34:08.222845 INFO: calibration group: precursor, predicting mz
20:34:08.223966 INFO: calibration group: precursor, predicting rt
20:34:08.225282 INFO: calibration group: precursor, predicting mobility
20:34:08.226035 INFO: calibration group: fragment, predicting mz
20:34:08.227992 INFO: === checking if optimization conditions were reached ===
20:34:08.228089 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
20:34:08.229755 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 9.9120.
20:34:08.229806 INFO: ==============================================
20:34:08.229887 INFO: Starting optimization step 4.
20:34:08.229949 PROGRESS: === Extracting elution groups 0 to 600 ===
20:34:08.230002 PROGRESS: Extracting batch of 1188 precursors
20:34:08.230993 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:34:08.231051 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:34:08.231091 INFO: FWHM in RT is 2.60 seconds, sigma is 0.57
20:34:08.231115 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.43
20:34:08.231814 INFO: Starting candidate selection
20:34:08.764310 INFO: Starting candidate scoring
20:34:08.901130 INFO: Finished candidate processing
20:34:08.901239 INFO: Collecting candidate features
20:34:08.909936 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2264)
20:34:08.913180 INFO: Collecting fragment features
20:34:08.917511 INFO: Finished candidate scoring
20:34:08.919003 PROGRESS: === Extracted 2264 precursors and 23273 fragments ===
20:34:08.920230 INFO: performing precursor FDR with 47 features
20:34:08.920272 INFO: Decoy channel: -1
20:34:08.920295 INFO: Competetive: True
20:34:08.922816 INFO: Setting torch num_threads to 2 for FDR classification task
20:34:08.924030 WARNING: dropped 1 decoy PSMs due to missing features
20:34:08.938505 INFO: Test AUC: 0.856
20:34:08.938589 INFO: Train AUC: 0.860
20:34:08.938618 INFO: AUC difference: 0.53%
20:34:09.119731 INFO: Resetting torch num_threads to 100
20:34:09.120302 INFO: === FDR correction performed with classifier version 7 ===
20:34:09.120946 PROGRESS: ============================= Precursor FDR =============================
20:34:09.121033 PROGRESS: Total precursors accumulated: 600
20:34:09.121090 PROGRESS: Target precursors: 578 (96.33%)
20:34:09.121139 PROGRESS: Decoy precursors: 22 (3.67%)
20:34:09.121186 PROGRESS: 
20:34:09.121233 PROGRESS: Precursor Summary:
20:34:09.122295 PROGRESS: Channel   0:	 0.05 FDR:   578; 0.01 FDR:   520; 0.001 FDR:   343
20:34:09.122387 PROGRESS: 
20:34:09.122442 PROGRESS: Protein Summary:
20:34:09.123684 PROGRESS: Channel   0:	 0.05 FDR:   543; 0.01 FDR:   486; 0.001 FDR:   322
20:34:09.123775 PROGRESS: =========================================================================
20:34:09.127289 INFO: fragments_df: keeping 4927 of 23273 [sum(precursor_idx_mask)=10654 sum(mass_error_mask)=23273 stop_rank=4927
20:34:09.131896 INFO: calibration group: precursor, fitting mz estimator 
20:34:09.268776 INFO: calibration group: precursor, fitting rt estimator 
20:34:09.410711 INFO: calibration group: precursor, fitting mobility estimator 
20:34:09.548758 INFO: calibration group: fragment, fitting mz estimator 
20:34:10.231162 INFO: Using score_cutoff 33.430014167404174 (fac=0.99, q=1)
20:34:10.231575 INFO: calibration group: precursor, predicting mz
20:34:10.232687 INFO: calibration group: precursor, predicting rt
20:34:10.234011 INFO: calibration group: precursor, predicting mobility
20:34:10.234769 INFO: calibration group: fragment, predicting mz
20:34:10.236743 INFO: === checking if optimization conditions were reached ===
20:34:10.236841 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
20:34:10.238563 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 10.2284.
20:34:10.238615 INFO: ==============================================
20:34:10.238698 INFO: Starting optimization step 5.
20:34:10.238761 PROGRESS: === Extracting elution groups 0 to 600 ===
20:34:10.238815 PROGRESS: Extracting batch of 1188 precursors
20:34:10.239773 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:34:10.239820 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:34:10.239855 INFO: FWHM in RT is 2.58 seconds, sigma is 0.57
20:34:10.239877 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.20
20:34:10.240610 INFO: Starting candidate selection
20:34:10.783865 INFO: Starting candidate scoring
20:34:10.908445 INFO: Finished candidate processing
20:34:10.908553 INFO: Collecting candidate features
20:34:10.920721 INFO: Collecting fragment features
20:34:10.925005 INFO: Finished candidate scoring
20:34:10.926571 PROGRESS: === Extracted 2259 precursors and 23243 fragments ===
20:34:10.926864 INFO: performing precursor FDR with 47 features
20:34:10.926900 INFO: Decoy channel: -1
20:34:10.926923 INFO: Competetive: True
20:34:10.929529 INFO: Setting torch num_threads to 2 for FDR classification task
20:34:10.942173 INFO: Test AUC: 0.828
20:34:10.942254 INFO: Train AUC: 0.877
20:34:10.942288 INFO: AUC difference: 5.65%
20:34:10.942312 WARNING: AUC difference > 5%. This may indicate overfitting.
20:34:11.131634 INFO: Resetting torch num_threads to 100
20:34:11.132477 INFO: === FDR correction performed with classifier version 7 ===
20:34:11.133430 PROGRESS: ============================= Precursor FDR =============================
20:34:11.133523 PROGRESS: Total precursors accumulated: 600
20:34:11.133583 PROGRESS: Target precursors: 578 (96.33%)
20:34:11.133632 PROGRESS: Decoy precursors: 22 (3.67%)
20:34:11.133678 PROGRESS: 
20:34:11.133722 PROGRESS: Precursor Summary:
20:34:11.134821 PROGRESS: Channel   0:	 0.05 FDR:   578; 0.01 FDR:   519; 0.001 FDR:   344
20:34:11.134909 PROGRESS: 
20:34:11.134964 PROGRESS: Protein Summary:
20:34:11.136224 PROGRESS: Channel   0:	 0.05 FDR:   543; 0.01 FDR:   485; 0.001 FDR:   322
20:34:11.136319 PROGRESS: =========================================================================
20:34:11.140152 INFO: fragments_df: keeping 4993 of 23243 [sum(precursor_idx_mask)=10592 sum(mass_error_mask)=23243 stop_rank=4993
20:34:11.146404 INFO: calibration group: precursor, fitting mz estimator 
20:34:11.298195 INFO: calibration group: precursor, fitting rt estimator 
20:34:11.417296 INFO: calibration group: precursor, fitting mobility estimator 
20:34:11.534320 INFO: calibration group: fragment, fitting mz estimator 
20:34:12.207455 INFO: Using score_cutoff 33.5717804649353 (fac=0.99, q=1)
20:34:12.207921 INFO: calibration group: precursor, predicting mz
20:34:12.209136 INFO: calibration group: precursor, predicting rt
20:34:12.210462 INFO: calibration group: precursor, predicting mobility
20:34:12.211240 INFO: calibration group: fragment, predicting mz
20:34:12.213733 INFO: === checking if optimization conditions were reached ===
20:34:12.213838 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
20:34:12.214952 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 9.9120 found after 6 searches.
20:34:12.215005 INFO: ==============================================
20:34:12.215104 PROGRESS: Optimization finished for rt_error.
20:34:12.219917 INFO: calibration group: precursor, predicting mz
20:34:12.220894 INFO: calibration group: precursor, predicting rt
20:34:12.222223 INFO: calibration group: precursor, predicting mobility
20:34:12.222992 INFO: calibration group: fragment, predicting mz
20:34:12.253362 INFO: Starting optimization step 0.
20:34:12.253612 PROGRESS: === Extracting elution groups 0 to 600 ===
20:34:12.253683 PROGRESS: Extracting batch of 1188 precursors
20:34:12.254862 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:34:12.254910 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:34:12.254949 INFO: FWHM in RT is 2.58 seconds, sigma is 0.57
20:34:12.254973 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.20
20:34:12.255955 INFO: Starting candidate selection
20:34:12.848640 INFO: Starting candidate scoring
20:34:13.117009 INFO: Finished candidate processing
20:34:13.117443 INFO: Collecting candidate features
20:34:13.147449 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2262)
20:34:13.154858 INFO: Collecting fragment features
20:34:13.171752 INFO: Finished candidate scoring
20:34:13.180333 PROGRESS: === Extracted 2262 precursors and 23272 fragments ===
20:34:13.181265 INFO: performing precursor FDR with 47 features
20:34:13.181334 INFO: Decoy channel: -1
20:34:13.181366 INFO: Competetive: True
20:34:13.189205 INFO: Setting torch num_threads to 2 for FDR classification task
20:34:13.192752 WARNING: dropped 1 decoy PSMs due to missing features
20:34:13.235096 INFO: Test AUC: 0.872
20:34:13.235426 INFO: Train AUC: 0.865
20:34:13.235484 INFO: AUC difference: 0.81%
20:34:13.524318 INFO: Resetting torch num_threads to 100
20:34:13.525531 INFO: === FDR correction performed with classifier version 12 ===
20:34:13.526738 PROGRESS: ============================= Precursor FDR =============================
20:34:13.526835 PROGRESS: Total precursors accumulated: 600
20:34:13.526898 PROGRESS: Target precursors: 579 (96.50%)
20:34:13.526951 PROGRESS: Decoy precursors: 21 (3.50%)
20:34:13.526997 PROGRESS: 
20:34:13.527055 PROGRESS: Precursor Summary:
20:34:13.528292 PROGRESS: Channel   0:	 0.05 FDR:   579; 0.01 FDR:   518; 0.001 FDR:   348
20:34:13.528388 PROGRESS: 
20:34:13.528464 PROGRESS: Protein Summary:
20:34:13.529863 PROGRESS: Channel   0:	 0.05 FDR:   544; 0.01 FDR:   484; 0.001 FDR:   326
20:34:13.530150 PROGRESS: =========================================================================
20:34:13.534147 INFO: fragments_df: keeping 4998 of 23272 [sum(precursor_idx_mask)=10572 sum(mass_error_mask)=23272 stop_rank=4998
20:34:13.542367 INFO: calibration group: precursor, fitting mz estimator 
20:34:13.716735 INFO: calibration group: precursor, fitting rt estimator 
20:34:13.897044 INFO: calibration group: precursor, fitting mobility estimator 
20:34:14.069002 INFO: calibration group: fragment, fitting mz estimator 
20:34:14.841887 INFO: Using score_cutoff 33.44027656517029 (fac=0.99, q=1)
20:34:14.843672 INFO: calibration group: precursor, predicting mz
20:34:14.845600 INFO: calibration group: precursor, predicting rt
20:34:14.847053 INFO: calibration group: precursor, predicting mobility
20:34:14.847851 INFO: calibration group: fragment, predicting mz
20:34:14.850417 INFO: === checking if optimization conditions were reached ===
20:34:14.850544 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
20:34:14.852259 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0582.
20:34:14.852316 INFO: ==============================================
20:34:14.852411 INFO: Starting optimization step 1.
20:34:14.852480 PROGRESS: === Extracting elution groups 0 to 600 ===
20:34:14.852546 PROGRESS: Extracting batch of 1188 precursors
20:34:14.854345 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:34:14.854396 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:34:14.854436 INFO: FWHM in RT is 2.58 seconds, sigma is 0.57
20:34:14.854460 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.20
20:34:14.855673 INFO: Starting candidate selection
20:34:15.409098 INFO: Starting candidate scoring
20:34:15.543850 INFO: Finished candidate processing
20:34:15.543982 INFO: Collecting candidate features
20:34:15.554967 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2260)
20:34:15.558236 INFO: Collecting fragment features
20:34:15.564444 INFO: Finished candidate scoring
20:34:15.566209 PROGRESS: === Extracted 2260 precursors and 22986 fragments ===
20:34:15.566531 INFO: performing precursor FDR with 47 features
20:34:15.566569 INFO: Decoy channel: -1
20:34:15.566592 INFO: Competetive: True
20:34:15.569713 INFO: Setting torch num_threads to 2 for FDR classification task
20:34:15.571054 WARNING: dropped 1 decoy PSMs due to missing features
20:34:15.584356 INFO: Test AUC: 0.847
20:34:15.584452 INFO: Train AUC: 0.868
20:34:15.584482 INFO: AUC difference: 2.45%
20:34:15.774883 INFO: Resetting torch num_threads to 100
20:34:15.775728 INFO: === FDR correction performed with classifier version 12 ===
20:34:15.776626 PROGRESS: ============================= Precursor FDR =============================
20:34:15.776721 PROGRESS: Total precursors accumulated: 599
20:34:15.776782 PROGRESS: Target precursors: 578 (96.49%)
20:34:15.776832 PROGRESS: Decoy precursors: 21 (3.51%)
20:34:15.776878 PROGRESS: 
20:34:15.776921 PROGRESS: Precursor Summary:
20:34:15.777967 PROGRESS: Channel   0:	 0.05 FDR:   578; 0.01 FDR:   518; 0.001 FDR:   347
20:34:15.778057 PROGRESS: 
20:34:15.778114 PROGRESS: Protein Summary:
20:34:15.779386 PROGRESS: Channel   0:	 0.05 FDR:   543; 0.01 FDR:   484; 0.001 FDR:   324
20:34:15.779479 PROGRESS: =========================================================================
20:34:15.783050 INFO: fragments_df: keeping 4925 of 22986 [sum(precursor_idx_mask)=10563 sum(mass_error_mask)=22986 stop_rank=4925
20:34:15.788818 INFO: calibration group: precursor, fitting mz estimator 
20:34:16.035198 INFO: calibration group: precursor, fitting rt estimator 
20:34:16.191849 INFO: calibration group: precursor, fitting mobility estimator 
20:34:16.331395 INFO: calibration group: fragment, fitting mz estimator 
20:34:17.109988 INFO: Using score_cutoff 33.11095133399963 (fac=0.99, q=1)
20:34:17.110489 INFO: calibration group: precursor, predicting mz
20:34:17.111836 INFO: calibration group: precursor, predicting rt
20:34:17.113187 INFO: calibration group: precursor, predicting mobility
20:34:17.113979 INFO: calibration group: fragment, predicting mz
20:34:17.116536 INFO: === checking if optimization conditions were reached ===
20:34:17.116649 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
20:34:17.118222 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0527.
20:34:17.118276 INFO: ==============================================
20:34:17.118360 INFO: Starting optimization step 2.
20:34:17.118428 PROGRESS: === Extracting elution groups 0 to 600 ===
20:34:17.118486 PROGRESS: Extracting batch of 1188 precursors
20:34:17.121048 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:34:17.121099 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:34:17.121136 INFO: FWHM in RT is 2.56 seconds, sigma is 0.56
20:34:17.121160 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.12
20:34:17.133117 INFO: Starting candidate selection
20:34:17.737090 INFO: Starting candidate scoring
20:34:17.874895 INFO: Finished candidate processing
20:34:17.879654 INFO: Collecting candidate features
20:34:17.891697 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2250)
20:34:17.895866 INFO: Collecting fragment features
20:34:17.901396 INFO: Finished candidate scoring
20:34:17.903581 PROGRESS: === Extracted 2250 precursors and 22840 fragments ===
20:34:17.903918 INFO: performing precursor FDR with 47 features
20:34:17.903964 INFO: Decoy channel: -1
20:34:17.903991 INFO: Competetive: True
20:34:17.907554 INFO: Setting torch num_threads to 2 for FDR classification task
20:34:17.909163 WARNING: dropped 1 decoy PSMs due to missing features
20:34:17.922758 INFO: Test AUC: 0.895
20:34:17.922838 INFO: Train AUC: 0.864
20:34:17.922876 INFO: AUC difference: 3.63%
20:34:18.107521 INFO: Resetting torch num_threads to 100
20:34:18.108139 INFO: === FDR correction performed with classifier version 12 ===
20:34:18.108818 PROGRESS: ============================= Precursor FDR =============================
20:34:18.108924 PROGRESS: Total precursors accumulated: 599
20:34:18.108999 PROGRESS: Target precursors: 578 (96.49%)
20:34:18.109065 PROGRESS: Decoy precursors: 21 (3.51%)
20:34:18.109127 PROGRESS: 
20:34:18.109189 PROGRESS: Precursor Summary:
20:34:18.110247 PROGRESS: Channel   0:	 0.05 FDR:   578; 0.01 FDR:   514; 0.001 FDR:   331
20:34:18.110344 PROGRESS: 
20:34:18.110411 PROGRESS: Protein Summary:
20:34:18.111688 PROGRESS: Channel   0:	 0.05 FDR:   543; 0.01 FDR:   480; 0.001 FDR:   308
20:34:18.111789 PROGRESS: =========================================================================
20:34:18.115254 INFO: fragments_df: keeping 4954 of 22840 [sum(precursor_idx_mask)=10449 sum(mass_error_mask)=22840 stop_rank=4954
20:34:18.121118 INFO: calibration group: precursor, fitting mz estimator 
20:34:18.246748 INFO: calibration group: precursor, fitting rt estimator 
20:34:18.370150 INFO: calibration group: precursor, fitting mobility estimator 
20:34:18.483881 INFO: calibration group: fragment, fitting mz estimator 
20:34:19.154051 INFO: Using score_cutoff 33.75215443611145 (fac=0.99, q=1)
20:34:19.154442 INFO: calibration group: precursor, predicting mz
20:34:19.155534 INFO: calibration group: precursor, predicting rt
20:34:19.156846 INFO: calibration group: precursor, predicting mobility
20:34:19.157601 INFO: calibration group: fragment, predicting mz
20:34:19.159674 INFO: === checking if optimization conditions were reached ===
20:34:19.159770 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
20:34:19.160494 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.0582 found after 3 searches.
20:34:19.160541 INFO: ==============================================
20:34:19.160622 PROGRESS: Optimization finished for mobility_error.
20:34:19.165343 INFO: calibration group: precursor, predicting mz
20:34:19.166153 INFO: calibration group: precursor, predicting rt
20:34:19.167445 INFO: calibration group: precursor, predicting mobility
20:34:19.168200 INFO: calibration group: fragment, predicting mz
20:34:19.193568 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
20:34:19.193694 PROGRESS: ==============================================
20:34:19.193779 PROGRESS: ms2_error      : 10.0474
20:34:19.193849 PROGRESS: ms1_error      : 10.5658
20:34:19.193906 PROGRESS: rt_error       : 9.9120
20:34:19.193955 PROGRESS: mobility_error : 0.0582
20:34:19.193999 PROGRESS: ==============================================
20:34:19.194676 INFO: calibration group: precursor, predicting mz
20:34:19.247963 INFO: calibration group: precursor, predicting rt
20:34:19.363081 INFO: calibration group: precursor, predicting mobility
20:34:19.389484 INFO: calibration group: fragment, predicting mz
20:34:19.629572 PROGRESS: Extracting batch of 189636 precursors
20:34:19.704608 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:34:19.704747 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:34:19.704796 INFO: FWHM in RT is 2.56 seconds, sigma is 0.56
20:34:19.704819 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.12
20:34:19.705674 INFO: Starting candidate selection
20:35:00.852300 INFO: Applying score cutoff of 33.11095133399963
20:35:00.858471 INFO: Removed 91131 precursors with score below cutoff
20:35:01.183636 INFO: Starting candidate scoring
20:35:08.188268 INFO: Finished candidate processing
20:35:08.188851 INFO: Collecting candidate features
20:35:08.716911 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 268736)
20:35:08.730419 INFO: Collecting fragment features
20:35:08.903264 INFO: Finished candidate scoring
20:35:09.038659 INFO: === FDR correction performed with classifier version 15 ===
20:35:09.039580 INFO: performing precursor FDR with 47 features
20:35:09.039636 INFO: Decoy channel: -1
20:35:09.039663 INFO: Competetive: True
20:35:09.126495 INFO: Setting torch num_threads to 2 for FDR classification task
20:35:09.167759 WARNING: dropped 1 decoy PSMs due to missing features
20:35:09.167940 WARNING: FDR calculation for 163245 target and 105490 decoy PSMs
20:35:09.167968 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
20:35:14.196678 INFO: Test AUC: 0.917
20:35:14.196833 INFO: Train AUC: 0.919
20:35:14.196865 INFO: AUC difference: 0.18%
20:35:14.435041 INFO: Resetting torch num_threads to 100
20:35:14.459679 INFO: Removing fragments below FDR threshold
20:35:14.519869 PROGRESS: ============================= Precursor FDR =============================
20:35:14.520182 PROGRESS: Total precursors accumulated: 91,201
20:35:14.520250 PROGRESS: Target precursors: 90,299 (99.01%)
20:35:14.520302 PROGRESS: Decoy precursors: 902 (0.99%)
20:35:14.520347 PROGRESS: 
20:35:14.520392 PROGRESS: Precursor Summary:
20:35:14.571813 PROGRESS: Channel   0:	 0.05 FDR: 90,299; 0.01 FDR: 90,299; 0.001 FDR: 84,736
20:35:14.572122 PROGRESS: 
20:35:14.572187 PROGRESS: Protein Summary:
20:35:14.648626 PROGRESS: Channel   0:	 0.05 FDR: 9,647; 0.01 FDR: 9,647; 0.001 FDR: 9,584
20:35:14.648924 PROGRESS: =========================================================================
20:35:15.353234 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
20:35:15.402648 PROGRESS: Loading raw file 2/6: ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
20:35:15.402833 INFO: Quantification results path: run_output/alphadia_1.10.4_Again_good_now/quant
20:35:15.402915 INFO: Creating folder run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/figures
20:35:15.403659 INFO: Initializing RawFileManager
20:35:15.403796 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
20:35:15.403860 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
20:35:15.403905 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
20:35:15.615850 INFO: Reading 39,128 frames with 2,860,596,893 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
20:35:21.668600 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d...
20:35:21.671729 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
20:35:21.678241 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
20:35:21.678616 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
20:35:21.679121 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
20:35:21.680959 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
20:35:21.696166 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
20:35:21.696510 INFO: Indexing quadrupole dimension
20:35:22.229160 INFO: Transposing detector events
20:35:30.705034 INFO: Finished transposing data
20:35:30.744840 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
20:35:30.746510 INFO: RT (min)            : 0.0 - 70.0
20:35:30.746606 INFO: RT duration (sec)   : 4199.8
20:35:30.746644 INFO: RT duration (min)   : 70.0
20:35:30.746676 INFO: Cycle len (scans)   : 9
20:35:30.746706 INFO: Cycle len (sec)     : 0.97
20:35:30.746733 INFO: Number of cycles    : 4347
20:35:30.746763 INFO: MS2 range (m/z)     : 400.0 - 1000.0
20:35:30.803183 INFO: Initializing CalibrationManager
20:35:30.803549 INFO: Loading calibration config
20:35:30.804295 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed'], 'function': LOESSRegression()}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed'], 'function': LOESSRegression(n_kernels=2)}], 'name': 'precursor'}]
20:35:30.804407 INFO: Calibration group :fragment, found 1 estimator(s)
20:35:30.804506 INFO: Calibration group :precursor, found 3 estimator(s)
20:35:30.804687 INFO: Initializing OptimizationManager
20:35:30.804797 INFO: initial parameter: ms1_error = 30
20:35:30.804847 INFO: initial parameter: ms2_error = 30
20:35:30.804905 INFO: initial parameter: rt_error = 2099.894844
20:35:30.804957 INFO: initial parameter: mobility_error = 0.1
20:35:30.805000 INFO: initial parameter: column_type = library
20:35:30.805038 INFO: initial parameter: num_candidates = 1
20:35:30.805076 INFO: initial parameter: classifier_version = -1
20:35:30.805119 INFO: initial parameter: fwhm_rt = 5
20:35:30.805161 INFO: initial parameter: fwhm_mobility = 0.01
20:35:30.805201 INFO: initial parameter: score_cutoff = 0
20:35:30.805274 INFO: Initializing TimingManager
20:35:30.805357 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
20:35:30.805513 INFO: FDRManager not loaded from disk.
20:35:30.805539 INFO: Initializing FDRManager
20:35:30.805583 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
20:35:30.842983 PROGRESS: 95,522 target precursors potentially observable (0 removed)
20:35:30.899168 PROGRESS: Starting initial search for precursors.
20:35:30.906830 INFO: Starting optimization step 0.
20:35:30.907007 PROGRESS: === Extracting elution groups 0 to 200 ===
20:35:30.907091 PROGRESS: Extracting batch of 395 precursors
20:35:30.908193 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:35:30.908244 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:35:30.908278 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:35:30.908299 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:35:30.909235 INFO: Starting candidate selection
20:36:01.037109 INFO: Starting candidate scoring
20:36:01.104198 INFO: Finished candidate processing
20:36:01.104310 INFO: Collecting candidate features
20:36:01.113921 INFO: Collecting fragment features
20:36:01.116297 INFO: Finished candidate scoring
20:36:01.117069 PROGRESS: === Extracted 394 precursors and 4349 fragments ===
20:36:01.117361 INFO: performing precursor FDR with 47 features
20:36:01.117399 INFO: Decoy channel: -1
20:36:01.117422 INFO: Competetive: True
20:36:01.118406 INFO: Setting torch num_threads to 2 for FDR classification task
20:36:01.129091 INFO: Test AUC: 0.480
20:36:01.129154 INFO: Train AUC: 0.439
20:36:01.129184 INFO: AUC difference: 9.34%
20:36:01.129205 WARNING: AUC difference > 5%. This may indicate overfitting.
20:36:01.306416 INFO: Resetting torch num_threads to 100
20:36:01.307009 INFO: === FDR correction performed with classifier version -1 ===
20:36:01.307677 PROGRESS: ============================= Precursor FDR =============================
20:36:01.307770 PROGRESS: Total precursors accumulated: 200
20:36:01.307830 PROGRESS: Target precursors: 93 (46.50%)
20:36:01.307881 PROGRESS: Decoy precursors: 107 (53.50%)
20:36:01.307939 PROGRESS: 
20:36:01.307988 PROGRESS: Precursor Summary:
20:36:01.308839 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
20:36:01.308928 PROGRESS: 
20:36:01.308985 PROGRESS: Protein Summary:
20:36:01.309910 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
20:36:01.310003 PROGRESS: =========================================================================
20:36:01.313559 INFO: Starting optimization step 1.
20:36:01.313664 PROGRESS: === Extracting elution groups 200 to 600 ===
20:36:01.313730 PROGRESS: Extracting batch of 793 precursors
20:36:01.314490 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:36:01.314538 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:36:01.314566 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:36:01.314590 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:36:01.315409 INFO: Starting candidate selection
20:36:06.700636 INFO: Starting candidate scoring
20:36:06.820221 INFO: Finished candidate processing
20:36:06.820333 INFO: Collecting candidate features
20:36:06.830207 INFO: Collecting fragment features
20:36:06.833028 INFO: Finished candidate scoring
20:36:06.834951 PROGRESS: === Extracted 1187 precursors and 13151 fragments ===
20:36:06.835718 INFO: performing precursor FDR with 47 features
20:36:06.835762 INFO: Decoy channel: -1
20:36:06.835786 INFO: Competetive: True
20:36:06.838430 INFO: Setting torch num_threads to 2 for FDR classification task
20:36:06.848763 INFO: Test AUC: 0.467
20:36:06.848825 INFO: Train AUC: 0.427
20:36:06.848856 INFO: AUC difference: 9.41%
20:36:06.848879 WARNING: AUC difference > 5%. This may indicate overfitting.
20:36:07.029297 INFO: Resetting torch num_threads to 100
20:36:07.029932 INFO: === FDR correction performed with classifier version -1 ===
20:36:07.030602 PROGRESS: ============================= Precursor FDR =============================
20:36:07.030694 PROGRESS: Total precursors accumulated: 600
20:36:07.030755 PROGRESS: Target precursors: 275 (45.83%)
20:36:07.030806 PROGRESS: Decoy precursors: 325 (54.17%)
20:36:07.030853 PROGRESS: 
20:36:07.030896 PROGRESS: Precursor Summary:
20:36:07.031739 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:36:07.031831 PROGRESS: 
20:36:07.031887 PROGRESS: Protein Summary:
20:36:07.032777 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:36:07.032865 PROGRESS: =========================================================================
20:36:07.037312 INFO: Starting optimization step 2.
20:36:07.037606 PROGRESS: === Extracting elution groups 600 to 1400 ===
20:36:07.037673 PROGRESS: Extracting batch of 1583 precursors
20:36:07.038589 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:36:07.038638 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:36:07.038666 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:36:07.038688 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:36:07.039452 INFO: Starting candidate selection
20:36:17.307616 INFO: Starting candidate scoring
20:36:17.470762 INFO: Finished candidate processing
20:36:17.470885 INFO: Collecting candidate features
20:36:17.483669 INFO: Collecting fragment features
20:36:17.487619 INFO: Finished candidate scoring
20:36:17.490348 PROGRESS: === Extracted 2770 precursors and 30827 fragments ===
20:36:17.491328 INFO: performing precursor FDR with 47 features
20:36:17.491373 INFO: Decoy channel: -1
20:36:17.491397 INFO: Competetive: True
20:36:17.494593 INFO: Setting torch num_threads to 2 for FDR classification task
20:36:17.510066 INFO: Test AUC: 0.454
20:36:17.510137 INFO: Train AUC: 0.428
20:36:17.510166 INFO: AUC difference: 6.17%
20:36:17.510187 WARNING: AUC difference > 5%. This may indicate overfitting.
20:36:17.685429 INFO: Resetting torch num_threads to 100
20:36:17.686212 INFO: === FDR correction performed with classifier version -1 ===
20:36:17.687010 PROGRESS: ============================= Precursor FDR =============================
20:36:17.687112 PROGRESS: Total precursors accumulated: 1,400
20:36:17.687180 PROGRESS: Target precursors: 627 (44.79%)
20:36:17.687235 PROGRESS: Decoy precursors: 773 (55.21%)
20:36:17.687282 PROGRESS: 
20:36:17.687328 PROGRESS: Precursor Summary:
20:36:17.688181 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:36:17.688267 PROGRESS: 
20:36:17.688322 PROGRESS: Protein Summary:
20:36:17.689212 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:36:17.689299 PROGRESS: =========================================================================
20:36:17.695832 INFO: Starting optimization step 3.
20:36:17.695943 PROGRESS: === Extracting elution groups 1400 to 3000 ===
20:36:17.696005 PROGRESS: Extracting batch of 3171 precursors
20:36:17.697133 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:36:17.697182 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:36:17.697210 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:36:17.697232 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:36:17.698028 INFO: Starting candidate selection
20:37:01.034924 INFO: Starting candidate scoring
20:37:01.348286 INFO: Finished candidate processing
20:37:01.348409 INFO: Collecting candidate features
20:37:01.364391 INFO: Collecting fragment features
20:37:01.369913 INFO: Finished candidate scoring
20:37:01.375480 PROGRESS: === Extracted 5940 precursors and 65994 fragments ===
20:37:01.376771 INFO: performing precursor FDR with 47 features
20:37:01.376819 INFO: Decoy channel: -1
20:37:01.376845 INFO: Competetive: True
20:37:01.381299 INFO: Setting torch num_threads to 2 for FDR classification task
20:37:01.407301 INFO: Test AUC: 0.449
20:37:01.407433 INFO: Train AUC: 0.437
20:37:01.407463 INFO: AUC difference: 2.85%
20:37:01.586438 INFO: Resetting torch num_threads to 100
20:37:01.587391 INFO: === FDR correction performed with classifier version -1 ===
20:37:01.588412 PROGRESS: ============================= Precursor FDR =============================
20:37:01.588508 PROGRESS: Total precursors accumulated: 3,000
20:37:01.588570 PROGRESS: Target precursors: 1,349 (44.97%)
20:37:01.588621 PROGRESS: Decoy precursors: 1,651 (55.03%)
20:37:01.588670 PROGRESS: 
20:37:01.588714 PROGRESS: Precursor Summary:
20:37:01.589579 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:37:01.589672 PROGRESS: 
20:37:01.589729 PROGRESS: Protein Summary:
20:37:01.590644 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:37:01.590732 PROGRESS: =========================================================================
20:37:01.601815 INFO: Starting optimization step 4.
20:37:01.601958 PROGRESS: === Extracting elution groups 3000 to 6200 ===
20:37:01.602025 PROGRESS: Extracting batch of 6347 precursors
20:37:01.604311 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:37:01.604362 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:37:01.604390 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:37:01.604412 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:37:01.605179 INFO: Starting candidate selection
20:38:01.106858 INFO: Starting candidate scoring
20:38:01.724597 INFO: Finished candidate processing
20:38:01.724779 INFO: Collecting candidate features
20:38:01.759383 INFO: Collecting fragment features
20:38:01.772378 INFO: Finished candidate scoring
20:38:01.796492 PROGRESS: === Extracted 12287 precursors and 136577 fragments ===
20:38:01.802882 INFO: performing precursor FDR with 47 features
20:38:01.802981 INFO: Decoy channel: -1
20:38:01.803014 INFO: Competetive: True
20:38:01.813353 INFO: Setting torch num_threads to 2 for FDR classification task
20:38:01.976387 INFO: Test AUC: 0.433
20:38:01.976839 INFO: Train AUC: 0.442
20:38:01.976909 INFO: AUC difference: 2.12%
20:38:02.183646 INFO: Resetting torch num_threads to 100
20:38:02.185160 INFO: === FDR correction performed with classifier version -1 ===
20:38:02.187298 PROGRESS: ============================= Precursor FDR =============================
20:38:02.187667 PROGRESS: Total precursors accumulated: 6,200
20:38:02.187735 PROGRESS: Target precursors: 2,747 (44.31%)
20:38:02.187788 PROGRESS: Decoy precursors: 3,453 (55.69%)
20:38:02.187840 PROGRESS: 
20:38:02.187890 PROGRESS: Precursor Summary:
20:38:02.188797 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:38:02.188886 PROGRESS: 
20:38:02.188941 PROGRESS: Protein Summary:
20:38:02.189880 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:38:02.189978 PROGRESS: =========================================================================
20:38:02.227494 INFO: Starting optimization step 5.
20:38:02.227814 PROGRESS: === Extracting elution groups 6200 to 12600 ===
20:38:02.227911 PROGRESS: Extracting batch of 12697 precursors
20:38:02.232568 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:38:02.232636 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:38:02.232675 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:38:02.232699 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:38:02.233679 INFO: Starting candidate selection
20:39:23.880795 INFO: Starting candidate scoring
20:39:25.519865 INFO: Finished candidate processing
20:39:25.520069 INFO: Collecting candidate features
20:39:25.594049 INFO: Collecting fragment features
20:39:25.627377 INFO: Finished candidate scoring
20:39:25.672997 PROGRESS: === Extracted 24983 precursors and 277757 fragments ===
20:39:25.680630 INFO: performing precursor FDR with 47 features
20:39:25.680768 INFO: Decoy channel: -1
20:39:25.680795 INFO: Competetive: True
20:39:25.701381 INFO: Setting torch num_threads to 2 for FDR classification task
20:39:26.084883 INFO: Test AUC: 0.805
20:39:26.085030 INFO: Train AUC: 0.811
20:39:26.085061 INFO: AUC difference: 0.74%
20:39:26.297124 INFO: Resetting torch num_threads to 100
20:39:26.301112 INFO: === FDR correction performed with classifier version -1 ===
20:39:26.306153 PROGRESS: ============================= Precursor FDR =============================
20:39:26.306342 PROGRESS: Total precursors accumulated: 12,600
20:39:26.306409 PROGRESS: Target precursors: 10,287 (81.64%)
20:39:26.306465 PROGRESS: Decoy precursors: 2,313 (18.36%)
20:39:26.306513 PROGRESS: 
20:39:26.306557 PROGRESS: Precursor Summary:
20:39:26.310081 PROGRESS: Channel   0:	 0.05 FDR: 7,162; 0.01 FDR: 5,153; 0.001 FDR: 2,282
20:39:26.310223 PROGRESS: 
20:39:26.310281 PROGRESS: Protein Summary:
20:39:26.314444 PROGRESS: Channel   0:	 0.05 FDR: 3,747; 0.01 FDR: 2,879; 0.001 FDR: 1,528
20:39:26.314606 PROGRESS: =========================================================================
20:39:26.356322 INFO: fragments_df: keeping 5000 of 277757 [sum(precursor_idx_mask)=57530 sum(mass_error_mask)=277757 stop_rank=5000
20:39:26.383727 INFO: calibration group: precursor, fitting mz estimator 
20:39:27.110488 INFO: calibration group: precursor, fitting rt estimator 
20:39:27.971898 INFO: calibration group: precursor, fitting mobility estimator 
20:39:28.747833 INFO: calibration group: fragment, fitting mz estimator 
20:39:29.454069 INFO: Using score_cutoff 51.54294149780274 (fac=0.99, q=1)
20:39:29.455407 INFO: calibration group: precursor, predicting mz
20:39:29.457644 INFO: calibration group: precursor, predicting rt
20:39:29.459086 INFO: calibration group: precursor, predicting mobility
20:39:29.459907 INFO: calibration group: fragment, predicting mz
20:39:29.462790 PROGRESS: Required number of precursors found. Starting search parameter optimization.
20:39:29.463003 INFO: Starting optimization step 6.
20:39:29.463120 PROGRESS: === Extracting elution groups 0 to 600 ===
20:39:29.463230 PROGRESS: Extracting batch of 1188 precursors
20:39:29.472650 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:39:29.472718 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:39:29.472792 INFO: FWHM in RT is 3.36 seconds, sigma is 0.74
20:39:29.472824 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.20
20:39:29.478482 INFO: Starting candidate selection
20:39:38.552921 INFO: Starting candidate scoring
20:39:38.799131 INFO: Finished candidate processing
20:39:38.799314 INFO: Collecting candidate features
20:39:38.831442 INFO: Collecting fragment features
20:39:38.841475 INFO: Finished candidate scoring
20:39:38.843710 PROGRESS: === Extracted 2268 precursors and 25121 fragments ===
20:39:38.844268 INFO: performing precursor FDR with 47 features
20:39:38.844328 INFO: Decoy channel: -1
20:39:38.844372 INFO: Competetive: True
20:39:38.850207 INFO: Setting torch num_threads to 2 for FDR classification task
20:39:38.870696 INFO: Test AUC: 0.734
20:39:38.870808 INFO: Train AUC: 0.721
20:39:38.870837 INFO: AUC difference: 1.86%
20:39:39.062749 INFO: Resetting torch num_threads to 100
20:39:39.063437 INFO: === FDR correction performed with classifier version 5 ===
20:39:39.064132 PROGRESS: ============================= Precursor FDR =============================
20:39:39.064223 PROGRESS: Total precursors accumulated: 600
20:39:39.064289 PROGRESS: Target precursors: 497 (82.83%)
20:39:39.064341 PROGRESS: Decoy precursors: 103 (17.17%)
20:39:39.064388 PROGRESS: 
20:39:39.064432 PROGRESS: Precursor Summary:
20:39:39.065421 PROGRESS: Channel   0:	 0.05 FDR:   351; 0.01 FDR:   250; 0.001 FDR:   186
20:39:39.065513 PROGRESS: 
20:39:39.065569 PROGRESS: Protein Summary:
20:39:39.066732 PROGRESS: Channel   0:	 0.05 FDR:   327; 0.01 FDR:   236; 0.001 FDR:   179
20:39:39.066828 PROGRESS: =========================================================================
20:39:39.078405 INFO: fragments_df: keeping 2864 of 25121 [sum(precursor_idx_mask)=5076 sum(mass_error_mask)=25121 stop_rank=2864
20:39:39.084724 INFO: calibration group: precursor, fitting mz estimator 
20:39:39.207694 INFO: calibration group: precursor, fitting rt estimator 
20:39:39.328799 INFO: calibration group: precursor, fitting mobility estimator 
20:39:39.455274 INFO: calibration group: fragment, fitting mz estimator 
20:39:39.856643 INFO: Using score_cutoff 53.03313901290893 (fac=0.99, q=1)
20:39:39.857078 INFO: calibration group: precursor, predicting mz
20:39:39.858271 INFO: calibration group: precursor, predicting rt
20:39:39.859624 INFO: calibration group: precursor, predicting mobility
20:39:39.860401 INFO: calibration group: fragment, predicting mz
20:39:39.862437 INFO: === checking if optimization conditions were reached ===
20:39:39.863797 PROGRESS: ❌ ms2_error      : 10.0474 > 10.0474 or insufficient steps taken.
20:39:39.864710 PROGRESS: ❌ ms1_error      : 10.5658 > 10.5658 or insufficient steps taken.
20:39:39.864759 INFO: ==============================================
20:39:39.864848 INFO: Starting optimization step 7.
20:39:39.864914 PROGRESS: === Extracting elution groups 0 to 600 ===
20:39:39.864971 PROGRESS: Extracting batch of 1188 precursors
20:39:39.866114 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:39:39.866162 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:39:39.866202 INFO: FWHM in RT is 3.33 seconds, sigma is 0.73
20:39:39.866225 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.11
20:39:39.867050 INFO: Starting candidate selection
20:39:47.664083 INFO: Starting candidate scoring
20:39:47.776168 INFO: Finished candidate processing
20:39:47.776281 INFO: Collecting candidate features
20:39:47.788165 INFO: Collecting fragment features
20:39:47.792871 INFO: Finished candidate scoring
20:39:47.794375 PROGRESS: === Extracted 2284 precursors and 24600 fragments ===
20:39:47.794677 INFO: performing precursor FDR with 47 features
20:39:47.794714 INFO: Decoy channel: -1
20:39:47.794736 INFO: Competetive: True
20:39:47.797342 INFO: Setting torch num_threads to 2 for FDR classification task
20:39:47.810858 INFO: Test AUC: 0.787
20:39:47.810918 INFO: Train AUC: 0.769
20:39:47.810948 INFO: AUC difference: 2.31%
20:39:47.990887 INFO: Resetting torch num_threads to 100
20:39:47.991542 INFO: === FDR correction performed with classifier version 6 ===
20:39:47.992213 PROGRESS: ============================= Precursor FDR =============================
20:39:47.992305 PROGRESS: Total precursors accumulated: 600
20:39:47.992373 PROGRESS: Target precursors: 547 (91.17%)
20:39:47.992427 PROGRESS: Decoy precursors: 53 (8.83%)
20:39:47.992473 PROGRESS: 
20:39:47.992518 PROGRESS: Precursor Summary:
20:39:47.993537 PROGRESS: Channel   0:	 0.05 FDR:   507; 0.01 FDR:   402; 0.001 FDR:   273
20:39:47.993627 PROGRESS: 
20:39:47.993683 PROGRESS: Protein Summary:
20:39:47.994891 PROGRESS: Channel   0:	 0.05 FDR:   475; 0.01 FDR:   375; 0.001 FDR:   258
20:39:47.994992 PROGRESS: =========================================================================
20:39:47.998351 INFO: fragments_df: keeping 3980 of 24600 [sum(precursor_idx_mask)=8343 sum(mass_error_mask)=24600 stop_rank=3980
20:39:48.003530 INFO: calibration group: precursor, fitting mz estimator 
20:39:48.131282 INFO: calibration group: precursor, fitting rt estimator 
20:39:48.259798 INFO: calibration group: precursor, fitting mobility estimator 
20:39:48.391590 INFO: calibration group: fragment, fitting mz estimator 
20:39:48.938156 INFO: Using score_cutoff 42.37556532783508 (fac=0.99, q=1)
20:39:48.938575 INFO: calibration group: precursor, predicting mz
20:39:48.939757 INFO: calibration group: precursor, predicting rt
20:39:48.941085 INFO: calibration group: precursor, predicting mobility
20:39:48.941861 INFO: calibration group: fragment, predicting mz
20:39:48.943846 INFO: === checking if optimization conditions were reached ===
20:39:48.945350 PROGRESS: ✅ ms2_error      : 10.0474 <= 10.0474
20:39:48.946284 PROGRESS: ✅ ms1_error      : 10.5658 <= 10.5658
20:39:48.946337 INFO: ==============================================
20:39:48.946426 PROGRESS: Optimization finished for ms2_error, ms1_error.
20:39:48.951473 INFO: calibration group: precursor, predicting mz
20:39:48.952299 INFO: calibration group: precursor, predicting rt
20:39:48.953597 INFO: calibration group: precursor, predicting mobility
20:39:48.954365 INFO: calibration group: fragment, predicting mz
20:39:48.956314 INFO: Starting optimization step 0.
20:39:48.956414 PROGRESS: === Extracting elution groups 0 to 600 ===
20:39:48.956485 PROGRESS: Extracting batch of 1188 precursors
20:39:48.957584 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:39:48.957631 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:39:48.957668 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
20:39:48.957691 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.56
20:39:48.958486 INFO: Starting candidate selection
20:40:01.050233 INFO: Starting candidate scoring
20:40:01.182944 INFO: Finished candidate processing
20:40:01.183064 INFO: Collecting candidate features
20:40:01.195380 INFO: Collecting fragment features
20:40:01.200305 INFO: Finished candidate scoring
20:40:01.201806 PROGRESS: === Extracted 2266 precursors and 24354 fragments ===
20:40:01.202102 INFO: performing precursor FDR with 47 features
20:40:01.202139 INFO: Decoy channel: -1
20:40:01.202162 INFO: Competetive: True
20:40:01.204717 INFO: Setting torch num_threads to 2 for FDR classification task
20:40:01.217139 INFO: Test AUC: 0.818
20:40:01.217203 INFO: Train AUC: 0.781
20:40:01.217233 INFO: AUC difference: 4.72%
20:40:01.398167 INFO: Resetting torch num_threads to 100
20:40:01.398798 INFO: === FDR correction performed with classifier version 7 ===
20:40:01.399462 PROGRESS: ============================= Precursor FDR =============================
20:40:01.399558 PROGRESS: Total precursors accumulated: 600
20:40:01.399614 PROGRESS: Target precursors: 548 (91.33%)
20:40:01.399664 PROGRESS: Decoy precursors: 52 (8.67%)
20:40:01.399709 PROGRESS: 
20:40:01.399751 PROGRESS: Precursor Summary:
20:40:01.400770 PROGRESS: Channel   0:	 0.05 FDR:   512; 0.01 FDR:   374; 0.001 FDR:   267
20:40:01.400861 PROGRESS: 
20:40:01.400917 PROGRESS: Protein Summary:
20:40:01.402112 PROGRESS: Channel   0:	 0.05 FDR:   481; 0.01 FDR:   351; 0.001 FDR:   253
20:40:01.402205 PROGRESS: =========================================================================
20:40:01.405593 INFO: fragments_df: keeping 3909 of 24354 [sum(precursor_idx_mask)=7806 sum(mass_error_mask)=24354 stop_rank=3909
20:40:01.411137 INFO: calibration group: precursor, fitting mz estimator 
20:40:01.514420 INFO: calibration group: precursor, fitting rt estimator 
20:40:01.619658 INFO: calibration group: precursor, fitting mobility estimator 
20:40:01.733041 INFO: calibration group: fragment, fitting mz estimator 
20:40:02.194917 INFO: Using score_cutoff 43.71106593933105 (fac=0.99, q=1)
20:40:02.195349 INFO: calibration group: precursor, predicting mz
20:40:02.196534 INFO: calibration group: precursor, predicting rt
20:40:02.197879 INFO: calibration group: precursor, predicting mobility
20:40:02.198668 INFO: calibration group: fragment, predicting mz
20:40:02.200785 INFO: === checking if optimization conditions were reached ===
20:40:02.200904 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
20:40:02.202441 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 10.1540.
20:40:02.202494 INFO: ==============================================
20:40:02.202583 INFO: Starting optimization step 1.
20:40:02.202651 PROGRESS: === Extracting elution groups 0 to 600 ===
20:40:02.202708 PROGRESS: Extracting batch of 1188 precursors
20:40:02.203775 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:40:02.203826 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:40:02.203863 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
20:40:02.203885 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.53
20:40:02.204633 INFO: Starting candidate selection
20:40:02.719557 INFO: Starting candidate scoring
20:40:02.840777 INFO: Finished candidate processing
20:40:02.840882 INFO: Collecting candidate features
20:40:02.853077 INFO: Collecting fragment features
20:40:02.858512 INFO: Finished candidate scoring
20:40:02.860019 PROGRESS: === Extracted 2262 precursors and 23254 fragments ===
20:40:02.860317 INFO: performing precursor FDR with 47 features
20:40:02.860356 INFO: Decoy channel: -1
20:40:02.860379 INFO: Competetive: True
20:40:02.862935 INFO: Setting torch num_threads to 2 for FDR classification task
20:40:02.875003 INFO: Test AUC: 0.857
20:40:02.875078 INFO: Train AUC: 0.846
20:40:02.875108 INFO: AUC difference: 1.28%
20:40:03.054107 INFO: Resetting torch num_threads to 100
20:40:03.054744 INFO: === FDR correction performed with classifier version 7 ===
20:40:03.055608 PROGRESS: ============================= Precursor FDR =============================
20:40:03.055703 PROGRESS: Total precursors accumulated: 600
20:40:03.055762 PROGRESS: Target precursors: 580 (96.67%)
20:40:03.055812 PROGRESS: Decoy precursors: 20 (3.33%)
20:40:03.055858 PROGRESS: 
20:40:03.055902 PROGRESS: Precursor Summary:
20:40:03.056931 PROGRESS: Channel   0:	 0.05 FDR:   580; 0.01 FDR:   544; 0.001 FDR:   461
20:40:03.057021 PROGRESS: 
20:40:03.057076 PROGRESS: Protein Summary:
20:40:03.058334 PROGRESS: Channel   0:	 0.05 FDR:   543; 0.01 FDR:   510; 0.001 FDR:   431
20:40:03.058434 PROGRESS: =========================================================================
20:40:03.061929 INFO: fragments_df: keeping 5000 of 23254 [sum(precursor_idx_mask)=11170 sum(mass_error_mask)=23254 stop_rank=5000
20:40:03.067138 INFO: calibration group: precursor, fitting mz estimator 
20:40:03.205689 INFO: calibration group: precursor, fitting rt estimator 
20:40:03.350587 INFO: calibration group: precursor, fitting mobility estimator 
20:40:03.498810 INFO: calibration group: fragment, fitting mz estimator 
20:40:04.209051 INFO: Using score_cutoff 35.346160859298706 (fac=0.99, q=1)
20:40:04.209481 INFO: calibration group: precursor, predicting mz
20:40:04.210661 INFO: calibration group: precursor, predicting rt
20:40:04.211991 INFO: calibration group: precursor, predicting mobility
20:40:04.212759 INFO: calibration group: fragment, predicting mz
20:40:04.215817 INFO: === checking if optimization conditions were reached ===
20:40:04.215926 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
20:40:04.217617 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 10.7546.
20:40:04.217679 INFO: ==============================================
20:40:04.217785 INFO: Starting optimization step 2.
20:40:04.217854 PROGRESS: === Extracting elution groups 0 to 600 ===
20:40:04.217914 PROGRESS: Extracting batch of 1188 precursors
20:40:04.219219 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:40:04.219269 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:40:04.219303 INFO: FWHM in RT is 2.55 seconds, sigma is 0.56
20:40:04.219327 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.08
20:40:04.220051 INFO: Starting candidate selection
20:40:04.740444 INFO: Starting candidate scoring
20:40:04.863169 INFO: Finished candidate processing
20:40:04.863291 INFO: Collecting candidate features
20:40:04.872872 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2260)
20:40:04.876141 INFO: Collecting fragment features
20:40:04.881824 INFO: Finished candidate scoring
20:40:04.883466 PROGRESS: === Extracted 2260 precursors and 23250 fragments ===
20:40:04.883785 INFO: performing precursor FDR with 47 features
20:40:04.883828 INFO: Decoy channel: -1
20:40:04.883862 INFO: Competetive: True
20:40:04.886693 INFO: Setting torch num_threads to 2 for FDR classification task
20:40:04.888059 WARNING: dropped 1 target PSMs due to missing features
20:40:04.901162 INFO: Test AUC: 0.870
20:40:04.901285 INFO: Train AUC: 0.851
20:40:04.901316 INFO: AUC difference: 2.29%
20:40:05.077993 INFO: Resetting torch num_threads to 100
20:40:05.078568 INFO: === FDR correction performed with classifier version 7 ===
20:40:05.079270 PROGRESS: ============================= Precursor FDR =============================
20:40:05.079363 PROGRESS: Total precursors accumulated: 600
20:40:05.079420 PROGRESS: Target precursors: 583 (97.17%)
20:40:05.079468 PROGRESS: Decoy precursors: 17 (2.83%)
20:40:05.079513 PROGRESS: 
20:40:05.079565 PROGRESS: Precursor Summary:
20:40:05.080586 PROGRESS: Channel   0:	 0.05 FDR:   583; 0.01 FDR:   555; 0.001 FDR:   464
20:40:05.080676 PROGRESS: 
20:40:05.080732 PROGRESS: Protein Summary:
20:40:05.081981 PROGRESS: Channel   0:	 0.05 FDR:   545; 0.01 FDR:   520; 0.001 FDR:   432
20:40:05.082072 PROGRESS: =========================================================================
20:40:05.085520 INFO: fragments_df: keeping 5000 of 23250 [sum(precursor_idx_mask)=11349 sum(mass_error_mask)=23250 stop_rank=5000
20:40:05.090747 INFO: calibration group: precursor, fitting mz estimator 
20:40:05.207746 INFO: calibration group: precursor, fitting rt estimator 
20:40:05.330933 INFO: calibration group: precursor, fitting mobility estimator 
20:40:05.459471 INFO: calibration group: fragment, fitting mz estimator 
20:40:06.130944 INFO: Using score_cutoff 33.51990267333984 (fac=0.99, q=1)
20:40:06.131627 INFO: calibration group: precursor, predicting mz
20:40:06.132804 INFO: calibration group: precursor, predicting rt
20:40:06.134130 INFO: calibration group: precursor, predicting mobility
20:40:06.134891 INFO: calibration group: fragment, predicting mz
20:40:06.136934 INFO: === checking if optimization conditions were reached ===
20:40:06.137040 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
20:40:06.138800 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 11.6489.
20:40:06.138854 INFO: ==============================================
20:40:06.138941 INFO: Starting optimization step 3.
20:40:06.139007 PROGRESS: === Extracting elution groups 0 to 600 ===
20:40:06.139086 PROGRESS: Extracting batch of 1188 precursors
20:40:06.140227 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:40:06.140275 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:40:06.140311 INFO: FWHM in RT is 2.53 seconds, sigma is 0.56
20:40:06.140333 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.06
20:40:06.141115 INFO: Starting candidate selection
20:40:06.718477 INFO: Starting candidate scoring
20:40:06.848895 INFO: Finished candidate processing
20:40:06.849022 INFO: Collecting candidate features
20:40:06.857776 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2252)
20:40:06.860973 INFO: Collecting fragment features
20:40:06.865322 INFO: Finished candidate scoring
20:40:06.866809 PROGRESS: === Extracted 2252 precursors and 23178 fragments ===
20:40:06.867118 INFO: performing precursor FDR with 47 features
20:40:06.867157 INFO: Decoy channel: -1
20:40:06.867181 INFO: Competetive: True
20:40:06.869798 INFO: Setting torch num_threads to 2 for FDR classification task
20:40:06.871047 WARNING: dropped 1 decoy PSMs due to missing features
20:40:06.885805 INFO: Test AUC: 0.828
20:40:06.885904 INFO: Train AUC: 0.862
20:40:06.885934 INFO: AUC difference: 3.99%
20:40:07.067971 INFO: Resetting torch num_threads to 100
20:40:07.068589 INFO: === FDR correction performed with classifier version 7 ===
20:40:07.069261 PROGRESS: ============================= Precursor FDR =============================
20:40:07.069354 PROGRESS: Total precursors accumulated: 600
20:40:07.069413 PROGRESS: Target precursors: 580 (96.67%)
20:40:07.069466 PROGRESS: Decoy precursors: 20 (3.33%)
20:40:07.069512 PROGRESS: 
20:40:07.069557 PROGRESS: Precursor Summary:
20:40:07.070621 PROGRESS: Channel   0:	 0.05 FDR:   580; 0.01 FDR:   549; 0.001 FDR:   461
20:40:07.070713 PROGRESS: 
20:40:07.070768 PROGRESS: Protein Summary:
20:40:07.072042 PROGRESS: Channel   0:	 0.05 FDR:   542; 0.01 FDR:   513; 0.001 FDR:   429
20:40:07.072140 PROGRESS: =========================================================================
20:40:07.075624 INFO: fragments_df: keeping 5000 of 23178 [sum(precursor_idx_mask)=11226 sum(mass_error_mask)=23178 stop_rank=5000
20:40:07.081724 INFO: calibration group: precursor, fitting mz estimator 
20:40:07.218890 INFO: calibration group: precursor, fitting rt estimator 
20:40:07.366806 INFO: calibration group: precursor, fitting mobility estimator 
20:40:07.515294 INFO: calibration group: fragment, fitting mz estimator 
20:40:08.242969 INFO: Using score_cutoff 35.53571449127197 (fac=0.99, q=1)
20:40:08.243420 INFO: calibration group: precursor, predicting mz
20:40:08.244631 INFO: calibration group: precursor, predicting rt
20:40:08.245970 INFO: calibration group: precursor, predicting mobility
20:40:08.246735 INFO: calibration group: fragment, predicting mz
20:40:08.248869 INFO: === checking if optimization conditions were reached ===
20:40:08.248976 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
20:40:08.250769 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 11.7891.
20:40:08.250828 INFO: ==============================================
20:40:08.250918 INFO: Starting optimization step 4.
20:40:08.250987 PROGRESS: === Extracting elution groups 0 to 600 ===
20:40:08.251056 PROGRESS: Extracting batch of 1188 precursors
20:40:08.252254 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:40:08.252302 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:40:08.252339 INFO: FWHM in RT is 2.53 seconds, sigma is 0.56
20:40:08.252363 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.09
20:40:08.260102 INFO: Starting candidate selection
20:40:08.791984 INFO: Starting candidate scoring
20:40:08.897048 INFO: Finished candidate processing
20:40:08.897156 INFO: Collecting candidate features
20:40:08.906402 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2246)
20:40:08.909695 INFO: Collecting fragment features
20:40:08.914903 INFO: Finished candidate scoring
20:40:08.916522 PROGRESS: === Extracted 2246 precursors and 23132 fragments ===
20:40:08.916837 INFO: performing precursor FDR with 47 features
20:40:08.916875 INFO: Decoy channel: -1
20:40:08.916898 INFO: Competetive: True
20:40:08.919787 INFO: Setting torch num_threads to 2 for FDR classification task
20:40:08.921030 WARNING: dropped 1 decoy PSMs due to missing features
20:40:08.932636 INFO: Test AUC: 0.852
20:40:08.932725 INFO: Train AUC: 0.858
20:40:08.932755 INFO: AUC difference: 0.80%
20:40:09.108013 INFO: Resetting torch num_threads to 100
20:40:09.108634 INFO: === FDR correction performed with classifier version 7 ===
20:40:09.109301 PROGRESS: ============================= Precursor FDR =============================
20:40:09.109393 PROGRESS: Total precursors accumulated: 600
20:40:09.109455 PROGRESS: Target precursors: 580 (96.67%)
20:40:09.109505 PROGRESS: Decoy precursors: 20 (3.33%)
20:40:09.109552 PROGRESS: 
20:40:09.109598 PROGRESS: Precursor Summary:
20:40:09.110614 PROGRESS: Channel   0:	 0.05 FDR:   580; 0.01 FDR:   555; 0.001 FDR:   461
20:40:09.110706 PROGRESS: 
20:40:09.110763 PROGRESS: Protein Summary:
20:40:09.112031 PROGRESS: Channel   0:	 0.05 FDR:   542; 0.01 FDR:   519; 0.001 FDR:   428
20:40:09.112125 PROGRESS: =========================================================================
20:40:09.115578 INFO: fragments_df: keeping 5000 of 23132 [sum(precursor_idx_mask)=11310 sum(mass_error_mask)=23132 stop_rank=5000
20:40:09.121028 INFO: calibration group: precursor, fitting mz estimator 
20:40:09.275733 INFO: calibration group: precursor, fitting rt estimator 
20:40:09.436379 INFO: calibration group: precursor, fitting mobility estimator 
20:40:09.573272 INFO: calibration group: fragment, fitting mz estimator 
20:40:10.227863 INFO: Using score_cutoff 34.281164197540285 (fac=0.99, q=1)
20:40:10.228311 INFO: calibration group: precursor, predicting mz
20:40:10.229521 INFO: calibration group: precursor, predicting rt
20:40:10.230861 INFO: calibration group: precursor, predicting mobility
20:40:10.231642 INFO: calibration group: fragment, predicting mz
20:40:10.234141 INFO: === checking if optimization conditions were reached ===
20:40:10.234244 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
20:40:10.235287 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 10.1540 found after 5 searches.
20:40:10.235342 INFO: ==============================================
20:40:10.235430 PROGRESS: Optimization finished for rt_error.
20:40:10.240611 INFO: calibration group: precursor, predicting mz
20:40:10.241455 INFO: calibration group: precursor, predicting rt
20:40:10.242751 INFO: calibration group: precursor, predicting mobility
20:40:10.243532 INFO: calibration group: fragment, predicting mz
20:40:10.271685 INFO: Starting optimization step 0.
20:40:10.271846 PROGRESS: === Extracting elution groups 0 to 600 ===
20:40:10.271914 PROGRESS: Extracting batch of 1188 precursors
20:40:10.273093 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:40:10.273144 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:40:10.273181 INFO: FWHM in RT is 2.55 seconds, sigma is 0.56
20:40:10.273204 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.08
20:40:10.274046 INFO: Starting candidate selection
20:40:10.849930 INFO: Starting candidate scoring
20:40:10.969988 INFO: Finished candidate processing
20:40:10.970102 INFO: Collecting candidate features
20:40:10.979181 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2252)
20:40:10.982385 INFO: Collecting fragment features
20:40:10.986960 INFO: Finished candidate scoring
20:40:10.988482 PROGRESS: === Extracted 2252 precursors and 23181 fragments ===
20:40:10.988774 INFO: performing precursor FDR with 47 features
20:40:10.988811 INFO: Decoy channel: -1
20:40:10.988834 INFO: Competetive: True
20:40:10.991544 INFO: Setting torch num_threads to 2 for FDR classification task
20:40:10.992763 WARNING: dropped 1 target PSMs due to missing features
20:40:11.004729 INFO: Test AUC: 0.857
20:40:11.004794 INFO: Train AUC: 0.863
20:40:11.004823 INFO: AUC difference: 0.77%
20:40:11.184291 INFO: Resetting torch num_threads to 100
20:40:11.184930 INFO: === FDR correction performed with classifier version 9 ===
20:40:11.185822 PROGRESS: ============================= Precursor FDR =============================
20:40:11.185925 PROGRESS: Total precursors accumulated: 600
20:40:11.185989 PROGRESS: Target precursors: 577 (96.17%)
20:40:11.186042 PROGRESS: Decoy precursors: 23 (3.83%)
20:40:11.186100 PROGRESS: 
20:40:11.186147 PROGRESS: Precursor Summary:
20:40:11.187192 PROGRESS: Channel   0:	 0.05 FDR:   577; 0.01 FDR:   549; 0.001 FDR:   457
20:40:11.187301 PROGRESS: 
20:40:11.187359 PROGRESS: Protein Summary:
20:40:11.188643 PROGRESS: Channel   0:	 0.05 FDR:   539; 0.01 FDR:   514; 0.001 FDR:   424
20:40:11.188739 PROGRESS: =========================================================================
20:40:11.192264 INFO: fragments_df: keeping 5000 of 23181 [sum(precursor_idx_mask)=11188 sum(mass_error_mask)=23181 stop_rank=5000
20:40:11.197512 INFO: calibration group: precursor, fitting mz estimator 
20:40:11.335392 INFO: calibration group: precursor, fitting rt estimator 
20:40:11.481489 INFO: calibration group: precursor, fitting mobility estimator 
20:40:11.630067 INFO: calibration group: fragment, fitting mz estimator 
20:40:12.353211 INFO: Using score_cutoff 33.95067881011963 (fac=0.99, q=1)
20:40:12.353653 INFO: calibration group: precursor, predicting mz
20:40:12.354831 INFO: calibration group: precursor, predicting rt
20:40:12.356170 INFO: calibration group: precursor, predicting mobility
20:40:12.356932 INFO: calibration group: fragment, predicting mz
20:40:12.359010 INFO: === checking if optimization conditions were reached ===
20:40:12.359126 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
20:40:12.360499 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0584.
20:40:12.361039 INFO: ==============================================
20:40:12.361133 INFO: Starting optimization step 1.
20:40:12.361202 PROGRESS: === Extracting elution groups 0 to 600 ===
20:40:12.361265 PROGRESS: Extracting batch of 1188 precursors
20:40:12.362550 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:40:12.362601 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:40:12.362638 INFO: FWHM in RT is 2.53 seconds, sigma is 0.56
20:40:12.362664 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.06
20:40:12.363450 INFO: Starting candidate selection
20:40:12.864577 INFO: Starting candidate scoring
20:40:12.991160 INFO: Finished candidate processing
20:40:12.991275 INFO: Collecting candidate features
20:40:13.000590 WARNING: intensity_correlation has 2 NaNs ( 0.09 % out of 2245)
20:40:13.003888 INFO: Collecting fragment features
20:40:13.008177 INFO: Finished candidate scoring
20:40:13.009671 PROGRESS: === Extracted 2245 precursors and 22878 fragments ===
20:40:13.009962 INFO: performing precursor FDR with 47 features
20:40:13.009999 INFO: Decoy channel: -1
20:40:13.010021 INFO: Competetive: True
20:40:13.012682 INFO: Setting torch num_threads to 2 for FDR classification task
20:40:13.014019 WARNING: dropped 1 target PSMs due to missing features
20:40:13.014075 WARNING: dropped 1 decoy PSMs due to missing features
20:40:13.025175 INFO: Test AUC: 0.873
20:40:13.025251 INFO: Train AUC: 0.866
20:40:13.025281 INFO: AUC difference: 0.86%
20:40:13.202032 INFO: Resetting torch num_threads to 100
20:40:13.202660 INFO: === FDR correction performed with classifier version 9 ===
20:40:13.203368 PROGRESS: ============================= Precursor FDR =============================
20:40:13.203463 PROGRESS: Total precursors accumulated: 599
20:40:13.203521 PROGRESS: Target precursors: 578 (96.49%)
20:40:13.203571 PROGRESS: Decoy precursors: 21 (3.51%)
20:40:13.203615 PROGRESS: 
20:40:13.203659 PROGRESS: Precursor Summary:
20:40:13.204670 PROGRESS: Channel   0:	 0.05 FDR:   578; 0.01 FDR:   549; 0.001 FDR:   451
20:40:13.204763 PROGRESS: 
20:40:13.204825 PROGRESS: Protein Summary:
20:40:13.206066 PROGRESS: Channel   0:	 0.05 FDR:   540; 0.01 FDR:   514; 0.001 FDR:   418
20:40:13.206156 PROGRESS: =========================================================================
20:40:13.209690 INFO: fragments_df: keeping 5000 of 22878 [sum(precursor_idx_mask)=11186 sum(mass_error_mask)=22878 stop_rank=5000
20:40:13.215041 INFO: calibration group: precursor, fitting mz estimator 
20:40:13.351507 INFO: calibration group: precursor, fitting rt estimator 
20:40:13.497650 INFO: calibration group: precursor, fitting mobility estimator 
20:40:13.635394 INFO: calibration group: fragment, fitting mz estimator 
20:40:14.341393 INFO: Using score_cutoff 33.93954372711182 (fac=0.99, q=1)
20:40:14.341819 INFO: calibration group: precursor, predicting mz
20:40:14.343005 INFO: calibration group: precursor, predicting rt
20:40:14.344373 INFO: calibration group: precursor, predicting mobility
20:40:14.345133 INFO: calibration group: fragment, predicting mz
20:40:14.347219 INFO: === checking if optimization conditions were reached ===
20:40:14.347327 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
20:40:14.348789 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0524.
20:40:14.348843 INFO: ==============================================
20:40:14.348930 INFO: Starting optimization step 2.
20:40:14.348995 PROGRESS: === Extracting elution groups 0 to 600 ===
20:40:14.349054 PROGRESS: Extracting batch of 1188 precursors
20:40:14.350282 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:40:14.350328 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:40:14.350363 INFO: FWHM in RT is 2.51 seconds, sigma is 0.55
20:40:14.350386 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.02
20:40:14.351273 INFO: Starting candidate selection
20:40:14.878059 INFO: Starting candidate scoring
20:40:15.017608 INFO: Finished candidate processing
20:40:15.017723 INFO: Collecting candidate features
20:40:15.031199 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2244)
20:40:15.034603 INFO: Collecting fragment features
20:40:15.040124 INFO: Finished candidate scoring
20:40:15.041924 PROGRESS: === Extracted 2244 precursors and 22770 fragments ===
20:40:15.042286 INFO: performing precursor FDR with 47 features
20:40:15.042328 INFO: Decoy channel: -1
20:40:15.042354 INFO: Competetive: True
20:40:15.045446 INFO: Setting torch num_threads to 2 for FDR classification task
20:40:15.046903 WARNING: dropped 1 decoy PSMs due to missing features
20:40:15.061975 INFO: Test AUC: 0.878
20:40:15.062121 INFO: Train AUC: 0.865
20:40:15.062152 INFO: AUC difference: 1.55%
20:40:15.266283 INFO: Resetting torch num_threads to 100
20:40:15.266971 INFO: === FDR correction performed with classifier version 9 ===
20:40:15.267788 PROGRESS: ============================= Precursor FDR =============================
20:40:15.267889 PROGRESS: Total precursors accumulated: 599
20:40:15.267959 PROGRESS: Target precursors: 577 (96.33%)
20:40:15.268012 PROGRESS: Decoy precursors: 22 (3.67%)
20:40:15.268067 PROGRESS: 
20:40:15.268114 PROGRESS: Precursor Summary:
20:40:15.269337 PROGRESS: Channel   0:	 0.05 FDR:   577; 0.01 FDR:   558; 0.001 FDR:   450
20:40:15.269439 PROGRESS: 
20:40:15.269500 PROGRESS: Protein Summary:
20:40:15.270900 PROGRESS: Channel   0:	 0.05 FDR:   539; 0.01 FDR:   523; 0.001 FDR:   417
20:40:15.271001 PROGRESS: =========================================================================
20:40:15.274800 INFO: fragments_df: keeping 5000 of 22770 [sum(precursor_idx_mask)=11363 sum(mass_error_mask)=22770 stop_rank=5000
20:40:15.280478 INFO: calibration group: precursor, fitting mz estimator 
20:40:15.416865 INFO: calibration group: precursor, fitting rt estimator 
20:40:15.560189 INFO: calibration group: precursor, fitting mobility estimator 
20:40:15.694360 INFO: calibration group: fragment, fitting mz estimator 
20:40:16.422362 INFO: Using score_cutoff 33.308923123168945 (fac=0.99, q=1)
20:40:16.422825 INFO: calibration group: precursor, predicting mz
20:40:16.424190 INFO: calibration group: precursor, predicting rt
20:40:16.425641 INFO: calibration group: precursor, predicting mobility
20:40:16.426471 INFO: calibration group: fragment, predicting mz
20:40:16.428690 INFO: === checking if optimization conditions were reached ===
20:40:16.428801 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
20:40:16.429625 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.0524 found after 3 searches.
20:40:16.429677 INFO: ==============================================
20:40:16.429764 PROGRESS: Optimization finished for mobility_error.
20:40:16.435011 INFO: calibration group: precursor, predicting mz
20:40:16.435897 INFO: calibration group: precursor, predicting rt
20:40:16.437351 INFO: calibration group: precursor, predicting mobility
20:40:16.438193 INFO: calibration group: fragment, predicting mz
20:40:16.467378 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
20:40:16.467533 PROGRESS: ==============================================
20:40:16.467611 PROGRESS: ms2_error      : 10.0474
20:40:16.467672 PROGRESS: ms1_error      : 10.5658
20:40:16.467732 PROGRESS: rt_error       : 10.1540
20:40:16.467784 PROGRESS: mobility_error : 0.0524
20:40:16.467833 PROGRESS: ==============================================
20:40:16.469121 INFO: calibration group: precursor, predicting mz
20:40:16.491709 INFO: calibration group: precursor, predicting rt
20:40:16.636914 INFO: calibration group: precursor, predicting mobility
20:40:16.663697 INFO: calibration group: fragment, predicting mz
20:40:16.979655 PROGRESS: Extracting batch of 189636 precursors
20:40:17.076128 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:40:17.076373 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:40:17.076435 INFO: FWHM in RT is 2.50 seconds, sigma is 0.55
20:40:17.076460 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.95
20:40:17.099772 INFO: Starting candidate selection
20:40:37.327505 INFO: Applying score cutoff of 33.308923123168945
20:40:37.333993 INFO: Removed 93312 precursors with score below cutoff
20:40:37.680176 INFO: Starting candidate scoring
20:40:44.886223 INFO: Finished candidate processing
20:40:44.886339 INFO: Collecting candidate features
20:40:45.301094 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 266085)
20:40:45.314423 INFO: Collecting fragment features
20:40:45.495498 INFO: Finished candidate scoring
20:40:45.662757 INFO: === FDR correction performed with classifier version 15 ===
20:40:45.664278 INFO: performing precursor FDR with 47 features
20:40:45.664319 INFO: Decoy channel: -1
20:40:45.664344 INFO: Competetive: True
20:40:45.757909 INFO: Setting torch num_threads to 2 for FDR classification task
20:40:45.805304 WARNING: dropped 1 target PSMs due to missing features
20:40:45.805516 WARNING: FDR calculation for 162991 target and 103093 decoy PSMs
20:40:45.805544 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
20:40:50.960383 INFO: Test AUC: 0.915
20:40:50.960534 INFO: Train AUC: 0.920
20:40:50.960567 INFO: AUC difference: 0.61%
20:40:51.196626 INFO: Resetting torch num_threads to 100
20:40:51.213792 INFO: Removing fragments below FDR threshold
20:40:51.260605 PROGRESS: ============================= Precursor FDR =============================
20:40:51.260899 PROGRESS: Total precursors accumulated: 61,289
20:40:51.260966 PROGRESS: Target precursors: 60,683 (99.01%)
20:40:51.261028 PROGRESS: Decoy precursors: 606 (0.99%)
20:40:51.261078 PROGRESS: 
20:40:51.261127 PROGRESS: Precursor Summary:
20:40:51.288043 PROGRESS: Channel   0:	 0.05 FDR: 60,683; 0.01 FDR: 60,683; 0.001 FDR: 56,279
20:40:51.288346 PROGRESS: 
20:40:51.288409 PROGRESS: Protein Summary:
20:40:51.323807 PROGRESS: Channel   0:	 0.05 FDR: 8,974; 0.01 FDR: 8,974; 0.001 FDR: 8,842
20:40:51.324061 PROGRESS: =========================================================================
20:40:51.822110 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
20:40:51.877141 PROGRESS: Loading raw file 3/6: ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
20:40:51.877314 INFO: Quantification results path: run_output/alphadia_1.10.4_Again_good_now/quant
20:40:51.877393 INFO: Creating folder run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/figures
20:40:51.878018 INFO: Initializing RawFileManager
20:40:51.878138 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
20:40:51.878205 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
20:40:51.878246 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
20:40:52.088948 INFO: Reading 39,128 frames with 2,897,842,446 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
20:40:58.402713 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d...
20:40:58.406600 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
20:40:58.409590 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
20:40:58.409937 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
20:40:58.410426 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
20:40:58.412110 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
20:40:58.431012 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
20:40:58.431425 INFO: Indexing quadrupole dimension
20:40:59.040247 INFO: Transposing detector events
20:41:09.020033 INFO: Finished transposing data
20:41:09.050790 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
20:41:09.051758 INFO: RT (min)            : 0.0 - 70.0
20:41:09.051803 INFO: RT duration (sec)   : 4199.8
20:41:09.051827 INFO: RT duration (min)   : 70.0
20:41:09.051847 INFO: Cycle len (scans)   : 9
20:41:09.051866 INFO: Cycle len (sec)     : 0.97
20:41:09.051885 INFO: Number of cycles    : 4347
20:41:09.051903 INFO: MS2 range (m/z)     : 400.0 - 1000.0
20:41:09.116727 INFO: Initializing CalibrationManager
20:41:09.117059 INFO: Loading calibration config
20:41:09.117946 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed'], 'function': LOESSRegression()}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed'], 'function': LOESSRegression(n_kernels=2)}], 'name': 'precursor'}]
20:41:09.118034 INFO: Calibration group :fragment, found 1 estimator(s)
20:41:09.118147 INFO: Calibration group :precursor, found 3 estimator(s)
20:41:09.118328 INFO: Initializing OptimizationManager
20:41:09.118435 INFO: initial parameter: ms1_error = 30
20:41:09.118488 INFO: initial parameter: ms2_error = 30
20:41:09.118552 INFO: initial parameter: rt_error = 2099.8992935
20:41:09.118598 INFO: initial parameter: mobility_error = 0.1
20:41:09.118639 INFO: initial parameter: column_type = library
20:41:09.118678 INFO: initial parameter: num_candidates = 1
20:41:09.118717 INFO: initial parameter: classifier_version = -1
20:41:09.118756 INFO: initial parameter: fwhm_rt = 5
20:41:09.118797 INFO: initial parameter: fwhm_mobility = 0.01
20:41:09.118835 INFO: initial parameter: score_cutoff = 0
20:41:09.118912 INFO: Initializing TimingManager
20:41:09.118990 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
20:41:09.119180 INFO: FDRManager not loaded from disk.
20:41:09.119211 INFO: Initializing FDRManager
20:41:09.119258 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
20:41:09.152978 PROGRESS: 95,522 target precursors potentially observable (0 removed)
20:41:09.198851 PROGRESS: Starting initial search for precursors.
20:41:09.205689 INFO: Starting optimization step 0.
20:41:09.205863 PROGRESS: === Extracting elution groups 0 to 200 ===
20:41:09.205948 PROGRESS: Extracting batch of 395 precursors
20:41:09.207301 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:41:09.207354 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:41:09.207399 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:41:09.207423 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:41:09.208552 INFO: Starting candidate selection
20:41:12.889611 INFO: Starting candidate scoring
20:41:13.015790 INFO: Finished candidate processing
20:41:13.016002 INFO: Collecting candidate features
20:41:13.031836 INFO: Collecting fragment features
20:41:13.035203 INFO: Finished candidate scoring
20:41:13.036874 PROGRESS: === Extracted 394 precursors and 4340 fragments ===
20:41:13.037354 INFO: performing precursor FDR with 47 features
20:41:13.037404 INFO: Decoy channel: -1
20:41:13.037436 INFO: Competetive: True
20:41:13.039089 INFO: Setting torch num_threads to 2 for FDR classification task
20:41:13.056888 INFO: Test AUC: 0.244
20:41:13.057033 INFO: Train AUC: 0.436
20:41:13.057071 INFO: AUC difference: 43.97%
20:41:13.057098 WARNING: AUC difference > 5%. This may indicate overfitting.
20:41:13.255333 INFO: Resetting torch num_threads to 100
20:41:13.255949 INFO: === FDR correction performed with classifier version -1 ===
20:41:13.256612 PROGRESS: ============================= Precursor FDR =============================
20:41:13.256701 PROGRESS: Total precursors accumulated: 200
20:41:13.256762 PROGRESS: Target precursors: 83 (41.50%)
20:41:13.256813 PROGRESS: Decoy precursors: 117 (58.50%)
20:41:13.256858 PROGRESS: 
20:41:13.256901 PROGRESS: Precursor Summary:
20:41:13.257777 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
20:41:13.257865 PROGRESS: 
20:41:13.257920 PROGRESS: Protein Summary:
20:41:13.258856 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
20:41:13.258946 PROGRESS: =========================================================================
20:41:13.263394 INFO: Starting optimization step 1.
20:41:13.263512 PROGRESS: === Extracting elution groups 200 to 600 ===
20:41:13.263576 PROGRESS: Extracting batch of 793 precursors
20:41:13.265391 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:41:13.265440 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:41:13.265469 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:41:13.265490 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:41:13.269337 INFO: Starting candidate selection
20:41:20.502841 INFO: Starting candidate scoring
20:41:20.604745 INFO: Finished candidate processing
20:41:20.604848 INFO: Collecting candidate features
20:41:20.614367 INFO: Collecting fragment features
20:41:20.617326 INFO: Finished candidate scoring
20:41:20.619204 PROGRESS: === Extracted 1187 precursors and 13134 fragments ===
20:41:20.619943 INFO: performing precursor FDR with 47 features
20:41:20.619986 INFO: Decoy channel: -1
20:41:20.620009 INFO: Competetive: True
20:41:20.622768 INFO: Setting torch num_threads to 2 for FDR classification task
20:41:20.634187 INFO: Test AUC: 0.426
20:41:20.634247 INFO: Train AUC: 0.414
20:41:20.634275 INFO: AUC difference: 2.99%
20:41:20.832198 INFO: Resetting torch num_threads to 100
20:41:20.832812 INFO: === FDR correction performed with classifier version -1 ===
20:41:20.833483 PROGRESS: ============================= Precursor FDR =============================
20:41:20.833575 PROGRESS: Total precursors accumulated: 600
20:41:20.833633 PROGRESS: Target precursors: 255 (42.50%)
20:41:20.833691 PROGRESS: Decoy precursors: 345 (57.50%)
20:41:20.833738 PROGRESS: 
20:41:20.833781 PROGRESS: Precursor Summary:
20:41:20.834648 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
20:41:20.834736 PROGRESS: 
20:41:20.834790 PROGRESS: Protein Summary:
20:41:20.835737 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
20:41:20.835826 PROGRESS: =========================================================================
20:41:20.840496 INFO: Starting optimization step 2.
20:41:20.840597 PROGRESS: === Extracting elution groups 600 to 1400 ===
20:41:20.840662 PROGRESS: Extracting batch of 1583 precursors
20:41:20.841514 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:41:20.841559 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:41:20.841587 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:41:20.841609 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:41:20.842410 INFO: Starting candidate selection
20:41:31.207285 INFO: Starting candidate scoring
20:41:31.405321 INFO: Finished candidate processing
20:41:31.405432 INFO: Collecting candidate features
20:41:31.417199 INFO: Collecting fragment features
20:41:31.420881 INFO: Finished candidate scoring
20:41:31.423831 PROGRESS: === Extracted 2770 precursors and 30817 fragments ===
20:41:31.425021 INFO: performing precursor FDR with 47 features
20:41:31.425063 INFO: Decoy channel: -1
20:41:31.425086 INFO: Competetive: True
20:41:31.428926 INFO: Setting torch num_threads to 2 for FDR classification task
20:41:31.445015 INFO: Test AUC: 0.386
20:41:31.445097 INFO: Train AUC: 0.409
20:41:31.445126 INFO: AUC difference: 5.60%
20:41:31.445148 WARNING: AUC difference > 5%. This may indicate overfitting.
20:41:31.622975 INFO: Resetting torch num_threads to 100
20:41:31.623745 INFO: === FDR correction performed with classifier version -1 ===
20:41:31.624476 PROGRESS: ============================= Precursor FDR =============================
20:41:31.624571 PROGRESS: Total precursors accumulated: 1,400
20:41:31.624634 PROGRESS: Target precursors: 559 (39.93%)
20:41:31.624685 PROGRESS: Decoy precursors: 841 (60.07%)
20:41:31.624732 PROGRESS: 
20:41:31.624777 PROGRESS: Precursor Summary:
20:41:31.625618 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:41:31.625707 PROGRESS: 
20:41:31.625760 PROGRESS: Protein Summary:
20:41:31.626657 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:41:31.626743 PROGRESS: =========================================================================
20:41:31.634258 INFO: Starting optimization step 3.
20:41:31.634376 PROGRESS: === Extracting elution groups 1400 to 3000 ===
20:41:31.634440 PROGRESS: Extracting batch of 3171 precursors
20:41:31.635617 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:41:31.635669 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:41:31.635700 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:41:31.635722 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:41:31.636500 INFO: Starting candidate selection
20:41:51.634423 INFO: Starting candidate scoring
20:41:51.969798 INFO: Finished candidate processing
20:41:51.969905 INFO: Collecting candidate features
20:41:51.984430 INFO: Collecting fragment features
20:41:51.990110 INFO: Finished candidate scoring
20:41:51.997155 PROGRESS: === Extracted 5940 precursors and 65980 fragments ===
20:41:51.998467 INFO: performing precursor FDR with 47 features
20:41:51.998511 INFO: Decoy channel: -1
20:41:51.998535 INFO: Competetive: True
20:41:52.004045 INFO: Setting torch num_threads to 2 for FDR classification task
20:41:52.032056 INFO: Test AUC: 0.401
20:41:52.032174 INFO: Train AUC: 0.409
20:41:52.032205 INFO: AUC difference: 1.98%
20:41:52.211381 INFO: Resetting torch num_threads to 100
20:41:52.212249 INFO: === FDR correction performed with classifier version -1 ===
20:41:52.213227 PROGRESS: ============================= Precursor FDR =============================
20:41:52.213319 PROGRESS: Total precursors accumulated: 3,000
20:41:52.213391 PROGRESS: Target precursors: 1,223 (40.77%)
20:41:52.213444 PROGRESS: Decoy precursors: 1,777 (59.23%)
20:41:52.213491 PROGRESS: 
20:41:52.213536 PROGRESS: Precursor Summary:
20:41:52.214395 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:41:52.214484 PROGRESS: 
20:41:52.214539 PROGRESS: Protein Summary:
20:41:52.215464 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:41:52.215553 PROGRESS: =========================================================================
20:41:52.230514 INFO: Starting optimization step 4.
20:41:52.230654 PROGRESS: === Extracting elution groups 3000 to 6200 ===
20:41:52.230743 PROGRESS: Extracting batch of 6347 precursors
20:41:52.232553 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:41:52.232599 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:41:52.232645 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:41:52.232669 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:41:52.233581 INFO: Starting candidate selection
20:42:34.752702 INFO: Starting candidate scoring
20:42:35.463098 INFO: Finished candidate processing
20:42:35.463212 INFO: Collecting candidate features
20:42:35.484082 INFO: Collecting fragment features
20:42:35.492555 INFO: Finished candidate scoring
20:42:35.502346 PROGRESS: === Extracted 12287 precursors and 136580 fragments ===
20:42:35.504199 INFO: performing precursor FDR with 47 features
20:42:35.504267 INFO: Decoy channel: -1
20:42:35.504292 INFO: Competetive: True
20:42:35.510071 INFO: Setting torch num_threads to 2 for FDR classification task
20:42:35.555267 INFO: Test AUC: 0.406
20:42:35.555400 INFO: Train AUC: 0.408
20:42:35.555430 INFO: AUC difference: 0.47%
20:42:35.739647 INFO: Resetting torch num_threads to 100
20:42:35.742909 INFO: === FDR correction performed with classifier version -1 ===
20:42:35.744220 PROGRESS: ============================= Precursor FDR =============================
20:42:35.744330 PROGRESS: Total precursors accumulated: 6,200
20:42:35.744390 PROGRESS: Target precursors: 2,507 (40.44%)
20:42:35.744441 PROGRESS: Decoy precursors: 3,693 (59.56%)
20:42:35.744486 PROGRESS: 
20:42:35.744530 PROGRESS: Precursor Summary:
20:42:35.745443 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
20:42:35.745871 PROGRESS: 
20:42:35.745999 PROGRESS: Protein Summary:
20:42:35.746994 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
20:42:35.747262 PROGRESS: =========================================================================
20:42:35.765784 INFO: Starting optimization step 5.
20:42:35.766009 PROGRESS: === Extracting elution groups 6200 to 12600 ===
20:42:35.766079 PROGRESS: Extracting batch of 12697 precursors
20:42:35.769393 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:42:35.769445 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:42:35.769477 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:42:35.769499 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:42:35.770768 INFO: Starting candidate selection
20:43:58.809749 INFO: Starting candidate scoring
20:44:00.104025 INFO: Finished candidate processing
20:44:00.104172 INFO: Collecting candidate features
20:44:00.147537 INFO: Collecting fragment features
20:44:00.159947 INFO: Finished candidate scoring
20:44:00.179782 PROGRESS: === Extracted 24983 precursors and 277777 fragments ===
20:44:00.184012 INFO: performing precursor FDR with 47 features
20:44:00.184101 INFO: Decoy channel: -1
20:44:00.184128 INFO: Competetive: True
20:44:00.195374 INFO: Setting torch num_threads to 2 for FDR classification task
20:44:00.480555 INFO: Test AUC: 0.803
20:44:00.480699 INFO: Train AUC: 0.807
20:44:00.480730 INFO: AUC difference: 0.52%
20:44:00.678813 INFO: Resetting torch num_threads to 100
20:44:00.680546 INFO: === FDR correction performed with classifier version -1 ===
20:44:00.682469 PROGRESS: ============================= Precursor FDR =============================
20:44:00.682591 PROGRESS: Total precursors accumulated: 12,600
20:44:00.682667 PROGRESS: Target precursors: 10,212 (81.05%)
20:44:00.682722 PROGRESS: Decoy precursors: 2,388 (18.95%)
20:44:00.682769 PROGRESS: 
20:44:00.682814 PROGRESS: Precursor Summary:
20:44:00.685496 PROGRESS: Channel   0:	 0.05 FDR: 7,821; 0.01 FDR: 6,016; 0.001 FDR: 2,676
20:44:00.685610 PROGRESS: 
20:44:00.685673 PROGRESS: Protein Summary:
20:44:00.689368 PROGRESS: Channel   0:	 0.05 FDR: 3,934; 0.01 FDR: 3,209; 0.001 FDR: 1,702
20:44:00.689480 PROGRESS: =========================================================================
20:44:00.719561 INFO: fragments_df: keeping 5000 of 277777 [sum(precursor_idx_mask)=66795 sum(mass_error_mask)=277777 stop_rank=5000
20:44:00.729711 INFO: calibration group: precursor, fitting mz estimator 
20:44:01.647240 INFO: calibration group: precursor, fitting rt estimator 
20:44:02.548756 INFO: calibration group: precursor, fitting mobility estimator 
20:44:03.429116 INFO: calibration group: fragment, fitting mz estimator 
20:44:04.118691 INFO: Using score_cutoff 49.70660203742981 (fac=0.99, q=1)
20:44:04.119339 INFO: calibration group: precursor, predicting mz
20:44:04.120581 INFO: calibration group: precursor, predicting rt
20:44:04.121911 INFO: calibration group: precursor, predicting mobility
20:44:04.122706 INFO: calibration group: fragment, predicting mz
20:44:04.124818 PROGRESS: Required number of precursors found. Starting search parameter optimization.
20:44:04.124963 INFO: Starting optimization step 6.
20:44:04.125034 PROGRESS: === Extracting elution groups 0 to 600 ===
20:44:04.125102 PROGRESS: Extracting batch of 1188 precursors
20:44:04.126955 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:44:04.127003 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:44:04.127056 INFO: FWHM in RT is 3.26 seconds, sigma is 0.72
20:44:04.127079 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.09
20:44:04.127946 INFO: Starting candidate selection
20:44:12.966972 INFO: Starting candidate scoring
20:44:13.165574 INFO: Finished candidate processing
20:44:13.165708 INFO: Collecting candidate features
20:44:13.179681 INFO: Collecting fragment features
20:44:13.184633 INFO: Finished candidate scoring
20:44:13.186408 PROGRESS: === Extracted 2268 precursors and 25083 fragments ===
20:44:13.187447 INFO: performing precursor FDR with 47 features
20:44:13.187492 INFO: Decoy channel: -1
20:44:13.187517 INFO: Competetive: True
20:44:13.190884 INFO: Setting torch num_threads to 2 for FDR classification task
20:44:13.205323 INFO: Test AUC: 0.689
20:44:13.205404 INFO: Train AUC: 0.702
20:44:13.205436 INFO: AUC difference: 1.92%
20:44:13.387649 INFO: Resetting torch num_threads to 100
20:44:13.388372 INFO: === FDR correction performed with classifier version 5 ===
20:44:13.389072 PROGRESS: ============================= Precursor FDR =============================
20:44:13.389162 PROGRESS: Total precursors accumulated: 600
20:44:13.389226 PROGRESS: Target precursors: 496 (82.67%)
20:44:13.389279 PROGRESS: Decoy precursors: 104 (17.33%)
20:44:13.389324 PROGRESS: 
20:44:13.389367 PROGRESS: Precursor Summary:
20:44:13.390380 PROGRESS: Channel   0:	 0.05 FDR:   406; 0.01 FDR:   328; 0.001 FDR:   185
20:44:13.390472 PROGRESS: 
20:44:13.390529 PROGRESS: Protein Summary:
20:44:13.391704 PROGRESS: Channel   0:	 0.05 FDR:   379; 0.01 FDR:   305; 0.001 FDR:   177
20:44:13.391799 PROGRESS: =========================================================================
20:44:13.401929 INFO: fragments_df: keeping 3702 of 25083 [sum(precursor_idx_mask)=6834 sum(mass_error_mask)=25083 stop_rank=3702
20:44:13.408051 INFO: calibration group: precursor, fitting mz estimator 
20:44:13.534703 INFO: calibration group: precursor, fitting rt estimator 
20:44:13.661638 INFO: calibration group: precursor, fitting mobility estimator 
20:44:13.790499 INFO: calibration group: fragment, fitting mz estimator 
20:44:14.292913 INFO: Using score_cutoff 53.24904937820435 (fac=0.99, q=1)
20:44:14.293381 INFO: calibration group: precursor, predicting mz
20:44:14.294603 INFO: calibration group: precursor, predicting rt
20:44:14.295998 INFO: calibration group: precursor, predicting mobility
20:44:14.296789 INFO: calibration group: fragment, predicting mz
20:44:14.298779 INFO: === checking if optimization conditions were reached ===
20:44:14.300285 PROGRESS: ❌ ms2_error      : 10.2759 > 10.0474 or insufficient steps taken.
20:44:14.301218 PROGRESS: ❌ ms1_error      : 10.5658 > 10.5658 or insufficient steps taken.
20:44:14.301268 INFO: ==============================================
20:44:14.301361 INFO: Starting optimization step 7.
20:44:14.301429 PROGRESS: === Extracting elution groups 0 to 600 ===
20:44:14.301493 PROGRESS: Extracting batch of 1188 precursors
20:44:14.302770 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:44:14.302819 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:44:14.302860 INFO: FWHM in RT is 3.36 seconds, sigma is 0.74
20:44:14.302883 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.04
20:44:14.303707 INFO: Starting candidate selection
20:44:22.461802 INFO: Starting candidate scoring
20:44:22.595958 INFO: Finished candidate processing
20:44:22.596084 INFO: Collecting candidate features
20:44:22.608201 INFO: Collecting fragment features
20:44:22.612511 INFO: Finished candidate scoring
20:44:22.614052 PROGRESS: === Extracted 2266 precursors and 24420 fragments ===
20:44:22.614357 INFO: performing precursor FDR with 47 features
20:44:22.614393 INFO: Decoy channel: -1
20:44:22.614417 INFO: Competetive: True
20:44:22.617013 INFO: Setting torch num_threads to 2 for FDR classification task
20:44:22.629451 INFO: Test AUC: 0.761
20:44:22.629530 INFO: Train AUC: 0.756
20:44:22.629559 INFO: AUC difference: 0.70%
20:44:22.804761 INFO: Resetting torch num_threads to 100
20:44:22.805443 INFO: === FDR correction performed with classifier version 6 ===
20:44:22.806143 PROGRESS: ============================= Precursor FDR =============================
20:44:22.806237 PROGRESS: Total precursors accumulated: 600
20:44:22.806298 PROGRESS: Target precursors: 536 (89.33%)
20:44:22.806351 PROGRESS: Decoy precursors: 64 (10.67%)
20:44:22.806398 PROGRESS: 
20:44:22.806444 PROGRESS: Precursor Summary:
20:44:22.807492 PROGRESS: Channel   0:	 0.05 FDR:   492; 0.01 FDR:   420; 0.001 FDR:   332
20:44:22.807587 PROGRESS: 
20:44:22.807644 PROGRESS: Protein Summary:
20:44:22.808833 PROGRESS: Channel   0:	 0.05 FDR:   460; 0.01 FDR:   393; 0.001 FDR:   309
20:44:22.808934 PROGRESS: =========================================================================
20:44:22.812356 INFO: fragments_df: keeping 4188 of 24420 [sum(precursor_idx_mask)=8619 sum(mass_error_mask)=24420 stop_rank=4188
20:44:22.817064 INFO: calibration group: precursor, fitting mz estimator 
20:44:22.952115 INFO: calibration group: precursor, fitting rt estimator 
20:44:23.085381 INFO: calibration group: precursor, fitting mobility estimator 
20:44:23.219209 INFO: calibration group: fragment, fitting mz estimator 
20:44:23.790609 INFO: Using score_cutoff 42.27697436599731 (fac=0.99, q=1)
20:44:23.791070 INFO: calibration group: precursor, predicting mz
20:44:23.792294 INFO: calibration group: precursor, predicting rt
20:44:23.793628 INFO: calibration group: precursor, predicting mobility
20:44:23.794402 INFO: calibration group: fragment, predicting mz
20:44:23.796391 INFO: === checking if optimization conditions were reached ===
20:44:23.797848 PROGRESS: ✅ ms2_error      : 10.0474 <= 10.0474
20:44:23.798787 PROGRESS: ✅ ms1_error      : 10.5658 <= 10.5658
20:44:23.798836 INFO: ==============================================
20:44:23.798926 PROGRESS: Optimization finished for ms2_error, ms1_error.
20:44:23.803383 INFO: calibration group: precursor, predicting mz
20:44:23.804211 INFO: calibration group: precursor, predicting rt
20:44:23.805507 INFO: calibration group: precursor, predicting mobility
20:44:23.806287 INFO: calibration group: fragment, predicting mz
20:44:23.808321 INFO: Starting optimization step 0.
20:44:23.808428 PROGRESS: === Extracting elution groups 0 to 600 ===
20:44:23.808494 PROGRESS: Extracting batch of 1188 precursors
20:44:23.809384 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:44:23.809437 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:44:23.809473 INFO: FWHM in RT is 2.70 seconds, sigma is 0.59
20:44:23.809498 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.58
20:44:23.810252 INFO: Starting candidate selection
20:44:31.796733 INFO: Starting candidate scoring
20:44:31.919273 INFO: Finished candidate processing
20:44:31.919394 INFO: Collecting candidate features
20:44:31.931781 INFO: Collecting fragment features
20:44:31.936178 INFO: Finished candidate scoring
20:44:31.937832 PROGRESS: === Extracted 2259 precursors and 24253 fragments ===
20:44:31.938144 INFO: performing precursor FDR with 47 features
20:44:31.938182 INFO: Decoy channel: -1
20:44:31.938207 INFO: Competetive: True
20:44:31.940822 INFO: Setting torch num_threads to 2 for FDR classification task
20:44:31.954802 INFO: Test AUC: 0.798
20:44:31.954890 INFO: Train AUC: 0.772
20:44:31.954920 INFO: AUC difference: 3.42%
20:44:32.130513 INFO: Resetting torch num_threads to 100
20:44:32.131258 INFO: === FDR correction performed with classifier version 7 ===
20:44:32.131990 PROGRESS: ============================= Precursor FDR =============================
20:44:32.132083 PROGRESS: Total precursors accumulated: 600
20:44:32.132146 PROGRESS: Target precursors: 543 (90.50%)
20:44:32.132199 PROGRESS: Decoy precursors: 57 (9.50%)
20:44:32.132246 PROGRESS: 
20:44:32.132294 PROGRESS: Precursor Summary:
20:44:32.133349 PROGRESS: Channel   0:	 0.05 FDR:   505; 0.01 FDR:   417; 0.001 FDR:   271
20:44:32.133443 PROGRESS: 
20:44:32.133501 PROGRESS: Protein Summary:
20:44:32.134709 PROGRESS: Channel   0:	 0.05 FDR:   472; 0.01 FDR:   389; 0.001 FDR:   251
20:44:32.134803 PROGRESS: =========================================================================
20:44:32.138284 INFO: fragments_df: keeping 4353 of 24253 [sum(precursor_idx_mask)=8579 sum(mass_error_mask)=24253 stop_rank=4353
20:44:32.143265 INFO: calibration group: precursor, fitting mz estimator 
20:44:32.265961 INFO: calibration group: precursor, fitting rt estimator 
20:44:32.382296 INFO: calibration group: precursor, fitting mobility estimator 
20:44:32.494545 INFO: calibration group: fragment, fitting mz estimator 
20:44:33.040787 INFO: Using score_cutoff 42.682406602478025 (fac=0.99, q=1)
20:44:33.041234 INFO: calibration group: precursor, predicting mz
20:44:33.042452 INFO: calibration group: precursor, predicting rt
20:44:33.043781 INFO: calibration group: precursor, predicting mobility
20:44:33.044564 INFO: calibration group: fragment, predicting mz
20:44:33.046633 INFO: === checking if optimization conditions were reached ===
20:44:33.046739 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
20:44:33.048377 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 171.0916.
20:44:33.048431 INFO: ==============================================
20:44:33.048522 INFO: Starting optimization step 1.
20:44:33.048589 PROGRESS: === Extracting elution groups 0 to 600 ===
20:44:33.048645 PROGRESS: Extracting batch of 1188 precursors
20:44:33.050123 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:44:33.050172 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:44:33.050207 INFO: FWHM in RT is 2.69 seconds, sigma is 0.59
20:44:33.050230 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.54
20:44:33.051118 INFO: Starting candidate selection
20:44:34.060197 INFO: Starting candidate scoring
20:44:34.168519 INFO: Finished candidate processing
20:44:34.168646 INFO: Collecting candidate features
20:44:34.180992 INFO: Collecting fragment features
20:44:34.186242 INFO: Finished candidate scoring
20:44:34.187808 PROGRESS: === Extracted 2259 precursors and 23920 fragments ===
20:44:34.188114 INFO: performing precursor FDR with 47 features
20:44:34.188151 INFO: Decoy channel: -1
20:44:34.188175 INFO: Competetive: True
20:44:34.190780 INFO: Setting torch num_threads to 2 for FDR classification task
20:44:34.203242 INFO: Test AUC: 0.817
20:44:34.203311 INFO: Train AUC: 0.798
20:44:34.203341 INFO: AUC difference: 2.33%
20:44:34.383102 INFO: Resetting torch num_threads to 100
20:44:34.383766 INFO: === FDR correction performed with classifier version 7 ===
20:44:34.384454 PROGRESS: ============================= Precursor FDR =============================
20:44:34.384544 PROGRESS: Total precursors accumulated: 600
20:44:34.384606 PROGRESS: Target precursors: 570 (95.00%)
20:44:34.384658 PROGRESS: Decoy precursors: 30 (5.00%)
20:44:34.384719 PROGRESS: 
20:44:34.384768 PROGRESS: Precursor Summary:
20:44:34.385809 PROGRESS: Channel   0:	 0.05 FDR:   558; 0.01 FDR:   490; 0.001 FDR:   292
20:44:34.385900 PROGRESS: 
20:44:34.385956 PROGRESS: Protein Summary:
20:44:34.387198 PROGRESS: Channel   0:	 0.05 FDR:   522; 0.01 FDR:   460; 0.001 FDR:   271
20:44:34.387294 PROGRESS: =========================================================================
20:44:34.390800 INFO: fragments_df: keeping 4783 of 23920 [sum(precursor_idx_mask)=10029 sum(mass_error_mask)=23920 stop_rank=4783
20:44:34.395522 INFO: calibration group: precursor, fitting mz estimator 
20:44:34.531757 INFO: calibration group: precursor, fitting rt estimator 
20:44:34.672161 INFO: calibration group: precursor, fitting mobility estimator 
20:44:34.809975 INFO: calibration group: fragment, fitting mz estimator 
20:44:35.483185 INFO: Using score_cutoff 39.577435149765016 (fac=0.99, q=1)
20:44:35.483638 INFO: calibration group: precursor, predicting mz
20:44:35.485365 INFO: calibration group: precursor, predicting rt
20:44:35.486714 INFO: calibration group: precursor, predicting mobility
20:44:35.487508 INFO: calibration group: fragment, predicting mz
20:44:35.489755 INFO: === checking if optimization conditions were reached ===
20:44:35.489855 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
20:44:35.491582 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 62.1264.
20:44:35.491637 INFO: ==============================================
20:44:35.491725 INFO: Starting optimization step 2.
20:44:35.491790 PROGRESS: === Extracting elution groups 0 to 600 ===
20:44:35.491851 PROGRESS: Extracting batch of 1188 precursors
20:44:35.493117 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:44:35.493163 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:44:35.493198 INFO: FWHM in RT is 2.64 seconds, sigma is 0.58
20:44:35.493223 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.30
20:44:35.494015 INFO: Starting candidate selection
20:44:36.239863 INFO: Starting candidate scoring
20:44:36.361831 INFO: Finished candidate processing
20:44:36.361946 INFO: Collecting candidate features
20:44:36.374804 INFO: Collecting fragment features
20:44:36.378760 INFO: Finished candidate scoring
20:44:36.380321 PROGRESS: === Extracted 2255 precursors and 23654 fragments ===
20:44:36.380666 INFO: performing precursor FDR with 47 features
20:44:36.380708 INFO: Decoy channel: -1
20:44:36.380739 INFO: Competetive: True
20:44:36.383324 INFO: Setting torch num_threads to 2 for FDR classification task
20:44:36.395222 INFO: Test AUC: 0.843
20:44:36.395295 INFO: Train AUC: 0.828
20:44:36.395331 INFO: AUC difference: 1.75%
20:44:36.580211 INFO: Resetting torch num_threads to 100
20:44:36.581250 INFO: === FDR correction performed with classifier version 7 ===
20:44:36.582081 PROGRESS: ============================= Precursor FDR =============================
20:44:36.582178 PROGRESS: Total precursors accumulated: 600
20:44:36.582238 PROGRESS: Target precursors: 571 (95.17%)
20:44:36.582290 PROGRESS: Decoy precursors: 29 (4.83%)
20:44:36.582336 PROGRESS: 
20:44:36.582390 PROGRESS: Precursor Summary:
20:44:36.583588 PROGRESS: Channel   0:	 0.05 FDR:   571; 0.01 FDR:   516; 0.001 FDR:   285
20:44:36.583683 PROGRESS: 
20:44:36.583737 PROGRESS: Protein Summary:
20:44:36.585090 PROGRESS: Channel   0:	 0.05 FDR:   535; 0.01 FDR:   483; 0.001 FDR:   265
20:44:36.585194 PROGRESS: =========================================================================
20:44:36.589153 INFO: fragments_df: keeping 5000 of 23654 [sum(precursor_idx_mask)=10526 sum(mass_error_mask)=23654 stop_rank=5000
20:44:36.595923 INFO: calibration group: precursor, fitting mz estimator 
20:44:36.746661 INFO: calibration group: precursor, fitting rt estimator 
20:44:36.917188 INFO: calibration group: precursor, fitting mobility estimator 
20:44:37.069883 INFO: calibration group: fragment, fitting mz estimator 
20:44:37.769366 INFO: Using score_cutoff 36.477728548049924 (fac=0.99, q=1)
20:44:37.769838 INFO: calibration group: precursor, predicting mz
20:44:37.771078 INFO: calibration group: precursor, predicting rt
20:44:37.772405 INFO: calibration group: precursor, predicting mobility
20:44:37.773177 INFO: calibration group: fragment, predicting mz
20:44:37.775242 INFO: === checking if optimization conditions were reached ===
20:44:37.775344 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
20:44:37.777142 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 26.8712.
20:44:37.777195 INFO: ==============================================
20:44:37.777282 INFO: Starting optimization step 3.
20:44:37.777346 PROGRESS: === Extracting elution groups 0 to 600 ===
20:44:37.777413 PROGRESS: Extracting batch of 1188 precursors
20:44:37.778530 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:44:37.778579 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:44:37.778613 INFO: FWHM in RT is 2.60 seconds, sigma is 0.57
20:44:37.778636 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.17
20:44:37.779463 INFO: Starting candidate selection
20:44:38.410080 INFO: Starting candidate scoring
20:44:38.532397 INFO: Finished candidate processing
20:44:38.533428 INFO: Collecting candidate features
20:44:38.542676 WARNING: intensity_correlation has 2 NaNs ( 0.09 % out of 2263)
20:44:38.545810 INFO: Collecting fragment features
20:44:38.549823 INFO: Finished candidate scoring
20:44:38.551304 PROGRESS: === Extracted 2263 precursors and 23542 fragments ===
20:44:38.551607 INFO: performing precursor FDR with 47 features
20:44:38.551644 INFO: Decoy channel: -1
20:44:38.551668 INFO: Competetive: True
20:44:38.554140 INFO: Setting torch num_threads to 2 for FDR classification task
20:44:38.555376 WARNING: dropped 2 decoy PSMs due to missing features
20:44:38.567535 INFO: Test AUC: 0.865
20:44:38.567602 INFO: Train AUC: 0.843
20:44:38.567630 INFO: AUC difference: 2.67%
20:44:38.749713 INFO: Resetting torch num_threads to 100
20:44:38.750408 INFO: === FDR correction performed with classifier version 7 ===
20:44:38.751189 PROGRESS: ============================= Precursor FDR =============================
20:44:38.751282 PROGRESS: Total precursors accumulated: 600
20:44:38.751342 PROGRESS: Target precursors: 577 (96.17%)
20:44:38.751395 PROGRESS: Decoy precursors: 23 (3.83%)
20:44:38.751442 PROGRESS: 
20:44:38.751491 PROGRESS: Precursor Summary:
20:44:38.752548 PROGRESS: Channel   0:	 0.05 FDR:   577; 0.01 FDR:   514; 0.001 FDR:   317
20:44:38.752638 PROGRESS: 
20:44:38.752693 PROGRESS: Protein Summary:
20:44:38.753924 PROGRESS: Channel   0:	 0.05 FDR:   540; 0.01 FDR:   478; 0.001 FDR:   297
20:44:38.754015 PROGRESS: =========================================================================
20:44:38.757482 INFO: fragments_df: keeping 4945 of 23542 [sum(precursor_idx_mask)=10426 sum(mass_error_mask)=23542 stop_rank=4945
20:44:38.762166 INFO: calibration group: precursor, fitting mz estimator 
20:44:45.967168 INFO: calibration group: precursor, fitting rt estimator 
20:44:46.114570 INFO: calibration group: precursor, fitting mobility estimator 
20:44:46.256721 INFO: calibration group: fragment, fitting mz estimator 
20:44:46.905716 INFO: Using score_cutoff 35.40476895446778 (fac=0.99, q=1)
20:44:46.906172 INFO: calibration group: precursor, predicting mz
20:44:46.907443 INFO: calibration group: precursor, predicting rt
20:44:46.908802 INFO: calibration group: precursor, predicting mobility
20:44:46.909576 INFO: calibration group: fragment, predicting mz
20:44:46.911683 INFO: === checking if optimization conditions were reached ===
20:44:46.911787 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
20:44:46.913612 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 13.4082.
20:44:46.913673 INFO: ==============================================
20:44:46.913762 INFO: Starting optimization step 4.
20:44:46.913827 PROGRESS: === Extracting elution groups 0 to 600 ===
20:44:46.913882 PROGRESS: Extracting batch of 1188 precursors
20:44:46.914944 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:44:46.914991 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:44:46.915036 INFO: FWHM in RT is 2.59 seconds, sigma is 0.57
20:44:46.915059 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.16
20:44:46.930337 INFO: Starting candidate selection
20:44:47.470767 INFO: Starting candidate scoring
20:44:47.579780 INFO: Finished candidate processing
20:44:47.579901 INFO: Collecting candidate features
20:44:47.592672 INFO: Collecting fragment features
20:44:47.596656 INFO: Finished candidate scoring
20:44:47.598929 PROGRESS: === Extracted 2250 precursors and 23178 fragments ===
20:44:47.599268 INFO: performing precursor FDR with 47 features
20:44:47.599309 INFO: Decoy channel: -1
20:44:47.599340 INFO: Competetive: True
20:44:47.602445 INFO: Setting torch num_threads to 2 for FDR classification task
20:44:47.617871 INFO: Test AUC: 0.880
20:44:47.617941 INFO: Train AUC: 0.856
20:44:47.617971 INFO: AUC difference: 2.79%
20:44:47.803535 INFO: Resetting torch num_threads to 100
20:44:47.804210 INFO: === FDR correction performed with classifier version 7 ===
20:44:47.804934 PROGRESS: ============================= Precursor FDR =============================
20:44:47.805028 PROGRESS: Total precursors accumulated: 600
20:44:47.805089 PROGRESS: Target precursors: 581 (96.83%)
20:44:47.805140 PROGRESS: Decoy precursors: 19 (3.17%)
20:44:47.805186 PROGRESS: 
20:44:47.805229 PROGRESS: Precursor Summary:
20:44:47.806306 PROGRESS: Channel   0:	 0.05 FDR:   581; 0.01 FDR:   536; 0.001 FDR:   426
20:44:47.806401 PROGRESS: 
20:44:47.806460 PROGRESS: Protein Summary:
20:44:47.807736 PROGRESS: Channel   0:	 0.05 FDR:   544; 0.01 FDR:   500; 0.001 FDR:   398
20:44:47.807832 PROGRESS: =========================================================================
20:44:47.811378 INFO: fragments_df: keeping 5000 of 23178 [sum(precursor_idx_mask)=10811 sum(mass_error_mask)=23178 stop_rank=5000
20:44:47.820266 INFO: calibration group: precursor, fitting mz estimator 
20:44:47.942042 INFO: calibration group: precursor, fitting rt estimator 
20:44:48.063148 INFO: calibration group: precursor, fitting mobility estimator 
20:44:48.189922 INFO: calibration group: fragment, fitting mz estimator 
20:44:48.815796 INFO: Using score_cutoff 33.791177152633665 (fac=0.99, q=1)
20:44:48.816240 INFO: calibration group: precursor, predicting mz
20:44:48.817454 INFO: calibration group: precursor, predicting rt
20:44:48.818781 INFO: calibration group: precursor, predicting mobility
20:44:48.819551 INFO: calibration group: fragment, predicting mz
20:44:48.821530 INFO: === checking if optimization conditions were reached ===
20:44:48.821634 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
20:44:48.823488 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 11.9163.
20:44:48.823544 INFO: ==============================================
20:44:48.823636 INFO: Starting optimization step 5.
20:44:48.823704 PROGRESS: === Extracting elution groups 0 to 600 ===
20:44:48.823764 PROGRESS: Extracting batch of 1188 precursors
20:44:48.824828 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:44:48.824875 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:44:48.824911 INFO: FWHM in RT is 2.58 seconds, sigma is 0.57
20:44:48.824945 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.09
20:44:48.825676 INFO: Starting candidate selection
20:44:49.354066 INFO: Starting candidate scoring
20:44:49.475789 INFO: Finished candidate processing
20:44:49.475897 INFO: Collecting candidate features
20:44:49.488777 INFO: Collecting fragment features
20:44:49.493259 INFO: Finished candidate scoring
20:44:49.494996 PROGRESS: === Extracted 2252 precursors and 23193 fragments ===
20:44:49.495305 INFO: performing precursor FDR with 47 features
20:44:49.495342 INFO: Decoy channel: -1
20:44:49.495365 INFO: Competetive: True
20:44:49.497940 INFO: Setting torch num_threads to 2 for FDR classification task
20:44:49.510404 INFO: Test AUC: 0.871
20:44:49.510465 INFO: Train AUC: 0.864
20:44:49.510494 INFO: AUC difference: 0.76%
20:44:49.690382 INFO: Resetting torch num_threads to 100
20:44:49.690994 INFO: === FDR correction performed with classifier version 7 ===
20:44:49.692049 PROGRESS: ============================= Precursor FDR =============================
20:44:49.692143 PROGRESS: Total precursors accumulated: 600
20:44:49.692204 PROGRESS: Target precursors: 582 (97.00%)
20:44:49.692254 PROGRESS: Decoy precursors: 18 (3.00%)
20:44:49.692302 PROGRESS: 
20:44:49.692353 PROGRESS: Precursor Summary:
20:44:49.693416 PROGRESS: Channel   0:	 0.05 FDR:   582; 0.01 FDR:   546; 0.001 FDR:   425
20:44:49.693507 PROGRESS: 
20:44:49.693564 PROGRESS: Protein Summary:
20:44:49.694798 PROGRESS: Channel   0:	 0.05 FDR:   544; 0.01 FDR:   509; 0.001 FDR:   396
20:44:49.694897 PROGRESS: =========================================================================
20:44:49.698371 INFO: fragments_df: keeping 5000 of 23193 [sum(precursor_idx_mask)=11018 sum(mass_error_mask)=23193 stop_rank=5000
20:44:49.703526 INFO: calibration group: precursor, fitting mz estimator 
20:44:49.816958 INFO: calibration group: precursor, fitting rt estimator 
20:44:49.936712 INFO: calibration group: precursor, fitting mobility estimator 
20:44:50.063217 INFO: calibration group: fragment, fitting mz estimator 
20:44:50.684175 INFO: Using score_cutoff 33.5653479423523 (fac=0.99, q=1)
20:44:50.684597 INFO: calibration group: precursor, predicting mz
20:44:50.685762 INFO: calibration group: precursor, predicting rt
20:44:50.687099 INFO: calibration group: precursor, predicting mobility
20:44:50.687864 INFO: calibration group: fragment, predicting mz
20:44:50.689854 INFO: === checking if optimization conditions were reached ===
20:44:50.689957 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
20:44:50.691719 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 11.5770.
20:44:50.691774 INFO: ==============================================
20:44:50.691863 INFO: Starting optimization step 6.
20:44:50.691930 PROGRESS: === Extracting elution groups 0 to 600 ===
20:44:50.691996 PROGRESS: Extracting batch of 1188 precursors
20:44:50.693010 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:44:50.693057 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:44:50.693093 INFO: FWHM in RT is 2.57 seconds, sigma is 0.56
20:44:50.693116 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.09
20:44:50.693960 INFO: Starting candidate selection
20:44:51.209807 INFO: Starting candidate scoring
20:44:51.323824 INFO: Finished candidate processing
20:44:51.323932 INFO: Collecting candidate features
20:44:51.337101 INFO: Collecting fragment features
20:44:51.343840 INFO: Finished candidate scoring
20:44:51.345469 PROGRESS: === Extracted 2250 precursors and 23190 fragments ===
20:44:51.345759 INFO: performing precursor FDR with 47 features
20:44:51.345799 INFO: Decoy channel: -1
20:44:51.345823 INFO: Competetive: True
20:44:51.348481 INFO: Setting torch num_threads to 2 for FDR classification task
20:44:51.362659 INFO: Test AUC: 0.857
20:44:51.362726 INFO: Train AUC: 0.866
20:44:51.362755 INFO: AUC difference: 1.03%
20:44:51.541158 INFO: Resetting torch num_threads to 100
20:44:51.541775 INFO: === FDR correction performed with classifier version 7 ===
20:44:51.542444 PROGRESS: ============================= Precursor FDR =============================
20:44:51.542540 PROGRESS: Total precursors accumulated: 600
20:44:51.542599 PROGRESS: Target precursors: 583 (97.17%)
20:44:51.542649 PROGRESS: Decoy precursors: 17 (2.83%)
20:44:51.542693 PROGRESS: 
20:44:51.542736 PROGRESS: Precursor Summary:
20:44:51.543757 PROGRESS: Channel   0:	 0.05 FDR:   583; 0.01 FDR:   545; 0.001 FDR:   429
20:44:51.543852 PROGRESS: 
20:44:51.543910 PROGRESS: Protein Summary:
20:44:51.545120 PROGRESS: Channel   0:	 0.05 FDR:   545; 0.01 FDR:   508; 0.001 FDR:   400
20:44:51.545212 PROGRESS: =========================================================================
20:44:51.549122 INFO: fragments_df: keeping 5000 of 23190 [sum(precursor_idx_mask)=10995 sum(mass_error_mask)=23190 stop_rank=5000
20:44:51.554292 INFO: calibration group: precursor, fitting mz estimator 
20:44:51.669662 INFO: calibration group: precursor, fitting rt estimator 
20:44:51.790143 INFO: calibration group: precursor, fitting mobility estimator 
20:44:51.916430 INFO: calibration group: fragment, fitting mz estimator 
20:44:52.566206 INFO: Using score_cutoff 33.559153871154784 (fac=0.99, q=1)
20:44:52.566645 INFO: calibration group: precursor, predicting mz
20:44:52.567848 INFO: calibration group: precursor, predicting rt
20:44:52.569172 INFO: calibration group: precursor, predicting mobility
20:44:52.569936 INFO: calibration group: fragment, predicting mz
20:44:52.571927 INFO: === checking if optimization conditions were reached ===
20:44:52.572031 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
20:44:52.573033 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 11.5770 found after 7 searches.
20:44:52.573085 INFO: ==============================================
20:44:52.573173 PROGRESS: Optimization finished for rt_error.
20:44:52.577919 INFO: calibration group: precursor, predicting mz
20:44:52.578746 INFO: calibration group: precursor, predicting rt
20:44:52.581975 INFO: calibration group: precursor, predicting mobility
20:44:52.582757 INFO: calibration group: fragment, predicting mz
20:44:52.611118 INFO: Starting optimization step 0.
20:44:52.611261 PROGRESS: === Extracting elution groups 0 to 600 ===
20:44:52.611330 PROGRESS: Extracting batch of 1188 precursors
20:44:52.612453 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:44:52.612500 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:44:52.612542 INFO: FWHM in RT is 2.57 seconds, sigma is 0.56
20:44:52.612564 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.09
20:44:52.613372 INFO: Starting candidate selection
20:44:53.123502 INFO: Starting candidate scoring
20:44:53.239161 INFO: Finished candidate processing
20:44:53.239274 INFO: Collecting candidate features
20:44:53.249371 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2252)
20:44:53.252607 INFO: Collecting fragment features
20:44:53.259495 INFO: Finished candidate scoring
20:44:53.261053 PROGRESS: === Extracted 2252 precursors and 23194 fragments ===
20:44:53.261351 INFO: performing precursor FDR with 47 features
20:44:53.261388 INFO: Decoy channel: -1
20:44:53.261411 INFO: Competetive: True
20:44:53.264106 INFO: Setting torch num_threads to 2 for FDR classification task
20:44:53.265309 WARNING: dropped 1 target PSMs due to missing features
20:44:53.278725 INFO: Test AUC: 0.868
20:44:53.278790 INFO: Train AUC: 0.864
20:44:53.278818 INFO: AUC difference: 0.47%
20:44:53.459431 INFO: Resetting torch num_threads to 100
20:44:53.460037 INFO: === FDR correction performed with classifier version 14 ===
20:44:53.460712 PROGRESS: ============================= Precursor FDR =============================
20:44:53.460804 PROGRESS: Total precursors accumulated: 600
20:44:53.460864 PROGRESS: Target precursors: 582 (97.00%)
20:44:53.460913 PROGRESS: Decoy precursors: 18 (3.00%)
20:44:53.460958 PROGRESS: 
20:44:53.461002 PROGRESS: Precursor Summary:
20:44:53.462052 PROGRESS: Channel   0:	 0.05 FDR:   582; 0.01 FDR:   531; 0.001 FDR:   430
20:44:53.462142 PROGRESS: 
20:44:53.462199 PROGRESS: Protein Summary:
20:44:53.463445 PROGRESS: Channel   0:	 0.05 FDR:   545; 0.01 FDR:   496; 0.001 FDR:   401
20:44:53.463539 PROGRESS: =========================================================================
20:44:53.467087 INFO: fragments_df: keeping 5000 of 23194 [sum(precursor_idx_mask)=10697 sum(mass_error_mask)=23194 stop_rank=5000
20:44:53.472215 INFO: calibration group: precursor, fitting mz estimator 
20:44:53.586349 INFO: calibration group: precursor, fitting rt estimator 
20:44:53.706869 INFO: calibration group: precursor, fitting mobility estimator 
20:44:53.847404 INFO: calibration group: fragment, fitting mz estimator 
20:44:54.649708 INFO: Using score_cutoff 33.57629842758179 (fac=0.99, q=1)
20:44:54.650475 INFO: calibration group: precursor, predicting mz
20:44:54.651780 INFO: calibration group: precursor, predicting rt
20:44:54.653127 INFO: calibration group: precursor, predicting mobility
20:44:54.653920 INFO: calibration group: fragment, predicting mz
20:44:54.656223 INFO: === checking if optimization conditions were reached ===
20:44:54.656341 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
20:44:54.657799 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0563.
20:44:54.657852 INFO: ==============================================
20:44:54.657938 INFO: Starting optimization step 1.
20:44:54.658017 PROGRESS: === Extracting elution groups 0 to 600 ===
20:44:54.658079 PROGRESS: Extracting batch of 1188 precursors
20:44:54.662835 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:44:54.662886 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:44:54.662926 INFO: FWHM in RT is 2.59 seconds, sigma is 0.57
20:44:54.662950 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.11
20:44:54.695090 INFO: Starting candidate selection
20:44:55.184812 INFO: Starting candidate scoring
20:44:55.314777 INFO: Finished candidate processing
20:44:55.314883 INFO: Collecting candidate features
20:44:55.334930 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2245)
20:44:55.340584 INFO: Collecting fragment features
20:44:55.349114 INFO: Finished candidate scoring
20:44:55.351096 PROGRESS: === Extracted 2245 precursors and 22770 fragments ===
20:44:55.351612 INFO: performing precursor FDR with 47 features
20:44:55.351673 INFO: Decoy channel: -1
20:44:55.351712 INFO: Competetive: True
20:44:55.356411 INFO: Setting torch num_threads to 2 for FDR classification task
20:44:55.357619 WARNING: dropped 1 decoy PSMs due to missing features
20:44:55.372869 INFO: Test AUC: 0.854
20:44:55.372939 INFO: Train AUC: 0.866
20:44:55.372967 INFO: AUC difference: 1.33%
20:44:55.559172 INFO: Resetting torch num_threads to 100
20:44:55.559849 INFO: === FDR correction performed with classifier version 14 ===
20:44:55.560524 PROGRESS: ============================= Precursor FDR =============================
20:44:55.560624 PROGRESS: Total precursors accumulated: 599
20:44:55.560702 PROGRESS: Target precursors: 581 (96.99%)
20:44:55.560758 PROGRESS: Decoy precursors: 18 (3.01%)
20:44:55.560806 PROGRESS: 
20:44:55.560851 PROGRESS: Precursor Summary:
20:44:55.561927 PROGRESS: Channel   0:	 0.05 FDR:   581; 0.01 FDR:   529; 0.001 FDR:   414
20:44:55.562022 PROGRESS: 
20:44:55.562078 PROGRESS: Protein Summary:
20:44:55.563370 PROGRESS: Channel   0:	 0.05 FDR:   545; 0.01 FDR:   495; 0.001 FDR:   386
20:44:55.563467 PROGRESS: =========================================================================
20:44:55.567188 INFO: fragments_df: keeping 5000 of 22770 [sum(precursor_idx_mask)=10584 sum(mass_error_mask)=22770 stop_rank=5000
20:44:55.574983 INFO: calibration group: precursor, fitting mz estimator 
20:44:55.752577 INFO: calibration group: precursor, fitting rt estimator 
20:44:55.944600 INFO: calibration group: precursor, fitting mobility estimator 
20:44:56.090504 INFO: calibration group: fragment, fitting mz estimator 
20:44:56.807258 INFO: Using score_cutoff 33.41444734039307 (fac=0.99, q=1)
20:44:56.807841 INFO: calibration group: precursor, predicting mz
20:44:56.809193 INFO: calibration group: precursor, predicting rt
20:44:56.810550 INFO: calibration group: precursor, predicting mobility
20:44:56.811330 INFO: calibration group: fragment, predicting mz
20:44:56.813633 INFO: === checking if optimization conditions were reached ===
20:44:56.813750 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
20:44:56.815525 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0511.
20:44:56.815583 INFO: ==============================================
20:44:56.815678 INFO: Starting optimization step 2.
20:44:56.815742 PROGRESS: === Extracting elution groups 0 to 600 ===
20:44:56.815813 PROGRESS: Extracting batch of 1188 precursors
20:44:56.817257 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:44:56.817306 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:44:56.817349 INFO: FWHM in RT is 2.57 seconds, sigma is 0.56
20:44:56.817371 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.09
20:44:56.818261 INFO: Starting candidate selection
20:44:57.336516 INFO: Starting candidate scoring
20:44:57.447479 INFO: Finished candidate processing
20:44:57.447598 INFO: Collecting candidate features
20:44:57.456605 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2245)
20:44:57.459824 INFO: Collecting fragment features
20:44:57.464051 INFO: Finished candidate scoring
20:44:57.465631 PROGRESS: === Extracted 2245 precursors and 22704 fragments ===
20:44:57.465948 INFO: performing precursor FDR with 47 features
20:44:57.465984 INFO: Decoy channel: -1
20:44:57.466008 INFO: Competetive: True
20:44:57.468715 INFO: Setting torch num_threads to 2 for FDR classification task
20:44:57.470018 WARNING: dropped 1 decoy PSMs due to missing features
20:44:57.481855 INFO: Test AUC: 0.848
20:44:57.481936 INFO: Train AUC: 0.868
20:44:57.481965 INFO: AUC difference: 2.38%
20:44:57.663213 INFO: Resetting torch num_threads to 100
20:44:57.663934 INFO: === FDR correction performed with classifier version 14 ===
20:44:57.664654 PROGRESS: ============================= Precursor FDR =============================
20:44:57.664745 PROGRESS: Total precursors accumulated: 599
20:44:57.664803 PROGRESS: Target precursors: 581 (96.99%)
20:44:57.664851 PROGRESS: Decoy precursors: 18 (3.01%)
20:44:57.664896 PROGRESS: 
20:44:57.664939 PROGRESS: Precursor Summary:
20:44:57.666010 PROGRESS: Channel   0:	 0.05 FDR:   581; 0.01 FDR:   542; 0.001 FDR:   424
20:44:57.666101 PROGRESS: 
20:44:57.666164 PROGRESS: Protein Summary:
20:44:57.667436 PROGRESS: Channel   0:	 0.05 FDR:   544; 0.01 FDR:   506; 0.001 FDR:   395
20:44:57.667531 PROGRESS: =========================================================================
20:44:57.670938 INFO: fragments_df: keeping 5000 of 22704 [sum(precursor_idx_mask)=10857 sum(mass_error_mask)=22704 stop_rank=5000
20:44:57.676291 INFO: calibration group: precursor, fitting mz estimator 
20:44:57.816137 INFO: calibration group: precursor, fitting rt estimator 
20:44:57.959667 INFO: calibration group: precursor, fitting mobility estimator 
20:44:58.097246 INFO: calibration group: fragment, fitting mz estimator 
20:44:58.800973 INFO: Using score_cutoff 33.43287003250122 (fac=0.99, q=1)
20:44:58.801459 INFO: calibration group: precursor, predicting mz
20:44:58.802711 INFO: calibration group: precursor, predicting rt
20:44:58.804048 INFO: calibration group: precursor, predicting mobility
20:44:58.804817 INFO: calibration group: fragment, predicting mz
20:44:58.807087 INFO: === checking if optimization conditions were reached ===
20:44:58.807194 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
20:44:58.808065 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.0511 found after 3 searches.
20:44:58.808113 INFO: ==============================================
20:44:58.808208 PROGRESS: Optimization finished for mobility_error.
20:44:58.813008 INFO: calibration group: precursor, predicting mz
20:44:58.813862 INFO: calibration group: precursor, predicting rt
20:44:58.815168 INFO: calibration group: precursor, predicting mobility
20:44:58.815924 INFO: calibration group: fragment, predicting mz
20:44:58.842658 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
20:44:58.842825 PROGRESS: ==============================================
20:44:58.842899 PROGRESS: ms2_error      : 10.0474
20:44:58.842958 PROGRESS: ms1_error      : 10.5658
20:44:58.843012 PROGRESS: rt_error       : 11.5770
20:44:58.843072 PROGRESS: mobility_error : 0.0511
20:44:58.843121 PROGRESS: ==============================================
20:44:58.844017 INFO: calibration group: precursor, predicting mz
20:44:58.870939 INFO: calibration group: precursor, predicting rt
20:44:59.003316 INFO: calibration group: precursor, predicting mobility
20:44:59.028779 INFO: calibration group: fragment, predicting mz
20:44:59.321301 PROGRESS: Extracting batch of 189636 precursors
20:44:59.406841 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:44:59.407002 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:44:59.407066 INFO: FWHM in RT is 2.55 seconds, sigma is 0.56
20:44:59.407091 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.06
20:44:59.408003 INFO: Starting candidate selection
20:45:09.008738 INFO: Applying score cutoff of 33.43287003250122
20:45:09.014796 INFO: Removed 98607 precursors with score below cutoff
20:45:09.338383 INFO: Starting candidate scoring
20:45:15.752048 INFO: Finished candidate processing
20:45:15.752162 INFO: Collecting candidate features
20:45:16.180619 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 261432)
20:45:16.192776 INFO: Collecting fragment features
20:45:16.354231 INFO: Finished candidate scoring
20:45:16.524996 INFO: === FDR correction performed with classifier version 17 ===
20:45:16.525975 INFO: performing precursor FDR with 47 features
20:45:16.526010 INFO: Decoy channel: -1
20:45:16.526034 INFO: Competetive: True
20:45:16.612799 INFO: Setting torch num_threads to 2 for FDR classification task
20:45:16.655754 WARNING: dropped 1 decoy PSMs due to missing features
20:45:16.655934 WARNING: FDR calculation for 161537 target and 99894 decoy PSMs
20:45:16.655965 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
20:45:22.578900 INFO: Test AUC: 0.918
20:45:22.579046 INFO: Train AUC: 0.920
20:45:22.579078 INFO: AUC difference: 0.23%
20:45:22.816095 INFO: Resetting torch num_threads to 100
20:45:22.841338 INFO: Removing fragments below FDR threshold
20:45:22.903426 PROGRESS: ============================= Precursor FDR =============================
20:45:22.904331 PROGRESS: Total precursors accumulated: 91,474
20:45:22.904406 PROGRESS: Target precursors: 90,569 (99.01%)
20:45:22.904461 PROGRESS: Decoy precursors: 905 (0.99%)
20:45:22.904523 PROGRESS: 
20:45:22.904575 PROGRESS: Precursor Summary:
20:45:22.957100 PROGRESS: Channel   0:	 0.05 FDR: 90,569; 0.01 FDR: 90,569; 0.001 FDR: 84,639
20:45:22.957414 PROGRESS: 
20:45:22.957481 PROGRESS: Protein Summary:
20:45:23.034142 PROGRESS: Channel   0:	 0.05 FDR: 9,650; 0.01 FDR: 9,650; 0.001 FDR: 9,580
20:45:23.034456 PROGRESS: =========================================================================
20:45:23.734767 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
20:45:23.787262 PROGRESS: Loading raw file 4/6: ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
20:45:23.787435 INFO: Quantification results path: run_output/alphadia_1.10.4_Again_good_now/quant
20:45:23.787515 INFO: Creating folder run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/figures
20:45:23.788855 INFO: Initializing RawFileManager
20:45:23.788989 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
20:45:23.789051 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
20:45:23.789090 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
20:45:23.998693 INFO: Reading 39,128 frames with 2,751,035,867 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
20:45:29.896109 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d...
20:45:29.901790 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
20:45:29.907718 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
20:45:29.908052 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
20:45:29.908758 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
20:45:29.910051 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
20:45:29.935114 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
20:45:29.935589 INFO: Indexing quadrupole dimension
20:45:30.476428 INFO: Transposing detector events
20:45:39.358214 INFO: Finished transposing data
20:45:39.397476 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
20:45:39.399924 INFO: RT (min)            : 0.0 - 70.0
20:45:39.400026 INFO: RT duration (sec)   : 4199.8
20:45:39.400075 INFO: RT duration (min)   : 70.0
20:45:39.400110 INFO: Cycle len (scans)   : 9
20:45:39.400143 INFO: Cycle len (sec)     : 0.97
20:45:39.400173 INFO: Number of cycles    : 4347
20:45:39.400204 INFO: MS2 range (m/z)     : 400.0 - 1000.0
20:45:39.459354 INFO: Initializing CalibrationManager
20:45:39.459694 INFO: Loading calibration config
20:45:39.460457 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed'], 'function': LOESSRegression()}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed'], 'function': LOESSRegression(n_kernels=2)}], 'name': 'precursor'}]
20:45:39.460547 INFO: Calibration group :fragment, found 1 estimator(s)
20:45:39.460639 INFO: Calibration group :precursor, found 3 estimator(s)
20:45:39.460818 INFO: Initializing OptimizationManager
20:45:39.460925 INFO: initial parameter: ms1_error = 30
20:45:39.460974 INFO: initial parameter: ms2_error = 30
20:45:39.461038 INFO: initial parameter: rt_error = 2099.891532
20:45:39.461095 INFO: initial parameter: mobility_error = 0.1
20:45:39.461137 INFO: initial parameter: column_type = library
20:45:39.461177 INFO: initial parameter: num_candidates = 1
20:45:39.461215 INFO: initial parameter: classifier_version = -1
20:45:39.461255 INFO: initial parameter: fwhm_rt = 5
20:45:39.461296 INFO: initial parameter: fwhm_mobility = 0.01
20:45:39.461334 INFO: initial parameter: score_cutoff = 0
20:45:39.461406 INFO: Initializing TimingManager
20:45:39.461475 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
20:45:39.461596 INFO: FDRManager not loaded from disk.
20:45:39.461621 INFO: Initializing FDRManager
20:45:39.461662 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
20:45:39.497736 PROGRESS: 95,522 target precursors potentially observable (0 removed)
20:45:39.561866 PROGRESS: Starting initial search for precursors.
20:45:39.569451 INFO: Starting optimization step 0.
20:45:39.569644 PROGRESS: === Extracting elution groups 0 to 200 ===
20:45:39.569723 PROGRESS: Extracting batch of 395 precursors
20:45:39.570930 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:45:39.570982 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:45:39.571015 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:45:39.571046 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:45:39.573290 INFO: Starting candidate selection
20:45:42.863981 INFO: Starting candidate scoring
20:45:42.941318 INFO: Finished candidate processing
20:45:42.941424 INFO: Collecting candidate features
20:45:42.951362 INFO: Collecting fragment features
20:45:42.953978 INFO: Finished candidate scoring
20:45:42.954832 PROGRESS: === Extracted 394 precursors and 4353 fragments ===
20:45:42.955155 INFO: performing precursor FDR with 47 features
20:45:42.955196 INFO: Decoy channel: -1
20:45:42.955220 INFO: Competetive: True
20:45:42.956513 INFO: Setting torch num_threads to 2 for FDR classification task
20:45:42.969298 INFO: Test AUC: 0.428
20:45:42.969367 INFO: Train AUC: 0.492
20:45:42.969397 INFO: AUC difference: 13.01%
20:45:42.969420 WARNING: AUC difference > 5%. This may indicate overfitting.
20:45:43.160508 INFO: Resetting torch num_threads to 100
20:45:43.161136 INFO: === FDR correction performed with classifier version -1 ===
20:45:43.161844 PROGRESS: ============================= Precursor FDR =============================
20:45:43.161935 PROGRESS: Total precursors accumulated: 200
20:45:43.161996 PROGRESS: Target precursors: 102 (51.00%)
20:45:43.162049 PROGRESS: Decoy precursors: 98 (49.00%)
20:45:43.162097 PROGRESS: 
20:45:43.162143 PROGRESS: Precursor Summary:
20:45:43.162976 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:45:43.163074 PROGRESS: 
20:45:43.163131 PROGRESS: Protein Summary:
20:45:43.164026 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:45:43.164116 PROGRESS: =========================================================================
20:45:43.168397 INFO: Starting optimization step 1.
20:45:43.168512 PROGRESS: === Extracting elution groups 200 to 600 ===
20:45:43.168578 PROGRESS: Extracting batch of 793 precursors
20:45:43.169458 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:45:43.169505 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:45:43.169533 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:45:43.169556 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:45:43.170334 INFO: Starting candidate selection
20:45:48.681907 INFO: Starting candidate scoring
20:45:48.795320 INFO: Finished candidate processing
20:45:48.795439 INFO: Collecting candidate features
20:45:48.806946 INFO: Collecting fragment features
20:45:48.810353 INFO: Finished candidate scoring
20:45:48.812446 PROGRESS: === Extracted 1187 precursors and 13147 fragments ===
20:45:48.813340 INFO: performing precursor FDR with 47 features
20:45:48.813384 INFO: Decoy channel: -1
20:45:48.813409 INFO: Competetive: True
20:45:48.816706 INFO: Setting torch num_threads to 2 for FDR classification task
20:45:48.828818 INFO: Test AUC: 0.456
20:45:48.828922 INFO: Train AUC: 0.474
20:45:48.828956 INFO: AUC difference: 3.74%
20:45:49.032558 INFO: Resetting torch num_threads to 100
20:45:49.033358 INFO: === FDR correction performed with classifier version -1 ===
20:45:49.034180 PROGRESS: ============================= Precursor FDR =============================
20:45:49.034283 PROGRESS: Total precursors accumulated: 600
20:45:49.034348 PROGRESS: Target precursors: 288 (48.00%)
20:45:49.034399 PROGRESS: Decoy precursors: 312 (52.00%)
20:45:49.034446 PROGRESS: 
20:45:49.034490 PROGRESS: Precursor Summary:
20:45:49.035398 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
20:45:49.035508 PROGRESS: 
20:45:49.035573 PROGRESS: Protein Summary:
20:45:49.036708 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
20:45:49.036799 PROGRESS: =========================================================================
20:45:49.042834 INFO: Starting optimization step 2.
20:45:49.042958 PROGRESS: === Extracting elution groups 600 to 1400 ===
20:45:49.043040 PROGRESS: Extracting batch of 1583 precursors
20:45:49.044149 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:45:49.044199 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:45:49.044230 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:45:49.044259 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:45:49.046279 INFO: Starting candidate selection
20:45:59.334784 INFO: Starting candidate scoring
20:45:59.527392 INFO: Finished candidate processing
20:45:59.527509 INFO: Collecting candidate features
20:45:59.540008 INFO: Collecting fragment features
20:45:59.544581 INFO: Finished candidate scoring
20:45:59.547733 PROGRESS: === Extracted 2770 precursors and 30818 fragments ===
20:45:59.548702 INFO: performing precursor FDR with 47 features
20:45:59.548745 INFO: Decoy channel: -1
20:45:59.548771 INFO: Competetive: True
20:45:59.552325 INFO: Setting torch num_threads to 2 for FDR classification task
20:45:59.570216 INFO: Test AUC: 0.461
20:45:59.570316 INFO: Train AUC: 0.483
20:45:59.570346 INFO: AUC difference: 4.67%
20:45:59.748983 INFO: Resetting torch num_threads to 100
20:45:59.749805 INFO: === FDR correction performed with classifier version -1 ===
20:45:59.750633 PROGRESS: ============================= Precursor FDR =============================
20:45:59.750726 PROGRESS: Total precursors accumulated: 1,400
20:45:59.750788 PROGRESS: Target precursors: 687 (49.07%)
20:45:59.750839 PROGRESS: Decoy precursors: 713 (50.93%)
20:45:59.750885 PROGRESS: 
20:45:59.750931 PROGRESS: Precursor Summary:
20:45:59.751823 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:45:59.751914 PROGRESS: 
20:45:59.751969 PROGRESS: Protein Summary:
20:45:59.752898 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:45:59.752985 PROGRESS: =========================================================================
20:45:59.760413 INFO: Starting optimization step 3.
20:45:59.760531 PROGRESS: === Extracting elution groups 1400 to 3000 ===
20:45:59.760593 PROGRESS: Extracting batch of 3171 precursors
20:45:59.761688 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:45:59.761736 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:45:59.761764 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:45:59.761786 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:45:59.762559 INFO: Starting candidate selection
20:46:23.733154 INFO: Starting candidate scoring
20:46:24.021360 INFO: Finished candidate processing
20:46:24.021545 INFO: Collecting candidate features
20:46:24.058358 INFO: Collecting fragment features
20:46:24.067373 INFO: Finished candidate scoring
20:46:24.074708 PROGRESS: === Extracted 5940 precursors and 65962 fragments ===
20:46:24.077339 INFO: performing precursor FDR with 47 features
20:46:24.077423 INFO: Decoy channel: -1
20:46:24.077465 INFO: Competetive: True
20:46:24.085917 INFO: Setting torch num_threads to 2 for FDR classification task
20:46:24.112481 INFO: Test AUC: 0.475
20:46:24.112627 INFO: Train AUC: 0.479
20:46:24.112660 INFO: AUC difference: 0.78%
20:46:24.305626 INFO: Resetting torch num_threads to 100
20:46:24.306692 INFO: === FDR correction performed with classifier version -1 ===
20:46:24.307886 PROGRESS: ============================= Precursor FDR =============================
20:46:24.307985 PROGRESS: Total precursors accumulated: 3,000
20:46:24.308050 PROGRESS: Target precursors: 1,451 (48.37%)
20:46:24.308148 PROGRESS: Decoy precursors: 1,549 (51.63%)
20:46:24.308198 PROGRESS: 
20:46:24.308241 PROGRESS: Precursor Summary:
20:46:24.309289 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:46:24.309387 PROGRESS: 
20:46:24.309446 PROGRESS: Protein Summary:
20:46:24.310460 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:46:24.310547 PROGRESS: =========================================================================
20:46:24.325078 INFO: Starting optimization step 4.
20:46:24.325305 PROGRESS: === Extracting elution groups 3000 to 6200 ===
20:46:24.325373 PROGRESS: Extracting batch of 6347 precursors
20:46:24.327086 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:46:24.327177 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:46:24.327208 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:46:24.327229 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:46:24.328084 INFO: Starting candidate selection
20:47:03.637855 INFO: Starting candidate scoring
20:47:04.121597 INFO: Finished candidate processing
20:47:04.121706 INFO: Collecting candidate features
20:47:04.142868 INFO: Collecting fragment features
20:47:04.150792 INFO: Finished candidate scoring
20:47:04.162412 PROGRESS: === Extracted 12287 precursors and 136514 fragments ===
20:47:04.164292 INFO: performing precursor FDR with 47 features
20:47:04.164343 INFO: Decoy channel: -1
20:47:04.164366 INFO: Competetive: True
20:47:04.170493 INFO: Setting torch num_threads to 2 for FDR classification task
20:47:04.216283 INFO: Test AUC: 0.460
20:47:04.216404 INFO: Train AUC: 0.490
20:47:04.216435 INFO: AUC difference: 6.20%
20:47:04.216455 WARNING: AUC difference > 5%. This may indicate overfitting.
20:47:04.401193 INFO: Resetting torch num_threads to 100
20:47:04.402378 INFO: === FDR correction performed with classifier version -1 ===
20:47:04.404185 PROGRESS: ============================= Precursor FDR =============================
20:47:04.404289 PROGRESS: Total precursors accumulated: 6,200
20:47:04.404347 PROGRESS: Target precursors: 3,038 (49.00%)
20:47:04.404397 PROGRESS: Decoy precursors: 3,162 (51.00%)
20:47:04.404442 PROGRESS: 
20:47:04.404485 PROGRESS: Precursor Summary:
20:47:04.405361 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:47:04.405452 PROGRESS: 
20:47:04.405507 PROGRESS: Protein Summary:
20:47:04.406427 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:47:04.406514 PROGRESS: =========================================================================
20:47:04.427463 INFO: Starting optimization step 5.
20:47:04.427721 PROGRESS: === Extracting elution groups 6200 to 12600 ===
20:47:04.427793 PROGRESS: Extracting batch of 12697 precursors
20:47:04.431242 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:47:04.431297 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:47:04.431333 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:47:04.431355 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:47:04.432158 INFO: Starting candidate selection
20:48:23.509836 INFO: Starting candidate scoring
20:49:00.635552 INFO: Finished candidate processing
20:49:00.635886 INFO: Collecting candidate features
20:49:00.696115 INFO: Collecting fragment features
20:49:00.709877 INFO: Finished candidate scoring
20:49:00.730581 PROGRESS: === Extracted 24983 precursors and 277657 fragments ===
20:49:00.734729 INFO: performing precursor FDR with 47 features
20:49:00.734810 INFO: Decoy channel: -1
20:49:00.734836 INFO: Competetive: True
20:49:00.746042 INFO: Setting torch num_threads to 2 for FDR classification task
20:49:01.095977 INFO: Test AUC: 0.813
20:49:01.096123 INFO: Train AUC: 0.807
20:49:01.096154 INFO: AUC difference: 0.79%
20:49:01.300338 INFO: Resetting torch num_threads to 100
20:49:01.301990 INFO: === FDR correction performed with classifier version -1 ===
20:49:01.304096 PROGRESS: ============================= Precursor FDR =============================
20:49:01.304208 PROGRESS: Total precursors accumulated: 12,600
20:49:01.304270 PROGRESS: Target precursors: 10,229 (81.18%)
20:49:01.304323 PROGRESS: Decoy precursors: 2,371 (18.82%)
20:49:01.304378 PROGRESS: 
20:49:01.304425 PROGRESS: Precursor Summary:
20:49:01.306684 PROGRESS: Channel   0:	 0.05 FDR: 7,381; 0.01 FDR: 4,946; 0.001 FDR:    42
20:49:01.306781 PROGRESS: 
20:49:01.306839 PROGRESS: Protein Summary:
20:49:01.309934 PROGRESS: Channel   0:	 0.05 FDR: 3,752; 0.01 FDR: 2,727; 0.001 FDR:    40
20:49:01.310036 PROGRESS: =========================================================================
20:49:01.339350 INFO: fragments_df: keeping 5000 of 277657 [sum(precursor_idx_mask)=54666 sum(mass_error_mask)=277657 stop_rank=5000
20:49:01.351689 INFO: calibration group: precursor, fitting mz estimator 
20:49:01.966593 INFO: calibration group: precursor, fitting rt estimator 
20:49:02.600048 INFO: calibration group: precursor, fitting mobility estimator 
20:49:03.216172 INFO: calibration group: fragment, fitting mz estimator 
20:49:03.828780 INFO: Using score_cutoff 50.86614101028442 (fac=0.99, q=1)
20:49:03.829322 INFO: calibration group: precursor, predicting mz
20:49:03.830423 INFO: calibration group: precursor, predicting rt
20:49:03.831754 INFO: calibration group: precursor, predicting mobility
20:49:03.832527 INFO: calibration group: fragment, predicting mz
20:49:03.834497 PROGRESS: Required number of precursors found. Starting search parameter optimization.
20:49:03.834623 INFO: Starting optimization step 6.
20:49:03.834695 PROGRESS: === Extracting elution groups 0 to 600 ===
20:49:03.834761 PROGRESS: Extracting batch of 1188 precursors
20:49:03.835862 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:49:03.835910 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:49:03.835953 INFO: FWHM in RT is 3.32 seconds, sigma is 0.73
20:49:03.835978 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.22
20:49:03.836690 INFO: Starting candidate selection
20:49:12.052962 INFO: Starting candidate scoring
20:49:12.292023 INFO: Finished candidate processing
20:49:12.292144 INFO: Collecting candidate features
20:49:12.305734 INFO: Collecting fragment features
20:49:12.309827 INFO: Finished candidate scoring
20:49:12.311452 PROGRESS: === Extracted 2291 precursors and 25342 fragments ===
20:49:12.311753 INFO: performing precursor FDR with 47 features
20:49:12.311789 INFO: Decoy channel: -1
20:49:12.311812 INFO: Competetive: True
20:49:12.314503 INFO: Setting torch num_threads to 2 for FDR classification task
20:49:12.327607 INFO: Test AUC: 0.718
20:49:12.327698 INFO: Train AUC: 0.727
20:49:12.327728 INFO: AUC difference: 1.18%
20:49:12.517865 INFO: Resetting torch num_threads to 100
20:49:12.518600 INFO: === FDR correction performed with classifier version 5 ===
20:49:12.519345 PROGRESS: ============================= Precursor FDR =============================
20:49:12.519441 PROGRESS: Total precursors accumulated: 600
20:49:12.519510 PROGRESS: Target precursors: 503 (83.83%)
20:49:12.519564 PROGRESS: Decoy precursors: 97 (16.17%)
20:49:12.519612 PROGRESS: 
20:49:12.519657 PROGRESS: Precursor Summary:
20:49:12.520648 PROGRESS: Channel   0:	 0.05 FDR:   387; 0.01 FDR:   261; 0.001 FDR:    88
20:49:12.520740 PROGRESS: 
20:49:12.520796 PROGRESS: Protein Summary:
20:49:12.521928 PROGRESS: Channel   0:	 0.05 FDR:   362; 0.01 FDR:   245; 0.001 FDR:    84
20:49:12.522030 PROGRESS: =========================================================================
20:49:12.525988 INFO: fragments_df: keeping 3092 of 25342 [sum(precursor_idx_mask)=5435 sum(mass_error_mask)=25342 stop_rank=3092
20:49:12.531222 INFO: calibration group: precursor, fitting mz estimator 
20:49:12.677458 INFO: calibration group: precursor, fitting rt estimator 
20:49:12.800283 INFO: calibration group: precursor, fitting mobility estimator 
20:49:12.924044 INFO: calibration group: fragment, fitting mz estimator 
20:49:13.338059 INFO: Using score_cutoff 52.90896656799317 (fac=0.99, q=1)
20:49:13.338483 INFO: calibration group: precursor, predicting mz
20:49:13.339637 INFO: calibration group: precursor, predicting rt
20:49:13.340964 INFO: calibration group: precursor, predicting mobility
20:49:13.341741 INFO: calibration group: fragment, predicting mz
20:49:13.343870 INFO: === checking if optimization conditions were reached ===
20:49:13.345433 PROGRESS: ❌ ms2_error      : 10.0474 > 10.0474 or insufficient steps taken.
20:49:13.346343 PROGRESS: ❌ ms1_error      : 10.5658 > 10.5658 or insufficient steps taken.
20:49:13.346391 INFO: ==============================================
20:49:13.346476 INFO: Starting optimization step 7.
20:49:13.346540 PROGRESS: === Extracting elution groups 0 to 600 ===
20:49:13.346596 PROGRESS: Extracting batch of 1188 precursors
20:49:13.347702 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:49:13.347749 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:49:13.347784 INFO: FWHM in RT is 3.33 seconds, sigma is 0.73
20:49:13.347807 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.27
20:49:13.348511 INFO: Starting candidate selection
20:49:21.737570 INFO: Starting candidate scoring
20:49:21.863178 INFO: Finished candidate processing
20:49:21.863292 INFO: Collecting candidate features
20:49:21.875580 INFO: Collecting fragment features
20:49:21.880351 INFO: Finished candidate scoring
20:49:21.882336 PROGRESS: === Extracted 2295 precursors and 24689 fragments ===
20:49:21.882657 INFO: performing precursor FDR with 47 features
20:49:21.882696 INFO: Decoy channel: -1
20:49:21.882720 INFO: Competetive: True
20:49:21.885453 INFO: Setting torch num_threads to 2 for FDR classification task
20:49:21.898448 INFO: Test AUC: 0.752
20:49:21.898558 INFO: Train AUC: 0.756
20:49:21.898587 INFO: AUC difference: 0.58%
20:49:22.075576 INFO: Resetting torch num_threads to 100
20:49:22.076327 INFO: === FDR correction performed with classifier version 6 ===
20:49:22.077087 PROGRESS: ============================= Precursor FDR =============================
20:49:22.077180 PROGRESS: Total precursors accumulated: 600
20:49:22.077241 PROGRESS: Target precursors: 544 (90.67%)
20:49:22.077291 PROGRESS: Decoy precursors: 56 (9.33%)
20:49:22.077340 PROGRESS: 
20:49:22.077384 PROGRESS: Precursor Summary:
20:49:22.078426 PROGRESS: Channel   0:	 0.05 FDR:   499; 0.01 FDR:   395; 0.001 FDR:   184
20:49:22.078518 PROGRESS: 
20:49:22.078573 PROGRESS: Protein Summary:
20:49:22.079777 PROGRESS: Channel   0:	 0.05 FDR:   466; 0.01 FDR:   367; 0.001 FDR:   177
20:49:22.079894 PROGRESS: =========================================================================
20:49:22.083368 INFO: fragments_df: keeping 4017 of 24689 [sum(precursor_idx_mask)=8216 sum(mass_error_mask)=24689 stop_rank=4017
20:49:22.088140 INFO: calibration group: precursor, fitting mz estimator 
20:49:22.222903 INFO: calibration group: precursor, fitting rt estimator 
20:49:22.355907 INFO: calibration group: precursor, fitting mobility estimator 
20:49:22.486743 INFO: calibration group: fragment, fitting mz estimator 
20:49:23.031227 INFO: Using score_cutoff 41.25511568984985 (fac=0.99, q=1)
20:49:23.031636 INFO: calibration group: precursor, predicting mz
20:49:23.032752 INFO: calibration group: precursor, predicting rt
20:49:23.034066 INFO: calibration group: precursor, predicting mobility
20:49:23.034837 INFO: calibration group: fragment, predicting mz
20:49:23.036876 INFO: === checking if optimization conditions were reached ===
20:49:23.038328 PROGRESS: ✅ ms2_error      : 10.0474 <= 10.0474
20:49:23.039263 PROGRESS: ✅ ms1_error      : 10.5658 <= 10.5658
20:49:23.039313 INFO: ==============================================
20:49:23.039401 PROGRESS: Optimization finished for ms2_error, ms1_error.
20:49:23.043752 INFO: calibration group: precursor, predicting mz
20:49:23.044565 INFO: calibration group: precursor, predicting rt
20:49:23.045870 INFO: calibration group: precursor, predicting mobility
20:49:23.046635 INFO: calibration group: fragment, predicting mz
20:49:23.048652 INFO: Starting optimization step 0.
20:49:23.048755 PROGRESS: === Extracting elution groups 0 to 600 ===
20:49:23.048818 PROGRESS: Extracting batch of 1188 precursors
20:49:23.049737 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:49:23.049784 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:49:23.049828 INFO: FWHM in RT is 2.83 seconds, sigma is 0.62
20:49:23.049851 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.59
20:49:23.050614 INFO: Starting candidate selection
20:50:01.030544 INFO: Starting candidate scoring
20:50:01.156482 INFO: Finished candidate processing
20:50:01.156592 INFO: Collecting candidate features
20:50:01.168444 INFO: Collecting fragment features
20:50:01.172980 INFO: Finished candidate scoring
20:50:01.174402 PROGRESS: === Extracted 2283 precursors and 24461 fragments ===
20:50:01.174685 INFO: performing precursor FDR with 47 features
20:50:01.174722 INFO: Decoy channel: -1
20:50:01.174746 INFO: Competetive: True
20:50:01.177193 INFO: Setting torch num_threads to 2 for FDR classification task
20:50:01.189465 INFO: Test AUC: 0.737
20:50:01.189530 INFO: Train AUC: 0.768
20:50:01.189558 INFO: AUC difference: 4.02%
20:50:01.370880 INFO: Resetting torch num_threads to 100
20:50:01.371475 INFO: === FDR correction performed with classifier version 7 ===
20:50:01.372170 PROGRESS: ============================= Precursor FDR =============================
20:50:01.372261 PROGRESS: Total precursors accumulated: 600
20:50:01.372321 PROGRESS: Target precursors: 540 (90.00%)
20:50:01.372372 PROGRESS: Decoy precursors: 60 (10.00%)
20:50:01.372419 PROGRESS: 
20:50:01.372462 PROGRESS: Precursor Summary:
20:50:01.373480 PROGRESS: Channel   0:	 0.05 FDR:   485; 0.01 FDR:   402; 0.001 FDR:   182
20:50:01.373570 PROGRESS: 
20:50:01.373627 PROGRESS: Protein Summary:
20:50:01.374783 PROGRESS: Channel   0:	 0.05 FDR:   453; 0.01 FDR:   373; 0.001 FDR:   175
20:50:01.374873 PROGRESS: =========================================================================
20:50:01.378168 INFO: fragments_df: keeping 4182 of 24461 [sum(precursor_idx_mask)=8282 sum(mass_error_mask)=24461 stop_rank=4182
20:50:01.382807 INFO: calibration group: precursor, fitting mz estimator 
20:50:01.494245 INFO: calibration group: precursor, fitting rt estimator 
20:50:01.606199 INFO: calibration group: precursor, fitting mobility estimator 
20:50:01.718359 INFO: calibration group: fragment, fitting mz estimator 
20:50:02.228367 INFO: Using score_cutoff 41.43263504219055 (fac=0.99, q=1)
20:50:02.228806 INFO: calibration group: precursor, predicting mz
20:50:02.229943 INFO: calibration group: precursor, predicting rt
20:50:02.231277 INFO: calibration group: precursor, predicting mobility
20:50:02.232056 INFO: calibration group: fragment, predicting mz
20:50:02.234253 INFO: === checking if optimization conditions were reached ===
20:50:02.234396 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
20:50:02.236054 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 346.2049.
20:50:02.236110 INFO: ==============================================
20:50:02.236199 INFO: Starting optimization step 1.
20:50:02.236262 PROGRESS: === Extracting elution groups 0 to 600 ===
20:50:02.236319 PROGRESS: Extracting batch of 1188 precursors
20:50:02.237345 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:50:02.237394 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:50:02.237428 INFO: FWHM in RT is 2.71 seconds, sigma is 0.60
20:50:02.237451 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.48
20:50:02.238288 INFO: Starting candidate selection
20:50:03.771185 INFO: Starting candidate scoring
20:50:03.895708 INFO: Finished candidate processing
20:50:03.895818 INFO: Collecting candidate features
20:50:03.908180 INFO: Collecting fragment features
20:50:03.912888 INFO: Finished candidate scoring
20:50:03.914482 PROGRESS: === Extracted 2285 precursors and 24205 fragments ===
20:50:03.914784 INFO: performing precursor FDR with 47 features
20:50:03.914825 INFO: Decoy channel: -1
20:50:03.914850 INFO: Competetive: True
20:50:03.917416 INFO: Setting torch num_threads to 2 for FDR classification task
20:50:03.929914 INFO: Test AUC: 0.819
20:50:03.929983 INFO: Train AUC: 0.781
20:50:03.930027 INFO: AUC difference: 4.89%
20:50:04.105156 INFO: Resetting torch num_threads to 100
20:50:04.105750 INFO: === FDR correction performed with classifier version 7 ===
20:50:04.106417 PROGRESS: ============================= Precursor FDR =============================
20:50:04.106509 PROGRESS: Total precursors accumulated: 600
20:50:04.106569 PROGRESS: Target precursors: 561 (93.50%)
20:50:04.106620 PROGRESS: Decoy precursors: 39 (6.50%)
20:50:04.106665 PROGRESS: 
20:50:04.106712 PROGRESS: Precursor Summary:
20:50:04.107787 PROGRESS: Channel   0:	 0.05 FDR:   536; 0.01 FDR:   427; 0.001 FDR:   333
20:50:04.107889 PROGRESS: 
20:50:04.107948 PROGRESS: Protein Summary:
20:50:04.109156 PROGRESS: Channel   0:	 0.05 FDR:   501; 0.01 FDR:   398; 0.001 FDR:   310
20:50:04.109246 PROGRESS: =========================================================================
20:50:04.112597 INFO: fragments_df: keeping 4333 of 24205 [sum(precursor_idx_mask)=8798 sum(mass_error_mask)=24205 stop_rank=4333
20:50:04.117347 INFO: calibration group: precursor, fitting mz estimator 
20:50:04.246489 INFO: calibration group: precursor, fitting rt estimator 
20:50:04.381799 INFO: calibration group: precursor, fitting mobility estimator 
20:50:04.516229 INFO: calibration group: fragment, fitting mz estimator 
20:50:05.113681 INFO: Using score_cutoff 41.15085926055908 (fac=0.99, q=1)
20:50:05.114116 INFO: calibration group: precursor, predicting mz
20:50:05.115271 INFO: calibration group: precursor, predicting rt
20:50:05.116597 INFO: calibration group: precursor, predicting mobility
20:50:05.117372 INFO: calibration group: fragment, predicting mz
20:50:05.119480 INFO: === checking if optimization conditions were reached ===
20:50:05.119581 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
20:50:05.121189 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 244.4048.
20:50:05.121245 INFO: ==============================================
20:50:05.121334 INFO: Starting optimization step 2.
20:50:05.121405 PROGRESS: === Extracting elution groups 0 to 600 ===
20:50:05.121468 PROGRESS: Extracting batch of 1188 precursors
20:50:05.122533 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:50:05.122586 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:50:05.122625 INFO: FWHM in RT is 2.70 seconds, sigma is 0.59
20:50:05.122651 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.43
20:50:05.123390 INFO: Starting candidate selection
20:50:06.405400 INFO: Starting candidate scoring
20:50:06.512002 INFO: Finished candidate processing
20:50:06.512107 INFO: Collecting candidate features
20:50:06.523787 INFO: Collecting fragment features
20:50:06.528660 INFO: Finished candidate scoring
20:50:06.530081 PROGRESS: === Extracted 2274 precursors and 24029 fragments ===
20:50:06.530358 INFO: performing precursor FDR with 47 features
20:50:06.530394 INFO: Decoy channel: -1
20:50:06.530416 INFO: Competetive: True
20:50:06.532901 INFO: Setting torch num_threads to 2 for FDR classification task
20:50:06.544685 INFO: Test AUC: 0.790
20:50:06.544754 INFO: Train AUC: 0.792
20:50:06.544784 INFO: AUC difference: 0.19%
20:50:06.721193 INFO: Resetting torch num_threads to 100
20:50:06.721779 INFO: === FDR correction performed with classifier version 7 ===
20:50:06.722456 PROGRESS: ============================= Precursor FDR =============================
20:50:06.722548 PROGRESS: Total precursors accumulated: 600
20:50:06.722609 PROGRESS: Target precursors: 559 (93.17%)
20:50:06.722659 PROGRESS: Decoy precursors: 41 (6.83%)
20:50:06.722705 PROGRESS: 
20:50:06.722757 PROGRESS: Precursor Summary:
20:50:06.723816 PROGRESS: Channel   0:	 0.05 FDR:   545; 0.01 FDR:   430; 0.001 FDR:   359
20:50:06.723909 PROGRESS: 
20:50:06.723964 PROGRESS: Protein Summary:
20:50:06.725159 PROGRESS: Channel   0:	 0.05 FDR:   511; 0.01 FDR:   404; 0.001 FDR:   336
20:50:06.725248 PROGRESS: =========================================================================
20:50:06.728533 INFO: fragments_df: keeping 4335 of 24029 [sum(precursor_idx_mask)=8843 sum(mass_error_mask)=24029 stop_rank=4335
20:50:06.733272 INFO: calibration group: precursor, fitting mz estimator 
20:50:06.850216 INFO: calibration group: precursor, fitting rt estimator 
20:50:06.962496 INFO: calibration group: precursor, fitting mobility estimator 
20:50:07.076513 INFO: calibration group: fragment, fitting mz estimator 
20:50:07.603531 INFO: Using score_cutoff 41.16428402824402 (fac=0.99, q=1)
20:50:07.603942 INFO: calibration group: precursor, predicting mz
20:50:07.605041 INFO: calibration group: precursor, predicting rt
20:50:07.606370 INFO: calibration group: precursor, predicting mobility
20:50:07.607151 INFO: calibration group: fragment, predicting mz
20:50:07.609148 INFO: === checking if optimization conditions were reached ===
20:50:07.609273 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
20:50:07.610978 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 141.3867.
20:50:07.611055 INFO: ==============================================
20:50:07.611146 INFO: Starting optimization step 3.
20:50:07.611211 PROGRESS: === Extracting elution groups 0 to 600 ===
20:50:07.611278 PROGRESS: Extracting batch of 1188 precursors
20:50:07.612405 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:50:07.612453 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:50:07.612489 INFO: FWHM in RT is 2.70 seconds, sigma is 0.59
20:50:07.612512 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.39
20:50:07.613228 INFO: Starting candidate selection
20:50:08.591297 INFO: Starting candidate scoring
20:50:08.714807 INFO: Finished candidate processing
20:50:08.714916 INFO: Collecting candidate features
20:50:08.726603 INFO: Collecting fragment features
20:50:08.730590 INFO: Finished candidate scoring
20:50:08.731996 PROGRESS: === Extracted 2276 precursors and 23930 fragments ===
20:50:08.732281 INFO: performing precursor FDR with 47 features
20:50:08.732317 INFO: Decoy channel: -1
20:50:08.732340 INFO: Competetive: True
20:50:08.734875 INFO: Setting torch num_threads to 2 for FDR classification task
20:50:08.746860 INFO: Test AUC: 0.846
20:50:08.746923 INFO: Train AUC: 0.802
20:50:08.746953 INFO: AUC difference: 5.47%
20:50:08.746974 WARNING: AUC difference > 5%. This may indicate overfitting.
20:50:08.921574 INFO: Resetting torch num_threads to 100
20:50:08.922157 INFO: === FDR correction performed with classifier version 7 ===
20:50:08.922809 PROGRESS: ============================= Precursor FDR =============================
20:50:08.922898 PROGRESS: Total precursors accumulated: 600
20:50:08.922958 PROGRESS: Target precursors: 560 (93.33%)
20:50:08.923007 PROGRESS: Decoy precursors: 40 (6.67%)
20:50:08.923067 PROGRESS: 
20:50:08.923112 PROGRESS: Precursor Summary:
20:50:08.924149 PROGRESS: Channel   0:	 0.05 FDR:   544; 0.01 FDR:   433; 0.001 FDR:   347
20:50:08.924241 PROGRESS: 
20:50:08.924298 PROGRESS: Protein Summary:
20:50:08.925517 PROGRESS: Channel   0:	 0.05 FDR:   511; 0.01 FDR:   406; 0.001 FDR:   323
20:50:08.925608 PROGRESS: =========================================================================
20:50:08.928947 INFO: fragments_df: keeping 4330 of 23930 [sum(precursor_idx_mask)=8823 sum(mass_error_mask)=23930 stop_rank=4330
20:50:08.933863 INFO: calibration group: precursor, fitting mz estimator 
20:50:09.050740 INFO: calibration group: precursor, fitting rt estimator 
20:50:09.162834 INFO: calibration group: precursor, fitting mobility estimator 
20:50:09.275982 INFO: calibration group: fragment, fitting mz estimator 
20:50:09.802943 INFO: Using score_cutoff 40.95848148651123 (fac=0.99, q=1)
20:50:09.803369 INFO: calibration group: precursor, predicting mz
20:50:09.804482 INFO: calibration group: precursor, predicting rt
20:50:09.805794 INFO: calibration group: precursor, predicting mobility
20:50:09.806565 INFO: calibration group: fragment, predicting mz
20:50:09.808573 INFO: === checking if optimization conditions were reached ===
20:50:09.808685 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
20:50:09.810364 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 12.9990.
20:50:09.810416 INFO: ==============================================
20:50:09.810500 INFO: Starting optimization step 4.
20:50:09.810564 PROGRESS: === Extracting elution groups 0 to 600 ===
20:50:09.810620 PROGRESS: Extracting batch of 1188 precursors
20:50:09.811641 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:50:09.811696 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:50:09.811730 INFO: FWHM in RT is 2.70 seconds, sigma is 0.59
20:50:09.811752 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.39
20:50:09.812473 INFO: Starting candidate selection
20:50:10.323075 INFO: Starting candidate scoring
20:50:10.415941 INFO: Finished candidate processing
20:50:10.416045 INFO: Collecting candidate features
20:50:10.425475 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2253)
20:50:10.428684 INFO: Collecting fragment features
20:50:10.432699 INFO: Finished candidate scoring
20:50:10.434197 PROGRESS: === Extracted 2253 precursors and 23032 fragments ===
20:50:10.434491 INFO: performing precursor FDR with 47 features
20:50:10.434528 INFO: Decoy channel: -1
20:50:10.434551 INFO: Competetive: True
20:50:10.437101 INFO: Setting torch num_threads to 2 for FDR classification task
20:50:10.438298 WARNING: dropped 1 decoy PSMs due to missing features
20:50:10.449485 INFO: Test AUC: 0.907
20:50:10.449544 INFO: Train AUC: 0.851
20:50:10.449575 INFO: AUC difference: 6.48%
20:50:10.449601 WARNING: AUC difference > 5%. This may indicate overfitting.
20:50:10.626769 INFO: Resetting torch num_threads to 100
20:50:10.627352 INFO: === FDR correction performed with classifier version 7 ===
20:50:10.628016 PROGRESS: ============================= Precursor FDR =============================
20:50:10.628109 PROGRESS: Total precursors accumulated: 600
20:50:10.628171 PROGRESS: Target precursors: 584 (97.33%)
20:50:10.628224 PROGRESS: Decoy precursors: 16 (2.67%)
20:50:10.628271 PROGRESS: 
20:50:10.628315 PROGRESS: Precursor Summary:
20:50:10.629370 PROGRESS: Channel   0:	 0.05 FDR:   584; 0.01 FDR:   521; 0.001 FDR:   378
20:50:10.629465 PROGRESS: 
20:50:10.629521 PROGRESS: Protein Summary:
20:50:10.630755 PROGRESS: Channel   0:	 0.05 FDR:   548; 0.01 FDR:   488; 0.001 FDR:   352
20:50:10.630850 PROGRESS: =========================================================================
20:50:10.634200 INFO: fragments_df: keeping 4928 of 23032 [sum(precursor_idx_mask)=10584 sum(mass_error_mask)=23032 stop_rank=4928
20:50:10.638861 INFO: calibration group: precursor, fitting mz estimator 
20:50:10.768170 INFO: calibration group: precursor, fitting rt estimator 
20:50:10.884695 INFO: calibration group: precursor, fitting mobility estimator 
20:50:11.003902 INFO: calibration group: fragment, fitting mz estimator 
20:50:11.619968 INFO: Using score_cutoff 34.03990962982178 (fac=0.99, q=1)
20:50:11.620381 INFO: calibration group: precursor, predicting mz
20:50:11.621510 INFO: calibration group: precursor, predicting rt
20:50:11.622855 INFO: calibration group: precursor, predicting mobility
20:50:11.623637 INFO: calibration group: fragment, predicting mz
20:50:11.625685 INFO: === checking if optimization conditions were reached ===
20:50:11.625783 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
20:50:11.627541 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 11.2582.
20:50:11.627598 INFO: ==============================================
20:50:11.627688 INFO: Starting optimization step 5.
20:50:11.627754 PROGRESS: === Extracting elution groups 0 to 600 ===
20:50:11.627813 PROGRESS: Extracting batch of 1188 precursors
20:50:11.628918 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:50:11.628966 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:50:11.629011 INFO: FWHM in RT is 2.56 seconds, sigma is 0.56
20:50:11.629035 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.17
20:50:11.629730 INFO: Starting candidate selection
20:50:12.153023 INFO: Starting candidate scoring
20:50:12.274543 INFO: Finished candidate processing
20:50:12.274649 INFO: Collecting candidate features
20:50:12.283578 WARNING: intensity_correlation has 2 NaNs ( 0.09 % out of 2240)
20:50:12.286734 INFO: Collecting fragment features
20:50:12.290976 INFO: Finished candidate scoring
20:50:12.292387 PROGRESS: === Extracted 2240 precursors and 22928 fragments ===
20:50:12.292668 INFO: performing precursor FDR with 47 features
20:50:12.292704 INFO: Decoy channel: -1
20:50:12.292726 INFO: Competetive: True
20:50:12.295168 INFO: Setting torch num_threads to 2 for FDR classification task
20:50:12.296345 WARNING: dropped 2 decoy PSMs due to missing features
20:50:12.307309 INFO: Test AUC: 0.854
20:50:12.307375 INFO: Train AUC: 0.859
20:50:12.307407 INFO: AUC difference: 0.48%
20:50:12.484203 INFO: Resetting torch num_threads to 100
20:50:12.484762 INFO: === FDR correction performed with classifier version 7 ===
20:50:12.485464 PROGRESS: ============================= Precursor FDR =============================
20:50:12.485554 PROGRESS: Total precursors accumulated: 600
20:50:12.485613 PROGRESS: Target precursors: 576 (96.00%)
20:50:12.485664 PROGRESS: Decoy precursors: 24 (4.00%)
20:50:12.485710 PROGRESS: 
20:50:12.485754 PROGRESS: Precursor Summary:
20:50:12.486792 PROGRESS: Channel   0:	 0.05 FDR:   576; 0.01 FDR:   505; 0.001 FDR:   375
20:50:12.486880 PROGRESS: 
20:50:12.486936 PROGRESS: Protein Summary:
20:50:12.488216 PROGRESS: Channel   0:	 0.05 FDR:   541; 0.01 FDR:   472; 0.001 FDR:   349
20:50:12.488312 PROGRESS: =========================================================================
20:50:12.491781 INFO: fragments_df: keeping 4883 of 22928 [sum(precursor_idx_mask)=10267 sum(mass_error_mask)=22928 stop_rank=4883
20:50:12.496445 INFO: calibration group: precursor, fitting mz estimator 
20:50:12.618019 INFO: calibration group: precursor, fitting rt estimator 
20:50:12.734009 INFO: calibration group: precursor, fitting mobility estimator 
20:50:12.855486 INFO: calibration group: fragment, fitting mz estimator 
20:50:13.469639 INFO: Using score_cutoff 35.52654170379639 (fac=0.99, q=1)
20:50:13.470055 INFO: calibration group: precursor, predicting mz
20:50:13.471160 INFO: calibration group: precursor, predicting rt
20:50:13.472473 INFO: calibration group: precursor, predicting mobility
20:50:13.473239 INFO: calibration group: fragment, predicting mz
20:50:13.475256 INFO: === checking if optimization conditions were reached ===
20:50:13.475355 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
20:50:13.477076 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 8.6063.
20:50:13.477133 INFO: ==============================================
20:50:13.477220 INFO: Starting optimization step 6.
20:50:13.477285 PROGRESS: === Extracting elution groups 0 to 600 ===
20:50:13.477341 PROGRESS: Extracting batch of 1188 precursors
20:50:13.478399 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:50:13.478444 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:50:13.478480 INFO: FWHM in RT is 2.58 seconds, sigma is 0.57
20:50:13.478505 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.18
20:50:13.479191 INFO: Starting candidate selection
20:50:13.985056 INFO: Starting candidate scoring
20:50:14.103655 INFO: Finished candidate processing
20:50:14.103768 INFO: Collecting candidate features
20:50:14.116381 INFO: Collecting fragment features
20:50:14.120922 INFO: Finished candidate scoring
20:50:14.122647 PROGRESS: === Extracted 2244 precursors and 22985 fragments ===
20:50:14.122951 INFO: performing precursor FDR with 47 features
20:50:14.122989 INFO: Decoy channel: -1
20:50:14.123013 INFO: Competetive: True
20:50:14.125612 INFO: Setting torch num_threads to 2 for FDR classification task
20:50:14.138469 INFO: Test AUC: 0.838
20:50:14.138537 INFO: Train AUC: 0.864
20:50:14.138567 INFO: AUC difference: 2.99%
20:50:14.313677 INFO: Resetting torch num_threads to 100
20:50:14.314248 INFO: === FDR correction performed with classifier version 7 ===
20:50:14.314957 PROGRESS: ============================= Precursor FDR =============================
20:50:14.315060 PROGRESS: Total precursors accumulated: 600
20:50:14.315119 PROGRESS: Target precursors: 577 (96.17%)
20:50:14.315171 PROGRESS: Decoy precursors: 23 (3.83%)
20:50:14.315218 PROGRESS: 
20:50:14.315261 PROGRESS: Precursor Summary:
20:50:14.316291 PROGRESS: Channel   0:	 0.05 FDR:   577; 0.01 FDR:   534; 0.001 FDR:   453
20:50:14.316384 PROGRESS: 
20:50:14.316440 PROGRESS: Protein Summary:
20:50:14.317681 PROGRESS: Channel   0:	 0.05 FDR:   542; 0.01 FDR:   501; 0.001 FDR:   426
20:50:14.317769 PROGRESS: =========================================================================
20:50:14.321347 INFO: fragments_df: keeping 4999 of 22985 [sum(precursor_idx_mask)=10854 sum(mass_error_mask)=22985 stop_rank=4999
20:50:14.326561 INFO: calibration group: precursor, fitting mz estimator 
20:50:14.479678 INFO: calibration group: precursor, fitting rt estimator 
20:50:14.613870 INFO: calibration group: precursor, fitting mobility estimator 
20:50:14.776572 INFO: calibration group: fragment, fitting mz estimator 
20:50:15.450605 INFO: Using score_cutoff 33.23889220962525 (fac=0.99, q=1)
20:50:15.451042 INFO: calibration group: precursor, predicting mz
20:50:15.452170 INFO: calibration group: precursor, predicting rt
20:50:15.453507 INFO: calibration group: precursor, predicting mobility
20:50:15.454283 INFO: calibration group: fragment, predicting mz
20:50:15.456338 INFO: === checking if optimization conditions were reached ===
20:50:15.456436 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
20:50:15.458242 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 10.1958.
20:50:15.458295 INFO: ==============================================
20:50:15.458381 INFO: Starting optimization step 7.
20:50:15.458446 PROGRESS: === Extracting elution groups 0 to 600 ===
20:50:15.458504 PROGRESS: Extracting batch of 1188 precursors
20:50:15.459656 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:50:15.459703 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:50:15.459738 INFO: FWHM in RT is 2.57 seconds, sigma is 0.56
20:50:15.459760 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.15
20:50:15.476970 INFO: Starting candidate selection
20:50:15.988369 INFO: Starting candidate scoring
20:50:16.096221 INFO: Finished candidate processing
20:50:16.096351 INFO: Collecting candidate features
20:50:16.107673 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2249)
20:50:16.111067 INFO: Collecting fragment features
20:50:16.115844 INFO: Finished candidate scoring
20:50:16.117430 PROGRESS: === Extracted 2249 precursors and 23041 fragments ===
20:50:16.117734 INFO: performing precursor FDR with 47 features
20:50:16.117771 INFO: Decoy channel: -1
20:50:16.117795 INFO: Competetive: True
20:50:16.120467 INFO: Setting torch num_threads to 2 for FDR classification task
20:50:16.121700 WARNING: dropped 1 decoy PSMs due to missing features
20:50:16.132793 INFO: Test AUC: 0.878
20:50:16.132855 INFO: Train AUC: 0.854
20:50:16.132883 INFO: AUC difference: 2.82%
20:50:16.311141 INFO: Resetting torch num_threads to 100
20:50:16.311717 INFO: === FDR correction performed with classifier version 7 ===
20:50:16.312378 PROGRESS: ============================= Precursor FDR =============================
20:50:16.312471 PROGRESS: Total precursors accumulated: 600
20:50:16.312531 PROGRESS: Target precursors: 576 (96.00%)
20:50:16.312582 PROGRESS: Decoy precursors: 24 (4.00%)
20:50:16.312629 PROGRESS: 
20:50:16.312675 PROGRESS: Precursor Summary:
20:50:16.313713 PROGRESS: Channel   0:	 0.05 FDR:   576; 0.01 FDR:   471; 0.001 FDR:   430
20:50:16.313807 PROGRESS: 
20:50:16.313865 PROGRESS: Protein Summary:
20:50:16.315150 PROGRESS: Channel   0:	 0.05 FDR:   542; 0.01 FDR:   443; 0.001 FDR:   403
20:50:16.315246 PROGRESS: =========================================================================
20:50:16.318588 INFO: fragments_df: keeping 4702 of 23041 [sum(precursor_idx_mask)=9592 sum(mass_error_mask)=23041 stop_rank=4702
20:50:16.323430 INFO: calibration group: precursor, fitting mz estimator 
20:50:16.467227 INFO: calibration group: precursor, fitting rt estimator 
20:50:16.607596 INFO: calibration group: precursor, fitting mobility estimator 
20:50:16.747241 INFO: calibration group: fragment, fitting mz estimator 
20:50:17.374826 INFO: Using score_cutoff 36.08204030227661 (fac=0.99, q=1)
20:50:17.375257 INFO: calibration group: precursor, predicting mz
20:50:17.376377 INFO: calibration group: precursor, predicting rt
20:50:17.377698 INFO: calibration group: precursor, predicting mobility
20:50:17.378469 INFO: calibration group: fragment, predicting mz
20:50:17.380482 INFO: === checking if optimization conditions were reached ===
20:50:17.380583 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
20:50:17.382296 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 9.6960.
20:50:17.382349 INFO: ==============================================
20:50:17.382437 INFO: Starting optimization step 8.
20:50:17.382502 PROGRESS: === Extracting elution groups 0 to 600 ===
20:50:17.382559 PROGRESS: Extracting batch of 1188 precursors
20:50:17.383584 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:50:17.383631 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:50:17.383665 INFO: FWHM in RT is 2.63 seconds, sigma is 0.58
20:50:17.383687 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.26
20:50:17.384606 INFO: Starting candidate selection
20:50:17.894195 INFO: Starting candidate scoring
20:50:18.009470 INFO: Finished candidate processing
20:50:18.009578 INFO: Collecting candidate features
20:50:18.018645 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2244)
20:50:18.021864 INFO: Collecting fragment features
20:50:18.025949 INFO: Finished candidate scoring
20:50:18.027599 PROGRESS: === Extracted 2244 precursors and 22982 fragments ===
20:50:18.028692 INFO: performing precursor FDR with 47 features
20:50:18.028732 INFO: Decoy channel: -1
20:50:18.028755 INFO: Competetive: True
20:50:18.031394 INFO: Setting torch num_threads to 2 for FDR classification task
20:50:18.032633 WARNING: dropped 1 decoy PSMs due to missing features
20:50:18.043805 INFO: Test AUC: 0.843
20:50:18.043873 INFO: Train AUC: 0.861
20:50:18.043903 INFO: AUC difference: 2.10%
20:50:18.220811 INFO: Resetting torch num_threads to 100
20:50:18.221397 INFO: === FDR correction performed with classifier version 7 ===
20:50:18.222125 PROGRESS: ============================= Precursor FDR =============================
20:50:18.222218 PROGRESS: Total precursors accumulated: 600
20:50:18.222278 PROGRESS: Target precursors: 580 (96.67%)
20:50:18.222330 PROGRESS: Decoy precursors: 20 (3.33%)
20:50:18.222378 PROGRESS: 
20:50:18.222423 PROGRESS: Precursor Summary:
20:50:18.223481 PROGRESS: Channel   0:	 0.05 FDR:   580; 0.01 FDR:   518; 0.001 FDR:   427
20:50:18.223582 PROGRESS: 
20:50:18.223640 PROGRESS: Protein Summary:
20:50:18.224894 PROGRESS: Channel   0:	 0.05 FDR:   544; 0.01 FDR:   486; 0.001 FDR:   401
20:50:18.224984 PROGRESS: =========================================================================
20:50:18.228350 INFO: fragments_df: keeping 4941 of 22982 [sum(precursor_idx_mask)=10553 sum(mass_error_mask)=22982 stop_rank=4941
20:50:18.232984 INFO: calibration group: precursor, fitting mz estimator 
20:50:18.378028 INFO: calibration group: precursor, fitting rt estimator 
20:50:18.520009 INFO: calibration group: precursor, fitting mobility estimator 
20:50:18.660669 INFO: calibration group: fragment, fitting mz estimator 
20:50:19.320094 INFO: Using score_cutoff 33.5726545097351 (fac=0.99, q=1)
20:50:19.320524 INFO: calibration group: precursor, predicting mz
20:50:19.321675 INFO: calibration group: precursor, predicting rt
20:50:19.322994 INFO: calibration group: precursor, predicting mobility
20:50:19.323777 INFO: calibration group: fragment, predicting mz
20:50:19.325778 INFO: === checking if optimization conditions were reached ===
20:50:19.325876 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
20:50:19.326893 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 8.6063 found after 9 searches.
20:50:19.326942 INFO: ==============================================
20:50:19.327041 PROGRESS: Optimization finished for rt_error.
20:50:19.331438 INFO: calibration group: precursor, predicting mz
20:50:19.332279 INFO: calibration group: precursor, predicting rt
20:50:19.333577 INFO: calibration group: precursor, predicting mobility
20:50:19.334355 INFO: calibration group: fragment, predicting mz
20:50:19.361444 INFO: Starting optimization step 0.
20:50:19.361648 PROGRESS: === Extracting elution groups 0 to 600 ===
20:50:19.361714 PROGRESS: Extracting batch of 1188 precursors
20:50:19.362925 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:50:19.362972 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:50:19.363010 INFO: FWHM in RT is 2.57 seconds, sigma is 0.56
20:50:19.363044 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.15
20:50:19.364930 INFO: Starting candidate selection
20:50:19.890996 INFO: Starting candidate scoring
20:50:19.990687 INFO: Finished candidate processing
20:50:19.990795 INFO: Collecting candidate features
20:50:20.002580 INFO: Collecting fragment features
20:50:20.006462 INFO: Finished candidate scoring
20:50:20.007911 PROGRESS: === Extracted 2242 precursors and 22942 fragments ===
20:50:20.008191 INFO: performing precursor FDR with 47 features
20:50:20.008225 INFO: Decoy channel: -1
20:50:20.008248 INFO: Competetive: True
20:50:20.010846 INFO: Setting torch num_threads to 2 for FDR classification task
20:50:20.022845 INFO: Test AUC: 0.859
20:50:20.022912 INFO: Train AUC: 0.853
20:50:20.022940 INFO: AUC difference: 0.79%
20:50:20.204097 INFO: Resetting torch num_threads to 100
20:50:20.204697 INFO: === FDR correction performed with classifier version 14 ===
20:50:20.205367 PROGRESS: ============================= Precursor FDR =============================
20:50:20.205458 PROGRESS: Total precursors accumulated: 600
20:50:20.205517 PROGRESS: Target precursors: 577 (96.17%)
20:50:20.205568 PROGRESS: Decoy precursors: 23 (3.83%)
20:50:20.205615 PROGRESS: 
20:50:20.205660 PROGRESS: Precursor Summary:
20:50:20.206690 PROGRESS: Channel   0:	 0.05 FDR:   577; 0.01 FDR:   532; 0.001 FDR:   449
20:50:20.206782 PROGRESS: 
20:50:20.206837 PROGRESS: Protein Summary:
20:50:20.208126 PROGRESS: Channel   0:	 0.05 FDR:   542; 0.01 FDR:   499; 0.001 FDR:   422
20:50:20.208223 PROGRESS: =========================================================================
20:50:20.211621 INFO: fragments_df: keeping 4986 of 22942 [sum(precursor_idx_mask)=10836 sum(mass_error_mask)=22942 stop_rank=4986
20:50:20.216315 INFO: calibration group: precursor, fitting mz estimator 
20:50:20.346858 INFO: calibration group: precursor, fitting rt estimator 
20:50:20.467332 INFO: calibration group: precursor, fitting mobility estimator 
20:50:20.590617 INFO: calibration group: fragment, fitting mz estimator 
20:50:21.216124 INFO: Using score_cutoff 33.51360769271851 (fac=0.99, q=1)
20:50:21.216558 INFO: calibration group: precursor, predicting mz
20:50:21.217667 INFO: calibration group: precursor, predicting rt
20:50:21.219003 INFO: calibration group: precursor, predicting mobility
20:50:21.219788 INFO: calibration group: fragment, predicting mz
20:50:21.221820 INFO: === checking if optimization conditions were reached ===
20:50:21.221918 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
20:50:21.223305 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0586.
20:50:21.223359 INFO: ==============================================
20:50:21.223464 INFO: Starting optimization step 1.
20:50:21.223546 PROGRESS: === Extracting elution groups 0 to 600 ===
20:50:21.223608 PROGRESS: Extracting batch of 1188 precursors
20:50:21.224904 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:50:21.224951 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:50:21.224986 INFO: FWHM in RT is 2.56 seconds, sigma is 0.56
20:50:21.225008 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.15
20:50:21.225741 INFO: Starting candidate selection
20:50:21.726854 INFO: Starting candidate scoring
20:50:21.835386 INFO: Finished candidate processing
20:50:21.835536 INFO: Collecting candidate features
20:50:21.850235 INFO: Collecting fragment features
20:50:21.854616 INFO: Finished candidate scoring
20:50:21.856213 PROGRESS: === Extracted 2234 precursors and 22589 fragments ===
20:50:21.856513 INFO: performing precursor FDR with 47 features
20:50:21.856549 INFO: Decoy channel: -1
20:50:21.856573 INFO: Competetive: True
20:50:21.859257 INFO: Setting torch num_threads to 2 for FDR classification task
20:50:21.871805 INFO: Test AUC: 0.847
20:50:21.871872 INFO: Train AUC: 0.858
20:50:21.871901 INFO: AUC difference: 1.37%
20:50:22.048126 INFO: Resetting torch num_threads to 100
20:50:22.048722 INFO: === FDR correction performed with classifier version 14 ===
20:50:22.049388 PROGRESS: ============================= Precursor FDR =============================
20:50:22.049477 PROGRESS: Total precursors accumulated: 599
20:50:22.049536 PROGRESS: Target precursors: 577 (96.33%)
20:50:22.049587 PROGRESS: Decoy precursors: 22 (3.67%)
20:50:22.049633 PROGRESS: 
20:50:22.049677 PROGRESS: Precursor Summary:
20:50:22.050699 PROGRESS: Channel   0:	 0.05 FDR:   577; 0.01 FDR:   528; 0.001 FDR:   407
20:50:22.050789 PROGRESS: 
20:50:22.050843 PROGRESS: Protein Summary:
20:50:22.052086 PROGRESS: Channel   0:	 0.05 FDR:   542; 0.01 FDR:   495; 0.001 FDR:   380
20:50:22.052178 PROGRESS: =========================================================================
20:50:22.055637 INFO: fragments_df: keeping 4971 of 22589 [sum(precursor_idx_mask)=10711 sum(mass_error_mask)=22589 stop_rank=4971
20:50:22.062496 INFO: calibration group: precursor, fitting mz estimator 
20:50:22.221650 INFO: calibration group: precursor, fitting rt estimator 
20:50:22.367666 INFO: calibration group: precursor, fitting mobility estimator 
20:50:22.504205 INFO: calibration group: fragment, fitting mz estimator 
20:50:23.238104 INFO: Using score_cutoff 33.21396799736023 (fac=0.99, q=1)
20:50:23.238535 INFO: calibration group: precursor, predicting mz
20:50:23.239712 INFO: calibration group: precursor, predicting rt
20:50:23.241029 INFO: calibration group: precursor, predicting mobility
20:50:23.241792 INFO: calibration group: fragment, predicting mz
20:50:23.243777 INFO: === checking if optimization conditions were reached ===
20:50:23.243882 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
20:50:23.245310 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0507.
20:50:23.245363 INFO: ==============================================
20:50:23.245447 INFO: Starting optimization step 2.
20:50:23.245511 PROGRESS: === Extracting elution groups 0 to 600 ===
20:50:23.245566 PROGRESS: Extracting batch of 1188 precursors
20:50:23.246675 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:50:23.246722 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:50:23.246757 INFO: FWHM in RT is 2.58 seconds, sigma is 0.57
20:50:23.246778 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.15
20:50:23.247576 INFO: Starting candidate selection
20:50:23.750960 INFO: Starting candidate scoring
20:50:23.921224 INFO: Finished candidate processing
20:50:23.921397 INFO: Collecting candidate features
20:50:23.932422 WARNING: intensity_correlation has 2 NaNs ( 0.09 % out of 2230)
20:50:23.935837 INFO: Collecting fragment features
20:50:23.940852 INFO: Finished candidate scoring
20:50:23.945280 PROGRESS: === Extracted 2230 precursors and 22314 fragments ===
20:50:23.945623 INFO: performing precursor FDR with 47 features
20:50:23.945659 INFO: Decoy channel: -1
20:50:23.945682 INFO: Competetive: True
20:50:23.949134 INFO: Setting torch num_threads to 2 for FDR classification task
20:50:23.950697 WARNING: dropped 2 decoy PSMs due to missing features
20:50:23.964506 INFO: Test AUC: 0.828
20:50:23.964582 INFO: Train AUC: 0.866
20:50:23.964613 INFO: AUC difference: 4.34%
20:50:24.157416 INFO: Resetting torch num_threads to 100
20:50:24.159466 INFO: === FDR correction performed with classifier version 14 ===
20:50:24.160384 PROGRESS: ============================= Precursor FDR =============================
20:50:24.160478 PROGRESS: Total precursors accumulated: 599
20:50:24.160547 PROGRESS: Target precursors: 579 (96.66%)
20:50:24.160598 PROGRESS: Decoy precursors: 20 (3.34%)
20:50:24.160643 PROGRESS: 
20:50:24.160690 PROGRESS: Precursor Summary:
20:50:24.161908 PROGRESS: Channel   0:	 0.05 FDR:   579; 0.01 FDR:   531; 0.001 FDR:   445
20:50:24.161999 PROGRESS: 
20:50:24.162051 PROGRESS: Protein Summary:
20:50:24.163369 PROGRESS: Channel   0:	 0.05 FDR:   542; 0.01 FDR:   498; 0.001 FDR:   419
20:50:24.163462 PROGRESS: =========================================================================
20:50:24.167520 INFO: fragments_df: keeping 4885 of 22314 [sum(precursor_idx_mask)=10648 sum(mass_error_mask)=22314 stop_rank=4885
20:50:24.175929 INFO: calibration group: precursor, fitting mz estimator 
20:50:24.362543 INFO: calibration group: precursor, fitting rt estimator 
20:50:24.509040 INFO: calibration group: precursor, fitting mobility estimator 
20:50:24.652625 INFO: calibration group: fragment, fitting mz estimator 
20:50:25.306998 INFO: Using score_cutoff 30.875380090713502 (fac=0.99, q=1)
20:50:25.307686 INFO: calibration group: precursor, predicting mz
20:50:25.309154 INFO: calibration group: precursor, predicting rt
20:50:25.310522 INFO: calibration group: precursor, predicting mobility
20:50:25.311301 INFO: calibration group: fragment, predicting mz
20:50:25.313335 INFO: === checking if optimization conditions were reached ===
20:50:25.313467 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
20:50:25.314527 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.1000 found after 3 searches.
20:50:25.314577 INFO: ==============================================
20:50:25.314669 PROGRESS: Optimization finished for mobility_error.
20:50:25.321477 INFO: calibration group: precursor, predicting mz
20:50:25.322324 INFO: calibration group: precursor, predicting rt
20:50:25.323631 INFO: calibration group: precursor, predicting mobility
20:50:25.324383 INFO: calibration group: fragment, predicting mz
20:50:25.353512 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
20:50:25.353689 PROGRESS: ==============================================
20:50:25.353762 PROGRESS: ms2_error      : 10.0474
20:50:25.353828 PROGRESS: ms1_error      : 10.5658
20:50:25.353888 PROGRESS: rt_error       : 8.6063
20:50:25.353935 PROGRESS: mobility_error : 0.1000
20:50:25.353979 PROGRESS: ==============================================
20:50:25.355066 INFO: calibration group: precursor, predicting mz
20:50:25.380657 INFO: calibration group: precursor, predicting rt
20:50:25.496364 INFO: calibration group: precursor, predicting mobility
20:50:25.524298 INFO: calibration group: fragment, predicting mz
20:50:25.829398 PROGRESS: Extracting batch of 189636 precursors
20:50:25.952132 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:50:25.952366 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:50:25.952436 INFO: FWHM in RT is 2.56 seconds, sigma is 0.56
20:50:25.952459 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.15
20:50:25.956067 INFO: Starting candidate selection
20:51:00.914652 INFO: Applying score cutoff of 33.51360769271851
20:51:00.924157 INFO: Removed 90524 precursors with score below cutoff
20:51:01.360827 INFO: Starting candidate scoring
20:51:08.308046 INFO: Finished candidate processing
20:51:08.308222 INFO: Collecting candidate features
20:51:08.745868 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 269847)
20:51:08.761134 INFO: Collecting fragment features
20:51:08.925029 INFO: Finished candidate scoring
20:51:09.066940 INFO: === FDR correction performed with classifier version 17 ===
20:51:09.068348 INFO: performing precursor FDR with 47 features
20:51:09.068393 INFO: Decoy channel: -1
20:51:09.068418 INFO: Competetive: True
20:51:09.147432 INFO: Setting torch num_threads to 2 for FDR classification task
20:51:09.186539 WARNING: dropped 1 decoy PSMs due to missing features
20:51:09.186721 WARNING: FDR calculation for 163038 target and 106808 decoy PSMs
20:51:09.186748 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
20:51:14.658704 INFO: Test AUC: 0.916
20:51:14.658859 INFO: Train AUC: 0.918
20:51:14.658891 INFO: AUC difference: 0.29%
20:51:14.891340 INFO: Resetting torch num_threads to 100
20:51:14.915386 INFO: Removing fragments below FDR threshold
20:51:14.978321 PROGRESS: ============================= Precursor FDR =============================
20:51:14.978615 PROGRESS: Total precursors accumulated: 91,129
20:51:14.978682 PROGRESS: Target precursors: 90,227 (99.01%)
20:51:14.978734 PROGRESS: Decoy precursors: 902 (0.99%)
20:51:14.978781 PROGRESS: 
20:51:14.978827 PROGRESS: Precursor Summary:
20:51:15.029298 PROGRESS: Channel   0:	 0.05 FDR: 90,227; 0.01 FDR: 90,227; 0.001 FDR: 84,951
20:51:15.029610 PROGRESS: 
20:51:15.029674 PROGRESS: Protein Summary:
20:51:15.107714 PROGRESS: Channel   0:	 0.05 FDR: 9,609; 0.01 FDR: 9,609; 0.001 FDR: 9,524
20:51:15.108008 PROGRESS: =========================================================================
20:51:15.838218 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
20:51:15.889336 PROGRESS: Loading raw file 5/6: ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
20:51:15.889498 INFO: Quantification results path: run_output/alphadia_1.10.4_Again_good_now/quant
20:51:15.889574 INFO: Creating folder run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/figures
20:51:15.890168 INFO: Initializing RawFileManager
20:51:15.890273 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
20:51:15.890322 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
20:51:15.890359 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
20:51:16.094853 INFO: Reading 39,128 frames with 2,766,418,119 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
20:51:23.271841 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d...
20:51:23.279060 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
20:51:23.287127 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
20:51:23.287549 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
20:51:23.288166 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
20:51:23.290254 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
20:51:23.307066 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
20:51:23.307490 INFO: Indexing quadrupole dimension
20:51:24.106689 INFO: Transposing detector events
20:51:35.504625 INFO: Finished transposing data
20:51:35.544844 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
20:51:35.545666 INFO: RT (min)            : 0.0 - 70.0
20:51:35.545758 INFO: RT duration (sec)   : 4199.9
20:51:35.545812 INFO: RT duration (min)   : 70.0
20:51:35.545881 INFO: Cycle len (scans)   : 9
20:51:35.545927 INFO: Cycle len (sec)     : 0.97
20:51:35.545971 INFO: Number of cycles    : 4347
20:51:35.546014 INFO: MS2 range (m/z)     : 400.0 - 1000.0
20:51:35.586929 INFO: Initializing CalibrationManager
20:51:35.587260 INFO: Loading calibration config
20:51:35.587756 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed'], 'function': LOESSRegression()}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed'], 'function': LOESSRegression(n_kernels=2)}], 'name': 'precursor'}]
20:51:35.587847 INFO: Calibration group :fragment, found 1 estimator(s)
20:51:35.587925 INFO: Calibration group :precursor, found 3 estimator(s)
20:51:35.588056 INFO: Initializing OptimizationManager
20:51:35.588154 INFO: initial parameter: ms1_error = 30
20:51:35.588202 INFO: initial parameter: ms2_error = 30
20:51:35.588269 INFO: initial parameter: rt_error = 2099.9331315
20:51:35.588318 INFO: initial parameter: mobility_error = 0.1
20:51:35.588360 INFO: initial parameter: column_type = library
20:51:35.588401 INFO: initial parameter: num_candidates = 1
20:51:35.588441 INFO: initial parameter: classifier_version = -1
20:51:35.588480 INFO: initial parameter: fwhm_rt = 5
20:51:35.588521 INFO: initial parameter: fwhm_mobility = 0.01
20:51:35.588561 INFO: initial parameter: score_cutoff = 0
20:51:35.588615 INFO: Initializing TimingManager
20:51:35.588665 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
20:51:35.588741 INFO: FDRManager not loaded from disk.
20:51:35.588762 INFO: Initializing FDRManager
20:51:35.588794 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
20:51:35.624604 PROGRESS: 95,522 target precursors potentially observable (0 removed)
20:51:35.681432 PROGRESS: Starting initial search for precursors.
20:51:35.688058 INFO: Starting optimization step 0.
20:51:35.688232 PROGRESS: === Extracting elution groups 0 to 200 ===
20:51:35.688302 PROGRESS: Extracting batch of 395 precursors
20:51:35.689123 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:51:35.689173 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:51:35.689201 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:51:35.689223 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:51:35.690154 INFO: Starting candidate selection
20:52:01.015811 INFO: Starting candidate scoring
20:52:01.082525 INFO: Finished candidate processing
20:52:01.082632 INFO: Collecting candidate features
20:52:01.091758 INFO: Collecting fragment features
20:52:01.093934 INFO: Finished candidate scoring
20:52:01.094719 PROGRESS: === Extracted 394 precursors and 4341 fragments ===
20:52:01.095032 INFO: performing precursor FDR with 47 features
20:52:01.095072 INFO: Decoy channel: -1
20:52:01.095096 INFO: Competetive: True
20:52:01.096527 INFO: Setting torch num_threads to 2 for FDR classification task
20:52:01.106106 INFO: Test AUC: 0.332
20:52:01.106166 INFO: Train AUC: 0.509
20:52:01.106196 INFO: AUC difference: 34.63%
20:52:01.106219 WARNING: AUC difference > 5%. This may indicate overfitting.
20:52:01.282040 INFO: Resetting torch num_threads to 100
20:52:01.282569 INFO: === FDR correction performed with classifier version -1 ===
20:52:01.283196 PROGRESS: ============================= Precursor FDR =============================
20:52:01.283288 PROGRESS: Total precursors accumulated: 200
20:52:01.283350 PROGRESS: Target precursors: 96 (48.00%)
20:52:01.283416 PROGRESS: Decoy precursors: 104 (52.00%)
20:52:01.283465 PROGRESS: 
20:52:01.283511 PROGRESS: Precursor Summary:
20:52:01.284344 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:52:01.284431 PROGRESS: 
20:52:01.284485 PROGRESS: Protein Summary:
20:52:01.285375 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:52:01.285465 PROGRESS: =========================================================================
20:52:01.289079 INFO: Starting optimization step 1.
20:52:01.289182 PROGRESS: === Extracting elution groups 200 to 600 ===
20:52:01.289243 PROGRESS: Extracting batch of 793 precursors
20:52:01.290021 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:52:01.290068 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:52:01.290096 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:52:01.290118 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:52:01.292348 INFO: Starting candidate selection
20:52:07.193156 INFO: Starting candidate scoring
20:52:07.295963 INFO: Finished candidate processing
20:52:07.296077 INFO: Collecting candidate features
20:52:07.305690 INFO: Collecting fragment features
20:52:07.308377 INFO: Finished candidate scoring
20:52:07.310574 PROGRESS: === Extracted 1187 precursors and 13130 fragments ===
20:52:07.311362 INFO: performing precursor FDR with 47 features
20:52:07.311408 INFO: Decoy channel: -1
20:52:07.311433 INFO: Competetive: True
20:52:07.314321 INFO: Setting torch num_threads to 2 for FDR classification task
20:52:07.324239 INFO: Test AUC: 0.475
20:52:07.324302 INFO: Train AUC: 0.463
20:52:07.324333 INFO: AUC difference: 2.46%
20:52:07.496681 INFO: Resetting torch num_threads to 100
20:52:07.497467 INFO: === FDR correction performed with classifier version -1 ===
20:52:07.498126 PROGRESS: ============================= Precursor FDR =============================
20:52:07.498219 PROGRESS: Total precursors accumulated: 600
20:52:07.498280 PROGRESS: Target precursors: 273 (45.50%)
20:52:07.498329 PROGRESS: Decoy precursors: 327 (54.50%)
20:52:07.498376 PROGRESS: 
20:52:07.498420 PROGRESS: Precursor Summary:
20:52:07.499265 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:52:07.499357 PROGRESS: 
20:52:07.499413 PROGRESS: Protein Summary:
20:52:07.500306 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:52:07.500397 PROGRESS: =========================================================================
20:52:07.505504 INFO: Starting optimization step 2.
20:52:07.505623 PROGRESS: === Extracting elution groups 600 to 1400 ===
20:52:07.505686 PROGRESS: Extracting batch of 1583 precursors
20:52:07.506587 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:52:07.506635 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:52:07.506666 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:52:07.506687 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:52:07.507731 INFO: Starting candidate selection
20:52:18.079149 INFO: Starting candidate scoring
20:52:18.343397 INFO: Finished candidate processing
20:52:18.343620 INFO: Collecting candidate features
20:52:18.360568 INFO: Collecting fragment features
20:52:18.367359 INFO: Finished candidate scoring
20:52:18.382743 PROGRESS: === Extracted 2770 precursors and 30811 fragments ===
20:52:18.384560 INFO: performing precursor FDR with 47 features
20:52:18.384609 INFO: Decoy channel: -1
20:52:18.384636 INFO: Competetive: True
20:52:18.395025 INFO: Setting torch num_threads to 2 for FDR classification task
20:52:18.418400 INFO: Test AUC: 0.465
20:52:18.418505 INFO: Train AUC: 0.457
20:52:18.418535 INFO: AUC difference: 1.82%
20:52:18.617485 INFO: Resetting torch num_threads to 100
20:52:18.619032 INFO: === FDR correction performed with classifier version -1 ===
20:52:18.620158 PROGRESS: ============================= Precursor FDR =============================
20:52:18.620257 PROGRESS: Total precursors accumulated: 1,400
20:52:18.620319 PROGRESS: Target precursors: 636 (45.43%)
20:52:18.620372 PROGRESS: Decoy precursors: 764 (54.57%)
20:52:18.620421 PROGRESS: 
20:52:18.620468 PROGRESS: Precursor Summary:
20:52:18.621402 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
20:52:18.621498 PROGRESS: 
20:52:18.621553 PROGRESS: Protein Summary:
20:52:18.622551 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
20:52:18.622646 PROGRESS: =========================================================================
20:52:18.646510 INFO: Starting optimization step 3.
20:52:18.646711 PROGRESS: === Extracting elution groups 1400 to 3000 ===
20:52:18.646810 PROGRESS: Extracting batch of 3171 precursors
20:52:18.648557 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:52:18.648615 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:52:18.648659 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:52:18.648682 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:52:18.734749 INFO: Starting candidate selection
20:53:01.021200 INFO: Starting candidate scoring
20:53:01.402952 INFO: Finished candidate processing
20:53:01.403181 INFO: Collecting candidate features
20:53:01.428332 INFO: Collecting fragment features
20:53:01.436405 INFO: Finished candidate scoring
20:53:01.443385 PROGRESS: === Extracted 5940 precursors and 65973 fragments ===
20:53:01.445619 INFO: performing precursor FDR with 47 features
20:53:01.445712 INFO: Decoy channel: -1
20:53:01.445755 INFO: Competetive: True
20:53:01.453186 INFO: Setting torch num_threads to 2 for FDR classification task
20:53:01.480861 INFO: Test AUC: 0.469
20:53:01.481042 INFO: Train AUC: 0.461
20:53:01.481074 INFO: AUC difference: 1.76%
20:53:01.668289 INFO: Resetting torch num_threads to 100
20:53:01.669380 INFO: === FDR correction performed with classifier version -1 ===
20:53:01.670404 PROGRESS: ============================= Precursor FDR =============================
20:53:01.670505 PROGRESS: Total precursors accumulated: 3,000
20:53:01.670566 PROGRESS: Target precursors: 1,387 (46.23%)
20:53:01.670620 PROGRESS: Decoy precursors: 1,613 (53.77%)
20:53:01.670664 PROGRESS: 
20:53:01.670709 PROGRESS: Precursor Summary:
20:53:01.671622 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:53:01.671731 PROGRESS: 
20:53:01.671789 PROGRESS: Protein Summary:
20:53:01.672738 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:53:01.672832 PROGRESS: =========================================================================
20:53:01.695836 INFO: Starting optimization step 4.
20:53:01.696171 PROGRESS: === Extracting elution groups 3000 to 6200 ===
20:53:01.696242 PROGRESS: Extracting batch of 6347 precursors
20:53:01.698477 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:53:01.698584 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:53:01.698620 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:53:01.698643 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:53:01.721729 INFO: Starting candidate selection
20:54:01.019452 INFO: Starting candidate scoring
20:54:01.460258 INFO: Finished candidate processing
20:54:01.460365 INFO: Collecting candidate features
20:54:01.479545 INFO: Collecting fragment features
20:54:01.487302 INFO: Finished candidate scoring
20:54:01.495766 PROGRESS: === Extracted 12286 precursors and 136535 fragments ===
20:54:01.497605 INFO: performing precursor FDR with 47 features
20:54:01.497663 INFO: Decoy channel: -1
20:54:01.497688 INFO: Competetive: True
20:54:01.504062 INFO: Setting torch num_threads to 2 for FDR classification task
20:54:01.547162 INFO: Test AUC: 0.463
20:54:01.547287 INFO: Train AUC: 0.458
20:54:01.547318 INFO: AUC difference: 1.18%
20:54:01.734082 INFO: Resetting torch num_threads to 100
20:54:01.735234 INFO: === FDR correction performed with classifier version -1 ===
20:54:01.736555 PROGRESS: ============================= Precursor FDR =============================
20:54:01.736658 PROGRESS: Total precursors accumulated: 6,200
20:54:01.736718 PROGRESS: Target precursors: 2,858 (46.10%)
20:54:01.736770 PROGRESS: Decoy precursors: 3,342 (53.90%)
20:54:01.736814 PROGRESS: 
20:54:01.736860 PROGRESS: Precursor Summary:
20:54:01.737747 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:54:01.737837 PROGRESS: 
20:54:01.737891 PROGRESS: Protein Summary:
20:54:01.738831 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:54:01.738919 PROGRESS: =========================================================================
20:54:01.763178 INFO: Starting optimization step 5.
20:54:01.763436 PROGRESS: === Extracting elution groups 6200 to 12600 ===
20:54:01.763505 PROGRESS: Extracting batch of 12697 precursors
20:54:01.766198 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:54:01.766252 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:54:01.766281 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:54:01.766304 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:54:01.767056 INFO: Starting candidate selection
20:55:23.600342 INFO: Starting candidate scoring
20:55:24.427827 INFO: Finished candidate processing
20:55:24.427986 INFO: Collecting candidate features
20:55:24.477938 INFO: Collecting fragment features
20:55:24.489808 INFO: Finished candidate scoring
20:55:24.509609 PROGRESS: === Extracted 24982 precursors and 277638 fragments ===
20:55:24.514175 INFO: performing precursor FDR with 47 features
20:55:24.514270 INFO: Decoy channel: -1
20:55:24.514295 INFO: Competetive: True
20:55:24.525837 INFO: Setting torch num_threads to 2 for FDR classification task
20:55:24.825619 INFO: Test AUC: 0.816
20:55:24.825782 INFO: Train AUC: 0.812
20:55:24.825812 INFO: AUC difference: 0.56%
20:55:25.055324 INFO: Resetting torch num_threads to 100
20:55:25.058156 INFO: === FDR correction performed with classifier version -1 ===
20:55:25.061216 PROGRESS: ============================= Precursor FDR =============================
20:55:25.061411 PROGRESS: Total precursors accumulated: 12,600
20:55:25.061481 PROGRESS: Target precursors: 10,250 (81.35%)
20:55:25.061536 PROGRESS: Decoy precursors: 2,350 (18.65%)
20:55:25.061584 PROGRESS: 
20:55:25.061643 PROGRESS: Precursor Summary:
20:55:25.064655 PROGRESS: Channel   0:	 0.05 FDR: 7,329; 0.01 FDR: 5,547; 0.001 FDR:     7
20:55:25.064801 PROGRESS: 
20:55:25.064860 PROGRESS: Protein Summary:
20:55:25.068405 PROGRESS: Channel   0:	 0.05 FDR: 3,734; 0.01 FDR: 3,007; 0.001 FDR:     6
20:55:25.068538 PROGRESS: =========================================================================
20:55:25.100764 INFO: fragments_df: keeping 5000 of 277638 [sum(precursor_idx_mask)=61853 sum(mass_error_mask)=277638 stop_rank=5000
20:55:25.121985 INFO: calibration group: precursor, fitting mz estimator 
20:55:25.854993 INFO: calibration group: precursor, fitting rt estimator 
20:55:26.604563 INFO: calibration group: precursor, fitting mobility estimator 
20:55:27.327216 INFO: calibration group: fragment, fitting mz estimator 
20:55:27.957305 INFO: Using score_cutoff 50.2861501991272 (fac=0.99, q=1)
20:55:27.957983 INFO: calibration group: precursor, predicting mz
20:55:27.959317 INFO: calibration group: precursor, predicting rt
20:55:27.960677 INFO: calibration group: precursor, predicting mobility
20:55:27.961470 INFO: calibration group: fragment, predicting mz
20:55:27.963473 PROGRESS: Required number of precursors found. Starting search parameter optimization.
20:55:27.963669 INFO: Starting optimization step 6.
20:55:27.963745 PROGRESS: === Extracting elution groups 0 to 600 ===
20:55:27.963826 PROGRESS: Extracting batch of 1188 precursors
20:55:27.965358 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:55:27.965407 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:55:27.965465 INFO: FWHM in RT is 3.22 seconds, sigma is 0.71
20:55:27.965499 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.09
20:55:27.966338 INFO: Starting candidate selection
20:55:37.053905 INFO: Starting candidate scoring
20:55:37.392421 INFO: Finished candidate processing
20:55:37.392763 INFO: Collecting candidate features
20:55:37.408549 INFO: Collecting fragment features
20:55:37.414347 INFO: Finished candidate scoring
20:55:37.419375 PROGRESS: === Extracted 2282 precursors and 25244 fragments ===
20:55:37.419798 INFO: performing precursor FDR with 47 features
20:55:37.419838 INFO: Decoy channel: -1
20:55:37.419864 INFO: Competetive: True
20:55:37.423605 INFO: Setting torch num_threads to 2 for FDR classification task
20:55:37.441313 INFO: Test AUC: 0.672
20:55:37.441389 INFO: Train AUC: 0.732
20:55:37.441418 INFO: AUC difference: 8.17%
20:55:37.441440 WARNING: AUC difference > 5%. This may indicate overfitting.
20:55:37.632007 INFO: Resetting torch num_threads to 100
20:55:37.633134 INFO: === FDR correction performed with classifier version 5 ===
20:55:37.634194 PROGRESS: ============================= Precursor FDR =============================
20:55:37.634296 PROGRESS: Total precursors accumulated: 600
20:55:37.634367 PROGRESS: Target precursors: 504 (84.00%)
20:55:37.634421 PROGRESS: Decoy precursors: 96 (16.00%)
20:55:37.634469 PROGRESS: 
20:55:37.634514 PROGRESS: Precursor Summary:
20:55:37.635592 PROGRESS: Channel   0:	 0.05 FDR:   408; 0.01 FDR:   204; 0.001 FDR:     2
20:55:37.635685 PROGRESS: 
20:55:37.635740 PROGRESS: Protein Summary:
20:55:37.636861 PROGRESS: Channel   0:	 0.05 FDR:   383; 0.01 FDR:   193; 0.001 FDR:     2
20:55:37.636963 PROGRESS: =========================================================================
20:55:37.642030 INFO: fragments_df: keeping 2363 of 25244 [sum(precursor_idx_mask)=4203 sum(mass_error_mask)=25244 stop_rank=2363
20:55:37.649558 INFO: calibration group: precursor, fitting mz estimator 
20:55:37.807276 INFO: calibration group: precursor, fitting rt estimator 
20:55:37.959990 INFO: calibration group: precursor, fitting mobility estimator 
20:55:38.105556 INFO: calibration group: fragment, fitting mz estimator 
20:55:38.461690 INFO: Using score_cutoff 52.710952443695064 (fac=0.99, q=1)
20:55:38.462394 INFO: calibration group: precursor, predicting mz
20:55:38.464440 INFO: calibration group: precursor, predicting rt
20:55:38.466208 INFO: calibration group: precursor, predicting mobility
20:55:38.467091 INFO: calibration group: fragment, predicting mz
20:55:38.469604 INFO: === checking if optimization conditions were reached ===
20:55:38.471174 PROGRESS: ❌ ms2_error      : 10.0474 > 10.0474 or insufficient steps taken.
20:55:38.472214 PROGRESS: ❌ ms1_error      : 10.5658 > 10.5658 or insufficient steps taken.
20:55:38.472269 INFO: ==============================================
20:55:38.472379 INFO: Starting optimization step 7.
20:55:38.472450 PROGRESS: === Extracting elution groups 0 to 600 ===
20:55:38.472517 PROGRESS: Extracting batch of 1188 precursors
20:55:38.474376 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:55:38.474438 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:55:38.474479 INFO: FWHM in RT is 3.28 seconds, sigma is 0.72
20:55:38.474505 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.30
20:55:38.476750 INFO: Starting candidate selection
20:56:01.021449 INFO: Starting candidate scoring
20:56:01.156677 INFO: Finished candidate processing
20:56:01.156802 INFO: Collecting candidate features
20:56:01.172126 INFO: Collecting fragment features
20:56:01.178926 INFO: Finished candidate scoring
20:56:01.181036 PROGRESS: === Extracted 2283 precursors and 24621 fragments ===
20:56:01.181404 INFO: performing precursor FDR with 47 features
20:56:01.181450 INFO: Decoy channel: -1
20:56:01.181481 INFO: Competetive: True
20:56:01.184878 INFO: Setting torch num_threads to 2 for FDR classification task
20:56:01.198818 INFO: Test AUC: 0.791
20:56:01.198907 INFO: Train AUC: 0.758
20:56:01.198936 INFO: AUC difference: 4.36%
20:56:01.374562 INFO: Resetting torch num_threads to 100
20:56:01.375172 INFO: === FDR correction performed with classifier version 6 ===
20:56:01.375828 PROGRESS: ============================= Precursor FDR =============================
20:56:01.375923 PROGRESS: Total precursors accumulated: 600
20:56:01.375984 PROGRESS: Target precursors: 542 (90.33%)
20:56:01.376034 PROGRESS: Decoy precursors: 58 (9.67%)
20:56:01.376080 PROGRESS: 
20:56:01.376124 PROGRESS: Precursor Summary:
20:56:01.377136 PROGRESS: Channel   0:	 0.05 FDR:   487; 0.01 FDR:   423; 0.001 FDR:   220
20:56:01.377226 PROGRESS: 
20:56:01.377283 PROGRESS: Protein Summary:
20:56:01.378450 PROGRESS: Channel   0:	 0.05 FDR:   456; 0.01 FDR:   394; 0.001 FDR:   211
20:56:01.378552 PROGRESS: =========================================================================
20:56:01.381954 INFO: fragments_df: keeping 4209 of 24621 [sum(precursor_idx_mask)=8806 sum(mass_error_mask)=24621 stop_rank=4209
20:56:01.386931 INFO: calibration group: precursor, fitting mz estimator 
20:56:01.505415 INFO: calibration group: precursor, fitting rt estimator 
20:56:01.618860 INFO: calibration group: precursor, fitting mobility estimator 
20:56:01.734442 INFO: calibration group: fragment, fitting mz estimator 
20:56:02.238903 INFO: Using score_cutoff 41.13674213790894 (fac=0.99, q=1)
20:56:02.239340 INFO: calibration group: precursor, predicting mz
20:56:02.240460 INFO: calibration group: precursor, predicting rt
20:56:02.241778 INFO: calibration group: precursor, predicting mobility
20:56:02.242542 INFO: calibration group: fragment, predicting mz
20:56:02.244524 INFO: === checking if optimization conditions were reached ===
20:56:02.245975 PROGRESS: ✅ ms2_error      : 10.0474 <= 10.0474
20:56:02.246895 PROGRESS: ✅ ms1_error      : 10.5658 <= 10.5658
20:56:02.246944 INFO: ==============================================
20:56:02.247040 PROGRESS: Optimization finished for ms2_error, ms1_error.
20:56:02.251677 INFO: calibration group: precursor, predicting mz
20:56:02.252492 INFO: calibration group: precursor, predicting rt
20:56:02.253782 INFO: calibration group: precursor, predicting mobility
20:56:02.254540 INFO: calibration group: fragment, predicting mz
20:56:02.256542 INFO: Starting optimization step 0.
20:56:02.256646 PROGRESS: === Extracting elution groups 0 to 600 ===
20:56:02.256710 PROGRESS: Extracting batch of 1188 precursors
20:56:02.257608 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:56:02.257655 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:56:02.257692 INFO: FWHM in RT is 2.67 seconds, sigma is 0.59
20:56:02.257716 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.46
20:56:02.258470 INFO: Starting candidate selection
20:56:09.538805 INFO: Starting candidate scoring
20:56:09.662615 INFO: Finished candidate processing
20:56:09.662719 INFO: Collecting candidate features
20:56:09.674714 INFO: Collecting fragment features
20:56:09.678698 INFO: Finished candidate scoring
20:56:09.680182 PROGRESS: === Extracted 2265 precursors and 24319 fragments ===
20:56:09.680468 INFO: performing precursor FDR with 47 features
20:56:09.680505 INFO: Decoy channel: -1
20:56:09.680529 INFO: Competetive: True
20:56:09.683111 INFO: Setting torch num_threads to 2 for FDR classification task
20:56:09.696208 INFO: Test AUC: 0.769
20:56:09.696275 INFO: Train AUC: 0.782
20:56:09.696305 INFO: AUC difference: 1.66%
20:56:09.870150 INFO: Resetting torch num_threads to 100
20:56:09.870741 INFO: === FDR correction performed with classifier version 7 ===
20:56:09.871442 PROGRESS: ============================= Precursor FDR =============================
20:56:09.871537 PROGRESS: Total precursors accumulated: 600
20:56:09.871598 PROGRESS: Target precursors: 539 (89.83%)
20:56:09.871650 PROGRESS: Decoy precursors: 61 (10.17%)
20:56:09.871696 PROGRESS: 
20:56:09.871740 PROGRESS: Precursor Summary:
20:56:09.872735 PROGRESS: Channel   0:	 0.05 FDR:   484; 0.01 FDR:   406; 0.001 FDR:    35
20:56:09.872827 PROGRESS: 
20:56:09.872885 PROGRESS: Protein Summary:
20:56:09.874025 PROGRESS: Channel   0:	 0.05 FDR:   454; 0.01 FDR:   378; 0.001 FDR:    35
20:56:09.874127 PROGRESS: =========================================================================
20:56:09.877481 INFO: fragments_df: keeping 4213 of 24319 [sum(precursor_idx_mask)=8276 sum(mass_error_mask)=24319 stop_rank=4213
20:56:09.882639 INFO: calibration group: precursor, fitting mz estimator 
20:56:10.011817 INFO: calibration group: precursor, fitting rt estimator 
20:56:10.145128 INFO: calibration group: precursor, fitting mobility estimator 
20:56:10.256371 INFO: calibration group: fragment, fitting mz estimator 
20:56:10.762617 INFO: Using score_cutoff 42.216091163635255 (fac=0.99, q=1)
20:56:10.763044 INFO: calibration group: precursor, predicting mz
20:56:10.764165 INFO: calibration group: precursor, predicting rt
20:56:10.765489 INFO: calibration group: precursor, predicting mobility
20:56:10.766257 INFO: calibration group: fragment, predicting mz
20:56:10.768244 INFO: === checking if optimization conditions were reached ===
20:56:10.768352 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
20:56:10.769923 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 114.3425.
20:56:10.769974 INFO: ==============================================
20:56:10.770058 INFO: Starting optimization step 1.
20:56:10.770122 PROGRESS: === Extracting elution groups 0 to 600 ===
20:56:10.770176 PROGRESS: Extracting batch of 1188 precursors
20:56:10.771141 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:56:10.771192 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:56:10.771228 INFO: FWHM in RT is 2.63 seconds, sigma is 0.58
20:56:10.771249 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.49
20:56:10.772048 INFO: Starting candidate selection
20:56:11.604881 INFO: Starting candidate scoring
20:56:11.711574 INFO: Finished candidate processing
20:56:11.711701 INFO: Collecting candidate features
20:56:11.725618 INFO: Collecting fragment features
20:56:11.730493 INFO: Finished candidate scoring
20:56:11.732523 PROGRESS: === Extracted 2260 precursors and 23626 fragments ===
20:56:11.732840 INFO: performing precursor FDR with 47 features
20:56:11.732880 INFO: Decoy channel: -1
20:56:11.732904 INFO: Competetive: True
20:56:11.735738 INFO: Setting torch num_threads to 2 for FDR classification task
20:56:11.749659 INFO: Test AUC: 0.835
20:56:11.749727 INFO: Train AUC: 0.813
20:56:11.749756 INFO: AUC difference: 2.73%
20:56:11.932690 INFO: Resetting torch num_threads to 100
20:56:11.933478 INFO: === FDR correction performed with classifier version 7 ===
20:56:11.934252 PROGRESS: ============================= Precursor FDR =============================
20:56:11.934346 PROGRESS: Total precursors accumulated: 600
20:56:11.934412 PROGRESS: Target precursors: 571 (95.17%)
20:56:11.934464 PROGRESS: Decoy precursors: 29 (4.83%)
20:56:11.934512 PROGRESS: 
20:56:11.934559 PROGRESS: Precursor Summary:
20:56:11.935699 PROGRESS: Channel   0:	 0.05 FDR:   568; 0.01 FDR:   483; 0.001 FDR:   193
20:56:11.935795 PROGRESS: 
20:56:11.935851 PROGRESS: Protein Summary:
20:56:11.937099 PROGRESS: Channel   0:	 0.05 FDR:   532; 0.01 FDR:   451; 0.001 FDR:   187
20:56:11.937193 PROGRESS: =========================================================================
20:56:11.940734 INFO: fragments_df: keeping 4616 of 23626 [sum(precursor_idx_mask)=9731 sum(mass_error_mask)=23626 stop_rank=4616
20:56:11.945826 INFO: calibration group: precursor, fitting mz estimator 
20:56:12.063764 INFO: calibration group: precursor, fitting rt estimator 
20:56:12.186350 INFO: calibration group: precursor, fitting mobility estimator 
20:56:12.310083 INFO: calibration group: fragment, fitting mz estimator 
20:56:12.893129 INFO: Using score_cutoff 38.32078256378174 (fac=0.99, q=1)
20:56:12.893626 INFO: calibration group: precursor, predicting mz
20:56:12.894963 INFO: calibration group: precursor, predicting rt
20:56:12.896300 INFO: calibration group: precursor, predicting mobility
20:56:12.897083 INFO: calibration group: fragment, predicting mz
20:56:12.899149 INFO: === checking if optimization conditions were reached ===
20:56:12.899253 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
20:56:12.900973 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 15.0307.
20:56:12.901027 INFO: ==============================================
20:56:12.901114 INFO: Starting optimization step 2.
20:56:12.901179 PROGRESS: === Extracting elution groups 0 to 600 ===
20:56:12.901238 PROGRESS: Extracting batch of 1188 precursors
20:56:12.902405 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:56:12.902453 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:56:12.902489 INFO: FWHM in RT is 2.59 seconds, sigma is 0.57
20:56:12.902512 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.23
20:56:12.906334 INFO: Starting candidate selection
20:56:13.432454 INFO: Starting candidate scoring
20:56:13.533670 INFO: Finished candidate processing
20:56:13.534794 INFO: Collecting candidate features
20:56:13.544987 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2251)
20:56:13.548191 INFO: Collecting fragment features
20:56:13.553053 INFO: Finished candidate scoring
20:56:13.554862 PROGRESS: === Extracted 2251 precursors and 23018 fragments ===
20:56:13.555186 INFO: performing precursor FDR with 47 features
20:56:13.555226 INFO: Decoy channel: -1
20:56:13.555251 INFO: Competetive: True
20:56:13.557931 INFO: Setting torch num_threads to 2 for FDR classification task
20:56:13.559250 WARNING: dropped 1 decoy PSMs due to missing features
20:56:13.573042 INFO: Test AUC: 0.883
20:56:13.573118 INFO: Train AUC: 0.857
20:56:13.573146 INFO: AUC difference: 3.03%
20:56:13.753952 INFO: Resetting torch num_threads to 100
20:56:13.754682 INFO: === FDR correction performed with classifier version 7 ===
20:56:13.755435 PROGRESS: ============================= Precursor FDR =============================
20:56:13.755531 PROGRESS: Total precursors accumulated: 600
20:56:13.755594 PROGRESS: Target precursors: 589 (98.17%)
20:56:13.755644 PROGRESS: Decoy precursors: 11 (1.83%)
20:56:13.755692 PROGRESS: 
20:56:13.755745 PROGRESS: Precursor Summary:
20:56:13.757075 PROGRESS: Channel   0:	 0.05 FDR:   589; 0.01 FDR:   573; 0.001 FDR:   486
20:56:13.757185 PROGRESS: 
20:56:13.757245 PROGRESS: Protein Summary:
20:56:13.758529 PROGRESS: Channel   0:	 0.05 FDR:   551; 0.01 FDR:   536; 0.001 FDR:   454
20:56:13.758623 PROGRESS: =========================================================================
20:56:13.762450 INFO: fragments_df: keeping 5000 of 23018 [sum(precursor_idx_mask)=11483 sum(mass_error_mask)=23018 stop_rank=5000
20:56:13.767506 INFO: calibration group: precursor, fitting mz estimator 
20:56:13.911326 INFO: calibration group: precursor, fitting rt estimator 
20:56:14.056389 INFO: calibration group: precursor, fitting mobility estimator 
20:56:14.205935 INFO: calibration group: fragment, fitting mz estimator 
20:56:14.966925 INFO: Using score_cutoff 31.373875930023193 (fac=0.99, q=1)
20:56:14.967411 INFO: calibration group: precursor, predicting mz
20:56:14.968692 INFO: calibration group: precursor, predicting rt
20:56:14.970024 INFO: calibration group: precursor, predicting mobility
20:56:14.970792 INFO: calibration group: fragment, predicting mz
20:56:14.972810 INFO: === checking if optimization conditions were reached ===
20:56:14.972913 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
20:56:14.974782 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 13.0362.
20:56:14.974838 INFO: ==============================================
20:56:14.974927 INFO: Starting optimization step 3.
20:56:14.974995 PROGRESS: === Extracting elution groups 0 to 600 ===
20:56:14.975073 PROGRESS: Extracting batch of 1188 precursors
20:56:14.976290 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:56:14.976338 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:56:14.976382 INFO: FWHM in RT is 2.51 seconds, sigma is 0.55
20:56:14.976407 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.98
20:56:14.977122 INFO: Starting candidate selection
20:56:15.498527 INFO: Starting candidate scoring
20:56:15.638589 INFO: Finished candidate processing
20:56:15.638697 INFO: Collecting candidate features
20:56:15.649839 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2246)
20:56:15.653211 INFO: Collecting fragment features
20:56:15.660177 INFO: Finished candidate scoring
20:56:15.661769 PROGRESS: === Extracted 2246 precursors and 22936 fragments ===
20:56:15.662081 INFO: performing precursor FDR with 47 features
20:56:15.662118 INFO: Decoy channel: -1
20:56:15.662143 INFO: Competetive: True
20:56:15.664832 INFO: Setting torch num_threads to 2 for FDR classification task
20:56:15.666110 WARNING: dropped 1 decoy PSMs due to missing features
20:56:15.680057 INFO: Test AUC: 0.863
20:56:15.680128 INFO: Train AUC: 0.872
20:56:15.680156 INFO: AUC difference: 1.05%
20:56:15.863074 INFO: Resetting torch num_threads to 100
20:56:15.863787 INFO: === FDR correction performed with classifier version 7 ===
20:56:15.864537 PROGRESS: ============================= Precursor FDR =============================
20:56:15.864632 PROGRESS: Total precursors accumulated: 600
20:56:15.864693 PROGRESS: Target precursors: 588 (98.00%)
20:56:15.864744 PROGRESS: Decoy precursors: 12 (2.00%)
20:56:15.864792 PROGRESS: 
20:56:15.864838 PROGRESS: Precursor Summary:
20:56:15.866671 PROGRESS: Channel   0:	 0.05 FDR:   588; 0.01 FDR:   541; 0.001 FDR:   252
20:56:15.866767 PROGRESS: 
20:56:15.866821 PROGRESS: Protein Summary:
20:56:15.868094 PROGRESS: Channel   0:	 0.05 FDR:   550; 0.01 FDR:   505; 0.001 FDR:   240
20:56:15.868192 PROGRESS: =========================================================================
20:56:15.871673 INFO: fragments_df: keeping 5000 of 22936 [sum(precursor_idx_mask)=10849 sum(mass_error_mask)=22936 stop_rank=5000
20:56:15.878609 INFO: calibration group: precursor, fitting mz estimator 
20:56:16.019565 INFO: calibration group: precursor, fitting rt estimator 
20:56:16.141826 INFO: calibration group: precursor, fitting mobility estimator 
20:56:16.267310 INFO: calibration group: fragment, fitting mz estimator 
20:56:16.913373 INFO: Using score_cutoff 32.60829796600342 (fac=0.99, q=1)
20:56:16.913847 INFO: calibration group: precursor, predicting mz
20:56:16.915125 INFO: calibration group: precursor, predicting rt
20:56:16.916461 INFO: calibration group: precursor, predicting mobility
20:56:16.917238 INFO: calibration group: fragment, predicting mz
20:56:16.919237 INFO: === checking if optimization conditions were reached ===
20:56:16.919343 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
20:56:16.921174 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 11.1594.
20:56:16.921228 INFO: ==============================================
20:56:16.921317 INFO: Starting optimization step 4.
20:56:16.921382 PROGRESS: === Extracting elution groups 0 to 600 ===
20:56:16.921456 PROGRESS: Extracting batch of 1188 precursors
20:56:16.922653 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:56:16.922701 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:56:16.922737 INFO: FWHM in RT is 2.48 seconds, sigma is 0.55
20:56:16.922759 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.03
20:56:16.923555 INFO: Starting candidate selection
20:56:17.443253 INFO: Starting candidate scoring
20:56:17.568588 INFO: Finished candidate processing
20:56:17.568713 INFO: Collecting candidate features
20:56:17.578159 WARNING: intensity_correlation has 2 NaNs ( 0.09 % out of 2245)
20:56:17.581357 INFO: Collecting fragment features
20:56:17.586344 INFO: Finished candidate scoring
20:56:17.588053 PROGRESS: === Extracted 2245 precursors and 22948 fragments ===
20:56:17.588381 INFO: performing precursor FDR with 47 features
20:56:17.588418 INFO: Decoy channel: -1
20:56:17.588442 INFO: Competetive: True
20:56:17.591134 INFO: Setting torch num_threads to 2 for FDR classification task
20:56:17.592420 WARNING: dropped 2 decoy PSMs due to missing features
20:56:17.605992 INFO: Test AUC: 0.864
20:56:17.606097 INFO: Train AUC: 0.861
20:56:17.606127 INFO: AUC difference: 0.34%
20:56:17.791835 INFO: Resetting torch num_threads to 100
20:56:17.792584 INFO: === FDR correction performed with classifier version 7 ===
20:56:17.793333 PROGRESS: ============================= Precursor FDR =============================
20:56:17.793426 PROGRESS: Total precursors accumulated: 600
20:56:17.793488 PROGRESS: Target precursors: 585 (97.50%)
20:56:17.793538 PROGRESS: Decoy precursors: 15 (2.50%)
20:56:17.793582 PROGRESS: 
20:56:17.793625 PROGRESS: Precursor Summary:
20:56:17.794723 PROGRESS: Channel   0:	 0.05 FDR:   585; 0.01 FDR:   550; 0.001 FDR:   449
20:56:17.794818 PROGRESS: 
20:56:17.794876 PROGRESS: Protein Summary:
20:56:17.796178 PROGRESS: Channel   0:	 0.05 FDR:   547; 0.01 FDR:   514; 0.001 FDR:   418
20:56:17.796272 PROGRESS: =========================================================================
20:56:17.800064 INFO: fragments_df: keeping 5000 of 22948 [sum(precursor_idx_mask)=11038 sum(mass_error_mask)=22948 stop_rank=5000
20:56:17.804896 INFO: calibration group: precursor, fitting mz estimator 
20:56:17.922016 INFO: calibration group: precursor, fitting rt estimator 
20:56:18.044675 INFO: calibration group: precursor, fitting mobility estimator 
20:56:18.177061 INFO: calibration group: fragment, fitting mz estimator 
20:56:18.818199 INFO: Using score_cutoff 32.68444228363037 (fac=0.99, q=1)
20:56:18.818614 INFO: calibration group: precursor, predicting mz
20:56:18.819772 INFO: calibration group: precursor, predicting rt
20:56:18.821106 INFO: calibration group: precursor, predicting mobility
20:56:18.821859 INFO: calibration group: fragment, predicting mz
20:56:18.823864 INFO: === checking if optimization conditions were reached ===
20:56:18.823963 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
20:56:18.825719 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 11.3252.
20:56:18.825773 INFO: ==============================================
20:56:18.825857 INFO: Starting optimization step 5.
20:56:18.825922 PROGRESS: === Extracting elution groups 0 to 600 ===
20:56:18.825978 PROGRESS: Extracting batch of 1188 precursors
20:56:18.827093 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:56:18.827141 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:56:18.827176 INFO: FWHM in RT is 2.46 seconds, sigma is 0.54
20:56:18.827198 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.01
20:56:18.827961 INFO: Starting candidate selection
20:56:19.333709 INFO: Starting candidate scoring
20:56:19.437997 INFO: Finished candidate processing
20:56:19.438112 INFO: Collecting candidate features
20:56:19.447073 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2243)
20:56:19.450180 INFO: Collecting fragment features
20:56:19.454248 INFO: Finished candidate scoring
20:56:19.455838 PROGRESS: === Extracted 2243 precursors and 22930 fragments ===
20:56:19.456140 INFO: performing precursor FDR with 47 features
20:56:19.456176 INFO: Decoy channel: -1
20:56:19.456199 INFO: Competetive: True
20:56:19.458823 INFO: Setting torch num_threads to 2 for FDR classification task
20:56:19.460048 WARNING: dropped 1 decoy PSMs due to missing features
20:56:19.471835 INFO: Test AUC: 0.851
20:56:19.471926 INFO: Train AUC: 0.865
20:56:19.471956 INFO: AUC difference: 1.63%
20:56:19.716517 INFO: Resetting torch num_threads to 100
20:56:19.717600 INFO: === FDR correction performed with classifier version 7 ===
20:56:19.718856 PROGRESS: ============================= Precursor FDR =============================
20:56:19.719168 PROGRESS: Total precursors accumulated: 600
20:56:19.719410 PROGRESS: Target precursors: 585 (97.50%)
20:56:19.719641 PROGRESS: Decoy precursors: 15 (2.50%)
20:56:19.719869 PROGRESS: 
20:56:19.720093 PROGRESS: Precursor Summary:
20:56:19.721880 PROGRESS: Channel   0:	 0.05 FDR:   585; 0.01 FDR:   540; 0.001 FDR:   452
20:56:19.722139 PROGRESS: 
20:56:19.722234 PROGRESS: Protein Summary:
20:56:19.724066 PROGRESS: Channel   0:	 0.05 FDR:   547; 0.01 FDR:   504; 0.001 FDR:   420
20:56:19.724376 PROGRESS: =========================================================================
20:56:19.729835 INFO: fragments_df: keeping 5000 of 22930 [sum(precursor_idx_mask)=10824 sum(mass_error_mask)=22930 stop_rank=5000
20:56:19.738075 INFO: calibration group: precursor, fitting mz estimator 
20:56:19.893816 INFO: calibration group: precursor, fitting rt estimator 
20:56:20.053960 INFO: calibration group: precursor, fitting mobility estimator 
20:56:20.227756 INFO: calibration group: fragment, fitting mz estimator 
20:56:20.953929 INFO: Using score_cutoff 32.99931960411072 (fac=0.99, q=1)
20:56:20.954364 INFO: calibration group: precursor, predicting mz
20:56:20.955515 INFO: calibration group: precursor, predicting rt
20:56:20.956837 INFO: calibration group: precursor, predicting mobility
20:56:20.957592 INFO: calibration group: fragment, predicting mz
20:56:20.959555 INFO: === checking if optimization conditions were reached ===
20:56:20.959654 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
20:56:20.960649 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 11.1594 found after 6 searches.
20:56:20.960700 INFO: ==============================================
20:56:20.960786 PROGRESS: Optimization finished for rt_error.
20:56:20.965602 INFO: calibration group: precursor, predicting mz
20:56:20.966428 INFO: calibration group: precursor, predicting rt
20:56:20.967737 INFO: calibration group: precursor, predicting mobility
20:56:20.968498 INFO: calibration group: fragment, predicting mz
20:56:20.998161 INFO: Starting optimization step 0.
20:56:20.998414 PROGRESS: === Extracting elution groups 0 to 600 ===
20:56:20.998486 PROGRESS: Extracting batch of 1188 precursors
20:56:20.999748 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:56:20.999796 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:56:20.999834 INFO: FWHM in RT is 2.46 seconds, sigma is 0.54
20:56:20.999857 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 3.01
20:56:21.000989 INFO: Starting candidate selection
20:56:21.525390 INFO: Starting candidate scoring
20:56:21.645204 INFO: Finished candidate processing
20:56:21.645315 INFO: Collecting candidate features
20:56:21.654510 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2240)
20:56:21.657725 INFO: Collecting fragment features
20:56:21.662264 INFO: Finished candidate scoring
20:56:21.664003 PROGRESS: === Extracted 2240 precursors and 22906 fragments ===
20:56:21.664299 INFO: performing precursor FDR with 47 features
20:56:21.664340 INFO: Decoy channel: -1
20:56:21.664363 INFO: Competetive: True
20:56:21.667137 INFO: Setting torch num_threads to 2 for FDR classification task
20:56:21.668448 WARNING: dropped 1 decoy PSMs due to missing features
20:56:21.680588 INFO: Test AUC: 0.836
20:56:21.680654 INFO: Train AUC: 0.867
20:56:21.680683 INFO: AUC difference: 3.49%
20:56:21.856813 INFO: Resetting torch num_threads to 100
20:56:21.857435 INFO: === FDR correction performed with classifier version 12 ===
20:56:21.858122 PROGRESS: ============================= Precursor FDR =============================
20:56:21.858213 PROGRESS: Total precursors accumulated: 600
20:56:21.858273 PROGRESS: Target precursors: 584 (97.33%)
20:56:21.858323 PROGRESS: Decoy precursors: 16 (2.67%)
20:56:21.858369 PROGRESS: 
20:56:21.858413 PROGRESS: Precursor Summary:
20:56:21.859490 PROGRESS: Channel   0:	 0.05 FDR:   584; 0.01 FDR:   540; 0.001 FDR:   446
20:56:21.859585 PROGRESS: 
20:56:21.859651 PROGRESS: Protein Summary:
20:56:21.860943 PROGRESS: Channel   0:	 0.05 FDR:   546; 0.01 FDR:   504; 0.001 FDR:   414
20:56:21.861036 PROGRESS: =========================================================================
20:56:21.864601 INFO: fragments_df: keeping 5000 of 22906 [sum(precursor_idx_mask)=10811 sum(mass_error_mask)=22906 stop_rank=5000
20:56:21.870025 INFO: calibration group: precursor, fitting mz estimator 
20:56:22.030540 INFO: calibration group: precursor, fitting rt estimator 
20:56:22.171246 INFO: calibration group: precursor, fitting mobility estimator 
20:56:22.316450 INFO: calibration group: fragment, fitting mz estimator 
20:56:23.013686 INFO: Using score_cutoff 33.0528799621582 (fac=0.99, q=1)
20:56:23.014101 INFO: calibration group: precursor, predicting mz
20:56:23.015224 INFO: calibration group: precursor, predicting rt
20:56:23.016539 INFO: calibration group: precursor, predicting mobility
20:56:23.017292 INFO: calibration group: fragment, predicting mz
20:56:23.019574 INFO: === checking if optimization conditions were reached ===
20:56:23.019680 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
20:56:23.021018 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0627.
20:56:23.021075 INFO: ==============================================
20:56:23.021158 INFO: Starting optimization step 1.
20:56:23.021224 PROGRESS: === Extracting elution groups 0 to 600 ===
20:56:23.021282 PROGRESS: Extracting batch of 1188 precursors
20:56:23.022603 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:56:23.022649 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:56:23.022684 INFO: FWHM in RT is 2.48 seconds, sigma is 0.54
20:56:23.022708 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.03
20:56:23.023767 INFO: Starting candidate selection
20:56:23.529119 INFO: Starting candidate scoring
20:56:23.646310 INFO: Finished candidate processing
20:56:23.646415 INFO: Collecting candidate features
20:56:23.655175 WARNING: intensity_correlation has 2 NaNs ( 0.09 % out of 2245)
20:56:23.658310 INFO: Collecting fragment features
20:56:23.662218 INFO: Finished candidate scoring
20:56:23.663695 PROGRESS: === Extracted 2245 precursors and 22708 fragments ===
20:56:23.663980 INFO: performing precursor FDR with 47 features
20:56:23.664017 INFO: Decoy channel: -1
20:56:23.664039 INFO: Competetive: True
20:56:23.666816 INFO: Setting torch num_threads to 2 for FDR classification task
20:56:23.668181 WARNING: dropped 1 target PSMs due to missing features
20:56:23.668231 WARNING: dropped 1 decoy PSMs due to missing features
20:56:23.680143 INFO: Test AUC: 0.846
20:56:23.680210 INFO: Train AUC: 0.868
20:56:23.680239 INFO: AUC difference: 2.52%
20:56:23.854713 INFO: Resetting torch num_threads to 100
20:56:23.855289 INFO: === FDR correction performed with classifier version 12 ===
20:56:23.856396 PROGRESS: ============================= Precursor FDR =============================
20:56:23.856488 PROGRESS: Total precursors accumulated: 599
20:56:23.856547 PROGRESS: Target precursors: 583 (97.33%)
20:56:23.856598 PROGRESS: Decoy precursors: 16 (2.67%)
20:56:23.856646 PROGRESS: 
20:56:23.856692 PROGRESS: Precursor Summary:
20:56:23.857724 PROGRESS: Channel   0:	 0.05 FDR:   583; 0.01 FDR:   543; 0.001 FDR:   436
20:56:23.857818 PROGRESS: 
20:56:23.857874 PROGRESS: Protein Summary:
20:56:23.859128 PROGRESS: Channel   0:	 0.05 FDR:   545; 0.01 FDR:   507; 0.001 FDR:   404
20:56:23.859223 PROGRESS: =========================================================================
20:56:23.862696 INFO: fragments_df: keeping 5000 of 22708 [sum(precursor_idx_mask)=10869 sum(mass_error_mask)=22708 stop_rank=5000
20:56:23.868748 INFO: calibration group: precursor, fitting mz estimator 
20:56:24.008775 INFO: calibration group: precursor, fitting rt estimator 
20:56:24.148765 INFO: calibration group: precursor, fitting mobility estimator 
20:56:24.287575 INFO: calibration group: fragment, fitting mz estimator 
20:56:24.979986 INFO: Using score_cutoff 33.059987580871585 (fac=0.99, q=1)
20:56:24.980402 INFO: calibration group: precursor, predicting mz
20:56:24.981532 INFO: calibration group: precursor, predicting rt
20:56:24.982846 INFO: calibration group: precursor, predicting mobility
20:56:24.983624 INFO: calibration group: fragment, predicting mz
20:56:24.985633 INFO: === checking if optimization conditions were reached ===
20:56:24.985738 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
20:56:24.987162 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0541.
20:56:24.987218 INFO: ==============================================
20:56:24.987303 INFO: Starting optimization step 2.
20:56:24.987368 PROGRESS: === Extracting elution groups 0 to 600 ===
20:56:24.987425 PROGRESS: Extracting batch of 1188 precursors
20:56:24.988503 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:56:24.988549 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:56:24.988584 INFO: FWHM in RT is 2.47 seconds, sigma is 0.54
20:56:24.988608 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.03
20:56:24.990415 INFO: Starting candidate selection
20:56:25.488539 INFO: Starting candidate scoring
20:56:25.586506 INFO: Finished candidate processing
20:56:25.586609 INFO: Collecting candidate features
20:56:25.595447 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2245)
20:56:25.598472 INFO: Collecting fragment features
20:56:25.603067 INFO: Finished candidate scoring
20:56:25.604535 PROGRESS: === Extracted 2245 precursors and 22636 fragments ===
20:56:25.604817 INFO: performing precursor FDR with 47 features
20:56:25.604853 INFO: Decoy channel: -1
20:56:25.604876 INFO: Competetive: True
20:56:25.607429 INFO: Setting torch num_threads to 2 for FDR classification task
20:56:25.608599 WARNING: dropped 1 decoy PSMs due to missing features
20:56:25.619801 INFO: Test AUC: 0.873
20:56:25.619865 INFO: Train AUC: 0.860
20:56:25.619895 INFO: AUC difference: 1.47%
20:56:25.795563 INFO: Resetting torch num_threads to 100
20:56:25.796114 INFO: === FDR correction performed with classifier version 12 ===
20:56:25.796750 PROGRESS: ============================= Precursor FDR =============================
20:56:25.796849 PROGRESS: Total precursors accumulated: 599
20:56:25.796910 PROGRESS: Target precursors: 585 (97.66%)
20:56:25.796960 PROGRESS: Decoy precursors: 14 (2.34%)
20:56:25.797006 PROGRESS: 
20:56:25.797051 PROGRESS: Precursor Summary:
20:56:25.798111 PROGRESS: Channel   0:	 0.05 FDR:   585; 0.01 FDR:   550; 0.001 FDR:   433
20:56:25.798205 PROGRESS: 
20:56:25.798262 PROGRESS: Protein Summary:
20:56:25.799558 PROGRESS: Channel   0:	 0.05 FDR:   547; 0.01 FDR:   514; 0.001 FDR:   401
20:56:25.799656 PROGRESS: =========================================================================
20:56:25.803071 INFO: fragments_df: keeping 5000 of 22636 [sum(precursor_idx_mask)=10967 sum(mass_error_mask)=22636 stop_rank=5000
20:56:25.808138 INFO: calibration group: precursor, fitting mz estimator 
20:56:25.948339 INFO: calibration group: precursor, fitting rt estimator 
20:56:26.089289 INFO: calibration group: precursor, fitting mobility estimator 
20:56:26.226404 INFO: calibration group: fragment, fitting mz estimator 
20:56:26.916436 INFO: Using score_cutoff 32.2564559223175 (fac=0.99, q=1)
20:56:26.916858 INFO: calibration group: precursor, predicting mz
20:56:26.917985 INFO: calibration group: precursor, predicting rt
20:56:26.919318 INFO: calibration group: precursor, predicting mobility
20:56:26.920080 INFO: calibration group: fragment, predicting mz
20:56:26.922439 INFO: === checking if optimization conditions were reached ===
20:56:26.922539 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
20:56:26.923278 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.0541 found after 3 searches.
20:56:26.923326 INFO: ==============================================
20:56:26.923409 PROGRESS: Optimization finished for mobility_error.
20:56:26.928266 INFO: calibration group: precursor, predicting mz
20:56:26.929099 INFO: calibration group: precursor, predicting rt
20:56:26.930376 INFO: calibration group: precursor, predicting mobility
20:56:26.931139 INFO: calibration group: fragment, predicting mz
20:56:26.957354 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
20:56:26.957498 PROGRESS: ==============================================
20:56:26.957568 PROGRESS: ms2_error      : 10.0474
20:56:26.957624 PROGRESS: ms1_error      : 10.5658
20:56:26.957675 PROGRESS: rt_error       : 11.1594
20:56:26.957724 PROGRESS: mobility_error : 0.0541
20:56:26.957767 PROGRESS: ==============================================
20:56:26.958454 INFO: calibration group: precursor, predicting mz
20:56:26.985058 INFO: calibration group: precursor, predicting rt
20:56:27.104032 INFO: calibration group: precursor, predicting mobility
20:56:27.131062 INFO: calibration group: fragment, predicting mz
20:56:27.406410 PROGRESS: Extracting batch of 189636 precursors
20:56:27.463854 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:56:27.463995 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:56:27.464043 INFO: FWHM in RT is 2.47 seconds, sigma is 0.54
20:56:27.464068 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.03
20:56:27.467578 INFO: Starting candidate selection
20:57:00.878653 INFO: Applying score cutoff of 32.2564559223175
20:57:00.884892 INFO: Removed 88106 precursors with score below cutoff
20:57:01.232190 INFO: Starting candidate scoring
20:57:08.251304 INFO: Finished candidate processing
20:57:08.251482 INFO: Collecting candidate features
20:57:08.682728 INFO: Collecting fragment features
20:57:08.844924 INFO: Finished candidate scoring
20:57:09.035785 INFO: === FDR correction performed with classifier version 16 ===
20:57:09.036623 INFO: performing precursor FDR with 47 features
20:57:09.036675 INFO: Decoy channel: -1
20:57:09.036704 INFO: Competetive: True
20:57:09.111823 INFO: Setting torch num_threads to 2 for FDR classification task
20:57:09.143059 WARNING: FDR calculation for 164234 target and 107586 decoy PSMs
20:57:09.143206 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
20:57:14.822900 INFO: Test AUC: 0.920
20:57:14.823048 INFO: Train AUC: 0.925
20:57:14.823082 INFO: AUC difference: 0.50%
20:57:15.059033 INFO: Resetting torch num_threads to 100
20:57:15.079223 INFO: Removing fragments below FDR threshold
20:57:15.136531 PROGRESS: ============================= Precursor FDR =============================
20:57:15.136838 PROGRESS: Total precursors accumulated: 92,382
20:57:15.136908 PROGRESS: Target precursors: 91,468 (99.01%)
20:57:15.136960 PROGRESS: Decoy precursors: 914 (0.99%)
20:57:15.137007 PROGRESS: 
20:57:15.137050 PROGRESS: Precursor Summary:
20:57:15.176225 PROGRESS: Channel   0:	 0.05 FDR: 91,468; 0.01 FDR: 91,468; 0.001 FDR: 85,894
20:57:15.176512 PROGRESS: 
20:57:15.176576 PROGRESS: Protein Summary:
20:57:15.233833 PROGRESS: Channel   0:	 0.05 FDR: 9,634; 0.01 FDR: 9,634; 0.001 FDR: 9,569
20:57:15.234122 PROGRESS: =========================================================================
20:57:15.929573 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
20:57:15.980328 PROGRESS: Loading raw file 6/6: ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
20:57:15.980489 INFO: Quantification results path: run_output/alphadia_1.10.4_Again_good_now/quant
20:57:15.980571 INFO: Creating folder run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/figures
20:57:15.981320 INFO: Initializing RawFileManager
20:57:15.981440 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
20:57:15.981494 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
20:57:15.981530 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
20:57:16.184293 INFO: Reading 39,129 frames with 2,804,178,635 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
20:57:22.615828 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d...
20:57:22.618998 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
20:57:22.629381 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
20:57:22.629733 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
20:57:22.630196 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
20:57:22.632119 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
20:57:22.646952 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
20:57:22.647185 INFO: Indexing quadrupole dimension
20:57:23.153233 INFO: Transposing detector events
20:57:32.033380 INFO: Finished transposing data
20:57:32.073095 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
20:57:32.073859 INFO: RT (min)            : 0.0 - 70.0
20:57:32.073948 INFO: RT duration (sec)   : 4199.8
20:57:32.074004 INFO: RT duration (min)   : 70.0
20:57:32.074054 INFO: Cycle len (scans)   : 9
20:57:32.074100 INFO: Cycle len (sec)     : 0.97
20:57:32.074143 INFO: Number of cycles    : 4347
20:57:32.074188 INFO: MS2 range (m/z)     : 400.0 - 1000.0
20:57:32.115078 INFO: Initializing CalibrationManager
20:57:32.115407 INFO: Loading calibration config
20:57:32.115910 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed'], 'function': LOESSRegression()}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed'], 'function': LOESSRegression(n_kernels=2)}], 'name': 'precursor'}]
20:57:32.115995 INFO: Calibration group :fragment, found 1 estimator(s)
20:57:32.116079 INFO: Calibration group :precursor, found 3 estimator(s)
20:57:32.116219 INFO: Initializing OptimizationManager
20:57:32.116321 INFO: initial parameter: ms1_error = 30
20:57:32.116370 INFO: initial parameter: ms2_error = 30
20:57:32.116433 INFO: initial parameter: rt_error = 2099.9231665
20:57:32.116480 INFO: initial parameter: mobility_error = 0.1
20:57:32.116539 INFO: initial parameter: column_type = library
20:57:32.116582 INFO: initial parameter: num_candidates = 1
20:57:32.116621 INFO: initial parameter: classifier_version = -1
20:57:32.116660 INFO: initial parameter: fwhm_rt = 5
20:57:32.116702 INFO: initial parameter: fwhm_mobility = 0.01
20:57:32.116741 INFO: initial parameter: score_cutoff = 0
20:57:32.116797 INFO: Initializing TimingManager
20:57:32.116848 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
20:57:32.116933 INFO: FDRManager not loaded from disk.
20:57:32.116957 INFO: Initializing FDRManager
20:57:32.116989 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
20:57:32.147400 PROGRESS: 95,522 target precursors potentially observable (0 removed)
20:57:32.191992 PROGRESS: Starting initial search for precursors.
20:57:32.198491 INFO: Starting optimization step 0.
20:57:32.198663 PROGRESS: === Extracting elution groups 0 to 200 ===
20:57:32.198736 PROGRESS: Extracting batch of 395 precursors
20:57:32.199673 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:57:32.199737 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:57:32.199773 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:57:32.199795 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:57:32.200701 INFO: Starting candidate selection
20:58:01.075311 INFO: Starting candidate scoring
20:58:01.151369 INFO: Finished candidate processing
20:58:01.151475 INFO: Collecting candidate features
20:58:01.160757 INFO: Collecting fragment features
20:58:01.163071 INFO: Finished candidate scoring
20:58:01.163898 PROGRESS: === Extracted 394 precursors and 4351 fragments ===
20:58:01.164227 INFO: performing precursor FDR with 47 features
20:58:01.164267 INFO: Decoy channel: -1
20:58:01.164299 INFO: Competetive: True
20:58:01.165301 INFO: Setting torch num_threads to 2 for FDR classification task
20:58:01.174909 INFO: Test AUC: 0.492
20:58:01.174968 INFO: Train AUC: 0.458
20:58:01.175005 INFO: AUC difference: 7.41%
20:58:01.175057 WARNING: AUC difference > 5%. This may indicate overfitting.
20:58:01.388731 INFO: Resetting torch num_threads to 100
20:58:01.389379 INFO: === FDR correction performed with classifier version -1 ===
20:58:01.390146 PROGRESS: ============================= Precursor FDR =============================
20:58:01.390245 PROGRESS: Total precursors accumulated: 200
20:58:01.390312 PROGRESS: Target precursors: 86 (43.00%)
20:58:01.390370 PROGRESS: Decoy precursors: 114 (57.00%)
20:58:01.390423 PROGRESS: 
20:58:01.390474 PROGRESS: Precursor Summary:
20:58:01.391500 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:58:01.391599 PROGRESS: 
20:58:01.391662 PROGRESS: Protein Summary:
20:58:01.392748 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
20:58:01.392843 PROGRESS: =========================================================================
20:58:01.396464 INFO: Starting optimization step 1.
20:58:01.396568 PROGRESS: === Extracting elution groups 200 to 600 ===
20:58:01.396629 PROGRESS: Extracting batch of 793 precursors
20:58:01.397385 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:58:01.397429 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:58:01.397458 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:58:01.397480 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:58:01.409184 INFO: Starting candidate selection
20:58:07.399998 INFO: Starting candidate scoring
20:58:07.516761 INFO: Finished candidate processing
20:58:07.516883 INFO: Collecting candidate features
20:58:07.528463 INFO: Collecting fragment features
20:58:07.531241 INFO: Finished candidate scoring
20:58:07.535524 PROGRESS: === Extracted 1187 precursors and 13129 fragments ===
20:58:07.536363 INFO: performing precursor FDR with 47 features
20:58:07.536407 INFO: Decoy channel: -1
20:58:07.536430 INFO: Competetive: True
20:58:07.539476 INFO: Setting torch num_threads to 2 for FDR classification task
20:58:07.550338 INFO: Test AUC: 0.481
20:58:07.550400 INFO: Train AUC: 0.436
20:58:07.550430 INFO: AUC difference: 10.28%
20:58:07.550452 WARNING: AUC difference > 5%. This may indicate overfitting.
20:58:07.731522 INFO: Resetting torch num_threads to 100
20:58:07.732301 INFO: === FDR correction performed with classifier version -1 ===
20:58:07.733049 PROGRESS: ============================= Precursor FDR =============================
20:58:07.733146 PROGRESS: Total precursors accumulated: 600
20:58:07.733206 PROGRESS: Target precursors: 253 (42.17%)
20:58:07.733257 PROGRESS: Decoy precursors: 347 (57.83%)
20:58:07.733310 PROGRESS: 
20:58:07.733360 PROGRESS: Precursor Summary:
20:58:07.734238 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
20:58:07.734327 PROGRESS: 
20:58:07.734384 PROGRESS: Protein Summary:
20:58:07.735353 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
20:58:07.735443 PROGRESS: =========================================================================
20:58:07.744220 INFO: Starting optimization step 2.
20:58:07.744339 PROGRESS: === Extracting elution groups 600 to 1400 ===
20:58:07.744412 PROGRESS: Extracting batch of 1583 precursors
20:58:07.745476 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:58:07.745524 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:58:07.745554 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:58:07.745575 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:58:07.746367 INFO: Starting candidate selection
20:58:17.945798 INFO: Starting candidate scoring
20:58:18.140146 INFO: Finished candidate processing
20:58:18.140322 INFO: Collecting candidate features
20:58:18.162775 INFO: Collecting fragment features
20:58:18.167200 INFO: Finished candidate scoring
20:58:18.171933 PROGRESS: === Extracted 2770 precursors and 30802 fragments ===
20:58:18.173077 INFO: performing precursor FDR with 47 features
20:58:18.173127 INFO: Decoy channel: -1
20:58:18.173156 INFO: Competetive: True
20:58:18.177092 INFO: Setting torch num_threads to 2 for FDR classification task
20:58:18.194145 INFO: Test AUC: 0.473
20:58:18.194263 INFO: Train AUC: 0.433
20:58:18.194293 INFO: AUC difference: 9.24%
20:58:18.194315 WARNING: AUC difference > 5%. This may indicate overfitting.
20:58:18.378259 INFO: Resetting torch num_threads to 100
20:58:18.379092 INFO: === FDR correction performed with classifier version -1 ===
20:58:18.379852 PROGRESS: ============================= Precursor FDR =============================
20:58:18.379944 PROGRESS: Total precursors accumulated: 1,400
20:58:18.380003 PROGRESS: Target precursors: 601 (42.93%)
20:58:18.380053 PROGRESS: Decoy precursors: 799 (57.07%)
20:58:18.380099 PROGRESS: 
20:58:18.380143 PROGRESS: Precursor Summary:
20:58:18.381042 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
20:58:18.381138 PROGRESS: 
20:58:18.381196 PROGRESS: Protein Summary:
20:58:18.382194 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
20:58:18.382286 PROGRESS: =========================================================================
20:58:18.392536 INFO: Starting optimization step 3.
20:58:18.392653 PROGRESS: === Extracting elution groups 1400 to 3000 ===
20:58:18.392736 PROGRESS: Extracting batch of 3171 precursors
20:58:18.394129 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:58:18.394176 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:58:18.394222 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:58:18.394243 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:58:18.395187 INFO: Starting candidate selection
20:59:00.982896 INFO: Starting candidate scoring
20:59:01.271541 INFO: Finished candidate processing
20:59:01.271761 INFO: Collecting candidate features
20:59:01.286693 INFO: Collecting fragment features
20:59:01.291117 INFO: Finished candidate scoring
20:59:01.296234 PROGRESS: === Extracted 5940 precursors and 65987 fragments ===
20:59:01.297528 INFO: performing precursor FDR with 47 features
20:59:01.297575 INFO: Decoy channel: -1
20:59:01.297600 INFO: Competetive: True
20:59:01.302043 INFO: Setting torch num_threads to 2 for FDR classification task
20:59:01.328044 INFO: Test AUC: 0.428
20:59:01.328166 INFO: Train AUC: 0.447
20:59:01.328196 INFO: AUC difference: 4.40%
20:59:01.506695 INFO: Resetting torch num_threads to 100
20:59:01.507674 INFO: === FDR correction performed with classifier version -1 ===
20:59:01.508630 PROGRESS: ============================= Precursor FDR =============================
20:59:01.508722 PROGRESS: Total precursors accumulated: 3,000
20:59:01.508785 PROGRESS: Target precursors: 1,311 (43.70%)
20:59:01.508835 PROGRESS: Decoy precursors: 1,689 (56.30%)
20:59:01.508881 PROGRESS: 
20:59:01.508924 PROGRESS: Precursor Summary:
20:59:01.509820 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
20:59:01.509908 PROGRESS: 
20:59:01.509963 PROGRESS: Protein Summary:
20:59:01.510925 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
20:59:01.511013 PROGRESS: =========================================================================
20:59:01.523423 INFO: Starting optimization step 4.
20:59:01.523572 PROGRESS: === Extracting elution groups 3000 to 6200 ===
20:59:01.523635 PROGRESS: Extracting batch of 6347 precursors
20:59:01.525254 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
20:59:01.525301 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
20:59:01.525329 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
20:59:01.525350 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
20:59:01.560411 INFO: Starting candidate selection
21:00:01.046353 INFO: Starting candidate scoring
21:00:01.825475 INFO: Finished candidate processing
21:00:01.825588 INFO: Collecting candidate features
21:00:01.844939 INFO: Collecting fragment features
21:00:01.851930 INFO: Finished candidate scoring
21:00:01.862733 PROGRESS: === Extracted 12287 precursors and 136570 fragments ===
21:00:01.864678 INFO: performing precursor FDR with 47 features
21:00:01.864742 INFO: Decoy channel: -1
21:00:01.864768 INFO: Competetive: True
21:00:01.870912 INFO: Setting torch num_threads to 2 for FDR classification task
21:00:01.910529 INFO: Test AUC: 0.452
21:00:01.910663 INFO: Train AUC: 0.439
21:00:01.910694 INFO: AUC difference: 3.02%
21:00:02.107705 INFO: Resetting torch num_threads to 100
21:00:02.109398 INFO: === FDR correction performed with classifier version -1 ===
21:00:02.110934 PROGRESS: ============================= Precursor FDR =============================
21:00:02.111055 PROGRESS: Total precursors accumulated: 6,200
21:00:02.111122 PROGRESS: Target precursors: 2,657 (42.85%)
21:00:02.111196 PROGRESS: Decoy precursors: 3,543 (57.15%)
21:00:02.111245 PROGRESS: 
21:00:02.111289 PROGRESS: Precursor Summary:
21:00:02.112215 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
21:00:02.112303 PROGRESS: 
21:00:02.112359 PROGRESS: Protein Summary:
21:00:02.113351 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
21:00:02.113445 PROGRESS: =========================================================================
21:00:02.143651 INFO: Starting optimization step 5.
21:00:02.144023 PROGRESS: === Extracting elution groups 6200 to 12600 ===
21:00:02.144113 PROGRESS: Extracting batch of 12697 precursors
21:00:02.149030 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
21:00:02.149110 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
21:00:02.149161 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
21:00:02.149188 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
21:00:02.243820 INFO: Starting candidate selection
21:02:35.516507 INFO: Starting candidate scoring
21:02:36.351073 INFO: Finished candidate processing
21:02:36.351200 INFO: Collecting candidate features
21:02:36.381062 INFO: Collecting fragment features
21:02:36.391978 INFO: Finished candidate scoring
21:02:36.410604 PROGRESS: === Extracted 24983 precursors and 277758 fragments ===
21:02:36.413697 INFO: performing precursor FDR with 47 features
21:02:36.413772 INFO: Decoy channel: -1
21:02:36.413797 INFO: Competetive: True
21:02:36.423871 INFO: Setting torch num_threads to 2 for FDR classification task
21:02:36.726522 INFO: Test AUC: 0.802
21:02:36.726661 INFO: Train AUC: 0.806
21:02:36.726693 INFO: AUC difference: 0.45%
21:02:36.923720 INFO: Resetting torch num_threads to 100
21:02:36.925174 INFO: === FDR correction performed with classifier version -1 ===
21:02:36.927007 PROGRESS: ============================= Precursor FDR =============================
21:02:36.927134 PROGRESS: Total precursors accumulated: 12,600
21:02:36.927204 PROGRESS: Target precursors: 10,179 (80.79%)
21:02:36.927263 PROGRESS: Decoy precursors: 2,421 (19.21%)
21:02:36.927310 PROGRESS: 
21:02:36.927353 PROGRESS: Precursor Summary:
21:02:36.929522 PROGRESS: Channel   0:	 0.05 FDR: 7,210; 0.01 FDR: 3,965; 0.001 FDR:   126
21:02:36.929627 PROGRESS: 
21:02:36.929703 PROGRESS: Protein Summary:
21:02:36.932559 PROGRESS: Channel   0:	 0.05 FDR: 3,699; 0.01 FDR: 2,288; 0.001 FDR:   117
21:02:36.932658 PROGRESS: =========================================================================
21:02:36.959105 INFO: fragments_df: keeping 5000 of 277758 [sum(precursor_idx_mask)=43942 sum(mass_error_mask)=277758 stop_rank=5000
21:02:36.971117 INFO: calibration group: precursor, fitting mz estimator 
21:02:37.439893 INFO: calibration group: precursor, fitting rt estimator 
21:02:37.912678 INFO: calibration group: precursor, fitting mobility estimator 
21:02:38.379313 INFO: calibration group: fragment, fitting mz estimator 
21:02:39.038867 INFO: Using score_cutoff 52.51374423522949 (fac=0.99, q=1)
21:02:39.039435 INFO: calibration group: precursor, predicting mz
21:02:39.040771 INFO: calibration group: precursor, predicting rt
21:02:39.042997 INFO: calibration group: precursor, predicting mobility
21:02:39.043952 INFO: calibration group: fragment, predicting mz
21:02:39.051757 PROGRESS: Required number of precursors found. Starting search parameter optimization.
21:02:39.051920 INFO: Starting optimization step 6.
21:02:39.051989 PROGRESS: === Extracting elution groups 0 to 1400 ===
21:02:39.052053 PROGRESS: Extracting batch of 2771 precursors
21:02:39.053583 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
21:02:39.053632 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
21:02:39.053677 INFO: FWHM in RT is 3.30 seconds, sigma is 0.73
21:02:39.053699 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.33
21:02:39.054576 INFO: Starting candidate selection
21:03:03.882672 INFO: Starting candidate scoring
21:03:04.290503 INFO: Finished candidate processing
21:03:04.290627 INFO: Collecting candidate features
21:03:04.307603 INFO: Collecting fragment features
21:03:04.312815 INFO: Finished candidate scoring
21:03:04.315871 PROGRESS: === Extracted 5329 precursors and 59238 fragments ===
21:03:04.316185 INFO: performing precursor FDR with 47 features
21:03:04.316222 INFO: Decoy channel: -1
21:03:04.316245 INFO: Competetive: True
21:03:04.319402 INFO: Setting torch num_threads to 2 for FDR classification task
21:03:04.342320 INFO: Test AUC: 0.694
21:03:04.342430 INFO: Train AUC: 0.720
21:03:04.342460 INFO: AUC difference: 3.66%
21:03:04.523251 INFO: Resetting torch num_threads to 100
21:03:04.523944 INFO: === FDR correction performed with classifier version 5 ===
21:03:04.524702 PROGRESS: ============================= Precursor FDR =============================
21:03:04.524791 PROGRESS: Total precursors accumulated: 1,400
21:03:04.524857 PROGRESS: Target precursors: 1,189 (84.93%)
21:03:04.524911 PROGRESS: Decoy precursors: 211 (15.07%)
21:03:04.524956 PROGRESS: 
21:03:04.525000 PROGRESS: Precursor Summary:
21:03:04.526071 PROGRESS: Channel   0:	 0.05 FDR:   889; 0.01 FDR:   417; 0.001 FDR:   146
21:03:04.526161 PROGRESS: 
21:03:04.526217 PROGRESS: Protein Summary:
21:03:04.527472 PROGRESS: Channel   0:	 0.05 FDR:   773; 0.01 FDR:   387; 0.001 FDR:   141
21:03:04.527566 PROGRESS: =========================================================================
21:03:04.533661 INFO: fragments_df: keeping 5000 of 59238 [sum(precursor_idx_mask)=8865 sum(mass_error_mask)=59238 stop_rank=5000
21:03:04.540203 INFO: calibration group: precursor, fitting mz estimator 
21:03:04.674443 INFO: calibration group: precursor, fitting rt estimator 
21:03:04.806843 INFO: calibration group: precursor, fitting mobility estimator 
21:03:04.929229 INFO: calibration group: fragment, fitting mz estimator 
21:03:05.547352 INFO: Using score_cutoff 52.82535223388672 (fac=0.99, q=1)
21:03:05.547753 INFO: calibration group: precursor, predicting mz
21:03:05.549043 INFO: calibration group: precursor, predicting rt
21:03:05.551329 INFO: calibration group: precursor, predicting mobility
21:03:05.552293 INFO: calibration group: fragment, predicting mz
21:03:05.556514 INFO: === checking if optimization conditions were reached ===
21:03:05.558147 PROGRESS: ❌ ms2_error      : 10.0474 > 10.0474 or insufficient steps taken.
21:03:05.559087 PROGRESS: ❌ ms1_error      : 10.5658 > 10.5658 or insufficient steps taken.
21:03:05.559137 INFO: ==============================================
21:03:05.559221 INFO: Starting optimization step 7.
21:03:05.559294 PROGRESS: === Extracting elution groups 0 to 1400 ===
21:03:05.559351 PROGRESS: Extracting batch of 2771 precursors
21:03:05.560546 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
21:03:05.560593 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
21:03:05.560628 INFO: FWHM in RT is 3.25 seconds, sigma is 0.72
21:03:05.560651 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.32
21:03:05.561415 INFO: Starting candidate selection
21:03:21.661311 INFO: Starting candidate scoring
21:03:21.890479 INFO: Finished candidate processing
21:03:21.890622 INFO: Collecting candidate features
21:03:21.910610 INFO: Collecting fragment features
21:03:21.916278 INFO: Finished candidate scoring
21:03:21.919325 PROGRESS: === Extracted 5355 precursors and 57824 fragments ===
21:03:21.919633 INFO: performing precursor FDR with 47 features
21:03:21.919671 INFO: Decoy channel: -1
21:03:21.919694 INFO: Competetive: True
21:03:21.922781 INFO: Setting torch num_threads to 2 for FDR classification task
21:03:21.944183 INFO: Test AUC: 0.736
21:03:21.944275 INFO: Train AUC: 0.761
21:03:21.944305 INFO: AUC difference: 3.19%
21:03:22.121083 INFO: Resetting torch num_threads to 100
21:03:22.121799 INFO: === FDR correction performed with classifier version 6 ===
21:03:22.122511 PROGRESS: ============================= Precursor FDR =============================
21:03:22.122602 PROGRESS: Total precursors accumulated: 1,400
21:03:22.122667 PROGRESS: Target precursors: 1,254 (89.57%)
21:03:22.122717 PROGRESS: Decoy precursors: 146 (10.43%)
21:03:22.122761 PROGRESS: 
21:03:22.122804 PROGRESS: Precursor Summary:
21:03:22.124255 PROGRESS: Channel   0:	 0.05 FDR: 1,109; 0.01 FDR:   632; 0.001 FDR:   223
21:03:22.124365 PROGRESS: 
21:03:22.124425 PROGRESS: Protein Summary:
21:03:22.125806 PROGRESS: Channel   0:	 0.05 FDR:   969; 0.01 FDR:   560; 0.001 FDR:   216
21:03:22.125904 PROGRESS: =========================================================================
21:03:22.132056 INFO: fragments_df: keeping 5000 of 57824 [sum(precursor_idx_mask)=13125 sum(mass_error_mask)=57824 stop_rank=5000
21:03:22.136735 INFO: calibration group: precursor, fitting mz estimator 
21:03:22.265649 INFO: calibration group: precursor, fitting rt estimator 
21:03:22.393062 INFO: calibration group: precursor, fitting mobility estimator 
21:03:22.522716 INFO: calibration group: fragment, fitting mz estimator 
21:03:23.161614 INFO: Using score_cutoff 44.408350888824465 (fac=0.99, q=1)
21:03:23.162044 INFO: calibration group: precursor, predicting mz
21:03:23.163221 INFO: calibration group: precursor, predicting rt
21:03:23.164556 INFO: calibration group: precursor, predicting mobility
21:03:23.165342 INFO: calibration group: fragment, predicting mz
21:03:23.167895 INFO: === checking if optimization conditions were reached ===
21:03:23.169770 PROGRESS: ✅ ms2_error      : 10.0474 <= 10.0474
21:03:23.170746 PROGRESS: ✅ ms1_error      : 10.5658 <= 10.5658
21:03:23.170796 INFO: ==============================================
21:03:23.170882 PROGRESS: Optimization finished for ms2_error, ms1_error.
21:03:23.175607 INFO: calibration group: precursor, predicting mz
21:03:23.176432 INFO: calibration group: precursor, predicting rt
21:03:23.177739 INFO: calibration group: precursor, predicting mobility
21:03:23.178512 INFO: calibration group: fragment, predicting mz
21:03:23.180425 INFO: Starting optimization step 0.
21:03:23.180526 PROGRESS: === Extracting elution groups 0 to 600 ===
21:03:23.180588 PROGRESS: Extracting batch of 1188 precursors
21:03:23.181531 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
21:03:23.181578 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
21:03:23.181613 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
21:03:23.181636 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.99
21:03:23.182355 INFO: Starting candidate selection
21:03:30.721955 INFO: Starting candidate scoring
21:03:30.844834 INFO: Finished candidate processing
21:03:30.844940 INFO: Collecting candidate features
21:03:30.870793 INFO: Collecting fragment features
21:03:30.878041 INFO: Finished candidate scoring
21:03:30.880133 PROGRESS: === Extracted 2278 precursors and 24422 fragments ===
21:03:30.880566 INFO: performing precursor FDR with 47 features
21:03:30.880626 INFO: Decoy channel: -1
21:03:30.880665 INFO: Competetive: True
21:03:30.884685 INFO: Setting torch num_threads to 2 for FDR classification task
21:03:30.900079 INFO: Test AUC: 0.767
21:03:30.900147 INFO: Train AUC: 0.774
21:03:30.900176 INFO: AUC difference: 0.89%
21:03:31.087305 INFO: Resetting torch num_threads to 100
21:03:31.088321 INFO: === FDR correction performed with classifier version 7 ===
21:03:31.089395 PROGRESS: ============================= Precursor FDR =============================
21:03:31.089505 PROGRESS: Total precursors accumulated: 600
21:03:31.089580 PROGRESS: Target precursors: 544 (90.67%)
21:03:31.089640 PROGRESS: Decoy precursors: 56 (9.33%)
21:03:31.089694 PROGRESS: 
21:03:31.089746 PROGRESS: Precursor Summary:
21:03:31.091220 PROGRESS: Channel   0:	 0.05 FDR:   488; 0.01 FDR:   391; 0.001 FDR:   130
21:03:31.091340 PROGRESS: 
21:03:31.091407 PROGRESS: Protein Summary:
21:03:31.092851 PROGRESS: Channel   0:	 0.05 FDR:   459; 0.01 FDR:   365; 0.001 FDR:   127
21:03:31.092951 PROGRESS: =========================================================================
21:03:31.096870 INFO: fragments_df: keeping 4068 of 24422 [sum(precursor_idx_mask)=7925 sum(mass_error_mask)=24422 stop_rank=4068
21:03:31.102792 INFO: calibration group: precursor, fitting mz estimator 
21:03:31.241076 INFO: calibration group: precursor, fitting rt estimator 
21:03:31.384564 INFO: calibration group: precursor, fitting mobility estimator 
21:03:31.532802 INFO: calibration group: fragment, fitting mz estimator 
21:03:32.107315 INFO: Using score_cutoff 42.8890120010376 (fac=0.99, q=1)
21:03:32.107827 INFO: calibration group: precursor, predicting mz
21:03:32.109044 INFO: calibration group: precursor, predicting rt
21:03:32.110420 INFO: calibration group: precursor, predicting mobility
21:03:32.111228 INFO: calibration group: fragment, predicting mz
21:03:32.113311 INFO: === checking if optimization conditions were reached ===
21:03:32.113423 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
21:03:32.115073 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 272.3057.
21:03:32.115133 INFO: ==============================================
21:03:32.115228 INFO: Starting optimization step 1.
21:03:32.115292 PROGRESS: === Extracting elution groups 0 to 600 ===
21:03:32.115353 PROGRESS: Extracting batch of 1188 precursors
21:03:32.116387 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
21:03:32.116435 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
21:03:32.116470 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
21:03:32.116493 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.74
21:03:32.117995 INFO: Starting candidate selection
21:03:33.409299 INFO: Starting candidate scoring
21:03:33.519260 INFO: Finished candidate processing
21:03:33.519369 INFO: Collecting candidate features
21:03:33.531346 INFO: Collecting fragment features
21:03:33.535731 INFO: Finished candidate scoring
21:03:33.537162 PROGRESS: === Extracted 2254 precursors and 23862 fragments ===
21:03:33.537431 INFO: performing precursor FDR with 47 features
21:03:33.537466 INFO: Decoy channel: -1
21:03:33.537490 INFO: Competetive: True
21:03:33.539958 INFO: Setting torch num_threads to 2 for FDR classification task
21:03:33.551969 INFO: Test AUC: 0.779
21:03:33.552036 INFO: Train AUC: 0.802
21:03:33.552065 INFO: AUC difference: 2.91%
21:03:33.732914 INFO: Resetting torch num_threads to 100
21:03:33.733485 INFO: === FDR correction performed with classifier version 7 ===
21:03:33.734141 PROGRESS: ============================= Precursor FDR =============================
21:03:33.734230 PROGRESS: Total precursors accumulated: 600
21:03:33.734286 PROGRESS: Target precursors: 559 (93.17%)
21:03:33.734335 PROGRESS: Decoy precursors: 41 (6.83%)
21:03:33.734389 PROGRESS: 
21:03:33.734432 PROGRESS: Precursor Summary:
21:03:33.735453 PROGRESS: Channel   0:	 0.05 FDR:   542; 0.01 FDR:   409; 0.001 FDR:    67
21:03:33.735543 PROGRESS: 
21:03:33.735597 PROGRESS: Protein Summary:
21:03:33.736744 PROGRESS: Channel   0:	 0.05 FDR:   507; 0.01 FDR:   382; 0.001 FDR:    65
21:03:33.736831 PROGRESS: =========================================================================
21:03:33.739996 INFO: fragments_df: keeping 4232 of 23862 [sum(precursor_idx_mask)=8268 sum(mass_error_mask)=23862 stop_rank=4232
21:03:33.744856 INFO: calibration group: precursor, fitting mz estimator 
21:03:33.874372 INFO: calibration group: precursor, fitting rt estimator 
21:03:34.005123 INFO: calibration group: precursor, fitting mobility estimator 
21:03:34.122041 INFO: calibration group: fragment, fitting mz estimator 
21:03:34.628222 INFO: Using score_cutoff 40.183693190002444 (fac=0.99, q=1)
21:03:34.628631 INFO: calibration group: precursor, predicting mz
21:03:34.629747 INFO: calibration group: precursor, predicting rt
21:03:34.631078 INFO: calibration group: precursor, predicting mobility
21:03:34.631847 INFO: calibration group: fragment, predicting mz
21:03:34.634007 INFO: === checking if optimization conditions were reached ===
21:03:34.634106 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
21:03:34.635724 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 195.6603.
21:03:34.635784 INFO: ==============================================
21:03:34.635875 INFO: Starting optimization step 2.
21:03:34.635939 PROGRESS: === Extracting elution groups 0 to 600 ===
21:03:34.635994 PROGRESS: Extracting batch of 1188 precursors
21:03:34.636988 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
21:03:34.637036 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
21:03:34.637071 INFO: FWHM in RT is 2.69 seconds, sigma is 0.59
21:03:34.637095 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.62
21:03:34.637849 INFO: Starting candidate selection
21:03:35.700271 INFO: Starting candidate scoring
21:03:35.810653 INFO: Finished candidate processing
21:03:35.810760 INFO: Collecting candidate features
21:03:35.822409 INFO: Collecting fragment features
21:03:35.826728 INFO: Finished candidate scoring
21:03:35.828357 PROGRESS: === Extracted 2256 precursors and 23824 fragments ===
21:03:35.828643 INFO: performing precursor FDR with 47 features
21:03:35.828682 INFO: Decoy channel: -1
21:03:35.828706 INFO: Competetive: True
21:03:35.831288 INFO: Setting torch num_threads to 2 for FDR classification task
21:03:35.843391 INFO: Test AUC: 0.778
21:03:35.843454 INFO: Train AUC: 0.814
21:03:35.843482 INFO: AUC difference: 4.44%
21:03:45.132769 INFO: Resetting torch num_threads to 100
21:03:45.133355 INFO: === FDR correction performed with classifier version 7 ===
21:03:45.134022 PROGRESS: ============================= Precursor FDR =============================
21:03:45.134112 PROGRESS: Total precursors accumulated: 600
21:03:45.134170 PROGRESS: Target precursors: 562 (93.67%)
21:03:45.134220 PROGRESS: Decoy precursors: 38 (6.33%)
21:03:45.134265 PROGRESS: 
21:03:45.134319 PROGRESS: Precursor Summary:
21:03:45.135389 PROGRESS: Channel   0:	 0.05 FDR:   543; 0.01 FDR:   410; 0.001 FDR:    58
21:03:45.135482 PROGRESS: 
21:03:45.135537 PROGRESS: Protein Summary:
21:03:45.136691 PROGRESS: Channel   0:	 0.05 FDR:   508; 0.01 FDR:   383; 0.001 FDR:    56
21:03:45.136781 PROGRESS: =========================================================================
21:03:45.140053 INFO: fragments_df: keeping 4178 of 23824 [sum(precursor_idx_mask)=8260 sum(mass_error_mask)=23824 stop_rank=4178
21:03:45.144696 INFO: calibration group: precursor, fitting mz estimator 
21:03:45.255454 INFO: calibration group: precursor, fitting rt estimator 
21:03:45.369378 INFO: calibration group: precursor, fitting mobility estimator 
21:03:45.484994 INFO: calibration group: fragment, fitting mz estimator 
21:03:45.973072 INFO: Using score_cutoff 37.241856398391725 (fac=0.99, q=1)
21:03:45.973490 INFO: calibration group: precursor, predicting mz
21:03:45.974602 INFO: calibration group: precursor, predicting rt
21:03:45.975947 INFO: calibration group: precursor, predicting mobility
21:03:45.976721 INFO: calibration group: fragment, predicting mz
21:03:45.978853 INFO: === checking if optimization conditions were reached ===
21:03:45.978952 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
21:03:45.980671 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 25.0289.
21:03:45.980725 INFO: ==============================================
21:03:45.980811 INFO: Starting optimization step 3.
21:03:45.980876 PROGRESS: === Extracting elution groups 0 to 600 ===
21:03:45.980939 PROGRESS: Extracting batch of 1188 precursors
21:03:45.981897 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
21:03:45.981945 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
21:03:45.981979 INFO: FWHM in RT is 2.68 seconds, sigma is 0.59
21:03:45.982002 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.62
21:03:45.987627 INFO: Starting candidate selection
21:03:46.541849 INFO: Starting candidate scoring
21:03:46.655517 INFO: Finished candidate processing
21:03:46.655634 INFO: Collecting candidate features
21:03:46.663847 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2253)
21:03:46.667102 INFO: Collecting fragment features
21:03:46.670465 INFO: Finished candidate scoring
21:03:46.672224 PROGRESS: === Extracted 2253 precursors and 23274 fragments ===
21:03:46.672512 INFO: performing precursor FDR with 47 features
21:03:46.672549 INFO: Decoy channel: -1
21:03:46.672571 INFO: Competetive: True
21:03:46.675095 INFO: Setting torch num_threads to 2 for FDR classification task
21:03:46.676291 WARNING: dropped 1 decoy PSMs due to missing features
21:03:46.687600 INFO: Test AUC: 0.860
21:03:46.687670 INFO: Train AUC: 0.844
21:03:46.687699 INFO: AUC difference: 1.86%
21:03:46.870070 INFO: Resetting torch num_threads to 100
21:03:46.870791 INFO: === FDR correction performed with classifier version 7 ===
21:03:46.871686 PROGRESS: ============================= Precursor FDR =============================
21:03:46.871789 PROGRESS: Total precursors accumulated: 600
21:03:46.871861 PROGRESS: Target precursors: 583 (97.17%)
21:03:46.871921 PROGRESS: Decoy precursors: 17 (2.83%)
21:03:46.871968 PROGRESS: 
21:03:46.872014 PROGRESS: Precursor Summary:
21:03:46.873214 PROGRESS: Channel   0:	 0.05 FDR:   583; 0.01 FDR:   510; 0.001 FDR:    30
21:03:46.873314 PROGRESS: 
21:03:46.873382 PROGRESS: Protein Summary:
21:03:46.874933 PROGRESS: Channel   0:	 0.05 FDR:   546; 0.01 FDR:   477; 0.001 FDR:    30
21:03:46.875047 PROGRESS: =========================================================================
21:03:46.880370 INFO: fragments_df: keeping 4795 of 23274 [sum(precursor_idx_mask)=10247 sum(mass_error_mask)=23274 stop_rank=4795
21:03:46.888000 INFO: calibration group: precursor, fitting mz estimator 
21:03:47.040651 INFO: calibration group: precursor, fitting rt estimator 
21:03:47.190102 INFO: calibration group: precursor, fitting mobility estimator 
21:03:47.334210 INFO: calibration group: fragment, fitting mz estimator 
21:03:48.021845 INFO: Using score_cutoff 35.57453708839416 (fac=0.99, q=1)
21:03:48.022705 INFO: calibration group: precursor, predicting mz
21:03:48.024832 INFO: calibration group: precursor, predicting rt
21:03:48.026469 INFO: calibration group: precursor, predicting mobility
21:03:48.027342 INFO: calibration group: fragment, predicting mz
21:03:48.029810 INFO: === checking if optimization conditions were reached ===
21:03:48.029938 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
21:03:48.032309 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 10.0173.
21:03:48.032381 INFO: ==============================================
21:03:48.032485 INFO: Starting optimization step 4.
21:03:48.032585 PROGRESS: === Extracting elution groups 0 to 600 ===
21:03:48.032654 PROGRESS: Extracting batch of 1188 precursors
21:03:48.034261 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
21:03:48.034312 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
21:03:48.034353 INFO: FWHM in RT is 2.58 seconds, sigma is 0.57
21:03:48.034376 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.27
21:03:48.043388 INFO: Starting candidate selection
21:03:48.576305 INFO: Starting candidate scoring
21:03:48.682666 INFO: Finished candidate processing
21:03:48.682776 INFO: Collecting candidate features
21:03:48.694116 INFO: Collecting fragment features
21:03:48.697528 INFO: Finished candidate scoring
21:03:48.699077 PROGRESS: === Extracted 2245 precursors and 22908 fragments ===
21:03:48.699365 INFO: performing precursor FDR with 47 features
21:03:48.699403 INFO: Decoy channel: -1
21:03:48.699425 INFO: Competetive: True
21:03:48.701890 INFO: Setting torch num_threads to 2 for FDR classification task
21:03:48.713923 INFO: Test AUC: 0.883
21:03:48.713986 INFO: Train AUC: 0.867
21:03:48.714020 INFO: AUC difference: 1.95%
21:03:48.892042 INFO: Resetting torch num_threads to 100
21:03:48.892609 INFO: === FDR correction performed with classifier version 7 ===
21:03:48.893254 PROGRESS: ============================= Precursor FDR =============================
21:03:48.893344 PROGRESS: Total precursors accumulated: 600
21:03:48.893403 PROGRESS: Target precursors: 582 (97.00%)
21:03:48.893452 PROGRESS: Decoy precursors: 18 (3.00%)
21:03:48.893499 PROGRESS: 
21:03:48.893543 PROGRESS: Precursor Summary:
21:03:48.894579 PROGRESS: Channel   0:	 0.05 FDR:   582; 0.01 FDR:   537; 0.001 FDR:   492
21:03:48.894670 PROGRESS: 
21:03:48.894725 PROGRESS: Protein Summary:
21:03:48.896000 PROGRESS: Channel   0:	 0.05 FDR:   546; 0.01 FDR:   504; 0.001 FDR:   462
21:03:48.896099 PROGRESS: =========================================================================
21:03:48.899607 INFO: fragments_df: keeping 5000 of 22908 [sum(precursor_idx_mask)=10798 sum(mass_error_mask)=22908 stop_rank=5000
21:03:48.904280 INFO: calibration group: precursor, fitting mz estimator 
21:03:49.037664 INFO: calibration group: precursor, fitting rt estimator 
21:03:49.157114 INFO: calibration group: precursor, fitting mobility estimator 
21:03:49.281803 INFO: calibration group: fragment, fitting mz estimator 
21:03:49.945980 INFO: Using score_cutoff 34.43885760498046 (fac=0.99, q=1)
21:03:49.946410 INFO: calibration group: precursor, predicting mz
21:03:49.947574 INFO: calibration group: precursor, predicting rt
21:03:49.949176 INFO: calibration group: precursor, predicting mobility
21:03:49.949935 INFO: calibration group: fragment, predicting mz
21:03:49.951903 INFO: === checking if optimization conditions were reached ===
21:03:49.952000 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
21:03:49.953747 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 9.8478.
21:03:49.953799 INFO: ==============================================
21:03:49.953884 INFO: Starting optimization step 5.
21:03:49.953948 PROGRESS: === Extracting elution groups 0 to 600 ===
21:03:49.954004 PROGRESS: Extracting batch of 1188 precursors
21:03:49.954953 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
21:03:49.955000 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
21:03:49.955041 INFO: FWHM in RT is 2.58 seconds, sigma is 0.57
21:03:49.955066 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.16
21:03:49.955828 INFO: Starting candidate selection
21:03:50.472876 INFO: Starting candidate scoring
21:03:50.614329 INFO: Finished candidate processing
21:03:50.614467 INFO: Collecting candidate features
21:03:50.625304 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2244)
21:03:50.628586 INFO: Collecting fragment features
21:03:50.634309 INFO: Finished candidate scoring
21:03:50.635986 PROGRESS: === Extracted 2244 precursors and 22892 fragments ===
21:03:50.636319 INFO: performing precursor FDR with 47 features
21:03:50.636357 INFO: Decoy channel: -1
21:03:50.636380 INFO: Competetive: True
21:03:50.639121 INFO: Setting torch num_threads to 2 for FDR classification task
21:03:50.640393 WARNING: dropped 1 decoy PSMs due to missing features
21:03:50.654591 INFO: Test AUC: 0.878
21:03:50.654664 INFO: Train AUC: 0.860
21:03:50.654694 INFO: AUC difference: 2.13%
21:03:50.844002 INFO: Resetting torch num_threads to 100
21:03:50.845030 INFO: === FDR correction performed with classifier version 7 ===
21:03:50.845903 PROGRESS: ============================= Precursor FDR =============================
21:03:50.845999 PROGRESS: Total precursors accumulated: 600
21:03:50.846061 PROGRESS: Target precursors: 579 (96.50%)
21:03:50.846116 PROGRESS: Decoy precursors: 21 (3.50%)
21:03:50.846163 PROGRESS: 
21:03:50.846209 PROGRESS: Precursor Summary:
21:03:50.847339 PROGRESS: Channel   0:	 0.05 FDR:   579; 0.01 FDR:   522; 0.001 FDR:   432
21:03:50.847442 PROGRESS: 
21:03:50.847501 PROGRESS: Protein Summary:
21:03:50.848808 PROGRESS: Channel   0:	 0.05 FDR:   543; 0.01 FDR:   489; 0.001 FDR:   406
21:03:50.848906 PROGRESS: =========================================================================
21:03:50.852662 INFO: fragments_df: keeping 4985 of 22892 [sum(precursor_idx_mask)=10471 sum(mass_error_mask)=22892 stop_rank=4985
21:03:50.859511 INFO: calibration group: precursor, fitting mz estimator 
21:03:51.003460 INFO: calibration group: precursor, fitting rt estimator 
21:03:51.151570 INFO: calibration group: precursor, fitting mobility estimator 
21:03:51.298782 INFO: calibration group: fragment, fitting mz estimator 
21:03:52.004755 INFO: Using score_cutoff 35.396416207122805 (fac=0.99, q=1)
21:03:52.005365 INFO: calibration group: precursor, predicting mz
21:03:52.006978 INFO: calibration group: precursor, predicting rt
21:03:52.008345 INFO: calibration group: precursor, predicting mobility
21:03:52.009138 INFO: calibration group: fragment, predicting mz
21:03:52.011395 INFO: === checking if optimization conditions were reached ===
21:03:52.011513 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
21:03:52.012818 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 9.8478 found after 6 searches.
21:03:52.012872 INFO: ==============================================
21:03:52.012963 PROGRESS: Optimization finished for rt_error.
21:03:52.019478 INFO: calibration group: precursor, predicting mz
21:03:52.020376 INFO: calibration group: precursor, predicting rt
21:03:52.021713 INFO: calibration group: precursor, predicting mobility
21:03:52.022502 INFO: calibration group: fragment, predicting mz
21:03:52.053793 INFO: Starting optimization step 0.
21:03:52.053976 PROGRESS: === Extracting elution groups 0 to 600 ===
21:03:52.054050 PROGRESS: Extracting batch of 1188 precursors
21:03:52.055351 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
21:03:52.055403 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
21:03:52.055445 INFO: FWHM in RT is 2.58 seconds, sigma is 0.57
21:03:52.055468 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.20
21:03:52.056539 INFO: Starting candidate selection
21:03:52.648281 INFO: Starting candidate scoring
21:03:52.876329 INFO: Finished candidate processing
21:03:52.876497 INFO: Collecting candidate features
21:03:52.888585 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2240)
21:03:52.891854 INFO: Collecting fragment features
21:03:52.899366 INFO: Finished candidate scoring
21:03:52.901230 PROGRESS: === Extracted 2240 precursors and 22845 fragments ===
21:03:52.901598 INFO: performing precursor FDR with 47 features
21:03:52.901637 INFO: Decoy channel: -1
21:03:52.901663 INFO: Competetive: True
21:03:52.904698 INFO: Setting torch num_threads to 2 for FDR classification task
21:03:52.906061 WARNING: dropped 1 decoy PSMs due to missing features
21:03:52.921189 INFO: Test AUC: 0.855
21:03:52.921272 INFO: Train AUC: 0.867
21:03:52.921301 INFO: AUC difference: 1.38%
21:03:53.108008 INFO: Resetting torch num_threads to 100
21:03:53.108871 INFO: === FDR correction performed with classifier version 13 ===
21:03:53.109605 PROGRESS: ============================= Precursor FDR =============================
21:03:53.109696 PROGRESS: Total precursors accumulated: 600
21:03:53.109757 PROGRESS: Target precursors: 579 (96.50%)
21:03:53.109808 PROGRESS: Decoy precursors: 21 (3.50%)
21:03:53.109854 PROGRESS: 
21:03:53.109899 PROGRESS: Precursor Summary:
21:03:53.110951 PROGRESS: Channel   0:	 0.05 FDR:   579; 0.01 FDR:   532; 0.001 FDR:   433
21:03:53.111052 PROGRESS: 
21:03:53.111122 PROGRESS: Protein Summary:
21:03:53.112410 PROGRESS: Channel   0:	 0.05 FDR:   543; 0.01 FDR:   499; 0.001 FDR:   407
21:03:53.112506 PROGRESS: =========================================================================
21:03:53.116114 INFO: fragments_df: keeping 5000 of 22845 [sum(precursor_idx_mask)=10680 sum(mass_error_mask)=22845 stop_rank=5000
21:03:53.121940 INFO: calibration group: precursor, fitting mz estimator 
21:03:53.261968 INFO: calibration group: precursor, fitting rt estimator 
21:03:53.402867 INFO: calibration group: precursor, fitting mobility estimator 
21:03:53.545283 INFO: calibration group: fragment, fitting mz estimator 
21:03:54.259249 INFO: Using score_cutoff 35.23750422019958 (fac=0.99, q=1)
21:03:54.259729 INFO: calibration group: precursor, predicting mz
21:03:54.261021 INFO: calibration group: precursor, predicting rt
21:03:54.262352 INFO: calibration group: precursor, predicting mobility
21:03:54.263135 INFO: calibration group: fragment, predicting mz
21:03:54.265388 INFO: === checking if optimization conditions were reached ===
21:03:54.265502 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
21:03:54.266888 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0635.
21:03:54.266939 INFO: ==============================================
21:03:54.267035 INFO: Starting optimization step 1.
21:03:54.267107 PROGRESS: === Extracting elution groups 0 to 600 ===
21:03:54.267167 PROGRESS: Extracting batch of 1188 precursors
21:03:54.268658 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
21:03:54.268707 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
21:03:54.268743 INFO: FWHM in RT is 2.57 seconds, sigma is 0.57
21:03:54.268765 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.15
21:03:54.271557 INFO: Starting candidate selection
21:03:54.773850 INFO: Starting candidate scoring
21:03:54.890640 INFO: Finished candidate processing
21:03:54.890763 INFO: Collecting candidate features
21:03:54.901046 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2242)
21:03:54.904302 INFO: Collecting fragment features
21:03:54.910509 INFO: Finished candidate scoring
21:03:54.912056 PROGRESS: === Extracted 2242 precursors and 22605 fragments ===
21:03:54.912349 INFO: performing precursor FDR with 47 features
21:03:54.912384 INFO: Decoy channel: -1
21:03:54.912406 INFO: Competetive: True
21:03:54.915150 INFO: Setting torch num_threads to 2 for FDR classification task
21:03:54.916439 WARNING: dropped 1 decoy PSMs due to missing features
21:03:54.928526 INFO: Test AUC: 0.901
21:03:54.928590 INFO: Train AUC: 0.857
21:03:54.928617 INFO: AUC difference: 5.17%
21:03:54.928638 WARNING: AUC difference > 5%. This may indicate overfitting.
21:03:55.116573 INFO: Resetting torch num_threads to 100
21:03:55.117340 INFO: === FDR correction performed with classifier version 13 ===
21:03:55.118059 PROGRESS: ============================= Precursor FDR =============================
21:03:55.118149 PROGRESS: Total precursors accumulated: 599
21:03:55.118207 PROGRESS: Target precursors: 577 (96.33%)
21:03:55.118256 PROGRESS: Decoy precursors: 22 (3.67%)
21:03:55.118301 PROGRESS: 
21:03:55.118344 PROGRESS: Precursor Summary:
21:03:55.119382 PROGRESS: Channel   0:	 0.05 FDR:   577; 0.01 FDR:   532; 0.001 FDR:   491
21:03:55.119471 PROGRESS: 
21:03:55.119526 PROGRESS: Protein Summary:
21:03:55.120791 PROGRESS: Channel   0:	 0.05 FDR:   541; 0.01 FDR:   499; 0.001 FDR:   459
21:03:55.120883 PROGRESS: =========================================================================
21:03:55.124333 INFO: fragments_df: keeping 5000 of 22605 [sum(precursor_idx_mask)=10645 sum(mass_error_mask)=22605 stop_rank=5000
21:03:55.129697 INFO: calibration group: precursor, fitting mz estimator 
21:03:55.279689 INFO: calibration group: precursor, fitting rt estimator 
21:03:55.421557 INFO: calibration group: precursor, fitting mobility estimator 
21:03:55.567429 INFO: calibration group: fragment, fitting mz estimator 
21:03:56.286233 INFO: Using score_cutoff 34.891441846847535 (fac=0.99, q=1)
21:03:56.286708 INFO: calibration group: precursor, predicting mz
21:03:56.288007 INFO: calibration group: precursor, predicting rt
21:03:56.289345 INFO: calibration group: precursor, predicting mobility
21:03:56.290110 INFO: calibration group: fragment, predicting mz
21:03:56.292965 INFO: === checking if optimization conditions were reached ===
21:03:56.293077 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
21:03:56.294614 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0521.
21:03:56.294668 INFO: ==============================================
21:03:56.294756 INFO: Starting optimization step 2.
21:03:56.294824 PROGRESS: === Extracting elution groups 0 to 600 ===
21:03:56.294883 PROGRESS: Extracting batch of 1188 precursors
21:03:56.296447 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
21:03:56.296498 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
21:03:56.296535 INFO: FWHM in RT is 2.57 seconds, sigma is 0.57
21:03:56.296558 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.15
21:03:56.297420 INFO: Starting candidate selection
21:03:56.807185 INFO: Starting candidate scoring
21:03:56.927890 INFO: Finished candidate processing
21:03:56.928015 INFO: Collecting candidate features
21:03:56.938539 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2250)
21:03:56.941785 INFO: Collecting fragment features
21:03:56.947714 INFO: Finished candidate scoring
21:03:56.949158 PROGRESS: === Extracted 2250 precursors and 22611 fragments ===
21:03:56.949459 INFO: performing precursor FDR with 47 features
21:03:56.949496 INFO: Decoy channel: -1
21:03:56.949519 INFO: Competetive: True
21:03:56.952145 INFO: Setting torch num_threads to 2 for FDR classification task
21:03:56.953386 WARNING: dropped 1 decoy PSMs due to missing features
21:03:56.967689 INFO: Test AUC: 0.858
21:03:56.967760 INFO: Train AUC: 0.869
21:03:56.967788 INFO: AUC difference: 1.31%
21:03:57.151301 INFO: Resetting torch num_threads to 100
21:03:57.152027 INFO: === FDR correction performed with classifier version 13 ===
21:03:57.152743 PROGRESS: ============================= Precursor FDR =============================
21:03:57.152844 PROGRESS: Total precursors accumulated: 599
21:03:57.152907 PROGRESS: Target precursors: 578 (96.49%)
21:03:57.152958 PROGRESS: Decoy precursors: 21 (3.51%)
21:03:57.153005 PROGRESS: 
21:03:57.153051 PROGRESS: Precursor Summary:
21:03:57.154103 PROGRESS: Channel   0:	 0.05 FDR:   578; 0.01 FDR:   532; 0.001 FDR:   489
21:03:57.154197 PROGRESS: 
21:03:57.154254 PROGRESS: Protein Summary:
21:03:57.155570 PROGRESS: Channel   0:	 0.05 FDR:   542; 0.01 FDR:   499; 0.001 FDR:   457
21:03:57.155665 PROGRESS: =========================================================================
21:03:57.159163 INFO: fragments_df: keeping 5000 of 22611 [sum(precursor_idx_mask)=10632 sum(mass_error_mask)=22611 stop_rank=5000
21:03:57.164469 INFO: calibration group: precursor, fitting mz estimator 
21:03:57.309875 INFO: calibration group: precursor, fitting rt estimator 
21:03:57.452474 INFO: calibration group: precursor, fitting mobility estimator 
21:03:57.590723 INFO: calibration group: fragment, fitting mz estimator 
21:03:58.350377 INFO: Using score_cutoff 34.612476045227055 (fac=0.99, q=1)
21:03:58.351074 INFO: calibration group: precursor, predicting mz
21:03:58.352910 INFO: calibration group: precursor, predicting rt
21:03:58.354419 INFO: calibration group: precursor, predicting mobility
21:03:58.355264 INFO: calibration group: fragment, predicting mz
21:03:58.358489 INFO: === checking if optimization conditions were reached ===
21:03:58.358626 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
21:03:58.359754 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.0635 found after 3 searches.
21:03:58.359817 INFO: ==============================================
21:03:58.359912 PROGRESS: Optimization finished for mobility_error.
21:03:58.367395 INFO: calibration group: precursor, predicting mz
21:03:58.369140 INFO: calibration group: precursor, predicting rt
21:03:58.370635 INFO: calibration group: precursor, predicting mobility
21:03:58.371483 INFO: calibration group: fragment, predicting mz
21:03:58.414848 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
21:03:58.415275 PROGRESS: ==============================================
21:03:58.415402 PROGRESS: ms2_error      : 10.0474
21:03:58.415466 PROGRESS: ms1_error      : 10.5658
21:03:58.415524 PROGRESS: rt_error       : 9.8478
21:03:58.415576 PROGRESS: mobility_error : 0.0635
21:03:58.415622 PROGRESS: ==============================================
21:03:58.416777 INFO: calibration group: precursor, predicting mz
21:03:58.452581 INFO: calibration group: precursor, predicting rt
21:03:58.614393 INFO: calibration group: precursor, predicting mobility
21:03:58.645352 INFO: calibration group: fragment, predicting mz
21:03:59.004263 PROGRESS: Extracting batch of 189636 precursors
21:03:59.060964 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
21:03:59.061152 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
21:03:59.061205 INFO: FWHM in RT is 2.57 seconds, sigma is 0.57
21:03:59.061229 INFO: FWHM in mobility is 0.007 1/K_0, sigma is 3.15
21:03:59.070065 INFO: Starting candidate selection
21:04:08.436239 INFO: Applying score cutoff of 34.891441846847535
21:04:08.442112 INFO: Removed 112287 precursors with score below cutoff
21:04:08.777294 INFO: Starting candidate scoring
21:04:15.920860 INFO: Finished candidate processing
21:04:15.921026 INFO: Collecting candidate features
21:04:16.321274 INFO: Collecting fragment features
21:04:16.473892 INFO: Finished candidate scoring
21:04:16.599759 INFO: === FDR correction performed with classifier version 15 ===
21:04:16.600793 INFO: performing precursor FDR with 47 features
21:04:16.600843 INFO: Decoy channel: -1
21:04:16.600868 INFO: Competetive: True
21:04:16.670614 INFO: Setting torch num_threads to 2 for FDR classification task
21:04:16.698178 WARNING: FDR calculation for 157155 target and 91261 decoy PSMs
21:04:16.698333 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
21:04:22.091251 INFO: Test AUC: 0.926
21:04:22.091405 INFO: Train AUC: 0.928
21:04:22.091438 INFO: AUC difference: 0.23%
21:04:22.328575 INFO: Resetting torch num_threads to 100
21:04:22.355205 INFO: Removing fragments below FDR threshold
21:04:22.418811 PROGRESS: ============================= Precursor FDR =============================
21:04:22.419635 PROGRESS: Total precursors accumulated: 91,116
21:04:22.419712 PROGRESS: Target precursors: 90,214 (99.01%)
21:04:22.419767 PROGRESS: Decoy precursors: 902 (0.99%)
21:04:22.419816 PROGRESS: 
21:04:22.419865 PROGRESS: Precursor Summary:
21:04:22.472464 PROGRESS: Channel   0:	 0.05 FDR: 90,214; 0.01 FDR: 90,214; 0.001 FDR: 85,994
21:04:22.472796 PROGRESS: 
21:04:22.472871 PROGRESS: Protein Summary:
21:04:22.558509 PROGRESS: Channel   0:	 0.05 FDR: 9,610; 0.01 FDR: 9,610; 0.001 FDR: 9,539
21:04:22.558837 PROGRESS: =========================================================================
21:04:23.321950 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
21:04:23.884200 PROGRESS: Processing search outputs
21:04:23.884367 PROGRESS: Performing protein grouping and FDR
21:04:23.884428 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
21:04:23.986647 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
21:04:24.059545 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
21:04:24.128960 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
21:04:24.208227 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
21:04:24.276792 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
21:04:24.345221 INFO: Building combined output
21:04:24.534251 INFO: Performing protein inference
21:04:25.089137 INFO: Inference strategy: library. Using library grouping for protein inference
21:04:25.093393 INFO: Performing protein FDR
21:04:27.909372 INFO: Normalizing q-values using 9,663 targets and 2,809 decoys
21:04:27.919004 INFO: Test AUC: 0.999
21:04:27.919099 INFO: Train AUC: 1.000
21:04:27.919138 INFO: AUC difference: 0.05%
21:04:28.716582 PROGRESS: ================ Protein FDR =================
21:04:28.716763 PROGRESS: Unique protein groups in output
21:04:28.716796 PROGRESS:   1% protein FDR: 9,655
21:04:28.716823 PROGRESS: 
21:04:28.716842 PROGRESS: Unique precursor in output
21:04:28.716860 PROGRESS:   1% protein FDR: 94,791
21:04:28.716892 PROGRESS: ================================================
21:04:28.813162 PROGRESS: Building search statistics
21:04:28.974557 INFO: Loaded OptimizationManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/optimization_manager.pkl
21:04:28.974817 INFO: Initializing OptimizationManager
21:04:28.975239 INFO: Loaded CalibrationManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/calibration_manager.pkl
21:04:28.975324 INFO: Initializing CalibrationManager
21:04:28.975599 INFO: Loaded RawFileManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/raw_file_manager.pkl
21:04:28.975677 INFO: Initializing RawFileManager
21:04:29.011102 INFO: Loaded OptimizationManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/optimization_manager.pkl
21:04:29.011343 INFO: Initializing OptimizationManager
21:04:29.011586 INFO: Loaded CalibrationManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/calibration_manager.pkl
21:04:29.011666 INFO: Initializing CalibrationManager
21:04:29.011884 INFO: Loaded RawFileManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/raw_file_manager.pkl
21:04:29.011959 INFO: Initializing RawFileManager
21:04:29.052087 INFO: Loaded OptimizationManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/optimization_manager.pkl
21:04:29.052327 INFO: Initializing OptimizationManager
21:04:29.052580 INFO: Loaded CalibrationManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/calibration_manager.pkl
21:04:29.052657 INFO: Initializing CalibrationManager
21:04:29.052876 INFO: Loaded RawFileManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/raw_file_manager.pkl
21:04:29.052966 INFO: Initializing RawFileManager
21:04:29.091732 INFO: Loaded OptimizationManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/optimization_manager.pkl
21:04:29.093243 INFO: Initializing OptimizationManager
21:04:29.093581 INFO: Loaded CalibrationManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/calibration_manager.pkl
21:04:29.093660 INFO: Initializing CalibrationManager
21:04:29.093890 INFO: Loaded RawFileManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/raw_file_manager.pkl
21:04:29.093978 INFO: Initializing RawFileManager
21:04:29.135217 INFO: Loaded OptimizationManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/optimization_manager.pkl
21:04:29.135478 INFO: Initializing OptimizationManager
21:04:29.135720 INFO: Loaded CalibrationManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/calibration_manager.pkl
21:04:29.135790 INFO: Initializing CalibrationManager
21:04:29.136018 INFO: Loaded RawFileManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/raw_file_manager.pkl
21:04:29.136091 INFO: Initializing RawFileManager
21:04:29.174818 INFO: Loaded OptimizationManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/optimization_manager.pkl
21:04:29.175081 INFO: Initializing OptimizationManager
21:04:29.175319 INFO: Loaded CalibrationManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/calibration_manager.pkl
21:04:29.175390 INFO: Initializing CalibrationManager
21:04:29.175586 INFO: Loaded RawFileManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/raw_file_manager.pkl
21:04:29.175656 INFO: Initializing RawFileManager
21:04:29.178664 INFO: Writing stat output to disk
21:04:29.178779 INFO: Saving run_output/alphadia_1.10.4_Again_good_now/stat.tsv to disk
21:04:29.189664 PROGRESS: Building internal statistics
21:04:29.190084 INFO: Loaded TimingManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/timing_manager.pkl
21:04:29.190132 INFO: Initializing TimingManager
21:04:29.190590 INFO: Loaded TimingManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/timing_manager.pkl
21:04:29.190634 INFO: Initializing TimingManager
21:04:29.190812 INFO: Loaded TimingManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/timing_manager.pkl
21:04:29.190849 INFO: Initializing TimingManager
21:04:29.191014 INFO: Loaded TimingManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/timing_manager.pkl
21:04:29.191064 INFO: Initializing TimingManager
21:04:29.191230 INFO: Loaded TimingManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/timing_manager.pkl
21:04:29.191266 INFO: Initializing TimingManager
21:04:29.191422 INFO: Loaded TimingManager from run_output/alphadia_1.10.4_Again_good_now/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/timing_manager.pkl
21:04:29.191457 INFO: Initializing TimingManager
21:04:29.191955 INFO: Writing internal output to disk
21:04:29.192003 INFO: Saving run_output/alphadia_1.10.4_Again_good_now/internal.tsv to disk
21:04:29.192645 PROGRESS: Performing label free quantification
21:04:29.313931 INFO: Accumulating fragment data
21:04:29.314137 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
21:04:29.385945 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
21:04:30.809461 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
21:04:32.278988 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
21:04:33.715231 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
21:04:35.128455 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
21:04:36.980322 PROGRESS: Performing label free quantification on the precursor level
21:04:36.980492 INFO: Filtering fragments by quality
21:04:37.287137 INFO: Performing label-free quantification using directLFQ
21:04:38.236766 INFO: 94791 lfq-groups total
21:05:44.824567 INFO: using 100 processes
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21:05:45.140054 INFO: lfq-object 100
21:05:45.156741 INFO: lfq-object 300
21:05:45.175301 INFO: lfq-object 500
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21:05:45.293224 INFO: lfq-object 600
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21:05:45.344281 INFO: lfq-object 1000
21:05:45.362686 INFO: lfq-object 1200
21:05:45.410207 INFO: lfq-object 700
21:05:45.441548 INFO: lfq-object 900
21:05:45.459448 INFO: lfq-object 1100
21:05:45.477935 INFO: lfq-object 1300
21:05:45.496703 INFO: lfq-object 1500
21:05:45.541451 INFO: lfq-object 1700
21:05:45.571730 INFO: lfq-object 1900
21:05:45.596282 INFO: lfq-object 1400
21:05:45.614686 INFO: lfq-object 1600
21:05:45.660122 INFO: lfq-object 1800
21:05:45.689092 INFO: lfq-object 2000
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21:05:45.810543 INFO: lfq-object 2100
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21:05:46.067088 INFO: lfq-object 2800
21:05:46.084492 INFO: lfq-object 3000
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21:05:46.800239 INFO: lfq-object 5000
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21:05:47.216108 INFO: lfq-object 6200
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21:05:48.880510 INFO: lfq-object 10000
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21:06:34.987763 INFO: lfq-object 85100
21:06:35.106627 INFO: lfq-object 85200
21:06:35.119927 INFO: lfq-object 85400
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21:06:35.214048 INFO: lfq-object 85800
21:06:35.225020 INFO: lfq-object 85300
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21:06:35.285319 INFO: lfq-object 85700
21:06:35.339851 INFO: lfq-object 85900
21:06:35.394237 INFO: lfq-object 86100
21:06:35.406576 INFO: lfq-object 86300
21:06:35.476405 INFO: lfq-object 86000
21:06:35.523915 INFO: lfq-object 86400
21:06:35.537358 INFO: lfq-object 86600
21:06:35.561620 INFO: lfq-object 86200
21:06:35.639217 INFO: lfq-object 86500
21:06:35.659232 INFO: lfq-object 86700
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21:06:36.373476 INFO: lfq-object 88100
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21:06:36.432192 INFO: lfq-object 88500
21:06:36.505933 INFO: lfq-object 88700
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21:06:36.547055 INFO: lfq-object 88600
21:06:36.624490 INFO: lfq-object 88800
21:06:36.646889 INFO: lfq-object 89200
21:06:36.649114 INFO: lfq-object 89000
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21:06:36.723057 INFO: lfq-object 89600
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21:06:37.005862 INFO: lfq-object 90000
21:06:55.874034 INFO: lfq-object 90100
21:06:55.985391 INFO: lfq-object 90300
21:06:56.027933 INFO: lfq-object 90200
21:06:56.121139 INFO: lfq-object 90400
21:06:56.207621 INFO: lfq-object 90600
21:06:56.248339 INFO: lfq-object 90500
21:06:56.259297 INFO: lfq-object 90800
21:06:56.384925 INFO: lfq-object 90700
21:06:56.400001 INFO: lfq-object 90900
21:06:56.440061 INFO: lfq-object 91300
21:06:56.445495 INFO: lfq-object 91100
21:06:56.518154 INFO: lfq-object 91500
21:06:56.524741 INFO: lfq-object 91000
21:06:56.560259 INFO: lfq-object 91400
21:06:56.560620 INFO: lfq-object 91200
21:06:56.637772 INFO: lfq-object 91600
21:06:56.657099 INFO: lfq-object 91800
21:06:56.669127 INFO: lfq-object 92000
21:06:56.738146 INFO: lfq-object 92200
21:06:56.755582 INFO: lfq-object 91700
21:06:56.770498 INFO: lfq-object 91900
21:06:56.790671 INFO: lfq-object 92100
21:06:56.860620 INFO: lfq-object 92300
21:06:56.976366 INFO: lfq-object 92500
21:06:56.983651 INFO: lfq-object 92400
21:06:57.013162 INFO: lfq-object 92700
21:06:57.100981 INFO: lfq-object 92600
21:06:57.150575 INFO: lfq-object 92800
21:06:57.223194 INFO: lfq-object 93200
21:06:57.227176 INFO: lfq-object 93000
21:06:57.285195 INFO: lfq-object 93400
21:06:57.290971 INFO: lfq-object 92900
21:06:57.341887 INFO: lfq-object 93300
21:06:57.346859 INFO: lfq-object 93100
21:06:57.405525 INFO: lfq-object 93500
21:06:57.456950 INFO: lfq-object 93700
21:06:57.467963 INFO: lfq-object 93900
21:06:57.519535 INFO: lfq-object 93600
21:06:57.532742 INFO: lfq-object 94100
21:06:57.579916 INFO: lfq-object 93800
21:06:57.612056 INFO: lfq-object 94000
21:06:57.652205 INFO: lfq-object 94200
21:06:57.714283 INFO: lfq-object 94400
21:06:57.767064 INFO: lfq-object 94600
21:06:57.769913 INFO: lfq-object 94300
21:06:57.829154 INFO: lfq-object 94500
21:06:57.883916 INFO: lfq-object 94700
21:07:03.459815 INFO: Writing precursor output to disk
21:07:03.460305 INFO: Saving run_output/alphadia_1.10.4_Again_good_now/precursor.matrix.tsv to disk
21:07:03.968732 PROGRESS: Performing label free quantification on the pg level
21:07:03.968858 INFO: Filtering fragments by quality
21:07:04.276029 INFO: Performing label-free quantification using directLFQ
21:07:04.592584 INFO: 9655 lfq-groups total
21:07:51.987265 INFO: using 100 processes
21:07:52.093047 INFO: lfq-object 0
21:07:52.114598 INFO: lfq-object 100
21:07:52.158921 INFO: lfq-object 200
21:07:52.187119 INFO: lfq-object 300
21:07:52.218256 INFO: lfq-object 400
21:07:52.254435 INFO: lfq-object 500
21:07:52.283885 INFO: lfq-object 600
21:07:52.309423 INFO: lfq-object 700
21:07:52.351114 INFO: lfq-object 800
21:07:52.376423 INFO: lfq-object 900
21:07:52.406721 INFO: lfq-object 1000
21:07:52.470045 INFO: lfq-object 1100
21:07:52.506504 INFO: lfq-object 1200
21:07:52.537721 INFO: lfq-object 1300
21:07:52.567183 INFO: lfq-object 1400
21:07:52.605314 INFO: lfq-object 1500
21:07:52.656804 INFO: lfq-object 1600
21:07:52.729249 INFO: lfq-object 1800
21:07:52.792011 INFO: lfq-object 1900
21:07:52.822994 INFO: lfq-object 2000
21:07:52.850713 INFO: lfq-object 1700
21:07:52.874435 INFO: lfq-object 2100
21:07:52.927617 INFO: lfq-object 2200
21:07:52.966464 INFO: lfq-object 2300
21:07:53.025270 INFO: lfq-object 2500
21:07:53.103244 INFO: lfq-object 2600
21:07:53.141561 INFO: lfq-object 2700
21:07:53.174844 INFO: lfq-object 2400
21:07:53.178832 INFO: lfq-object 2800
21:07:53.202889 INFO: lfq-object 2900
21:07:53.226780 INFO: lfq-object 3000
21:07:53.264402 INFO: lfq-object 3100
21:07:53.385176 INFO: lfq-object 3300
21:07:53.424508 INFO: lfq-object 3200
21:07:53.438628 INFO: lfq-object 3400
21:07:53.493444 INFO: lfq-object 3500
21:07:53.542298 INFO: lfq-object 3600
21:07:53.580999 INFO: lfq-object 3700
21:07:53.632840 INFO: lfq-object 3800
21:07:53.677680 INFO: lfq-object 3900
21:07:53.708989 INFO: lfq-object 4000
21:07:53.759180 INFO: lfq-object 4100
21:07:53.789732 INFO: lfq-object 4200
21:07:53.881919 INFO: lfq-object 4300
21:07:53.913722 INFO: lfq-object 4400
21:07:53.942381 INFO: lfq-object 4500
21:07:53.973615 INFO: lfq-object 4600
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21:07:54.047663 INFO: lfq-object 4800
21:07:54.078906 INFO: lfq-object 4900
21:07:54.139139 INFO: lfq-object 5000
21:07:54.198282 INFO: lfq-object 5100
21:07:54.227847 INFO: lfq-object 5200
21:07:54.291150 INFO: lfq-object 5300
21:07:54.358857 INFO: lfq-object 5400
21:07:54.387935 INFO: lfq-object 5500
21:07:54.415316 INFO: lfq-object 5600
21:07:54.479443 INFO: lfq-object 5700
21:07:54.540673 INFO: lfq-object 5800
21:07:54.565430 INFO: lfq-object 5900
21:07:54.602636 INFO: lfq-object 6000
21:07:54.632120 INFO: lfq-object 6100
21:07:54.677026 INFO: lfq-object 6200
21:07:54.717673 INFO: lfq-object 6300
21:07:54.790727 INFO: lfq-object 6500
21:07:54.820288 INFO: lfq-object 6600
21:07:54.860444 INFO: lfq-object 6700
21:07:54.874441 INFO: lfq-object 6400
21:07:54.892318 INFO: lfq-object 6800
21:07:54.947734 INFO: lfq-object 6900
21:07:55.015746 INFO: lfq-object 7000
21:07:55.056901 INFO: lfq-object 7100
21:07:55.089431 INFO: lfq-object 7200
21:07:55.124736 INFO: lfq-object 7300
21:07:55.156716 INFO: lfq-object 7400
21:07:55.191234 INFO: lfq-object 7500
21:07:55.232444 INFO: lfq-object 7600
21:07:55.261709 INFO: lfq-object 7700
21:07:55.301442 INFO: lfq-object 7800
21:07:55.342516 INFO: lfq-object 7900
21:07:55.374178 INFO: lfq-object 8000
21:07:55.413599 INFO: lfq-object 8100
21:07:55.450645 INFO: lfq-object 8200
21:07:55.491629 INFO: lfq-object 8300
21:07:55.526893 INFO: lfq-object 8400
21:07:55.560966 INFO: lfq-object 8500
21:07:55.612655 INFO: lfq-object 8600
21:07:55.684100 INFO: lfq-object 8700
21:07:55.743222 INFO: lfq-object 8800
21:07:55.791421 INFO: lfq-object 8900
21:07:55.861590 INFO: lfq-object 9000
21:07:55.886592 INFO: lfq-object 9100
21:07:55.922878 INFO: lfq-object 9200
21:07:55.960984 INFO: lfq-object 9300
21:07:56.017797 INFO: lfq-object 9400
21:07:56.054240 INFO: lfq-object 9500
21:07:56.089993 INFO: lfq-object 9600
21:07:58.603494 INFO: Writing pg output to disk
21:07:58.603699 INFO: Saving run_output/alphadia_1.10.4_Again_good_now/pg.matrix.tsv to disk
21:07:58.881061 INFO: Writing psm output to disk
21:07:58.881225 INFO: Saving run_output/alphadia_1.10.4_Again_good_now/precursors.tsv to disk
21:08:28.388702 PROGRESS: Building spectral library
21:08:28.494832 INFO: Building MBR spectral library
21:08:28.494995 INFO: Running MbrLibraryBuilder
21:08:28.777408 INFO: MBR spectral library contains 94,791 precursors, 9,655 proteins
21:08:28.777603 INFO: Writing MBR spectral library to disk
21:08:29.491306 PROGRESS: =================== Search Finished ===================
21:08:29.548112 WARNING: WARNING: Temp mmap arrays were written to /tmp/temp_mmap_l3_9h41f. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 569,245,208,576
