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0:00:00.013728 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.013753 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.013781 PROGRESS:            |_|                           
0:00:00.013803 PROGRESS: 
0:00:00.013826 PROGRESS: version: 1.10.3
0:00:00.013860 INFO: hostname: thestral
0:00:00.013913 INFO: date: 2025-04-18 11:03:14
0:00:00.013936 INFO: ================ AlphaX Environment ===============
0:00:00.013957 INFO: alphatims       : 1.0.8
0:00:00.013975 INFO: alpharaw        : 0.4.5
0:00:00.013994 INFO: alphabase       : 1.5.0
0:00:00.014011 INFO: alphapeptdeep   : 1.3.0
0:00:00.014028 INFO: directlfq       : 0.2.19
0:00:00.014045 INFO: ===================================================
0:00:00.014061 INFO: ================= Pip Environment =================
0:00:00.072435 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 alphadia==1.10.3 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 PyYAML==6.0.2
0:00:00.072529 INFO: ===================================================
0:00:00.072560 INFO: Running step 'library'
0:00:00.072673 INFO: loading config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:00:00.083240 INFO: loading additional config provided via CLI
0:00:00.083310 INFO: loading additional config provided via CLI parameters
0:00:00.083543 INFO: Updating config with 'user defined'
0:00:00.083623 INFO: Updating config with 'user defined (cli)'
0:00:00.083646 INFO: Updating config with 'multistep search'
0:00:00.083684 INFO: ├──version: 1
0:00:00.083710 INFO: ├──workflow_name: None
0:00:00.083736 INFO: [32;20m├──output_directory: run_output/alphadia_1.10_defaultMBR/library [multistep search, default: None][0m
0:00:00.083758 INFO: ├──library_path: None
0:00:00.083776 INFO: ├──raw_paths:
0:00:00.083799 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d [user defined (cli), default: None][0m
0:00:00.083819 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d [user defined (cli), default: None][0m
0:00:00.083838 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d [user defined (cli), default: None][0m
0:00:00.083861 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d [user defined (cli), default: None][0m
0:00:00.083879 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d [user defined (cli), default: None][0m
0:00:00.083897 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d [user defined (cli), default: None][0m
0:00:00.083916 INFO: ├──fasta_paths:
0:00:00.083935 INFO: │   [32;20m- ./ProteoBenchFASTA_DDAQuantification.fasta [user defined (cli), default: None][0m
0:00:00.083955 INFO: ├──quant_directory: None
0:00:00.083972 INFO: ├──general
0:00:00.083991 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
0:00:00.084010 INFO: │   ├──transfer_step_enabled: False
0:00:00.084028 INFO: │   ├──mbr_step_enabled: True
0:00:00.084046 INFO: │   ├──reuse_calibration: False
0:00:00.084064 INFO: │   ├──reuse_quant: False
0:00:00.084083 INFO: │   ├──astral_ms1: False
0:00:00.084100 INFO: │   ├──log_level: INFO
0:00:00.084119 INFO: │   ├──mmap_detector_events: False
0:00:00.084139 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
0:00:00.084156 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.084175 INFO: │   └──save_mbr_library: True
0:00:00.084193 INFO: ├──library_loading
0:00:00.084211 INFO: │   └──rt_heuristic: 180
0:00:00.084230 INFO: ├──library_prediction
0:00:00.084248 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.084268 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.084289 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.084308 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
0:00:00.084326 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.084345 INFO: │   ├──missed_cleavages: 1
0:00:00.084363 INFO: │   ├──precursor_len:
0:00:00.084381 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.084400 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.084418 INFO: │   ├──precursor_charge:
0:00:00.084436 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.084456 INFO: │   │   [32;20m- 4[0m
0:00:00.084473 INFO: │   ├──precursor_mz:
0:00:00.084491 INFO: │   │   [32;20m- 400[0m
0:00:00.084509 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
0:00:00.084528 INFO: │   ├──fragment_mz:
0:00:00.084546 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
0:00:00.084564 INFO: │   │   [32;20m- 2000[0m
0:00:00.084584 INFO: │   ├──nce: 25
0:00:00.084602 INFO: │   ├──fragment_types:
0:00:00.084620 INFO: │   │   [32;20m- b[0m
0:00:00.084637 INFO: │   │   [32;20m- y[0m
0:00:00.084655 INFO: │   ├──max_fragment_charge: 2
0:00:00.084673 INFO: │   [32;20m├──instrument: timsTOF [user defined, default: Lumos][0m
0:00:00.084699 INFO: │   ├──peptdeep_model_path: None
0:00:00.084718 INFO: │   └──peptdeep_model_type: generic
0:00:00.084736 INFO: ├──custom_modifications:
0:00:00.084754 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.084773 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.084792 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.084810 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.084828 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.084845 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.084863 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.084881 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.084900 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.084918 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.084936 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.084953 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.084970 INFO: │   ├──name: Label:13C(12)@K
0:00:00.084989 INFO: │   └──composition: C(12)
0:00:00.085008 INFO: ├──search
0:00:00.085034 INFO: │   [32;20m├──target_ms1_tolerance: 10 [user defined, default: 5][0m
0:00:00.085053 INFO: │   [32;20m├──target_ms2_tolerance: 15 [user defined, default: 10][0m
0:00:00.085071 INFO: │   ├──target_rt_tolerance: 0
0:00:00.085089 INFO: │   ├──target_mobility_tolerance: 0
0:00:00.085107 INFO: │   ├──quant_window: 3
0:00:00.085124 INFO: │   [32;20m├──target_num_candidates: 2 [user defined, default: 3][0m
0:00:00.085143 INFO: │   ├──channel_filter: 
0:00:00.085160 INFO: │   ├──exclude_shared_ions: True
0:00:00.085178 INFO: │   ├──compete_for_fragments: True
0:00:00.085196 INFO: │   ├──quant_all: True
0:00:00.085215 INFO: │   ├──top_k_fragments: 12
0:00:00.085232 INFO: │   └──experimental_xic: True
0:00:00.085251 INFO: ├──calibration
0:00:00.085268 INFO: │   ├──batch_size: 8000
0:00:00.085286 INFO: │   ├──optimization_lock_target: 200
0:00:00.085305 INFO: │   ├──max_steps: 20
0:00:00.085322 INFO: │   ├──min_steps: 2
0:00:00.085340 INFO: │   ├──max_skips: 1
0:00:00.085359 INFO: │   ├──norm_rt_mode: linear
0:00:00.085376 INFO: │   ├──max_fragments: 5000
0:00:00.085398 INFO: │   └──min_correlation: 0.7
0:00:00.085416 INFO: ├──search_initial
0:00:00.085433 INFO: │   ├──initial_num_candidates: 1
0:00:00.085451 INFO: │   ├──initial_ms1_tolerance: 30
0:00:00.085469 INFO: │   ├──initial_ms2_tolerance: 30
0:00:00.085487 INFO: │   ├──initial_mobility_tolerance: 0.1
0:00:00.085505 INFO: │   └──initial_rt_tolerance: 0.5
0:00:00.085523 INFO: ├──selection_config
0:00:00.085541 INFO: │   ├──peak_len_rt: 10.0
0:00:00.085559 INFO: │   ├──sigma_scale_rt: 0.5
0:00:00.085580 INFO: │   ├──peak_len_mobility: 0.01
0:00:00.085599 INFO: │   ├──sigma_scale_mobility: 1.0
0:00:00.085617 INFO: │   ├──top_k_precursors: 3
0:00:00.085636 INFO: │   ├──kernel_size: 30
0:00:00.085654 INFO: │   ├──f_mobility: 1.0
0:00:00.085672 INFO: │   ├──f_rt: 0.99
0:00:00.085692 INFO: │   ├──center_fraction: 0.5
0:00:00.085709 INFO: │   ├──min_size_mobility: 8
0:00:00.085727 INFO: │   ├──min_size_rt: 3
0:00:00.085746 INFO: │   ├──max_size_mobility: 20
0:00:00.085764 INFO: │   ├──max_size_rt: 15
0:00:00.085782 INFO: │   ├──group_channels: False
0:00:00.085801 INFO: │   ├──use_weighted_score: True
0:00:00.085819 INFO: │   ├──join_close_candidates: False
0:00:00.085838 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
0:00:00.085858 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
0:00:00.085875 INFO: ├──scoring_config
0:00:00.085893 INFO: │   ├──score_grouped: False
0:00:00.085911 INFO: │   ├──top_k_isotopes: 3
0:00:00.085934 INFO: │   ├──reference_channel: -1
0:00:00.085952 INFO: │   ├──precursor_mz_tolerance: 10
0:00:00.085970 INFO: │   └──fragment_mz_tolerance: 15
0:00:00.085989 INFO: ├──library_multiplexing
0:00:00.086007 INFO: │   ├──enabled: False
0:00:00.086025 INFO: │   ├──input_channel: 0
0:00:00.086042 INFO: │   └──multiplex_mapping:
0:00:00.086058 INFO: ├──multiplexing
0:00:00.086076 INFO: │   ├──enabled: False
0:00:00.086094 INFO: │   ├──target_channels: 4,8
0:00:00.086111 INFO: │   ├──decoy_channel: 12
0:00:00.086130 INFO: │   ├──reference_channel: 0
0:00:00.086147 INFO: │   └──competetive_scoring: True
0:00:00.086163 INFO: ├──fdr
0:00:00.086182 INFO: │   ├──fdr: 0.01
0:00:00.086199 INFO: │   ├──group_level: proteins
0:00:00.086216 INFO: │   ├──inference_strategy: heuristic
0:00:00.086234 INFO: │   ├──competetive_scoring: True
0:00:00.086252 INFO: │   ├──keep_decoys: False
0:00:00.086269 INFO: │   ├──channel_wise_fdr: False
0:00:00.086287 INFO: │   ├──enable_two_step_classifier: False
0:00:00.086306 INFO: │   ├──two_step_classifier_max_iterations: 5
0:00:00.086323 INFO: │   └──enable_nn_hyperparameter_tuning: False
0:00:00.086341 INFO: ├──search_output
0:00:00.086358 INFO: │   ├──file_format: tsv
0:00:00.086375 INFO: │   ├──peptide_level_lfq: False
0:00:00.086395 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
0:00:00.086414 INFO: │   ├──min_k_fragments: 12
0:00:00.086432 INFO: │   ├──min_correlation: 0.9
0:00:00.086450 INFO: │   ├──num_samples_quadratic: 50
0:00:00.086468 INFO: │   ├──min_nonnan: 3
0:00:00.086486 INFO: │   ├──normalize_lfq: True
0:00:00.086504 INFO: │   └──save_fragment_quant_matrix: False
0:00:00.086522 INFO: ├──optimization
0:00:00.086540 INFO: │   ├──order_of_optimization: None
0:00:00.086558 INFO: │   ├──ms2_error
0:00:00.086576 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.086594 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.086612 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.086630 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.086647 INFO: │   │   ├──try_narrower_values: True
0:00:00.086666 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.086684 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.086703 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.086721 INFO: │   ├──ms1_error
0:00:00.086739 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.086756 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.086774 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.086794 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.086812 INFO: │   │   ├──try_narrower_values: False
0:00:00.086832 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.086850 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.086868 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.086886 INFO: │   ├──mobility_error
0:00:00.086904 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.086921 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.086941 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.086958 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.086976 INFO: │   │   ├──try_narrower_values: False
0:00:00.086994 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.087012 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.087030 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.087049 INFO: │   └──rt_error
0:00:00.087067 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.087086 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.087110 INFO: │       ├──automatic_update_percentile_range: 0.99
0:00:00.087128 INFO: │       ├──automatic_update_factor: 1.1
0:00:00.087146 INFO: │       ├──try_narrower_values: True
0:00:00.087165 INFO: │       ├──maximal_decrease: 0.2
0:00:00.087183 INFO: │       ├──favour_narrower_optimum: True
0:00:00.087200 INFO: │       └──maximum_decrease_from_maximum: 0.1
0:00:00.087218 INFO: ├──optimization_manager
0:00:00.087236 INFO: │   ├──fwhm_rt: 5
0:00:00.087253 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.087273 INFO: │   └──score_cutoff: 0
0:00:00.087289 INFO: ├──transfer_library
0:00:00.087307 INFO: │   ├──enabled: False
0:00:00.087326 INFO: │   ├──fragment_types:
0:00:00.087343 INFO: │   │   [32;20m- b[0m
0:00:00.087360 INFO: │   │   [32;20m- y[0m
0:00:00.087378 INFO: │   ├──max_charge: 2
0:00:00.087395 INFO: │   ├──top_k_samples: 3
0:00:00.087412 INFO: │   ├──norm_delta_max: True
0:00:00.087430 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.087449 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.087466 INFO: └──transfer_learning
0:00:00.087484 INFO:     ├──enabled: False
0:00:00.087501 INFO:     ├──batch_size: 2000
0:00:00.087518 INFO:     ├──max_lr: 0.0001
0:00:00.087537 INFO:     ├──train_fraction: 0.7
0:00:00.087554 INFO:     ├──validation_fraction: 0.2
0:00:00.087572 INFO:     ├──test_fraction: 0.1
0:00:00.087590 INFO:     ├──test_interval: 1
0:00:00.087607 INFO:     ├──lr_patience: 3
0:00:00.087625 INFO:     ├──epochs: 51
0:00:00.087643 INFO:     ├──warmup_epochs: 5
0:00:00.087661 INFO:     ├──nce: 25
0:00:00.087681 INFO:     [32;20m└──instrument: timsTOF [user defined, default: Lumos][0m
0:00:00.092294 INFO: Registering 7 custom modifications
0:00:00.121167 PROGRESS: No library provided. Building library from fasta files.
0:00:00.121258 INFO: Running FastaDigest
0:00:00.967935 INFO: Digesting fasta file
0:00:07.583493 INFO: Adding modifications
0:01:39.319825 INFO: Removing non-canonical amino acids
0:01:45.373568 INFO: Fasta library contains 5,215,079 precursors
0:01:45.373820 PROGRESS: Predicting library properties.
0:01:45.373897 INFO: Running PeptDeepPrediction
0:01:45.373972 INFO: Device set to cpu
0:01:46.281418 INFO: Loading PeptDeep models of type generic
0:01:47.048252 INFO: Predicting RT, MS2 and mobility
0:01:47.048419 INFO: Using multiprocessing with 100 processes ...
0:01:47.425628 INFO: Predicting rt,ms2,mobility ...
0:07:18.064366 INFO: Adding fragment mz information
0:07:18.344745 INFO: Adding fragment intensity information
0:07:18.625608 INFO: Adding precursor information
0:07:18.950080 INFO: Running PrecursorInitializer
0:07:18.983123 INFO: Running AnnotateFasta
0:07:19.129470 INFO: Dropping decoys from input library before annotation
0:07:45.422943 INFO: Running IsotopeGenerator
0:08:11.324868 INFO: Running RTNormalization
0:08:11.325538 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:08:11.325639 INFO: Saving library to run_output/alphadia_1.10_defaultMBR/library/speclib.hdf
0:08:42.802726 INFO: Running DecoyGenerator
0:10:32.865701 INFO: Running FlattenLibrary
0:11:00.404921 INFO: Running InitFlatColumns
0:11:00.591121 INFO: Running LogFlatLibraryStats
0:11:00.591253 INFO: ============ Library Stats ============
0:11:00.591291 INFO: Number of precursors: 10,400,392
0:11:02.016786 INFO: 	thereof targets:5,215,079
0:11:02.016936 INFO: 	thereof decoys: 5,185,313
0:11:02.087806 INFO: Number of elution groups: 5,215,079
0:11:02.087937 INFO: 	average size: 1.99
0:11:02.422220 INFO: Number of proteins: 117,993
0:11:02.447512 INFO: Number of channels: 1 ([0])
0:11:02.447677 INFO: Isotopes Distribution for 4 isotopes
0:11:02.447705 INFO: =======================================
0:11:02.455192 INFO: Searching 6 files:
0:11:02.455305 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:11:02.455339 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
0:11:02.455358 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
0:11:02.455376 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
0:11:02.455393 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
0:11:02.455410 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
0:11:02.455430 INFO: Using 1 fasta files:
0:11:02.455448 INFO:   ./ProteoBenchFASTA_DDAQuantification.fasta
0:11:02.455472 INFO: Using library: None
0:11:02.455491 INFO: Saving output to: run_output/alphadia_1.10_defaultMBR/library
0:11:02.455514 PROGRESS: Starting Search Workflows
0:11:02.455575 PROGRESS: Loading raw file 1/6: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
0:11:02.455619 INFO: Quantification results path: run_output/alphadia_1.10_defaultMBR/library/quant
0:11:02.455675 INFO: Creating parent folder for workflows at run_output/alphadia_1.10_defaultMBR/library/quant
0:11:02.455791 INFO: Creating workflow folder for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494 at run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
0:11:02.456155 INFO: Initializing RawFileManager
0:11:02.456256 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:11:02.456299 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:11:02.456330 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:11:02.669260 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
0:11:12.199809 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d...
0:11:12.204075 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:11:12.216608 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:11:12.216931 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:11:12.217279 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:11:12.218947 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:11:12.227157 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:11:12.227340 INFO: Indexing quadrupole dimension
0:11:12.750655 INFO: Transposing detector events
0:11:23.092883 INFO: Finished transposing data
0:11:23.117125 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:11:23.118103 INFO: RT (min)            : 0.0 - 70.0
0:11:23.118146 INFO: RT duration (sec)   : 4199.9
0:11:23.118170 INFO: RT duration (min)   : 70.0
0:11:23.118192 INFO: Cycle len (scans)   : 9
0:11:23.118209 INFO: Cycle len (sec)     : 0.97
0:11:23.118226 INFO: Number of cycles    : 4347
0:11:23.118243 INFO: MS2 range (m/z)     : 400.0 - 1000.0
0:11:24.388867 INFO: Initializing CalibrationManager
0:11:24.389187 INFO: Loading calibration config
0:11:24.389307 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'}]
0:11:24.389388 INFO: Calibration group :fragment, found 1 estimator(s)
0:11:24.389515 INFO: Calibration group :precursor, found 3 estimator(s)
0:11:24.389656 INFO: Initializing OptimizationManager
0:11:24.389752 INFO: initial parameter: ms1_error = 30
0:11:24.389805 INFO: initial parameter: ms2_error = 30
0:11:24.389856 INFO: initial parameter: rt_error = 2099.928159
0:11:24.389912 INFO: initial parameter: mobility_error = 0.1
0:11:24.389962 INFO: initial parameter: column_type = library
0:11:24.390005 INFO: initial parameter: num_candidates = 1
0:11:24.390047 INFO: initial parameter: classifier_version = -1
0:11:24.390090 INFO: initial parameter: fwhm_rt = 5
0:11:24.390133 INFO: initial parameter: fwhm_mobility = 0.01
0:11:24.390174 INFO: initial parameter: score_cutoff = 0
0:11:24.390237 INFO: Initializing TimingManager
0:11:24.390300 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
0:11:24.390413 INFO: FDRManager not loaded from disk.
0:11:24.390439 INFO: Initializing FDRManager
0:11:24.390481 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:11:25.655167 PROGRESS: 5,215,079 target precursors potentially observable (0 removed)
0:11:27.465775 PROGRESS: Starting initial search for precursors.
0:11:28.345971 INFO: Starting optimization step 0.
0:11:28.346220 PROGRESS: === Extracting elution groups 0 to 8000 ===
0:11:28.346315 PROGRESS: Extracting batch of 15771 precursors
0:11:30.410017 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:11:30.410133 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:11:30.410166 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:11:30.410188 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:11:34.201686 INFO: Starting candidate selection
0:14:28.660038 INFO: Starting candidate scoring
0:22:20.226206 INFO: Finished candidate processing
0:22:20.226415 INFO: Collecting candidate features
0:22:20.835553 WARNING: intensity_correlation has 2 NaNs ( 0.01 % out of 13800)
0:22:20.839242 INFO: Collecting fragment features
0:22:23.290375 INFO: Finished candidate scoring
0:22:23.305374 PROGRESS: === Extracted 13800 precursors and 138628 fragments ===
0:22:23.305741 INFO: performing precursor FDR with 47 features
0:22:23.305779 INFO: Decoy channel: -1
0:22:23.305803 INFO: Competetive: True
0:22:23.309601 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:23.312070 WARNING: dropped 2 target PSMs due to missing features
0:22:23.948226 INFO: Test AUC: 0.512
0:22:23.948348 INFO: Train AUC: 0.522
0:22:23.948380 INFO: AUC difference: 1.95%
0:22:24.033337 INFO: Resetting torch num_threads to 128
0:22:24.033780 INFO: === FDR correction performed with classifier version -1 ===
0:22:24.035722 PROGRESS: ============================= Precursor FDR =============================
0:22:24.035815 PROGRESS: Total precursors accumulated: 7,060
0:22:24.035874 PROGRESS: Target precursors: 3,782 (53.57%)
0:22:24.035925 PROGRESS: Decoy precursors: 3,278 (46.43%)
0:22:24.035971 PROGRESS: 
0:22:24.036016 PROGRESS: Precursor Summary:
0:22:24.036937 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:24.037031 PROGRESS: 
0:22:24.037090 PROGRESS: Protein Summary:
0:22:24.038036 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:24.038122 PROGRESS: =========================================================================
0:22:24.182451 INFO: Starting optimization step 1.
0:22:24.182701 PROGRESS: === Extracting elution groups 8000 to 24000 ===
0:22:24.182771 PROGRESS: Extracting batch of 31534 precursors
0:22:24.189507 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:22:24.189576 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:22:24.189610 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:22:24.189632 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:22:24.191525 INFO: Starting candidate selection
0:24:56.506916 INFO: Starting candidate scoring
0:24:57.993671 INFO: Finished candidate processing
0:24:57.993861 INFO: Collecting candidate features
0:24:58.085174 WARNING: intensity_correlation has 4 NaNs ( 0.01 % out of 27420)
0:24:58.089432 INFO: Collecting fragment features
0:24:58.112530 INFO: Finished candidate scoring
0:24:58.204394 PROGRESS: === Extracted 41220 precursors and 413058 fragments ===
0:24:58.211066 INFO: performing precursor FDR with 47 features
0:24:58.211189 INFO: Decoy channel: -1
0:24:58.211216 INFO: Competetive: True
0:24:58.234369 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:58.244698 WARNING: dropped 4 target PSMs due to missing features
0:24:58.244852 WARNING: dropped 2 decoy PSMs due to missing features
0:24:59.071791 INFO: Test AUC: 0.547
0:24:59.072026 INFO: Train AUC: 0.560
0:24:59.072061 INFO: AUC difference: 2.22%
0:24:59.165590 INFO: Resetting torch num_threads to 128
0:24:59.168791 INFO: === FDR correction performed with classifier version -1 ===
0:24:59.172354 PROGRESS: ============================= Precursor FDR =============================
0:24:59.172498 PROGRESS: Total precursors accumulated: 21,106
0:24:59.172565 PROGRESS: Target precursors: 12,160 (57.61%)
0:24:59.172620 PROGRESS: Decoy precursors: 8,946 (42.39%)
0:24:59.172669 PROGRESS: 
0:24:59.172716 PROGRESS: Precursor Summary:
0:24:59.173832 PROGRESS: Channel   0:	 0.05 FDR:   212; 0.01 FDR:   126; 0.001 FDR:    92
0:24:59.173925 PROGRESS: 
0:24:59.173985 PROGRESS: Protein Summary:
0:24:59.175164 PROGRESS: Channel   0:	 0.05 FDR:   207; 0.01 FDR:   122; 0.001 FDR:    90
0:24:59.175252 PROGRESS: =========================================================================
0:24:59.390552 INFO: Starting optimization step 2.
0:24:59.390814 PROGRESS: === Extracting elution groups 24000 to 56000 ===
0:24:59.390897 PROGRESS: Extracting batch of 63016 precursors
0:24:59.405886 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:24:59.406002 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:24:59.406045 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:24:59.406067 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:24:59.407012 INFO: Starting candidate selection
0:30:08.045154 INFO: Starting candidate scoring
0:30:11.007423 INFO: Finished candidate processing
0:30:11.007588 INFO: Collecting candidate features
0:30:11.132896 WARNING: intensity_correlation has 13 NaNs ( 0.02 % out of 55011)
0:30:11.133218 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 55011)
0:30:11.138120 INFO: Collecting fragment features
0:30:11.178003 INFO: Finished candidate scoring
0:30:11.268731 PROGRESS: === Extracted 96231 precursors and 963854 fragments ===
0:30:11.281568 INFO: performing precursor FDR with 47 features
0:30:11.281697 INFO: Decoy channel: -1
0:30:11.281728 INFO: Competetive: True
0:30:11.327344 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:11.347596 WARNING: dropped 10 target PSMs due to missing features
0:30:11.347727 WARNING: dropped 9 decoy PSMs due to missing features
0:30:13.007945 INFO: Test AUC: 0.552
0:30:13.008070 INFO: Train AUC: 0.574
0:30:13.008106 INFO: AUC difference: 3.72%
0:30:13.099327 INFO: Resetting torch num_threads to 128
0:30:13.104451 INFO: === FDR correction performed with classifier version -1 ===
0:30:13.113016 PROGRESS: ============================= Precursor FDR =============================
0:30:13.113297 PROGRESS: Total precursors accumulated: 49,318
0:30:13.113384 PROGRESS: Target precursors: 29,361 (59.53%)
0:30:13.113449 PROGRESS: Decoy precursors: 19,957 (40.47%)
0:30:13.113510 PROGRESS: 
0:30:13.113569 PROGRESS: Precursor Summary:
0:30:13.114962 PROGRESS: Channel   0:	 0.05 FDR:   513; 0.01 FDR:   357; 0.001 FDR:   280
0:30:13.115073 PROGRESS: 
0:30:13.115141 PROGRESS: Protein Summary:
0:30:13.116611 PROGRESS: Channel   0:	 0.05 FDR:   476; 0.01 FDR:   332; 0.001 FDR:   263
0:30:13.116713 PROGRESS: =========================================================================
0:30:13.130900 INFO: fragments_df_filtered: 3215
0:30:13.346711 INFO: calibration group: precursor, fitting mz estimator 
0:30:13.398381 INFO: calibration group: precursor, fitting rt estimator 
0:30:13.450402 INFO: calibration group: precursor, fitting mobility estimator 
0:30:13.510586 INFO: calibration group: fragment, fitting mz estimator 
0:30:13.745805 INFO: calibration group: precursor, predicting mz
0:30:13.761294 INFO: calibration group: precursor, predicting rt
0:30:13.834866 INFO: calibration group: precursor, predicting mobility
0:30:13.851612 INFO: calibration group: fragment, predicting mz
0:30:13.990680 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:30:13.991012 INFO: Starting optimization step 3.
0:30:13.991104 PROGRESS: === Extracting elution groups 0 to 56000 ===
0:30:13.991202 PROGRESS: Extracting batch of 110321 precursors
0:30:14.030641 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:30:14.030788 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:30:14.030860 INFO: FWHM in RT is 3.17 seconds, sigma is 0.70
0:30:14.030891 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.01
0:30:14.041707 INFO: Starting candidate selection
0:39:06.556201 INFO: Starting candidate scoring
0:39:16.626737 INFO: Finished candidate processing
0:39:16.626912 INFO: Collecting candidate features
0:39:17.072323 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 189250)
0:39:17.087318 INFO: Collecting fragment features
0:39:17.208680 INFO: Finished candidate scoring
0:39:17.412232 PROGRESS: === Extracted 189250 precursors and 1926296 fragments ===
0:39:17.412731 INFO: performing precursor FDR with 47 features
0:39:17.412773 INFO: Decoy channel: -1
0:39:17.412797 INFO: Competetive: True
0:39:17.472178 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:17.504766 WARNING: dropped 1 target PSMs due to missing features
0:39:20.644804 INFO: Test AUC: 0.565
0:39:20.645011 INFO: Train AUC: 0.585
0:39:20.645053 INFO: AUC difference: 3.46%
0:39:20.743784 INFO: Resetting torch num_threads to 128
0:39:20.750187 INFO: === FDR correction performed with classifier version 2 ===
0:39:20.760299 PROGRESS: ============================= Precursor FDR =============================
0:39:20.760550 PROGRESS: Total precursors accumulated: 50,259
0:39:20.760616 PROGRESS: Target precursors: 31,560 (62.79%)
0:39:20.760669 PROGRESS: Decoy precursors: 18,699 (37.21%)
0:39:20.760716 PROGRESS: 
0:39:20.760762 PROGRESS: Precursor Summary:
0:39:20.762211 PROGRESS: Channel   0:	 0.05 FDR:   550; 0.01 FDR:   354; 0.001 FDR:   197
0:39:20.762319 PROGRESS: 
0:39:20.762378 PROGRESS: Protein Summary:
0:39:20.763823 PROGRESS: Channel   0:	 0.05 FDR:   506; 0.01 FDR:   326; 0.001 FDR:   183
0:39:20.763914 PROGRESS: =========================================================================
0:39:20.778630 INFO: fragments_df_filtered: 4254
0:39:20.997275 INFO: calibration group: precursor, fitting mz estimator 
0:39:21.039268 INFO: calibration group: precursor, fitting rt estimator 
0:39:21.079803 INFO: calibration group: precursor, fitting mobility estimator 
0:39:21.121862 INFO: calibration group: fragment, fitting mz estimator 
0:39:21.385606 INFO: calibration group: precursor, predicting mz
0:39:21.401090 INFO: calibration group: precursor, predicting rt
0:39:21.471919 INFO: calibration group: precursor, predicting mobility
0:39:21.489889 INFO: calibration group: fragment, predicting mz
0:39:21.649795 INFO: === checking if optimization conditions were reached ===
0:39:21.652556 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
0:39:21.653749 PROGRESS: ❌ ms1_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:39:21.653805 INFO: ==============================================
0:39:21.653928 INFO: Starting optimization step 4.
0:39:21.654008 PROGRESS: === Extracting elution groups 0 to 56000 ===
0:39:21.654123 PROGRESS: Extracting batch of 110321 precursors
0:39:21.702082 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:39:21.702242 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:39:21.702340 INFO: FWHM in RT is 3.42 seconds, sigma is 0.75
0:39:21.702368 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.18
0:39:21.703325 INFO: Starting candidate selection
0:47:23.634869 INFO: Starting candidate scoring
0:47:29.388422 INFO: Finished candidate processing
0:47:29.388588 INFO: Collecting candidate features
0:47:29.730146 WARNING: intensity_correlation has 11 NaNs ( 0.01 % out of 189091)
0:47:29.730555 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 189091)
0:47:29.740349 INFO: Collecting fragment features
0:47:29.854435 INFO: Finished candidate scoring
0:47:29.960553 PROGRESS: === Extracted 189091 precursors and 1858584 fragments ===
0:47:29.960949 INFO: performing precursor FDR with 47 features
0:47:29.960994 INFO: Decoy channel: -1
0:47:29.961020 INFO: Competetive: True
0:47:30.015150 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:30.047873 WARNING: dropped 6 target PSMs due to missing features
0:47:30.048011 WARNING: dropped 7 decoy PSMs due to missing features
0:47:33.161277 INFO: Test AUC: 0.556
0:47:33.161398 INFO: Train AUC: 0.585
0:47:33.161429 INFO: AUC difference: 5.03%
0:47:33.161451 WARNING: AUC difference > 5%. This may indicate overfitting.
0:47:33.255042 INFO: Resetting torch num_threads to 128
0:47:33.260261 INFO: === FDR correction performed with classifier version 3 ===
0:47:33.268644 PROGRESS: ============================= Precursor FDR =============================
0:47:33.268893 PROGRESS: Total precursors accumulated: 50,227
0:47:33.268959 PROGRESS: Target precursors: 31,049 (61.82%)
0:47:33.269013 PROGRESS: Decoy precursors: 19,178 (38.18%)
0:47:33.269074 PROGRESS: 
0:47:33.269121 PROGRESS: Precursor Summary:
0:47:33.270563 PROGRESS: Channel   0:	 0.05 FDR:   907; 0.01 FDR:   628; 0.001 FDR:   162
0:47:33.270658 PROGRESS: 
0:47:33.270716 PROGRESS: Protein Summary:
0:47:33.272248 PROGRESS: Channel   0:	 0.05 FDR:   829; 0.01 FDR:   574; 0.001 FDR:   150
0:47:33.272338 PROGRESS: =========================================================================
0:47:33.285713 INFO: fragments_df_filtered: 5000
0:47:33.458680 INFO: calibration group: precursor, fitting mz estimator 
0:47:33.510073 INFO: calibration group: precursor, fitting rt estimator 
0:47:33.566007 INFO: calibration group: precursor, fitting mobility estimator 
0:47:33.620777 INFO: calibration group: fragment, fitting mz estimator 
0:47:34.037389 INFO: calibration group: precursor, predicting mz
0:47:34.044247 INFO: calibration group: precursor, predicting rt
0:47:34.072219 INFO: calibration group: precursor, predicting mobility
0:47:34.078389 INFO: calibration group: fragment, predicting mz
0:47:34.128410 INFO: === checking if optimization conditions were reached ===
0:47:34.130836 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
0:47:34.132020 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
0:47:34.132073 INFO: ==============================================
0:47:34.132180 PROGRESS: Optimization finished for ms2_error, ms1_error.
0:47:34.305323 INFO: calibration group: precursor, predicting mz
0:47:34.312413 INFO: calibration group: precursor, predicting rt
0:47:34.340440 INFO: calibration group: precursor, predicting mobility
0:47:34.346624 INFO: calibration group: fragment, predicting mz
0:47:34.395638 INFO: Starting optimization step 0.
0:47:34.395890 PROGRESS: === Extracting elution groups 0 to 24000 ===
0:47:34.395978 PROGRESS: Extracting batch of 47305 precursors
0:47:34.412686 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:47:34.412818 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:47:34.412878 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
0:47:34.412905 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.24
0:47:34.421674 INFO: Starting candidate selection
0:51:03.942048 INFO: Starting candidate scoring
0:51:06.444516 INFO: Finished candidate processing
0:51:06.444622 INFO: Collecting candidate features
0:51:06.574752 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 81093)
0:51:06.581255 INFO: Collecting fragment features
0:51:06.637916 INFO: Finished candidate scoring
0:51:06.681484 PROGRESS: === Extracted 81093 precursors and 794933 fragments ===
0:51:06.681940 INFO: performing precursor FDR with 47 features
0:51:06.681980 INFO: Decoy channel: -1
0:51:06.682004 INFO: Competetive: True
0:51:06.706305 INFO: Setting torch num_threads to 2 for FDR classification task
0:51:06.719466 WARNING: dropped 2 decoy PSMs due to missing features
0:51:07.957144 INFO: Test AUC: 0.567
0:51:07.957268 INFO: Train AUC: 0.604
0:51:07.957298 INFO: AUC difference: 6.01%
0:51:07.957319 WARNING: AUC difference > 5%. This may indicate overfitting.
0:51:08.054497 INFO: Resetting torch num_threads to 128
0:51:08.057003 INFO: === FDR correction performed with classifier version 4 ===
0:51:08.060534 PROGRESS: ============================= Precursor FDR =============================
0:51:08.060677 PROGRESS: Total precursors accumulated: 21,525
0:51:08.060743 PROGRESS: Target precursors: 13,687 (63.59%)
0:51:08.060797 PROGRESS: Decoy precursors: 7,838 (36.41%)
0:51:08.060845 PROGRESS: 
0:51:08.060890 PROGRESS: Precursor Summary:
0:51:08.062040 PROGRESS: Channel   0:	 0.05 FDR:   453; 0.01 FDR:   285; 0.001 FDR:   241
0:51:08.062140 PROGRESS: 
0:51:08.062202 PROGRESS: Protein Summary:
0:51:08.063487 PROGRESS: Channel   0:	 0.05 FDR:   439; 0.01 FDR:   275; 0.001 FDR:   233
0:51:08.063578 PROGRESS: =========================================================================
0:51:08.093283 INFO: fragments_df_filtered: 3170
0:51:08.260699 INFO: calibration group: precursor, fitting mz estimator 
0:51:08.302313 INFO: calibration group: precursor, fitting rt estimator 
0:51:08.340787 INFO: calibration group: precursor, fitting mobility estimator 
0:51:08.378821 INFO: calibration group: fragment, fitting mz estimator 
0:51:08.542900 INFO: calibration group: precursor, predicting mz
0:51:08.550414 INFO: calibration group: precursor, predicting rt
0:51:08.579051 INFO: calibration group: precursor, predicting mobility
0:51:08.585569 INFO: calibration group: fragment, predicting mz
0:51:08.637850 INFO: === checking if optimization conditions were reached ===
0:51:08.638097 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:51:08.640391 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 657.5069.
0:51:08.640452 INFO: ==============================================
0:51:08.640549 INFO: Starting optimization step 1.
0:51:08.640623 PROGRESS: === Extracting elution groups 0 to 24000 ===
0:51:08.640701 PROGRESS: Extracting batch of 47305 precursors
0:51:08.651881 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:51:08.651993 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:51:08.652048 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
0:51:08.652076 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.21
0:51:08.660801 INFO: Starting candidate selection
0:52:22.272565 INFO: Starting candidate scoring
0:52:24.690182 INFO: Finished candidate processing
0:52:24.690374 INFO: Collecting candidate features
0:52:24.864012 WARNING: intensity_correlation has 20 NaNs ( 0.03 % out of 79549)
0:52:24.864369 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 79549)
0:52:24.870974 INFO: Collecting fragment features
0:52:24.931449 INFO: Finished candidate scoring
0:52:24.984003 PROGRESS: === Extracted 79549 precursors and 767799 fragments ===
0:52:24.984651 INFO: performing precursor FDR with 47 features
0:52:24.984698 INFO: Decoy channel: -1
0:52:24.984724 INFO: Competetive: True
0:52:25.025754 INFO: Setting torch num_threads to 2 for FDR classification task
0:52:25.046398 WARNING: dropped 10 target PSMs due to missing features
0:52:25.046552 WARNING: dropped 13 decoy PSMs due to missing features
0:52:26.544764 INFO: Test AUC: 0.556
0:52:26.544923 INFO: Train AUC: 0.591
0:52:26.544953 INFO: AUC difference: 5.93%
0:52:26.544975 WARNING: AUC difference > 5%. This may indicate overfitting.
0:52:26.643042 INFO: Resetting torch num_threads to 128
0:52:26.646982 INFO: === FDR correction performed with classifier version 4 ===
0:52:26.651376 PROGRESS: ============================= Precursor FDR =============================
0:52:26.651546 PROGRESS: Total precursors accumulated: 21,276
0:52:26.651610 PROGRESS: Target precursors: 13,053 (61.35%)
0:52:26.651662 PROGRESS: Decoy precursors: 8,223 (38.65%)
0:52:26.651710 PROGRESS: 
0:52:26.651762 PROGRESS: Precursor Summary:
0:52:26.652915 PROGRESS: Channel   0:	 0.05 FDR:   370; 0.01 FDR:   253; 0.001 FDR:   158
0:52:26.653016 PROGRESS: 
0:52:26.653092 PROGRESS: Protein Summary:
0:52:26.654350 PROGRESS: Channel   0:	 0.05 FDR:   358; 0.01 FDR:   245; 0.001 FDR:   152
0:52:26.654441 PROGRESS: =========================================================================
0:52:26.661285 INFO: fragments_df_filtered: 2853
0:52:26.861241 INFO: calibration group: precursor, fitting mz estimator 
0:52:26.912239 INFO: calibration group: precursor, fitting rt estimator 
0:52:26.953239 INFO: calibration group: precursor, fitting mobility estimator 
0:52:26.992040 INFO: calibration group: fragment, fitting mz estimator 
0:52:27.140834 INFO: calibration group: precursor, predicting mz
0:52:27.148912 INFO: calibration group: precursor, predicting rt
0:52:27.177733 INFO: calibration group: precursor, predicting mobility
0:52:27.184748 INFO: calibration group: fragment, predicting mz
0:52:27.239184 INFO: === checking if optimization conditions were reached ===
0:52:27.239506 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:52:27.242004 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 427.6862.
0:52:27.242079 INFO: ==============================================
0:52:27.242186 INFO: Starting optimization step 2.
0:52:27.242265 PROGRESS: === Extracting elution groups 0 to 24000 ===
0:52:27.242358 PROGRESS: Extracting batch of 47305 precursors
0:52:27.259036 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:52:27.259183 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:52:27.259263 INFO: FWHM in RT is 2.97 seconds, sigma is 0.65
0:52:27.259290 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.20
0:52:27.268220 INFO: Starting candidate selection
0:53:10.244527 INFO: Starting candidate scoring
0:53:11.425505 INFO: Finished candidate processing
0:53:11.425606 INFO: Collecting candidate features
0:53:11.569908 WARNING: intensity_correlation has 513 NaNs ( 0.72 % out of 71163)
0:53:11.570205 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 71163)
0:53:11.575846 INFO: Collecting fragment features
0:53:11.610558 INFO: Finished candidate scoring
0:53:11.650272 PROGRESS: === Extracted 71163 precursors and 364943 fragments ===
0:53:11.650737 INFO: performing precursor FDR with 47 features
0:53:11.650777 INFO: Decoy channel: -1
0:53:11.650801 INFO: Competetive: True
0:53:11.673014 INFO: Setting torch num_threads to 2 for FDR classification task
0:53:11.685835 WARNING: dropped 258 target PSMs due to missing features
0:53:11.685956 WARNING: dropped 259 decoy PSMs due to missing features
0:53:12.806444 INFO: Test AUC: 0.529
0:53:12.806566 INFO: Train AUC: 0.559
0:53:12.806596 INFO: AUC difference: 5.38%
0:53:12.806619 WARNING: AUC difference > 5%. This may indicate overfitting.
0:53:12.896770 INFO: Resetting torch num_threads to 128
0:53:12.899144 INFO: === FDR correction performed with classifier version 4 ===
0:53:12.902451 PROGRESS: ============================= Precursor FDR =============================
0:53:12.902584 PROGRESS: Total precursors accumulated: 20,332
0:53:12.902647 PROGRESS: Target precursors: 11,521 (56.66%)
0:53:12.902699 PROGRESS: Decoy precursors: 8,811 (43.34%)
0:53:12.902746 PROGRESS: 
0:53:12.902792 PROGRESS: Precursor Summary:
0:53:12.903774 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
0:53:12.903862 PROGRESS: 
0:53:12.903917 PROGRESS: Protein Summary:
0:53:12.904967 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
0:53:12.905076 PROGRESS: =========================================================================
0:53:13.104319 INFO: calibration group: precursor, predicting mz
0:53:13.113791 INFO: calibration group: precursor, predicting rt
0:53:13.153474 INFO: calibration group: precursor, predicting mobility
0:53:13.165237 INFO: calibration group: fragment, predicting mz
0:53:13.238726 INFO: === skipping optimization until target number of precursors are found ===
0:53:13.239092 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
0:53:13.239176 INFO: Starting optimization step 3.
0:53:13.239249 PROGRESS: === Extracting elution groups 24000 to 56000 ===
0:53:13.239329 PROGRESS: Extracting batch of 63016 precursors
0:53:13.261367 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:53:13.261519 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:53:13.261574 INFO: FWHM in RT is 2.97 seconds, sigma is 0.65
0:53:13.261598 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.20
0:53:13.262639 INFO: Starting candidate selection
0:54:13.355608 INFO: Starting candidate scoring
0:54:14.903696 INFO: Finished candidate processing
0:54:14.903888 INFO: Collecting candidate features
0:54:15.134936 WARNING: intensity_correlation has 750 NaNs ( 0.79 % out of 94887)
0:54:15.135314 WARNING: height_correlation has 8 NaNs ( 0.01 % out of 94887)
0:54:15.142328 INFO: Collecting fragment features
0:54:15.202347 INFO: Finished candidate scoring
0:54:15.382699 PROGRESS: === Extracted 166050 precursors and 853859 fragments ===
0:54:15.402530 INFO: performing precursor FDR with 47 features
0:54:15.402682 INFO: Decoy channel: -1
0:54:15.402711 INFO: Competetive: True
0:54:15.494665 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:15.537174 WARNING: dropped 654 target PSMs due to missing features
0:54:15.537331 WARNING: dropped 616 decoy PSMs due to missing features
0:54:18.970560 INFO: Test AUC: 0.526
0:54:18.970877 INFO: Train AUC: 0.562
0:54:18.970931 INFO: AUC difference: 6.52%
0:54:18.970954 WARNING: AUC difference > 5%. This may indicate overfitting.
0:54:19.072313 INFO: Resetting torch num_threads to 128
0:54:19.083011 INFO: === FDR correction performed with classifier version 4 ===
0:54:19.093629 PROGRESS: ============================= Precursor FDR =============================
0:54:19.093939 PROGRESS: Total precursors accumulated: 47,422
0:54:19.094008 PROGRESS: Target precursors: 27,002 (56.94%)
0:54:19.094064 PROGRESS: Decoy precursors: 20,420 (43.06%)
0:54:19.094115 PROGRESS: 
0:54:19.094163 PROGRESS: Precursor Summary:
0:54:19.095481 PROGRESS: Channel   0:	 0.05 FDR:    86; 0.01 FDR:    12; 0.001 FDR:    12
0:54:19.095574 PROGRESS: 
0:54:19.095633 PROGRESS: Protein Summary:
0:54:19.096891 PROGRESS: Channel   0:	 0.05 FDR:    85; 0.01 FDR:    12; 0.001 FDR:    12
0:54:19.097003 PROGRESS: =========================================================================
0:54:19.749760 INFO: calibration group: precursor, predicting mz
0:54:19.768405 INFO: calibration group: precursor, predicting rt
0:54:19.843756 INFO: calibration group: precursor, predicting mobility
0:54:19.862426 INFO: calibration group: fragment, predicting mz
0:54:20.018857 INFO: === skipping optimization until target number of precursors are found ===
0:54:20.019222 PROGRESS: === Optimization of rt_error has been skipped 2 time(s); maximum number is 1 ===
0:54:20.020183 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 2099.9282 found after 2 searches.
0:54:20.020276 PROGRESS: Optimization finished for rt_error.
0:54:20.219248 INFO: calibration group: precursor, predicting mz
0:54:20.227492 INFO: calibration group: precursor, predicting rt
0:54:20.256586 INFO: calibration group: precursor, predicting mobility
0:54:20.263814 INFO: calibration group: fragment, predicting mz
0:54:20.349192 INFO: Starting optimization step 0.
0:54:20.349452 PROGRESS: === Extracting elution groups 0 to 24000 ===
0:54:20.349549 PROGRESS: Extracting batch of 47305 precursors
0:54:20.365434 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:54:20.365590 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:54:20.365644 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
0:54:20.365668 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.21
0:54:20.366864 INFO: Starting candidate selection
0:57:46.835896 INFO: Starting candidate scoring
0:57:48.048880 INFO: Finished candidate processing
0:57:48.049080 INFO: Collecting candidate features
0:57:48.216952 WARNING: intensity_correlation has 413 NaNs ( 0.55 % out of 75065)
0:57:48.217313 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 75065)
0:57:48.223492 INFO: Collecting fragment features
0:57:48.265490 INFO: Finished candidate scoring
0:57:48.313667 PROGRESS: === Extracted 75065 precursors and 393423 fragments ===
0:57:48.314221 INFO: performing precursor FDR with 47 features
0:57:48.314264 INFO: Decoy channel: -1
0:57:48.314288 INFO: Competetive: True
0:57:48.343859 INFO: Setting torch num_threads to 2 for FDR classification task
0:57:48.359433 WARNING: dropped 199 target PSMs due to missing features
0:57:48.359564 WARNING: dropped 215 decoy PSMs due to missing features
0:57:49.735950 INFO: Test AUC: 0.526
0:57:49.736091 INFO: Train AUC: 0.571
0:57:49.736122 INFO: AUC difference: 7.84%
0:57:49.736143 WARNING: AUC difference > 5%. This may indicate overfitting.
0:57:49.827793 INFO: Resetting torch num_threads to 128
0:57:49.830765 INFO: === FDR correction performed with classifier version 5 ===
0:57:49.834527 PROGRESS: ============================= Precursor FDR =============================
0:57:49.834679 PROGRESS: Total precursors accumulated: 21,013
0:57:49.834743 PROGRESS: Target precursors: 12,273 (58.41%)
0:57:49.834794 PROGRESS: Decoy precursors: 8,740 (41.59%)
0:57:49.834842 PROGRESS: 
0:57:49.834890 PROGRESS: Precursor Summary:
0:57:49.835905 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
0:57:49.835994 PROGRESS: 
0:57:49.836051 PROGRESS: Protein Summary:
0:57:49.837106 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
0:57:49.837199 PROGRESS: =========================================================================
0:57:50.065747 INFO: calibration group: precursor, predicting mz
0:57:50.075745 INFO: calibration group: precursor, predicting rt
0:57:50.114841 INFO: calibration group: precursor, predicting mobility
0:57:50.125766 INFO: calibration group: fragment, predicting mz
0:57:50.203429 INFO: === skipping optimization until target number of precursors are found ===
0:57:50.203791 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
0:57:50.203875 INFO: Starting optimization step 1.
0:57:50.203954 PROGRESS: === Extracting elution groups 24000 to 56000 ===
0:57:50.204042 PROGRESS: Extracting batch of 63016 precursors
0:57:50.229332 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:57:50.229498 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:57:50.229564 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
0:57:50.229593 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.21
0:57:50.242531 INFO: Starting candidate selection
1:02:36.467374 INFO: Starting candidate scoring
1:02:40.326386 INFO: Finished candidate processing
1:02:40.326529 INFO: Collecting candidate features
1:02:40.558748 WARNING: intensity_correlation has 602 NaNs ( 0.60 % out of 100375)
1:02:40.559103 WARNING: height_correlation has 15 NaNs ( 0.01 % out of 100375)
1:02:40.566093 INFO: Collecting fragment features
1:02:40.620199 INFO: Finished candidate scoring
1:02:40.769282 PROGRESS: === Extracted 175440 precursors and 921603 fragments ===
1:02:40.788192 INFO: performing precursor FDR with 47 features
1:02:40.788341 INFO: Decoy channel: -1
1:02:40.788368 INFO: Competetive: True
1:02:40.876392 INFO: Setting torch num_threads to 2 for FDR classification task
1:02:40.915560 WARNING: dropped 500 target PSMs due to missing features
1:02:40.915713 WARNING: dropped 522 decoy PSMs due to missing features
1:02:43.940989 INFO: Test AUC: 0.535
1:02:43.941716 INFO: Train AUC: 0.566
1:02:43.941756 INFO: AUC difference: 5.58%
1:02:43.941799 WARNING: AUC difference > 5%. This may indicate overfitting.
1:02:44.920984 INFO: Resetting torch num_threads to 128
1:02:44.929202 INFO: === FDR correction performed with classifier version 5 ===
1:02:44.938930 PROGRESS: ============================= Precursor FDR =============================
1:02:44.939239 PROGRESS: Total precursors accumulated: 49,070
1:02:44.939312 PROGRESS: Target precursors: 28,614 (58.31%)
1:02:44.939372 PROGRESS: Decoy precursors: 20,456 (41.69%)
1:02:44.939427 PROGRESS: 
1:02:44.939480 PROGRESS: Precursor Summary:
1:02:44.940750 PROGRESS: Channel   0:	 0.05 FDR:    40; 0.01 FDR:    33; 0.001 FDR:    33
1:02:44.940845 PROGRESS: 
1:02:44.940907 PROGRESS: Protein Summary:
1:02:44.942304 PROGRESS: Channel   0:	 0.05 FDR:    40; 0.01 FDR:    33; 0.001 FDR:    33
1:02:44.942400 PROGRESS: =========================================================================
1:02:45.353721 INFO: calibration group: precursor, predicting mz
1:02:45.374138 INFO: calibration group: precursor, predicting rt
1:02:45.450009 INFO: calibration group: precursor, predicting mobility
1:02:45.470914 INFO: calibration group: fragment, predicting mz
1:02:45.640079 INFO: === skipping optimization until target number of precursors are found ===
1:02:45.640405 PROGRESS: === Optimization of mobility_error has been skipped 2 time(s); maximum number is 1 ===
1:02:45.640476 INFO: Starting optimization step 2.
1:02:45.640550 PROGRESS: === Extracting elution groups 56000 to 120000 ===
1:02:45.640624 PROGRESS: Extracting batch of 126066 precursors
1:02:45.688194 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:02:45.688340 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:02:45.688390 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
1:02:45.688413 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.21
1:02:45.689461 INFO: Starting candidate selection
1:11:48.958948 INFO: Starting candidate scoring
1:11:52.102490 INFO: Finished candidate processing
1:11:52.102604 INFO: Collecting candidate features
1:11:52.462605 WARNING: intensity_correlation has 1059 NaNs ( 0.53 % out of 200647)
1:11:52.463029 WARNING: height_correlation has 33 NaNs ( 0.02 % out of 200647)
1:11:52.473134 INFO: Collecting fragment features
1:11:52.578685 INFO: Finished candidate scoring
1:11:52.849957 PROGRESS: === Extracted 376087 precursors and 1976873 fragments ===
1:11:52.889613 INFO: performing precursor FDR with 47 features
1:11:52.889766 INFO: Decoy channel: -1
1:11:52.889793 INFO: Competetive: True
1:11:53.054452 INFO: Setting torch num_threads to 2 for FDR classification task
1:11:53.129746 WARNING: dropped 1059 target PSMs due to missing features
1:11:53.129896 WARNING: dropped 1040 decoy PSMs due to missing features
1:11:59.986587 INFO: Test AUC: 0.534
1:11:59.986753 INFO: Train AUC: 0.561
1:11:59.986784 INFO: AUC difference: 4.83%
1:12:00.102601 INFO: Resetting torch num_threads to 128
1:12:00.123347 INFO: === FDR correction performed with classifier version 5 ===
1:12:00.144675 PROGRESS: ============================= Precursor FDR =============================
1:12:00.145000 PROGRESS: Total precursors accumulated: 105,197
1:12:00.145075 PROGRESS: Target precursors: 60,433 (57.45%)
1:12:00.145128 PROGRESS: Decoy precursors: 44,764 (42.55%)
1:12:00.145174 PROGRESS: 
1:12:00.145219 PROGRESS: Precursor Summary:
1:12:00.146826 PROGRESS: Channel   0:	 0.05 FDR:     9; 0.01 FDR:     9; 0.001 FDR:     9
1:12:00.146936 PROGRESS: 
1:12:00.146994 PROGRESS: Protein Summary:
1:12:00.148462 PROGRESS: Channel   0:	 0.05 FDR:     9; 0.01 FDR:     9; 0.001 FDR:     9
1:12:00.148554 PROGRESS: =========================================================================
1:12:00.614668 INFO: calibration group: precursor, predicting mz
1:12:00.650013 INFO: calibration group: precursor, predicting rt
1:12:00.803391 INFO: calibration group: precursor, predicting mobility
1:12:00.839725 INFO: calibration group: fragment, predicting mz
1:12:01.142419 INFO: === skipping optimization until target number of precursors are found ===
1:12:01.142808 PROGRESS: === Optimization of mobility_error has been skipped 3 time(s); maximum number is 1 ===
1:12:01.142882 INFO: Starting optimization step 3.
1:12:01.142950 PROGRESS: === Extracting elution groups 120000 to 248000 ===
1:12:01.143025 PROGRESS: Extracting batch of 252186 precursors
1:12:01.206981 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:12:01.207128 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:12:01.207181 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
1:12:01.207204 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.21
1:12:01.208116 INFO: Starting candidate selection
1:30:07.317619 INFO: Starting candidate scoring
1:30:13.269396 INFO: Finished candidate processing
1:30:13.269710 INFO: Collecting candidate features
1:30:14.316409 WARNING: intensity_correlation has 2167 NaNs ( 0.54 % out of 401465)
1:30:14.317154 WARNING: height_correlation has 44 NaNs ( 0.01 % out of 401465)
1:30:14.334482 INFO: Collecting fragment features
1:30:14.544478 INFO: Finished candidate scoring
1:30:15.135372 PROGRESS: === Extracted 777552 precursors and 4085872 fragments ===
1:30:15.213188 INFO: performing precursor FDR with 47 features
1:30:15.213333 INFO: Decoy channel: -1
1:30:15.213365 INFO: Competetive: True
1:30:15.572729 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:15.731577 WARNING: dropped 2171 target PSMs due to missing features
1:30:15.731722 WARNING: dropped 2113 decoy PSMs due to missing features
1:30:30.211701 INFO: Test AUC: 0.540
1:30:30.212241 INFO: Train AUC: 0.554
1:30:30.212278 INFO: AUC difference: 2.50%
1:30:30.358061 INFO: Resetting torch num_threads to 128
1:30:30.400563 INFO: === FDR correction performed with classifier version 5 ===
1:30:30.442867 PROGRESS: ============================= Precursor FDR =============================
1:30:30.443198 PROGRESS: Total precursors accumulated: 217,382
1:30:30.443268 PROGRESS: Target precursors: 124,222 (57.14%)
1:30:30.443322 PROGRESS: Decoy precursors: 93,160 (42.86%)
1:30:30.443373 PROGRESS: 
1:30:30.443420 PROGRESS: Precursor Summary:
1:30:30.445616 PROGRESS: Channel   0:	 0.05 FDR:     6; 0.01 FDR:     6; 0.001 FDR:     6
1:30:30.445714 PROGRESS: 
1:30:30.445773 PROGRESS: Protein Summary:
1:30:30.447724 PROGRESS: Channel   0:	 0.05 FDR:     6; 0.01 FDR:     6; 0.001 FDR:     6
1:30:30.447816 PROGRESS: =========================================================================
1:30:31.109444 INFO: calibration group: precursor, predicting mz
1:30:31.176859 INFO: calibration group: precursor, predicting rt
1:30:31.488518 INFO: calibration group: precursor, predicting mobility
1:30:31.555471 INFO: calibration group: fragment, predicting mz
1:30:32.154299 INFO: === skipping optimization until target number of precursors are found ===
1:30:32.154642 PROGRESS: === Optimization of mobility_error has been skipped 4 time(s); maximum number is 1 ===
1:30:32.154726 INFO: Starting optimization step 4.
1:30:32.154800 PROGRESS: === Extracting elution groups 248000 to 504000 ===
1:30:32.154877 PROGRESS: Extracting batch of 504181 precursors
1:30:32.284122 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:30:32.284264 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:30:32.284313 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
1:30:32.284338 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.21
1:30:32.285355 INFO: Starting candidate selection
2:07:02.324940 INFO: Starting candidate scoring
2:07:13.554530 INFO: Finished candidate processing
2:07:13.554655 INFO: Collecting candidate features
2:07:15.417050 WARNING: intensity_correlation has 4290 NaNs ( 0.53 % out of 802989)
2:07:15.417975 WARNING: height_correlation has 94 NaNs ( 0.01 % out of 802989)
2:07:15.446930 INFO: Collecting fragment features
2:07:15.856626 INFO: Finished candidate scoring
2:07:16.947586 PROGRESS: === Extracted 1580541 precursors and 8301822 fragments ===
2:07:17.106165 INFO: performing precursor FDR with 47 features
2:07:17.106329 INFO: Decoy channel: -1
2:07:17.106357 INFO: Competetive: True
2:07:17.947540 INFO: Setting torch num_threads to 2 for FDR classification task
2:07:18.322565 WARNING: dropped 4399 target PSMs due to missing features
2:07:18.322745 WARNING: dropped 4223 decoy PSMs due to missing features
2:07:53.171002 INFO: Test AUC: 0.540
2:07:53.172180 INFO: Train AUC: 0.550
2:07:53.172230 INFO: AUC difference: 1.83%
2:07:53.388579 INFO: Resetting torch num_threads to 128
2:07:53.466345 INFO: === FDR correction performed with classifier version 5 ===
2:07:53.559738 PROGRESS: ============================= Precursor FDR =============================
2:07:53.560057 PROGRESS: Total precursors accumulated: 442,047
2:07:53.560130 PROGRESS: Target precursors: 251,126 (56.81%)
2:07:53.560183 PROGRESS: Decoy precursors: 190,921 (43.19%)
2:07:53.560230 PROGRESS: 
2:07:53.560276 PROGRESS: Precursor Summary:
2:07:53.563836 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
2:07:53.563973 PROGRESS: 
2:07:53.564032 PROGRESS: Protein Summary:
2:07:53.567029 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
2:07:53.567127 PROGRESS: =========================================================================
2:07:55.017123 INFO: calibration group: precursor, predicting mz
2:07:55.177324 INFO: calibration group: precursor, predicting rt
2:07:55.844507 INFO: calibration group: precursor, predicting mobility
2:07:55.985459 INFO: calibration group: fragment, predicting mz
2:07:57.252331 INFO: === skipping optimization until target number of precursors are found ===
2:07:57.252667 PROGRESS: === Optimization of mobility_error has been skipped 5 time(s); maximum number is 1 ===
2:07:57.252758 INFO: Starting optimization step 5.
2:07:57.252828 PROGRESS: === Extracting elution groups 504000 to 1016000 ===
2:07:57.252923 PROGRESS: Extracting batch of 1008477 precursors
2:07:57.515118 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:07:57.515259 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:07:57.515322 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
2:07:57.515347 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.21
2:07:57.519940 INFO: Starting candidate selection
3:19:07.848990 INFO: Starting candidate scoring
3:19:30.882062 INFO: Finished candidate processing
3:19:30.883003 INFO: Collecting candidate features
3:19:34.189100 WARNING: intensity_correlation has 8870 NaNs ( 0.55 % out of 1605760)
3:19:34.190666 WARNING: height_correlation has 190 NaNs ( 0.01 % out of 1605760)
3:19:34.244178 INFO: Collecting fragment features
3:19:35.140599 INFO: Finished candidate scoring
3:19:37.694389 PROGRESS: === Extracted 3186301 precursors and 16729805 fragments ===
3:19:37.999759 INFO: performing precursor FDR with 47 features
3:19:37.999918 INFO: Decoy channel: -1
3:19:37.999948 INFO: Competetive: True
3:19:39.469643 INFO: Setting torch num_threads to 2 for FDR classification task
3:19:40.082896 WARNING: dropped 8878 target PSMs due to missing features
3:19:40.083056 WARNING: dropped 8722 decoy PSMs due to missing features
3:20:39.324523 INFO: Test AUC: 0.543
3:20:39.324847 INFO: Train AUC: 0.548
3:20:39.324890 INFO: AUC difference: 0.87%
3:20:39.647635 INFO: Resetting torch num_threads to 128
3:20:39.808903 INFO: === FDR correction performed with classifier version 5 ===
3:20:39.983328 PROGRESS: ============================= Precursor FDR =============================
3:20:39.983709 PROGRESS: Total precursors accumulated: 891,162
3:20:39.983793 PROGRESS: Target precursors: 505,948 (56.77%)
3:20:39.983847 PROGRESS: Decoy precursors: 385,214 (43.23%)
3:20:39.983898 PROGRESS: 
3:20:39.983946 PROGRESS: Precursor Summary:
3:20:39.989108 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:20:39.989231 PROGRESS: 
3:20:39.989288 PROGRESS: Protein Summary:
3:20:39.993819 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:20:39.993933 PROGRESS: =========================================================================
3:20:41.813332 INFO: calibration group: precursor, predicting mz
3:20:42.150891 INFO: calibration group: precursor, predicting rt
3:20:43.435355 INFO: calibration group: precursor, predicting mobility
3:20:43.726228 INFO: calibration group: fragment, predicting mz
3:20:46.217619 INFO: === skipping optimization until target number of precursors are found ===
3:20:46.217949 PROGRESS: === Optimization of mobility_error has been skipped 6 time(s); maximum number is 1 ===
3:20:46.218030 INFO: Starting optimization step 6.
3:20:46.218100 PROGRESS: === Extracting elution groups 1016000 to 2040000 ===
3:20:46.218193 PROGRESS: Extracting batch of 2017059 precursors
3:20:46.707590 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
3:20:46.707734 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
3:20:46.707785 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
3:20:46.707810 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.21
3:20:46.708819 INFO: Starting candidate selection
5:42:18.902237 INFO: Starting candidate scoring
5:43:05.520154 INFO: Finished candidate processing
5:43:05.520736 INFO: Collecting candidate features
5:43:12.054885 WARNING: intensity_correlation has 17757 NaNs ( 0.55 % out of 3211952)
5:43:12.057824 WARNING: height_correlation has 401 NaNs ( 0.01 % out of 3211952)
5:43:12.164128 INFO: Collecting fragment features
5:43:13.970177 INFO: Finished candidate scoring
5:43:18.076760 PROGRESS: === Extracted 6398253 precursors and 33591196 fragments ===
5:43:18.707494 INFO: performing precursor FDR with 47 features
5:43:18.707651 INFO: Decoy channel: -1
5:43:18.707682 INFO: Competetive: True
5:43:21.570783 INFO: Setting torch num_threads to 2 for FDR classification task
5:43:22.975197 WARNING: dropped 18002 target PSMs due to missing features
5:43:22.975350 WARNING: dropped 17574 decoy PSMs due to missing features
5:45:44.378172 INFO: Test AUC: 0.548
5:45:44.378703 INFO: Train AUC: 0.551
5:45:44.378747 INFO: AUC difference: 0.47%
5:45:44.896162 INFO: Resetting torch num_threads to 128
5:45:45.267864 INFO: === FDR correction performed with classifier version 5 ===
5:45:45.613115 PROGRESS: ============================= Precursor FDR =============================
5:45:45.613502 PROGRESS: Total precursors accumulated: 1,789,439
5:45:45.613572 PROGRESS: Target precursors: 1,019,993 (57.00%)
5:45:45.613646 PROGRESS: Decoy precursors: 769,446 (43.00%)
5:45:45.613699 PROGRESS: 
5:45:45.613745 PROGRESS: Precursor Summary:
5:45:45.622937 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
5:45:45.623115 PROGRESS: 
5:45:45.623174 PROGRESS: Protein Summary:
5:45:45.631536 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
5:45:45.631694 PROGRESS: =========================================================================
5:45:49.152978 INFO: calibration group: precursor, predicting mz
5:45:49.716976 INFO: calibration group: precursor, predicting rt
5:45:52.274537 INFO: calibration group: precursor, predicting mobility
5:45:52.831982 INFO: calibration group: fragment, predicting mz
5:45:57.820853 INFO: === skipping optimization until target number of precursors are found ===
5:45:57.821237 PROGRESS: === Optimization of mobility_error has been skipped 7 time(s); maximum number is 1 ===
5:45:57.821340 INFO: Starting optimization step 7.
5:45:57.821420 PROGRESS: === Extracting elution groups 2040000 to 4088000 ===
5:45:57.821523 PROGRESS: Extracting batch of 4034279 precursors
5:45:59.068232 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:45:59.068421 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:45:59.068495 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
5:45:59.068528 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.21
5:45:59.074066 INFO: Starting candidate selection
10:27:28.114071 INFO: Starting candidate scoring
10:29:02.017102 INFO: Finished candidate processing
10:29:02.018110 INFO: Collecting candidate features
10:29:15.419712 WARNING: intensity_correlation has 35210 NaNs ( 0.55 % out of 6424454)
10:29:15.426100 WARNING: height_correlation has 807 NaNs ( 0.01 % out of 6424454)
10:29:15.638309 INFO: Collecting fragment features
10:29:19.292155 INFO: Finished candidate scoring
10:29:30.479921 PROGRESS: === Extracted 12822707 precursors and 67325241 fragments ===
10:29:31.762975 INFO: performing precursor FDR with 47 features
10:29:31.763112 INFO: Decoy channel: -1
10:29:31.763140 INFO: Competetive: True
10:29:36.911824 INFO: Setting torch num_threads to 2 for FDR classification task
10:29:39.276779 WARNING: dropped 36160 target PSMs due to missing features
10:29:39.276925 WARNING: dropped 35076 decoy PSMs due to missing features
10:33:50.961308 INFO: Test AUC: 0.548
10:33:50.961551 INFO: Train AUC: 0.553
10:33:50.961592 INFO: AUC difference: 0.96%
10:33:51.789894 INFO: Resetting torch num_threads to 128
10:33:52.416725 INFO: === FDR correction performed with classifier version 5 ===
10:33:53.051484 PROGRESS: ============================= Precursor FDR =============================
10:33:53.051805 PROGRESS: Total precursors accumulated: 3,586,209
10:33:53.051872 PROGRESS: Target precursors: 2,036,853 (56.80%)
10:33:53.051923 PROGRESS: Decoy precursors: 1,549,356 (43.20%)
10:33:53.051972 PROGRESS: 
10:33:53.052022 PROGRESS: Precursor Summary:
10:33:53.070100 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
10:33:53.070367 PROGRESS: 
10:33:53.070432 PROGRESS: Protein Summary:
10:33:53.087967 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
10:33:53.088191 PROGRESS: =========================================================================
10:33:55.133592 INFO: calibration group: precursor, predicting mz
10:33:55.444574 INFO: calibration group: precursor, predicting rt
10:33:56.850198 INFO: calibration group: precursor, predicting mobility
10:33:57.158901 INFO: calibration group: fragment, predicting mz
10:33:59.916966 INFO: === skipping optimization until target number of precursors are found ===
10:33:59.917256 PROGRESS: === Optimization of mobility_error has been skipped 8 time(s); maximum number is 1 ===
10:33:59.917342 INFO: Starting optimization step 8.
10:33:59.918074 PROGRESS: === Extracting elution groups 4088000 to 5215079 ===
10:33:59.918162 PROGRESS: Extracting batch of 2220101 precursors
10:34:00.431594 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:34:00.431721 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:34:00.431770 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
10:34:00.431794 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.21
10:34:00.433185 INFO: Starting candidate selection
13:08:54.923277 INFO: Starting candidate scoring
13:09:47.501815 INFO: Finished candidate processing
13:09:47.502527 INFO: Collecting candidate features
13:09:54.584251 WARNING: intensity_correlation has 19187 NaNs ( 0.54 % out of 3537316)
13:09:54.587495 WARNING: height_correlation has 474 NaNs ( 0.01 % out of 3537316)
13:09:54.705083 INFO: Collecting fragment features
13:09:56.748783 INFO: Finished candidate scoring
13:10:06.000874 PROGRESS: === Extracted 16360023 precursors and 85888408 fragments ===
13:10:07.556221 INFO: performing precursor FDR with 47 features
13:10:07.556359 INFO: Decoy channel: -1
13:10:07.556392 INFO: Competetive: True
13:10:14.230803 INFO: Setting torch num_threads to 2 for FDR classification task
13:10:17.244230 WARNING: dropped 46153 target PSMs due to missing features
13:10:17.244375 WARNING: dropped 44562 decoy PSMs due to missing features
13:16:08.569692 INFO: Test AUC: 0.538
13:16:08.569964 INFO: Train AUC: 0.554
13:16:08.570015 INFO: AUC difference: 2.98%
13:16:09.550333 INFO: Resetting torch num_threads to 128
13:16:10.544191 INFO: === FDR correction performed with classifier version 5 ===
13:16:11.386899 PROGRESS: ============================= Precursor FDR =============================
13:16:11.387202 PROGRESS: Total precursors accumulated: 4,575,603
13:16:11.387269 PROGRESS: Target precursors: 2,598,453 (56.79%)
13:16:11.387330 PROGRESS: Decoy precursors: 1,977,150 (43.21%)
13:16:11.387379 PROGRESS: 
13:16:11.387424 PROGRESS: Precursor Summary:
13:16:11.410981 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
13:16:11.411250 PROGRESS: 
13:16:11.411315 PROGRESS: Protein Summary:
13:16:11.433956 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
13:16:11.434185 PROGRESS: =========================================================================
13:16:11.535534 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
13:16:11.535851 PROGRESS: ==============================================
13:16:12.025543 INFO: fragments_df_filtered: 0
13:16:12.488140 WARNING: No more batches to process. Will proceed to extraction using best parameters available in optimization manager.
13:16:12.488422 WARNING: Using current optimal value for ms2_error: 15.00.
13:16:12.957860 WARNING: No more batches to process. Will proceed to extraction using best parameters available in optimization manager.
13:16:12.958113 WARNING: Using current optimal value for ms1_error: 10.00.
13:16:13.419358 WARNING: No more batches to process. Will proceed to extraction using best parameters available in optimization manager.
13:16:13.421469 WARNING: Using current optimal value for rt_error: 2099.93.
13:16:13.892861 WARNING: No more batches to process. Will proceed to extraction using best parameters available in optimization manager.
13:16:13.894003 WARNING: Using current optimal value for mobility_error: 0.10.
13:16:13.900912 PROGRESS: ms2_error      : 15.0000
13:16:13.901131 PROGRESS: ms1_error      : 10.0000
13:16:13.901196 PROGRESS: rt_error       : 2099.9282
13:16:13.901247 PROGRESS: mobility_error : 0.1000
13:16:13.901293 PROGRESS: ==============================================
13:16:14.166251 INFO: calibration group: precursor, predicting mz
13:16:15.669114 INFO: calibration group: precursor, predicting rt
13:16:22.119638 INFO: calibration group: precursor, predicting mobility
13:16:23.610231 INFO: calibration group: fragment, predicting mz
13:16:36.110446 PROGRESS: Extracting batch of 10272670 precursors
13:16:38.524239 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:16:38.524372 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:16:38.524433 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
13:16:38.524460 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.21
13:16:38.525644 INFO: Starting candidate selection
1 day, 1:06:26.819884 INFO: Applying score cutoff of 37.72792678833008
1 day, 1:06:26.848193 INFO: Removed 17625041 precursors with score below cutoff
1 day, 1:06:29.292562 INFO: Starting candidate scoring
1 day, 1:06:34.365007 INFO: Finished candidate processing
1 day, 1:06:34.366084 INFO: Collecting candidate features
1 day, 1:06:36.803639 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 250134)
1 day, 1:06:36.804151 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 250134)
1 day, 1:06:36.820106 INFO: Collecting fragment features
1 day, 1:06:37.373019 INFO: Finished candidate scoring
1 day, 1:06:38.134122 INFO: === FDR correction performed with classifier version 17 ===
1 day, 1:06:38.135711 INFO: performing precursor FDR with 47 features
1 day, 1:06:38.135753 INFO: Decoy channel: -1
1 day, 1:06:38.135786 INFO: Competetive: True
1 day, 1:06:38.265282 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:06:38.365479 WARNING: dropped 1 target PSMs due to missing features
1 day, 1:06:38.365697 WARNING: FDR calculation for 132360 target and 117773 decoy PSMs
1 day, 1:06:38.365738 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1 day, 1:06:43.444875 INFO: Test AUC: 0.548
1 day, 1:06:43.445075 INFO: Train AUC: 0.568
1 day, 1:06:43.445110 INFO: AUC difference: 3.49%
1 day, 1:06:43.551962 INFO: Resetting torch num_threads to 128
1 day, 1:06:43.565067 INFO: Removing fragments below FDR threshold
1 day, 1:06:43.737351 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:06:43.737613 PROGRESS: Total precursors accumulated: 22
1 day, 1:06:43.737679 PROGRESS: Target precursors: 22 (100.00%)
1 day, 1:06:43.737732 PROGRESS: Decoy precursors: 0 (0.00%)
1 day, 1:06:43.737790 PROGRESS: 
1 day, 1:06:43.737843 PROGRESS: Precursor Summary:
1 day, 1:06:43.738857 PROGRESS: Channel   0:	 0.05 FDR:    22; 0.01 FDR:    22; 0.001 FDR:    22
1 day, 1:06:43.738947 PROGRESS: 
1 day, 1:06:43.739002 PROGRESS: Protein Summary:
1 day, 1:06:43.740082 PROGRESS: Channel   0:	 0.05 FDR:    22; 0.01 FDR:    22; 0.001 FDR:    22
1 day, 1:06:43.740178 PROGRESS: =========================================================================
1 day, 1:06:43.759561 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 1:06:44.634658 PROGRESS: Loading raw file 2/6: ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 1:06:44.634818 INFO: Quantification results path: run_output/alphadia_1.10_defaultMBR/library/quant
1 day, 1:06:44.634901 INFO: Creating workflow folder for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500 at run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 1:06:44.635923 INFO: Initializing RawFileManager
1 day, 1:06:44.636053 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 1:06:44.636106 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 1:06:44.636145 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 1:06:44.857958 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
1 day, 1:06:53.510993 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d...
1 day, 1:06:53.512442 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 1:06:53.515754 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 1:06:53.515990 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 1:06:53.516342 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 1:06:53.518069 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 1:06:53.533038 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 1:06:53.533262 INFO: Indexing quadrupole dimension
1 day, 1:06:54.038338 INFO: Transposing detector events
1 day, 1:07:02.817459 INFO: Finished transposing data
1 day, 1:07:02.856778 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 1:07:02.858984 INFO: RT (min)            : 0.0 - 70.0
1 day, 1:07:02.859082 INFO: RT duration (sec)   : 4199.8
1 day, 1:07:02.859140 INFO: RT duration (min)   : 70.0
1 day, 1:07:02.859195 INFO: Cycle len (scans)   : 9
1 day, 1:07:02.859241 INFO: Cycle len (sec)     : 0.97
1 day, 1:07:02.859285 INFO: Number of cycles    : 4347
1 day, 1:07:02.859329 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 1:07:04.148746 INFO: Initializing CalibrationManager
1 day, 1:07:04.149036 INFO: Loading calibration config
1 day, 1:07:04.150441 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'}]
1 day, 1:07:04.150574 INFO: Calibration group :fragment, found 1 estimator(s)
1 day, 1:07:04.150699 INFO: Calibration group :precursor, found 3 estimator(s)
1 day, 1:07:04.150898 INFO: Initializing OptimizationManager
1 day, 1:07:04.151052 INFO: initial parameter: ms1_error = 30
1 day, 1:07:04.151109 INFO: initial parameter: ms2_error = 30
1 day, 1:07:04.151170 INFO: initial parameter: rt_error = 2099.894844
1 day, 1:07:04.151220 INFO: initial parameter: mobility_error = 0.1
1 day, 1:07:04.151267 INFO: initial parameter: column_type = library
1 day, 1:07:04.151309 INFO: initial parameter: num_candidates = 1
1 day, 1:07:04.151352 INFO: initial parameter: classifier_version = -1
1 day, 1:07:04.151393 INFO: initial parameter: fwhm_rt = 5
1 day, 1:07:04.151435 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 1:07:04.151478 INFO: initial parameter: score_cutoff = 0
1 day, 1:07:04.151547 INFO: Initializing TimingManager
1 day, 1:07:04.151609 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 1:07:04.151723 INFO: FDRManager not loaded from disk.
1 day, 1:07:04.151749 INFO: Initializing FDRManager
1 day, 1:07:04.151783 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 1:07:05.442800 PROGRESS: 5,215,079 target precursors potentially observable (0 removed)
1 day, 1:07:07.300380 PROGRESS: Starting initial search for precursors.
1 day, 1:07:07.563779 INFO: Starting optimization step 0.
1 day, 1:07:07.564022 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 1:07:07.564100 PROGRESS: Extracting batch of 15771 precursors
1 day, 1:07:07.567754 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:07:07.567813 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:07:07.567847 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 1:07:07.567869 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 1:07:07.568953 INFO: Starting candidate selection
1 day, 1:08:28.569718 INFO: Starting candidate scoring
1 day, 1:08:29.344234 INFO: Finished candidate processing
1 day, 1:08:29.344337 INFO: Collecting candidate features
1 day, 1:08:29.377996 INFO: Collecting fragment features
1 day, 1:08:29.391760 INFO: Finished candidate scoring
1 day, 1:08:29.400192 PROGRESS: === Extracted 13798 precursors and 138660 fragments ===
1 day, 1:08:29.400597 INFO: performing precursor FDR with 47 features
1 day, 1:08:29.400635 INFO: Decoy channel: -1
1 day, 1:08:29.400658 INFO: Competetive: True
1 day, 1:08:29.406198 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:08:29.558410 INFO: Test AUC: 0.498
1 day, 1:08:29.558531 INFO: Train AUC: 0.507
1 day, 1:08:29.558565 INFO: AUC difference: 1.80%
1 day, 1:08:29.645404 INFO: Resetting torch num_threads to 100
1 day, 1:08:29.646520 INFO: === FDR correction performed with classifier version -1 ===
1 day, 1:08:29.647943 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:08:29.648055 PROGRESS: Total precursors accumulated: 7,064
1 day, 1:08:29.648117 PROGRESS: Target precursors: 3,719 (52.65%)
1 day, 1:08:29.648168 PROGRESS: Decoy precursors: 3,345 (47.35%)
1 day, 1:08:29.648215 PROGRESS: 
1 day, 1:08:29.648263 PROGRESS: Precursor Summary:
1 day, 1:08:29.649171 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1 day, 1:08:29.649262 PROGRESS: 
1 day, 1:08:29.649321 PROGRESS: Protein Summary:
1 day, 1:08:29.650286 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1 day, 1:08:29.650376 PROGRESS: =========================================================================
1 day, 1:08:29.809812 INFO: Starting optimization step 1.
1 day, 1:08:29.810074 PROGRESS: === Extracting elution groups 8000 to 24000 ===
1 day, 1:08:29.810189 PROGRESS: Extracting batch of 31534 precursors
1 day, 1:08:29.817285 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:08:29.817364 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:08:29.817401 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 1:08:29.817423 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 1:08:29.818310 INFO: Starting candidate selection
1 day, 1:11:02.398656 INFO: Starting candidate scoring
1 day, 1:11:03.895349 INFO: Finished candidate processing
1 day, 1:11:03.895456 INFO: Collecting candidate features
1 day, 1:11:03.948931 WARNING: intensity_correlation has 8 NaNs ( 0.03 % out of 27432)
1 day, 1:11:03.953120 INFO: Collecting fragment features
1 day, 1:11:03.974856 INFO: Finished candidate scoring
1 day, 1:11:04.015870 PROGRESS: === Extracted 41230 precursors and 413491 fragments ===
1 day, 1:11:04.021157 INFO: performing precursor FDR with 47 features
1 day, 1:11:04.021221 INFO: Decoy channel: -1
1 day, 1:11:04.021246 INFO: Competetive: True
1 day, 1:11:04.042859 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:11:04.050958 WARNING: dropped 4 target PSMs due to missing features
1 day, 1:11:04.051078 WARNING: dropped 4 decoy PSMs due to missing features
1 day, 1:11:04.558204 INFO: Test AUC: 0.545
1 day, 1:11:04.558330 INFO: Train AUC: 0.557
1 day, 1:11:04.558362 INFO: AUC difference: 2.15%
1 day, 1:11:04.647245 INFO: Resetting torch num_threads to 100
1 day, 1:11:04.649602 INFO: === FDR correction performed with classifier version -1 ===
1 day, 1:11:04.652821 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:11:04.652979 PROGRESS: Total precursors accumulated: 21,126
1 day, 1:11:04.653060 PROGRESS: Target precursors: 12,187 (57.69%)
1 day, 1:11:04.653119 PROGRESS: Decoy precursors: 8,939 (42.31%)
1 day, 1:11:04.653169 PROGRESS: 
1 day, 1:11:04.653218 PROGRESS: Precursor Summary:
1 day, 1:11:04.654262 PROGRESS: Channel   0:	 0.05 FDR:   137; 0.01 FDR:    49; 0.001 FDR:    49
1 day, 1:11:04.654356 PROGRESS: 
1 day, 1:11:04.654413 PROGRESS: Protein Summary:
1 day, 1:11:04.655504 PROGRESS: Channel   0:	 0.05 FDR:   135; 0.01 FDR:    48; 0.001 FDR:    48
1 day, 1:11:04.655596 PROGRESS: =========================================================================
1 day, 1:11:04.859193 INFO: Starting optimization step 2.
1 day, 1:11:04.859458 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1 day, 1:11:04.859540 PROGRESS: Extracting batch of 63016 precursors
1 day, 1:11:04.875033 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:11:04.875157 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:11:04.875195 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 1:11:04.875217 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 1:11:04.876609 INFO: Starting candidate selection
1 day, 1:16:06.751732 INFO: Starting candidate scoring
1 day, 1:16:09.784554 INFO: Finished candidate processing
1 day, 1:16:09.784730 INFO: Collecting candidate features
1 day, 1:16:09.912221 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 55032)
1 day, 1:16:09.917479 INFO: Collecting fragment features
1 day, 1:16:09.960748 INFO: Finished candidate scoring
1 day, 1:16:10.048288 PROGRESS: === Extracted 96262 precursors and 964952 fragments ===
1 day, 1:16:10.061786 INFO: performing precursor FDR with 47 features
1 day, 1:16:10.061915 INFO: Decoy channel: -1
1 day, 1:16:10.061947 INFO: Competetive: True
1 day, 1:16:10.112270 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:16:10.136748 WARNING: dropped 6 target PSMs due to missing features
1 day, 1:16:10.136879 WARNING: dropped 5 decoy PSMs due to missing features
1 day, 1:16:11.819061 INFO: Test AUC: 0.561
1 day, 1:16:11.819195 INFO: Train AUC: 0.576
1 day, 1:16:11.819227 INFO: AUC difference: 2.48%
1 day, 1:16:11.911075 INFO: Resetting torch num_threads to 100
1 day, 1:16:11.917570 INFO: === FDR correction performed with classifier version -1 ===
1 day, 1:16:11.927685 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:16:11.927978 PROGRESS: Total precursors accumulated: 49,371
1 day, 1:16:11.928044 PROGRESS: Target precursors: 29,448 (59.65%)
1 day, 1:16:11.928096 PROGRESS: Decoy precursors: 19,923 (40.35%)
1 day, 1:16:11.928147 PROGRESS: 
1 day, 1:16:11.928195 PROGRESS: Precursor Summary:
1 day, 1:16:11.929598 PROGRESS: Channel   0:	 0.05 FDR:   500; 0.01 FDR:   355; 0.001 FDR:   264
1 day, 1:16:11.929701 PROGRESS: 
1 day, 1:16:11.929760 PROGRESS: Protein Summary:
1 day, 1:16:11.931180 PROGRESS: Channel   0:	 0.05 FDR:   465; 0.01 FDR:   330; 0.001 FDR:   249
1 day, 1:16:11.931276 PROGRESS: =========================================================================
1 day, 1:16:11.945161 INFO: fragments_df_filtered: 3185
1 day, 1:16:12.170446 INFO: calibration group: precursor, fitting mz estimator 
1 day, 1:16:12.211876 INFO: calibration group: precursor, fitting rt estimator 
1 day, 1:16:12.254721 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 1:16:12.297554 INFO: calibration group: fragment, fitting mz estimator 
1 day, 1:16:12.463502 INFO: calibration group: precursor, predicting mz
1 day, 1:16:12.479199 INFO: calibration group: precursor, predicting rt
1 day, 1:16:12.545442 INFO: calibration group: precursor, predicting mobility
1 day, 1:16:12.561480 INFO: calibration group: fragment, predicting mz
1 day, 1:16:12.700697 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 1:16:12.701000 INFO: Starting optimization step 3.
1 day, 1:16:12.701091 PROGRESS: === Extracting elution groups 0 to 56000 ===
1 day, 1:16:12.701165 PROGRESS: Extracting batch of 110321 precursors
1 day, 1:16:12.733293 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:16:12.733426 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:16:12.733476 INFO: FWHM in RT is 3.37 seconds, sigma is 0.74
1 day, 1:16:12.733500 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.08
1 day, 1:16:12.742331 INFO: Starting candidate selection
1 day, 1:25:03.302301 INFO: Starting candidate scoring
1 day, 1:25:13.695481 INFO: Finished candidate processing
1 day, 1:25:13.696210 INFO: Collecting candidate features
1 day, 1:25:14.056127 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 189241)
1 day, 1:25:14.066494 INFO: Collecting fragment features
1 day, 1:25:14.197193 INFO: Finished candidate scoring
1 day, 1:25:14.411733 PROGRESS: === Extracted 189241 precursors and 1927635 fragments ===
1 day, 1:25:14.412343 INFO: performing precursor FDR with 47 features
1 day, 1:25:14.412384 INFO: Decoy channel: -1
1 day, 1:25:14.412408 INFO: Competetive: True
1 day, 1:25:14.483477 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:25:14.516521 WARNING: dropped 1 target PSMs due to missing features
1 day, 1:25:18.521345 INFO: Test AUC: 0.567
1 day, 1:25:18.521500 INFO: Train AUC: 0.586
1 day, 1:25:18.521534 INFO: AUC difference: 3.16%
1 day, 1:25:18.623981 INFO: Resetting torch num_threads to 100
1 day, 1:25:18.630870 INFO: === FDR correction performed with classifier version 2 ===
1 day, 1:25:18.640921 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:25:18.641282 PROGRESS: Total precursors accumulated: 50,242
1 day, 1:25:18.641349 PROGRESS: Target precursors: 31,520 (62.74%)
1 day, 1:25:18.641404 PROGRESS: Decoy precursors: 18,722 (37.26%)
1 day, 1:25:18.641455 PROGRESS: 
1 day, 1:25:18.641504 PROGRESS: Precursor Summary:
1 day, 1:25:18.642982 PROGRESS: Channel   0:	 0.05 FDR:   646; 0.01 FDR:   354; 0.001 FDR:   323
1 day, 1:25:18.643082 PROGRESS: 
1 day, 1:25:18.643139 PROGRESS: Protein Summary:
1 day, 1:25:18.644686 PROGRESS: Channel   0:	 0.05 FDR:   601; 0.01 FDR:   327; 0.001 FDR:   297
1 day, 1:25:18.644782 PROGRESS: =========================================================================
1 day, 1:25:18.660375 INFO: fragments_df_filtered: 4450
1 day, 1:25:19.192606 INFO: calibration group: precursor, fitting mz estimator 
1 day, 1:25:19.241823 INFO: calibration group: precursor, fitting rt estimator 
1 day, 1:25:19.280786 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 1:25:19.320564 INFO: calibration group: fragment, fitting mz estimator 
1 day, 1:25:19.608270 INFO: calibration group: precursor, predicting mz
1 day, 1:25:19.624424 INFO: calibration group: precursor, predicting rt
1 day, 1:25:19.691678 INFO: calibration group: precursor, predicting mobility
1 day, 1:25:19.708488 INFO: calibration group: fragment, predicting mz
1 day, 1:25:19.841377 INFO: === checking if optimization conditions were reached ===
1 day, 1:25:19.843596 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 1:25:19.844568 PROGRESS: ❌ ms1_error      : 10.0000 > 10.0000 or insufficient steps taken.
1 day, 1:25:19.844617 INFO: ==============================================
1 day, 1:25:19.844723 INFO: Starting optimization step 4.
1 day, 1:25:19.844795 PROGRESS: === Extracting elution groups 0 to 56000 ===
1 day, 1:25:19.844868 PROGRESS: Extracting batch of 110321 precursors
1 day, 1:25:19.876734 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:25:19.876877 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:25:19.876940 INFO: FWHM in RT is 3.18 seconds, sigma is 0.70
1 day, 1:25:19.876968 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.01
1 day, 1:25:19.885641 INFO: Starting candidate selection
1 day, 1:33:34.153246 INFO: Starting candidate scoring
1 day, 1:33:39.644168 INFO: Finished candidate processing
1 day, 1:33:39.644355 INFO: Collecting candidate features
1 day, 1:33:39.986919 WARNING: intensity_correlation has 11 NaNs ( 0.01 % out of 189057)
1 day, 1:33:39.987333 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 189057)
1 day, 1:33:39.997160 INFO: Collecting fragment features
1 day, 1:33:40.118677 INFO: Finished candidate scoring
1 day, 1:33:40.204024 PROGRESS: === Extracted 189057 precursors and 1857654 fragments ===
1 day, 1:33:40.204968 INFO: performing precursor FDR with 47 features
1 day, 1:33:40.205011 INFO: Decoy channel: -1
1 day, 1:33:40.205088 INFO: Competetive: True
1 day, 1:33:40.275669 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:33:40.312258 WARNING: dropped 7 target PSMs due to missing features
1 day, 1:33:40.312403 WARNING: dropped 5 decoy PSMs due to missing features
1 day, 1:33:43.777351 INFO: Test AUC: 0.558
1 day, 1:33:43.777491 INFO: Train AUC: 0.587
1 day, 1:33:43.777521 INFO: AUC difference: 4.95%
1 day, 1:33:43.874303 INFO: Resetting torch num_threads to 100
1 day, 1:33:43.880453 INFO: === FDR correction performed with classifier version 3 ===
1 day, 1:33:43.889597 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:33:43.889904 PROGRESS: Total precursors accumulated: 50,230
1 day, 1:33:43.889969 PROGRESS: Target precursors: 30,931 (61.58%)
1 day, 1:33:43.890021 PROGRESS: Decoy precursors: 19,299 (38.42%)
1 day, 1:33:43.890071 PROGRESS: 
1 day, 1:33:43.890117 PROGRESS: Precursor Summary:
1 day, 1:33:43.891645 PROGRESS: Channel   0:	 0.05 FDR:   908; 0.01 FDR:   688; 0.001 FDR:   375
1 day, 1:33:43.891743 PROGRESS: 
1 day, 1:33:43.891801 PROGRESS: Protein Summary:
1 day, 1:33:43.893396 PROGRESS: Channel   0:	 0.05 FDR:   833; 0.01 FDR:   624; 0.001 FDR:   346
1 day, 1:33:43.893495 PROGRESS: =========================================================================
1 day, 1:33:43.909707 INFO: fragments_df_filtered: 5000
1 day, 1:33:44.090229 INFO: calibration group: precursor, fitting mz estimator 
1 day, 1:33:44.148200 INFO: calibration group: precursor, fitting rt estimator 
1 day, 1:33:44.195070 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 1:33:44.238852 INFO: calibration group: fragment, fitting mz estimator 
1 day, 1:33:44.586013 INFO: calibration group: precursor, predicting mz
1 day, 1:33:44.593305 INFO: calibration group: precursor, predicting rt
1 day, 1:33:44.621791 INFO: calibration group: precursor, predicting mobility
1 day, 1:33:44.628364 INFO: calibration group: fragment, predicting mz
1 day, 1:33:44.684305 INFO: === checking if optimization conditions were reached ===
1 day, 1:33:44.686734 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 1:33:44.687940 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
1 day, 1:33:44.687996 INFO: ==============================================
1 day, 1:33:44.688127 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 1:33:44.861186 INFO: calibration group: precursor, predicting mz
1 day, 1:33:44.868461 INFO: calibration group: precursor, predicting rt
1 day, 1:33:44.897036 INFO: calibration group: precursor, predicting mobility
1 day, 1:33:44.903609 INFO: calibration group: fragment, predicting mz
1 day, 1:33:44.955577 INFO: Starting optimization step 0.
1 day, 1:33:44.955865 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 1:33:44.955988 PROGRESS: Extracting batch of 47305 precursors
1 day, 1:33:44.974459 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:33:44.974605 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:33:44.974684 INFO: FWHM in RT is 2.99 seconds, sigma is 0.66
1 day, 1:33:44.974715 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.19
1 day, 1:33:44.983655 INFO: Starting candidate selection
1 day, 1:37:19.996823 INFO: Starting candidate scoring
1 day, 1:37:22.597631 INFO: Finished candidate processing
1 day, 1:37:22.597804 INFO: Collecting candidate features
1 day, 1:37:22.756747 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 81003)
1 day, 1:37:22.763893 INFO: Collecting fragment features
1 day, 1:37:22.817103 INFO: Finished candidate scoring
1 day, 1:37:22.855478 PROGRESS: === Extracted 81003 precursors and 794739 fragments ===
1 day, 1:37:22.855950 INFO: performing precursor FDR with 47 features
1 day, 1:37:22.855989 INFO: Decoy channel: -1
1 day, 1:37:22.856013 INFO: Competetive: True
1 day, 1:37:22.884290 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:37:22.900390 WARNING: dropped 2 target PSMs due to missing features
1 day, 1:37:22.900533 WARNING: dropped 2 decoy PSMs due to missing features
1 day, 1:37:24.158684 INFO: Test AUC: 0.564
1 day, 1:37:24.158820 INFO: Train AUC: 0.607
1 day, 1:37:24.158850 INFO: AUC difference: 7.12%
1 day, 1:37:24.158873 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 1:37:24.247398 INFO: Resetting torch num_threads to 100
1 day, 1:37:24.250448 INFO: === FDR correction performed with classifier version 4 ===
1 day, 1:37:24.254225 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:37:24.254376 PROGRESS: Total precursors accumulated: 21,511
1 day, 1:37:24.254441 PROGRESS: Target precursors: 13,642 (63.42%)
1 day, 1:37:24.254493 PROGRESS: Decoy precursors: 7,869 (36.58%)
1 day, 1:37:24.254542 PROGRESS: 
1 day, 1:37:24.254589 PROGRESS: Precursor Summary:
1 day, 1:37:24.255694 PROGRESS: Channel   0:	 0.05 FDR:   427; 0.01 FDR:   326; 0.001 FDR:   163
1 day, 1:37:24.255790 PROGRESS: 
1 day, 1:37:24.255848 PROGRESS: Protein Summary:
1 day, 1:37:24.257100 PROGRESS: Channel   0:	 0.05 FDR:   411; 0.01 FDR:   311; 0.001 FDR:   159
1 day, 1:37:24.257200 PROGRESS: =========================================================================
1 day, 1:37:24.290535 INFO: fragments_df_filtered: 3406
1 day, 1:37:24.460176 INFO: calibration group: precursor, fitting mz estimator 
1 day, 1:37:24.500651 INFO: calibration group: precursor, fitting rt estimator 
1 day, 1:37:24.538359 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 1:37:24.577261 INFO: calibration group: fragment, fitting mz estimator 
1 day, 1:37:24.760518 INFO: calibration group: precursor, predicting mz
1 day, 1:37:24.767700 INFO: calibration group: precursor, predicting rt
1 day, 1:37:24.797010 INFO: calibration group: precursor, predicting mobility
1 day, 1:37:24.803641 INFO: calibration group: fragment, predicting mz
1 day, 1:37:24.856565 INFO: === checking if optimization conditions were reached ===
1 day, 1:37:24.856858 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 1:37:24.858745 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 823.9262.
1 day, 1:37:24.858803 INFO: ==============================================
1 day, 1:37:24.858903 INFO: Starting optimization step 1.
1 day, 1:37:24.858974 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 1:37:24.859046 PROGRESS: Extracting batch of 47305 precursors
1 day, 1:37:24.872496 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:37:24.872621 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:37:24.872670 INFO: FWHM in RT is 3.00 seconds, sigma is 0.66
1 day, 1:37:24.872693 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.20
1 day, 1:37:24.881506 INFO: Starting candidate selection
1 day, 1:39:05.830101 INFO: Starting candidate scoring
1 day, 1:39:08.305823 INFO: Finished candidate processing
1 day, 1:39:08.305939 INFO: Collecting candidate features
1 day, 1:39:08.443850 WARNING: intensity_correlation has 23 NaNs ( 0.03 % out of 79822)
1 day, 1:39:08.444177 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 79822)
1 day, 1:39:08.450417 INFO: Collecting fragment features
1 day, 1:39:08.507312 INFO: Finished candidate scoring
1 day, 1:39:08.549477 PROGRESS: === Extracted 79822 precursors and 774234 fragments ===
1 day, 1:39:08.549973 INFO: performing precursor FDR with 47 features
1 day, 1:39:08.550012 INFO: Decoy channel: -1
1 day, 1:39:08.550037 INFO: Competetive: True
1 day, 1:39:08.582925 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:39:08.602288 WARNING: dropped 8 target PSMs due to missing features
1 day, 1:39:08.602420 WARNING: dropped 15 decoy PSMs due to missing features
1 day, 1:39:10.170279 INFO: Test AUC: 0.556
1 day, 1:39:10.170410 INFO: Train AUC: 0.597
1 day, 1:39:10.170440 INFO: AUC difference: 7.01%
1 day, 1:39:10.170461 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 1:39:10.261607 INFO: Resetting torch num_threads to 100
1 day, 1:39:10.264898 INFO: === FDR correction performed with classifier version 4 ===
1 day, 1:39:10.268979 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:39:10.269136 PROGRESS: Total precursors accumulated: 21,339
1 day, 1:39:10.269202 PROGRESS: Target precursors: 13,320 (62.42%)
1 day, 1:39:10.269255 PROGRESS: Decoy precursors: 8,019 (37.58%)
1 day, 1:39:10.269302 PROGRESS: 
1 day, 1:39:10.269347 PROGRESS: Precursor Summary:
1 day, 1:39:10.270525 PROGRESS: Channel   0:	 0.05 FDR:   445; 0.01 FDR:   346; 0.001 FDR:   241
1 day, 1:39:10.270618 PROGRESS: 
1 day, 1:39:10.270677 PROGRESS: Protein Summary:
1 day, 1:39:10.271970 PROGRESS: Channel   0:	 0.05 FDR:   427; 0.01 FDR:   330; 0.001 FDR:   233
1 day, 1:39:10.272061 PROGRESS: =========================================================================
1 day, 1:39:10.279824 INFO: fragments_df_filtered: 3533
1 day, 1:39:10.476846 INFO: calibration group: precursor, fitting mz estimator 
1 day, 1:39:10.525686 INFO: calibration group: precursor, fitting rt estimator 
1 day, 1:39:11.534267 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 1:39:11.582042 INFO: calibration group: fragment, fitting mz estimator 
1 day, 1:39:11.845605 INFO: calibration group: precursor, predicting mz
1 day, 1:39:11.853485 INFO: calibration group: precursor, predicting rt
1 day, 1:39:11.882806 INFO: calibration group: precursor, predicting mobility
1 day, 1:39:11.889495 INFO: calibration group: fragment, predicting mz
1 day, 1:39:11.945710 INFO: === checking if optimization conditions were reached ===
1 day, 1:39:11.946018 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 1:39:11.948567 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 518.1030.
1 day, 1:39:11.948629 INFO: ==============================================
1 day, 1:39:11.948751 INFO: Starting optimization step 2.
1 day, 1:39:11.948828 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 1:39:11.948900 PROGRESS: Extracting batch of 47305 precursors
1 day, 1:39:11.967072 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:39:11.967190 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:39:11.967240 INFO: FWHM in RT is 2.98 seconds, sigma is 0.65
1 day, 1:39:11.967263 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.14
1 day, 1:39:11.976152 INFO: Starting candidate selection
1 day, 1:40:06.666094 INFO: Starting candidate scoring
1 day, 1:40:09.163707 INFO: Finished candidate processing
1 day, 1:40:09.163819 INFO: Collecting candidate features
1 day, 1:40:09.301202 WARNING: intensity_correlation has 24 NaNs ( 0.03 % out of 78716)
1 day, 1:40:09.301554 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 78716)
1 day, 1:40:09.309216 INFO: Collecting fragment features
1 day, 1:40:09.365187 INFO: Finished candidate scoring
1 day, 1:40:09.401996 PROGRESS: === Extracted 78716 precursors and 757897 fragments ===
1 day, 1:40:09.402479 INFO: performing precursor FDR with 47 features
1 day, 1:40:09.402541 INFO: Decoy channel: -1
1 day, 1:40:09.402566 INFO: Competetive: True
1 day, 1:40:09.432089 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:40:09.448872 WARNING: dropped 12 target PSMs due to missing features
1 day, 1:40:09.448999 WARNING: dropped 12 decoy PSMs due to missing features
1 day, 1:40:10.728510 INFO: Test AUC: 0.558
1 day, 1:40:10.728653 INFO: Train AUC: 0.597
1 day, 1:40:10.728686 INFO: AUC difference: 6.52%
1 day, 1:40:10.728710 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 1:40:10.819145 INFO: Resetting torch num_threads to 100
1 day, 1:40:10.822254 INFO: === FDR correction performed with classifier version 4 ===
1 day, 1:40:10.826014 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:40:10.826173 PROGRESS: Total precursors accumulated: 21,121
1 day, 1:40:10.826237 PROGRESS: Target precursors: 13,097 (62.01%)
1 day, 1:40:10.826291 PROGRESS: Decoy precursors: 8,024 (37.99%)
1 day, 1:40:10.826340 PROGRESS: 
1 day, 1:40:10.826389 PROGRESS: Precursor Summary:
1 day, 1:40:10.827579 PROGRESS: Channel   0:	 0.05 FDR:   519; 0.01 FDR:   332; 0.001 FDR:   253
1 day, 1:40:10.827686 PROGRESS: 
1 day, 1:40:10.827744 PROGRESS: Protein Summary:
1 day, 1:40:10.829042 PROGRESS: Channel   0:	 0.05 FDR:   497; 0.01 FDR:   317; 0.001 FDR:   244
1 day, 1:40:10.829148 PROGRESS: =========================================================================
1 day, 1:40:10.836324 INFO: fragments_df_filtered: 3442
1 day, 1:40:11.008335 INFO: calibration group: precursor, fitting mz estimator 
1 day, 1:40:11.054695 INFO: calibration group: precursor, fitting rt estimator 
1 day, 1:40:11.104813 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 1:40:11.153085 INFO: calibration group: fragment, fitting mz estimator 
1 day, 1:40:11.340294 INFO: calibration group: precursor, predicting mz
1 day, 1:40:11.347751 INFO: calibration group: precursor, predicting rt
1 day, 1:40:11.376126 INFO: calibration group: precursor, predicting mobility
1 day, 1:40:11.382888 INFO: calibration group: fragment, predicting mz
1 day, 1:40:11.437297 INFO: === checking if optimization conditions were reached ===
1 day, 1:40:11.437581 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 1:40:11.439683 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 380.0282.
1 day, 1:40:11.439736 INFO: ==============================================
1 day, 1:40:11.439835 INFO: Starting optimization step 3.
1 day, 1:40:11.439909 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 1:40:11.439982 PROGRESS: Extracting batch of 47305 precursors
1 day, 1:40:11.452848 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:40:11.452967 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:40:11.453060 INFO: FWHM in RT is 3.02 seconds, sigma is 0.66
1 day, 1:40:11.453098 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.14
1 day, 1:40:11.461987 INFO: Starting candidate selection
1 day, 1:40:51.935110 INFO: Starting candidate scoring
1 day, 1:40:54.323905 INFO: Finished candidate processing
1 day, 1:40:54.324095 INFO: Collecting candidate features
1 day, 1:40:54.495410 WARNING: intensity_correlation has 37 NaNs ( 0.05 % out of 78382)
1 day, 1:40:54.495765 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 78382)
1 day, 1:40:54.502121 INFO: Collecting fragment features
1 day, 1:40:54.577720 INFO: Finished candidate scoring
1 day, 1:40:54.620772 PROGRESS: === Extracted 78382 precursors and 750977 fragments ===
1 day, 1:40:54.621476 INFO: performing precursor FDR with 47 features
1 day, 1:40:54.621517 INFO: Decoy channel: -1
1 day, 1:40:54.621543 INFO: Competetive: True
1 day, 1:40:54.663862 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:40:54.682584 WARNING: dropped 18 target PSMs due to missing features
1 day, 1:40:54.682727 WARNING: dropped 20 decoy PSMs due to missing features
1 day, 1:40:56.185932 INFO: Test AUC: 0.551
1 day, 1:40:56.186089 INFO: Train AUC: 0.592
1 day, 1:40:56.186121 INFO: AUC difference: 7.02%
1 day, 1:40:56.186143 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 1:40:56.282261 INFO: Resetting torch num_threads to 100
1 day, 1:40:56.285672 INFO: === FDR correction performed with classifier version 4 ===
1 day, 1:40:56.290038 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:40:56.290195 PROGRESS: Total precursors accumulated: 21,086
1 day, 1:40:56.290271 PROGRESS: Target precursors: 12,775 (60.59%)
1 day, 1:40:56.290326 PROGRESS: Decoy precursors: 8,311 (39.41%)
1 day, 1:40:56.290374 PROGRESS: 
1 day, 1:40:56.290418 PROGRESS: Precursor Summary:
1 day, 1:40:56.291607 PROGRESS: Channel   0:	 0.05 FDR:   456; 0.01 FDR:   333; 0.001 FDR:     0
1 day, 1:40:56.291707 PROGRESS: 
1 day, 1:40:56.291765 PROGRESS: Protein Summary:
1 day, 1:40:56.293066 PROGRESS: Channel   0:	 0.05 FDR:   435; 0.01 FDR:   318; 0.001 FDR:     0
1 day, 1:40:56.293164 PROGRESS: =========================================================================
1 day, 1:40:56.300754 INFO: fragments_df_filtered: 3473
1 day, 1:40:56.811049 INFO: calibration group: precursor, fitting mz estimator 
1 day, 1:40:56.859920 INFO: calibration group: precursor, fitting rt estimator 
1 day, 1:40:56.913254 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 1:40:56.964430 INFO: calibration group: fragment, fitting mz estimator 
1 day, 1:40:57.223657 INFO: calibration group: precursor, predicting mz
1 day, 1:40:57.231162 INFO: calibration group: precursor, predicting rt
1 day, 1:40:57.259646 INFO: calibration group: precursor, predicting mobility
1 day, 1:40:57.266443 INFO: calibration group: fragment, predicting mz
1 day, 1:40:57.322632 INFO: === checking if optimization conditions were reached ===
1 day, 1:40:57.322932 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 1:40:57.325479 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 337.2455.
1 day, 1:40:57.325536 INFO: ==============================================
1 day, 1:40:57.325649 INFO: Starting optimization step 4.
1 day, 1:40:57.325734 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 1:40:57.325824 PROGRESS: Extracting batch of 47305 precursors
1 day, 1:40:57.340997 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:40:57.341140 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:40:57.341217 INFO: FWHM in RT is 3.04 seconds, sigma is 0.67
1 day, 1:40:57.341245 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.13
1 day, 1:40:57.350380 INFO: Starting candidate selection
1 day, 1:41:33.021588 INFO: Starting candidate scoring
1 day, 1:41:35.484071 INFO: Finished candidate processing
1 day, 1:41:35.484281 INFO: Collecting candidate features
1 day, 1:41:35.636871 WARNING: intensity_correlation has 36 NaNs ( 0.05 % out of 78146)
1 day, 1:41:35.637205 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 78146)
1 day, 1:41:35.643285 INFO: Collecting fragment features
1 day, 1:41:35.698951 INFO: Finished candidate scoring
1 day, 1:41:35.735062 PROGRESS: === Extracted 78146 precursors and 746871 fragments ===
1 day, 1:41:35.735571 INFO: performing precursor FDR with 47 features
1 day, 1:41:35.735611 INFO: Decoy channel: -1
1 day, 1:41:35.735636 INFO: Competetive: True
1 day, 1:41:35.764736 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:41:35.781274 WARNING: dropped 21 target PSMs due to missing features
1 day, 1:41:35.781415 WARNING: dropped 17 decoy PSMs due to missing features
1 day, 1:41:37.189786 INFO: Test AUC: 0.546
1 day, 1:41:37.189925 INFO: Train AUC: 0.585
1 day, 1:41:37.189956 INFO: AUC difference: 6.67%
1 day, 1:41:37.189977 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 1:41:37.282233 INFO: Resetting torch num_threads to 100
1 day, 1:41:37.285403 INFO: === FDR correction performed with classifier version 4 ===
1 day, 1:41:37.289644 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:41:37.289803 PROGRESS: Total precursors accumulated: 21,043
1 day, 1:41:37.289868 PROGRESS: Target precursors: 12,762 (60.65%)
1 day, 1:41:37.289920 PROGRESS: Decoy precursors: 8,281 (39.35%)
1 day, 1:41:37.289969 PROGRESS: 
1 day, 1:41:37.290015 PROGRESS: Precursor Summary:
1 day, 1:41:37.291197 PROGRESS: Channel   0:	 0.05 FDR:   486; 0.01 FDR:   366; 0.001 FDR:   319
1 day, 1:41:37.291293 PROGRESS: 
1 day, 1:41:37.291348 PROGRESS: Protein Summary:
1 day, 1:41:37.292636 PROGRESS: Channel   0:	 0.05 FDR:   468; 0.01 FDR:   351; 0.001 FDR:   306
1 day, 1:41:37.292739 PROGRESS: =========================================================================
1 day, 1:41:37.300652 INFO: fragments_df_filtered: 3645
1 day, 1:41:37.491972 INFO: calibration group: precursor, fitting mz estimator 
1 day, 1:41:37.532896 INFO: calibration group: precursor, fitting rt estimator 
1 day, 1:41:37.575968 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 1:41:37.615410 INFO: calibration group: fragment, fitting mz estimator 
1 day, 1:41:37.818109 INFO: calibration group: precursor, predicting mz
1 day, 1:41:37.825316 INFO: calibration group: precursor, predicting rt
1 day, 1:41:37.853242 INFO: calibration group: precursor, predicting mobility
1 day, 1:41:37.859874 INFO: calibration group: fragment, predicting mz
1 day, 1:41:37.914095 INFO: === checking if optimization conditions were reached ===
1 day, 1:41:37.914408 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 1:41:37.916882 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 347.5745.
1 day, 1:41:37.916946 INFO: ==============================================
1 day, 1:41:37.917070 INFO: Starting optimization step 5.
1 day, 1:41:37.917156 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 1:41:37.917243 PROGRESS: Extracting batch of 47305 precursors
1 day, 1:41:37.935293 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:41:37.935429 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:41:37.935489 INFO: FWHM in RT is 3.02 seconds, sigma is 0.66
1 day, 1:41:37.935527 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.04
1 day, 1:41:37.944500 INFO: Starting candidate selection
1 day, 1:42:13.178677 INFO: Starting candidate scoring
1 day, 1:42:15.596127 INFO: Finished candidate processing
1 day, 1:42:15.596302 INFO: Collecting candidate features
1 day, 1:42:15.758022 WARNING: intensity_correlation has 40 NaNs ( 0.05 % out of 78164)
1 day, 1:42:15.758339 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 78164)
1 day, 1:42:15.764664 INFO: Collecting fragment features
1 day, 1:42:15.821599 INFO: Finished candidate scoring
1 day, 1:42:15.858211 PROGRESS: === Extracted 78164 precursors and 746669 fragments ===
1 day, 1:42:15.858696 INFO: performing precursor FDR with 47 features
1 day, 1:42:15.858750 INFO: Decoy channel: -1
1 day, 1:42:15.858778 INFO: Competetive: True
1 day, 1:42:15.891990 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:42:15.909466 WARNING: dropped 26 target PSMs due to missing features
1 day, 1:42:15.909604 WARNING: dropped 16 decoy PSMs due to missing features
1 day, 1:42:17.316033 INFO: Test AUC: 0.548
1 day, 1:42:17.316173 INFO: Train AUC: 0.595
1 day, 1:42:17.316204 INFO: AUC difference: 7.96%
1 day, 1:42:17.316225 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 1:42:17.407295 INFO: Resetting torch num_threads to 100
1 day, 1:42:17.410278 INFO: === FDR correction performed with classifier version 4 ===
1 day, 1:42:17.414194 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:42:17.414340 PROGRESS: Total precursors accumulated: 21,050
1 day, 1:42:17.414405 PROGRESS: Target precursors: 12,900 (61.28%)
1 day, 1:42:17.414458 PROGRESS: Decoy precursors: 8,150 (38.72%)
1 day, 1:42:17.414507 PROGRESS: 
1 day, 1:42:17.414554 PROGRESS: Precursor Summary:
1 day, 1:42:17.415739 PROGRESS: Channel   0:	 0.05 FDR:   448; 0.01 FDR:   349; 0.001 FDR:   271
1 day, 1:42:17.415849 PROGRESS: 
1 day, 1:42:17.415906 PROGRESS: Protein Summary:
1 day, 1:42:17.417207 PROGRESS: Channel   0:	 0.05 FDR:   430; 0.01 FDR:   334; 0.001 FDR:   261
1 day, 1:42:17.417300 PROGRESS: =========================================================================
1 day, 1:42:17.425318 INFO: fragments_df_filtered: 3572
1 day, 1:42:17.597734 INFO: calibration group: precursor, fitting mz estimator 
1 day, 1:42:17.645982 INFO: calibration group: precursor, fitting rt estimator 
1 day, 1:42:17.698230 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 1:42:17.747763 INFO: calibration group: fragment, fitting mz estimator 
1 day, 1:42:18.014642 INFO: calibration group: precursor, predicting mz
1 day, 1:42:18.022253 INFO: calibration group: precursor, predicting rt
1 day, 1:42:18.050701 INFO: calibration group: precursor, predicting mobility
1 day, 1:42:18.057549 INFO: calibration group: fragment, predicting mz
1 day, 1:42:18.111580 INFO: === checking if optimization conditions were reached ===
1 day, 1:42:18.111893 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 1:42:18.113412 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 337.2455 found after 6 searches.
1 day, 1:42:18.113474 INFO: ==============================================
1 day, 1:42:18.113596 PROGRESS: Optimization finished for rt_error.
1 day, 1:42:18.278795 INFO: calibration group: precursor, predicting mz
1 day, 1:42:18.286644 INFO: calibration group: precursor, predicting rt
1 day, 1:42:18.315283 INFO: calibration group: precursor, predicting mobility
1 day, 1:42:18.322077 INFO: calibration group: fragment, predicting mz
1 day, 1:42:18.402932 INFO: Starting optimization step 0.
1 day, 1:42:18.403171 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 1:42:18.403260 PROGRESS: Extracting batch of 47305 precursors
1 day, 1:42:18.416943 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:42:18.417060 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:42:18.417121 INFO: FWHM in RT is 3.02 seconds, sigma is 0.66
1 day, 1:42:18.417152 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.04
1 day, 1:42:18.425946 INFO: Starting candidate selection
1 day, 1:42:54.860210 INFO: Starting candidate scoring
1 day, 1:42:57.324422 INFO: Finished candidate processing
1 day, 1:42:57.324527 INFO: Collecting candidate features
1 day, 1:42:57.481662 WARNING: intensity_correlation has 37 NaNs ( 0.05 % out of 78150)
1 day, 1:42:57.482189 WARNING: height_correlation has 4 NaNs ( 0.01 % out of 78150)
1 day, 1:42:57.495326 INFO: Collecting fragment features
1 day, 1:42:57.550916 INFO: Finished candidate scoring
1 day, 1:42:57.590486 PROGRESS: === Extracted 78150 precursors and 746286 fragments ===
1 day, 1:42:57.590968 INFO: performing precursor FDR with 47 features
1 day, 1:42:57.591006 INFO: Decoy channel: -1
1 day, 1:42:57.591028 INFO: Competetive: True
1 day, 1:42:57.616777 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:42:57.631756 WARNING: dropped 22 target PSMs due to missing features
1 day, 1:42:57.631884 WARNING: dropped 16 decoy PSMs due to missing features
1 day, 1:42:58.826119 INFO: Test AUC: 0.572
1 day, 1:42:58.826243 INFO: Train AUC: 0.611
1 day, 1:42:58.826272 INFO: AUC difference: 6.36%
1 day, 1:42:58.826293 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 1:42:58.917226 INFO: Resetting torch num_threads to 100
1 day, 1:42:58.919756 INFO: === FDR correction performed with classifier version 9 ===
1 day, 1:42:58.923318 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:42:58.923457 PROGRESS: Total precursors accumulated: 21,046
1 day, 1:42:58.923536 PROGRESS: Target precursors: 13,390 (63.62%)
1 day, 1:42:58.923589 PROGRESS: Decoy precursors: 7,656 (36.38%)
1 day, 1:42:58.923635 PROGRESS: 
1 day, 1:42:58.923679 PROGRESS: Precursor Summary:
1 day, 1:42:58.924828 PROGRESS: Channel   0:	 0.05 FDR:   520; 0.01 FDR:   319; 0.001 FDR:   284
1 day, 1:42:58.924925 PROGRESS: 
1 day, 1:42:58.924985 PROGRESS: Protein Summary:
1 day, 1:42:58.926300 PROGRESS: Channel   0:	 0.05 FDR:   499; 0.01 FDR:   305; 0.001 FDR:   273
1 day, 1:42:58.926394 PROGRESS: =========================================================================
1 day, 1:42:58.933696 INFO: fragments_df_filtered: 3310
1 day, 1:42:59.101474 INFO: calibration group: precursor, fitting mz estimator 
1 day, 1:42:59.152798 INFO: calibration group: precursor, fitting rt estimator 
1 day, 1:42:59.194051 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 1:42:59.231876 INFO: calibration group: fragment, fitting mz estimator 
1 day, 1:42:59.409806 INFO: calibration group: precursor, predicting mz
1 day, 1:42:59.417966 INFO: calibration group: precursor, predicting rt
1 day, 1:42:59.446440 INFO: calibration group: precursor, predicting mobility
1 day, 1:42:59.453419 INFO: calibration group: fragment, predicting mz
1 day, 1:42:59.509118 INFO: === checking if optimization conditions were reached ===
1 day, 1:42:59.509450 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 1:42:59.511424 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0869.
1 day, 1:42:59.511479 INFO: ==============================================
1 day, 1:42:59.511588 INFO: Starting optimization step 1.
1 day, 1:42:59.511675 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 1:42:59.511771 PROGRESS: Extracting batch of 47305 precursors
1 day, 1:42:59.527876 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:42:59.528005 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:42:59.528080 INFO: FWHM in RT is 3.07 seconds, sigma is 0.67
1 day, 1:42:59.528107 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.21
1 day, 1:42:59.536977 INFO: Starting candidate selection
1 day, 1:43:29.491840 INFO: Starting candidate scoring
1 day, 1:43:31.891628 INFO: Finished candidate processing
1 day, 1:43:31.891798 INFO: Collecting candidate features
1 day, 1:43:32.045994 WARNING: intensity_correlation has 32 NaNs ( 0.04 % out of 77479)
1 day, 1:43:32.046315 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 77479)
1 day, 1:43:32.052404 INFO: Collecting fragment features
1 day, 1:43:32.102030 INFO: Finished candidate scoring
1 day, 1:43:32.146395 PROGRESS: === Extracted 77479 precursors and 738454 fragments ===
1 day, 1:43:32.146826 INFO: performing precursor FDR with 47 features
1 day, 1:43:32.146865 INFO: Decoy channel: -1
1 day, 1:43:32.146892 INFO: Competetive: True
1 day, 1:43:32.173994 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:43:32.188769 WARNING: dropped 20 target PSMs due to missing features
1 day, 1:43:32.188898 WARNING: dropped 14 decoy PSMs due to missing features
1 day, 1:43:33.412838 INFO: Test AUC: 0.562
1 day, 1:43:33.412961 INFO: Train AUC: 0.600
1 day, 1:43:33.412991 INFO: AUC difference: 6.27%
1 day, 1:43:33.413013 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 1:43:33.500075 INFO: Resetting torch num_threads to 100
1 day, 1:43:33.502806 INFO: === FDR correction performed with classifier version 9 ===
1 day, 1:43:33.506542 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:43:33.506696 PROGRESS: Total precursors accumulated: 20,899
1 day, 1:43:33.506772 PROGRESS: Target precursors: 13,080 (62.59%)
1 day, 1:43:33.506837 PROGRESS: Decoy precursors: 7,819 (37.41%)
1 day, 1:43:33.506898 PROGRESS: 
1 day, 1:43:33.506956 PROGRESS: Precursor Summary:
1 day, 1:43:33.508123 PROGRESS: Channel   0:	 0.05 FDR:   502; 0.01 FDR:   335; 0.001 FDR:   236
1 day, 1:43:33.508227 PROGRESS: 
1 day, 1:43:33.508294 PROGRESS: Protein Summary:
1 day, 1:43:33.509638 PROGRESS: Channel   0:	 0.05 FDR:   481; 0.01 FDR:   322; 0.001 FDR:   228
1 day, 1:43:33.509743 PROGRESS: =========================================================================
1 day, 1:43:33.516958 INFO: fragments_df_filtered: 3388
1 day, 1:43:33.684221 INFO: calibration group: precursor, fitting mz estimator 
1 day, 1:43:33.729421 INFO: calibration group: precursor, fitting rt estimator 
1 day, 1:43:33.781091 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 1:43:33.831329 INFO: calibration group: fragment, fitting mz estimator 
1 day, 1:43:34.080548 INFO: calibration group: precursor, predicting mz
1 day, 1:43:34.088078 INFO: calibration group: precursor, predicting rt
1 day, 1:43:34.116060 INFO: calibration group: precursor, predicting mobility
1 day, 1:43:34.122843 INFO: calibration group: fragment, predicting mz
1 day, 1:43:34.174574 INFO: === checking if optimization conditions were reached ===
1 day, 1:43:34.174867 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 1:43:34.176683 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0655.
1 day, 1:43:34.176743 INFO: ==============================================
1 day, 1:43:34.176855 INFO: Starting optimization step 2.
1 day, 1:43:34.176934 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 1:43:34.177018 PROGRESS: Extracting batch of 47305 precursors
1 day, 1:43:34.188480 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:43:34.188587 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:43:34.188648 INFO: FWHM in RT is 3.01 seconds, sigma is 0.66
1 day, 1:43:34.188679 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.15
1 day, 1:43:34.197422 INFO: Starting candidate selection
1 day, 1:43:56.939150 INFO: Starting candidate scoring
1 day, 1:43:59.301059 INFO: Finished candidate processing
1 day, 1:43:59.301192 INFO: Collecting candidate features
1 day, 1:43:59.479430 WARNING: intensity_correlation has 32 NaNs ( 0.04 % out of 75879)
1 day, 1:43:59.479734 WARNING: height_correlation has 9 NaNs ( 0.01 % out of 75879)
1 day, 1:43:59.485777 INFO: Collecting fragment features
1 day, 1:43:59.534829 INFO: Finished candidate scoring
1 day, 1:43:59.585652 PROGRESS: === Extracted 75879 precursors and 718384 fragments ===
1 day, 1:43:59.586121 INFO: performing precursor FDR with 47 features
1 day, 1:43:59.586159 INFO: Decoy channel: -1
1 day, 1:43:59.586184 INFO: Competetive: True
1 day, 1:43:59.609620 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:43:59.624380 WARNING: dropped 18 target PSMs due to missing features
1 day, 1:43:59.624504 WARNING: dropped 18 decoy PSMs due to missing features
1 day, 1:44:00.848303 INFO: Test AUC: 0.558
1 day, 1:44:00.848488 INFO: Train AUC: 0.608
1 day, 1:44:00.848521 INFO: AUC difference: 8.13%
1 day, 1:44:00.848544 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 1:44:01.804227 INFO: Resetting torch num_threads to 100
1 day, 1:44:01.806788 INFO: === FDR correction performed with classifier version 9 ===
1 day, 1:44:01.811034 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:44:01.811177 PROGRESS: Total precursors accumulated: 20,521
1 day, 1:44:01.811249 PROGRESS: Target precursors: 12,699 (61.88%)
1 day, 1:44:01.811302 PROGRESS: Decoy precursors: 7,822 (38.12%)
1 day, 1:44:01.811351 PROGRESS: 
1 day, 1:44:01.811396 PROGRESS: Precursor Summary:
1 day, 1:44:01.812603 PROGRESS: Channel   0:	 0.05 FDR:   532; 0.01 FDR:   353; 0.001 FDR:   260
1 day, 1:44:01.812704 PROGRESS: 
1 day, 1:44:01.812767 PROGRESS: Protein Summary:
1 day, 1:44:01.814092 PROGRESS: Channel   0:	 0.05 FDR:   511; 0.01 FDR:   338; 0.001 FDR:   252
1 day, 1:44:01.814197 PROGRESS: =========================================================================
1 day, 1:44:01.823981 INFO: fragments_df_filtered: 3575
1 day, 1:44:01.997235 INFO: calibration group: precursor, fitting mz estimator 
1 day, 1:44:02.043897 INFO: calibration group: precursor, fitting rt estimator 
1 day, 1:44:02.095565 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 1:44:02.143358 INFO: calibration group: fragment, fitting mz estimator 
1 day, 1:44:02.409846 INFO: calibration group: precursor, predicting mz
1 day, 1:44:02.417338 INFO: calibration group: precursor, predicting rt
1 day, 1:44:02.445693 INFO: calibration group: precursor, predicting mobility
1 day, 1:44:02.452688 INFO: calibration group: fragment, predicting mz
1 day, 1:44:02.507494 INFO: === checking if optimization conditions were reached ===
1 day, 1:44:02.507747 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 1:44:02.509571 PROGRESS: ❌ mobility_error : optimization incomplete after 3 search(es). Will search with parameter 0.0552.
1 day, 1:44:02.509627 INFO: ==============================================
1 day, 1:44:02.509720 INFO: Starting optimization step 3.
1 day, 1:44:02.509785 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 1:44:02.509843 PROGRESS: Extracting batch of 47305 precursors
1 day, 1:44:02.522814 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:44:02.522922 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:44:02.522978 INFO: FWHM in RT is 2.99 seconds, sigma is 0.66
1 day, 1:44:02.523002 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.15
1 day, 1:44:02.531937 INFO: Starting candidate selection
1 day, 1:44:21.950231 INFO: Starting candidate scoring
1 day, 1:44:24.348661 INFO: Finished candidate processing
1 day, 1:44:24.348766 INFO: Collecting candidate features
1 day, 1:44:24.471056 WARNING: intensity_correlation has 35 NaNs ( 0.05 % out of 75038)
1 day, 1:44:24.471348 WARNING: height_correlation has 8 NaNs ( 0.01 % out of 75038)
1 day, 1:44:24.477239 INFO: Collecting fragment features
1 day, 1:44:24.528026 INFO: Finished candidate scoring
1 day, 1:44:24.562858 PROGRESS: === Extracted 75038 precursors and 707202 fragments ===
1 day, 1:44:24.563257 INFO: performing precursor FDR with 47 features
1 day, 1:44:24.563295 INFO: Decoy channel: -1
1 day, 1:44:24.563317 INFO: Competetive: True
1 day, 1:44:24.584832 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:44:24.599190 WARNING: dropped 18 target PSMs due to missing features
1 day, 1:44:24.599322 WARNING: dropped 21 decoy PSMs due to missing features
1 day, 1:44:25.705868 INFO: Test AUC: 0.555
1 day, 1:44:25.705998 INFO: Train AUC: 0.610
1 day, 1:44:25.706029 INFO: AUC difference: 9.08%
1 day, 1:44:25.706051 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 1:44:25.792881 INFO: Resetting torch num_threads to 100
1 day, 1:44:25.795427 INFO: === FDR correction performed with classifier version 9 ===
1 day, 1:44:25.798751 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:44:25.798894 PROGRESS: Total precursors accumulated: 20,329
1 day, 1:44:25.798968 PROGRESS: Target precursors: 12,778 (62.86%)
1 day, 1:44:25.799021 PROGRESS: Decoy precursors: 7,551 (37.14%)
1 day, 1:44:25.799069 PROGRESS: 
1 day, 1:44:25.799113 PROGRESS: Precursor Summary:
1 day, 1:44:25.800267 PROGRESS: Channel   0:	 0.05 FDR:   465; 0.01 FDR:   361; 0.001 FDR:   295
1 day, 1:44:25.800703 PROGRESS: 
1 day, 1:44:25.800764 PROGRESS: Protein Summary:
1 day, 1:44:25.802064 PROGRESS: Channel   0:	 0.05 FDR:   449; 0.01 FDR:   348; 0.001 FDR:   286
1 day, 1:44:25.802160 PROGRESS: =========================================================================
1 day, 1:44:25.809230 INFO: fragments_df_filtered: 3575
1 day, 1:44:25.974584 INFO: calibration group: precursor, fitting mz estimator 
1 day, 1:44:26.022135 INFO: calibration group: precursor, fitting rt estimator 
1 day, 1:44:26.062487 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 1:44:26.098007 INFO: calibration group: fragment, fitting mz estimator 
1 day, 1:44:26.296582 INFO: calibration group: precursor, predicting mz
1 day, 1:44:26.304273 INFO: calibration group: precursor, predicting rt
1 day, 1:44:26.335050 INFO: calibration group: precursor, predicting mobility
1 day, 1:44:26.342085 INFO: calibration group: fragment, predicting mz
1 day, 1:44:26.396200 INFO: === checking if optimization conditions were reached ===
1 day, 1:44:26.396486 PROGRESS: === Optimization of mobility_error has been performed 4 time(s); minimum number is 2 ===
1 day, 1:44:26.398653 PROGRESS: ❌ mobility_error : optimization incomplete after 4 search(es). Will search with parameter 0.0472.
1 day, 1:44:26.398715 INFO: ==============================================
1 day, 1:44:26.398818 INFO: Starting optimization step 4.
1 day, 1:44:26.398890 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 1:44:26.398957 PROGRESS: Extracting batch of 47305 precursors
1 day, 1:44:26.414967 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:44:26.415150 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:44:26.415251 INFO: FWHM in RT is 3.01 seconds, sigma is 0.66
1 day, 1:44:26.415313 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.14
1 day, 1:44:26.440416 INFO: Starting candidate selection
1 day, 1:44:43.362312 INFO: Starting candidate scoring
1 day, 1:44:45.755904 INFO: Finished candidate processing
1 day, 1:44:45.756098 INFO: Collecting candidate features
1 day, 1:44:45.923101 WARNING: intensity_correlation has 32 NaNs ( 0.04 % out of 74190)
1 day, 1:44:45.923475 WARNING: height_correlation has 6 NaNs ( 0.01 % out of 74190)
1 day, 1:44:45.931390 INFO: Collecting fragment features
1 day, 1:44:45.981774 INFO: Finished candidate scoring
1 day, 1:44:46.022688 PROGRESS: === Extracted 74190 precursors and 695272 fragments ===
1 day, 1:44:46.023166 INFO: performing precursor FDR with 47 features
1 day, 1:44:46.023229 INFO: Decoy channel: -1
1 day, 1:44:46.023252 INFO: Competetive: True
1 day, 1:44:46.053176 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:44:46.071937 WARNING: dropped 19 target PSMs due to missing features
1 day, 1:44:46.072089 WARNING: dropped 17 decoy PSMs due to missing features
1 day, 1:44:47.466031 INFO: Test AUC: 0.551
1 day, 1:44:47.466198 INFO: Train AUC: 0.608
1 day, 1:44:47.466230 INFO: AUC difference: 9.42%
1 day, 1:44:47.466253 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 1:44:47.561101 INFO: Resetting torch num_threads to 100
1 day, 1:44:47.567058 INFO: === FDR correction performed with classifier version 9 ===
1 day, 1:44:47.571500 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:44:47.571673 PROGRESS: Total precursors accumulated: 20,130
1 day, 1:44:47.571739 PROGRESS: Target precursors: 12,582 (62.50%)
1 day, 1:44:47.571792 PROGRESS: Decoy precursors: 7,548 (37.50%)
1 day, 1:44:47.571841 PROGRESS: 
1 day, 1:44:47.571885 PROGRESS: Precursor Summary:
1 day, 1:44:47.573146 PROGRESS: Channel   0:	 0.05 FDR:   522; 0.01 FDR:   345; 0.001 FDR:   292
1 day, 1:44:47.573260 PROGRESS: 
1 day, 1:44:47.573317 PROGRESS: Protein Summary:
1 day, 1:44:47.574641 PROGRESS: Channel   0:	 0.05 FDR:   505; 0.01 FDR:   331; 0.001 FDR:   280
1 day, 1:44:47.574736 PROGRESS: =========================================================================
1 day, 1:44:47.582315 INFO: fragments_df_filtered: 3488
1 day, 1:44:48.017382 INFO: calibration group: precursor, fitting mz estimator 
1 day, 1:44:48.059030 INFO: calibration group: precursor, fitting rt estimator 
1 day, 1:44:48.103027 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 1:44:48.147646 INFO: calibration group: fragment, fitting mz estimator 
1 day, 1:44:48.349532 INFO: calibration group: precursor, predicting mz
1 day, 1:44:48.358721 INFO: calibration group: precursor, predicting rt
1 day, 1:44:48.387559 INFO: calibration group: precursor, predicting mobility
1 day, 1:44:48.394340 INFO: calibration group: fragment, predicting mz
1 day, 1:44:48.450727 INFO: === checking if optimization conditions were reached ===
1 day, 1:44:48.451146 PROGRESS: === Optimization of mobility_error has been performed 5 time(s); minimum number is 2 ===
1 day, 1:44:48.452591 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.0552 found after 5 searches.
1 day, 1:44:48.452657 INFO: ==============================================
1 day, 1:44:48.452793 PROGRESS: Optimization finished for mobility_error.
1 day, 1:44:48.854022 INFO: calibration group: precursor, predicting mz
1 day, 1:44:48.864244 INFO: calibration group: precursor, predicting rt
1 day, 1:44:48.893266 INFO: calibration group: precursor, predicting mobility
1 day, 1:44:48.900164 INFO: calibration group: fragment, predicting mz
1 day, 1:44:48.991137 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 1:44:48.992218 PROGRESS: ==============================================
1 day, 1:44:48.992300 PROGRESS: ms2_error      : 15.0000
1 day, 1:44:48.992364 PROGRESS: ms1_error      : 10.0000
1 day, 1:44:48.992420 PROGRESS: rt_error       : 337.2455
1 day, 1:44:48.992469 PROGRESS: mobility_error : 0.0552
1 day, 1:44:48.992515 PROGRESS: ==============================================
1 day, 1:44:48.995860 INFO: calibration group: precursor, predicting mz
1 day, 1:44:50.475921 INFO: calibration group: precursor, predicting rt
1 day, 1:44:56.882426 INFO: calibration group: precursor, predicting mobility
1 day, 1:44:58.306406 INFO: calibration group: fragment, predicting mz
1 day, 1:45:10.901245 PROGRESS: Extracting batch of 10272670 precursors
1 day, 1:45:13.434195 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:45:13.434339 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:45:13.434395 INFO: FWHM in RT is 3.01 seconds, sigma is 0.66
1 day, 1:45:13.434424 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.14
1 day, 1:45:13.435772 INFO: Starting candidate selection
1 day, 2:50:32.984135 INFO: Applying score cutoff of 30.928431854248046
1 day, 2:50:33.450665 INFO: Removed 3994143 precursors with score below cutoff
1 day, 2:50:36.451672 INFO: Starting candidate scoring
1 day, 2:56:54.131408 INFO: Finished candidate processing
1 day, 2:56:54.131826 INFO: Collecting candidate features
1 day, 2:57:17.770659 WARNING: intensity_correlation has 27 NaNs ( 0.00 % out of 13187751)
1 day, 2:57:18.217708 INFO: Collecting fragment features
1 day, 2:57:27.511107 INFO: Finished candidate scoring
1 day, 2:57:39.545234 INFO: === FDR correction performed with classifier version 14 ===
1 day, 2:57:39.552114 INFO: performing precursor FDR with 47 features
1 day, 2:57:39.552194 INFO: Decoy channel: -1
1 day, 2:57:39.552222 INFO: Competetive: True
1 day, 2:57:43.067622 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 2:57:45.244787 WARNING: dropped 9 target PSMs due to missing features
1 day, 2:57:45.244949 WARNING: dropped 18 decoy PSMs due to missing features
1 day, 3:02:23.097534 INFO: Test AUC: 0.564
1 day, 3:02:23.097813 INFO: Train AUC: 0.573
1 day, 3:02:23.097870 INFO: AUC difference: 1.55%
1 day, 3:02:23.950665 INFO: Resetting torch num_threads to 100
1 day, 3:02:24.267488 INFO: Removing fragments below FDR threshold
1 day, 3:02:25.214689 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:02:25.215037 PROGRESS: Total precursors accumulated: 74,760
1 day, 3:02:25.215105 PROGRESS: Target precursors: 74,020 (99.01%)
1 day, 3:02:25.215162 PROGRESS: Decoy precursors: 740 (0.99%)
1 day, 3:02:25.215213 PROGRESS: 
1 day, 3:02:25.215261 PROGRESS: Precursor Summary:
1 day, 3:02:25.244607 PROGRESS: Channel   0:	 0.05 FDR: 74,020; 0.01 FDR: 74,020; 0.001 FDR: 53,225
1 day, 3:02:25.244902 PROGRESS: 
1 day, 3:02:25.244971 PROGRESS: Protein Summary:
1 day, 3:02:25.290147 PROGRESS: Channel   0:	 0.05 FDR: 11,487; 0.01 FDR: 11,487; 0.001 FDR: 9,015
1 day, 3:02:25.290431 PROGRESS: =========================================================================
1 day, 3:02:25.953989 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 3:02:26.387246 PROGRESS: Loading raw file 3/6: ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 3:02:26.387441 INFO: Quantification results path: run_output/alphadia_1.10_defaultMBR/library/quant
1 day, 3:02:26.387538 INFO: Creating workflow folder for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506 at run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 3:02:26.388282 INFO: Initializing RawFileManager
1 day, 3:02:26.388438 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 3:02:26.388517 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 3:02:26.388580 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 3:02:26.611107 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
1 day, 3:02:35.889735 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d...
1 day, 3:02:35.891165 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 3:02:35.893280 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 3:02:35.893534 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 3:02:35.893908 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 3:02:35.895299 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 3:02:35.910779 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 3:02:35.911022 INFO: Indexing quadrupole dimension
1 day, 3:02:36.414557 INFO: Transposing detector events
1 day, 3:02:46.222103 INFO: Finished transposing data
1 day, 3:02:46.261180 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 3:02:46.262326 INFO: RT (min)            : 0.0 - 70.0
1 day, 3:02:46.262418 INFO: RT duration (sec)   : 4199.8
1 day, 3:02:46.262471 INFO: RT duration (min)   : 70.0
1 day, 3:02:46.262519 INFO: Cycle len (scans)   : 9
1 day, 3:02:46.262565 INFO: Cycle len (sec)     : 0.97
1 day, 3:02:46.262609 INFO: Number of cycles    : 4347
1 day, 3:02:46.262655 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 3:02:47.531200 INFO: Initializing CalibrationManager
1 day, 3:02:47.531597 INFO: Loading calibration config
1 day, 3:02:47.532354 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'}]
1 day, 3:02:47.532467 INFO: Calibration group :fragment, found 1 estimator(s)
1 day, 3:02:47.532585 INFO: Calibration group :precursor, found 3 estimator(s)
1 day, 3:02:47.532796 INFO: Initializing OptimizationManager
1 day, 3:02:47.532936 INFO: initial parameter: ms1_error = 30
1 day, 3:02:47.532992 INFO: initial parameter: ms2_error = 30
1 day, 3:02:47.533067 INFO: initial parameter: rt_error = 2099.8992935
1 day, 3:02:47.533129 INFO: initial parameter: mobility_error = 0.1
1 day, 3:02:47.533177 INFO: initial parameter: column_type = library
1 day, 3:02:47.533224 INFO: initial parameter: num_candidates = 1
1 day, 3:02:47.533267 INFO: initial parameter: classifier_version = -1
1 day, 3:02:47.533309 INFO: initial parameter: fwhm_rt = 5
1 day, 3:02:47.533353 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 3:02:47.533395 INFO: initial parameter: score_cutoff = 0
1 day, 3:02:47.533466 INFO: Initializing TimingManager
1 day, 3:02:47.533547 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 3:02:47.533679 INFO: FDRManager not loaded from disk.
1 day, 3:02:47.533707 INFO: Initializing FDRManager
1 day, 3:02:47.533761 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 3:02:48.956459 PROGRESS: 5,215,079 target precursors potentially observable (0 removed)
1 day, 3:02:50.808788 PROGRESS: Starting initial search for precursors.
1 day, 3:02:51.061202 INFO: Starting optimization step 0.
1 day, 3:02:51.061476 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 3:02:51.061567 PROGRESS: Extracting batch of 15771 precursors
1 day, 3:02:51.066211 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:02:51.066268 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:02:51.066307 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 3:02:51.066331 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 3:02:51.067415 INFO: Starting candidate selection
1 day, 3:04:09.955090 INFO: Starting candidate scoring
1 day, 3:04:10.746943 INFO: Finished candidate processing
1 day, 3:04:10.747129 INFO: Collecting candidate features
1 day, 3:04:10.780493 WARNING: intensity_correlation has 3 NaNs ( 0.02 % out of 13798)
1 day, 3:04:10.784214 INFO: Collecting fragment features
1 day, 3:04:10.798366 INFO: Finished candidate scoring
1 day, 3:04:10.807191 PROGRESS: === Extracted 13798 precursors and 138685 fragments ===
1 day, 3:04:10.807644 INFO: performing precursor FDR with 47 features
1 day, 3:04:10.807683 INFO: Decoy channel: -1
1 day, 3:04:10.807709 INFO: Competetive: True
1 day, 3:04:10.815042 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:04:10.818130 WARNING: dropped 2 target PSMs due to missing features
1 day, 3:04:10.818188 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 3:04:10.962376 INFO: Test AUC: 0.526
1 day, 3:04:10.962511 INFO: Train AUC: 0.540
1 day, 3:04:10.962548 INFO: AUC difference: 2.54%
1 day, 3:04:11.053252 INFO: Resetting torch num_threads to 100
1 day, 3:04:11.054731 INFO: === FDR correction performed with classifier version -1 ===
1 day, 3:04:11.056532 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:04:11.056646 PROGRESS: Total precursors accumulated: 7,068
1 day, 3:04:11.056709 PROGRESS: Target precursors: 4,011 (56.75%)
1 day, 3:04:11.056775 PROGRESS: Decoy precursors: 3,057 (43.25%)
1 day, 3:04:11.056824 PROGRESS: 
1 day, 3:04:11.056872 PROGRESS: Precursor Summary:
1 day, 3:04:11.057793 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 3:04:11.057887 PROGRESS: 
1 day, 3:04:11.057944 PROGRESS: Protein Summary:
1 day, 3:04:11.058888 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 3:04:11.058978 PROGRESS: =========================================================================
1 day, 3:04:11.561580 INFO: Starting optimization step 1.
1 day, 3:04:11.561885 PROGRESS: === Extracting elution groups 8000 to 24000 ===
1 day, 3:04:11.561983 PROGRESS: Extracting batch of 31534 precursors
1 day, 3:04:11.573162 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:04:11.573254 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:04:11.573293 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 3:04:11.573318 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 3:04:11.574797 INFO: Starting candidate selection
1 day, 3:06:43.469784 INFO: Starting candidate scoring
1 day, 3:06:44.971563 INFO: Finished candidate processing
1 day, 3:06:44.971750 INFO: Collecting candidate features
1 day, 3:06:45.055761 WARNING: intensity_correlation has 4 NaNs ( 0.01 % out of 27442)
1 day, 3:06:45.056042 WARNING: height_correlation has 2 NaNs ( 0.01 % out of 27442)
1 day, 3:06:45.059855 INFO: Collecting fragment features
1 day, 3:06:45.079904 INFO: Finished candidate scoring
1 day, 3:06:45.121184 PROGRESS: === Extracted 41240 precursors and 413448 fragments ===
1 day, 3:06:45.127169 INFO: performing precursor FDR with 47 features
1 day, 3:06:45.127268 INFO: Decoy channel: -1
1 day, 3:06:45.127296 INFO: Competetive: True
1 day, 3:06:45.151298 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:06:45.161169 WARNING: dropped 4 target PSMs due to missing features
1 day, 3:06:45.161312 WARNING: dropped 4 decoy PSMs due to missing features
1 day, 3:06:45.887953 INFO: Test AUC: 0.560
1 day, 3:06:45.888104 INFO: Train AUC: 0.576
1 day, 3:06:45.888137 INFO: AUC difference: 2.84%
1 day, 3:06:45.979357 INFO: Resetting torch num_threads to 100
1 day, 3:06:45.982557 INFO: === FDR correction performed with classifier version -1 ===
1 day, 3:06:45.985811 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:06:45.985965 PROGRESS: Total precursors accumulated: 21,123
1 day, 3:06:45.986032 PROGRESS: Target precursors: 12,745 (60.34%)
1 day, 3:06:45.986086 PROGRESS: Decoy precursors: 8,378 (39.66%)
1 day, 3:06:45.986136 PROGRESS: 
1 day, 3:06:45.986185 PROGRESS: Precursor Summary:
1 day, 3:06:45.987227 PROGRESS: Channel   0:	 0.05 FDR:    68; 0.01 FDR:    19; 0.001 FDR:    19
1 day, 3:06:45.987322 PROGRESS: 
1 day, 3:06:45.987383 PROGRESS: Protein Summary:
1 day, 3:06:45.988453 PROGRESS: Channel   0:	 0.05 FDR:    67; 0.01 FDR:    19; 0.001 FDR:    19
1 day, 3:06:45.988546 PROGRESS: =========================================================================
1 day, 3:06:46.224954 INFO: Starting optimization step 2.
1 day, 3:06:46.225276 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1 day, 3:06:46.225400 PROGRESS: Extracting batch of 63016 precursors
1 day, 3:06:46.244635 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:06:46.244775 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:06:46.244827 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 3:06:46.244854 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 3:06:46.245835 INFO: Starting candidate selection
1 day, 3:11:44.881603 INFO: Starting candidate scoring
1 day, 3:11:47.810637 INFO: Finished candidate processing
1 day, 3:11:47.810740 INFO: Collecting candidate features
1 day, 3:11:47.936523 WARNING: intensity_correlation has 13 NaNs ( 0.02 % out of 55035)
1 day, 3:11:47.941748 INFO: Collecting fragment features
1 day, 3:11:47.982997 INFO: Finished candidate scoring
1 day, 3:11:48.078864 PROGRESS: === Extracted 96275 precursors and 964711 fragments ===
1 day, 3:11:48.091734 INFO: performing precursor FDR with 47 features
1 day, 3:11:48.091834 INFO: Decoy channel: -1
1 day, 3:11:48.091860 INFO: Competetive: True
1 day, 3:11:48.138482 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:11:48.160799 WARNING: dropped 13 target PSMs due to missing features
1 day, 3:11:48.160926 WARNING: dropped 8 decoy PSMs due to missing features
1 day, 3:11:49.838372 INFO: Test AUC: 0.562
1 day, 3:11:49.838514 INFO: Train AUC: 0.577
1 day, 3:11:49.838547 INFO: AUC difference: 2.60%
1 day, 3:11:49.936846 INFO: Resetting torch num_threads to 100
1 day, 3:11:49.943234 INFO: === FDR correction performed with classifier version -1 ===
1 day, 3:11:49.953125 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:11:49.953412 PROGRESS: Total precursors accumulated: 49,354
1 day, 3:11:49.953478 PROGRESS: Target precursors: 29,511 (59.79%)
1 day, 3:11:49.953531 PROGRESS: Decoy precursors: 19,843 (40.21%)
1 day, 3:11:49.953581 PROGRESS: 
1 day, 3:11:49.953630 PROGRESS: Precursor Summary:
1 day, 3:11:49.955001 PROGRESS: Channel   0:	 0.05 FDR:   475; 0.01 FDR:   329; 0.001 FDR:   132
1 day, 3:11:49.955097 PROGRESS: 
1 day, 3:11:49.955157 PROGRESS: Protein Summary:
1 day, 3:11:49.956564 PROGRESS: Channel   0:	 0.05 FDR:   441; 0.01 FDR:   307; 0.001 FDR:   129
1 day, 3:11:49.956657 PROGRESS: =========================================================================
1 day, 3:11:49.970303 INFO: fragments_df_filtered: 3066
1 day, 3:11:50.200318 INFO: calibration group: precursor, fitting mz estimator 
1 day, 3:11:50.247712 INFO: calibration group: precursor, fitting rt estimator 
1 day, 3:11:50.300103 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 3:11:50.352028 INFO: calibration group: fragment, fitting mz estimator 
1 day, 3:11:50.532810 INFO: calibration group: precursor, predicting mz
1 day, 3:11:50.548405 INFO: calibration group: precursor, predicting rt
1 day, 3:11:50.613152 INFO: calibration group: precursor, predicting mobility
1 day, 3:11:50.628880 INFO: calibration group: fragment, predicting mz
1 day, 3:11:50.765596 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 3:11:50.765924 INFO: Starting optimization step 3.
1 day, 3:11:50.766001 PROGRESS: === Extracting elution groups 0 to 56000 ===
1 day, 3:11:50.766090 PROGRESS: Extracting batch of 110321 precursors
1 day, 3:11:50.796707 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:11:50.796829 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:11:50.796896 INFO: FWHM in RT is 3.36 seconds, sigma is 0.74
1 day, 3:11:50.796921 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.28
1 day, 3:11:50.805794 INFO: Starting candidate selection
1 day, 3:20:52.528348 INFO: Starting candidate scoring
1 day, 3:21:03.548522 INFO: Finished candidate processing
1 day, 3:21:03.548697 INFO: Collecting candidate features
1 day, 3:21:03.908461 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 189481)
1 day, 3:21:03.918391 INFO: Collecting fragment features
1 day, 3:21:04.041554 INFO: Finished candidate scoring
1 day, 3:21:04.146090 PROGRESS: === Extracted 189481 precursors and 1931263 fragments ===
1 day, 3:21:04.146608 INFO: performing precursor FDR with 47 features
1 day, 3:21:04.146650 INFO: Decoy channel: -1
1 day, 3:21:04.146672 INFO: Competetive: True
1 day, 3:21:04.234237 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:21:04.273141 WARNING: dropped 1 target PSMs due to missing features
1 day, 3:21:08.278032 INFO: Test AUC: 0.563
1 day, 3:21:08.278180 INFO: Train AUC: 0.590
1 day, 3:21:08.278212 INFO: AUC difference: 4.50%
1 day, 3:21:09.914309 INFO: Resetting torch num_threads to 100
1 day, 3:21:09.922220 INFO: === FDR correction performed with classifier version 2 ===
1 day, 3:21:09.933970 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:21:09.934310 PROGRESS: Total precursors accumulated: 50,306
1 day, 3:21:09.934376 PROGRESS: Target precursors: 31,706 (63.03%)
1 day, 3:21:09.934428 PROGRESS: Decoy precursors: 18,600 (36.97%)
1 day, 3:21:09.934479 PROGRESS: 
1 day, 3:21:09.934525 PROGRESS: Precursor Summary:
1 day, 3:21:09.936100 PROGRESS: Channel   0:	 0.05 FDR:   637; 0.01 FDR:   401; 0.001 FDR:   333
1 day, 3:21:09.936202 PROGRESS: 
1 day, 3:21:09.936258 PROGRESS: Protein Summary:
1 day, 3:21:09.937776 PROGRESS: Channel   0:	 0.05 FDR:   589; 0.01 FDR:   374; 0.001 FDR:   308
1 day, 3:21:09.937877 PROGRESS: =========================================================================
1 day, 3:21:09.949448 INFO: fragments_df_filtered: 4929
1 day, 3:21:10.501689 INFO: calibration group: precursor, fitting mz estimator 
1 day, 3:21:10.547322 INFO: calibration group: precursor, fitting rt estimator 
1 day, 3:21:10.589176 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 3:21:10.630535 INFO: calibration group: fragment, fitting mz estimator 
1 day, 3:21:10.971127 INFO: calibration group: precursor, predicting mz
1 day, 3:21:10.986646 INFO: calibration group: precursor, predicting rt
1 day, 3:21:11.053780 INFO: calibration group: precursor, predicting mobility
1 day, 3:21:11.071177 INFO: calibration group: fragment, predicting mz
1 day, 3:21:11.205656 INFO: === checking if optimization conditions were reached ===
1 day, 3:21:11.208418 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 3:21:11.209599 PROGRESS: ❌ ms1_error      : 10.0000 > 10.0000 or insufficient steps taken.
1 day, 3:21:11.209659 INFO: ==============================================
1 day, 3:21:11.209780 INFO: Starting optimization step 4.
1 day, 3:21:11.209857 PROGRESS: === Extracting elution groups 0 to 56000 ===
1 day, 3:21:11.209929 PROGRESS: Extracting batch of 110321 precursors
1 day, 3:21:11.261910 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:21:11.262064 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:21:11.262113 INFO: FWHM in RT is 3.24 seconds, sigma is 0.71
1 day, 3:21:11.262138 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.11
1 day, 3:21:11.262957 INFO: Starting candidate selection
1 day, 3:29:16.312476 INFO: Starting candidate scoring
1 day, 3:29:22.023467 INFO: Finished candidate processing
1 day, 3:29:22.023670 INFO: Collecting candidate features
1 day, 3:29:22.399886 WARNING: intensity_correlation has 7 NaNs ( 0.00 % out of 189216)
1 day, 3:29:22.400358 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 189216)
1 day, 3:29:22.410386 INFO: Collecting fragment features
1 day, 3:29:22.527258 INFO: Finished candidate scoring
1 day, 3:29:22.625831 PROGRESS: === Extracted 189216 precursors and 1859322 fragments ===
1 day, 3:29:22.626390 INFO: performing precursor FDR with 47 features
1 day, 3:29:22.626433 INFO: Decoy channel: -1
1 day, 3:29:22.626462 INFO: Competetive: True
1 day, 3:29:22.705777 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:29:22.752223 WARNING: dropped 1 target PSMs due to missing features
1 day, 3:29:22.752368 WARNING: dropped 7 decoy PSMs due to missing features
1 day, 3:29:26.045501 INFO: Test AUC: 0.563
1 day, 3:29:26.045644 INFO: Train AUC: 0.591
1 day, 3:29:26.045674 INFO: AUC difference: 4.71%
1 day, 3:29:26.146783 INFO: Resetting torch num_threads to 100
1 day, 3:29:26.154850 INFO: === FDR correction performed with classifier version 3 ===
1 day, 3:29:26.166547 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:29:26.166884 PROGRESS: Total precursors accumulated: 50,233
1 day, 3:29:26.166951 PROGRESS: Target precursors: 31,192 (62.09%)
1 day, 3:29:26.167006 PROGRESS: Decoy precursors: 19,041 (37.91%)
1 day, 3:29:26.167056 PROGRESS: 
1 day, 3:29:26.167106 PROGRESS: Precursor Summary:
1 day, 3:29:26.168756 PROGRESS: Channel   0:	 0.05 FDR:   845; 0.01 FDR:   613; 0.001 FDR:   507
1 day, 3:29:26.168856 PROGRESS: 
1 day, 3:29:26.168916 PROGRESS: Protein Summary:
1 day, 3:29:26.170630 PROGRESS: Channel   0:	 0.05 FDR:   773; 0.01 FDR:   563; 0.001 FDR:   462
1 day, 3:29:26.170728 PROGRESS: =========================================================================
1 day, 3:29:26.185362 INFO: fragments_df_filtered: 5000
1 day, 3:29:26.372616 INFO: calibration group: precursor, fitting mz estimator 
1 day, 3:29:26.418720 INFO: calibration group: precursor, fitting rt estimator 
1 day, 3:29:26.460413 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 3:29:26.502450 INFO: calibration group: fragment, fitting mz estimator 
1 day, 3:29:26.852413 INFO: calibration group: precursor, predicting mz
1 day, 3:29:26.860192 INFO: calibration group: precursor, predicting rt
1 day, 3:29:26.888680 INFO: calibration group: precursor, predicting mobility
1 day, 3:29:26.895098 INFO: calibration group: fragment, predicting mz
1 day, 3:29:26.947499 INFO: === checking if optimization conditions were reached ===
1 day, 3:29:26.949792 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 3:29:26.950829 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
1 day, 3:29:26.950884 INFO: ==============================================
1 day, 3:29:26.951008 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 3:29:27.121891 INFO: calibration group: precursor, predicting mz
1 day, 3:29:27.129837 INFO: calibration group: precursor, predicting rt
1 day, 3:29:27.158461 INFO: calibration group: precursor, predicting mobility
1 day, 3:29:27.164910 INFO: calibration group: fragment, predicting mz
1 day, 3:29:27.219252 INFO: Starting optimization step 0.
1 day, 3:29:27.219551 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 3:29:27.219679 PROGRESS: Extracting batch of 47305 precursors
1 day, 3:29:27.236205 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:29:27.236329 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:29:27.236397 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 3:29:27.236427 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.21
1 day, 3:29:27.242335 INFO: Starting candidate selection
1 day, 3:32:59.271960 INFO: Starting candidate scoring
1 day, 3:33:01.885791 INFO: Finished candidate processing
1 day, 3:33:01.885968 INFO: Collecting candidate features
1 day, 3:33:02.046961 WARNING: intensity_correlation has 5 NaNs ( 0.01 % out of 80948)
1 day, 3:33:02.053521 INFO: Collecting fragment features
1 day, 3:33:02.110731 INFO: Finished candidate scoring
1 day, 3:33:02.149791 PROGRESS: === Extracted 80948 precursors and 793851 fragments ===
1 day, 3:33:02.150299 INFO: performing precursor FDR with 47 features
1 day, 3:33:02.150343 INFO: Decoy channel: -1
1 day, 3:33:02.150376 INFO: Competetive: True
1 day, 3:33:02.177706 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:33:02.194205 WARNING: dropped 2 target PSMs due to missing features
1 day, 3:33:02.194346 WARNING: dropped 3 decoy PSMs due to missing features
1 day, 3:33:03.489976 INFO: Test AUC: 0.571
1 day, 3:33:03.490115 INFO: Train AUC: 0.617
1 day, 3:33:03.490150 INFO: AUC difference: 7.46%
1 day, 3:33:03.490178 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:33:03.584275 INFO: Resetting torch num_threads to 100
1 day, 3:33:03.587397 INFO: === FDR correction performed with classifier version 4 ===
1 day, 3:33:03.591443 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:33:03.591614 PROGRESS: Total precursors accumulated: 21,509
1 day, 3:33:03.591687 PROGRESS: Target precursors: 13,862 (64.45%)
1 day, 3:33:03.591755 PROGRESS: Decoy precursors: 7,647 (35.55%)
1 day, 3:33:03.591814 PROGRESS: 
1 day, 3:33:03.591870 PROGRESS: Precursor Summary:
1 day, 3:33:03.593070 PROGRESS: Channel   0:	 0.05 FDR:   412; 0.01 FDR:   303; 0.001 FDR:   272
1 day, 3:33:03.593176 PROGRESS: 
1 day, 3:33:03.593244 PROGRESS: Protein Summary:
1 day, 3:33:03.594556 PROGRESS: Channel   0:	 0.05 FDR:   394; 0.01 FDR:   290; 0.001 FDR:   261
1 day, 3:33:03.594659 PROGRESS: =========================================================================
1 day, 3:33:03.703060 INFO: fragments_df_filtered: 3426
1 day, 3:33:03.875810 INFO: calibration group: precursor, fitting mz estimator 
1 day, 3:33:03.920367 INFO: calibration group: precursor, fitting rt estimator 
1 day, 3:33:03.970046 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 3:33:04.019847 INFO: calibration group: fragment, fitting mz estimator 
1 day, 3:33:04.226938 INFO: calibration group: precursor, predicting mz
1 day, 3:33:04.234389 INFO: calibration group: precursor, predicting rt
1 day, 3:33:04.262859 INFO: calibration group: precursor, predicting mobility
1 day, 3:33:04.269786 INFO: calibration group: fragment, predicting mz
1 day, 3:33:04.325547 INFO: === checking if optimization conditions were reached ===
1 day, 3:33:04.325863 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 3:33:04.328012 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 573.1103.
1 day, 3:33:04.328086 INFO: ==============================================
1 day, 3:33:04.328197 INFO: Starting optimization step 1.
1 day, 3:33:04.328273 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 3:33:04.328352 PROGRESS: Extracting batch of 47305 precursors
1 day, 3:33:04.344582 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:33:04.344708 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:33:04.344760 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 3:33:04.344782 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.14
1 day, 3:33:04.353748 INFO: Starting candidate selection
1 day, 3:34:01.495453 INFO: Starting candidate scoring
1 day, 3:34:04.001189 INFO: Finished candidate processing
1 day, 3:34:04.002506 INFO: Collecting candidate features
1 day, 3:34:04.171015 WARNING: intensity_correlation has 18 NaNs ( 0.02 % out of 78858)
1 day, 3:34:04.182371 INFO: Collecting fragment features
1 day, 3:34:04.249315 INFO: Finished candidate scoring
1 day, 3:34:04.330499 PROGRESS: === Extracted 78858 precursors and 759378 fragments ===
1 day, 3:34:04.331185 INFO: performing precursor FDR with 47 features
1 day, 3:34:04.331228 INFO: Decoy channel: -1
1 day, 3:34:04.331255 INFO: Competetive: True
1 day, 3:34:04.370842 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:34:04.389201 WARNING: dropped 10 target PSMs due to missing features
1 day, 3:34:04.389347 WARNING: dropped 8 decoy PSMs due to missing features
1 day, 3:34:06.001616 INFO: Test AUC: 0.560
1 day, 3:34:06.001757 INFO: Train AUC: 0.604
1 day, 3:34:06.001788 INFO: AUC difference: 7.28%
1 day, 3:34:06.001810 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:34:06.100820 INFO: Resetting torch num_threads to 100
1 day, 3:34:06.104133 INFO: === FDR correction performed with classifier version 4 ===
1 day, 3:34:06.108193 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:34:06.108357 PROGRESS: Total precursors accumulated: 21,175
1 day, 3:34:06.108424 PROGRESS: Target precursors: 13,241 (62.53%)
1 day, 3:34:06.108482 PROGRESS: Decoy precursors: 7,934 (37.47%)
1 day, 3:34:06.108531 PROGRESS: 
1 day, 3:34:06.108583 PROGRESS: Precursor Summary:
1 day, 3:34:06.109767 PROGRESS: Channel   0:	 0.05 FDR:   402; 0.01 FDR:   257; 0.001 FDR:   248
1 day, 3:34:06.109866 PROGRESS: 
1 day, 3:34:06.109925 PROGRESS: Protein Summary:
1 day, 3:34:06.111209 PROGRESS: Channel   0:	 0.05 FDR:   384; 0.01 FDR:   248; 0.001 FDR:   239
1 day, 3:34:06.111305 PROGRESS: =========================================================================
1 day, 3:34:06.117872 INFO: fragments_df_filtered: 2969
1 day, 3:34:06.321497 INFO: calibration group: precursor, fitting mz estimator 
1 day, 3:34:06.367491 INFO: calibration group: precursor, fitting rt estimator 
1 day, 3:34:06.406537 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 3:34:06.444776 INFO: calibration group: fragment, fitting mz estimator 
1 day, 3:34:06.592945 INFO: calibration group: precursor, predicting mz
1 day, 3:34:06.600781 INFO: calibration group: precursor, predicting rt
1 day, 3:34:06.629724 INFO: calibration group: precursor, predicting mobility
1 day, 3:34:06.636762 INFO: calibration group: fragment, predicting mz
1 day, 3:34:06.692641 INFO: === checking if optimization conditions were reached ===
1 day, 3:34:06.692991 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 3:34:06.695544 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 299.9589.
1 day, 3:34:06.695605 INFO: ==============================================
1 day, 3:34:06.695719 INFO: Starting optimization step 2.
1 day, 3:34:06.695796 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 3:34:06.695894 PROGRESS: Extracting batch of 47305 precursors
1 day, 3:34:06.714781 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:34:06.714921 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:34:06.714984 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 3:34:06.715010 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.24
1 day, 3:34:06.724020 INFO: Starting candidate selection
1 day, 3:34:38.603897 INFO: Starting candidate scoring
1 day, 3:34:40.880422 INFO: Finished candidate processing
1 day, 3:34:40.880736 INFO: Collecting candidate features
1 day, 3:34:41.046925 WARNING: intensity_correlation has 31 NaNs ( 0.04 % out of 77860)
1 day, 3:34:41.047252 WARNING: height_correlation has 6 NaNs ( 0.01 % out of 77860)
1 day, 3:34:41.053271 INFO: Collecting fragment features
1 day, 3:34:41.119005 INFO: Finished candidate scoring
1 day, 3:34:41.158962 PROGRESS: === Extracted 77860 precursors and 740519 fragments ===
1 day, 3:34:41.159499 INFO: performing precursor FDR with 47 features
1 day, 3:34:41.159539 INFO: Decoy channel: -1
1 day, 3:34:41.159563 INFO: Competetive: True
1 day, 3:34:41.190389 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:34:41.205938 WARNING: dropped 16 target PSMs due to missing features
1 day, 3:34:41.206078 WARNING: dropped 17 decoy PSMs due to missing features
1 day, 3:34:42.494284 INFO: Test AUC: 0.551
1 day, 3:34:42.494419 INFO: Train AUC: 0.594
1 day, 3:34:42.494449 INFO: AUC difference: 7.25%
1 day, 3:34:42.494472 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:34:42.580986 INFO: Resetting torch num_threads to 100
1 day, 3:34:42.584033 INFO: === FDR correction performed with classifier version 4 ===
1 day, 3:34:42.587924 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:34:42.588079 PROGRESS: Total precursors accumulated: 20,993
1 day, 3:34:42.588143 PROGRESS: Target precursors: 13,009 (61.97%)
1 day, 3:34:42.588197 PROGRESS: Decoy precursors: 7,984 (38.03%)
1 day, 3:34:42.588247 PROGRESS: 
1 day, 3:34:42.588292 PROGRESS: Precursor Summary:
1 day, 3:34:42.589462 PROGRESS: Channel   0:	 0.05 FDR:   401; 0.01 FDR:   331; 0.001 FDR:   286
1 day, 3:34:42.589561 PROGRESS: 
1 day, 3:34:42.589619 PROGRESS: Protein Summary:
1 day, 3:34:42.590883 PROGRESS: Channel   0:	 0.05 FDR:   383; 0.01 FDR:   317; 0.001 FDR:   274
1 day, 3:34:42.590980 PROGRESS: =========================================================================
1 day, 3:34:42.597949 INFO: fragments_df_filtered: 3563
1 day, 3:34:42.766155 INFO: calibration group: precursor, fitting mz estimator 
1 day, 3:34:42.803023 INFO: calibration group: precursor, fitting rt estimator 
1 day, 3:34:42.842141 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 3:34:42.879969 INFO: calibration group: fragment, fitting mz estimator 
1 day, 3:34:43.076808 INFO: calibration group: precursor, predicting mz
1 day, 3:34:43.084454 INFO: calibration group: precursor, predicting rt
1 day, 3:34:43.113133 INFO: calibration group: precursor, predicting mobility
1 day, 3:34:43.119933 INFO: calibration group: fragment, predicting mz
1 day, 3:34:43.174365 INFO: === checking if optimization conditions were reached ===
1 day, 3:34:43.174664 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 3:34:43.176682 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 176.8322.
1 day, 3:34:43.176736 INFO: ==============================================
1 day, 3:34:43.176831 INFO: Starting optimization step 3.
1 day, 3:34:43.176899 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 3:34:43.176971 PROGRESS: Extracting batch of 47305 precursors
1 day, 3:34:43.189211 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:34:43.189325 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:34:43.189375 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 3:34:43.189399 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.13
1 day, 3:34:43.205606 INFO: Starting candidate selection
1 day, 3:35:03.351156 INFO: Starting candidate scoring
1 day, 3:35:05.741954 INFO: Finished candidate processing
1 day, 3:35:05.742136 INFO: Collecting candidate features
1 day, 3:35:05.889034 WARNING: intensity_correlation has 34 NaNs ( 0.04 % out of 77618)
1 day, 3:35:05.889338 WARNING: height_correlation has 4 NaNs ( 0.01 % out of 77618)
1 day, 3:35:05.895230 INFO: Collecting fragment features
1 day, 3:35:05.941743 INFO: Finished candidate scoring
1 day, 3:35:05.977760 PROGRESS: === Extracted 77618 precursors and 731529 fragments ===
1 day, 3:35:05.978184 INFO: performing precursor FDR with 47 features
1 day, 3:35:05.978223 INFO: Decoy channel: -1
1 day, 3:35:05.978247 INFO: Competetive: True
1 day, 3:35:06.002802 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:35:06.018293 WARNING: dropped 21 target PSMs due to missing features
1 day, 3:35:06.018438 WARNING: dropped 15 decoy PSMs due to missing features
1 day, 3:35:07.260310 INFO: Test AUC: 0.546
1 day, 3:35:07.260449 INFO: Train AUC: 0.591
1 day, 3:35:07.260481 INFO: AUC difference: 7.55%
1 day, 3:35:07.260503 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:35:07.345741 INFO: Resetting torch num_threads to 100
1 day, 3:35:07.348716 INFO: === FDR correction performed with classifier version 4 ===
1 day, 3:35:07.352349 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:35:07.352504 PROGRESS: Total precursors accumulated: 20,953
1 day, 3:35:07.352582 PROGRESS: Target precursors: 12,882 (61.48%)
1 day, 3:35:07.352636 PROGRESS: Decoy precursors: 8,071 (38.52%)
1 day, 3:35:07.352691 PROGRESS: 
1 day, 3:35:07.352738 PROGRESS: Precursor Summary:
1 day, 3:35:07.353880 PROGRESS: Channel   0:	 0.05 FDR:   425; 0.01 FDR:   309; 0.001 FDR:   276
1 day, 3:35:07.353975 PROGRESS: 
1 day, 3:35:07.354031 PROGRESS: Protein Summary:
1 day, 3:35:07.355280 PROGRESS: Channel   0:	 0.05 FDR:   406; 0.01 FDR:   296; 0.001 FDR:   267
1 day, 3:35:07.355376 PROGRESS: =========================================================================
1 day, 3:35:07.361785 INFO: fragments_df_filtered: 3388
1 day, 3:35:07.534142 INFO: calibration group: precursor, fitting mz estimator 
1 day, 3:35:07.578702 INFO: calibration group: precursor, fitting rt estimator 
1 day, 3:35:07.619514 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 3:35:07.659148 INFO: calibration group: fragment, fitting mz estimator 
1 day, 3:35:07.842419 INFO: calibration group: precursor, predicting mz
1 day, 3:35:07.849543 INFO: calibration group: precursor, predicting rt
1 day, 3:35:07.877943 INFO: calibration group: precursor, predicting mobility
1 day, 3:35:07.884765 INFO: calibration group: fragment, predicting mz
1 day, 3:35:07.934762 INFO: === checking if optimization conditions were reached ===
1 day, 3:35:07.935081 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 3:35:07.937484 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 128.2918.
1 day, 3:35:07.937550 INFO: ==============================================
1 day, 3:35:07.937676 INFO: Starting optimization step 4.
1 day, 3:35:07.937761 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 3:35:07.937836 PROGRESS: Extracting batch of 47305 precursors
1 day, 3:35:07.954945 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:35:07.955081 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:35:07.955130 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 3:35:07.955158 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.08
1 day, 3:35:07.963926 INFO: Starting candidate selection
1 day, 3:35:22.497582 INFO: Starting candidate scoring
1 day, 3:35:24.966613 INFO: Finished candidate processing
1 day, 3:35:24.966722 INFO: Collecting candidate features
1 day, 3:35:25.093137 WARNING: intensity_correlation has 47 NaNs ( 0.06 % out of 77258)
1 day, 3:35:25.093493 WARNING: height_correlation has 6 NaNs ( 0.01 % out of 77258)
1 day, 3:35:25.099477 INFO: Collecting fragment features
1 day, 3:35:25.161531 INFO: Finished candidate scoring
1 day, 3:35:25.196479 PROGRESS: === Extracted 77258 precursors and 724876 fragments ===
1 day, 3:35:25.197160 INFO: performing precursor FDR with 47 features
1 day, 3:35:25.197202 INFO: Decoy channel: -1
1 day, 3:35:25.197226 INFO: Competetive: True
1 day, 3:35:25.231813 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:35:25.248865 WARNING: dropped 25 target PSMs due to missing features
1 day, 3:35:25.248997 WARNING: dropped 24 decoy PSMs due to missing features
1 day, 3:35:26.560815 INFO: Test AUC: 0.548
1 day, 3:35:26.560950 INFO: Train AUC: 0.591
1 day, 3:35:26.560980 INFO: AUC difference: 7.22%
1 day, 3:35:26.561002 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:35:26.656089 INFO: Resetting torch num_threads to 100
1 day, 3:35:26.659143 INFO: === FDR correction performed with classifier version 4 ===
1 day, 3:35:26.662797 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:35:26.662955 PROGRESS: Total precursors accumulated: 20,874
1 day, 3:35:26.663020 PROGRESS: Target precursors: 12,812 (61.38%)
1 day, 3:35:26.663072 PROGRESS: Decoy precursors: 8,062 (38.62%)
1 day, 3:35:26.663122 PROGRESS: 
1 day, 3:35:26.663168 PROGRESS: Precursor Summary:
1 day, 3:35:26.664282 PROGRESS: Channel   0:	 0.05 FDR:   446; 0.01 FDR:   336; 0.001 FDR:   326
1 day, 3:35:26.664378 PROGRESS: 
1 day, 3:35:26.664434 PROGRESS: Protein Summary:
1 day, 3:35:26.665719 PROGRESS: Channel   0:	 0.05 FDR:   427; 0.01 FDR:   321; 0.001 FDR:   312
1 day, 3:35:26.665817 PROGRESS: =========================================================================
1 day, 3:35:26.672746 INFO: fragments_df_filtered: 3589
1 day, 3:35:26.843423 INFO: calibration group: precursor, fitting mz estimator 
1 day, 3:35:26.880862 INFO: calibration group: precursor, fitting rt estimator 
1 day, 3:35:26.919137 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 3:35:26.957121 INFO: calibration group: fragment, fitting mz estimator 
1 day, 3:35:27.156203 INFO: calibration group: precursor, predicting mz
1 day, 3:35:27.163583 INFO: calibration group: precursor, predicting rt
1 day, 3:35:27.192280 INFO: calibration group: precursor, predicting mobility
1 day, 3:35:27.198938 INFO: calibration group: fragment, predicting mz
1 day, 3:35:27.250906 INFO: === checking if optimization conditions were reached ===
1 day, 3:35:27.251243 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 3:35:27.253666 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 111.6870.
1 day, 3:35:27.253731 INFO: ==============================================
1 day, 3:35:27.253844 INFO: Starting optimization step 5.
1 day, 3:35:27.253921 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 3:35:27.254021 PROGRESS: Extracting batch of 47305 precursors
1 day, 3:35:27.270939 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:35:27.271065 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:35:27.272136 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 3:35:27.272177 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.03
1 day, 3:35:27.281239 INFO: Starting candidate selection
1 day, 3:35:40.232525 INFO: Starting candidate scoring
1 day, 3:35:42.687949 INFO: Finished candidate processing
1 day, 3:35:42.688066 INFO: Collecting candidate features
1 day, 3:35:42.808410 WARNING: intensity_correlation has 43 NaNs ( 0.06 % out of 77229)
1 day, 3:35:42.808795 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 77229)
1 day, 3:35:42.818658 INFO: Collecting fragment features
1 day, 3:35:42.862497 INFO: Finished candidate scoring
1 day, 3:35:42.921347 PROGRESS: === Extracted 77229 precursors and 722948 fragments ===
1 day, 3:35:42.921775 INFO: performing precursor FDR with 47 features
1 day, 3:35:42.921814 INFO: Decoy channel: -1
1 day, 3:35:42.921844 INFO: Competetive: True
1 day, 3:35:42.944356 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:35:42.959618 WARNING: dropped 28 target PSMs due to missing features
1 day, 3:35:42.959770 WARNING: dropped 17 decoy PSMs due to missing features
1 day, 3:35:44.207454 INFO: Test AUC: 0.534
1 day, 3:35:44.207596 INFO: Train AUC: 0.587
1 day, 3:35:44.207631 INFO: AUC difference: 8.98%
1 day, 3:35:44.207655 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:35:44.293792 INFO: Resetting torch num_threads to 100
1 day, 3:35:44.328093 INFO: === FDR correction performed with classifier version 4 ===
1 day, 3:35:44.331909 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:35:44.332055 PROGRESS: Total precursors accumulated: 20,885
1 day, 3:35:44.332126 PROGRESS: Target precursors: 12,672 (60.68%)
1 day, 3:35:44.332186 PROGRESS: Decoy precursors: 8,213 (39.32%)
1 day, 3:35:44.332242 PROGRESS: 
1 day, 3:35:44.332295 PROGRESS: Precursor Summary:
1 day, 3:35:44.333478 PROGRESS: Channel   0:	 0.05 FDR:   428; 0.01 FDR:   341; 0.001 FDR:   237
1 day, 3:35:44.333578 PROGRESS: 
1 day, 3:35:44.333641 PROGRESS: Protein Summary:
1 day, 3:35:44.334903 PROGRESS: Channel   0:	 0.05 FDR:   410; 0.01 FDR:   327; 0.001 FDR:   228
1 day, 3:35:44.334998 PROGRESS: =========================================================================
1 day, 3:35:44.341979 INFO: fragments_df_filtered: 3611
1 day, 3:35:44.550043 INFO: calibration group: precursor, fitting mz estimator 
1 day, 3:35:44.595238 INFO: calibration group: precursor, fitting rt estimator 
1 day, 3:35:45.693552 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 3:35:45.741836 INFO: calibration group: fragment, fitting mz estimator 
1 day, 3:35:46.010309 INFO: calibration group: precursor, predicting mz
1 day, 3:35:46.018826 INFO: calibration group: precursor, predicting rt
1 day, 3:35:46.049271 INFO: calibration group: precursor, predicting mobility
1 day, 3:35:46.056544 INFO: calibration group: fragment, predicting mz
1 day, 3:35:46.112041 INFO: === checking if optimization conditions were reached ===
1 day, 3:35:46.112334 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 3:35:46.114429 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 108.5777.
1 day, 3:35:46.114490 INFO: ==============================================
1 day, 3:35:46.114602 INFO: Starting optimization step 6.
1 day, 3:35:46.114687 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 3:35:46.114764 PROGRESS: Extracting batch of 47305 precursors
1 day, 3:35:46.132864 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:35:46.132991 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:35:46.133054 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 3:35:46.133088 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.08
1 day, 3:35:46.142994 INFO: Starting candidate selection
1 day, 3:35:58.791351 INFO: Starting candidate scoring
1 day, 3:36:01.289227 INFO: Finished candidate processing
1 day, 3:36:01.289364 INFO: Collecting candidate features
1 day, 3:36:01.414364 WARNING: intensity_correlation has 50 NaNs ( 0.06 % out of 76964)
1 day, 3:36:01.414666 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 76964)
1 day, 3:36:01.421417 INFO: Collecting fragment features
1 day, 3:36:01.472060 INFO: Finished candidate scoring
1 day, 3:36:01.508333 PROGRESS: === Extracted 76964 precursors and 721072 fragments ===
1 day, 3:36:01.508754 INFO: performing precursor FDR with 47 features
1 day, 3:36:01.508791 INFO: Decoy channel: -1
1 day, 3:36:01.508819 INFO: Competetive: True
1 day, 3:36:01.534676 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:36:01.550028 WARNING: dropped 29 target PSMs due to missing features
1 day, 3:36:01.550178 WARNING: dropped 24 decoy PSMs due to missing features
1 day, 3:36:02.765891 INFO: Test AUC: 0.547
1 day, 3:36:02.766039 INFO: Train AUC: 0.586
1 day, 3:36:02.766074 INFO: AUC difference: 6.61%
1 day, 3:36:02.766100 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:36:02.851244 INFO: Resetting torch num_threads to 100
1 day, 3:36:02.854304 INFO: === FDR correction performed with classifier version 4 ===
1 day, 3:36:02.857943 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:36:02.858123 PROGRESS: Total precursors accumulated: 20,810
1 day, 3:36:02.858196 PROGRESS: Target precursors: 12,643 (60.75%)
1 day, 3:36:02.858259 PROGRESS: Decoy precursors: 8,167 (39.25%)
1 day, 3:36:02.858316 PROGRESS: 
1 day, 3:36:02.858369 PROGRESS: Precursor Summary:
1 day, 3:36:02.859576 PROGRESS: Channel   0:	 0.05 FDR:   421; 0.01 FDR:   351; 0.001 FDR:   324
1 day, 3:36:02.860264 PROGRESS: 
1 day, 3:36:02.860341 PROGRESS: Protein Summary:
1 day, 3:36:02.861672 PROGRESS: Channel   0:	 0.05 FDR:   403; 0.01 FDR:   337; 0.001 FDR:   312
1 day, 3:36:02.861779 PROGRESS: =========================================================================
1 day, 3:36:02.869012 INFO: fragments_df_filtered: 3649
1 day, 3:36:03.037331 INFO: calibration group: precursor, fitting mz estimator 
1 day, 3:36:03.074069 INFO: calibration group: precursor, fitting rt estimator 
1 day, 3:36:03.114120 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 3:36:03.152121 INFO: calibration group: fragment, fitting mz estimator 
1 day, 3:36:03.358338 INFO: calibration group: precursor, predicting mz
1 day, 3:36:03.365955 INFO: calibration group: precursor, predicting rt
1 day, 3:36:03.394612 INFO: calibration group: precursor, predicting mobility
1 day, 3:36:03.401560 INFO: calibration group: fragment, predicting mz
1 day, 3:36:03.454770 INFO: === checking if optimization conditions were reached ===
1 day, 3:36:03.455086 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 3:36:03.456435 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 108.5777 found after 7 searches.
1 day, 3:36:03.456493 INFO: ==============================================
1 day, 3:36:03.456598 PROGRESS: Optimization finished for rt_error.
1 day, 3:36:03.623091 INFO: calibration group: precursor, predicting mz
1 day, 3:36:03.630770 INFO: calibration group: precursor, predicting rt
1 day, 3:36:03.660267 INFO: calibration group: precursor, predicting mobility
1 day, 3:36:03.667166 INFO: calibration group: fragment, predicting mz
1 day, 3:36:03.746317 INFO: Starting optimization step 0.
1 day, 3:36:03.746560 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 3:36:03.746634 PROGRESS: Extracting batch of 47305 precursors
1 day, 3:36:03.758784 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:36:03.758906 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:36:03.758946 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 3:36:03.758970 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.00
1 day, 3:36:03.767920 INFO: Starting candidate selection
1 day, 3:36:16.353378 INFO: Starting candidate scoring
1 day, 3:36:18.795371 INFO: Finished candidate processing
1 day, 3:36:18.795559 INFO: Collecting candidate features
1 day, 3:36:18.936878 WARNING: intensity_correlation has 53 NaNs ( 0.07 % out of 77120)
1 day, 3:36:18.937226 WARNING: height_correlation has 9 NaNs ( 0.01 % out of 77120)
1 day, 3:36:18.944850 INFO: Collecting fragment features
1 day, 3:36:19.007239 INFO: Finished candidate scoring
1 day, 3:36:19.057781 PROGRESS: === Extracted 77120 precursors and 722107 fragments ===
1 day, 3:36:19.058189 INFO: performing precursor FDR with 47 features
1 day, 3:36:19.058227 INFO: Decoy channel: -1
1 day, 3:36:19.058251 INFO: Competetive: True
1 day, 3:36:19.083263 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:36:19.098624 WARNING: dropped 30 target PSMs due to missing features
1 day, 3:36:19.098767 WARNING: dropped 26 decoy PSMs due to missing features
1 day, 3:36:20.381869 INFO: Test AUC: 0.560
1 day, 3:36:20.382032 INFO: Train AUC: 0.602
1 day, 3:36:20.382062 INFO: AUC difference: 7.01%
1 day, 3:36:20.382084 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:36:20.477371 INFO: Resetting torch num_threads to 100
1 day, 3:36:20.480695 INFO: === FDR correction performed with classifier version 11 ===
1 day, 3:36:20.484682 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:36:20.484845 PROGRESS: Total precursors accumulated: 20,843
1 day, 3:36:20.484917 PROGRESS: Target precursors: 12,981 (62.28%)
1 day, 3:36:20.484974 PROGRESS: Decoy precursors: 7,862 (37.72%)
1 day, 3:36:20.485035 PROGRESS: 
1 day, 3:36:20.485085 PROGRESS: Precursor Summary:
1 day, 3:36:20.486328 PROGRESS: Channel   0:	 0.05 FDR:   461; 0.01 FDR:   357; 0.001 FDR:   336
1 day, 3:36:20.486426 PROGRESS: 
1 day, 3:36:20.486485 PROGRESS: Protein Summary:
1 day, 3:36:20.487808 PROGRESS: Channel   0:	 0.05 FDR:   441; 0.01 FDR:   343; 0.001 FDR:   322
1 day, 3:36:20.487904 PROGRESS: =========================================================================
1 day, 3:36:20.495607 INFO: fragments_df_filtered: 3746
1 day, 3:36:20.684521 INFO: calibration group: precursor, fitting mz estimator 
1 day, 3:36:20.730015 INFO: calibration group: precursor, fitting rt estimator 
1 day, 3:36:20.781474 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 3:36:20.829729 INFO: calibration group: fragment, fitting mz estimator 
1 day, 3:36:21.111460 INFO: calibration group: precursor, predicting mz
1 day, 3:36:21.119456 INFO: calibration group: precursor, predicting rt
1 day, 3:36:21.149210 INFO: calibration group: precursor, predicting mobility
1 day, 3:36:21.156217 INFO: calibration group: fragment, predicting mz
1 day, 3:36:21.210830 INFO: === checking if optimization conditions were reached ===
1 day, 3:36:21.211138 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 3:36:21.213961 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0728.
1 day, 3:36:21.214118 INFO: ==============================================
1 day, 3:36:21.214267 INFO: Starting optimization step 1.
1 day, 3:36:21.214337 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 3:36:21.214410 PROGRESS: Extracting batch of 47305 precursors
1 day, 3:36:21.229161 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:36:21.229279 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:36:21.229331 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 3:36:21.229358 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.95
1 day, 3:36:21.238368 INFO: Starting candidate selection
1 day, 3:36:30.624423 INFO: Starting candidate scoring
1 day, 3:36:32.983388 INFO: Finished candidate processing
1 day, 3:36:32.983563 INFO: Collecting candidate features
1 day, 3:36:33.134370 WARNING: intensity_correlation has 55 NaNs ( 0.07 % out of 75719)
1 day, 3:36:33.134758 WARNING: height_correlation has 8 NaNs ( 0.01 % out of 75719)
1 day, 3:36:33.142567 INFO: Collecting fragment features
1 day, 3:36:33.196464 INFO: Finished candidate scoring
1 day, 3:36:33.232827 PROGRESS: === Extracted 75719 precursors and 704011 fragments ===
1 day, 3:36:33.233324 INFO: performing precursor FDR with 47 features
1 day, 3:36:33.233369 INFO: Decoy channel: -1
1 day, 3:36:33.233395 INFO: Competetive: True
1 day, 3:36:33.259926 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:36:33.275501 WARNING: dropped 23 target PSMs due to missing features
1 day, 3:36:33.275639 WARNING: dropped 37 decoy PSMs due to missing features
1 day, 3:36:34.483883 INFO: Test AUC: 0.563
1 day, 3:36:34.484025 INFO: Train AUC: 0.615
1 day, 3:36:34.484056 INFO: AUC difference: 8.38%
1 day, 3:36:34.484079 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:36:34.571700 INFO: Resetting torch num_threads to 100
1 day, 3:36:34.574811 INFO: === FDR correction performed with classifier version 11 ===
1 day, 3:36:34.578562 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:36:34.578737 PROGRESS: Total precursors accumulated: 20,491
1 day, 3:36:34.578823 PROGRESS: Target precursors: 12,979 (63.34%)
1 day, 3:36:34.578899 PROGRESS: Decoy precursors: 7,512 (36.66%)
1 day, 3:36:34.578964 PROGRESS: 
1 day, 3:36:34.579028 PROGRESS: Precursor Summary:
1 day, 3:36:34.580296 PROGRESS: Channel   0:	 0.05 FDR:   523; 0.01 FDR:   325; 0.001 FDR:   314
1 day, 3:36:34.580402 PROGRESS: 
1 day, 3:36:34.580476 PROGRESS: Protein Summary:
1 day, 3:36:34.581836 PROGRESS: Channel   0:	 0.05 FDR:   500; 0.01 FDR:   313; 0.001 FDR:   302
1 day, 3:36:34.581934 PROGRESS: =========================================================================
1 day, 3:36:34.588519 INFO: fragments_df_filtered: 3452
1 day, 3:36:34.753047 INFO: calibration group: precursor, fitting mz estimator 
1 day, 3:36:34.789308 INFO: calibration group: precursor, fitting rt estimator 
1 day, 3:36:34.829824 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 3:36:34.869079 INFO: calibration group: fragment, fitting mz estimator 
1 day, 3:36:35.056117 INFO: calibration group: precursor, predicting mz
1 day, 3:36:35.063676 INFO: calibration group: precursor, predicting rt
1 day, 3:36:35.092361 INFO: calibration group: precursor, predicting mobility
1 day, 3:36:35.099353 INFO: calibration group: fragment, predicting mz
1 day, 3:36:35.152509 INFO: === checking if optimization conditions were reached ===
1 day, 3:36:35.152800 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 3:36:35.154880 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0550.
1 day, 3:36:35.154944 INFO: ==============================================
1 day, 3:36:35.155052 INFO: Starting optimization step 2.
1 day, 3:36:35.155130 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 3:36:35.155204 PROGRESS: Extracting batch of 47305 precursors
1 day, 3:36:35.172709 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:36:35.172848 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:36:35.172896 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 3:36:35.172926 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.12
1 day, 3:36:35.181905 INFO: Starting candidate selection
1 day, 3:36:42.921656 INFO: Starting candidate scoring
1 day, 3:36:45.301528 INFO: Finished candidate processing
1 day, 3:36:45.301712 INFO: Collecting candidate features
1 day, 3:36:45.460288 WARNING: intensity_correlation has 64 NaNs ( 0.09 % out of 73886)
1 day, 3:36:45.460676 WARNING: height_correlation has 13 NaNs ( 0.02 % out of 73886)
1 day, 3:36:45.469417 INFO: Collecting fragment features
1 day, 3:36:45.523584 INFO: Finished candidate scoring
1 day, 3:36:45.592955 PROGRESS: === Extracted 73886 precursors and 682131 fragments ===
1 day, 3:36:45.593395 INFO: performing precursor FDR with 47 features
1 day, 3:36:45.593434 INFO: Decoy channel: -1
1 day, 3:36:45.593458 INFO: Competetive: True
1 day, 3:36:45.623355 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:36:45.641428 WARNING: dropped 31 target PSMs due to missing features
1 day, 3:36:45.641575 WARNING: dropped 39 decoy PSMs due to missing features
1 day, 3:36:47.033999 INFO: Test AUC: 0.560
1 day, 3:36:47.034143 INFO: Train AUC: 0.600
1 day, 3:36:47.034174 INFO: AUC difference: 6.74%
1 day, 3:36:47.034195 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:36:47.130583 INFO: Resetting torch num_threads to 100
1 day, 3:36:47.133800 INFO: === FDR correction performed with classifier version 11 ===
1 day, 3:36:47.138097 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:36:47.138278 PROGRESS: Total precursors accumulated: 20,063
1 day, 3:36:47.138343 PROGRESS: Target precursors: 12,447 (62.04%)
1 day, 3:36:47.138396 PROGRESS: Decoy precursors: 7,616 (37.96%)
1 day, 3:36:47.138445 PROGRESS: 
1 day, 3:36:47.138491 PROGRESS: Precursor Summary:
1 day, 3:36:47.139673 PROGRESS: Channel   0:	 0.05 FDR:   434; 0.01 FDR:   357; 0.001 FDR:   277
1 day, 3:36:47.139779 PROGRESS: 
1 day, 3:36:47.139837 PROGRESS: Protein Summary:
1 day, 3:36:47.141139 PROGRESS: Channel   0:	 0.05 FDR:   415; 0.01 FDR:   344; 0.001 FDR:   268
1 day, 3:36:47.141235 PROGRESS: =========================================================================
1 day, 3:36:47.148660 INFO: fragments_df_filtered: 3644
1 day, 3:36:47.666241 INFO: calibration group: precursor, fitting mz estimator 
1 day, 3:36:47.708598 INFO: calibration group: precursor, fitting rt estimator 
1 day, 3:36:47.752370 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 3:36:47.791655 INFO: calibration group: fragment, fitting mz estimator 
1 day, 3:36:47.998402 INFO: calibration group: precursor, predicting mz
1 day, 3:36:48.006356 INFO: calibration group: precursor, predicting rt
1 day, 3:36:48.035260 INFO: calibration group: precursor, predicting mobility
1 day, 3:36:48.042312 INFO: calibration group: fragment, predicting mz
1 day, 3:36:48.097195 INFO: === checking if optimization conditions were reached ===
1 day, 3:36:48.097537 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 3:36:48.100055 PROGRESS: ❌ mobility_error : optimization incomplete after 3 search(es). Will search with parameter 0.0442.
1 day, 3:36:48.100122 INFO: ==============================================
1 day, 3:36:48.100235 INFO: Starting optimization step 3.
1 day, 3:36:48.100316 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 3:36:48.100390 PROGRESS: Extracting batch of 47305 precursors
1 day, 3:36:48.122216 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:36:48.122368 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:36:48.122424 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 3:36:48.122454 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.08
1 day, 3:36:48.131424 INFO: Starting candidate selection
1 day, 3:36:54.392955 INFO: Starting candidate scoring
1 day, 3:36:56.787871 INFO: Finished candidate processing
1 day, 3:36:56.788047 INFO: Collecting candidate features
1 day, 3:36:56.931693 WARNING: intensity_correlation has 64 NaNs ( 0.09 % out of 73048)
1 day, 3:36:56.932003 WARNING: height_correlation has 8 NaNs ( 0.01 % out of 73048)
1 day, 3:36:56.937778 INFO: Collecting fragment features
1 day, 3:36:56.989704 INFO: Finished candidate scoring
1 day, 3:36:57.023230 PROGRESS: === Extracted 73048 precursors and 667746 fragments ===
1 day, 3:36:57.023713 INFO: performing precursor FDR with 47 features
1 day, 3:36:57.023753 INFO: Decoy channel: -1
1 day, 3:36:57.023779 INFO: Competetive: True
1 day, 3:36:57.047528 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:36:57.061894 WARNING: dropped 31 target PSMs due to missing features
1 day, 3:36:57.062033 WARNING: dropped 36 decoy PSMs due to missing features
1 day, 3:36:58.158468 INFO: Test AUC: 0.557
1 day, 3:36:58.158608 INFO: Train AUC: 0.600
1 day, 3:36:58.158639 INFO: AUC difference: 7.06%
1 day, 3:36:58.158661 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:36:58.247386 INFO: Resetting torch num_threads to 100
1 day, 3:36:58.250284 INFO: === FDR correction performed with classifier version 11 ===
1 day, 3:36:58.253583 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:36:58.253728 PROGRESS: Total precursors accumulated: 19,862
1 day, 3:36:58.253793 PROGRESS: Target precursors: 12,381 (62.34%)
1 day, 3:36:58.253847 PROGRESS: Decoy precursors: 7,481 (37.66%)
1 day, 3:36:58.253896 PROGRESS: 
1 day, 3:36:58.253942 PROGRESS: Precursor Summary:
1 day, 3:36:58.255061 PROGRESS: Channel   0:	 0.05 FDR:   453; 0.01 FDR:   355; 0.001 FDR:   260
1 day, 3:36:58.255157 PROGRESS: 
1 day, 3:36:58.255213 PROGRESS: Protein Summary:
1 day, 3:36:58.256477 PROGRESS: Channel   0:	 0.05 FDR:   434; 0.01 FDR:   342; 0.001 FDR:   250
1 day, 3:36:58.256572 PROGRESS: =========================================================================
1 day, 3:36:58.263573 INFO: fragments_df_filtered: 3667
1 day, 3:36:58.448148 INFO: calibration group: precursor, fitting mz estimator 
1 day, 3:36:58.494950 INFO: calibration group: precursor, fitting rt estimator 
1 day, 3:36:58.546730 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 3:36:58.592601 INFO: calibration group: fragment, fitting mz estimator 
1 day, 3:36:58.869020 INFO: calibration group: precursor, predicting mz
1 day, 3:36:58.876389 INFO: calibration group: precursor, predicting rt
1 day, 3:36:58.904739 INFO: calibration group: precursor, predicting mobility
1 day, 3:36:58.911485 INFO: calibration group: fragment, predicting mz
1 day, 3:36:58.963023 INFO: === checking if optimization conditions were reached ===
1 day, 3:36:58.963315 PROGRESS: === Optimization of mobility_error has been performed 4 time(s); minimum number is 2 ===
1 day, 3:36:58.965293 PROGRESS: ❌ mobility_error : optimization incomplete after 4 search(es). Will search with parameter 0.0407.
1 day, 3:36:58.965353 INFO: ==============================================
1 day, 3:36:58.965454 INFO: Starting optimization step 4.
1 day, 3:36:58.965521 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 3:36:58.965588 PROGRESS: Extracting batch of 47305 precursors
1 day, 3:36:58.977952 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:36:58.978073 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:36:58.978124 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 3:36:58.978147 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.01
1 day, 3:36:58.986818 INFO: Starting candidate selection
1 day, 3:37:04.153800 INFO: Starting candidate scoring
1 day, 3:37:05.449723 INFO: Finished candidate processing
1 day, 3:37:05.449842 INFO: Collecting candidate features
1 day, 3:37:05.556163 WARNING: intensity_correlation has 455 NaNs ( 0.69 % out of 66290)
1 day, 3:37:05.556501 WARNING: height_correlation has 9 NaNs ( 0.01 % out of 66290)
1 day, 3:37:05.563697 INFO: Collecting fragment features
1 day, 3:37:05.595958 INFO: Finished candidate scoring
1 day, 3:37:05.628222 PROGRESS: === Extracted 66290 precursors and 371537 fragments ===
1 day, 3:37:05.628630 INFO: performing precursor FDR with 47 features
1 day, 3:37:05.628671 INFO: Decoy channel: -1
1 day, 3:37:05.628695 INFO: Competetive: True
1 day, 3:37:05.647437 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:37:05.660165 WARNING: dropped 238 target PSMs due to missing features
1 day, 3:37:05.660310 WARNING: dropped 221 decoy PSMs due to missing features
1 day, 3:37:06.647996 INFO: Test AUC: 0.528
1 day, 3:37:06.648135 INFO: Train AUC: 0.584
1 day, 3:37:06.648166 INFO: AUC difference: 9.68%
1 day, 3:37:06.648189 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:37:06.734476 INFO: Resetting torch num_threads to 100
1 day, 3:37:06.737195 INFO: === FDR correction performed with classifier version 11 ===
1 day, 3:37:06.740359 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:37:06.740509 PROGRESS: Total precursors accumulated: 18,875
1 day, 3:37:06.740574 PROGRESS: Target precursors: 11,308 (59.91%)
1 day, 3:37:06.740635 PROGRESS: Decoy precursors: 7,567 (40.09%)
1 day, 3:37:06.740685 PROGRESS: 
1 day, 3:37:06.740734 PROGRESS: Precursor Summary:
1 day, 3:37:06.743323 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1 day, 3:37:06.743429 PROGRESS: 
1 day, 3:37:06.743487 PROGRESS: Protein Summary:
1 day, 3:37:06.744516 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1 day, 3:37:06.744608 PROGRESS: =========================================================================
1 day, 3:37:07.029206 INFO: calibration group: precursor, predicting mz
1 day, 3:37:07.038793 INFO: calibration group: precursor, predicting rt
1 day, 3:37:07.078076 INFO: calibration group: precursor, predicting mobility
1 day, 3:37:07.087750 INFO: calibration group: fragment, predicting mz
1 day, 3:37:07.158586 INFO: === skipping optimization until target number of precursors are found ===
1 day, 3:37:07.158890 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
1 day, 3:37:07.158955 INFO: Starting optimization step 5.
1 day, 3:37:07.159041 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1 day, 3:37:07.159117 PROGRESS: Extracting batch of 63016 precursors
1 day, 3:37:07.175909 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:37:07.176046 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:37:07.176097 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 3:37:07.176126 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.01
1 day, 3:37:07.177088 INFO: Starting candidate selection
1 day, 3:37:13.750426 INFO: Starting candidate scoring
1 day, 3:37:15.443235 INFO: Finished candidate processing
1 day, 3:37:15.443345 INFO: Collecting candidate features
1 day, 3:37:15.583160 WARNING: intensity_correlation has 606 NaNs ( 0.69 % out of 88431)
1 day, 3:37:15.583532 WARNING: height_correlation has 21 NaNs ( 0.02 % out of 88431)
1 day, 3:37:15.591551 INFO: Collecting fragment features
1 day, 3:37:15.637098 INFO: Finished candidate scoring
1 day, 3:37:15.713950 PROGRESS: === Extracted 154721 precursors and 867858 fragments ===
1 day, 3:37:15.728372 INFO: performing precursor FDR with 47 features
1 day, 3:37:15.728484 INFO: Decoy channel: -1
1 day, 3:37:15.728509 INFO: Competetive: True
1 day, 3:37:15.789018 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:37:15.819179 WARNING: dropped 551 target PSMs due to missing features
1 day, 3:37:15.819326 WARNING: dropped 522 decoy PSMs due to missing features
1 day, 3:37:18.521247 INFO: Test AUC: 0.534
1 day, 3:37:18.521390 INFO: Train AUC: 0.579
1 day, 3:37:18.521420 INFO: AUC difference: 7.78%
1 day, 3:37:18.521441 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:37:18.614262 INFO: Resetting torch num_threads to 100
1 day, 3:37:18.621595 INFO: === FDR correction performed with classifier version 11 ===
1 day, 3:37:18.629389 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:37:18.629676 PROGRESS: Total precursors accumulated: 44,110
1 day, 3:37:18.629740 PROGRESS: Target precursors: 26,272 (59.56%)
1 day, 3:37:18.629791 PROGRESS: Decoy precursors: 17,838 (40.44%)
1 day, 3:37:18.629839 PROGRESS: 
1 day, 3:37:18.629885 PROGRESS: Precursor Summary:
1 day, 3:37:18.631032 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1 day, 3:37:18.631130 PROGRESS: 
1 day, 3:37:18.631186 PROGRESS: Protein Summary:
1 day, 3:37:18.632316 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1 day, 3:37:18.632410 PROGRESS: =========================================================================
1 day, 3:37:18.954072 INFO: calibration group: precursor, predicting mz
1 day, 3:37:18.971831 INFO: calibration group: precursor, predicting rt
1 day, 3:37:19.050257 INFO: calibration group: precursor, predicting mobility
1 day, 3:37:19.070485 INFO: calibration group: fragment, predicting mz
1 day, 3:37:19.227144 INFO: === skipping optimization until target number of precursors are found ===
1 day, 3:37:19.227435 PROGRESS: === Optimization of mobility_error has been skipped 2 time(s); maximum number is 1 ===
1 day, 3:37:19.227784 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.0442 found after 4 searches.
1 day, 3:37:19.227857 PROGRESS: Optimization finished for mobility_error.
1 day, 3:37:19.419647 INFO: calibration group: precursor, predicting mz
1 day, 3:37:19.427437 INFO: calibration group: precursor, predicting rt
1 day, 3:37:19.456136 INFO: calibration group: precursor, predicting mobility
1 day, 3:37:19.463625 INFO: calibration group: fragment, predicting mz
1 day, 3:37:19.542095 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 3:37:19.542334 PROGRESS: ==============================================
1 day, 3:37:19.542428 PROGRESS: ms2_error      : 15.0000
1 day, 3:37:19.542512 PROGRESS: ms1_error      : 10.0000
1 day, 3:37:19.542586 PROGRESS: rt_error       : 108.5777
1 day, 3:37:19.542659 PROGRESS: mobility_error : 0.0442
1 day, 3:37:19.542723 PROGRESS: ==============================================
1 day, 3:37:19.545810 INFO: calibration group: precursor, predicting mz
1 day, 3:37:21.048802 INFO: calibration group: precursor, predicting rt
1 day, 3:37:27.530135 INFO: calibration group: precursor, predicting mobility
1 day, 3:37:28.995516 INFO: calibration group: fragment, predicting mz
1 day, 3:37:41.507685 PROGRESS: Extracting batch of 10272670 precursors
1 day, 3:37:43.982903 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:37:43.983043 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:37:43.983094 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 3:37:43.983120 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.01
1 day, 3:37:43.987659 INFO: Starting candidate selection
1 day, 3:55:14.038565 INFO: Applying score cutoff of 13.930057899475097
1 day, 3:55:14.583282 INFO: Removed 2371988 precursors with score below cutoff
1 day, 3:55:17.063764 INFO: Starting candidate scoring
1 day, 3:59:04.117699 INFO: Finished candidate processing
1 day, 3:59:04.118330 INFO: Collecting candidate features
1 day, 3:59:28.296463 WARNING: intensity_correlation has 81345 NaNs ( 0.59 % out of 13820635)
1 day, 3:59:28.310421 WARNING: height_correlation has 1557 NaNs ( 0.01 % out of 13820635)
1 day, 3:59:28.765506 INFO: Collecting fragment features
1 day, 3:59:36.546146 INFO: Finished candidate scoring
1 day, 3:59:51.646327 INFO: === FDR correction performed with classifier version 15 ===
1 day, 3:59:51.650632 INFO: performing precursor FDR with 47 features
1 day, 3:59:51.650709 INFO: Decoy channel: -1
1 day, 3:59:51.650744 INFO: Competetive: True
1 day, 3:59:55.296233 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:59:57.549162 WARNING: dropped 41241 target PSMs due to missing features
1 day, 3:59:57.549321 WARNING: dropped 41007 decoy PSMs due to missing features
1 day, 4:04:08.147853 INFO: Test AUC: 0.545
1 day, 4:04:08.148132 INFO: Train AUC: 0.557
1 day, 4:04:08.148173 INFO: AUC difference: 2.27%
1 day, 4:04:08.995384 INFO: Resetting torch num_threads to 100
1 day, 4:04:09.306761 INFO: Removing fragments below FDR threshold
1 day, 4:04:09.450331 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:04:09.450649 PROGRESS: Total precursors accumulated: 0
1 day, 4:04:09.450724 PROGRESS: Target precursors: 0 (0.00%)
1 day, 4:04:09.450781 PROGRESS: Decoy precursors: 0 (0.00%)
1 day, 4:04:09.450833 PROGRESS: 
1 day, 4:04:09.450887 PROGRESS: Precursor Summary:
1 day, 4:04:09.451028 PROGRESS: 
1 day, 4:04:09.451098 PROGRESS: Protein Summary:
1 day, 4:04:09.451176 PROGRESS: =========================================================================
1 day, 4:04:09.629513 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 4:04:10.061352 PROGRESS: Loading raw file 4/6: ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 4:04:10.062224 INFO: Quantification results path: run_output/alphadia_1.10_defaultMBR/library/quant
1 day, 4:04:10.062335 INFO: Creating workflow folder for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496 at run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 4:04:10.063188 INFO: Initializing RawFileManager
1 day, 4:04:10.063318 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:04:10.063387 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:04:10.063429 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:04:10.285106 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
1 day, 4:04:20.201121 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d...
1 day, 4:04:20.202393 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:04:20.205784 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:04:20.206073 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:04:20.206463 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:04:20.207638 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:04:20.224046 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:04:20.224288 INFO: Indexing quadrupole dimension
1 day, 4:04:20.709221 INFO: Transposing detector events
1 day, 4:04:30.041433 INFO: Finished transposing data
1 day, 4:04:30.079049 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 4:04:30.080030 INFO: RT (min)            : 0.0 - 70.0
1 day, 4:04:30.080127 INFO: RT duration (sec)   : 4199.8
1 day, 4:04:30.080185 INFO: RT duration (min)   : 70.0
1 day, 4:04:30.080242 INFO: Cycle len (scans)   : 9
1 day, 4:04:30.080288 INFO: Cycle len (sec)     : 0.97
1 day, 4:04:30.080335 INFO: Number of cycles    : 4347
1 day, 4:04:30.080380 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 4:04:31.494115 INFO: Initializing CalibrationManager
1 day, 4:04:31.494415 INFO: Loading calibration config
1 day, 4:04:31.494824 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'}]
1 day, 4:04:31.494916 INFO: Calibration group :fragment, found 1 estimator(s)
1 day, 4:04:31.494983 INFO: Calibration group :precursor, found 3 estimator(s)
1 day, 4:04:31.495106 INFO: Initializing OptimizationManager
1 day, 4:04:31.495241 INFO: initial parameter: ms1_error = 30
1 day, 4:04:31.495293 INFO: initial parameter: ms2_error = 30
1 day, 4:04:31.495356 INFO: initial parameter: rt_error = 2099.891532
1 day, 4:04:31.495417 INFO: initial parameter: mobility_error = 0.1
1 day, 4:04:31.495464 INFO: initial parameter: column_type = library
1 day, 4:04:31.495508 INFO: initial parameter: num_candidates = 1
1 day, 4:04:31.495553 INFO: initial parameter: classifier_version = -1
1 day, 4:04:31.495598 INFO: initial parameter: fwhm_rt = 5
1 day, 4:04:31.495640 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 4:04:31.495682 INFO: initial parameter: score_cutoff = 0
1 day, 4:04:31.495736 INFO: Initializing TimingManager
1 day, 4:04:31.495786 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 4:04:31.495860 INFO: FDRManager not loaded from disk.
1 day, 4:04:31.495885 INFO: Initializing FDRManager
1 day, 4:04:31.495911 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 4:04:32.783127 PROGRESS: 5,215,079 target precursors potentially observable (0 removed)
1 day, 4:04:34.642774 PROGRESS: Starting initial search for precursors.
1 day, 4:04:34.888385 INFO: Starting optimization step 0.
1 day, 4:04:34.888653 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 4:04:34.888724 PROGRESS: Extracting batch of 15771 precursors
1 day, 4:04:34.892370 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:04:34.892427 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:04:34.892457 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:04:34.892482 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:04:34.893417 INFO: Starting candidate selection
1 day, 4:05:52.383754 INFO: Starting candidate scoring
1 day, 4:05:53.120112 INFO: Finished candidate processing
1 day, 4:05:53.120435 INFO: Collecting candidate features
1 day, 4:05:53.197586 WARNING: intensity_correlation has 4 NaNs ( 0.03 % out of 13802)
1 day, 4:05:53.201350 INFO: Collecting fragment features
1 day, 4:05:53.214498 INFO: Finished candidate scoring
1 day, 4:05:53.230680 PROGRESS: === Extracted 13802 precursors and 138314 fragments ===
1 day, 4:05:53.231171 INFO: performing precursor FDR with 47 features
1 day, 4:05:53.231210 INFO: Decoy channel: -1
1 day, 4:05:53.231238 INFO: Competetive: True
1 day, 4:05:53.236643 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:05:53.239878 WARNING: dropped 3 target PSMs due to missing features
1 day, 4:05:53.239937 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 4:05:53.402307 INFO: Test AUC: 0.510
1 day, 4:05:53.402440 INFO: Train AUC: 0.516
1 day, 4:05:53.402475 INFO: AUC difference: 0.99%
1 day, 4:05:53.485892 INFO: Resetting torch num_threads to 100
1 day, 4:05:53.487299 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:05:53.488914 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:05:53.489045 PROGRESS: Total precursors accumulated: 7,060
1 day, 4:05:53.489126 PROGRESS: Target precursors: 3,698 (52.38%)
1 day, 4:05:53.489195 PROGRESS: Decoy precursors: 3,362 (47.62%)
1 day, 4:05:53.489263 PROGRESS: 
1 day, 4:05:53.489320 PROGRESS: Precursor Summary:
1 day, 4:05:53.490221 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 4:05:53.490319 PROGRESS: 
1 day, 4:05:53.490386 PROGRESS: Protein Summary:
1 day, 4:05:53.491334 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 4:05:53.491436 PROGRESS: =========================================================================
1 day, 4:05:53.654286 INFO: Starting optimization step 1.
1 day, 4:05:53.654592 PROGRESS: === Extracting elution groups 8000 to 24000 ===
1 day, 4:05:53.654681 PROGRESS: Extracting batch of 31534 precursors
1 day, 4:05:53.662746 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:05:53.662829 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:05:53.662875 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:05:53.662899 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:05:53.663937 INFO: Starting candidate selection
1 day, 4:08:29.712946 INFO: Starting candidate scoring
1 day, 4:08:31.154310 INFO: Finished candidate processing
1 day, 4:08:31.154428 INFO: Collecting candidate features
1 day, 4:08:31.212761 WARNING: intensity_correlation has 4 NaNs ( 0.01 % out of 27402)
1 day, 4:08:31.213104 WARNING: height_correlation has 2 NaNs ( 0.01 % out of 27402)
1 day, 4:08:31.219737 INFO: Collecting fragment features
1 day, 4:08:31.240469 INFO: Finished candidate scoring
1 day, 4:08:31.283892 PROGRESS: === Extracted 41204 precursors and 412093 fragments ===
1 day, 4:08:31.290364 INFO: performing precursor FDR with 47 features
1 day, 4:08:31.290452 INFO: Decoy channel: -1
1 day, 4:08:31.290477 INFO: Competetive: True
1 day, 4:08:31.313692 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:08:31.323153 WARNING: dropped 5 target PSMs due to missing features
1 day, 4:08:31.323288 WARNING: dropped 3 decoy PSMs due to missing features
1 day, 4:08:31.997327 INFO: Test AUC: 0.554
1 day, 4:08:31.997469 INFO: Train AUC: 0.560
1 day, 4:08:31.997499 INFO: AUC difference: 1.08%
1 day, 4:08:32.089072 INFO: Resetting torch num_threads to 100
1 day, 4:08:32.107023 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:08:32.110433 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:08:32.110585 PROGRESS: Total precursors accumulated: 21,106
1 day, 4:08:32.110652 PROGRESS: Target precursors: 12,436 (58.92%)
1 day, 4:08:32.110707 PROGRESS: Decoy precursors: 8,670 (41.08%)
1 day, 4:08:32.110757 PROGRESS: 
1 day, 4:08:32.110804 PROGRESS: Precursor Summary:
1 day, 4:08:32.111878 PROGRESS: Channel   0:	 0.05 FDR:    61; 0.01 FDR:    44; 0.001 FDR:    44
1 day, 4:08:32.111972 PROGRESS: 
1 day, 4:08:32.112030 PROGRESS: Protein Summary:
1 day, 4:08:32.113143 PROGRESS: Channel   0:	 0.05 FDR:    60; 0.01 FDR:    43; 0.001 FDR:    43
1 day, 4:08:32.113235 PROGRESS: =========================================================================
1 day, 4:08:32.336965 INFO: Starting optimization step 2.
1 day, 4:08:32.337275 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1 day, 4:08:32.337360 PROGRESS: Extracting batch of 63016 precursors
1 day, 4:08:32.376720 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:08:32.376856 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:08:32.376894 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:08:32.376916 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:08:32.377917 INFO: Starting candidate selection
1 day, 4:13:31.780607 INFO: Starting candidate scoring
1 day, 4:13:34.576194 INFO: Finished candidate processing
1 day, 4:13:34.577376 INFO: Collecting candidate features
1 day, 4:13:34.699610 WARNING: intensity_correlation has 10 NaNs ( 0.02 % out of 54958)
1 day, 4:13:34.699909 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 54958)
1 day, 4:13:34.706543 INFO: Collecting fragment features
1 day, 4:13:34.746860 INFO: Finished candidate scoring
1 day, 4:13:34.832222 PROGRESS: === Extracted 96162 precursors and 961862 fragments ===
1 day, 4:13:34.844600 INFO: performing precursor FDR with 47 features
1 day, 4:13:34.844701 INFO: Decoy channel: -1
1 day, 4:13:34.844728 INFO: Competetive: True
1 day, 4:13:34.888402 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:13:34.910585 WARNING: dropped 12 target PSMs due to missing features
1 day, 4:13:34.910727 WARNING: dropped 7 decoy PSMs due to missing features
1 day, 4:13:36.642508 INFO: Test AUC: 0.560
1 day, 4:13:36.642652 INFO: Train AUC: 0.584
1 day, 4:13:36.642682 INFO: AUC difference: 4.07%
1 day, 4:13:36.735847 INFO: Resetting torch num_threads to 100
1 day, 4:13:36.741493 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:13:36.750948 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:13:36.751265 PROGRESS: Total precursors accumulated: 49,289
1 day, 4:13:36.751332 PROGRESS: Target precursors: 29,985 (60.84%)
1 day, 4:13:36.751401 PROGRESS: Decoy precursors: 19,304 (39.16%)
1 day, 4:13:36.751450 PROGRESS: 
1 day, 4:13:36.751497 PROGRESS: Precursor Summary:
1 day, 4:13:36.752986 PROGRESS: Channel   0:	 0.05 FDR:   490; 0.01 FDR:   368; 0.001 FDR:   191
1 day, 4:13:36.753097 PROGRESS: 
1 day, 4:13:36.753160 PROGRESS: Protein Summary:
1 day, 4:13:36.754590 PROGRESS: Channel   0:	 0.05 FDR:   454; 0.01 FDR:   340; 0.001 FDR:   185
1 day, 4:13:36.754683 PROGRESS: =========================================================================
1 day, 4:13:36.768941 INFO: fragments_df_filtered: 3246
1 day, 4:13:37.000444 INFO: calibration group: precursor, fitting mz estimator 
1 day, 4:13:37.039852 INFO: calibration group: precursor, fitting rt estimator 
1 day, 4:13:37.080358 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 4:13:37.121238 INFO: calibration group: fragment, fitting mz estimator 
1 day, 4:13:37.289942 INFO: calibration group: precursor, predicting mz
1 day, 4:13:37.305906 INFO: calibration group: precursor, predicting rt
1 day, 4:13:37.371234 INFO: calibration group: precursor, predicting mobility
1 day, 4:13:37.385948 INFO: calibration group: fragment, predicting mz
1 day, 4:13:37.524875 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 4:13:37.525208 INFO: Starting optimization step 3.
1 day, 4:13:37.525305 PROGRESS: === Extracting elution groups 0 to 56000 ===
1 day, 4:13:37.525384 PROGRESS: Extracting batch of 110321 precursors
1 day, 4:13:37.554773 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:13:37.554912 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:13:37.554964 INFO: FWHM in RT is 3.29 seconds, sigma is 0.72
1 day, 4:13:37.554989 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.07
1 day, 4:13:37.563736 INFO: Starting candidate selection
1 day, 4:22:33.620155 INFO: Starting candidate scoring
1 day, 4:22:43.462940 INFO: Finished candidate processing
1 day, 4:22:43.463142 INFO: Collecting candidate features
1 day, 4:22:43.789795 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 189298)
1 day, 4:22:43.800116 INFO: Collecting fragment features
1 day, 4:22:43.928700 INFO: Finished candidate scoring
1 day, 4:22:44.027528 PROGRESS: === Extracted 189298 precursors and 1924909 fragments ===
1 day, 4:22:44.028042 INFO: performing precursor FDR with 47 features
1 day, 4:22:44.028083 INFO: Decoy channel: -1
1 day, 4:22:44.028112 INFO: Competetive: True
1 day, 4:22:44.093043 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:22:44.130131 WARNING: dropped 2 target PSMs due to missing features
1 day, 4:22:44.130277 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 4:22:47.779152 INFO: Test AUC: 0.573
1 day, 4:22:47.779293 INFO: Train AUC: 0.592
1 day, 4:22:47.779331 INFO: AUC difference: 3.34%
1 day, 4:22:47.878297 INFO: Resetting torch num_threads to 100
1 day, 4:22:47.884372 INFO: === FDR correction performed with classifier version 2 ===
1 day, 4:22:47.893698 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:22:47.894020 PROGRESS: Total precursors accumulated: 50,272
1 day, 4:22:47.894096 PROGRESS: Target precursors: 31,807 (63.27%)
1 day, 4:22:47.894171 PROGRESS: Decoy precursors: 18,465 (36.73%)
1 day, 4:22:47.894235 PROGRESS: 
1 day, 4:22:47.894298 PROGRESS: Precursor Summary:
1 day, 4:22:47.895753 PROGRESS: Channel   0:	 0.05 FDR:   606; 0.01 FDR:   404; 0.001 FDR:   211
1 day, 4:22:47.895864 PROGRESS: 
1 day, 4:22:47.895934 PROGRESS: Protein Summary:
1 day, 4:22:47.897418 PROGRESS: Channel   0:	 0.05 FDR:   564; 0.01 FDR:   377; 0.001 FDR:   202
1 day, 4:22:47.897524 PROGRESS: =========================================================================
1 day, 4:22:47.908848 INFO: fragments_df_filtered: 4736
1 day, 4:22:48.131573 INFO: calibration group: precursor, fitting mz estimator 
1 day, 4:22:48.181299 INFO: calibration group: precursor, fitting rt estimator 
1 day, 4:22:48.235159 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 4:22:48.277343 INFO: calibration group: fragment, fitting mz estimator 
1 day, 4:22:48.593965 INFO: calibration group: precursor, predicting mz
1 day, 4:22:48.609274 INFO: calibration group: precursor, predicting rt
1 day, 4:22:48.678761 INFO: calibration group: precursor, predicting mobility
1 day, 4:22:48.695543 INFO: calibration group: fragment, predicting mz
1 day, 4:22:48.841416 INFO: === checking if optimization conditions were reached ===
1 day, 4:22:48.844018 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 4:22:48.845196 PROGRESS: ❌ ms1_error      : 10.0000 > 10.0000 or insufficient steps taken.
1 day, 4:22:48.845252 INFO: ==============================================
1 day, 4:22:48.845365 INFO: Starting optimization step 4.
1 day, 4:22:48.845442 PROGRESS: === Extracting elution groups 0 to 56000 ===
1 day, 4:22:48.845522 PROGRESS: Extracting batch of 110321 precursors
1 day, 4:22:48.887152 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:22:48.887301 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:22:48.887363 INFO: FWHM in RT is 3.27 seconds, sigma is 0.72
1 day, 4:22:48.887393 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.09
1 day, 4:22:48.890849 INFO: Starting candidate selection
1 day, 4:30:45.595671 INFO: Starting candidate scoring
1 day, 4:30:51.125854 INFO: Finished candidate processing
1 day, 4:30:51.126046 INFO: Collecting candidate features
1 day, 4:30:51.487588 WARNING: intensity_correlation has 6 NaNs ( 0.00 % out of 188990)
1 day, 4:30:51.488092 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 188990)
1 day, 4:30:51.501045 INFO: Collecting fragment features
1 day, 4:30:51.626128 INFO: Finished candidate scoring
1 day, 4:30:51.740306 PROGRESS: === Extracted 188990 precursors and 1853558 fragments ===
1 day, 4:30:51.740801 INFO: performing precursor FDR with 47 features
1 day, 4:30:51.740842 INFO: Decoy channel: -1
1 day, 4:30:51.740867 INFO: Competetive: True
1 day, 4:30:51.812799 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:30:51.855789 WARNING: dropped 4 target PSMs due to missing features
1 day, 4:30:51.855950 WARNING: dropped 3 decoy PSMs due to missing features
1 day, 4:30:55.603076 INFO: Test AUC: 0.561
1 day, 4:30:55.603220 INFO: Train AUC: 0.593
1 day, 4:30:55.603252 INFO: AUC difference: 5.43%
1 day, 4:30:55.603275 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:30:55.701716 INFO: Resetting torch num_threads to 100
1 day, 4:30:55.709138 INFO: === FDR correction performed with classifier version 3 ===
1 day, 4:30:55.720448 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:30:55.720772 PROGRESS: Total precursors accumulated: 50,200
1 day, 4:30:55.720839 PROGRESS: Target precursors: 31,261 (62.27%)
1 day, 4:30:55.720892 PROGRESS: Decoy precursors: 18,939 (37.73%)
1 day, 4:30:55.720942 PROGRESS: 
1 day, 4:30:55.720990 PROGRESS: Precursor Summary:
1 day, 4:30:55.722606 PROGRESS: Channel   0:	 0.05 FDR:   856; 0.01 FDR:   623; 0.001 FDR:   380
1 day, 4:30:55.722707 PROGRESS: 
1 day, 4:30:55.722766 PROGRESS: Protein Summary:
1 day, 4:30:55.724380 PROGRESS: Channel   0:	 0.05 FDR:   780; 0.01 FDR:   563; 0.001 FDR:   347
1 day, 4:30:55.724478 PROGRESS: =========================================================================
1 day, 4:30:55.740648 INFO: fragments_df_filtered: 5000
1 day, 4:30:55.931506 INFO: calibration group: precursor, fitting mz estimator 
1 day, 4:30:55.985672 INFO: calibration group: precursor, fitting rt estimator 
1 day, 4:30:56.040953 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 4:30:56.093825 INFO: calibration group: fragment, fitting mz estimator 
1 day, 4:30:56.513629 INFO: calibration group: precursor, predicting mz
1 day, 4:30:56.521525 INFO: calibration group: precursor, predicting rt
1 day, 4:30:56.549796 INFO: calibration group: precursor, predicting mobility
1 day, 4:30:56.556335 INFO: calibration group: fragment, predicting mz
1 day, 4:30:56.609565 INFO: === checking if optimization conditions were reached ===
1 day, 4:30:56.611771 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 4:30:56.612774 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
1 day, 4:30:56.612828 INFO: ==============================================
1 day, 4:30:56.612930 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 4:30:56.782667 INFO: calibration group: precursor, predicting mz
1 day, 4:30:56.790482 INFO: calibration group: precursor, predicting rt
1 day, 4:30:56.818752 INFO: calibration group: precursor, predicting mobility
1 day, 4:30:56.825211 INFO: calibration group: fragment, predicting mz
1 day, 4:30:56.877812 INFO: Starting optimization step 0.
1 day, 4:30:56.878099 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 4:30:56.878185 PROGRESS: Extracting batch of 47305 precursors
1 day, 4:30:56.893579 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:30:56.893710 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:30:56.893763 INFO: FWHM in RT is 2.93 seconds, sigma is 0.64
1 day, 4:30:56.893787 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.12
1 day, 4:30:56.905252 INFO: Starting candidate selection
1 day, 4:34:22.894164 INFO: Starting candidate scoring
1 day, 4:34:25.378247 INFO: Finished candidate processing
1 day, 4:34:25.378372 INFO: Collecting candidate features
1 day, 4:34:25.520619 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 81108)
1 day, 4:34:25.529571 INFO: Collecting fragment features
1 day, 4:34:25.583163 INFO: Finished candidate scoring
1 day, 4:34:25.623681 PROGRESS: === Extracted 81108 precursors and 793934 fragments ===
1 day, 4:34:25.624191 INFO: performing precursor FDR with 47 features
1 day, 4:34:25.624233 INFO: Decoy channel: -1
1 day, 4:34:25.624261 INFO: Competetive: True
1 day, 4:34:25.656072 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:34:25.676376 WARNING: dropped 1 target PSMs due to missing features
1 day, 4:34:26.999712 INFO: Test AUC: 0.559
1 day, 4:34:26.999859 INFO: Train AUC: 0.617
1 day, 4:34:26.999890 INFO: AUC difference: 9.41%
1 day, 4:34:26.999912 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:34:27.089878 INFO: Resetting torch num_threads to 100
1 day, 4:34:27.093655 INFO: === FDR correction performed with classifier version 4 ===
1 day, 4:34:27.097626 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:34:27.097774 PROGRESS: Total precursors accumulated: 21,521
1 day, 4:34:27.097838 PROGRESS: Target precursors: 13,690 (63.61%)
1 day, 4:34:27.097893 PROGRESS: Decoy precursors: 7,831 (36.39%)
1 day, 4:34:27.097943 PROGRESS: 
1 day, 4:34:27.097990 PROGRESS: Precursor Summary:
1 day, 4:34:27.099124 PROGRESS: Channel   0:	 0.05 FDR:   386; 0.01 FDR:   245; 0.001 FDR:   196
1 day, 4:34:27.099224 PROGRESS: 
1 day, 4:34:27.099285 PROGRESS: Protein Summary:
1 day, 4:34:27.100529 PROGRESS: Channel   0:	 0.05 FDR:   372; 0.01 FDR:   239; 0.001 FDR:   190
1 day, 4:34:27.100626 PROGRESS: =========================================================================
1 day, 4:34:27.132518 INFO: fragments_df_filtered: 2750
1 day, 4:34:27.317519 INFO: calibration group: precursor, fitting mz estimator 
1 day, 4:34:27.363418 INFO: calibration group: precursor, fitting rt estimator 
1 day, 4:34:27.414558 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 4:34:27.464722 INFO: calibration group: fragment, fitting mz estimator 
1 day, 4:34:27.630617 INFO: calibration group: precursor, predicting mz
1 day, 4:34:27.638109 INFO: calibration group: precursor, predicting rt
1 day, 4:34:27.666725 INFO: calibration group: precursor, predicting mobility
1 day, 4:34:27.673389 INFO: calibration group: fragment, predicting mz
1 day, 4:34:27.725447 INFO: === checking if optimization conditions were reached ===
1 day, 4:34:27.725804 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 4:34:27.727962 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 363.0382.
1 day, 4:34:27.728048 INFO: ==============================================
1 day, 4:34:27.728162 INFO: Starting optimization step 1.
1 day, 4:34:27.728245 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 4:34:27.728330 PROGRESS: Extracting batch of 47305 precursors
1 day, 4:34:27.749980 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:34:27.750112 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:34:27.750172 INFO: FWHM in RT is 3.01 seconds, sigma is 0.66
1 day, 4:34:27.750220 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.21
1 day, 4:34:27.759354 INFO: Starting candidate selection
1 day, 4:35:07.362859 INFO: Starting candidate scoring
1 day, 4:35:09.723699 INFO: Finished candidate processing
1 day, 4:35:09.723875 INFO: Collecting candidate features
1 day, 4:35:09.888788 WARNING: intensity_correlation has 39 NaNs ( 0.05 % out of 77944)
1 day, 4:35:09.889588 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 77944)
1 day, 4:35:09.898966 INFO: Collecting fragment features
1 day, 4:35:09.954815 INFO: Finished candidate scoring
1 day, 4:35:10.001761 PROGRESS: === Extracted 77944 precursors and 743017 fragments ===
1 day, 4:35:10.002231 INFO: performing precursor FDR with 47 features
1 day, 4:35:10.002269 INFO: Decoy channel: -1
1 day, 4:35:10.002293 INFO: Competetive: True
1 day, 4:35:10.032414 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:35:10.047951 WARNING: dropped 22 target PSMs due to missing features
1 day, 4:35:10.048093 WARNING: dropped 17 decoy PSMs due to missing features
1 day, 4:35:11.333784 INFO: Test AUC: 0.511
1 day, 4:35:11.334009 INFO: Train AUC: 0.599
1 day, 4:35:11.334041 INFO: AUC difference: 14.68%
1 day, 4:35:11.334064 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:35:11.425162 INFO: Resetting torch num_threads to 100
1 day, 4:35:11.429133 INFO: === FDR correction performed with classifier version 4 ===
1 day, 4:35:11.432997 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:35:11.433163 PROGRESS: Total precursors accumulated: 20,983
1 day, 4:35:11.433230 PROGRESS: Target precursors: 12,961 (61.77%)
1 day, 4:35:11.433281 PROGRESS: Decoy precursors: 8,022 (38.23%)
1 day, 4:35:11.433336 PROGRESS: 
1 day, 4:35:11.433382 PROGRESS: Precursor Summary:
1 day, 4:35:11.434549 PROGRESS: Channel   0:	 0.05 FDR:   407; 0.01 FDR:   322; 0.001 FDR:   282
1 day, 4:35:11.434648 PROGRESS: 
1 day, 4:35:11.434706 PROGRESS: Protein Summary:
1 day, 4:35:11.435956 PROGRESS: Channel   0:	 0.05 FDR:   391; 0.01 FDR:   311; 0.001 FDR:   273
1 day, 4:35:11.436050 PROGRESS: =========================================================================
1 day, 4:35:11.445255 INFO: fragments_df_filtered: 3444
1 day, 4:35:11.646101 INFO: calibration group: precursor, fitting mz estimator 
1 day, 4:35:11.696069 INFO: calibration group: precursor, fitting rt estimator 
1 day, 4:35:11.748792 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 4:35:11.797349 INFO: calibration group: fragment, fitting mz estimator 
1 day, 4:35:12.050128 INFO: calibration group: precursor, predicting mz
1 day, 4:35:12.057560 INFO: calibration group: precursor, predicting rt
1 day, 4:35:12.086435 INFO: calibration group: precursor, predicting mobility
1 day, 4:35:12.093011 INFO: calibration group: fragment, predicting mz
1 day, 4:35:12.146224 INFO: === checking if optimization conditions were reached ===
1 day, 4:35:12.146514 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 4:35:12.148476 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 335.0451.
1 day, 4:35:12.148540 INFO: ==============================================
1 day, 4:35:12.148642 INFO: Starting optimization step 2.
1 day, 4:35:12.148717 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 4:35:12.148796 PROGRESS: Extracting batch of 47305 precursors
1 day, 4:35:12.160954 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:35:12.161072 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:35:12.161131 INFO: FWHM in RT is 3.01 seconds, sigma is 0.66
1 day, 4:35:12.161159 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.09
1 day, 4:35:12.170097 INFO: Starting candidate selection
1 day, 4:35:47.938976 INFO: Starting candidate scoring
1 day, 4:35:50.269687 INFO: Finished candidate processing
1 day, 4:35:50.269856 INFO: Collecting candidate features
1 day, 4:35:50.424368 WARNING: intensity_correlation has 34 NaNs ( 0.04 % out of 77847)
1 day, 4:35:50.424723 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 77847)
1 day, 4:35:50.432954 INFO: Collecting fragment features
1 day, 4:35:50.481861 INFO: Finished candidate scoring
1 day, 4:35:50.518704 PROGRESS: === Extracted 77847 precursors and 741047 fragments ===
1 day, 4:35:50.519174 INFO: performing precursor FDR with 47 features
1 day, 4:35:50.519212 INFO: Decoy channel: -1
1 day, 4:35:50.519236 INFO: Competetive: True
1 day, 4:35:50.544517 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:35:50.559686 WARNING: dropped 18 target PSMs due to missing features
1 day, 4:35:50.559826 WARNING: dropped 17 decoy PSMs due to missing features
1 day, 4:35:51.771723 INFO: Test AUC: 0.512
1 day, 4:35:51.771863 INFO: Train AUC: 0.600
1 day, 4:35:51.771892 INFO: AUC difference: 14.62%
1 day, 4:35:51.771917 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:35:51.859090 INFO: Resetting torch num_threads to 100
1 day, 4:35:51.862103 INFO: === FDR correction performed with classifier version 4 ===
1 day, 4:35:51.865679 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:35:51.865837 PROGRESS: Total precursors accumulated: 20,957
1 day, 4:35:51.865901 PROGRESS: Target precursors: 12,970 (61.89%)
1 day, 4:35:51.865952 PROGRESS: Decoy precursors: 7,987 (38.11%)
1 day, 4:35:51.866001 PROGRESS: 
1 day, 4:35:51.866047 PROGRESS: Precursor Summary:
1 day, 4:35:51.867155 PROGRESS: Channel   0:	 0.05 FDR:   430; 0.01 FDR:   339; 0.001 FDR:   292
1 day, 4:35:51.867249 PROGRESS: 
1 day, 4:35:51.867306 PROGRESS: Protein Summary:
1 day, 4:35:51.868575 PROGRESS: Channel   0:	 0.05 FDR:   414; 0.01 FDR:   327; 0.001 FDR:   282
1 day, 4:35:51.868678 PROGRESS: =========================================================================
1 day, 4:35:51.875773 INFO: fragments_df_filtered: 3564
1 day, 4:35:52.052202 INFO: calibration group: precursor, fitting mz estimator 
1 day, 4:35:52.091577 INFO: calibration group: precursor, fitting rt estimator 
1 day, 4:35:52.132786 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 4:35:52.171638 INFO: calibration group: fragment, fitting mz estimator 
1 day, 4:35:52.368040 INFO: calibration group: precursor, predicting mz
1 day, 4:35:52.375291 INFO: calibration group: precursor, predicting rt
1 day, 4:35:52.403415 INFO: calibration group: precursor, predicting mobility
1 day, 4:35:52.410025 INFO: calibration group: fragment, predicting mz
1 day, 4:35:52.461591 INFO: === checking if optimization conditions were reached ===
1 day, 4:35:52.461908 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 4:35:52.464436 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 265.3358.
1 day, 4:35:52.464501 INFO: ==============================================
1 day, 4:35:52.464610 INFO: Starting optimization step 3.
1 day, 4:35:52.464689 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 4:35:52.464767 PROGRESS: Extracting batch of 47305 precursors
1 day, 4:35:52.481933 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:35:52.482058 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:35:52.482113 INFO: FWHM in RT is 2.99 seconds, sigma is 0.66
1 day, 4:35:52.482141 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.09
1 day, 4:35:52.490994 INFO: Starting candidate selection
1 day, 4:36:21.142754 INFO: Starting candidate scoring
1 day, 4:36:23.485472 INFO: Finished candidate processing
1 day, 4:36:23.485579 INFO: Collecting candidate features
1 day, 4:36:23.622277 WARNING: intensity_correlation has 33 NaNs ( 0.04 % out of 77966)
1 day, 4:36:23.622597 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 77966)
1 day, 4:36:23.628621 INFO: Collecting fragment features
1 day, 4:36:23.682459 INFO: Finished candidate scoring
1 day, 4:36:23.721174 PROGRESS: === Extracted 77966 precursors and 738470 fragments ===
1 day, 4:36:23.721644 INFO: performing precursor FDR with 47 features
1 day, 4:36:23.721683 INFO: Decoy channel: -1
1 day, 4:36:23.721709 INFO: Competetive: True
1 day, 4:36:23.747034 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:36:23.762226 WARNING: dropped 24 target PSMs due to missing features
1 day, 4:36:23.762368 WARNING: dropped 12 decoy PSMs due to missing features
1 day, 4:36:25.013774 INFO: Test AUC: 0.553
1 day, 4:36:25.013914 INFO: Train AUC: 0.600
1 day, 4:36:25.013944 INFO: AUC difference: 7.80%
1 day, 4:36:25.013965 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:36:25.101829 INFO: Resetting torch num_threads to 100
1 day, 4:36:25.104886 INFO: === FDR correction performed with classifier version 4 ===
1 day, 4:36:25.108519 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:36:25.108682 PROGRESS: Total precursors accumulated: 21,030
1 day, 4:36:25.108765 PROGRESS: Target precursors: 12,955 (61.60%)
1 day, 4:36:25.108820 PROGRESS: Decoy precursors: 8,075 (38.40%)
1 day, 4:36:25.108871 PROGRESS: 
1 day, 4:36:25.108917 PROGRESS: Precursor Summary:
1 day, 4:36:25.110058 PROGRESS: Channel   0:	 0.05 FDR:   444; 0.01 FDR:   340; 0.001 FDR:   205
1 day, 4:36:25.110179 PROGRESS: 
1 day, 4:36:25.110235 PROGRESS: Protein Summary:
1 day, 4:36:25.111480 PROGRESS: Channel   0:	 0.05 FDR:   424; 0.01 FDR:   327; 0.001 FDR:   199
1 day, 4:36:25.111576 PROGRESS: =========================================================================
1 day, 4:36:25.118487 INFO: fragments_df_filtered: 3566
1 day, 4:36:25.295277 INFO: calibration group: precursor, fitting mz estimator 
1 day, 4:36:25.343396 INFO: calibration group: precursor, fitting rt estimator 
1 day, 4:36:26.544850 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 4:36:26.595147 INFO: calibration group: fragment, fitting mz estimator 
1 day, 4:36:26.856891 INFO: calibration group: precursor, predicting mz
1 day, 4:36:26.864409 INFO: calibration group: precursor, predicting rt
1 day, 4:36:26.893022 INFO: calibration group: precursor, predicting mobility
1 day, 4:36:26.899841 INFO: calibration group: fragment, predicting mz
1 day, 4:36:26.953701 INFO: === checking if optimization conditions were reached ===
1 day, 4:36:26.954015 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 4:36:26.958753 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 179.9808.
1 day, 4:36:26.958824 INFO: ==============================================
1 day, 4:36:26.958940 INFO: Starting optimization step 4.
1 day, 4:36:26.959035 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 4:36:26.959107 PROGRESS: Extracting batch of 47305 precursors
1 day, 4:36:26.976042 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:36:26.976160 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:36:26.976213 INFO: FWHM in RT is 3.00 seconds, sigma is 0.66
1 day, 4:36:26.976241 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.07
1 day, 4:36:26.985206 INFO: Starting candidate selection
1 day, 4:36:46.279330 INFO: Starting candidate scoring
1 day, 4:36:48.630839 INFO: Finished candidate processing
1 day, 4:36:48.631014 INFO: Collecting candidate features
1 day, 4:36:48.782800 WARNING: intensity_correlation has 35 NaNs ( 0.05 % out of 77354)
1 day, 4:36:48.783126 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 77354)
1 day, 4:36:48.789058 INFO: Collecting fragment features
1 day, 4:36:48.835550 INFO: Finished candidate scoring
1 day, 4:36:48.877570 PROGRESS: === Extracted 77354 precursors and 728037 fragments ===
1 day, 4:36:48.877992 INFO: performing precursor FDR with 47 features
1 day, 4:36:48.878030 INFO: Decoy channel: -1
1 day, 4:36:48.878054 INFO: Competetive: True
1 day, 4:36:48.903600 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:36:48.919691 WARNING: dropped 24 target PSMs due to missing features
1 day, 4:36:48.919829 WARNING: dropped 13 decoy PSMs due to missing features
1 day, 4:36:50.173316 INFO: Test AUC: 0.550
1 day, 4:36:50.173459 INFO: Train AUC: 0.590
1 day, 4:36:50.173491 INFO: AUC difference: 6.89%
1 day, 4:36:50.173514 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:36:50.260738 INFO: Resetting torch num_threads to 100
1 day, 4:36:50.263738 INFO: === FDR correction performed with classifier version 4 ===
1 day, 4:36:50.267473 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:36:50.267644 PROGRESS: Total precursors accumulated: 20,896
1 day, 4:36:50.267708 PROGRESS: Target precursors: 12,653 (60.55%)
1 day, 4:36:50.267760 PROGRESS: Decoy precursors: 8,243 (39.45%)
1 day, 4:36:50.267811 PROGRESS: 
1 day, 4:36:50.267857 PROGRESS: Precursor Summary:
1 day, 4:36:50.269009 PROGRESS: Channel   0:	 0.05 FDR:   446; 0.01 FDR:   339; 0.001 FDR:   157
1 day, 4:36:50.269120 PROGRESS: 
1 day, 4:36:50.269179 PROGRESS: Protein Summary:
1 day, 4:36:50.270427 PROGRESS: Channel   0:	 0.05 FDR:   426; 0.01 FDR:   325; 0.001 FDR:   152
1 day, 4:36:50.270521 PROGRESS: =========================================================================
1 day, 4:36:50.277245 INFO: fragments_df_filtered: 3509
1 day, 4:36:50.454510 INFO: calibration group: precursor, fitting mz estimator 
1 day, 4:36:50.503402 INFO: calibration group: precursor, fitting rt estimator 
1 day, 4:36:50.553998 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 4:36:50.604641 INFO: calibration group: fragment, fitting mz estimator 
1 day, 4:36:50.863887 INFO: calibration group: precursor, predicting mz
1 day, 4:36:50.871492 INFO: calibration group: precursor, predicting rt
1 day, 4:36:50.899934 INFO: calibration group: precursor, predicting mobility
1 day, 4:36:50.906704 INFO: calibration group: fragment, predicting mz
1 day, 4:36:50.959639 INFO: === checking if optimization conditions were reached ===
1 day, 4:36:50.959954 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 4:36:50.962315 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 156.6826.
1 day, 4:36:50.962383 INFO: ==============================================
1 day, 4:36:50.962498 INFO: Starting optimization step 5.
1 day, 4:36:50.962573 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 4:36:50.962640 PROGRESS: Extracting batch of 47305 precursors
1 day, 4:36:50.979077 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:36:50.979202 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:36:50.979248 INFO: FWHM in RT is 3.03 seconds, sigma is 0.67
1 day, 4:36:50.979276 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.06
1 day, 4:36:50.988221 INFO: Starting candidate selection
1 day, 4:37:08.310198 INFO: Starting candidate scoring
1 day, 4:37:10.665717 INFO: Finished candidate processing
1 day, 4:37:10.665883 INFO: Collecting candidate features
1 day, 4:37:10.816468 WARNING: intensity_correlation has 40 NaNs ( 0.05 % out of 77188)
1 day, 4:37:10.816771 WARNING: height_correlation has 8 NaNs ( 0.01 % out of 77188)
1 day, 4:37:10.822733 INFO: Collecting fragment features
1 day, 4:37:10.872656 INFO: Finished candidate scoring
1 day, 4:37:10.911640 PROGRESS: === Extracted 77188 precursors and 725307 fragments ===
1 day, 4:37:10.912135 INFO: performing precursor FDR with 47 features
1 day, 4:37:10.912184 INFO: Decoy channel: -1
1 day, 4:37:10.912211 INFO: Competetive: True
1 day, 4:37:10.940051 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:37:10.955892 WARNING: dropped 26 target PSMs due to missing features
1 day, 4:37:10.956033 WARNING: dropped 16 decoy PSMs due to missing features
1 day, 4:37:12.190437 INFO: Test AUC: 0.506
1 day, 4:37:12.190568 INFO: Train AUC: 0.592
1 day, 4:37:12.190597 INFO: AUC difference: 14.52%
1 day, 4:37:12.190617 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:37:12.278734 INFO: Resetting torch num_threads to 100
1 day, 4:37:12.281950 INFO: === FDR correction performed with classifier version 4 ===
1 day, 4:37:12.285750 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:37:12.285926 PROGRESS: Total precursors accumulated: 20,882
1 day, 4:37:12.285989 PROGRESS: Target precursors: 12,643 (60.54%)
1 day, 4:37:12.286041 PROGRESS: Decoy precursors: 8,239 (39.46%)
1 day, 4:37:12.286092 PROGRESS: 
1 day, 4:37:12.286139 PROGRESS: Precursor Summary:
1 day, 4:37:12.287313 PROGRESS: Channel   0:	 0.05 FDR:   429; 0.01 FDR:   324; 0.001 FDR:   272
1 day, 4:37:12.287408 PROGRESS: 
1 day, 4:37:12.287462 PROGRESS: Protein Summary:
1 day, 4:37:12.288727 PROGRESS: Channel   0:	 0.05 FDR:   412; 0.01 FDR:   311; 0.001 FDR:   262
1 day, 4:37:12.288818 PROGRESS: =========================================================================
1 day, 4:37:12.295406 INFO: fragments_df_filtered: 3391
1 day, 4:37:12.461777 INFO: calibration group: precursor, fitting mz estimator 
1 day, 4:37:12.510777 INFO: calibration group: precursor, fitting rt estimator 
1 day, 4:37:12.551335 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 4:37:12.592882 INFO: calibration group: fragment, fitting mz estimator 
1 day, 4:37:12.777397 INFO: calibration group: precursor, predicting mz
1 day, 4:37:12.785011 INFO: calibration group: precursor, predicting rt
1 day, 4:37:12.813735 INFO: calibration group: precursor, predicting mobility
1 day, 4:37:12.820576 INFO: calibration group: fragment, predicting mz
1 day, 4:37:12.874811 INFO: === checking if optimization conditions were reached ===
1 day, 4:37:12.875128 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 4:37:12.877501 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 129.0891.
1 day, 4:37:12.877564 INFO: ==============================================
1 day, 4:37:12.877676 INFO: Starting optimization step 6.
1 day, 4:37:12.877752 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 4:37:12.877831 PROGRESS: Extracting batch of 47305 precursors
1 day, 4:37:12.894706 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:37:12.894828 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:37:12.894885 INFO: FWHM in RT is 2.99 seconds, sigma is 0.66
1 day, 4:37:12.894916 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.11
1 day, 4:37:12.903921 INFO: Starting candidate selection
1 day, 4:37:27.565516 INFO: Starting candidate scoring
1 day, 4:37:29.879757 INFO: Finished candidate processing
1 day, 4:37:29.879877 INFO: Collecting candidate features
1 day, 4:37:30.005459 WARNING: intensity_correlation has 46 NaNs ( 0.06 % out of 77010)
1 day, 4:37:30.005860 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 77010)
1 day, 4:37:30.015350 INFO: Collecting fragment features
1 day, 4:37:30.058959 INFO: Finished candidate scoring
1 day, 4:37:30.107368 PROGRESS: === Extracted 77010 precursors and 721073 fragments ===
1 day, 4:37:30.107772 INFO: performing precursor FDR with 47 features
1 day, 4:37:30.107811 INFO: Decoy channel: -1
1 day, 4:37:30.107835 INFO: Competetive: True
1 day, 4:37:30.130642 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:37:30.145880 WARNING: dropped 21 target PSMs due to missing features
1 day, 4:37:30.146019 WARNING: dropped 26 decoy PSMs due to missing features
1 day, 4:37:31.355726 INFO: Test AUC: 0.546
1 day, 4:37:31.355870 INFO: Train AUC: 0.598
1 day, 4:37:31.355900 INFO: AUC difference: 8.55%
1 day, 4:37:31.355921 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:37:31.445679 INFO: Resetting torch num_threads to 100
1 day, 4:37:31.448751 INFO: === FDR correction performed with classifier version 4 ===
1 day, 4:37:31.452466 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:37:31.452650 PROGRESS: Total precursors accumulated: 20,843
1 day, 4:37:31.452717 PROGRESS: Target precursors: 12,753 (61.19%)
1 day, 4:37:31.452769 PROGRESS: Decoy precursors: 8,090 (38.81%)
1 day, 4:37:31.452819 PROGRESS: 
1 day, 4:37:31.452863 PROGRESS: Precursor Summary:
1 day, 4:37:31.454035 PROGRESS: Channel   0:	 0.05 FDR:   463; 0.01 FDR:   337; 0.001 FDR:   283
1 day, 4:37:31.454151 PROGRESS: 
1 day, 4:37:31.454211 PROGRESS: Protein Summary:
1 day, 4:37:31.455491 PROGRESS: Channel   0:	 0.05 FDR:   444; 0.01 FDR:   323; 0.001 FDR:   272
1 day, 4:37:31.455587 PROGRESS: =========================================================================
1 day, 4:37:31.462259 INFO: fragments_df_filtered: 3451
1 day, 4:37:31.640205 INFO: calibration group: precursor, fitting mz estimator 
1 day, 4:37:31.685173 INFO: calibration group: precursor, fitting rt estimator 
1 day, 4:37:31.723482 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 4:37:31.764190 INFO: calibration group: fragment, fitting mz estimator 
1 day, 4:37:31.951048 INFO: calibration group: precursor, predicting mz
1 day, 4:37:31.958686 INFO: calibration group: precursor, predicting rt
1 day, 4:37:31.987612 INFO: calibration group: precursor, predicting mobility
1 day, 4:37:31.994385 INFO: calibration group: fragment, predicting mz
1 day, 4:37:32.047363 INFO: === checking if optimization conditions were reached ===
1 day, 4:37:32.047663 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 4:37:32.049720 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 114.0027.
1 day, 4:37:32.049786 INFO: ==============================================
1 day, 4:37:32.049891 INFO: Starting optimization step 7.
1 day, 4:37:32.049970 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 4:37:32.050039 PROGRESS: Extracting batch of 47305 precursors
1 day, 4:37:32.062141 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:37:32.062258 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:37:32.062305 INFO: FWHM in RT is 2.99 seconds, sigma is 0.66
1 day, 4:37:32.062332 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.05
1 day, 4:37:32.071250 INFO: Starting candidate selection
1 day, 4:37:44.893738 INFO: Starting candidate scoring
1 day, 4:37:47.274486 INFO: Finished candidate processing
1 day, 4:37:47.274670 INFO: Collecting candidate features
1 day, 4:37:47.442320 WARNING: intensity_correlation has 48 NaNs ( 0.06 % out of 76867)
1 day, 4:37:47.442707 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 76867)
1 day, 4:37:47.451426 INFO: Collecting fragment features
1 day, 4:37:47.509899 INFO: Finished candidate scoring
1 day, 4:37:47.554749 PROGRESS: === Extracted 76867 precursors and 718263 fragments ===
1 day, 4:37:47.555290 INFO: performing precursor FDR with 47 features
1 day, 4:37:47.555330 INFO: Decoy channel: -1
1 day, 4:37:47.555354 INFO: Competetive: True
1 day, 4:37:47.591342 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:37:47.610829 WARNING: dropped 24 target PSMs due to missing features
1 day, 4:37:47.610972 WARNING: dropped 25 decoy PSMs due to missing features
1 day, 4:37:49.140729 INFO: Test AUC: 0.540
1 day, 4:37:49.140875 INFO: Train AUC: 0.600
1 day, 4:37:49.140905 INFO: AUC difference: 10.02%
1 day, 4:37:49.140927 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:37:49.239569 INFO: Resetting torch num_threads to 100
1 day, 4:37:49.242933 INFO: === FDR correction performed with classifier version 4 ===
1 day, 4:37:49.247404 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:37:49.247575 PROGRESS: Total precursors accumulated: 20,796
1 day, 4:37:49.247638 PROGRESS: Target precursors: 12,735 (61.24%)
1 day, 4:37:49.247691 PROGRESS: Decoy precursors: 8,061 (38.76%)
1 day, 4:37:49.247737 PROGRESS: 
1 day, 4:37:49.247782 PROGRESS: Precursor Summary:
1 day, 4:37:49.248977 PROGRESS: Channel   0:	 0.05 FDR:   417; 0.01 FDR:   331; 0.001 FDR:   297
1 day, 4:37:49.249079 PROGRESS: 
1 day, 4:37:49.249138 PROGRESS: Protein Summary:
1 day, 4:37:49.250428 PROGRESS: Channel   0:	 0.05 FDR:   401; 0.01 FDR:   318; 0.001 FDR:   284
1 day, 4:37:49.250522 PROGRESS: =========================================================================
1 day, 4:37:49.257899 INFO: fragments_df_filtered: 3452
1 day, 4:37:49.452842 INFO: calibration group: precursor, fitting mz estimator 
1 day, 4:37:49.498648 INFO: calibration group: precursor, fitting rt estimator 
1 day, 4:37:49.542123 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 4:37:49.584507 INFO: calibration group: fragment, fitting mz estimator 
1 day, 4:37:49.773618 INFO: calibration group: precursor, predicting mz
1 day, 4:37:49.781497 INFO: calibration group: precursor, predicting rt
1 day, 4:37:49.810452 INFO: calibration group: precursor, predicting mobility
1 day, 4:37:49.817480 INFO: calibration group: fragment, predicting mz
1 day, 4:37:49.872015 INFO: === checking if optimization conditions were reached ===
1 day, 4:37:49.872367 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
1 day, 4:37:49.875185 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 109.7940.
1 day, 4:37:49.875248 INFO: ==============================================
1 day, 4:37:49.875371 INFO: Starting optimization step 8.
1 day, 4:37:49.875449 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 4:37:49.875526 PROGRESS: Extracting batch of 47305 precursors
1 day, 4:37:49.894051 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:37:49.894167 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:37:49.894243 INFO: FWHM in RT is 2.99 seconds, sigma is 0.66
1 day, 4:37:49.894274 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.05
1 day, 4:37:49.901625 INFO: Starting candidate selection
1 day, 4:38:02.621637 INFO: Starting candidate scoring
1 day, 4:38:04.985353 INFO: Finished candidate processing
1 day, 4:38:04.985530 INFO: Collecting candidate features
1 day, 4:38:05.148310 WARNING: intensity_correlation has 51 NaNs ( 0.07 % out of 76918)
1 day, 4:38:05.148699 WARNING: height_correlation has 9 NaNs ( 0.01 % out of 76918)
1 day, 4:38:05.157507 INFO: Collecting fragment features
1 day, 4:38:05.209746 INFO: Finished candidate scoring
1 day, 4:38:05.254352 PROGRESS: === Extracted 76918 precursors and 718658 fragments ===
1 day, 4:38:05.254781 INFO: performing precursor FDR with 47 features
1 day, 4:38:05.254820 INFO: Decoy channel: -1
1 day, 4:38:05.254843 INFO: Competetive: True
1 day, 4:38:05.285499 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:38:05.304174 WARNING: dropped 24 target PSMs due to missing features
1 day, 4:38:05.304324 WARNING: dropped 29 decoy PSMs due to missing features
1 day, 4:38:06.798994 INFO: Test AUC: 0.549
1 day, 4:38:06.799143 INFO: Train AUC: 0.599
1 day, 4:38:06.799173 INFO: AUC difference: 8.32%
1 day, 4:38:06.799197 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:38:06.892242 INFO: Resetting torch num_threads to 100
1 day, 4:38:06.895524 INFO: === FDR correction performed with classifier version 4 ===
1 day, 4:38:06.899794 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:38:06.899971 PROGRESS: Total precursors accumulated: 20,814
1 day, 4:38:06.900037 PROGRESS: Target precursors: 12,752 (61.27%)
1 day, 4:38:06.900101 PROGRESS: Decoy precursors: 8,062 (38.73%)
1 day, 4:38:06.900158 PROGRESS: 
1 day, 4:38:06.900204 PROGRESS: Precursor Summary:
1 day, 4:38:06.901403 PROGRESS: Channel   0:	 0.05 FDR:   429; 0.01 FDR:   306; 0.001 FDR:   247
1 day, 4:38:06.901501 PROGRESS: 
1 day, 4:38:06.901558 PROGRESS: Protein Summary:
1 day, 4:38:06.902823 PROGRESS: Channel   0:	 0.05 FDR:   412; 0.01 FDR:   293; 0.001 FDR:   239
1 day, 4:38:06.902916 PROGRESS: =========================================================================
1 day, 4:38:06.909595 INFO: fragments_df_filtered: 3205
1 day, 4:38:07.135614 INFO: calibration group: precursor, fitting mz estimator 
1 day, 4:38:07.179408 INFO: calibration group: precursor, fitting rt estimator 
1 day, 4:38:07.220927 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 4:38:07.263103 INFO: calibration group: fragment, fitting mz estimator 
1 day, 4:38:07.431053 INFO: calibration group: precursor, predicting mz
1 day, 4:38:07.438938 INFO: calibration group: precursor, predicting rt
1 day, 4:38:07.467856 INFO: calibration group: precursor, predicting mobility
1 day, 4:38:07.474806 INFO: calibration group: fragment, predicting mz
1 day, 4:38:07.530119 INFO: === checking if optimization conditions were reached ===
1 day, 4:38:07.530465 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
1 day, 4:38:07.532104 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 109.7940 found after 9 searches.
1 day, 4:38:07.532163 INFO: ==============================================
1 day, 4:38:07.532275 PROGRESS: Optimization finished for rt_error.
1 day, 4:38:07.733203 INFO: calibration group: precursor, predicting mz
1 day, 4:38:07.741343 INFO: calibration group: precursor, predicting rt
1 day, 4:38:07.770436 INFO: calibration group: precursor, predicting mobility
1 day, 4:38:07.777406 INFO: calibration group: fragment, predicting mz
1 day, 4:38:07.870199 INFO: Starting optimization step 0.
1 day, 4:38:07.870474 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 4:38:07.870559 PROGRESS: Extracting batch of 47305 precursors
1 day, 4:38:07.891878 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:38:07.892020 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:38:07.892075 INFO: FWHM in RT is 3.02 seconds, sigma is 0.66
1 day, 4:38:07.892104 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.10
1 day, 4:38:07.893157 INFO: Starting candidate selection
1 day, 4:38:19.984383 INFO: Starting candidate scoring
1 day, 4:38:22.362898 INFO: Finished candidate processing
1 day, 4:38:22.363089 INFO: Collecting candidate features
1 day, 4:38:22.518187 WARNING: intensity_correlation has 42 NaNs ( 0.05 % out of 76888)
1 day, 4:38:22.518497 WARNING: height_correlation has 6 NaNs ( 0.01 % out of 76888)
1 day, 4:38:22.524446 INFO: Collecting fragment features
1 day, 4:38:22.573827 INFO: Finished candidate scoring
1 day, 4:38:22.610667 PROGRESS: === Extracted 76888 precursors and 718726 fragments ===
1 day, 4:38:22.611162 INFO: performing precursor FDR with 47 features
1 day, 4:38:22.611201 INFO: Decoy channel: -1
1 day, 4:38:22.611226 INFO: Competetive: True
1 day, 4:38:22.638353 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:38:22.654192 WARNING: dropped 24 target PSMs due to missing features
1 day, 4:38:22.654331 WARNING: dropped 19 decoy PSMs due to missing features
1 day, 4:38:23.826991 INFO: Test AUC: 0.569
1 day, 4:38:23.827130 INFO: Train AUC: 0.622
1 day, 4:38:23.827163 INFO: AUC difference: 8.56%
1 day, 4:38:23.827188 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:38:23.915677 INFO: Resetting torch num_threads to 100
1 day, 4:38:23.918719 INFO: === FDR correction performed with classifier version 13 ===
1 day, 4:38:23.922412 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:38:23.922575 PROGRESS: Total precursors accumulated: 20,806
1 day, 4:38:23.922641 PROGRESS: Target precursors: 13,227 (63.57%)
1 day, 4:38:23.922705 PROGRESS: Decoy precursors: 7,579 (36.43%)
1 day, 4:38:23.922774 PROGRESS: 
1 day, 4:38:23.922824 PROGRESS: Precursor Summary:
1 day, 4:38:23.923988 PROGRESS: Channel   0:	 0.05 FDR:   473; 0.01 FDR:   302; 0.001 FDR:   241
1 day, 4:38:23.924093 PROGRESS: 
1 day, 4:38:23.924149 PROGRESS: Protein Summary:
1 day, 4:38:23.925419 PROGRESS: Channel   0:	 0.05 FDR:   454; 0.01 FDR:   291; 0.001 FDR:   233
1 day, 4:38:23.925515 PROGRESS: =========================================================================
1 day, 4:38:23.931774 INFO: fragments_df_filtered: 3175
1 day, 4:38:24.109950 INFO: calibration group: precursor, fitting mz estimator 
1 day, 4:38:24.161211 INFO: calibration group: precursor, fitting rt estimator 
1 day, 4:38:24.206294 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 4:38:24.244833 INFO: calibration group: fragment, fitting mz estimator 
1 day, 4:38:24.407386 INFO: calibration group: precursor, predicting mz
1 day, 4:38:24.414945 INFO: calibration group: precursor, predicting rt
1 day, 4:38:24.443213 INFO: calibration group: precursor, predicting mobility
1 day, 4:38:24.450084 INFO: calibration group: fragment, predicting mz
1 day, 4:38:24.503247 INFO: === checking if optimization conditions were reached ===
1 day, 4:38:24.503579 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 4:38:24.505538 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0522.
1 day, 4:38:24.505605 INFO: ==============================================
1 day, 4:38:24.505725 INFO: Starting optimization step 1.
1 day, 4:38:24.505812 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 4:38:24.505901 PROGRESS: Extracting batch of 47305 precursors
1 day, 4:38:24.523196 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:38:24.523325 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:38:24.523387 INFO: FWHM in RT is 3.04 seconds, sigma is 0.67
1 day, 4:38:24.523417 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.10
1 day, 4:38:24.532145 INFO: Starting candidate selection
1 day, 4:38:32.082567 INFO: Starting candidate scoring
1 day, 4:38:34.373250 INFO: Finished candidate processing
1 day, 4:38:34.373426 INFO: Collecting candidate features
1 day, 4:38:34.490898 WARNING: intensity_correlation has 58 NaNs ( 0.08 % out of 73646)
1 day, 4:38:34.491207 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 73646)
1 day, 4:38:34.498047 INFO: Collecting fragment features
1 day, 4:38:34.549583 INFO: Finished candidate scoring
1 day, 4:38:34.586055 PROGRESS: === Extracted 73646 precursors and 677746 fragments ===
1 day, 4:38:34.586458 INFO: performing precursor FDR with 47 features
1 day, 4:38:34.586496 INFO: Decoy channel: -1
1 day, 4:38:34.586520 INFO: Competetive: True
1 day, 4:38:34.610570 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:38:34.625133 WARNING: dropped 31 target PSMs due to missing features
1 day, 4:38:34.625270 WARNING: dropped 29 decoy PSMs due to missing features
1 day, 4:38:35.737775 INFO: Test AUC: 0.567
1 day, 4:38:35.737911 INFO: Train AUC: 0.603
1 day, 4:38:35.737941 INFO: AUC difference: 6.07%
1 day, 4:38:35.737961 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:38:35.825420 INFO: Resetting torch num_threads to 100
1 day, 4:38:35.828336 INFO: === FDR correction performed with classifier version 13 ===
1 day, 4:38:35.831776 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:38:35.831947 PROGRESS: Total precursors accumulated: 19,996
1 day, 4:38:35.832013 PROGRESS: Target precursors: 12,497 (62.50%)
1 day, 4:38:35.832067 PROGRESS: Decoy precursors: 7,499 (37.50%)
1 day, 4:38:35.832119 PROGRESS: 
1 day, 4:38:35.832167 PROGRESS: Precursor Summary:
1 day, 4:38:35.834527 PROGRESS: Channel   0:	 0.05 FDR:   472; 0.01 FDR:   328; 0.001 FDR:   298
1 day, 4:38:35.834628 PROGRESS: 
1 day, 4:38:35.834687 PROGRESS: Protein Summary:
1 day, 4:38:35.835950 PROGRESS: Channel   0:	 0.05 FDR:   454; 0.01 FDR:   317; 0.001 FDR:   289
1 day, 4:38:35.836064 PROGRESS: =========================================================================
1 day, 4:38:35.842447 INFO: fragments_df_filtered: 3410
1 day, 4:38:36.008550 INFO: calibration group: precursor, fitting mz estimator 
1 day, 4:38:36.058214 INFO: calibration group: precursor, fitting rt estimator 
1 day, 4:38:36.095852 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 4:38:36.132401 INFO: calibration group: fragment, fitting mz estimator 
1 day, 4:38:36.317584 INFO: calibration group: precursor, predicting mz
1 day, 4:38:36.324785 INFO: calibration group: precursor, predicting rt
1 day, 4:38:36.352940 INFO: calibration group: precursor, predicting mobility
1 day, 4:38:36.359353 INFO: calibration group: fragment, predicting mz
1 day, 4:38:36.409858 INFO: === checking if optimization conditions were reached ===
1 day, 4:38:36.410171 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 4:38:36.412185 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0497.
1 day, 4:38:36.412250 INFO: ==============================================
1 day, 4:38:36.412374 INFO: Starting optimization step 2.
1 day, 4:38:36.412453 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 4:38:36.412526 PROGRESS: Extracting batch of 47305 precursors
1 day, 4:38:36.429041 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:38:36.429169 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:38:36.429220 INFO: FWHM in RT is 3.00 seconds, sigma is 0.66
1 day, 4:38:36.429251 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.10
1 day, 4:38:36.438072 INFO: Starting candidate selection
1 day, 4:38:43.146973 INFO: Starting candidate scoring
1 day, 4:38:45.457990 INFO: Finished candidate processing
1 day, 4:38:45.458107 INFO: Collecting candidate features
1 day, 4:38:45.614879 WARNING: intensity_correlation has 60 NaNs ( 0.08 % out of 72956)
1 day, 4:38:45.615228 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 72956)
1 day, 4:38:45.621266 INFO: Collecting fragment features
1 day, 4:38:45.691592 INFO: Finished candidate scoring
1 day, 4:38:45.737185 PROGRESS: === Extracted 72956 precursors and 668555 fragments ===
1 day, 4:38:45.737844 INFO: performing precursor FDR with 47 features
1 day, 4:38:45.737886 INFO: Decoy channel: -1
1 day, 4:38:45.737911 INFO: Competetive: True
1 day, 4:38:45.776632 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:38:45.793955 WARNING: dropped 35 target PSMs due to missing features
1 day, 4:38:45.794095 WARNING: dropped 29 decoy PSMs due to missing features
1 day, 4:38:47.221699 INFO: Test AUC: 0.557
1 day, 4:38:47.221840 INFO: Train AUC: 0.608
1 day, 4:38:47.221871 INFO: AUC difference: 8.39%
1 day, 4:38:47.221895 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:38:47.316336 INFO: Resetting torch num_threads to 100
1 day, 4:38:47.319637 INFO: === FDR correction performed with classifier version 13 ===
1 day, 4:38:47.323592 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:38:47.323766 PROGRESS: Total precursors accumulated: 19,830
1 day, 4:38:47.323829 PROGRESS: Target precursors: 12,368 (62.37%)
1 day, 4:38:47.323892 PROGRESS: Decoy precursors: 7,462 (37.63%)
1 day, 4:38:47.323943 PROGRESS: 
1 day, 4:38:47.323988 PROGRESS: Precursor Summary:
1 day, 4:38:47.325187 PROGRESS: Channel   0:	 0.05 FDR:   444; 0.01 FDR:   321; 0.001 FDR:   299
1 day, 4:38:47.325290 PROGRESS: 
1 day, 4:38:47.325345 PROGRESS: Protein Summary:
1 day, 4:38:47.326627 PROGRESS: Channel   0:	 0.05 FDR:   426; 0.01 FDR:   310; 0.001 FDR:   289
1 day, 4:38:47.326723 PROGRESS: =========================================================================
1 day, 4:38:47.333710 INFO: fragments_df_filtered: 3327
1 day, 4:38:47.527363 INFO: calibration group: precursor, fitting mz estimator 
1 day, 4:38:47.573175 INFO: calibration group: precursor, fitting rt estimator 
1 day, 4:38:47.612643 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 4:38:47.651086 INFO: calibration group: fragment, fitting mz estimator 
1 day, 4:38:47.829768 INFO: calibration group: precursor, predicting mz
1 day, 4:38:47.837620 INFO: calibration group: precursor, predicting rt
1 day, 4:38:47.866634 INFO: calibration group: precursor, predicting mobility
1 day, 4:38:47.873504 INFO: calibration group: fragment, predicting mz
1 day, 4:38:47.930044 INFO: === checking if optimization conditions were reached ===
1 day, 4:38:47.930402 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 4:38:47.932888 PROGRESS: ❌ mobility_error : optimization incomplete after 3 search(es). Will search with parameter 0.0420.
1 day, 4:38:47.932950 INFO: ==============================================
1 day, 4:38:47.933082 INFO: Starting optimization step 3.
1 day, 4:38:47.933165 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 4:38:47.933270 PROGRESS: Extracting batch of 47305 precursors
1 day, 4:38:47.955202 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:38:47.955335 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:38:47.955408 INFO: FWHM in RT is 3.01 seconds, sigma is 0.66
1 day, 4:38:47.955442 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.13
1 day, 4:38:47.956508 INFO: Starting candidate selection
1 day, 4:38:53.800843 INFO: Starting candidate scoring
1 day, 4:38:56.635248 INFO: Finished candidate processing
1 day, 4:38:56.635426 INFO: Collecting candidate features
1 day, 4:38:56.772563 WARNING: intensity_correlation has 58 NaNs ( 0.08 % out of 72008)
1 day, 4:38:56.772864 WARNING: height_correlation has 6 NaNs ( 0.01 % out of 72008)
1 day, 4:38:56.778658 INFO: Collecting fragment features
1 day, 4:38:56.823675 INFO: Finished candidate scoring
1 day, 4:38:56.857490 PROGRESS: === Extracted 72008 precursors and 654450 fragments ===
1 day, 4:38:56.857903 INFO: performing precursor FDR with 47 features
1 day, 4:38:56.857943 INFO: Decoy channel: -1
1 day, 4:38:56.857967 INFO: Competetive: True
1 day, 4:38:56.880257 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:38:56.898257 WARNING: dropped 35 target PSMs due to missing features
1 day, 4:38:56.898403 WARNING: dropped 26 decoy PSMs due to missing features
1 day, 4:38:58.120070 INFO: Test AUC: 0.554
1 day, 4:38:58.120208 INFO: Train AUC: 0.617
1 day, 4:38:58.120238 INFO: AUC difference: 10.28%
1 day, 4:38:58.120259 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:38:59.412881 INFO: Resetting torch num_threads to 100
1 day, 4:38:59.415785 INFO: === FDR correction performed with classifier version 13 ===
1 day, 4:38:59.419991 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:38:59.420141 PROGRESS: Total precursors accumulated: 19,629
1 day, 4:38:59.420206 PROGRESS: Target precursors: 12,412 (63.23%)
1 day, 4:38:59.420257 PROGRESS: Decoy precursors: 7,217 (36.77%)
1 day, 4:38:59.420307 PROGRESS: 
1 day, 4:38:59.420353 PROGRESS: Precursor Summary:
1 day, 4:38:59.421598 PROGRESS: Channel   0:	 0.05 FDR:   463; 0.01 FDR:   363; 0.001 FDR:   285
1 day, 4:38:59.421700 PROGRESS: 
1 day, 4:38:59.421755 PROGRESS: Protein Summary:
1 day, 4:38:59.423077 PROGRESS: Channel   0:	 0.05 FDR:   447; 0.01 FDR:   350; 0.001 FDR:   276
1 day, 4:38:59.423177 PROGRESS: =========================================================================
1 day, 4:38:59.430209 INFO: fragments_df_filtered: 3586
1 day, 4:38:59.609401 INFO: calibration group: precursor, fitting mz estimator 
1 day, 4:38:59.654315 INFO: calibration group: precursor, fitting rt estimator 
1 day, 4:38:59.706298 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 4:38:59.755334 INFO: calibration group: fragment, fitting mz estimator 
1 day, 4:39:00.024478 INFO: calibration group: precursor, predicting mz
1 day, 4:39:00.032000 INFO: calibration group: precursor, predicting rt
1 day, 4:39:00.060702 INFO: calibration group: precursor, predicting mobility
1 day, 4:39:00.067511 INFO: calibration group: fragment, predicting mz
1 day, 4:39:00.121666 INFO: === checking if optimization conditions were reached ===
1 day, 4:39:00.121983 PROGRESS: === Optimization of mobility_error has been performed 4 time(s); minimum number is 2 ===
1 day, 4:39:00.124170 PROGRESS: ❌ mobility_error : optimization incomplete after 4 search(es). Will search with parameter 0.0350.
1 day, 4:39:00.124232 INFO: ==============================================
1 day, 4:39:00.124364 INFO: Starting optimization step 4.
1 day, 4:39:00.124439 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 4:39:00.124508 PROGRESS: Extracting batch of 47305 precursors
1 day, 4:39:00.142010 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:39:00.142146 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:39:00.142194 INFO: FWHM in RT is 2.99 seconds, sigma is 0.66
1 day, 4:39:00.142222 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.04
1 day, 4:39:00.145536 INFO: Starting candidate selection
1 day, 4:39:05.351594 INFO: Starting candidate scoring
1 day, 4:39:07.581901 INFO: Finished candidate processing
1 day, 4:39:07.582603 INFO: Collecting candidate features
1 day, 4:39:07.706367 WARNING: intensity_correlation has 70 NaNs ( 0.10 % out of 71218)
1 day, 4:39:07.706681 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 71218)
1 day, 4:39:07.712714 INFO: Collecting fragment features
1 day, 4:39:07.758135 INFO: Finished candidate scoring
1 day, 4:39:07.801774 PROGRESS: === Extracted 71218 precursors and 639726 fragments ===
1 day, 4:39:07.802199 INFO: performing precursor FDR with 47 features
1 day, 4:39:07.802238 INFO: Decoy channel: -1
1 day, 4:39:07.802263 INFO: Competetive: True
1 day, 4:39:07.829563 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:39:07.846157 WARNING: dropped 30 target PSMs due to missing features
1 day, 4:39:07.846307 WARNING: dropped 41 decoy PSMs due to missing features
1 day, 4:39:09.256490 INFO: Test AUC: 0.499
1 day, 4:39:09.256636 INFO: Train AUC: 0.610
1 day, 4:39:09.256670 INFO: AUC difference: 18.13%
1 day, 4:39:09.256693 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:39:09.344787 INFO: Resetting torch num_threads to 100
1 day, 4:39:09.347933 INFO: === FDR correction performed with classifier version 13 ===
1 day, 4:39:09.351979 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:39:09.352133 PROGRESS: Total precursors accumulated: 19,456
1 day, 4:39:09.352197 PROGRESS: Target precursors: 12,241 (62.92%)
1 day, 4:39:09.352248 PROGRESS: Decoy precursors: 7,215 (37.08%)
1 day, 4:39:09.352296 PROGRESS: 
1 day, 4:39:09.352341 PROGRESS: Precursor Summary:
1 day, 4:39:09.353537 PROGRESS: Channel   0:	 0.05 FDR:   443; 0.01 FDR:   340; 0.001 FDR:   289
1 day, 4:39:09.353640 PROGRESS: 
1 day, 4:39:09.353698 PROGRESS: Protein Summary:
1 day, 4:39:09.354991 PROGRESS: Channel   0:	 0.05 FDR:   426; 0.01 FDR:   327; 0.001 FDR:   279
1 day, 4:39:09.355086 PROGRESS: =========================================================================
1 day, 4:39:09.362186 INFO: fragments_df_filtered: 3353
1 day, 4:39:09.558646 INFO: calibration group: precursor, fitting mz estimator 
1 day, 4:39:09.610215 INFO: calibration group: precursor, fitting rt estimator 
1 day, 4:39:09.662239 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 4:39:09.710740 INFO: calibration group: fragment, fitting mz estimator 
1 day, 4:39:09.923728 INFO: calibration group: precursor, predicting mz
1 day, 4:39:09.931770 INFO: calibration group: precursor, predicting rt
1 day, 4:39:09.960814 INFO: calibration group: precursor, predicting mobility
1 day, 4:39:09.967737 INFO: calibration group: fragment, predicting mz
1 day, 4:39:10.022268 INFO: === checking if optimization conditions were reached ===
1 day, 4:39:10.022554 PROGRESS: === Optimization of mobility_error has been performed 5 time(s); minimum number is 2 ===
1 day, 4:39:10.023592 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.0420 found after 5 searches.
1 day, 4:39:10.023644 INFO: ==============================================
1 day, 4:39:10.023737 PROGRESS: Optimization finished for mobility_error.
1 day, 4:39:10.212636 INFO: calibration group: precursor, predicting mz
1 day, 4:39:10.220623 INFO: calibration group: precursor, predicting rt
1 day, 4:39:10.249774 INFO: calibration group: precursor, predicting mobility
1 day, 4:39:10.256759 INFO: calibration group: fragment, predicting mz
1 day, 4:39:10.338002 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 4:39:10.338245 PROGRESS: ==============================================
1 day, 4:39:10.338322 PROGRESS: ms2_error      : 15.0000
1 day, 4:39:10.338380 PROGRESS: ms1_error      : 10.0000
1 day, 4:39:10.338433 PROGRESS: rt_error       : 109.7940
1 day, 4:39:10.338483 PROGRESS: mobility_error : 0.0420
1 day, 4:39:10.338529 PROGRESS: ==============================================
1 day, 4:39:10.341399 INFO: calibration group: precursor, predicting mz
1 day, 4:39:11.863498 INFO: calibration group: precursor, predicting rt
1 day, 4:39:18.431416 INFO: calibration group: precursor, predicting mobility
1 day, 4:39:19.889100 INFO: calibration group: fragment, predicting mz
1 day, 4:39:32.551238 PROGRESS: Extracting batch of 10272670 precursors
1 day, 4:39:34.879099 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:39:34.879247 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:39:34.879306 INFO: FWHM in RT is 2.99 seconds, sigma is 0.66
1 day, 4:39:34.879335 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.04
1 day, 4:39:34.880902 INFO: Starting candidate selection
1 day, 4:57:32.514129 INFO: Applying score cutoff of 32.54461517715454
1 day, 4:57:32.883866 INFO: Removed 6775189 precursors with score below cutoff
1 day, 4:57:36.041108 INFO: Starting candidate scoring
1 day, 5:02:39.083597 INFO: Finished candidate processing
1 day, 5:02:39.085609 INFO: Collecting candidate features
1 day, 5:02:58.054180 WARNING: intensity_correlation has 19 NaNs ( 0.00 % out of 10179236)
1 day, 5:02:58.405169 INFO: Collecting fragment features
1 day, 5:03:05.884300 INFO: Finished candidate scoring
1 day, 5:03:18.542470 INFO: === FDR correction performed with classifier version 17 ===
1 day, 5:03:18.557811 INFO: performing precursor FDR with 47 features
1 day, 5:03:18.557903 INFO: Decoy channel: -1
1 day, 5:03:18.557934 INFO: Competetive: True
1 day, 5:03:21.268260 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:03:22.969702 WARNING: dropped 9 target PSMs due to missing features
1 day, 5:03:22.969862 WARNING: dropped 10 decoy PSMs due to missing features
1 day, 5:06:43.082188 INFO: Test AUC: 0.536
1 day, 5:06:43.082472 INFO: Train AUC: 0.577
1 day, 5:06:43.082533 INFO: AUC difference: 7.11%
1 day, 5:06:43.082560 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 5:06:43.832031 INFO: Resetting torch num_threads to 100
1 day, 5:06:44.247534 INFO: Removing fragments below FDR threshold
1 day, 5:06:44.994672 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:06:44.995279 PROGRESS: Total precursors accumulated: 71,677
1 day, 5:06:44.995354 PROGRESS: Target precursors: 70,968 (99.01%)
1 day, 5:06:44.995410 PROGRESS: Decoy precursors: 709 (0.99%)
1 day, 5:06:44.995461 PROGRESS: 
1 day, 5:06:44.995507 PROGRESS: Precursor Summary:
1 day, 5:06:45.023085 PROGRESS: Channel   0:	 0.05 FDR: 70,968; 0.01 FDR: 70,968; 0.001 FDR: 52,858
1 day, 5:06:45.023355 PROGRESS: 
1 day, 5:06:45.023431 PROGRESS: Protein Summary:
1 day, 5:06:45.063654 PROGRESS: Channel   0:	 0.05 FDR: 11,368; 0.01 FDR: 11,368; 0.001 FDR: 8,952
1 day, 5:06:45.063910 PROGRESS: =========================================================================
1 day, 5:06:45.848576 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 5:06:46.281337 PROGRESS: Loading raw file 5/6: ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 5:06:46.281524 INFO: Quantification results path: run_output/alphadia_1.10_defaultMBR/library/quant
1 day, 5:06:46.281606 INFO: Creating workflow folder for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502 at run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 5:06:46.282345 INFO: Initializing RawFileManager
1 day, 5:06:46.282475 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 5:06:46.282540 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 5:06:46.282586 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 5:06:46.506040 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
1 day, 5:06:55.642844 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d...
1 day, 5:06:55.646131 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 5:06:55.648928 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 5:06:55.649221 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 5:06:55.649652 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 5:06:55.651430 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 5:06:55.667433 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 5:06:55.667733 INFO: Indexing quadrupole dimension
1 day, 5:06:56.163804 INFO: Transposing detector events
1 day, 5:07:05.651960 INFO: Finished transposing data
1 day, 5:07:05.689175 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 5:07:05.690246 INFO: RT (min)            : 0.0 - 70.0
1 day, 5:07:05.690337 INFO: RT duration (sec)   : 4199.9
1 day, 5:07:05.690396 INFO: RT duration (min)   : 70.0
1 day, 5:07:05.690449 INFO: Cycle len (scans)   : 9
1 day, 5:07:05.690494 INFO: Cycle len (sec)     : 0.97
1 day, 5:07:05.690536 INFO: Number of cycles    : 4347
1 day, 5:07:05.690579 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 5:07:07.038748 INFO: Initializing CalibrationManager
1 day, 5:07:07.039040 INFO: Loading calibration config
1 day, 5:07:07.039684 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'}]
1 day, 5:07:07.039774 INFO: Calibration group :fragment, found 1 estimator(s)
1 day, 5:07:07.039878 INFO: Calibration group :precursor, found 3 estimator(s)
1 day, 5:07:07.040067 INFO: Initializing OptimizationManager
1 day, 5:07:07.040170 INFO: initial parameter: ms1_error = 30
1 day, 5:07:07.040220 INFO: initial parameter: ms2_error = 30
1 day, 5:07:07.040280 INFO: initial parameter: rt_error = 2099.9331315
1 day, 5:07:07.040332 INFO: initial parameter: mobility_error = 0.1
1 day, 5:07:07.040377 INFO: initial parameter: column_type = library
1 day, 5:07:07.040418 INFO: initial parameter: num_candidates = 1
1 day, 5:07:07.040459 INFO: initial parameter: classifier_version = -1
1 day, 5:07:07.040499 INFO: initial parameter: fwhm_rt = 5
1 day, 5:07:07.040541 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 5:07:07.040582 INFO: initial parameter: score_cutoff = 0
1 day, 5:07:07.040648 INFO: Initializing TimingManager
1 day, 5:07:07.040710 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 5:07:07.040831 INFO: FDRManager not loaded from disk.
1 day, 5:07:07.040855 INFO: Initializing FDRManager
1 day, 5:07:07.040904 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 5:07:08.343185 PROGRESS: 5,215,079 target precursors potentially observable (0 removed)
1 day, 5:07:10.190801 PROGRESS: Starting initial search for precursors.
1 day, 5:07:10.444234 INFO: Starting optimization step 0.
1 day, 5:07:10.444473 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 5:07:10.444559 PROGRESS: Extracting batch of 15771 precursors
1 day, 5:07:10.448040 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 5:07:10.448095 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 5:07:10.448128 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 5:07:10.448150 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 5:07:10.449255 INFO: Starting candidate selection
1 day, 5:08:30.989736 INFO: Starting candidate scoring
1 day, 5:08:31.750243 INFO: Finished candidate processing
1 day, 5:08:31.750398 INFO: Collecting candidate features
1 day, 5:08:31.811239 WARNING: intensity_correlation has 1 NaNs ( 0.01 % out of 13769)
1 day, 5:08:31.817322 INFO: Collecting fragment features
1 day, 5:08:31.830137 INFO: Finished candidate scoring
1 day, 5:08:31.838317 PROGRESS: === Extracted 13769 precursors and 138111 fragments ===
1 day, 5:08:31.840005 INFO: performing precursor FDR with 47 features
1 day, 5:08:31.840053 INFO: Decoy channel: -1
1 day, 5:08:31.840077 INFO: Competetive: True
1 day, 5:08:31.844987 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:08:31.847817 WARNING: dropped 1 target PSMs due to missing features
1 day, 5:08:31.964303 INFO: Test AUC: 0.520
1 day, 5:08:31.964422 INFO: Train AUC: 0.526
1 day, 5:08:31.964458 INFO: AUC difference: 1.08%
1 day, 5:08:32.054943 INFO: Resetting torch num_threads to 100
1 day, 5:08:32.056781 INFO: === FDR correction performed with classifier version -1 ===
1 day, 5:08:32.058587 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:08:32.058722 PROGRESS: Total precursors accumulated: 7,051
1 day, 5:08:32.058786 PROGRESS: Target precursors: 3,754 (53.24%)
1 day, 5:08:32.058838 PROGRESS: Decoy precursors: 3,297 (46.76%)
1 day, 5:08:32.058886 PROGRESS: 
1 day, 5:08:32.058933 PROGRESS: Precursor Summary:
1 day, 5:08:32.059836 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 5:08:32.059927 PROGRESS: 
1 day, 5:08:32.059985 PROGRESS: Protein Summary:
1 day, 5:08:32.060923 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 5:08:32.061016 PROGRESS: =========================================================================
1 day, 5:08:32.562142 INFO: Starting optimization step 1.
1 day, 5:08:32.562484 PROGRESS: === Extracting elution groups 8000 to 24000 ===
1 day, 5:08:32.562569 PROGRESS: Extracting batch of 31534 precursors
1 day, 5:08:32.572921 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 5:08:32.573017 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 5:08:32.573075 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 5:08:32.573102 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 5:08:32.574152 INFO: Starting candidate selection
1 day, 5:11:05.686722 INFO: Starting candidate scoring
1 day, 5:11:07.107514 INFO: Finished candidate processing
1 day, 5:11:07.107649 INFO: Collecting candidate features
1 day, 5:11:07.202116 WARNING: intensity_correlation has 9 NaNs ( 0.03 % out of 27356)
1 day, 5:11:07.206388 INFO: Collecting fragment features
1 day, 5:11:07.226676 INFO: Finished candidate scoring
1 day, 5:11:07.276261 PROGRESS: === Extracted 41125 precursors and 411700 fragments ===
1 day, 5:11:07.281582 INFO: performing precursor FDR with 47 features
1 day, 5:11:07.281674 INFO: Decoy channel: -1
1 day, 5:11:07.281702 INFO: Competetive: True
1 day, 5:11:07.301575 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:11:07.310666 WARNING: dropped 5 target PSMs due to missing features
1 day, 5:11:07.310788 WARNING: dropped 5 decoy PSMs due to missing features
1 day, 5:11:07.839553 INFO: Test AUC: 0.556
1 day, 5:11:07.839747 INFO: Train AUC: 0.571
1 day, 5:11:07.839781 INFO: AUC difference: 2.51%
1 day, 5:11:07.932074 INFO: Resetting torch num_threads to 100
1 day, 5:11:07.935115 INFO: === FDR correction performed with classifier version -1 ===
1 day, 5:11:07.941110 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:11:07.941292 PROGRESS: Total precursors accumulated: 21,081
1 day, 5:11:07.941356 PROGRESS: Target precursors: 12,488 (59.24%)
1 day, 5:11:07.941411 PROGRESS: Decoy precursors: 8,593 (40.76%)
1 day, 5:11:07.941462 PROGRESS: 
1 day, 5:11:07.941511 PROGRESS: Precursor Summary:
1 day, 5:11:07.942638 PROGRESS: Channel   0:	 0.05 FDR:   217; 0.01 FDR:   108; 0.001 FDR:    74
1 day, 5:11:07.942737 PROGRESS: 
1 day, 5:11:07.942795 PROGRESS: Protein Summary:
1 day, 5:11:07.943928 PROGRESS: Channel   0:	 0.05 FDR:   210; 0.01 FDR:   105; 0.001 FDR:    72
1 day, 5:11:07.944021 PROGRESS: =========================================================================
1 day, 5:11:08.185118 INFO: Starting optimization step 2.
1 day, 5:11:08.185405 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1 day, 5:11:08.185486 PROGRESS: Extracting batch of 63016 precursors
1 day, 5:11:08.201520 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 5:11:08.201653 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 5:11:08.201700 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 5:11:08.201724 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 5:11:08.202642 INFO: Starting candidate selection
1 day, 5:16:07.057094 INFO: Starting candidate scoring
1 day, 5:16:09.888317 INFO: Finished candidate processing
1 day, 5:16:09.889342 INFO: Collecting candidate features
1 day, 5:16:09.997535 WARNING: intensity_correlation has 8 NaNs ( 0.01 % out of 54891)
1 day, 5:16:10.002839 INFO: Collecting fragment features
1 day, 5:16:10.044607 INFO: Finished candidate scoring
1 day, 5:16:10.183056 PROGRESS: === Extracted 96016 precursors and 961064 fragments ===
1 day, 5:16:10.197403 INFO: performing precursor FDR with 47 features
1 day, 5:16:10.197504 INFO: Decoy channel: -1
1 day, 5:16:10.197531 INFO: Competetive: True
1 day, 5:16:10.250833 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:16:10.276185 WARNING: dropped 10 target PSMs due to missing features
1 day, 5:16:10.276334 WARNING: dropped 8 decoy PSMs due to missing features
1 day, 5:16:12.038979 INFO: Test AUC: 0.560
1 day, 5:16:12.039157 INFO: Train AUC: 0.586
1 day, 5:16:12.039197 INFO: AUC difference: 4.39%
1 day, 5:16:12.138009 INFO: Resetting torch num_threads to 100
1 day, 5:16:12.144972 INFO: === FDR correction performed with classifier version -1 ===
1 day, 5:16:12.155491 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:16:12.155824 PROGRESS: Total precursors accumulated: 49,256
1 day, 5:16:12.155896 PROGRESS: Target precursors: 30,048 (61.00%)
1 day, 5:16:12.155959 PROGRESS: Decoy precursors: 19,208 (39.00%)
1 day, 5:16:12.156018 PROGRESS: 
1 day, 5:16:12.156075 PROGRESS: Precursor Summary:
1 day, 5:16:12.157614 PROGRESS: Channel   0:	 0.05 FDR:   517; 0.01 FDR:   264; 0.001 FDR:   164
1 day, 5:16:12.157734 PROGRESS: 
1 day, 5:16:12.157801 PROGRESS: Protein Summary:
1 day, 5:16:12.159216 PROGRESS: Channel   0:	 0.05 FDR:   480; 0.01 FDR:   247; 0.001 FDR:   157
1 day, 5:16:12.159316 PROGRESS: =========================================================================
1 day, 5:16:12.173011 INFO: fragments_df_filtered: 2515
1 day, 5:16:12.441787 INFO: calibration group: precursor, fitting mz estimator 
1 day, 5:16:12.485053 INFO: calibration group: precursor, fitting rt estimator 
1 day, 5:16:12.528258 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 5:16:12.570090 INFO: calibration group: fragment, fitting mz estimator 
1 day, 5:16:12.688953 INFO: calibration group: precursor, predicting mz
1 day, 5:16:12.705223 INFO: calibration group: precursor, predicting rt
1 day, 5:16:12.776463 INFO: calibration group: precursor, predicting mobility
1 day, 5:16:12.794895 INFO: calibration group: fragment, predicting mz
1 day, 5:16:12.940912 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 5:16:12.941349 INFO: Starting optimization step 3.
1 day, 5:16:12.941440 PROGRESS: === Extracting elution groups 0 to 56000 ===
1 day, 5:16:12.941542 PROGRESS: Extracting batch of 110321 precursors
1 day, 5:16:12.991878 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 5:16:12.992020 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 5:16:12.992085 INFO: FWHM in RT is 3.34 seconds, sigma is 0.73
1 day, 5:16:12.992115 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.25
1 day, 5:16:12.992983 INFO: Starting candidate selection
1 day, 5:24:59.334754 INFO: Starting candidate scoring
1 day, 5:25:09.131341 INFO: Finished candidate processing
1 day, 5:25:09.131655 INFO: Collecting candidate features
1 day, 5:25:09.480867 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 189444)
1 day, 5:25:09.481313 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 189444)
1 day, 5:25:09.491078 INFO: Collecting fragment features
1 day, 5:25:09.627432 INFO: Finished candidate scoring
1 day, 5:25:09.810677 PROGRESS: === Extracted 189444 precursors and 1928124 fragments ===
1 day, 5:25:09.811186 INFO: performing precursor FDR with 47 features
1 day, 5:25:09.811227 INFO: Decoy channel: -1
1 day, 5:25:09.811252 INFO: Competetive: True
1 day, 5:25:09.889267 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:25:09.933546 WARNING: dropped 1 target PSMs due to missing features
1 day, 5:25:09.933701 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 5:25:13.881278 INFO: Test AUC: 0.565
1 day, 5:25:13.881422 INFO: Train AUC: 0.594
1 day, 5:25:13.881455 INFO: AUC difference: 4.85%
1 day, 5:25:13.981011 INFO: Resetting torch num_threads to 100
1 day, 5:25:13.988259 INFO: === FDR correction performed with classifier version 2 ===
1 day, 5:25:13.999363 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:25:13.999669 PROGRESS: Total precursors accumulated: 50,280
1 day, 5:25:13.999733 PROGRESS: Target precursors: 31,765 (63.18%)
1 day, 5:25:13.999785 PROGRESS: Decoy precursors: 18,515 (36.82%)
1 day, 5:25:13.999833 PROGRESS: 
1 day, 5:25:13.999878 PROGRESS: Precursor Summary:
1 day, 5:25:14.001418 PROGRESS: Channel   0:	 0.05 FDR:   531; 0.01 FDR:   354; 0.001 FDR:   236
1 day, 5:25:14.001516 PROGRESS: 
1 day, 5:25:14.001572 PROGRESS: Protein Summary:
1 day, 5:25:14.003019 PROGRESS: Channel   0:	 0.05 FDR:   493; 0.01 FDR:   327; 0.001 FDR:   221
1 day, 5:25:14.003119 PROGRESS: =========================================================================
1 day, 5:25:14.018618 INFO: fragments_df_filtered: 4487
1 day, 5:25:14.555186 INFO: calibration group: precursor, fitting mz estimator 
1 day, 5:25:14.609693 INFO: calibration group: precursor, fitting rt estimator 
1 day, 5:25:14.658135 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 5:25:14.706894 INFO: calibration group: fragment, fitting mz estimator 
1 day, 5:25:15.063892 INFO: calibration group: precursor, predicting mz
1 day, 5:25:15.079678 INFO: calibration group: precursor, predicting rt
1 day, 5:25:15.146362 INFO: calibration group: precursor, predicting mobility
1 day, 5:25:15.161728 INFO: calibration group: fragment, predicting mz
1 day, 5:25:15.300652 INFO: === checking if optimization conditions were reached ===
1 day, 5:25:15.303001 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 5:25:15.303959 PROGRESS: ❌ ms1_error      : 10.0000 > 10.0000 or insufficient steps taken.
1 day, 5:25:15.304006 INFO: ==============================================
1 day, 5:25:15.304117 INFO: Starting optimization step 4.
1 day, 5:25:15.304188 PROGRESS: === Extracting elution groups 0 to 56000 ===
1 day, 5:25:15.304253 PROGRESS: Extracting batch of 110321 precursors
1 day, 5:25:15.338933 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 5:25:15.339070 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 5:25:15.339135 INFO: FWHM in RT is 3.18 seconds, sigma is 0.70
1 day, 5:25:15.339163 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.05
1 day, 5:25:15.348121 INFO: Starting candidate selection
1 day, 5:33:20.589612 INFO: Starting candidate scoring
1 day, 5:33:25.952936 INFO: Finished candidate processing
1 day, 5:33:25.953130 INFO: Collecting candidate features
1 day, 5:33:26.336351 WARNING: intensity_correlation has 8 NaNs ( 0.00 % out of 189371)
1 day, 5:33:26.346713 INFO: Collecting fragment features
1 day, 5:33:26.478556 INFO: Finished candidate scoring
1 day, 5:33:26.598025 PROGRESS: === Extracted 189371 precursors and 1858213 fragments ===
1 day, 5:33:26.598656 INFO: performing precursor FDR with 47 features
1 day, 5:33:26.598697 INFO: Decoy channel: -1
1 day, 5:33:26.598722 INFO: Competetive: True
1 day, 5:33:26.677485 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:33:26.722183 WARNING: dropped 2 target PSMs due to missing features
1 day, 5:33:26.722324 WARNING: dropped 6 decoy PSMs due to missing features
1 day, 5:33:30.444743 INFO: Test AUC: 0.559
1 day, 5:33:30.444906 INFO: Train AUC: 0.591
1 day, 5:33:30.444941 INFO: AUC difference: 5.50%
1 day, 5:33:30.444963 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 5:33:30.544967 INFO: Resetting torch num_threads to 100
1 day, 5:33:30.579670 INFO: === FDR correction performed with classifier version 3 ===
1 day, 5:33:30.592024 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:33:30.592302 PROGRESS: Total precursors accumulated: 50,235
1 day, 5:33:30.592367 PROGRESS: Target precursors: 31,145 (62.00%)
1 day, 5:33:30.592419 PROGRESS: Decoy precursors: 19,090 (38.00%)
1 day, 5:33:30.592466 PROGRESS: 
1 day, 5:33:30.592512 PROGRESS: Precursor Summary:
1 day, 5:33:30.594095 PROGRESS: Channel   0:	 0.05 FDR:   898; 0.01 FDR:   602; 0.001 FDR:   338
1 day, 5:33:30.594197 PROGRESS: 
1 day, 5:33:30.594255 PROGRESS: Protein Summary:
1 day, 5:33:30.595907 PROGRESS: Channel   0:	 0.05 FDR:   814; 0.01 FDR:   547; 0.001 FDR:   303
1 day, 5:33:30.596003 PROGRESS: =========================================================================
1 day, 5:33:30.612421 INFO: fragments_df_filtered: 5000
1 day, 5:33:30.810227 INFO: calibration group: precursor, fitting mz estimator 
1 day, 5:33:30.855377 INFO: calibration group: precursor, fitting rt estimator 
1 day, 5:33:30.899462 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 5:33:30.942007 INFO: calibration group: fragment, fitting mz estimator 
1 day, 5:33:31.293937 INFO: calibration group: precursor, predicting mz
1 day, 5:33:31.301193 INFO: calibration group: precursor, predicting rt
1 day, 5:33:31.329450 INFO: calibration group: precursor, predicting mobility
1 day, 5:33:31.335705 INFO: calibration group: fragment, predicting mz
1 day, 5:33:31.388494 INFO: === checking if optimization conditions were reached ===
1 day, 5:33:31.391182 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 5:33:31.392399 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
1 day, 5:33:31.392475 INFO: ==============================================
1 day, 5:33:31.392924 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 5:33:31.571186 INFO: calibration group: precursor, predicting mz
1 day, 5:33:31.578630 INFO: calibration group: precursor, predicting rt
1 day, 5:33:31.606909 INFO: calibration group: precursor, predicting mobility
1 day, 5:33:31.613185 INFO: calibration group: fragment, predicting mz
1 day, 5:33:31.666611 INFO: Starting optimization step 0.
1 day, 5:33:31.666909 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 5:33:31.667019 PROGRESS: Extracting batch of 47305 precursors
1 day, 5:33:31.736874 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 5:33:31.737037 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 5:33:31.737162 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 5:33:31.737194 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.19
1 day, 5:33:31.738283 INFO: Starting candidate selection
1 day, 5:37:06.778624 INFO: Starting candidate scoring
1 day, 5:37:09.249389 INFO: Finished candidate processing
1 day, 5:37:09.250580 INFO: Collecting candidate features
1 day, 5:37:09.388578 WARNING: intensity_correlation has 5 NaNs ( 0.01 % out of 81104)
1 day, 5:37:09.395422 INFO: Collecting fragment features
1 day, 5:37:09.462985 INFO: Finished candidate scoring
1 day, 5:37:09.499344 PROGRESS: === Extracted 81104 precursors and 793603 fragments ===
1 day, 5:37:09.499827 INFO: performing precursor FDR with 47 features
1 day, 5:37:09.499867 INFO: Decoy channel: -1
1 day, 5:37:09.499892 INFO: Competetive: True
1 day, 5:37:09.527957 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:37:09.544535 WARNING: dropped 3 target PSMs due to missing features
1 day, 5:37:09.544677 WARNING: dropped 2 decoy PSMs due to missing features
1 day, 5:37:11.088528 INFO: Test AUC: 0.567
1 day, 5:37:11.088668 INFO: Train AUC: 0.615
1 day, 5:37:11.088703 INFO: AUC difference: 7.92%
1 day, 5:37:11.088727 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 5:37:11.181306 INFO: Resetting torch num_threads to 100
1 day, 5:37:11.184149 INFO: === FDR correction performed with classifier version 4 ===
1 day, 5:37:11.187893 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:37:11.188053 PROGRESS: Total precursors accumulated: 21,515
1 day, 5:37:11.188117 PROGRESS: Target precursors: 13,823 (64.25%)
1 day, 5:37:11.188169 PROGRESS: Decoy precursors: 7,692 (35.75%)
1 day, 5:37:11.188219 PROGRESS: 
1 day, 5:37:11.188264 PROGRESS: Precursor Summary:
1 day, 5:37:11.189465 PROGRESS: Channel   0:	 0.05 FDR:   468; 0.01 FDR:   335; 0.001 FDR:   201
1 day, 5:37:11.189564 PROGRESS: 
1 day, 5:37:11.189620 PROGRESS: Protein Summary:
1 day, 5:37:11.190890 PROGRESS: Channel   0:	 0.05 FDR:   451; 0.01 FDR:   321; 0.001 FDR:   195
1 day, 5:37:11.190982 PROGRESS: =========================================================================
1 day, 5:37:11.265763 INFO: fragments_df_filtered: 3599
1 day, 5:37:11.438265 INFO: calibration group: precursor, fitting mz estimator 
1 day, 5:37:11.488243 INFO: calibration group: precursor, fitting rt estimator 
1 day, 5:37:11.539074 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 5:37:11.587950 INFO: calibration group: fragment, fitting mz estimator 
1 day, 5:37:11.857865 INFO: calibration group: precursor, predicting mz
1 day, 5:37:11.865277 INFO: calibration group: precursor, predicting rt
1 day, 5:37:11.893752 INFO: calibration group: precursor, predicting mobility
1 day, 5:37:11.900294 INFO: calibration group: fragment, predicting mz
1 day, 5:37:11.954262 INFO: === checking if optimization conditions were reached ===
1 day, 5:37:11.954539 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 5:37:11.956562 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 928.1790.
1 day, 5:37:11.956614 INFO: ==============================================
1 day, 5:37:11.956726 INFO: Starting optimization step 1.
1 day, 5:37:11.956795 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 5:37:11.956861 PROGRESS: Extracting batch of 47305 precursors
1 day, 5:37:11.968986 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 5:37:11.969117 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 5:37:11.969169 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 5:37:11.969193 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.95
1 day, 5:37:11.994045 INFO: Starting candidate selection
1 day, 5:38:48.530950 INFO: Starting candidate scoring
1 day, 5:38:50.758500 INFO: Finished candidate processing
1 day, 5:38:50.758858 INFO: Collecting candidate features
1 day, 5:38:50.970067 WARNING: intensity_correlation has 19 NaNs ( 0.02 % out of 80352)
1 day, 5:38:50.978398 INFO: Collecting fragment features
1 day, 5:38:51.037493 INFO: Finished candidate scoring
1 day, 5:38:51.086477 PROGRESS: === Extracted 80352 precursors and 779952 fragments ===
1 day, 5:38:51.087107 INFO: performing precursor FDR with 47 features
1 day, 5:38:51.087146 INFO: Decoy channel: -1
1 day, 5:38:51.087171 INFO: Competetive: True
1 day, 5:38:51.114974 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:38:51.130098 WARNING: dropped 11 target PSMs due to missing features
1 day, 5:38:51.130225 WARNING: dropped 8 decoy PSMs due to missing features
1 day, 5:38:52.695459 INFO: Test AUC: 0.562
1 day, 5:38:52.695585 INFO: Train AUC: 0.598
1 day, 5:38:52.695614 INFO: AUC difference: 6.15%
1 day, 5:38:52.695635 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 5:38:52.786844 INFO: Resetting torch num_threads to 100
1 day, 5:38:52.789377 INFO: === FDR correction performed with classifier version 4 ===
1 day, 5:38:52.792989 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:38:52.793150 PROGRESS: Total precursors accumulated: 21,408
1 day, 5:38:52.793215 PROGRESS: Target precursors: 13,446 (62.81%)
1 day, 5:38:52.793267 PROGRESS: Decoy precursors: 7,962 (37.19%)
1 day, 5:38:52.793315 PROGRESS: 
1 day, 5:38:52.793360 PROGRESS: Precursor Summary:
1 day, 5:38:52.794764 PROGRESS: Channel   0:	 0.05 FDR:   442; 0.01 FDR:   310; 0.001 FDR:   224
1 day, 5:38:52.794863 PROGRESS: 
1 day, 5:38:52.794917 PROGRESS: Protein Summary:
1 day, 5:38:52.796174 PROGRESS: Channel   0:	 0.05 FDR:   425; 0.01 FDR:   296; 0.001 FDR:   217
1 day, 5:38:52.796265 PROGRESS: =========================================================================
1 day, 5:38:52.802947 INFO: fragments_df_filtered: 3333
1 day, 5:38:52.973228 INFO: calibration group: precursor, fitting mz estimator 
1 day, 5:38:53.014513 INFO: calibration group: precursor, fitting rt estimator 
1 day, 5:38:53.052604 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 5:38:53.090311 INFO: calibration group: fragment, fitting mz estimator 
1 day, 5:38:53.269702 INFO: calibration group: precursor, predicting mz
1 day, 5:38:53.276796 INFO: calibration group: precursor, predicting rt
1 day, 5:38:53.305066 INFO: calibration group: precursor, predicting mobility
1 day, 5:38:53.311482 INFO: calibration group: fragment, predicting mz
1 day, 5:38:53.363619 INFO: === checking if optimization conditions were reached ===
1 day, 5:38:53.363904 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 5:38:53.365974 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 647.3889.
1 day, 5:38:53.366031 INFO: ==============================================
1 day, 5:38:53.366132 INFO: Starting optimization step 2.
1 day, 5:38:53.366211 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 5:38:53.366287 PROGRESS: Extracting batch of 47305 precursors
1 day, 5:38:53.378042 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 5:38:53.378159 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 5:38:53.378214 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 5:38:53.378257 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.99
1 day, 5:38:53.379335 INFO: Starting candidate selection
1 day, 5:39:58.406611 INFO: Starting candidate scoring
1 day, 5:39:59.869277 INFO: Finished candidate processing
1 day, 5:39:59.870418 INFO: Collecting candidate features
1 day, 5:40:00.037895 WARNING: intensity_correlation has 308 NaNs ( 0.41 % out of 74798)
1 day, 5:40:00.038260 WARNING: height_correlation has 11 NaNs ( 0.01 % out of 74798)
1 day, 5:40:00.044555 INFO: Collecting fragment features
1 day, 5:40:00.093980 INFO: Finished candidate scoring
1 day, 5:40:00.142174 PROGRESS: === Extracted 74798 precursors and 452989 fragments ===
1 day, 5:40:00.142768 INFO: performing precursor FDR with 47 features
1 day, 5:40:00.142815 INFO: Decoy channel: -1
1 day, 5:40:00.142842 INFO: Competetive: True
1 day, 5:40:00.182683 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:40:00.202167 WARNING: dropped 160 target PSMs due to missing features
1 day, 5:40:00.202326 WARNING: dropped 153 decoy PSMs due to missing features
1 day, 5:40:01.636956 INFO: Test AUC: 0.531
1 day, 5:40:01.637125 INFO: Train AUC: 0.576
1 day, 5:40:01.637156 INFO: AUC difference: 7.74%
1 day, 5:40:01.637178 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 5:40:01.732624 INFO: Resetting torch num_threads to 100
1 day, 5:40:01.736364 INFO: === FDR correction performed with classifier version 4 ===
1 day, 5:40:01.740930 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:40:01.741115 PROGRESS: Total precursors accumulated: 20,619
1 day, 5:40:01.741183 PROGRESS: Target precursors: 12,049 (58.44%)
1 day, 5:40:01.741235 PROGRESS: Decoy precursors: 8,570 (41.56%)
1 day, 5:40:01.741288 PROGRESS: 
1 day, 5:40:01.741337 PROGRESS: Precursor Summary:
1 day, 5:40:01.742339 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 5:40:01.742434 PROGRESS: 
1 day, 5:40:01.742492 PROGRESS: Protein Summary:
1 day, 5:40:01.743497 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 5:40:01.743590 PROGRESS: =========================================================================
1 day, 5:40:01.992794 INFO: calibration group: precursor, predicting mz
1 day, 5:40:02.002942 INFO: calibration group: precursor, predicting rt
1 day, 5:40:02.043308 INFO: calibration group: precursor, predicting mobility
1 day, 5:40:02.056288 INFO: calibration group: fragment, predicting mz
1 day, 5:40:02.127924 INFO: === skipping optimization until target number of precursors are found ===
1 day, 5:40:02.128212 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1 day, 5:40:02.128280 INFO: Starting optimization step 3.
1 day, 5:40:02.128349 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1 day, 5:40:02.128416 PROGRESS: Extracting batch of 63016 precursors
1 day, 5:40:02.144896 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 5:40:02.145016 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 5:40:02.145076 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 5:40:02.145100 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.99
1 day, 5:40:02.146115 INFO: Starting candidate selection
1 day, 5:41:27.484736 INFO: Starting candidate scoring
1 day, 5:41:29.248475 INFO: Finished candidate processing
1 day, 5:41:29.248677 INFO: Collecting candidate features
1 day, 5:41:29.509855 WARNING: intensity_correlation has 463 NaNs ( 0.47 % out of 99516)
1 day, 5:41:29.510178 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 99516)
1 day, 5:41:29.517235 INFO: Collecting fragment features
1 day, 5:41:29.583170 INFO: Finished candidate scoring
1 day, 5:41:29.718041 PROGRESS: === Extracted 174314 precursors and 1055981 fragments ===
1 day, 5:41:29.735101 INFO: performing precursor FDR with 47 features
1 day, 5:41:29.735219 INFO: Decoy channel: -1
1 day, 5:41:29.735247 INFO: Competetive: True
1 day, 5:41:29.807325 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:41:29.840042 WARNING: dropped 420 target PSMs due to missing features
1 day, 5:41:29.840171 WARNING: dropped 359 decoy PSMs due to missing features
1 day, 5:41:33.445148 INFO: Test AUC: 0.530
1 day, 5:41:33.445272 INFO: Train AUC: 0.574
1 day, 5:41:33.445308 INFO: AUC difference: 7.57%
1 day, 5:41:33.445336 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 5:41:33.541953 INFO: Resetting torch num_threads to 100
1 day, 5:41:33.549569 INFO: === FDR correction performed with classifier version 4 ===
1 day, 5:41:33.558201 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:41:33.558480 PROGRESS: Total precursors accumulated: 48,116
1 day, 5:41:33.558544 PROGRESS: Target precursors: 28,107 (58.42%)
1 day, 5:41:33.558595 PROGRESS: Decoy precursors: 20,009 (41.58%)
1 day, 5:41:33.558643 PROGRESS: 
1 day, 5:41:33.558690 PROGRESS: Precursor Summary:
1 day, 5:41:33.559908 PROGRESS: Channel   0:	 0.05 FDR:    11; 0.01 FDR:    11; 0.001 FDR:    11
1 day, 5:41:33.560000 PROGRESS: 
1 day, 5:41:33.560055 PROGRESS: Protein Summary:
1 day, 5:41:33.561271 PROGRESS: Channel   0:	 0.05 FDR:    11; 0.01 FDR:    11; 0.001 FDR:    11
1 day, 5:41:33.561365 PROGRESS: =========================================================================
1 day, 5:41:33.840167 INFO: calibration group: precursor, predicting mz
1 day, 5:41:33.857457 INFO: calibration group: precursor, predicting rt
1 day, 5:41:33.933183 INFO: calibration group: precursor, predicting mobility
1 day, 5:41:33.950620 INFO: calibration group: fragment, predicting mz
1 day, 5:41:34.107496 INFO: === skipping optimization until target number of precursors are found ===
1 day, 5:41:34.107787 PROGRESS: === Optimization of rt_error has been skipped 2 time(s); maximum number is 1 ===
1 day, 5:41:34.108499 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 928.1790 found after 2 searches.
1 day, 5:41:34.108569 PROGRESS: Optimization finished for rt_error.
1 day, 5:41:34.281830 INFO: calibration group: precursor, predicting mz
1 day, 5:41:34.289231 INFO: calibration group: precursor, predicting rt
1 day, 5:41:34.317988 INFO: calibration group: precursor, predicting mobility
1 day, 5:41:34.324592 INFO: calibration group: fragment, predicting mz
1 day, 5:41:34.404343 INFO: Starting optimization step 0.
1 day, 5:41:34.404544 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 5:41:34.404621 PROGRESS: Extracting batch of 47305 precursors
1 day, 5:41:34.415971 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 5:41:34.416085 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 5:41:34.416135 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 5:41:34.416160 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.99
1 day, 5:41:34.417172 INFO: Starting candidate selection
1 day, 5:43:10.220728 INFO: Starting candidate scoring
1 day, 5:43:11.722082 INFO: Finished candidate processing
1 day, 5:43:11.722193 INFO: Collecting candidate features
1 day, 5:43:11.847225 WARNING: intensity_correlation has 290 NaNs ( 0.38 % out of 75669)
1 day, 5:43:11.847545 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 75669)
1 day, 5:43:11.853446 INFO: Collecting fragment features
1 day, 5:43:11.896521 INFO: Finished candidate scoring
1 day, 5:43:11.938788 PROGRESS: === Extracted 75669 precursors and 461330 fragments ===
1 day, 5:43:11.939307 INFO: performing precursor FDR with 47 features
1 day, 5:43:11.939347 INFO: Decoy channel: -1
1 day, 5:43:11.939371 INFO: Competetive: True
1 day, 5:43:11.968514 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:43:11.983033 WARNING: dropped 151 target PSMs due to missing features
1 day, 5:43:11.983167 WARNING: dropped 144 decoy PSMs due to missing features
1 day, 5:43:13.516596 INFO: Test AUC: 0.533
1 day, 5:43:13.516725 INFO: Train AUC: 0.589
1 day, 5:43:13.516756 INFO: AUC difference: 9.55%
1 day, 5:43:13.516781 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 5:43:13.618341 INFO: Resetting torch num_threads to 100
1 day, 5:43:13.620868 INFO: === FDR correction performed with classifier version 6 ===
1 day, 5:43:13.624396 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:43:13.624571 PROGRESS: Total precursors accumulated: 20,819
1 day, 5:43:13.624638 PROGRESS: Target precursors: 12,454 (59.82%)
1 day, 5:43:13.624692 PROGRESS: Decoy precursors: 8,365 (40.18%)
1 day, 5:43:13.624741 PROGRESS: 
1 day, 5:43:13.624788 PROGRESS: Precursor Summary:
1 day, 5:43:13.625812 PROGRESS: Channel   0:	 0.05 FDR:    29; 0.01 FDR:     8; 0.001 FDR:     8
1 day, 5:43:13.625912 PROGRESS: 
1 day, 5:43:13.625969 PROGRESS: Protein Summary:
1 day, 5:43:13.627030 PROGRESS: Channel   0:	 0.05 FDR:    29; 0.01 FDR:     8; 0.001 FDR:     8
1 day, 5:43:13.627126 PROGRESS: =========================================================================
1 day, 5:43:13.835821 INFO: calibration group: precursor, predicting mz
1 day, 5:43:13.845471 INFO: calibration group: precursor, predicting rt
1 day, 5:43:13.884601 INFO: calibration group: precursor, predicting mobility
1 day, 5:43:13.895193 INFO: calibration group: fragment, predicting mz
1 day, 5:43:13.974809 INFO: === skipping optimization until target number of precursors are found ===
1 day, 5:43:13.975145 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
1 day, 5:43:13.975222 INFO: Starting optimization step 1.
1 day, 5:43:13.975302 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1 day, 5:43:13.975397 PROGRESS: Extracting batch of 63016 precursors
1 day, 5:43:13.998371 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 5:43:13.998524 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 5:43:13.998584 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 5:43:13.998616 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.99
1 day, 5:43:14.005848 INFO: Starting candidate selection
1 day, 5:45:21.771278 INFO: Starting candidate scoring
1 day, 5:45:23.683760 INFO: Finished candidate processing
1 day, 5:45:23.683867 INFO: Collecting candidate features
1 day, 5:45:23.843070 WARNING: intensity_correlation has 457 NaNs ( 0.45 % out of 100695)
1 day, 5:45:23.843399 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 100695)
1 day, 5:45:23.850243 INFO: Collecting fragment features
1 day, 5:45:23.914073 INFO: Finished candidate scoring
1 day, 5:45:24.047620 PROGRESS: === Extracted 176364 precursors and 1075771 fragments ===
1 day, 5:45:24.064608 INFO: performing precursor FDR with 47 features
1 day, 5:45:24.064744 INFO: Decoy channel: -1
1 day, 5:45:24.064772 INFO: Competetive: True
1 day, 5:45:24.141315 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:45:24.187221 WARNING: dropped 406 target PSMs due to missing features
1 day, 5:45:24.187351 WARNING: dropped 348 decoy PSMs due to missing features
1 day, 5:45:28.210539 INFO: Test AUC: 0.534
1 day, 5:45:28.210665 INFO: Train AUC: 0.578
1 day, 5:45:28.210696 INFO: AUC difference: 7.67%
1 day, 5:45:28.210720 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 5:45:28.306795 INFO: Resetting torch num_threads to 100
1 day, 5:45:28.314691 INFO: === FDR correction performed with classifier version 6 ===
1 day, 5:45:28.323644 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:45:28.323929 PROGRESS: Total precursors accumulated: 48,525
1 day, 5:45:28.323995 PROGRESS: Target precursors: 28,233 (58.18%)
1 day, 5:45:28.324049 PROGRESS: Decoy precursors: 20,292 (41.82%)
1 day, 5:45:28.324099 PROGRESS: 
1 day, 5:45:28.324146 PROGRESS: Precursor Summary:
1 day, 5:45:28.325307 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 5:45:28.325404 PROGRESS: 
1 day, 5:45:28.325459 PROGRESS: Protein Summary:
1 day, 5:45:28.326568 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 5:45:28.326658 PROGRESS: =========================================================================
1 day, 5:45:28.597790 INFO: calibration group: precursor, predicting mz
1 day, 5:45:28.615463 INFO: calibration group: precursor, predicting rt
1 day, 5:45:28.694064 INFO: calibration group: precursor, predicting mobility
1 day, 5:45:28.713520 INFO: calibration group: fragment, predicting mz
1 day, 5:45:28.883613 INFO: === skipping optimization until target number of precursors are found ===
1 day, 5:45:28.883954 PROGRESS: === Optimization of mobility_error has been skipped 2 time(s); maximum number is 1 ===
1 day, 5:45:28.884029 INFO: Starting optimization step 2.
1 day, 5:45:28.884111 PROGRESS: === Extracting elution groups 56000 to 120000 ===
1 day, 5:45:28.884192 PROGRESS: Extracting batch of 126066 precursors
1 day, 5:45:28.932334 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 5:45:28.932466 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 5:45:28.932518 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 5:45:28.932542 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.99
1 day, 5:45:28.933495 INFO: Starting candidate selection
1 day, 5:49:39.153967 INFO: Starting candidate scoring
1 day, 5:49:42.779376 INFO: Finished candidate processing
1 day, 5:49:42.779931 INFO: Collecting candidate features
1 day, 5:49:43.248710 WARNING: intensity_correlation has 825 NaNs ( 0.41 % out of 201454)
1 day, 5:49:43.249135 WARNING: height_correlation has 20 NaNs ( 0.01 % out of 201454)
1 day, 5:49:43.260936 INFO: Collecting fragment features
1 day, 5:49:43.374297 INFO: Finished candidate scoring
1 day, 5:49:43.629806 PROGRESS: === Extracted 377818 precursors and 2304509 fragments ===
1 day, 5:49:43.667153 INFO: performing precursor FDR with 47 features
1 day, 5:49:43.667293 INFO: Decoy channel: -1
1 day, 5:49:43.667324 INFO: Competetive: True
1 day, 5:49:43.833697 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:49:43.906306 WARNING: dropped 860 target PSMs due to missing features
1 day, 5:49:43.906452 WARNING: dropped 730 decoy PSMs due to missing features
1 day, 5:49:51.771276 INFO: Test AUC: 0.539
1 day, 5:49:51.771411 INFO: Train AUC: 0.562
1 day, 5:49:51.771442 INFO: AUC difference: 4.14%
1 day, 5:49:51.885738 INFO: Resetting torch num_threads to 100
1 day, 5:49:51.903959 INFO: === FDR correction performed with classifier version 6 ===
1 day, 5:49:51.924565 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:49:51.924897 PROGRESS: Total precursors accumulated: 103,965
1 day, 5:49:51.924973 PROGRESS: Target precursors: 59,778 (57.50%)
1 day, 5:49:51.925034 PROGRESS: Decoy precursors: 44,187 (42.50%)
1 day, 5:49:51.925086 PROGRESS: 
1 day, 5:49:51.925132 PROGRESS: Precursor Summary:
1 day, 5:49:51.926708 PROGRESS: Channel   0:	 0.05 FDR:    10; 0.01 FDR:    10; 0.001 FDR:    10
1 day, 5:49:51.926806 PROGRESS: 
1 day, 5:49:51.926864 PROGRESS: Protein Summary:
1 day, 5:49:51.928308 PROGRESS: Channel   0:	 0.05 FDR:    10; 0.01 FDR:    10; 0.001 FDR:    10
1 day, 5:49:51.928408 PROGRESS: =========================================================================
1 day, 5:49:52.338324 INFO: calibration group: precursor, predicting mz
1 day, 5:49:52.372378 INFO: calibration group: precursor, predicting rt
1 day, 5:49:52.526228 INFO: calibration group: precursor, predicting mobility
1 day, 5:49:52.560570 INFO: calibration group: fragment, predicting mz
1 day, 5:49:52.862743 INFO: === skipping optimization until target number of precursors are found ===
1 day, 5:49:52.863108 PROGRESS: === Optimization of mobility_error has been skipped 3 time(s); maximum number is 1 ===
1 day, 5:49:52.863196 INFO: Starting optimization step 3.
1 day, 5:49:52.863290 PROGRESS: === Extracting elution groups 120000 to 248000 ===
1 day, 5:49:52.863373 PROGRESS: Extracting batch of 252186 precursors
1 day, 5:49:52.929407 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 5:49:52.929542 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 5:49:52.929595 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 5:49:52.929632 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.99
1 day, 5:49:52.930501 INFO: Starting candidate selection
1 day, 5:58:18.836363 INFO: Starting candidate scoring
1 day, 5:58:25.854419 INFO: Finished candidate processing
1 day, 5:58:25.855713 INFO: Collecting candidate features
1 day, 5:58:26.595680 WARNING: intensity_correlation has 1682 NaNs ( 0.42 % out of 402483)
1 day, 5:58:26.596313 WARNING: height_correlation has 32 NaNs ( 0.01 % out of 402483)
1 day, 5:58:26.614506 INFO: Collecting fragment features
1 day, 5:58:26.830599 INFO: Finished candidate scoring
1 day, 5:58:27.274586 PROGRESS: === Extracted 780301 precursors and 4758413 fragments ===
1 day, 5:58:27.346816 INFO: performing precursor FDR with 47 features
1 day, 5:58:27.346953 INFO: Decoy channel: -1
1 day, 5:58:27.346979 INFO: Competetive: True
1 day, 5:58:27.700319 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:58:27.856907 WARNING: dropped 1771 target PSMs due to missing features
1 day, 5:58:27.857061 WARNING: dropped 1521 decoy PSMs due to missing features
1 day, 5:58:44.707110 INFO: Test AUC: 0.538
1 day, 5:58:44.707250 INFO: Train AUC: 0.560
1 day, 5:58:44.707281 INFO: AUC difference: 3.79%
1 day, 5:58:44.849686 INFO: Resetting torch num_threads to 100
1 day, 5:58:44.887431 INFO: === FDR correction performed with classifier version 6 ===
1 day, 5:58:44.926096 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:58:44.926393 PROGRESS: Total precursors accumulated: 214,670
1 day, 5:58:44.926461 PROGRESS: Target precursors: 122,628 (57.12%)
1 day, 5:58:44.926512 PROGRESS: Decoy precursors: 92,042 (42.88%)
1 day, 5:58:44.926561 PROGRESS: 
1 day, 5:58:44.926607 PROGRESS: Precursor Summary:
1 day, 5:58:44.928795 PROGRESS: Channel   0:	 0.05 FDR:    12; 0.01 FDR:    12; 0.001 FDR:    12
1 day, 5:58:44.928913 PROGRESS: 
1 day, 5:58:44.928971 PROGRESS: Protein Summary:
1 day, 5:58:44.930946 PROGRESS: Channel   0:	 0.05 FDR:    12; 0.01 FDR:    12; 0.001 FDR:    12
1 day, 5:58:44.931043 PROGRESS: =========================================================================
1 day, 5:58:45.561255 INFO: calibration group: precursor, predicting mz
1 day, 5:58:45.626595 INFO: calibration group: precursor, predicting rt
1 day, 5:58:45.939986 INFO: calibration group: precursor, predicting mobility
1 day, 5:58:46.008703 INFO: calibration group: fragment, predicting mz
1 day, 5:58:46.607587 INFO: === skipping optimization until target number of precursors are found ===
1 day, 5:58:46.607900 PROGRESS: === Optimization of mobility_error has been skipped 4 time(s); maximum number is 1 ===
1 day, 5:58:46.607976 INFO: Starting optimization step 4.
1 day, 5:58:46.608047 PROGRESS: === Extracting elution groups 248000 to 504000 ===
1 day, 5:58:46.608114 PROGRESS: Extracting batch of 504181 precursors
1 day, 5:58:46.730517 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 5:58:46.730647 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 5:58:46.730697 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 5:58:46.730721 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.99
1 day, 5:58:46.731654 INFO: Starting candidate selection
1 day, 6:15:25.816559 INFO: Starting candidate scoring
1 day, 6:15:39.397619 INFO: Finished candidate processing
1 day, 6:15:39.398015 INFO: Collecting candidate features
1 day, 6:15:41.347618 WARNING: intensity_correlation has 3391 NaNs ( 0.42 % out of 806192)
1 day, 6:15:41.348589 WARNING: height_correlation has 87 NaNs ( 0.01 % out of 806192)
1 day, 6:15:41.379760 INFO: Collecting fragment features
1 day, 6:15:41.824660 INFO: Finished candidate scoring
1 day, 6:15:42.819839 PROGRESS: === Extracted 1586493 precursors and 9669491 fragments ===
1 day, 6:15:42.991578 INFO: performing precursor FDR with 47 features
1 day, 6:15:42.991748 INFO: Decoy channel: -1
1 day, 6:15:42.991777 INFO: Competetive: True
1 day, 6:15:43.850148 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 6:15:44.222489 WARNING: dropped 3681 target PSMs due to missing features
1 day, 6:15:44.222664 WARNING: dropped 3053 decoy PSMs due to missing features
1 day, 6:16:16.208036 INFO: Test AUC: 0.543
1 day, 6:16:16.208494 INFO: Train AUC: 0.552
1 day, 6:16:16.208549 INFO: AUC difference: 1.56%
1 day, 6:16:16.424190 INFO: Resetting torch num_threads to 100
1 day, 6:16:16.609385 INFO: === FDR correction performed with classifier version 6 ===
1 day, 6:16:16.697370 PROGRESS: ============================= Precursor FDR =============================
1 day, 6:16:16.697690 PROGRESS: Total precursors accumulated: 436,463
1 day, 6:16:16.697758 PROGRESS: Target precursors: 247,942 (56.81%)
1 day, 6:16:16.697811 PROGRESS: Decoy precursors: 188,521 (43.19%)
1 day, 6:16:16.697862 PROGRESS: 
1 day, 6:16:16.697910 PROGRESS: Precursor Summary:
1 day, 6:16:16.701218 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1 day, 6:16:16.701328 PROGRESS: 
1 day, 6:16:16.701386 PROGRESS: Protein Summary:
1 day, 6:16:16.704253 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1 day, 6:16:16.704353 PROGRESS: =========================================================================
1 day, 6:16:17.777621 INFO: calibration group: precursor, predicting mz
1 day, 6:16:17.913176 INFO: calibration group: precursor, predicting rt
1 day, 6:16:18.531006 INFO: calibration group: precursor, predicting mobility
1 day, 6:16:18.662752 INFO: calibration group: fragment, predicting mz
1 day, 6:16:19.893827 INFO: === skipping optimization until target number of precursors are found ===
1 day, 6:16:19.894135 PROGRESS: === Optimization of mobility_error has been skipped 5 time(s); maximum number is 1 ===
1 day, 6:16:19.894228 INFO: Starting optimization step 5.
1 day, 6:16:19.894304 PROGRESS: === Extracting elution groups 504000 to 1016000 ===
1 day, 6:16:19.894378 PROGRESS: Extracting batch of 1008477 precursors
1 day, 6:16:20.142713 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 6:16:20.142840 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 6:16:20.142890 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 6:16:20.142915 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.99
1 day, 6:16:20.144304 INFO: Starting candidate selection
1 day, 6:49:50.718674 INFO: Starting candidate scoring
1 day, 6:50:18.587351 INFO: Finished candidate processing
1 day, 6:50:18.587566 INFO: Collecting candidate features
1 day, 6:50:21.791298 WARNING: intensity_correlation has 6797 NaNs ( 0.42 % out of 1611068)
1 day, 6:50:21.792906 WARNING: height_correlation has 143 NaNs ( 0.01 % out of 1611068)
1 day, 6:50:21.848133 INFO: Collecting fragment features
1 day, 6:50:22.760270 INFO: Finished candidate scoring
1 day, 6:50:25.549104 PROGRESS: === Extracted 3197561 precursors and 19486926 fragments ===
1 day, 6:50:25.860974 INFO: performing precursor FDR with 47 features
1 day, 6:50:25.861143 INFO: Decoy channel: -1
1 day, 6:50:25.861171 INFO: Competetive: True
1 day, 6:50:27.250880 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 6:50:27.859649 WARNING: dropped 7430 target PSMs due to missing features
1 day, 6:50:27.859800 WARNING: dropped 6194 decoy PSMs due to missing features
1 day, 6:51:25.729953 INFO: Test AUC: 0.546
1 day, 6:51:25.730195 INFO: Train AUC: 0.553
1 day, 6:51:25.730233 INFO: AUC difference: 1.23%
1 day, 6:51:26.039066 INFO: Resetting torch num_threads to 100
1 day, 6:51:26.201311 INFO: === FDR correction performed with classifier version 6 ===
1 day, 6:51:26.366532 PROGRESS: ============================= Precursor FDR =============================
1 day, 6:51:26.366887 PROGRESS: Total precursors accumulated: 879,771
1 day, 6:51:26.366958 PROGRESS: Target precursors: 502,623 (57.13%)
1 day, 6:51:26.367013 PROGRESS: Decoy precursors: 377,148 (42.87%)
1 day, 6:51:26.367065 PROGRESS: 
1 day, 6:51:26.367115 PROGRESS: Precursor Summary:
1 day, 6:51:26.372566 PROGRESS: Channel   0:	 0.05 FDR:    12; 0.01 FDR:    12; 0.001 FDR:    12
1 day, 6:51:26.372679 PROGRESS: 
1 day, 6:51:26.372762 PROGRESS: Protein Summary:
1 day, 6:51:26.377503 PROGRESS: Channel   0:	 0.05 FDR:    12; 0.01 FDR:    12; 0.001 FDR:    12
1 day, 6:51:26.377611 PROGRESS: =========================================================================
1 day, 6:51:28.072426 INFO: calibration group: precursor, predicting mz
1 day, 6:51:28.347723 INFO: calibration group: precursor, predicting rt
1 day, 6:51:29.613642 INFO: calibration group: precursor, predicting mobility
1 day, 6:51:29.882163 INFO: calibration group: fragment, predicting mz
1 day, 6:51:32.315285 INFO: === skipping optimization until target number of precursors are found ===
1 day, 6:51:32.315553 PROGRESS: === Optimization of mobility_error has been skipped 6 time(s); maximum number is 1 ===
1 day, 6:51:32.315634 INFO: Starting optimization step 6.
1 day, 6:51:32.315706 PROGRESS: === Extracting elution groups 1016000 to 2040000 ===
1 day, 6:51:32.315776 PROGRESS: Extracting batch of 2017059 precursors
1 day, 6:51:32.791675 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 6:51:32.791805 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 6:51:32.791855 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 6:51:32.791879 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.99
1 day, 6:51:32.818864 INFO: Starting candidate selection
1 day, 7:57:16.828232 INFO: Starting candidate scoring
1 day, 7:58:10.015085 INFO: Finished candidate processing
1 day, 7:58:10.015771 INFO: Collecting candidate features
1 day, 7:58:16.382296 WARNING: intensity_correlation has 13596 NaNs ( 0.42 % out of 3222947)
1 day, 7:58:16.385277 WARNING: height_correlation has 310 NaNs ( 0.01 % out of 3222947)
1 day, 7:58:16.491967 INFO: Collecting fragment features
1 day, 7:58:18.358294 INFO: Finished candidate scoring
1 day, 7:58:23.103320 PROGRESS: === Extracted 6420508 precursors and 39130648 fragments ===
1 day, 7:58:23.775283 INFO: performing precursor FDR with 47 features
1 day, 7:58:23.775416 INFO: Decoy channel: -1
1 day, 7:58:23.775444 INFO: Competetive: True
1 day, 7:58:26.497588 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 7:58:27.740328 WARNING: dropped 15012 target PSMs due to missing features
1 day, 7:58:27.740470 WARNING: dropped 12384 decoy PSMs due to missing features
1 day, 8:00:24.617821 INFO: Test AUC: 0.549
1 day, 8:00:24.618064 INFO: Train AUC: 0.553
1 day, 8:00:24.618102 INFO: AUC difference: 0.66%
1 day, 8:00:25.125573 INFO: Resetting torch num_threads to 100
1 day, 8:00:25.479246 INFO: === FDR correction performed with classifier version 6 ===
1 day, 8:00:25.803565 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:00:25.803899 PROGRESS: Total precursors accumulated: 1,766,169
1 day, 8:00:25.803979 PROGRESS: Target precursors: 1,012,938 (57.35%)
1 day, 8:00:25.804034 PROGRESS: Decoy precursors: 753,231 (42.65%)
1 day, 8:00:25.804082 PROGRESS: 
1 day, 8:00:25.804127 PROGRESS: Precursor Summary:
1 day, 8:00:25.813108 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 8:00:25.813269 PROGRESS: 
1 day, 8:00:25.813328 PROGRESS: Protein Summary:
1 day, 8:00:25.821530 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 8:00:25.821666 PROGRESS: =========================================================================
1 day, 8:00:28.971327 INFO: calibration group: precursor, predicting mz
1 day, 8:00:29.510397 INFO: calibration group: precursor, predicting rt
1 day, 8:00:32.038786 INFO: calibration group: precursor, predicting mobility
1 day, 8:00:32.553765 INFO: calibration group: fragment, predicting mz
1 day, 8:00:37.395103 INFO: === skipping optimization until target number of precursors are found ===
1 day, 8:00:37.395380 PROGRESS: === Optimization of mobility_error has been skipped 7 time(s); maximum number is 1 ===
1 day, 8:00:37.395460 INFO: Starting optimization step 7.
1 day, 8:00:37.395530 PROGRESS: === Extracting elution groups 2040000 to 4088000 ===
1 day, 8:00:37.395601 PROGRESS: Extracting batch of 4034279 precursors
1 day, 8:00:38.318393 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:00:38.318525 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:00:38.318575 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 8:00:38.318602 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.99
1 day, 8:00:38.322493 INFO: Starting candidate selection
1 day, 10:09:55.408623 INFO: Starting candidate scoring
1 day, 10:11:46.649007 INFO: Finished candidate processing
1 day, 10:11:46.649559 INFO: Collecting candidate features
1 day, 10:11:59.914125 WARNING: intensity_correlation has 27573 NaNs ( 0.43 % out of 6445452)
1 day, 10:11:59.919864 WARNING: height_correlation has 596 NaNs ( 0.01 % out of 6445452)
1 day, 10:12:00.134508 INFO: Collecting fragment features
1 day, 10:12:04.170379 INFO: Finished candidate scoring
1 day, 10:12:17.455229 PROGRESS: === Extracted 12865960 precursors and 78416882 fragments ===
1 day, 10:12:18.821954 INFO: performing precursor FDR with 47 features
1 day, 10:12:18.822089 INFO: Decoy channel: -1
1 day, 10:12:18.822120 INFO: Competetive: True
1 day, 10:12:24.568510 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 10:12:27.135487 WARNING: dropped 30138 target PSMs due to missing features
1 day, 10:12:27.135651 WARNING: dropped 25171 decoy PSMs due to missing features
1 day, 10:16:37.331042 INFO: Test AUC: 0.553
1 day, 10:16:37.331308 INFO: Train AUC: 0.555
1 day, 10:16:37.331351 INFO: AUC difference: 0.44%
1 day, 10:16:38.130588 INFO: Resetting torch num_threads to 100
1 day, 10:16:38.945898 INFO: === FDR correction performed with classifier version 6 ===
1 day, 10:16:39.597938 PROGRESS: ============================= Precursor FDR =============================
1 day, 10:16:39.598265 PROGRESS: Total precursors accumulated: 3,539,232
1 day, 10:16:39.598332 PROGRESS: Target precursors: 2,029,808 (57.35%)
1 day, 10:16:39.598387 PROGRESS: Decoy precursors: 1,509,424 (42.65%)
1 day, 10:16:39.598439 PROGRESS: 
1 day, 10:16:39.598487 PROGRESS: Precursor Summary:
1 day, 10:16:39.616879 PROGRESS: Channel   0:	 0.05 FDR:   984; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 10:16:39.617146 PROGRESS: 
1 day, 10:16:39.617213 PROGRESS: Protein Summary:
1 day, 10:16:39.635117 PROGRESS: Channel   0:	 0.05 FDR:   798; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 10:16:39.635354 PROGRESS: =========================================================================
1 day, 10:16:41.634058 INFO: calibration group: precursor, predicting mz
1 day, 10:16:41.943379 INFO: calibration group: precursor, predicting rt
1 day, 10:16:43.348363 INFO: calibration group: precursor, predicting mobility
1 day, 10:16:43.646237 INFO: calibration group: fragment, predicting mz
1 day, 10:16:46.370483 INFO: === skipping optimization until target number of precursors are found ===
1 day, 10:16:46.370787 PROGRESS: === Optimization of mobility_error has been skipped 8 time(s); maximum number is 1 ===
1 day, 10:16:46.370886 INFO: Starting optimization step 8.
1 day, 10:16:46.370969 PROGRESS: === Extracting elution groups 4088000 to 5215079 ===
1 day, 10:16:46.371046 PROGRESS: Extracting batch of 2220101 precursors
1 day, 10:16:46.896145 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 10:16:46.896278 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 10:16:46.896328 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 10:16:46.896353 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.99
1 day, 10:16:46.897605 INFO: Starting candidate selection
1 day, 11:28:13.935907 INFO: Starting candidate scoring
1 day, 11:29:15.345610 INFO: Finished candidate processing
1 day, 11:29:15.346430 INFO: Collecting candidate features
1 day, 11:29:22.772211 WARNING: intensity_correlation has 15033 NaNs ( 0.42 % out of 3548711)
1 day, 11:29:22.775837 WARNING: height_correlation has 313 NaNs ( 0.01 % out of 3548711)
1 day, 11:29:22.895730 INFO: Collecting fragment features
1 day, 11:29:25.006925 INFO: Finished candidate scoring
1 day, 11:29:34.921156 PROGRESS: === Extracted 16414671 precursors and 100023572 fragments ===
1 day, 11:29:36.624189 INFO: performing precursor FDR with 47 features
1 day, 11:29:36.624343 INFO: Decoy channel: -1
1 day, 11:29:36.624378 INFO: Competetive: True
1 day, 11:29:43.237189 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 11:29:46.254328 WARNING: dropped 38306 target PSMs due to missing features
1 day, 11:29:46.254509 WARNING: dropped 32200 decoy PSMs due to missing features
1 day, 11:35:38.091527 INFO: Test AUC: 0.550
1 day, 11:35:38.091811 INFO: Train AUC: 0.556
1 day, 11:35:38.091858 INFO: AUC difference: 1.00%
1 day, 11:35:39.063962 INFO: Resetting torch num_threads to 100
1 day, 11:35:40.071739 INFO: === FDR correction performed with classifier version 6 ===
1 day, 11:35:40.894245 PROGRESS: ============================= Precursor FDR =============================
1 day, 11:35:40.894596 PROGRESS: Total precursors accumulated: 4,515,476
1 day, 11:35:40.894661 PROGRESS: Target precursors: 2,582,159 (57.18%)
1 day, 11:35:40.894715 PROGRESS: Decoy precursors: 1,933,317 (42.82%)
1 day, 11:35:40.894764 PROGRESS: 
1 day, 11:35:40.894812 PROGRESS: Precursor Summary:
1 day, 11:35:40.918636 PROGRESS: Channel   0:	 0.05 FDR: 1,625; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 11:35:40.918936 PROGRESS: 
1 day, 11:35:40.919004 PROGRESS: Protein Summary:
1 day, 11:35:40.942572 PROGRESS: Channel   0:	 0.05 FDR: 1,221; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 11:35:40.942858 PROGRESS: =========================================================================
1 day, 11:35:41.061763 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 11:35:41.062109 PROGRESS: ==============================================
1 day, 11:35:41.677580 INFO: fragments_df_filtered: 0
1 day, 11:35:42.221453 WARNING: No more batches to process. Will proceed to extraction using best parameters available in optimization manager.
1 day, 11:35:42.221750 WARNING: Using current optimal value for ms2_error: 15.00.
1 day, 11:35:42.764882 WARNING: No more batches to process. Will proceed to extraction using best parameters available in optimization manager.
1 day, 11:35:42.765196 WARNING: Using current optimal value for ms1_error: 10.00.
1 day, 11:35:43.324761 WARNING: No more batches to process. Will proceed to extraction using best parameters available in optimization manager.
1 day, 11:35:43.326779 WARNING: Using current optimal value for rt_error: 928.18.
1 day, 11:35:43.886334 WARNING: No more batches to process. Will proceed to extraction using best parameters available in optimization manager.
1 day, 11:35:43.887595 WARNING: Using current optimal value for mobility_error: 0.10.
1 day, 11:35:43.895610 PROGRESS: ms2_error      : 15.0000
1 day, 11:35:43.895882 PROGRESS: ms1_error      : 10.0000
1 day, 11:35:43.895949 PROGRESS: rt_error       : 928.1790
1 day, 11:35:43.896000 PROGRESS: mobility_error : 0.1000
1 day, 11:35:43.896052 PROGRESS: ==============================================
1 day, 11:35:44.187120 INFO: calibration group: precursor, predicting mz
1 day, 11:35:45.630433 INFO: calibration group: precursor, predicting rt
1 day, 11:35:52.014192 INFO: calibration group: precursor, predicting mobility
1 day, 11:35:53.442992 INFO: calibration group: fragment, predicting mz
1 day, 11:36:05.765460 PROGRESS: Extracting batch of 10272670 precursors
1 day, 11:36:08.235186 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 11:36:08.235334 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 11:36:08.235389 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 11:36:08.235420 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.99
1 day, 11:36:08.236684 INFO: Starting candidate selection
1 day, 17:03:24.175734 INFO: Applying score cutoff of 16.388819221496583
1 day, 17:03:24.761183 INFO: Removed 756755 precursors with score below cutoff
1 day, 17:03:27.548187 INFO: Starting candidate scoring
1 day, 17:08:09.152647 INFO: Finished candidate processing
1 day, 17:08:09.154537 INFO: Collecting candidate features
1 day, 17:08:38.125089 WARNING: intensity_correlation has 63896 NaNs ( 0.40 % out of 16085008)
1 day, 17:08:38.139236 WARNING: height_correlation has 1153 NaNs ( 0.01 % out of 16085008)
1 day, 17:08:38.670293 INFO: Collecting fragment features
1 day, 17:08:47.720867 INFO: Finished candidate scoring
1 day, 17:09:09.410645 INFO: === FDR correction performed with classifier version 17 ===
1 day, 17:09:09.414616 INFO: performing precursor FDR with 47 features
1 day, 17:09:09.414698 INFO: Decoy channel: -1
1 day, 17:09:09.414726 INFO: Competetive: True
1 day, 17:09:13.653986 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:09:16.260779 WARNING: dropped 35212 target PSMs due to missing features
1 day, 17:09:16.260954 WARNING: dropped 29359 decoy PSMs due to missing features
1 day, 17:14:59.713294 INFO: Test AUC: 0.551
1 day, 17:14:59.713689 INFO: Train AUC: 0.557
1 day, 17:14:59.713736 INFO: AUC difference: 1.09%
1 day, 17:15:00.682325 INFO: Resetting torch num_threads to 100
1 day, 17:15:01.180504 INFO: Removing fragments below FDR threshold
1 day, 17:15:01.937288 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:15:01.937597 PROGRESS: Total precursors accumulated: 715
1 day, 17:15:01.937670 PROGRESS: Target precursors: 708 (99.02%)
1 day, 17:15:01.937724 PROGRESS: Decoy precursors: 7 (0.98%)
1 day, 17:15:01.937776 PROGRESS: 
1 day, 17:15:01.937823 PROGRESS: Precursor Summary:
1 day, 17:15:01.939094 PROGRESS: Channel   0:	 0.05 FDR:   708; 0.01 FDR:   708; 0.001 FDR:     1
1 day, 17:15:01.939214 PROGRESS: 
1 day, 17:15:01.939272 PROGRESS: Protein Summary:
1 day, 17:15:01.940656 PROGRESS: Channel   0:	 0.05 FDR:   584; 0.01 FDR:   584; 0.001 FDR:     1
1 day, 17:15:01.940757 PROGRESS: =========================================================================
1 day, 17:15:02.158285 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 17:15:03.005822 PROGRESS: Loading raw file 6/6: ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 17:15:03.005992 INFO: Quantification results path: run_output/alphadia_1.10_defaultMBR/library/quant
1 day, 17:15:03.006079 INFO: Creating workflow folder for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508 at run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 17:15:03.006932 INFO: Initializing RawFileManager
1 day, 17:15:03.007060 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 17:15:03.007116 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 17:15:03.007159 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 17:15:03.228743 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
1 day, 17:15:13.568964 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d...
1 day, 17:15:13.570095 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 17:15:13.574828 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 17:15:13.575064 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 17:15:13.575429 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 17:15:13.577392 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 17:15:13.592142 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 17:15:13.592327 INFO: Indexing quadrupole dimension
1 day, 17:15:14.079050 INFO: Transposing detector events
1 day, 17:15:22.229283 INFO: Finished transposing data
1 day, 17:15:22.266391 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 17:15:22.269588 INFO: RT (min)            : 0.0 - 70.0
1 day, 17:15:22.269689 INFO: RT duration (sec)   : 4199.8
1 day, 17:15:22.269749 INFO: RT duration (min)   : 70.0
1 day, 17:15:22.269802 INFO: Cycle len (scans)   : 9
1 day, 17:15:22.269849 INFO: Cycle len (sec)     : 0.97
1 day, 17:15:22.269894 INFO: Number of cycles    : 4347
1 day, 17:15:22.269941 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 17:15:23.892949 INFO: Initializing CalibrationManager
1 day, 17:15:23.893250 INFO: Loading calibration config
1 day, 17:15:23.893918 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'}]
1 day, 17:15:23.894022 INFO: Calibration group :fragment, found 1 estimator(s)
1 day, 17:15:23.894131 INFO: Calibration group :precursor, found 3 estimator(s)
1 day, 17:15:23.894331 INFO: Initializing OptimizationManager
1 day, 17:15:23.894457 INFO: initial parameter: ms1_error = 30
1 day, 17:15:23.894513 INFO: initial parameter: ms2_error = 30
1 day, 17:15:23.894578 INFO: initial parameter: rt_error = 2099.9231665
1 day, 17:15:23.894630 INFO: initial parameter: mobility_error = 0.1
1 day, 17:15:23.894679 INFO: initial parameter: column_type = library
1 day, 17:15:23.894727 INFO: initial parameter: num_candidates = 1
1 day, 17:15:23.894774 INFO: initial parameter: classifier_version = -1
1 day, 17:15:23.894818 INFO: initial parameter: fwhm_rt = 5
1 day, 17:15:23.894863 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 17:15:23.894906 INFO: initial parameter: score_cutoff = 0
1 day, 17:15:23.894972 INFO: Initializing TimingManager
1 day, 17:15:23.895038 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 17:15:23.895168 INFO: FDRManager not loaded from disk.
1 day, 17:15:23.895195 INFO: Initializing FDRManager
1 day, 17:15:23.895233 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 17:15:25.187639 PROGRESS: 5,215,079 target precursors potentially observable (0 removed)
1 day, 17:15:27.035182 PROGRESS: Starting initial search for precursors.
1 day, 17:15:27.315537 INFO: Starting optimization step 0.
1 day, 17:15:27.315780 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 17:15:27.315871 PROGRESS: Extracting batch of 15771 precursors
1 day, 17:15:27.319844 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:15:27.319901 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:15:27.319936 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 17:15:27.319959 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 17:15:27.320981 INFO: Starting candidate selection
1 day, 17:16:47.828307 INFO: Starting candidate scoring
1 day, 17:16:48.703660 INFO: Finished candidate processing
1 day, 17:16:48.703764 INFO: Collecting candidate features
1 day, 17:16:48.736517 WARNING: intensity_correlation has 3 NaNs ( 0.02 % out of 13756)
1 day, 17:16:48.736741 WARNING: height_correlation has 1 NaNs ( 0.01 % out of 13756)
1 day, 17:16:48.740366 INFO: Collecting fragment features
1 day, 17:16:48.755947 INFO: Finished candidate scoring
1 day, 17:16:48.763677 PROGRESS: === Extracted 13756 precursors and 138137 fragments ===
1 day, 17:16:48.764089 INFO: performing precursor FDR with 47 features
1 day, 17:16:48.764138 INFO: Decoy channel: -1
1 day, 17:16:48.764164 INFO: Competetive: True
1 day, 17:16:48.770182 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:16:48.773329 WARNING: dropped 2 target PSMs due to missing features
1 day, 17:16:48.773388 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 17:16:48.960999 INFO: Test AUC: 0.537
1 day, 17:16:48.961123 INFO: Train AUC: 0.538
1 day, 17:16:48.961153 INFO: AUC difference: 0.20%
1 day, 17:16:49.047330 INFO: Resetting torch num_threads to 100
1 day, 17:16:49.048491 INFO: === FDR correction performed with classifier version -1 ===
1 day, 17:16:49.049972 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:16:49.050086 PROGRESS: Total precursors accumulated: 7,046
1 day, 17:16:49.050149 PROGRESS: Target precursors: 3,908 (55.46%)
1 day, 17:16:49.050202 PROGRESS: Decoy precursors: 3,138 (44.54%)
1 day, 17:16:49.050249 PROGRESS: 
1 day, 17:16:49.050298 PROGRESS: Precursor Summary:
1 day, 17:16:49.051173 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 17:16:49.051269 PROGRESS: 
1 day, 17:16:49.051327 PROGRESS: Protein Summary:
1 day, 17:16:49.052260 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 17:16:49.052348 PROGRESS: =========================================================================
1 day, 17:16:49.205114 INFO: Starting optimization step 1.
1 day, 17:16:49.205377 PROGRESS: === Extracting elution groups 8000 to 24000 ===
1 day, 17:16:49.205457 PROGRESS: Extracting batch of 31534 precursors
1 day, 17:16:49.212803 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:16:49.212886 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:16:49.212928 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 17:16:49.212953 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 17:16:49.214103 INFO: Starting candidate selection
1 day, 17:19:25.148763 INFO: Starting candidate scoring
1 day, 17:19:26.536917 INFO: Finished candidate processing
1 day, 17:19:26.537126 INFO: Collecting candidate features
1 day, 17:19:26.640828 WARNING: intensity_correlation has 9 NaNs ( 0.03 % out of 27371)
1 day, 17:19:26.641090 WARNING: height_correlation has 2 NaNs ( 0.01 % out of 27371)
1 day, 17:19:26.645157 INFO: Collecting fragment features
1 day, 17:19:26.669731 INFO: Finished candidate scoring
1 day, 17:19:26.718667 PROGRESS: === Extracted 41127 precursors and 411965 fragments ===
1 day, 17:19:26.724046 INFO: performing precursor FDR with 47 features
1 day, 17:19:26.724118 INFO: Decoy channel: -1
1 day, 17:19:26.724145 INFO: Competetive: True
1 day, 17:19:26.746186 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:19:26.755142 WARNING: dropped 7 target PSMs due to missing features
1 day, 17:19:26.755261 WARNING: dropped 6 decoy PSMs due to missing features
1 day, 17:19:27.333236 INFO: Test AUC: 0.548
1 day, 17:19:27.333364 INFO: Train AUC: 0.577
1 day, 17:19:27.333394 INFO: AUC difference: 4.94%
1 day, 17:19:27.429164 INFO: Resetting torch num_threads to 100
1 day, 17:19:27.431579 INFO: === FDR correction performed with classifier version -1 ===
1 day, 17:19:27.435446 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:19:27.435609 PROGRESS: Total precursors accumulated: 21,077
1 day, 17:19:27.435675 PROGRESS: Target precursors: 12,701 (60.26%)
1 day, 17:19:27.435728 PROGRESS: Decoy precursors: 8,376 (39.74%)
1 day, 17:19:27.435780 PROGRESS: 
1 day, 17:19:27.435827 PROGRESS: Precursor Summary:
1 day, 17:19:27.436919 PROGRESS: Channel   0:	 0.05 FDR:   180; 0.01 FDR:   141; 0.001 FDR:    95
1 day, 17:19:27.437015 PROGRESS: 
1 day, 17:19:27.437087 PROGRESS: Protein Summary:
1 day, 17:19:27.438252 PROGRESS: Channel   0:	 0.05 FDR:   173; 0.01 FDR:   136; 0.001 FDR:    93
1 day, 17:19:27.438356 PROGRESS: =========================================================================
1 day, 17:19:27.634003 INFO: Starting optimization step 2.
1 day, 17:19:27.634270 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1 day, 17:19:27.634349 PROGRESS: Extracting batch of 63016 precursors
1 day, 17:19:27.650582 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:19:27.650702 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:19:27.650741 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 17:19:27.650766 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 17:19:27.651739 INFO: Starting candidate selection
1 day, 17:24:26.433604 INFO: Starting candidate scoring
1 day, 17:24:29.065175 INFO: Finished candidate processing
1 day, 17:24:29.065363 INFO: Collecting candidate features
1 day, 17:24:29.240582 WARNING: intensity_correlation has 16 NaNs ( 0.03 % out of 54858)
1 day, 17:24:29.240880 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 54858)
1 day, 17:24:29.247082 INFO: Collecting fragment features
1 day, 17:24:29.292861 INFO: Finished candidate scoring
1 day, 17:24:29.387219 PROGRESS: === Extracted 95985 precursors and 961483 fragments ===
1 day, 17:24:29.399437 INFO: performing precursor FDR with 47 features
1 day, 17:24:29.399564 INFO: Decoy channel: -1
1 day, 17:24:29.399589 INFO: Competetive: True
1 day, 17:24:30.924586 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:24:30.945270 WARNING: dropped 17 target PSMs due to missing features
1 day, 17:24:30.945400 WARNING: dropped 14 decoy PSMs due to missing features
1 day, 17:24:32.553128 INFO: Test AUC: 0.557
1 day, 17:24:32.553252 INFO: Train AUC: 0.591
1 day, 17:24:32.553282 INFO: AUC difference: 5.73%
1 day, 17:24:32.553304 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 17:24:32.644626 INFO: Resetting torch num_threads to 100
1 day, 17:24:32.649524 INFO: === FDR correction performed with classifier version -1 ===
1 day, 17:24:32.658435 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:24:32.658761 PROGRESS: Total precursors accumulated: 49,224
1 day, 17:24:32.658831 PROGRESS: Target precursors: 30,058 (61.06%)
1 day, 17:24:32.658886 PROGRESS: Decoy precursors: 19,166 (38.94%)
1 day, 17:24:32.658935 PROGRESS: 
1 day, 17:24:32.658981 PROGRESS: Precursor Summary:
1 day, 17:24:32.660494 PROGRESS: Channel   0:	 0.05 FDR:   563; 0.01 FDR:   364; 0.001 FDR:   108
1 day, 17:24:32.660597 PROGRESS: 
1 day, 17:24:32.660656 PROGRESS: Protein Summary:
1 day, 17:24:32.662103 PROGRESS: Channel   0:	 0.05 FDR:   520; 0.01 FDR:   335; 0.001 FDR:   106
1 day, 17:24:32.662201 PROGRESS: =========================================================================
1 day, 17:24:32.683760 INFO: fragments_df_filtered: 3296
1 day, 17:24:32.894634 INFO: calibration group: precursor, fitting mz estimator 
1 day, 17:24:32.932322 INFO: calibration group: precursor, fitting rt estimator 
1 day, 17:24:32.974832 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 17:24:33.016139 INFO: calibration group: fragment, fitting mz estimator 
1 day, 17:24:33.188246 INFO: calibration group: precursor, predicting mz
1 day, 17:24:33.207930 INFO: calibration group: precursor, predicting rt
1 day, 17:24:33.275254 INFO: calibration group: precursor, predicting mobility
1 day, 17:24:33.291304 INFO: calibration group: fragment, predicting mz
1 day, 17:24:33.429991 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 17:24:33.430274 INFO: Starting optimization step 3.
1 day, 17:24:33.430346 PROGRESS: === Extracting elution groups 0 to 56000 ===
1 day, 17:24:33.430407 PROGRESS: Extracting batch of 110321 precursors
1 day, 17:24:33.461444 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:24:33.461568 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:24:33.461615 INFO: FWHM in RT is 3.23 seconds, sigma is 0.71
1 day, 17:24:33.461654 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.18
1 day, 17:24:33.482102 INFO: Starting candidate selection
1 day, 17:33:21.873135 INFO: Starting candidate scoring
1 day, 17:33:31.755424 INFO: Finished candidate processing
1 day, 17:33:31.755626 INFO: Collecting candidate features
1 day, 17:33:32.145597 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 189429)
1 day, 17:33:32.146041 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 189429)
1 day, 17:33:32.156858 INFO: Collecting fragment features
1 day, 17:33:32.294318 INFO: Finished candidate scoring
1 day, 17:33:32.402869 PROGRESS: === Extracted 189429 precursors and 1928841 fragments ===
1 day, 17:33:32.403458 INFO: performing precursor FDR with 47 features
1 day, 17:33:32.403501 INFO: Decoy channel: -1
1 day, 17:33:32.403531 INFO: Competetive: True
1 day, 17:33:32.479460 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:33:32.518522 WARNING: dropped 2 decoy PSMs due to missing features
1 day, 17:33:36.513353 INFO: Test AUC: 0.564
1 day, 17:33:36.513482 INFO: Train AUC: 0.591
1 day, 17:33:36.513513 INFO: AUC difference: 4.46%
1 day, 17:33:36.612872 INFO: Resetting torch num_threads to 100
1 day, 17:33:36.618128 INFO: === FDR correction performed with classifier version 2 ===
1 day, 17:33:36.627058 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:33:36.627372 PROGRESS: Total precursors accumulated: 50,272
1 day, 17:33:36.627440 PROGRESS: Target precursors: 31,372 (62.40%)
1 day, 17:33:36.627493 PROGRESS: Decoy precursors: 18,900 (37.60%)
1 day, 17:33:36.627545 PROGRESS: 
1 day, 17:33:36.627592 PROGRESS: Precursor Summary:
1 day, 17:33:36.629068 PROGRESS: Channel   0:	 0.05 FDR:   611; 0.01 FDR:   449; 0.001 FDR:   149
1 day, 17:33:36.629180 PROGRESS: 
1 day, 17:33:36.629238 PROGRESS: Protein Summary:
1 day, 17:33:36.630736 PROGRESS: Channel   0:	 0.05 FDR:   568; 0.01 FDR:   417; 0.001 FDR:   143
1 day, 17:33:36.630835 PROGRESS: =========================================================================
1 day, 17:33:36.643028 INFO: fragments_df_filtered: 5000
1 day, 17:33:36.852103 INFO: calibration group: precursor, fitting mz estimator 
1 day, 17:33:36.893065 INFO: calibration group: precursor, fitting rt estimator 
1 day, 17:33:36.933890 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 17:33:36.974207 INFO: calibration group: fragment, fitting mz estimator 
1 day, 17:33:37.322549 INFO: calibration group: precursor, predicting mz
1 day, 17:33:37.337848 INFO: calibration group: precursor, predicting rt
1 day, 17:33:37.404536 INFO: calibration group: precursor, predicting mobility
1 day, 17:33:37.421411 INFO: calibration group: fragment, predicting mz
1 day, 17:33:37.563873 INFO: === checking if optimization conditions were reached ===
1 day, 17:33:37.566150 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 17:33:37.567121 PROGRESS: ❌ ms1_error      : 10.0000 > 10.0000 or insufficient steps taken.
1 day, 17:33:37.567171 INFO: ==============================================
1 day, 17:33:37.567270 INFO: Starting optimization step 4.
1 day, 17:33:37.567338 PROGRESS: === Extracting elution groups 0 to 56000 ===
1 day, 17:33:37.567406 PROGRESS: Extracting batch of 110321 precursors
1 day, 17:33:37.594867 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:33:37.595000 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:33:37.595052 INFO: FWHM in RT is 3.27 seconds, sigma is 0.72
1 day, 17:33:37.595077 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.08
1 day, 17:33:37.604041 INFO: Starting candidate selection
1 day, 17:41:42.265914 INFO: Starting candidate scoring
1 day, 17:41:47.746869 INFO: Finished candidate processing
1 day, 17:41:47.746980 INFO: Collecting candidate features
1 day, 17:41:48.050362 WARNING: intensity_correlation has 10 NaNs ( 0.01 % out of 189378)
1 day, 17:41:48.060739 INFO: Collecting fragment features
1 day, 17:41:48.177791 INFO: Finished candidate scoring
1 day, 17:41:48.261485 PROGRESS: === Extracted 189378 precursors and 1859279 fragments ===
1 day, 17:41:48.261936 INFO: performing precursor FDR with 47 features
1 day, 17:41:48.261975 INFO: Decoy channel: -1
1 day, 17:41:48.261999 INFO: Competetive: True
1 day, 17:41:48.329883 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:41:48.365051 WARNING: dropped 4 target PSMs due to missing features
1 day, 17:41:48.365184 WARNING: dropped 6 decoy PSMs due to missing features
1 day, 17:41:52.411575 INFO: Test AUC: 0.559
1 day, 17:41:52.411703 INFO: Train AUC: 0.585
1 day, 17:41:52.411732 INFO: AUC difference: 4.42%
1 day, 17:41:52.509423 INFO: Resetting torch num_threads to 100
1 day, 17:41:52.514584 INFO: === FDR correction performed with classifier version 3 ===
1 day, 17:41:52.523688 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:41:52.523989 PROGRESS: Total precursors accumulated: 50,234
1 day, 17:41:52.524056 PROGRESS: Target precursors: 30,636 (60.99%)
1 day, 17:41:52.524112 PROGRESS: Decoy precursors: 19,598 (39.01%)
1 day, 17:41:52.524164 PROGRESS: 
1 day, 17:41:52.524213 PROGRESS: Precursor Summary:
1 day, 17:41:52.525721 PROGRESS: Channel   0:	 0.05 FDR:   777; 0.01 FDR:   529; 0.001 FDR:   317
1 day, 17:41:52.525831 PROGRESS: 
1 day, 17:41:52.525892 PROGRESS: Protein Summary:
1 day, 17:41:52.527470 PROGRESS: Channel   0:	 0.05 FDR:   709; 0.01 FDR:   481; 0.001 FDR:   294
1 day, 17:41:52.527568 PROGRESS: =========================================================================
1 day, 17:41:52.540041 INFO: fragments_df_filtered: 5000
1 day, 17:41:52.713592 INFO: calibration group: precursor, fitting mz estimator 
1 day, 17:41:52.756531 INFO: calibration group: precursor, fitting rt estimator 
1 day, 17:41:52.798551 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 17:41:52.839592 INFO: calibration group: fragment, fitting mz estimator 
1 day, 17:41:53.188684 INFO: calibration group: precursor, predicting mz
1 day, 17:41:53.196136 INFO: calibration group: precursor, predicting rt
1 day, 17:41:53.224385 INFO: calibration group: precursor, predicting mobility
1 day, 17:41:53.231383 INFO: calibration group: fragment, predicting mz
1 day, 17:41:53.284384 INFO: === checking if optimization conditions were reached ===
1 day, 17:41:53.286534 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 17:41:53.287506 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
1 day, 17:41:53.287554 INFO: ==============================================
1 day, 17:41:53.287654 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 17:41:53.449152 INFO: calibration group: precursor, predicting mz
1 day, 17:41:53.456764 INFO: calibration group: precursor, predicting rt
1 day, 17:41:53.485070 INFO: calibration group: precursor, predicting mobility
1 day, 17:41:53.492051 INFO: calibration group: fragment, predicting mz
1 day, 17:41:53.543705 INFO: Starting optimization step 0.
1 day, 17:41:53.543933 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 17:41:53.544009 PROGRESS: Extracting batch of 47305 precursors
1 day, 17:41:53.560102 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:41:53.560235 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:41:53.560298 INFO: FWHM in RT is 2.90 seconds, sigma is 0.64
1 day, 17:41:53.560332 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.20
1 day, 17:41:53.569619 INFO: Starting candidate selection
1 day, 17:45:28.505224 INFO: Starting candidate scoring
1 day, 17:45:30.960099 INFO: Finished candidate processing
1 day, 17:45:30.961115 INFO: Collecting candidate features
1 day, 17:45:31.088927 WARNING: intensity_correlation has 5 NaNs ( 0.01 % out of 81016)
1 day, 17:45:31.096488 INFO: Collecting fragment features
1 day, 17:45:31.155047 INFO: Finished candidate scoring
1 day, 17:45:31.191908 PROGRESS: === Extracted 81016 precursors and 792525 fragments ===
1 day, 17:45:31.192385 INFO: performing precursor FDR with 47 features
1 day, 17:45:31.192436 INFO: Decoy channel: -1
1 day, 17:45:31.192460 INFO: Competetive: True
1 day, 17:45:31.220767 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:45:31.236843 WARNING: dropped 2 target PSMs due to missing features
1 day, 17:45:31.236968 WARNING: dropped 3 decoy PSMs due to missing features
1 day, 17:45:32.819080 INFO: Test AUC: 0.572
1 day, 17:45:32.819202 INFO: Train AUC: 0.614
1 day, 17:45:32.819232 INFO: AUC difference: 6.78%
1 day, 17:45:32.819254 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 17:45:32.909280 INFO: Resetting torch num_threads to 100
1 day, 17:45:32.911849 INFO: === FDR correction performed with classifier version 4 ===
1 day, 17:45:32.915532 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:45:32.915695 PROGRESS: Total precursors accumulated: 21,499
1 day, 17:45:32.915761 PROGRESS: Target precursors: 13,740 (63.91%)
1 day, 17:45:32.915830 PROGRESS: Decoy precursors: 7,759 (36.09%)
1 day, 17:45:32.915878 PROGRESS: 
1 day, 17:45:32.915927 PROGRESS: Precursor Summary:
1 day, 17:45:32.917042 PROGRESS: Channel   0:	 0.05 FDR:   441; 0.01 FDR:   223; 0.001 FDR:   135
1 day, 17:45:32.917140 PROGRESS: 
1 day, 17:45:32.917198 PROGRESS: Protein Summary:
1 day, 17:45:32.918432 PROGRESS: Channel   0:	 0.05 FDR:   422; 0.01 FDR:   215; 0.001 FDR:   131
1 day, 17:45:32.918525 PROGRESS: =========================================================================
1 day, 17:45:32.947092 INFO: fragments_df_filtered: 2695
1 day, 17:45:33.115001 INFO: calibration group: precursor, fitting mz estimator 
1 day, 17:45:33.155575 INFO: calibration group: precursor, fitting rt estimator 
1 day, 17:45:33.192651 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 17:45:33.230270 INFO: calibration group: fragment, fitting mz estimator 
1 day, 17:45:33.357792 INFO: calibration group: precursor, predicting mz
1 day, 17:45:33.365352 INFO: calibration group: precursor, predicting rt
1 day, 17:45:33.393607 INFO: calibration group: precursor, predicting mobility
1 day, 17:45:33.401155 INFO: calibration group: fragment, predicting mz
1 day, 17:45:33.455735 INFO: === checking if optimization conditions were reached ===
1 day, 17:45:33.456035 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 17:45:33.458158 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 359.4032.
1 day, 17:45:33.458220 INFO: ==============================================
1 day, 17:45:33.458325 INFO: Starting optimization step 1.
1 day, 17:45:33.458398 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 17:45:33.458470 PROGRESS: Extracting batch of 47305 precursors
1 day, 17:45:33.475363 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:45:33.475484 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:45:33.475540 INFO: FWHM in RT is 2.96 seconds, sigma is 0.65
1 day, 17:45:33.475567 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.17
1 day, 17:45:33.484679 INFO: Starting candidate selection
1 day, 17:46:13.789119 INFO: Starting candidate scoring
1 day, 17:46:15.931985 INFO: Finished candidate processing
1 day, 17:46:15.932186 INFO: Collecting candidate features
1 day, 17:46:16.124385 WARNING: intensity_correlation has 32 NaNs ( 0.04 % out of 77585)
1 day, 17:46:16.124693 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 77585)
1 day, 17:46:16.130842 INFO: Collecting fragment features
1 day, 17:46:16.193779 INFO: Finished candidate scoring
1 day, 17:46:16.247418 PROGRESS: === Extracted 77585 precursors and 740863 fragments ===
1 day, 17:46:16.247929 INFO: performing precursor FDR with 47 features
1 day, 17:46:16.247967 INFO: Decoy channel: -1
1 day, 17:46:16.247992 INFO: Competetive: True
1 day, 17:46:16.277950 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:46:16.295212 WARNING: dropped 15 target PSMs due to missing features
1 day, 17:46:16.295339 WARNING: dropped 18 decoy PSMs due to missing features
1 day, 17:46:17.845334 INFO: Test AUC: 0.540
1 day, 17:46:17.845454 INFO: Train AUC: 0.587
1 day, 17:46:17.845483 INFO: AUC difference: 7.86%
1 day, 17:46:17.845504 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 17:46:17.935736 INFO: Resetting torch num_threads to 100
1 day, 17:46:17.938236 INFO: === FDR correction performed with classifier version 4 ===
1 day, 17:46:17.941785 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:46:17.941943 PROGRESS: Total precursors accumulated: 20,919
1 day, 17:46:17.942008 PROGRESS: Target precursors: 12,780 (61.09%)
1 day, 17:46:17.942062 PROGRESS: Decoy precursors: 8,139 (38.91%)
1 day, 17:46:17.942109 PROGRESS: 
1 day, 17:46:17.942154 PROGRESS: Precursor Summary:
1 day, 17:46:17.943247 PROGRESS: Channel   0:	 0.05 FDR:   456; 0.01 FDR:   218; 0.001 FDR:     0
1 day, 17:46:17.943339 PROGRESS: 
1 day, 17:46:17.943396 PROGRESS: Protein Summary:
1 day, 17:46:17.944605 PROGRESS: Channel   0:	 0.05 FDR:   436; 0.01 FDR:   210; 0.001 FDR:     0
1 day, 17:46:17.944697 PROGRESS: =========================================================================
1 day, 17:46:17.950377 INFO: fragments_df_filtered: 2564
1 day, 17:46:18.121882 INFO: calibration group: precursor, fitting mz estimator 
1 day, 17:46:18.171175 INFO: calibration group: precursor, fitting rt estimator 
1 day, 17:46:18.209549 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 17:46:18.248412 INFO: calibration group: fragment, fitting mz estimator 
1 day, 17:46:18.371130 INFO: calibration group: precursor, predicting mz
1 day, 17:46:18.378815 INFO: calibration group: precursor, predicting rt
1 day, 17:46:18.407143 INFO: calibration group: precursor, predicting mobility
1 day, 17:46:18.415408 INFO: calibration group: fragment, predicting mz
1 day, 17:46:18.470242 INFO: === checking if optimization conditions were reached ===
1 day, 17:46:18.470498 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 17:46:18.472368 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 164.2230.
1 day, 17:46:18.472421 INFO: ==============================================
1 day, 17:46:18.472515 INFO: Starting optimization step 2.
1 day, 17:46:18.472580 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 17:46:18.472644 PROGRESS: Extracting batch of 47305 precursors
1 day, 17:46:18.484191 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:46:18.484293 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:46:18.484343 INFO: FWHM in RT is 2.96 seconds, sigma is 0.65
1 day, 17:46:18.484366 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.15
1 day, 17:46:18.493345 INFO: Starting candidate selection
1 day, 17:46:37.083113 INFO: Starting candidate scoring
1 day, 17:46:39.387483 INFO: Finished candidate processing
1 day, 17:46:39.387756 INFO: Collecting candidate features
1 day, 17:46:39.507144 WARNING: intensity_correlation has 43 NaNs ( 0.06 % out of 77242)
1 day, 17:46:39.507435 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 77242)
1 day, 17:46:39.513253 INFO: Collecting fragment features
1 day, 17:46:39.557643 INFO: Finished candidate scoring
1 day, 17:46:39.592804 PROGRESS: === Extracted 77242 precursors and 726855 fragments ===
1 day, 17:46:39.593190 INFO: performing precursor FDR with 47 features
1 day, 17:46:39.593228 INFO: Decoy channel: -1
1 day, 17:46:39.593252 INFO: Competetive: True
1 day, 17:46:39.615822 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:46:39.630248 WARNING: dropped 18 target PSMs due to missing features
1 day, 17:46:39.630378 WARNING: dropped 28 decoy PSMs due to missing features
1 day, 17:46:41.167894 INFO: Test AUC: 0.545
1 day, 17:46:41.168017 INFO: Train AUC: 0.583
1 day, 17:46:41.168047 INFO: AUC difference: 6.54%
1 day, 17:46:41.168069 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 17:46:41.254221 INFO: Resetting torch num_threads to 100
1 day, 17:46:41.256665 INFO: === FDR correction performed with classifier version 4 ===
1 day, 17:46:41.260203 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:46:41.260359 PROGRESS: Total precursors accumulated: 20,859
1 day, 17:46:41.260423 PROGRESS: Target precursors: 12,675 (60.77%)
1 day, 17:46:41.260473 PROGRESS: Decoy precursors: 8,184 (39.23%)
1 day, 17:46:41.260522 PROGRESS: 
1 day, 17:46:41.260567 PROGRESS: Precursor Summary:
1 day, 17:46:41.261705 PROGRESS: Channel   0:	 0.05 FDR:   466; 0.01 FDR:   314; 0.001 FDR:   258
1 day, 17:46:41.261801 PROGRESS: 
1 day, 17:46:41.261859 PROGRESS: Protein Summary:
1 day, 17:46:41.263118 PROGRESS: Channel   0:	 0.05 FDR:   445; 0.01 FDR:   301; 0.001 FDR:   247
1 day, 17:46:41.263212 PROGRESS: =========================================================================
1 day, 17:46:41.269421 INFO: fragments_df_filtered: 3406
1 day, 17:46:41.434344 INFO: calibration group: precursor, fitting mz estimator 
1 day, 17:46:41.481002 INFO: calibration group: precursor, fitting rt estimator 
1 day, 17:46:41.532013 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 17:46:41.581368 INFO: calibration group: fragment, fitting mz estimator 
1 day, 17:46:41.791194 INFO: calibration group: precursor, predicting mz
1 day, 17:46:41.799097 INFO: calibration group: precursor, predicting rt
1 day, 17:46:41.827661 INFO: calibration group: precursor, predicting mobility
1 day, 17:46:41.834568 INFO: calibration group: fragment, predicting mz
1 day, 17:46:41.888230 INFO: === checking if optimization conditions were reached ===
1 day, 17:46:41.888479 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 17:46:41.890412 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 137.8908.
1 day, 17:46:41.890466 INFO: ==============================================
1 day, 17:46:41.890557 INFO: Starting optimization step 3.
1 day, 17:46:41.890624 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 17:46:41.890682 PROGRESS: Extracting batch of 47305 precursors
1 day, 17:46:41.902031 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:46:41.902145 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:46:41.902186 INFO: FWHM in RT is 2.93 seconds, sigma is 0.64
1 day, 17:46:41.902210 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.98
1 day, 17:46:41.911145 INFO: Starting candidate selection
1 day, 17:46:56.874146 INFO: Starting candidate scoring
1 day, 17:46:59.238033 INFO: Finished candidate processing
1 day, 17:46:59.238197 INFO: Collecting candidate features
1 day, 17:46:59.386116 WARNING: intensity_correlation has 45 NaNs ( 0.06 % out of 76792)
1 day, 17:46:59.386402 WARNING: height_correlation has 4 NaNs ( 0.01 % out of 76792)
1 day, 17:46:59.392182 INFO: Collecting fragment features
1 day, 17:46:59.435023 INFO: Finished candidate scoring
1 day, 17:46:59.472191 PROGRESS: === Extracted 76792 precursors and 720204 fragments ===
1 day, 17:46:59.472564 INFO: performing precursor FDR with 47 features
1 day, 17:46:59.472602 INFO: Decoy channel: -1
1 day, 17:46:59.472627 INFO: Competetive: True
1 day, 17:46:59.495618 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:46:59.510195 WARNING: dropped 24 target PSMs due to missing features
1 day, 17:46:59.510318 WARNING: dropped 22 decoy PSMs due to missing features
1 day, 17:47:01.022101 INFO: Test AUC: 0.545
1 day, 17:47:01.022219 INFO: Train AUC: 0.581
1 day, 17:47:01.022249 INFO: AUC difference: 6.28%
1 day, 17:47:01.022270 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 17:47:01.110503 INFO: Resetting torch num_threads to 100
1 day, 17:47:01.112935 INFO: === FDR correction performed with classifier version 4 ===
1 day, 17:47:01.116482 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:47:01.116636 PROGRESS: Total precursors accumulated: 20,755
1 day, 17:47:01.116718 PROGRESS: Target precursors: 12,426 (59.87%)
1 day, 17:47:01.116775 PROGRESS: Decoy precursors: 8,329 (40.13%)
1 day, 17:47:01.116825 PROGRESS: 
1 day, 17:47:01.116872 PROGRESS: Precursor Summary:
1 day, 17:47:01.118036 PROGRESS: Channel   0:	 0.05 FDR:   485; 0.01 FDR:   310; 0.001 FDR:   233
1 day, 17:47:01.118138 PROGRESS: 
1 day, 17:47:01.118196 PROGRESS: Protein Summary:
1 day, 17:47:01.119456 PROGRESS: Channel   0:	 0.05 FDR:   463; 0.01 FDR:   298; 0.001 FDR:   226
1 day, 17:47:01.119549 PROGRESS: =========================================================================
1 day, 17:47:01.125679 INFO: fragments_df_filtered: 3347
1 day, 17:47:01.291062 INFO: calibration group: precursor, fitting mz estimator 
1 day, 17:47:01.329004 INFO: calibration group: precursor, fitting rt estimator 
1 day, 17:47:01.366968 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 17:47:01.407051 INFO: calibration group: fragment, fitting mz estimator 
1 day, 17:47:01.585429 INFO: calibration group: precursor, predicting mz
1 day, 17:47:01.592957 INFO: calibration group: precursor, predicting rt
1 day, 17:47:01.621740 INFO: calibration group: precursor, predicting mobility
1 day, 17:47:01.628542 INFO: calibration group: fragment, predicting mz
1 day, 17:47:01.683066 INFO: === checking if optimization conditions were reached ===
1 day, 17:47:01.683335 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 17:47:01.685814 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 120.0969.
1 day, 17:47:01.685876 INFO: ==============================================
1 day, 17:47:01.685979 INFO: Starting optimization step 4.
1 day, 17:47:01.686065 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 17:47:01.686136 PROGRESS: Extracting batch of 47305 precursors
1 day, 17:47:01.702955 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:47:01.703083 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:47:01.703131 INFO: FWHM in RT is 2.93 seconds, sigma is 0.64
1 day, 17:47:01.703160 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.04
1 day, 17:47:01.728270 INFO: Starting candidate selection
1 day, 17:47:15.084409 INFO: Starting candidate scoring
1 day, 17:47:17.394373 INFO: Finished candidate processing
1 day, 17:47:17.394485 INFO: Collecting candidate features
1 day, 17:47:17.542156 WARNING: intensity_correlation has 49 NaNs ( 0.06 % out of 76717)
1 day, 17:47:17.542516 WARNING: height_correlation has 4 NaNs ( 0.01 % out of 76717)
1 day, 17:47:17.548481 INFO: Collecting fragment features
1 day, 17:47:17.598696 INFO: Finished candidate scoring
1 day, 17:47:17.633620 PROGRESS: === Extracted 76717 precursors and 719010 fragments ===
1 day, 17:47:17.634131 INFO: performing precursor FDR with 47 features
1 day, 17:47:17.634171 INFO: Decoy channel: -1
1 day, 17:47:17.634204 INFO: Competetive: True
1 day, 17:47:17.660315 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:47:17.674568 WARNING: dropped 23 target PSMs due to missing features
1 day, 17:47:17.674694 WARNING: dropped 27 decoy PSMs due to missing features
1 day, 17:47:18.888919 INFO: Test AUC: 0.550
1 day, 17:47:18.889051 INFO: Train AUC: 0.591
1 day, 17:47:18.889088 INFO: AUC difference: 6.96%
1 day, 17:47:18.889115 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 17:47:18.975925 INFO: Resetting torch num_threads to 100
1 day, 17:47:18.978499 INFO: === FDR correction performed with classifier version 4 ===
1 day, 17:47:18.981966 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:47:18.982138 PROGRESS: Total precursors accumulated: 20,750
1 day, 17:47:18.982226 PROGRESS: Target precursors: 12,642 (60.93%)
1 day, 17:47:18.982296 PROGRESS: Decoy precursors: 8,108 (39.07%)
1 day, 17:47:18.982358 PROGRESS: 
1 day, 17:47:18.982415 PROGRESS: Precursor Summary:
1 day, 17:47:18.983644 PROGRESS: Channel   0:	 0.05 FDR:   487; 0.01 FDR:   325; 0.001 FDR:   245
1 day, 17:47:18.983758 PROGRESS: 
1 day, 17:47:18.983828 PROGRESS: Protein Summary:
1 day, 17:47:18.985174 PROGRESS: Channel   0:	 0.05 FDR:   464; 0.01 FDR:   313; 0.001 FDR:   238
1 day, 17:47:18.985279 PROGRESS: =========================================================================
1 day, 17:47:18.991967 INFO: fragments_df_filtered: 3402
1 day, 17:47:19.158171 INFO: calibration group: precursor, fitting mz estimator 
1 day, 17:47:19.203319 INFO: calibration group: precursor, fitting rt estimator 
1 day, 17:47:19.251398 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 17:47:19.303108 INFO: calibration group: fragment, fitting mz estimator 
1 day, 17:47:19.508205 INFO: calibration group: precursor, predicting mz
1 day, 17:47:19.515543 INFO: calibration group: precursor, predicting rt
1 day, 17:47:19.544321 INFO: calibration group: precursor, predicting mobility
1 day, 17:47:19.551083 INFO: calibration group: fragment, predicting mz
1 day, 17:47:19.605045 INFO: === checking if optimization conditions were reached ===
1 day, 17:47:19.605315 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 17:47:19.607366 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 112.9888.
1 day, 17:47:19.607420 INFO: ==============================================
1 day, 17:47:19.607537 INFO: Starting optimization step 5.
1 day, 17:47:19.607617 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 17:47:19.607695 PROGRESS: Extracting batch of 47305 precursors
1 day, 17:47:19.619421 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:47:19.619531 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:47:19.619590 INFO: FWHM in RT is 2.92 seconds, sigma is 0.64
1 day, 17:47:19.619619 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.98
1 day, 17:47:19.628736 INFO: Starting candidate selection
1 day, 17:47:32.186696 INFO: Starting candidate scoring
1 day, 17:47:34.494447 INFO: Finished candidate processing
1 day, 17:47:34.494654 INFO: Collecting candidate features
1 day, 17:47:34.631890 WARNING: intensity_correlation has 54 NaNs ( 0.07 % out of 76658)
1 day, 17:47:34.632185 WARNING: height_correlation has 5 NaNs ( 0.01 % out of 76658)
1 day, 17:47:34.638006 INFO: Collecting fragment features
1 day, 17:47:34.681860 INFO: Finished candidate scoring
1 day, 17:47:34.716261 PROGRESS: === Extracted 76658 precursors and 717919 fragments ===
1 day, 17:47:34.717871 INFO: performing precursor FDR with 47 features
1 day, 17:47:34.717914 INFO: Decoy channel: -1
1 day, 17:47:34.717937 INFO: Competetive: True
1 day, 17:47:34.740330 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:47:34.754628 WARNING: dropped 27 target PSMs due to missing features
1 day, 17:47:34.754752 WARNING: dropped 28 decoy PSMs due to missing features
1 day, 17:47:35.941512 INFO: Test AUC: 0.549
1 day, 17:47:35.941636 INFO: Train AUC: 0.584
1 day, 17:47:35.941666 INFO: AUC difference: 6.02%
1 day, 17:47:35.941687 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 17:47:36.027073 INFO: Resetting torch num_threads to 100
1 day, 17:47:36.029520 INFO: === FDR correction performed with classifier version 4 ===
1 day, 17:47:36.032909 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:47:36.033072 PROGRESS: Total precursors accumulated: 20,718
1 day, 17:47:36.033139 PROGRESS: Target precursors: 12,421 (59.95%)
1 day, 17:47:36.033193 PROGRESS: Decoy precursors: 8,297 (40.05%)
1 day, 17:47:36.033243 PROGRESS: 
1 day, 17:47:36.033289 PROGRESS: Precursor Summary:
1 day, 17:47:36.034410 PROGRESS: Channel   0:	 0.05 FDR:   469; 0.01 FDR:   316; 0.001 FDR:   281
1 day, 17:47:36.034508 PROGRESS: 
1 day, 17:47:36.034566 PROGRESS: Protein Summary:
1 day, 17:47:36.035826 PROGRESS: Channel   0:	 0.05 FDR:   448; 0.01 FDR:   304; 0.001 FDR:   270
1 day, 17:47:36.035921 PROGRESS: =========================================================================
1 day, 17:47:36.042150 INFO: fragments_df_filtered: 3350
1 day, 17:47:36.206849 INFO: calibration group: precursor, fitting mz estimator 
1 day, 17:47:36.244935 INFO: calibration group: precursor, fitting rt estimator 
1 day, 17:47:36.282606 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 17:47:36.322237 INFO: calibration group: fragment, fitting mz estimator 
1 day, 17:47:36.504015 INFO: calibration group: precursor, predicting mz
1 day, 17:47:36.511403 INFO: calibration group: precursor, predicting rt
1 day, 17:47:36.539803 INFO: calibration group: precursor, predicting mobility
1 day, 17:47:36.547201 INFO: calibration group: fragment, predicting mz
1 day, 17:47:36.599852 INFO: === checking if optimization conditions were reached ===
1 day, 17:47:36.600134 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 17:47:36.602474 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 112.5614.
1 day, 17:47:36.602540 INFO: ==============================================
1 day, 17:47:36.602654 INFO: Starting optimization step 6.
1 day, 17:47:36.602736 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 17:47:36.602805 PROGRESS: Extracting batch of 47305 precursors
1 day, 17:47:36.618891 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:47:36.619018 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:47:36.619067 INFO: FWHM in RT is 2.97 seconds, sigma is 0.65
1 day, 17:47:36.619097 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.12
1 day, 17:47:36.628009 INFO: Starting candidate selection
1 day, 17:47:48.337815 INFO: Starting candidate scoring
1 day, 17:47:49.393976 INFO: Finished candidate processing
1 day, 17:47:49.394113 INFO: Collecting candidate features
1 day, 17:47:49.496839 WARNING: intensity_correlation has 1102 NaNs ( 1.67 % out of 65909)
1 day, 17:47:49.497128 WARNING: height_correlation has 30 NaNs ( 0.05 % out of 65909)
1 day, 17:47:49.502627 INFO: Collecting fragment features
1 day, 17:47:49.534071 INFO: Finished candidate scoring
1 day, 17:47:49.567731 PROGRESS: === Extracted 65909 precursors and 309748 fragments ===
1 day, 17:47:49.568115 INFO: performing precursor FDR with 47 features
1 day, 17:47:49.568153 INFO: Decoy channel: -1
1 day, 17:47:49.568180 INFO: Competetive: True
1 day, 17:47:49.587890 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:47:49.599499 WARNING: dropped 566 target PSMs due to missing features
1 day, 17:47:49.599622 WARNING: dropped 549 decoy PSMs due to missing features
1 day, 17:47:50.599329 INFO: Test AUC: 0.510
1 day, 17:47:50.599452 INFO: Train AUC: 0.574
1 day, 17:47:50.599483 INFO: AUC difference: 11.20%
1 day, 17:47:50.599505 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 17:47:50.682910 INFO: Resetting torch num_threads to 100
1 day, 17:47:50.685156 INFO: === FDR correction performed with classifier version 4 ===
1 day, 17:47:50.688568 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:47:50.688712 PROGRESS: Total precursors accumulated: 19,574
1 day, 17:47:50.688783 PROGRESS: Target precursors: 11,116 (56.79%)
1 day, 17:47:50.688837 PROGRESS: Decoy precursors: 8,458 (43.21%)
1 day, 17:47:50.688888 PROGRESS: 
1 day, 17:47:50.688938 PROGRESS: Precursor Summary:
1 day, 17:47:50.689885 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 17:47:50.689991 PROGRESS: 
1 day, 17:47:50.690052 PROGRESS: Protein Summary:
1 day, 17:47:50.691039 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 17:47:50.691130 PROGRESS: =========================================================================
1 day, 17:47:50.883201 INFO: calibration group: precursor, predicting mz
1 day, 17:47:50.892663 INFO: calibration group: precursor, predicting rt
1 day, 17:47:50.932424 INFO: calibration group: precursor, predicting mobility
1 day, 17:47:50.942853 INFO: calibration group: fragment, predicting mz
1 day, 17:47:51.014052 INFO: === skipping optimization until target number of precursors are found ===
1 day, 17:47:51.014325 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1 day, 17:47:51.014389 INFO: Starting optimization step 7.
1 day, 17:47:51.014457 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1 day, 17:47:51.014520 PROGRESS: Extracting batch of 63016 precursors
1 day, 17:47:51.029621 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:47:51.029747 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:47:51.029790 INFO: FWHM in RT is 2.97 seconds, sigma is 0.65
1 day, 17:47:51.029813 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.12
1 day, 17:47:51.038877 INFO: Starting candidate selection
1 day, 17:48:06.029098 INFO: Starting candidate scoring
1 day, 17:48:07.434436 INFO: Finished candidate processing
1 day, 17:48:07.434598 INFO: Collecting candidate features
1 day, 17:48:07.599836 WARNING: intensity_correlation has 1433 NaNs ( 1.63 % out of 87915)
1 day, 17:48:07.600157 WARNING: height_correlation has 31 NaNs ( 0.04 % out of 87915)
1 day, 17:48:07.606477 INFO: Collecting fragment features
1 day, 17:48:07.651929 INFO: Finished candidate scoring
1 day, 17:48:07.752431 PROGRESS: === Extracted 153824 precursors and 721077 fragments ===
1 day, 17:48:07.765832 INFO: performing precursor FDR with 47 features
1 day, 17:48:07.765951 INFO: Decoy channel: -1
1 day, 17:48:07.765982 INFO: Competetive: True
1 day, 17:48:07.828803 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:48:07.858958 WARNING: dropped 1292 target PSMs due to missing features
1 day, 17:48:07.859096 WARNING: dropped 1272 decoy PSMs due to missing features
1 day, 17:48:10.585593 INFO: Test AUC: 0.520
1 day, 17:48:10.585707 INFO: Train AUC: 0.564
1 day, 17:48:10.585738 INFO: AUC difference: 7.75%
1 day, 17:48:10.585760 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 17:48:10.676279 INFO: Resetting torch num_threads to 100
1 day, 17:48:10.682641 INFO: === FDR correction performed with classifier version 4 ===
1 day, 17:48:10.690272 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:48:10.690573 PROGRESS: Total precursors accumulated: 45,714
1 day, 17:48:10.690642 PROGRESS: Target precursors: 25,720 (56.26%)
1 day, 17:48:10.690697 PROGRESS: Decoy precursors: 19,994 (43.74%)
1 day, 17:48:10.690748 PROGRESS: 
1 day, 17:48:10.690795 PROGRESS: Precursor Summary:
1 day, 17:48:10.691953 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1 day, 17:48:10.692048 PROGRESS: 
1 day, 17:48:10.692108 PROGRESS: Protein Summary:
1 day, 17:48:10.693284 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1 day, 17:48:10.693379 PROGRESS: =========================================================================
1 day, 17:48:10.959905 INFO: calibration group: precursor, predicting mz
1 day, 17:48:10.978278 INFO: calibration group: precursor, predicting rt
1 day, 17:48:11.054770 INFO: calibration group: precursor, predicting mobility
1 day, 17:48:11.076420 INFO: calibration group: fragment, predicting mz
1 day, 17:48:11.237650 INFO: === skipping optimization until target number of precursors are found ===
1 day, 17:48:11.237938 PROGRESS: === Optimization of rt_error has been skipped 2 time(s); maximum number is 1 ===
1 day, 17:48:11.238595 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 112.9888 found after 6 searches.
1 day, 17:48:11.238669 PROGRESS: Optimization finished for rt_error.
1 day, 17:48:11.410927 INFO: calibration group: precursor, predicting mz
1 day, 17:48:11.418567 INFO: calibration group: precursor, predicting rt
1 day, 17:48:11.447163 INFO: calibration group: precursor, predicting mobility
1 day, 17:48:11.454865 INFO: calibration group: fragment, predicting mz
1 day, 17:48:11.535239 INFO: Starting optimization step 0.
1 day, 17:48:11.535457 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 17:48:11.535538 PROGRESS: Extracting batch of 47305 precursors
1 day, 17:48:11.547054 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:48:11.547167 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:48:11.547219 INFO: FWHM in RT is 2.97 seconds, sigma is 0.65
1 day, 17:48:11.547244 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.12
1 day, 17:48:11.548388 INFO: Starting candidate selection
1 day, 17:48:23.139961 INFO: Starting candidate scoring
1 day, 17:48:24.209262 INFO: Finished candidate processing
1 day, 17:48:24.209381 INFO: Collecting candidate features
1 day, 17:48:24.315571 WARNING: intensity_correlation has 1108 NaNs ( 1.68 % out of 65927)
1 day, 17:48:24.315851 WARNING: height_correlation has 30 NaNs ( 0.05 % out of 65927)
1 day, 17:48:24.321369 INFO: Collecting fragment features
1 day, 17:48:24.352859 INFO: Finished candidate scoring
1 day, 17:48:24.387225 PROGRESS: === Extracted 65927 precursors and 309865 fragments ===
1 day, 17:48:24.387603 INFO: performing precursor FDR with 47 features
1 day, 17:48:24.387644 INFO: Decoy channel: -1
1 day, 17:48:24.387675 INFO: Competetive: True
1 day, 17:48:24.407215 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:48:24.418811 WARNING: dropped 562 target PSMs due to missing features
1 day, 17:48:24.418935 WARNING: dropped 559 decoy PSMs due to missing features
1 day, 17:48:25.424581 INFO: Test AUC: 0.527
1 day, 17:48:25.425265 INFO: Train AUC: 0.566
1 day, 17:48:25.425302 INFO: AUC difference: 6.92%
1 day, 17:48:25.425326 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 17:48:25.512371 INFO: Resetting torch num_threads to 100
1 day, 17:48:25.514607 INFO: === FDR correction performed with classifier version 10 ===
1 day, 17:48:25.517763 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:48:25.517908 PROGRESS: Total precursors accumulated: 19,573
1 day, 17:48:25.517974 PROGRESS: Target precursors: 11,016 (56.28%)
1 day, 17:48:25.518027 PROGRESS: Decoy precursors: 8,557 (43.72%)
1 day, 17:48:25.518076 PROGRESS: 
1 day, 17:48:25.518125 PROGRESS: Precursor Summary:
1 day, 17:48:25.519117 PROGRESS: Channel   0:	 0.05 FDR:     6; 0.01 FDR:     6; 0.001 FDR:     6
1 day, 17:48:25.519210 PROGRESS: 
1 day, 17:48:25.519265 PROGRESS: Protein Summary:
1 day, 17:48:25.520284 PROGRESS: Channel   0:	 0.05 FDR:     6; 0.01 FDR:     6; 0.001 FDR:     6
1 day, 17:48:25.520373 PROGRESS: =========================================================================
1 day, 17:48:25.673833 INFO: calibration group: precursor, predicting mz
1 day, 17:48:25.683381 INFO: calibration group: precursor, predicting rt
1 day, 17:48:25.721856 INFO: calibration group: precursor, predicting mobility
1 day, 17:48:25.732365 INFO: calibration group: fragment, predicting mz
1 day, 17:48:25.804423 INFO: === skipping optimization until target number of precursors are found ===
1 day, 17:48:25.804715 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
1 day, 17:48:25.804778 INFO: Starting optimization step 1.
1 day, 17:48:25.804848 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1 day, 17:48:25.804910 PROGRESS: Extracting batch of 63016 precursors
1 day, 17:48:25.820297 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:48:25.820424 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:48:25.820465 INFO: FWHM in RT is 2.97 seconds, sigma is 0.65
1 day, 17:48:25.820488 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.12
1 day, 17:48:25.821505 INFO: Starting candidate selection
1 day, 17:48:42.455943 INFO: Starting candidate scoring
1 day, 17:48:43.873012 INFO: Finished candidate processing
1 day, 17:48:43.873187 INFO: Collecting candidate features
1 day, 17:48:44.016017 WARNING: intensity_correlation has 1428 NaNs ( 1.62 % out of 87923)
1 day, 17:48:44.016417 WARNING: height_correlation has 31 NaNs ( 0.04 % out of 87923)
1 day, 17:48:44.026621 INFO: Collecting fragment features
1 day, 17:48:44.074786 INFO: Finished candidate scoring
1 day, 17:48:44.154572 PROGRESS: === Extracted 153850 precursors and 721242 fragments ===
1 day, 17:48:44.166933 INFO: performing precursor FDR with 47 features
1 day, 17:48:44.167059 INFO: Decoy channel: -1
1 day, 17:48:44.167087 INFO: Competetive: True
1 day, 17:48:44.230530 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:48:44.258214 WARNING: dropped 1296 target PSMs due to missing features
1 day, 17:48:44.258352 WARNING: dropped 1269 decoy PSMs due to missing features
1 day, 17:48:46.750659 INFO: Test AUC: 0.529
1 day, 17:48:46.750788 INFO: Train AUC: 0.564
1 day, 17:48:46.750818 INFO: AUC difference: 6.09%
1 day, 17:48:46.750840 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 17:48:46.842579 INFO: Resetting torch num_threads to 100
1 day, 17:48:46.849042 INFO: === FDR correction performed with classifier version 10 ===
1 day, 17:48:46.857138 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:48:46.857422 PROGRESS: Total precursors accumulated: 45,712
1 day, 17:48:46.857492 PROGRESS: Target precursors: 25,680 (56.18%)
1 day, 17:48:46.857546 PROGRESS: Decoy precursors: 20,032 (43.82%)
1 day, 17:48:46.857612 PROGRESS: 
1 day, 17:48:46.857659 PROGRESS: Precursor Summary:
1 day, 17:48:46.858838 PROGRESS: Channel   0:	 0.05 FDR:     7; 0.01 FDR:     7; 0.001 FDR:     7
1 day, 17:48:46.858934 PROGRESS: 
1 day, 17:48:46.858992 PROGRESS: Protein Summary:
1 day, 17:48:46.860149 PROGRESS: Channel   0:	 0.05 FDR:     7; 0.01 FDR:     7; 0.001 FDR:     7
1 day, 17:48:46.860244 PROGRESS: =========================================================================
1 day, 17:48:47.113766 INFO: calibration group: precursor, predicting mz
1 day, 17:48:47.131549 INFO: calibration group: precursor, predicting rt
1 day, 17:48:47.207249 INFO: calibration group: precursor, predicting mobility
1 day, 17:48:47.227574 INFO: calibration group: fragment, predicting mz
1 day, 17:48:47.391726 INFO: === skipping optimization until target number of precursors are found ===
1 day, 17:48:47.392019 PROGRESS: === Optimization of mobility_error has been skipped 2 time(s); maximum number is 1 ===
1 day, 17:48:47.392082 INFO: Starting optimization step 2.
1 day, 17:48:47.392150 PROGRESS: === Extracting elution groups 56000 to 120000 ===
1 day, 17:48:47.392210 PROGRESS: Extracting batch of 126066 precursors
1 day, 17:48:47.423588 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:48:47.423718 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:48:47.423768 INFO: FWHM in RT is 2.97 seconds, sigma is 0.65
1 day, 17:48:47.423793 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.12
1 day, 17:48:47.424909 INFO: Starting candidate selection
1 day, 17:49:17.256544 INFO: Starting candidate scoring
1 day, 17:49:19.880260 INFO: Finished candidate processing
1 day, 17:49:19.880425 INFO: Collecting candidate features
1 day, 17:49:20.178585 WARNING: intensity_correlation has 3005 NaNs ( 1.71 % out of 175609)
1 day, 17:49:20.178977 WARNING: height_correlation has 81 NaNs ( 0.05 % out of 175609)
1 day, 17:49:20.188161 INFO: Collecting fragment features
1 day, 17:49:20.283715 INFO: Finished candidate scoring
1 day, 17:49:20.482767 PROGRESS: === Extracted 329459 precursors and 1541001 fragments ===
1 day, 17:49:20.508322 INFO: performing precursor FDR with 47 features
1 day, 17:49:20.508459 INFO: Decoy channel: -1
1 day, 17:49:20.508486 INFO: Competetive: True
1 day, 17:49:20.647584 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:49:20.705495 WARNING: dropped 2854 target PSMs due to missing features
1 day, 17:49:20.705636 WARNING: dropped 2753 decoy PSMs due to missing features
1 day, 17:49:26.097325 INFO: Test AUC: 0.529
1 day, 17:49:26.097465 INFO: Train AUC: 0.556
1 day, 17:49:26.097496 INFO: AUC difference: 4.76%
1 day, 17:49:26.201892 INFO: Resetting torch num_threads to 100
1 day, 17:49:26.217192 INFO: === FDR correction performed with classifier version 10 ===
1 day, 17:49:26.235373 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:49:26.235649 PROGRESS: Total precursors accumulated: 97,967
1 day, 17:49:26.235723 PROGRESS: Target precursors: 54,618 (55.75%)
1 day, 17:49:26.235778 PROGRESS: Decoy precursors: 43,349 (44.25%)
1 day, 17:49:26.235826 PROGRESS: 
1 day, 17:49:26.235872 PROGRESS: Precursor Summary:
1 day, 17:49:26.237410 PROGRESS: Channel   0:	 0.05 FDR:    10; 0.01 FDR:    10; 0.001 FDR:    10
1 day, 17:49:26.237509 PROGRESS: 
1 day, 17:49:26.237566 PROGRESS: Protein Summary:
1 day, 17:49:26.238976 PROGRESS: Channel   0:	 0.05 FDR:    10; 0.01 FDR:    10; 0.001 FDR:    10
1 day, 17:49:26.239070 PROGRESS: =========================================================================
1 day, 17:49:26.660630 INFO: calibration group: precursor, predicting mz
1 day, 17:49:26.694714 INFO: calibration group: precursor, predicting rt
1 day, 17:49:26.846511 INFO: calibration group: precursor, predicting mobility
1 day, 17:49:26.881846 INFO: calibration group: fragment, predicting mz
1 day, 17:49:27.182734 INFO: === skipping optimization until target number of precursors are found ===
1 day, 17:49:27.183054 PROGRESS: === Optimization of mobility_error has been skipped 3 time(s); maximum number is 1 ===
1 day, 17:49:27.183130 INFO: Starting optimization step 3.
1 day, 17:49:27.183213 PROGRESS: === Extracting elution groups 120000 to 248000 ===
1 day, 17:49:27.183283 PROGRESS: Extracting batch of 252186 precursors
1 day, 17:49:27.245810 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:49:27.245943 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:49:27.245994 INFO: FWHM in RT is 2.97 seconds, sigma is 0.65
1 day, 17:49:27.246016 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.12
1 day, 17:49:27.247029 INFO: Starting candidate selection
1 day, 17:50:26.168698 INFO: Starting candidate scoring
1 day, 17:50:31.561855 INFO: Finished candidate processing
1 day, 17:50:31.562033 INFO: Collecting candidate features
1 day, 17:50:32.229355 WARNING: intensity_correlation has 5909 NaNs ( 1.68 % out of 351434)
1 day, 17:50:32.229915 WARNING: height_correlation has 158 NaNs ( 0.04 % out of 351434)
1 day, 17:50:32.244555 INFO: Collecting fragment features
1 day, 17:50:32.440062 INFO: Finished candidate scoring
1 day, 17:50:32.910722 PROGRESS: === Extracted 680893 precursors and 3184468 fragments ===
1 day, 17:50:32.969312 INFO: performing precursor FDR with 47 features
1 day, 17:50:32.969454 INFO: Decoy channel: -1
1 day, 17:50:32.969481 INFO: Competetive: True
1 day, 17:50:33.267516 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:50:33.404114 WARNING: dropped 5969 target PSMs due to missing features
1 day, 17:50:33.404273 WARNING: dropped 5640 decoy PSMs due to missing features
1 day, 17:50:46.085515 INFO: Test AUC: 0.518
1 day, 17:50:46.085664 INFO: Train AUC: 0.550
1 day, 17:50:46.085697 INFO: AUC difference: 5.82%
1 day, 17:50:46.085718 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 17:50:46.218993 INFO: Resetting torch num_threads to 100
1 day, 17:50:46.251297 INFO: === FDR correction performed with classifier version 10 ===
1 day, 17:50:46.289168 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:50:46.289523 PROGRESS: Total precursors accumulated: 202,522
1 day, 17:50:46.289588 PROGRESS: Target precursors: 112,592 (55.59%)
1 day, 17:50:46.289641 PROGRESS: Decoy precursors: 89,930 (44.41%)
1 day, 17:50:46.289690 PROGRESS: 
1 day, 17:50:46.289737 PROGRESS: Precursor Summary:
1 day, 17:50:46.291843 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1 day, 17:50:46.291944 PROGRESS: 
1 day, 17:50:46.292008 PROGRESS: Protein Summary:
1 day, 17:50:46.293909 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1 day, 17:50:46.294009 PROGRESS: =========================================================================
1 day, 17:50:46.921798 INFO: calibration group: precursor, predicting mz
1 day, 17:50:46.988159 INFO: calibration group: precursor, predicting rt
1 day, 17:50:47.301455 INFO: calibration group: precursor, predicting mobility
1 day, 17:50:47.373459 INFO: calibration group: fragment, predicting mz
1 day, 17:50:47.979356 INFO: === skipping optimization until target number of precursors are found ===
1 day, 17:50:47.979684 PROGRESS: === Optimization of mobility_error has been skipped 4 time(s); maximum number is 1 ===
1 day, 17:50:47.979759 INFO: Starting optimization step 4.
1 day, 17:50:47.979828 PROGRESS: === Extracting elution groups 248000 to 504000 ===
1 day, 17:50:47.979897 PROGRESS: Extracting batch of 504181 precursors
1 day, 17:50:48.103699 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:50:48.103840 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:50:48.103891 INFO: FWHM in RT is 2.97 seconds, sigma is 0.65
1 day, 17:50:48.103915 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.12
1 day, 17:50:48.104809 INFO: Starting candidate selection
1 day, 17:52:41.674897 INFO: Starting candidate scoring
1 day, 17:52:54.006785 INFO: Finished candidate processing
1 day, 17:52:54.006958 INFO: Collecting candidate features
1 day, 17:52:55.448265 WARNING: intensity_correlation has 11521 NaNs ( 1.64 % out of 702935)
1 day, 17:52:55.449159 WARNING: height_correlation has 296 NaNs ( 0.04 % out of 702935)
1 day, 17:52:55.474373 INFO: Collecting fragment features
1 day, 17:52:55.865563 INFO: Finished candidate scoring
1 day, 17:52:56.642632 PROGRESS: === Extracted 1383828 precursors and 6470363 fragments ===
1 day, 17:52:56.762367 INFO: performing precursor FDR with 47 features
1 day, 17:52:56.762504 INFO: Decoy channel: -1
1 day, 17:52:56.762534 INFO: Competetive: True
1 day, 17:52:57.366883 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:52:57.659904 WARNING: dropped 12099 target PSMs due to missing features
1 day, 17:52:57.660048 WARNING: dropped 11181 decoy PSMs due to missing features
1 day, 17:53:22.423123 INFO: Test AUC: 0.535
1 day, 17:53:22.423267 INFO: Train AUC: 0.547
1 day, 17:53:22.423306 INFO: AUC difference: 2.18%
1 day, 17:53:22.605375 INFO: Resetting torch num_threads to 100
1 day, 17:53:22.669815 INFO: === FDR correction performed with classifier version 10 ===
1 day, 17:53:22.742495 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:53:22.742847 PROGRESS: Total precursors accumulated: 411,828
1 day, 17:53:22.742918 PROGRESS: Target precursors: 228,104 (55.39%)
1 day, 17:53:22.742978 PROGRESS: Decoy precursors: 183,724 (44.61%)
1 day, 17:53:22.743032 PROGRESS: 
1 day, 17:53:22.743083 PROGRESS: Precursor Summary:
1 day, 17:53:22.746352 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1 day, 17:53:22.746473 PROGRESS: 
1 day, 17:53:22.746534 PROGRESS: Protein Summary:
1 day, 17:53:22.749277 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1 day, 17:53:22.749380 PROGRESS: =========================================================================
1 day, 17:53:23.704388 INFO: calibration group: precursor, predicting mz
1 day, 17:53:23.843301 INFO: calibration group: precursor, predicting rt
1 day, 17:53:24.469658 INFO: calibration group: precursor, predicting mobility
1 day, 17:53:24.607506 INFO: calibration group: fragment, predicting mz
1 day, 17:53:25.870774 INFO: === skipping optimization until target number of precursors are found ===
1 day, 17:53:25.871061 PROGRESS: === Optimization of mobility_error has been skipped 5 time(s); maximum number is 1 ===
1 day, 17:53:25.871164 INFO: Starting optimization step 5.
1 day, 17:53:25.871252 PROGRESS: === Extracting elution groups 504000 to 1016000 ===
1 day, 17:53:25.871340 PROGRESS: Extracting batch of 1008477 precursors
1 day, 17:53:26.117003 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:53:26.117144 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:53:26.117217 INFO: FWHM in RT is 2.97 seconds, sigma is 0.65
1 day, 17:53:26.117248 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.12
1 day, 17:53:26.118221 INFO: Starting candidate selection
1 day, 17:57:12.193126 INFO: Starting candidate scoring
1 day, 17:57:32.006037 INFO: Finished candidate processing
1 day, 17:57:32.006545 INFO: Collecting candidate features
1 day, 17:57:34.966227 WARNING: intensity_correlation has 22787 NaNs ( 1.62 % out of 1405606)
1 day, 17:57:34.967618 WARNING: height_correlation has 566 NaNs ( 0.04 % out of 1405606)
1 day, 17:57:35.015625 INFO: Collecting fragment features
1 day, 17:57:35.781620 INFO: Finished candidate scoring
1 day, 17:57:38.120566 PROGRESS: === Extracted 2789434 precursors and 13041701 fragments ===
1 day, 17:57:38.365039 INFO: performing precursor FDR with 47 features
1 day, 17:57:38.365165 INFO: Decoy channel: -1
1 day, 17:57:38.365195 INFO: Competetive: True
1 day, 17:57:39.607853 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 17:57:40.154268 WARNING: dropped 23919 target PSMs due to missing features
1 day, 17:57:40.154415 WARNING: dropped 22455 decoy PSMs due to missing features
1 day, 17:58:29.056545 INFO: Test AUC: 0.540
1 day, 17:58:29.056797 INFO: Train AUC: 0.547
1 day, 17:58:29.056836 INFO: AUC difference: 1.29%
1 day, 17:58:29.339377 INFO: Resetting torch num_threads to 100
1 day, 17:58:29.487337 INFO: === FDR correction performed with classifier version 10 ===
1 day, 17:58:29.641829 PROGRESS: ============================= Precursor FDR =============================
1 day, 17:58:29.642182 PROGRESS: Total precursors accumulated: 830,449
1 day, 17:58:29.642247 PROGRESS: Target precursors: 460,143 (55.41%)
1 day, 17:58:29.642298 PROGRESS: Decoy precursors: 370,306 (44.59%)
1 day, 17:58:29.642347 PROGRESS: 
1 day, 17:58:29.642392 PROGRESS: Precursor Summary:
1 day, 17:58:29.647342 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 17:58:29.647463 PROGRESS: 
1 day, 17:58:29.647520 PROGRESS: Protein Summary:
1 day, 17:58:29.651788 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 17:58:29.651896 PROGRESS: =========================================================================
1 day, 17:58:31.337794 INFO: calibration group: precursor, predicting mz
1 day, 17:58:31.627021 INFO: calibration group: precursor, predicting rt
1 day, 17:58:32.907491 INFO: calibration group: precursor, predicting mobility
1 day, 17:58:33.195879 INFO: calibration group: fragment, predicting mz
1 day, 17:58:35.729824 INFO: === skipping optimization until target number of precursors are found ===
1 day, 17:58:35.730096 PROGRESS: === Optimization of mobility_error has been skipped 6 time(s); maximum number is 1 ===
1 day, 17:58:35.730172 INFO: Starting optimization step 6.
1 day, 17:58:35.730241 PROGRESS: === Extracting elution groups 1016000 to 2040000 ===
1 day, 17:58:35.730310 PROGRESS: Extracting batch of 2017059 precursors
1 day, 17:58:36.215248 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 17:58:36.215379 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 17:58:36.215426 INFO: FWHM in RT is 2.97 seconds, sigma is 0.65
1 day, 17:58:36.215450 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.12
1 day, 17:58:36.216495 INFO: Starting candidate selection
1 day, 18:06:08.677301 INFO: Starting candidate scoring
1 day, 18:06:49.334146 INFO: Finished candidate processing
1 day, 18:06:49.334371 INFO: Collecting candidate features
1 day, 18:06:54.895133 WARNING: intensity_correlation has 46333 NaNs ( 1.65 % out of 2810872)
1 day, 18:06:54.897743 WARNING: height_correlation has 1175 NaNs ( 0.04 % out of 2810872)
1 day, 18:06:54.993690 INFO: Collecting fragment features
1 day, 18:06:56.582739 INFO: Finished candidate scoring
1 day, 18:07:01.843475 PROGRESS: === Extracted 5600306 precursors and 26186053 fragments ===
1 day, 18:07:02.364622 INFO: performing precursor FDR with 47 features
1 day, 18:07:02.364759 INFO: Decoy channel: -1
1 day, 18:07:02.364789 INFO: Competetive: True
1 day, 18:07:04.710940 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 18:07:05.769288 WARNING: dropped 48041 target PSMs due to missing features
1 day, 18:07:05.769438 WARNING: dropped 45317 decoy PSMs due to missing features
1 day, 18:08:39.533093 INFO: Test AUC: 0.543
1 day, 18:08:39.533339 INFO: Train AUC: 0.547
1 day, 18:08:39.533383 INFO: AUC difference: 0.64%
1 day, 18:08:39.975860 INFO: Resetting torch num_threads to 100
1 day, 18:08:40.278599 INFO: === FDR correction performed with classifier version 10 ===
1 day, 18:08:40.583127 PROGRESS: ============================= Precursor FDR =============================
1 day, 18:08:40.583468 PROGRESS: Total precursors accumulated: 1,666,966
1 day, 18:08:40.583535 PROGRESS: Target precursors: 929,774 (55.78%)
1 day, 18:08:40.583588 PROGRESS: Decoy precursors: 737,192 (44.22%)
1 day, 18:08:40.583638 PROGRESS: 
1 day, 18:08:40.583685 PROGRESS: Precursor Summary:
1 day, 18:08:40.592647 PROGRESS: Channel   0:	 0.05 FDR:     6; 0.01 FDR:     6; 0.001 FDR:     6
1 day, 18:08:40.592798 PROGRESS: 
1 day, 18:08:40.592857 PROGRESS: Protein Summary:
1 day, 18:08:40.600976 PROGRESS: Channel   0:	 0.05 FDR:     6; 0.01 FDR:     6; 0.001 FDR:     6
1 day, 18:08:40.601127 PROGRESS: =========================================================================
1 day, 18:08:43.707723 INFO: calibration group: precursor, predicting mz
1 day, 18:08:44.253416 INFO: calibration group: precursor, predicting rt
1 day, 18:08:46.777275 INFO: calibration group: precursor, predicting mobility
1 day, 18:08:47.332608 INFO: calibration group: fragment, predicting mz
1 day, 18:08:52.300974 INFO: === skipping optimization until target number of precursors are found ===
1 day, 18:08:52.301258 PROGRESS: === Optimization of mobility_error has been skipped 7 time(s); maximum number is 1 ===
1 day, 18:08:52.301348 INFO: Starting optimization step 7.
1 day, 18:08:52.301414 PROGRESS: === Extracting elution groups 2040000 to 4088000 ===
1 day, 18:08:52.301485 PROGRESS: Extracting batch of 4034279 precursors
1 day, 18:08:53.220826 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 18:08:53.220950 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 18:08:53.221000 INFO: FWHM in RT is 2.97 seconds, sigma is 0.65
1 day, 18:08:53.221035 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.12
1 day, 18:08:53.222274 INFO: Starting candidate selection
1 day, 18:23:59.315708 INFO: Starting candidate scoring
1 day, 18:25:20.343647 INFO: Finished candidate processing
1 day, 18:25:20.344159 INFO: Collecting candidate features
1 day, 18:25:31.240594 WARNING: intensity_correlation has 92975 NaNs ( 1.65 % out of 5620179)
1 day, 18:25:31.245666 WARNING: height_correlation has 2427 NaNs ( 0.04 % out of 5620179)
1 day, 18:25:31.431551 INFO: Collecting fragment features
1 day, 18:25:34.637425 INFO: Finished candidate scoring
1 day, 18:25:41.346387 PROGRESS: === Extracted 11220485 precursors and 52460522 fragments ===
1 day, 18:25:42.370475 INFO: performing precursor FDR with 47 features
1 day, 18:25:42.370608 INFO: Decoy channel: -1
1 day, 18:25:42.370638 INFO: Competetive: True
1 day, 18:25:46.933302 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 18:25:48.995420 WARNING: dropped 96269 target PSMs due to missing features
1 day, 18:25:48.995565 WARNING: dropped 91337 decoy PSMs due to missing features
1 day, 18:29:15.779953 INFO: Test AUC: 0.545
1 day, 18:29:15.780182 INFO: Train AUC: 0.548
1 day, 18:29:15.780219 INFO: AUC difference: 0.52%
1 day, 18:29:16.484305 INFO: Resetting torch num_threads to 100
1 day, 18:29:17.034324 INFO: === FDR correction performed with classifier version 10 ===
1 day, 18:29:17.637860 PROGRESS: ============================= Precursor FDR =============================
1 day, 18:29:17.638196 PROGRESS: Total precursors accumulated: 3,340,379
1 day, 18:29:17.638268 PROGRESS: Target precursors: 1,855,403 (55.54%)
1 day, 18:29:17.638323 PROGRESS: Decoy precursors: 1,484,976 (44.46%)
1 day, 18:29:17.638375 PROGRESS: 
1 day, 18:29:17.638443 PROGRESS: Precursor Summary:
1 day, 18:29:17.655052 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 18:29:17.655313 PROGRESS: 
1 day, 18:29:17.655376 PROGRESS: Protein Summary:
1 day, 18:29:17.671526 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1 day, 18:29:17.671748 PROGRESS: =========================================================================
1 day, 18:29:19.640043 INFO: calibration group: precursor, predicting mz
1 day, 18:29:19.958207 INFO: calibration group: precursor, predicting rt
1 day, 18:29:21.359593 INFO: calibration group: precursor, predicting mobility
1 day, 18:29:21.678687 INFO: calibration group: fragment, predicting mz
1 day, 18:29:24.478315 INFO: === skipping optimization until target number of precursors are found ===
1 day, 18:29:24.478601 PROGRESS: === Optimization of mobility_error has been skipped 8 time(s); maximum number is 1 ===
1 day, 18:29:24.478687 INFO: Starting optimization step 8.
1 day, 18:29:24.478762 PROGRESS: === Extracting elution groups 4088000 to 5215079 ===
1 day, 18:29:24.478841 PROGRESS: Extracting batch of 2220101 precursors
1 day, 18:29:25.004787 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 18:29:25.004920 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 18:29:25.004971 INFO: FWHM in RT is 2.97 seconds, sigma is 0.65
1 day, 18:29:25.004996 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.12
1 day, 18:29:25.006057 INFO: Starting candidate selection
1 day, 18:37:43.978028 INFO: Starting candidate scoring
1 day, 18:38:28.411030 INFO: Finished candidate processing
1 day, 18:38:28.411562 INFO: Collecting candidate features
1 day, 18:38:34.644504 WARNING: intensity_correlation has 51174 NaNs ( 1.66 % out of 3091246)
1 day, 18:38:34.647371 WARNING: height_correlation has 1253 NaNs ( 0.04 % out of 3091246)
1 day, 18:38:34.749555 INFO: Collecting fragment features
1 day, 18:38:36.512935 INFO: Finished candidate scoring
1 day, 18:38:42.378485 PROGRESS: === Extracted 14311731 precursors and 66906054 fragments ===
1 day, 18:38:43.728666 INFO: performing precursor FDR with 47 features
1 day, 18:38:43.728803 INFO: Decoy channel: -1
1 day, 18:38:43.728833 INFO: Competetive: True
1 day, 18:38:49.649457 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 18:38:52.305269 WARNING: dropped 122860 target PSMs due to missing features
1 day, 18:38:52.305414 WARNING: dropped 116591 decoy PSMs due to missing features
1 day, 18:45:23.826970 INFO: Test AUC: 0.545
1 day, 18:45:23.827212 INFO: Train AUC: 0.548
1 day, 18:45:23.827250 INFO: AUC difference: 0.60%
1 day, 18:45:25.059351 INFO: Resetting torch num_threads to 100
1 day, 18:45:25.788862 INFO: === FDR correction performed with classifier version 10 ===
1 day, 18:45:26.577315 PROGRESS: ============================= Precursor FDR =============================
1 day, 18:45:26.577648 PROGRESS: Total precursors accumulated: 4,261,164
1 day, 18:45:26.577740 PROGRESS: Target precursors: 2,361,718 (55.42%)
1 day, 18:45:26.577798 PROGRESS: Decoy precursors: 1,899,446 (44.58%)
1 day, 18:45:26.577848 PROGRESS: 
1 day, 18:45:26.577897 PROGRESS: Precursor Summary:
1 day, 18:45:26.601650 PROGRESS: Channel   0:	 0.05 FDR:    49; 0.01 FDR:     3; 0.001 FDR:     3
1 day, 18:45:26.601904 PROGRESS: 
1 day, 18:45:26.601969 PROGRESS: Protein Summary:
1 day, 18:45:26.624777 PROGRESS: Channel   0:	 0.05 FDR:    45; 0.01 FDR:     3; 0.001 FDR:     3
1 day, 18:45:26.625016 PROGRESS: =========================================================================
1 day, 18:45:26.720686 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 18:45:26.720994 PROGRESS: ==============================================
1 day, 18:45:27.205659 INFO: fragments_df_filtered: 58
1 day, 18:45:27.554934 WARNING: No more batches to process. Will proceed to extraction using best parameters available in optimization manager.
1 day, 18:45:27.555212 WARNING: Using current optimal value for ms2_error: 15.00.
1 day, 18:45:27.904058 WARNING: No more batches to process. Will proceed to extraction using best parameters available in optimization manager.
1 day, 18:45:27.904328 WARNING: Using current optimal value for ms1_error: 10.00.
1 day, 18:45:28.253296 WARNING: No more batches to process. Will proceed to extraction using best parameters available in optimization manager.
1 day, 18:45:28.255034 WARNING: Using current optimal value for rt_error: 112.99.
1 day, 18:45:28.602826 WARNING: No more batches to process. Will proceed to extraction using best parameters available in optimization manager.
1 day, 18:45:28.603843 WARNING: Using current optimal value for mobility_error: 0.10.
1 day, 18:45:28.609330 PROGRESS: ms2_error      : 15.0000
1 day, 18:45:28.609496 PROGRESS: ms1_error      : 10.0000
1 day, 18:45:28.609555 PROGRESS: rt_error       : 112.9888
1 day, 18:45:28.609605 PROGRESS: mobility_error : 0.1000
1 day, 18:45:28.609654 PROGRESS: ==============================================
1 day, 18:45:28.735965 INFO: calibration group: precursor, predicting mz
1 day, 18:45:30.208418 INFO: calibration group: precursor, predicting rt
1 day, 18:45:36.618520 INFO: calibration group: precursor, predicting mobility
1 day, 18:45:38.092106 INFO: calibration group: fragment, predicting mz
1 day, 18:45:50.772021 PROGRESS: Extracting batch of 10272670 precursors
1 day, 18:45:52.872109 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 18:45:52.872237 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 18:45:52.872286 INFO: FWHM in RT is 2.97 seconds, sigma is 0.65
1 day, 18:45:52.872312 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.12
1 day, 18:45:52.873245 INFO: Starting candidate selection
1 day, 19:24:31.737102 INFO: Applying score cutoff of 19.273183670043945
1 day, 19:24:32.129829 INFO: Removed 6964295 precursors with score below cutoff
1 day, 19:24:34.610301 INFO: Starting candidate scoring
1 day, 19:26:58.372094 INFO: Finished candidate processing
1 day, 19:26:58.372587 INFO: Collecting candidate features
1 day, 19:27:16.937750 WARNING: intensity_correlation has 119043 NaNs ( 1.19 % out of 10026843)
1 day, 19:27:16.946498 WARNING: height_correlation has 1779 NaNs ( 0.02 % out of 10026843)
1 day, 19:27:17.276631 INFO: Collecting fragment features
1 day, 19:27:22.907412 INFO: Finished candidate scoring
1 day, 19:27:33.984353 INFO: === FDR correction performed with classifier version 21 ===
1 day, 19:27:33.989353 INFO: performing precursor FDR with 47 features
1 day, 19:27:33.989429 INFO: Decoy channel: -1
1 day, 19:27:33.989459 INFO: Competetive: True
1 day, 19:27:36.703177 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:27:38.367440 WARNING: dropped 62257 target PSMs due to missing features
1 day, 19:27:38.367587 WARNING: dropped 57822 decoy PSMs due to missing features
1 day, 19:30:40.475855 INFO: Test AUC: 0.544
1 day, 19:30:40.476112 INFO: Train AUC: 0.548
1 day, 19:30:40.476150 INFO: AUC difference: 0.70%
1 day, 19:30:41.124534 INFO: Resetting torch num_threads to 100
1 day, 19:30:41.376329 INFO: Removing fragments below FDR threshold
1 day, 19:30:41.469179 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:30:41.469484 PROGRESS: Total precursors accumulated: 0
1 day, 19:30:41.469562 PROGRESS: Target precursors: 0 (0.00%)
1 day, 19:30:41.469617 PROGRESS: Decoy precursors: 0 (0.00%)
1 day, 19:30:41.469671 PROGRESS: 
1 day, 19:30:41.469722 PROGRESS: Precursor Summary:
1 day, 19:30:41.469860 PROGRESS: 
1 day, 19:30:41.469927 PROGRESS: Protein Summary:
1 day, 19:30:41.470003 PROGRESS: =========================================================================
1 day, 19:30:41.613632 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 19:31:04.685991 PROGRESS: Processing search outputs
1 day, 19:31:04.686146 PROGRESS: Performing protein grouping and FDR
1 day, 19:31:04.686187 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 19:31:04.721499 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 19:31:04.796762 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 19:31:04.802194 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 19:31:04.841212 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 19:31:04.849621 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 19:31:04.857166 INFO: Building combined output
1 day, 19:31:05.122480 INFO: Performing protein inference
1 day, 19:31:05.268548 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
1 day, 19:31:23.724998 INFO: Performing protein FDR
1 day, 19:31:28.002651 INFO: Normalizing q-values using 12,421 targets and 1,281 decoys
1 day, 19:31:28.011658 INFO: Test AUC: 0.891
1 day, 19:31:28.011713 INFO: Train AUC: 0.911
1 day, 19:31:28.011741 INFO: AUC difference: 2.17%
1 day, 19:31:29.494340 PROGRESS: ================ Protein FDR =================
1 day, 19:31:29.494478 PROGRESS: Unique protein groups in output
1 day, 19:31:29.494509 PROGRESS:   1% protein FDR: 8,253
1 day, 19:31:29.494531 PROGRESS: 
1 day, 19:31:29.494549 PROGRESS: Unique precursor in output
1 day, 19:31:29.494567 PROGRESS:   1% protein FDR: 82,039
1 day, 19:31:29.494585 PROGRESS: ================================================
1 day, 19:31:29.513350 PROGRESS: Building search statistics
1 day, 19:31:29.543371 INFO: Loaded OptimizationManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/optimization_manager.pkl
1 day, 19:31:29.543565 INFO: Initializing OptimizationManager
1 day, 19:31:29.543798 INFO: Loaded CalibrationManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/calibration_manager.pkl
1 day, 19:31:29.543873 INFO: Initializing CalibrationManager
1 day, 19:31:29.544065 INFO: Loaded RawFileManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/raw_file_manager.pkl
1 day, 19:31:29.544140 INFO: Initializing RawFileManager
1 day, 19:31:29.563887 INFO: Loaded OptimizationManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/optimization_manager.pkl
1 day, 19:31:29.564087 INFO: Initializing OptimizationManager
1 day, 19:31:29.564306 INFO: Loaded CalibrationManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/calibration_manager.pkl
1 day, 19:31:29.564389 INFO: Initializing CalibrationManager
1 day, 19:31:29.564577 INFO: Loaded RawFileManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/raw_file_manager.pkl
1 day, 19:31:29.564655 INFO: Initializing RawFileManager
1 day, 19:31:29.572140 INFO: Loaded OptimizationManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/optimization_manager.pkl
1 day, 19:31:29.572483 INFO: Initializing OptimizationManager
1 day, 19:31:29.572680 INFO: Loaded CalibrationManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/calibration_manager.pkl
1 day, 19:31:29.572757 INFO: Initializing CalibrationManager
1 day, 19:31:29.572947 INFO: Loaded RawFileManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/raw_file_manager.pkl
1 day, 19:31:29.573020 INFO: Initializing RawFileManager
1 day, 19:31:29.593644 INFO: Loaded OptimizationManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/optimization_manager.pkl
1 day, 19:31:29.593854 INFO: Initializing OptimizationManager
1 day, 19:31:29.594070 INFO: Loaded CalibrationManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/calibration_manager.pkl
1 day, 19:31:29.594148 INFO: Initializing CalibrationManager
1 day, 19:31:29.594352 INFO: Loaded RawFileManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/raw_file_manager.pkl
1 day, 19:31:29.594429 INFO: Initializing RawFileManager
1 day, 19:31:29.602222 INFO: Loaded OptimizationManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/optimization_manager.pkl
1 day, 19:31:29.602330 INFO: Initializing OptimizationManager
1 day, 19:31:29.602511 INFO: Loaded CalibrationManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/calibration_manager.pkl
1 day, 19:31:29.602584 INFO: Initializing CalibrationManager
1 day, 19:31:29.602753 INFO: Loaded RawFileManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/raw_file_manager.pkl
1 day, 19:31:29.602828 INFO: Initializing RawFileManager
1 day, 19:31:29.608904 INFO: Loaded OptimizationManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/optimization_manager.pkl
1 day, 19:31:29.609002 INFO: Initializing OptimizationManager
1 day, 19:31:29.609194 INFO: Loaded CalibrationManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/calibration_manager.pkl
1 day, 19:31:29.609266 INFO: Initializing CalibrationManager
1 day, 19:31:29.609430 INFO: Loaded RawFileManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/raw_file_manager.pkl
1 day, 19:31:29.609502 INFO: Initializing RawFileManager
1 day, 19:31:29.610585 INFO: Writing stat output to disk
1 day, 19:31:29.610637 INFO: Saving run_output/alphadia_1.10_defaultMBR/library/stat.tsv to disk
1 day, 19:31:29.613763 PROGRESS: Building internal statistics
1 day, 19:31:29.613954 INFO: Loaded TimingManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/timing_manager.pkl
1 day, 19:31:29.613994 INFO: Initializing TimingManager
1 day, 19:31:29.614203 INFO: Loaded TimingManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/timing_manager.pkl
1 day, 19:31:29.614244 INFO: Initializing TimingManager
1 day, 19:31:29.614412 INFO: Loaded TimingManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/timing_manager.pkl
1 day, 19:31:29.614449 INFO: Initializing TimingManager
1 day, 19:31:29.614605 INFO: Loaded TimingManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/timing_manager.pkl
1 day, 19:31:29.614641 INFO: Initializing TimingManager
1 day, 19:31:29.614794 INFO: Loaded TimingManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/timing_manager.pkl
1 day, 19:31:29.614830 INFO: Initializing TimingManager
1 day, 19:31:29.614977 INFO: Loaded TimingManager from run_output/alphadia_1.10_defaultMBR/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/timing_manager.pkl
1 day, 19:31:29.615012 INFO: Initializing TimingManager
1 day, 19:31:29.615341 INFO: Writing internal output to disk
1 day, 19:31:29.615383 INFO: Saving run_output/alphadia_1.10_defaultMBR/library/internal.tsv to disk
1 day, 19:31:29.615767 PROGRESS: Performing label free quantification
1 day, 19:31:29.637040 INFO: Accumulating fragment data
1 day, 19:31:29.637197 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 19:31:29.796524 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 19:31:30.589436 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 19:31:30.937771 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 19:31:32.038258 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 19:31:32.882965 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 19:31:33.457048 PROGRESS: Performing label free quantification on the precursor level
1 day, 19:31:33.457177 INFO: Filtering fragments by quality
1 day, 19:31:33.691065 INFO: Performing label-free quantification using directLFQ
1 day, 19:31:34.064174 INFO: to few values for normalization without missing values. Including missing values
1 day, 19:31:35.235312 INFO: 82039 lfq-groups total
1 day, 19:32:44.930786 INFO: using 100 processes
1 day, 19:32:45.273114 INFO: lfq-object 0
1 day, 19:32:45.366448 INFO: lfq-object 100
1 day, 19:32:45.411746 INFO: lfq-object 300
1 day, 19:32:45.458503 INFO: lfq-object 200
1 day, 19:32:45.477567 INFO: lfq-object 500
1 day, 19:32:45.503522 INFO: lfq-object 400
1 day, 19:32:45.523110 INFO: lfq-object 700
1 day, 19:32:45.542461 INFO: lfq-object 900
1 day, 19:32:45.565803 INFO: lfq-object 600
1 day, 19:32:45.613052 INFO: lfq-object 1100
1 day, 19:32:45.622195 INFO: lfq-object 800
1 day, 19:32:45.637378 INFO: lfq-object 1000
1 day, 19:32:45.667165 INFO: lfq-object 1300
1 day, 19:32:45.702373 INFO: lfq-object 1200
1 day, 19:32:45.750244 INFO: lfq-object 1500
1 day, 19:32:45.762196 INFO: lfq-object 1400
1 day, 19:32:45.840820 INFO: lfq-object 1600
1 day, 19:32:45.852813 INFO: lfq-object 1700
1 day, 19:32:45.949342 INFO: lfq-object 1800
1 day, 19:32:45.953471 INFO: lfq-object 1900
1 day, 19:32:46.043139 INFO: lfq-object 2000
1 day, 19:32:46.053246 INFO: lfq-object 2100
1 day, 19:32:46.139682 INFO: lfq-object 2300
1 day, 19:32:46.147605 INFO: lfq-object 2200
1 day, 19:32:46.187345 INFO: lfq-object 2500
1 day, 19:32:46.233005 INFO: lfq-object 2400
1 day, 19:32:46.274402 INFO: lfq-object 2700
1 day, 19:32:46.276997 INFO: lfq-object 2600
1 day, 19:32:46.337434 INFO: lfq-object 2900
1 day, 19:32:46.367722 INFO: lfq-object 2800
1 day, 19:32:46.402733 INFO: lfq-object 3100
1 day, 19:32:46.425839 INFO: lfq-object 3000
1 day, 19:32:46.466044 INFO: lfq-object 3300
1 day, 19:32:46.499328 INFO: lfq-object 3200
1 day, 19:32:46.554735 INFO: lfq-object 3400
1 day, 19:32:46.626505 INFO: lfq-object 3600
1 day, 19:32:46.648666 INFO: lfq-object 3500
1 day, 19:32:46.661524 INFO: lfq-object 3800
1 day, 19:32:46.720782 INFO: lfq-object 3700
1 day, 19:32:46.749845 INFO: lfq-object 3900
1 day, 19:32:46.766085 INFO: lfq-object 4000
1 day, 19:32:46.834126 INFO: lfq-object 4200
1 day, 19:32:46.858511 INFO: lfq-object 4100
1 day, 19:32:46.914034 INFO: lfq-object 4400
1 day, 19:32:46.932037 INFO: lfq-object 4300
1 day, 19:32:46.996849 INFO: lfq-object 4600
1 day, 19:32:47.001529 INFO: lfq-object 4500
1 day, 19:32:47.060791 INFO: lfq-object 4800
1 day, 19:32:47.089678 INFO: lfq-object 4700
1 day, 19:32:47.146884 INFO: lfq-object 5000
1 day, 19:32:47.151121 INFO: lfq-object 4900
1 day, 19:32:47.211093 INFO: lfq-object 5200
1 day, 19:32:47.243561 INFO: lfq-object 5100
1 day, 19:32:47.285552 INFO: lfq-object 5400
1 day, 19:32:47.316387 INFO: lfq-object 5300
1 day, 19:32:47.362737 INFO: lfq-object 5600
1 day, 19:32:47.374705 INFO: lfq-object 5500
1 day, 19:32:47.424594 INFO: lfq-object 5800
1 day, 19:32:47.474960 INFO: lfq-object 5700
1 day, 19:32:47.497708 INFO: lfq-object 6000
1 day, 19:32:47.516886 INFO: lfq-object 5900
1 day, 19:32:47.592781 INFO: lfq-object 6100
1 day, 19:32:50.315716 INFO: lfq-object 6200
1 day, 19:32:50.409244 INFO: lfq-object 6400
1 day, 19:32:50.412331 INFO: lfq-object 6300
1 day, 19:32:50.443786 INFO: lfq-object 6600
1 day, 19:32:50.499854 INFO: lfq-object 6500
1 day, 19:32:50.535037 INFO: lfq-object 6700
1 day, 19:32:50.552907 INFO: lfq-object 6800
1 day, 19:32:50.651141 INFO: lfq-object 6900
1 day, 19:32:50.741263 INFO: lfq-object 7100
1 day, 19:32:50.745575 INFO: lfq-object 7000
1 day, 19:32:50.834388 INFO: lfq-object 7200
1 day, 19:32:50.840480 INFO: lfq-object 7300
1 day, 19:32:50.895841 INFO: lfq-object 7500
1 day, 19:32:50.933276 INFO: lfq-object 7400
1 day, 19:32:50.946402 INFO: lfq-object 7700
1 day, 19:32:50.995332 INFO: lfq-object 7600
1 day, 19:32:51.020378 INFO: lfq-object 7900
1 day, 19:32:51.046095 INFO: lfq-object 7800
1 day, 19:32:51.097741 INFO: lfq-object 8100
1 day, 19:32:51.118781 INFO: lfq-object 8000
1 day, 19:32:51.150203 INFO: lfq-object 8300
1 day, 19:32:51.189332 INFO: lfq-object 8200
1 day, 19:32:51.237900 INFO: lfq-object 8400
1 day, 19:32:51.261283 INFO: lfq-object 8500
1 day, 19:32:51.313970 INFO: lfq-object 8700
1 day, 19:32:51.350426 INFO: lfq-object 8600
1 day, 19:32:51.408949 INFO: lfq-object 8800
1 day, 19:32:51.411553 INFO: lfq-object 8900
1 day, 19:32:51.487197 INFO: lfq-object 9100
1 day, 19:32:51.501266 INFO: lfq-object 9000
1 day, 19:32:51.574499 INFO: lfq-object 9200
1 day, 19:32:51.601446 INFO: lfq-object 9300
1 day, 19:32:51.677857 INFO: lfq-object 9500
1 day, 19:32:51.696799 INFO: lfq-object 9400
1 day, 19:32:51.738285 INFO: lfq-object 9700
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1 day, 19:32:51.831054 INFO: lfq-object 9800
1 day, 19:32:51.831910 INFO: lfq-object 9900
1 day, 19:32:51.859539 INFO: lfq-object 10100
1 day, 19:32:51.925732 INFO: lfq-object 10000
1 day, 19:32:51.945148 INFO: lfq-object 10200
1 day, 19:32:51.947128 INFO: lfq-object 10300
1 day, 19:32:52.051992 INFO: lfq-object 10400
1 day, 19:32:52.140737 INFO: lfq-object 10600
1 day, 19:32:52.144667 INFO: lfq-object 10500
1 day, 19:32:52.185072 INFO: lfq-object 10800
1 day, 19:32:52.230304 INFO: lfq-object 10700
1 day, 19:32:52.267589 INFO: lfq-object 11000
1 day, 19:32:52.278208 INFO: lfq-object 10900
1 day, 19:32:52.358869 INFO: lfq-object 11100
1 day, 19:32:52.383165 INFO: lfq-object 11200
1 day, 19:32:52.460164 INFO: lfq-object 11400
1 day, 19:32:52.478618 INFO: lfq-object 11300
1 day, 19:32:52.552970 INFO: lfq-object 11500
1 day, 19:32:52.562751 INFO: lfq-object 11600
1 day, 19:32:52.603898 INFO: lfq-object 11800
1 day, 19:32:52.659221 INFO: lfq-object 11700
1 day, 19:32:52.678877 INFO: lfq-object 12000
1 day, 19:32:52.694620 INFO: lfq-object 11900
1 day, 19:32:52.750914 INFO: lfq-object 12200
1 day, 19:32:52.778615 INFO: lfq-object 12100
1 day, 19:32:52.829533 INFO: lfq-object 12400
1 day, 19:32:52.846181 INFO: lfq-object 12300
1 day, 19:32:52.852449 INFO: lfq-object 12600
1 day, 19:32:52.924284 INFO: lfq-object 12500
1 day, 19:32:52.943110 INFO: lfq-object 12700
1 day, 19:32:52.950171 INFO: lfq-object 12800
1 day, 19:32:53.010892 INFO: lfq-object 13000
1 day, 19:32:53.045636 INFO: lfq-object 12900
1 day, 19:32:53.067510 INFO: lfq-object 13200
1 day, 19:32:53.106057 INFO: lfq-object 13100
1 day, 19:32:53.143606 INFO: lfq-object 13400
1 day, 19:32:53.161732 INFO: lfq-object 13300
1 day, 19:32:53.184836 INFO: lfq-object 13600
1 day, 19:32:53.236568 INFO: lfq-object 13500
1 day, 19:32:53.276448 INFO: lfq-object 13700
1 day, 19:32:53.370008 INFO: lfq-object 13800
1 day, 19:32:53.369960 INFO: lfq-object 13900
1 day, 19:32:53.462848 INFO: lfq-object 14000
1 day, 19:32:53.472492 INFO: lfq-object 14100
1 day, 19:32:53.546862 INFO: lfq-object 14300
1 day, 19:32:53.561125 INFO: lfq-object 14200
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1 day, 19:33:39.956500 INFO: Writing precursor output to disk
1 day, 19:33:39.956800 INFO: Saving run_output/alphadia_1.10_defaultMBR/library/precursor.matrix.tsv to disk
1 day, 19:33:40.256849 PROGRESS: Performing label free quantification on the pg level
1 day, 19:33:40.256957 INFO: Filtering fragments by quality
1 day, 19:33:40.501283 INFO: Performing label-free quantification using directLFQ
1 day, 19:33:40.585169 INFO: to few values for normalization without missing values. Including missing values
1 day, 19:33:40.637851 INFO: 8253 lfq-groups total
1 day, 19:34:38.049301 INFO: using 100 processes
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1 day, 19:34:39.251107 INFO: lfq-object 2800
1 day, 19:34:39.306841 INFO: lfq-object 2900
1 day, 19:34:39.360645 INFO: lfq-object 3000
1 day, 19:34:39.406588 INFO: lfq-object 3100
1 day, 19:34:39.457697 INFO: lfq-object 3200
1 day, 19:34:39.495131 INFO: lfq-object 3300
1 day, 19:34:39.551625 INFO: lfq-object 3400
1 day, 19:34:39.605068 INFO: lfq-object 3500
1 day, 19:34:39.659521 INFO: lfq-object 3600
1 day, 19:34:39.689733 INFO: lfq-object 3700
1 day, 19:34:39.747677 INFO: lfq-object 3800
1 day, 19:34:39.777558 INFO: lfq-object 3900
1 day, 19:34:39.820688 INFO: lfq-object 4000
1 day, 19:34:39.863634 INFO: lfq-object 4100
1 day, 19:34:39.911435 INFO: lfq-object 4200
1 day, 19:34:39.984066 INFO: lfq-object 4400
1 day, 19:34:39.994783 INFO: lfq-object 4300
1 day, 19:34:40.032037 INFO: lfq-object 4500
1 day, 19:34:40.067412 INFO: lfq-object 4600
1 day, 19:34:40.141730 INFO: lfq-object 4700
1 day, 19:34:40.171113 INFO: lfq-object 4800
1 day, 19:34:40.196626 INFO: lfq-object 4900
1 day, 19:34:40.235079 INFO: lfq-object 5000
1 day, 19:34:40.306247 INFO: lfq-object 5100
1 day, 19:34:40.353687 INFO: lfq-object 5200
1 day, 19:34:40.392111 INFO: lfq-object 5300
1 day, 19:34:40.438839 INFO: lfq-object 5400
1 day, 19:34:40.496005 INFO: lfq-object 5500
1 day, 19:34:40.550163 INFO: lfq-object 5600
1 day, 19:34:40.590546 INFO: lfq-object 5700
1 day, 19:34:40.634358 INFO: lfq-object 5800
1 day, 19:34:40.706251 INFO: lfq-object 5900
1 day, 19:34:40.768299 INFO: lfq-object 6000
1 day, 19:34:40.804901 INFO: lfq-object 6100
1 day, 19:34:40.827110 INFO: lfq-object 6200
1 day, 19:34:40.854682 INFO: lfq-object 6300
1 day, 19:34:40.933943 INFO: lfq-object 6400
1 day, 19:34:40.942538 INFO: lfq-object 6500
1 day, 19:34:40.970484 INFO: lfq-object 6600
1 day, 19:34:41.018735 INFO: lfq-object 6700
1 day, 19:34:41.080607 INFO: lfq-object 6800
1 day, 19:34:41.117091 INFO: lfq-object 6900
1 day, 19:34:41.153878 INFO: lfq-object 7000
1 day, 19:34:41.190946 INFO: lfq-object 7100
1 day, 19:34:41.249511 INFO: lfq-object 7200
1 day, 19:34:41.303601 INFO: lfq-object 7300
1 day, 19:34:41.342445 INFO: lfq-object 7400
1 day, 19:34:41.389215 INFO: lfq-object 7500
1 day, 19:34:41.452620 INFO: lfq-object 7600
1 day, 19:34:41.485219 INFO: lfq-object 7700
1 day, 19:34:41.511447 INFO: lfq-object 7800
1 day, 19:34:41.553454 INFO: lfq-object 7900
1 day, 19:34:41.612118 INFO: lfq-object 8000
1 day, 19:34:41.656154 INFO: lfq-object 8100
1 day, 19:34:41.693172 INFO: lfq-object 8200
1 day, 19:34:44.619056 INFO: Writing pg output to disk
1 day, 19:34:44.619234 INFO: Saving run_output/alphadia_1.10_defaultMBR/library/pg.matrix.tsv to disk
1 day, 19:34:44.723868 INFO: Writing psm output to disk
1 day, 19:34:44.724012 INFO: Saving run_output/alphadia_1.10_defaultMBR/library/precursors.tsv to disk
1 day, 19:34:52.536367 PROGRESS: Building spectral library
1 day, 19:34:52.560998 INFO: Building MBR spectral library
1 day, 19:34:52.561147 INFO: Running MbrLibraryBuilder
1 day, 19:34:53.913669 INFO: MBR spectral library contains 82,039 precursors, 8,253 proteins
1 day, 19:34:53.913809 INFO: Writing MBR spectral library to disk
1 day, 19:34:54.925928 PROGRESS: =================== Search Finished ===================
1 day, 19:34:55.898103 INFO: Running step 'mbr'
1 day, 19:34:55.901054 INFO: Extracted extra_config from previous step: defaultdict(<class 'dict'>, {'search': {'target_ms1_tolerance': 10.0, 'target_ms2_tolerance': 15.0}})
1 day, 19:34:55.901194 INFO: loading config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
1 day, 19:34:55.912693 INFO: loading additional config provided via CLI
1 day, 19:34:55.912766 INFO: loading additional config provided via CLI parameters
1 day, 19:34:55.913016 INFO: Updating config with 'user defined'
1 day, 19:34:55.913129 INFO: Updating config with 'user defined (cli)'
1 day, 19:34:55.913154 INFO: Updating config with 'multistep search'
1 day, 19:34:55.913196 INFO: ├──version: 1
1 day, 19:34:55.913222 INFO: ├──workflow_name: None
1 day, 19:34:55.913247 INFO: [32;20m├──output_directory: run_output/alphadia_1.10_defaultMBR [multistep search, default: None][0m
1 day, 19:34:55.913270 INFO: [32;20m├──library_path: run_output/alphadia_1.10_defaultMBR/library/speclib.mbr.hdf [multistep search, default: None][0m
1 day, 19:34:55.913292 INFO: ├──raw_paths:
1 day, 19:34:55.913311 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d [user defined (cli), default: None][0m
1 day, 19:34:55.913331 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d [user defined (cli), default: None][0m
1 day, 19:34:55.913351 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d [user defined (cli), default: None][0m
1 day, 19:34:55.913369 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d [user defined (cli), default: None][0m
1 day, 19:34:55.913402 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d [user defined (cli), default: None][0m
1 day, 19:34:55.913421 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d [user defined (cli), default: None][0m
1 day, 19:34:55.913440 INFO: ├──fasta_paths:
1 day, 19:34:55.913460 INFO: ├──quant_directory: None
1 day, 19:34:55.913479 INFO: ├──general
1 day, 19:34:55.913501 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
1 day, 19:34:55.913525 INFO: │   ├──transfer_step_enabled: False
1 day, 19:34:55.913544 INFO: │   ├──mbr_step_enabled: True
1 day, 19:34:55.913563 INFO: │   ├──reuse_calibration: False
1 day, 19:34:55.913583 INFO: │   ├──reuse_quant: False
1 day, 19:34:55.913601 INFO: │   ├──astral_ms1: False
1 day, 19:34:55.913619 INFO: │   ├──log_level: INFO
1 day, 19:34:55.913639 INFO: │   ├──mmap_detector_events: False
1 day, 19:34:55.913661 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
1 day, 19:34:55.913681 INFO: │   ├──save_library: True
1 day, 19:34:55.913701 INFO: │   └──save_mbr_library: True
1 day, 19:34:55.913720 INFO: ├──library_loading
1 day, 19:34:55.913742 INFO: │   └──rt_heuristic: 180
1 day, 19:34:55.913760 INFO: ├──library_prediction
1 day, 19:34:55.913779 INFO: │   ├──enabled: False
1 day, 19:34:55.913799 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
1 day, 19:34:55.913818 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
1 day, 19:34:55.913836 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
1 day, 19:34:55.913856 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
1 day, 19:34:55.913875 INFO: │   ├──missed_cleavages: 1
1 day, 19:34:55.913893 INFO: │   ├──precursor_len:
1 day, 19:34:55.913913 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
1 day, 19:34:55.913932 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
1 day, 19:34:55.913949 INFO: │   ├──precursor_charge:
1 day, 19:34:55.913969 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
1 day, 19:34:55.913986 INFO: │   │   [32;20m- 4[0m
1 day, 19:34:55.914004 INFO: │   ├──precursor_mz:
1 day, 19:34:55.914023 INFO: │   │   [32;20m- 400[0m
1 day, 19:34:55.914041 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
1 day, 19:34:55.914059 INFO: │   ├──fragment_mz:
1 day, 19:34:55.914078 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
1 day, 19:34:55.914099 INFO: │   │   [32;20m- 2000[0m
1 day, 19:34:55.914117 INFO: │   ├──nce: 25
1 day, 19:34:55.914136 INFO: │   ├──fragment_types:
1 day, 19:34:55.914155 INFO: │   │   [32;20m- b[0m
1 day, 19:34:55.914172 INFO: │   │   [32;20m- y[0m
1 day, 19:34:55.914193 INFO: │   ├──max_fragment_charge: 2
1 day, 19:34:55.914212 INFO: │   [32;20m├──instrument: timsTOF [user defined, default: Lumos][0m
1 day, 19:34:55.914230 INFO: │   ├──peptdeep_model_path: None
1 day, 19:34:55.914251 INFO: │   └──peptdeep_model_type: generic
1 day, 19:34:55.914269 INFO: ├──custom_modifications:
1 day, 19:34:55.914289 INFO: │   ├──name: Dimethyl:d12@K
1 day, 19:34:55.914309 INFO: │   └──composition: H(-2)2H(8)13C(2)
1 day, 19:34:55.914327 INFO: │   ├──name: Dimethyl:d12@Any_N-term
1 day, 19:34:55.914346 INFO: │   └──composition: H(-2)2H(8)13C(2)
1 day, 19:34:55.914366 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
1 day, 19:34:55.914384 INFO: │   └──composition: H(-2)2H(8)13C(2)
1 day, 19:34:55.914402 INFO: │   ├──name: mTRAQ:d12@K
1 day, 19:34:55.914422 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
1 day, 19:34:55.914440 INFO: │   ├──name: mTRAQ:d12@Any_N-term
1 day, 19:34:55.914457 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
1 day, 19:34:55.914484 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
1 day, 19:34:55.914501 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
1 day, 19:34:55.914522 INFO: │   ├──name: Label:13C(12)@K
1 day, 19:34:55.914543 INFO: │   └──composition: C(12)
1 day, 19:34:55.914561 INFO: ├──search
1 day, 19:34:55.914585 INFO: │   [32;20m├──target_ms1_tolerance: 10.0 [multistep search, default: 5][0m
1 day, 19:34:55.914605 INFO: │   [32;20m├──target_ms2_tolerance: 15.0 [multistep search, default: 10][0m
1 day, 19:34:55.914623 INFO: │   ├──target_rt_tolerance: 0
1 day, 19:34:55.914644 INFO: │   ├──target_mobility_tolerance: 0
1 day, 19:34:55.914662 INFO: │   ├──quant_window: 3
1 day, 19:34:55.914681 INFO: │   [32;20m├──target_num_candidates: 2 [user defined, default: 3][0m
1 day, 19:34:55.914700 INFO: │   ├──channel_filter: 
1 day, 19:34:55.914719 INFO: │   ├──exclude_shared_ions: True
1 day, 19:34:55.914737 INFO: │   ├──compete_for_fragments: True
1 day, 19:34:55.914756 INFO: │   ├──quant_all: True
1 day, 19:34:55.914775 INFO: │   ├──top_k_fragments: 12
1 day, 19:34:55.914796 INFO: │   └──experimental_xic: True
1 day, 19:34:55.914817 INFO: ├──calibration
1 day, 19:34:55.914837 INFO: │   ├──batch_size: 8000
1 day, 19:34:55.914857 INFO: │   ├──optimization_lock_target: 200
1 day, 19:34:55.914876 INFO: │   ├──max_steps: 20
1 day, 19:34:55.914894 INFO: │   ├──min_steps: 2
1 day, 19:34:55.914914 INFO: │   ├──max_skips: 1
1 day, 19:34:55.914932 INFO: │   ├──norm_rt_mode: linear
1 day, 19:34:55.914951 INFO: │   ├──max_fragments: 5000
1 day, 19:34:55.914976 INFO: │   └──min_correlation: 0.7
1 day, 19:34:55.914994 INFO: ├──search_initial
1 day, 19:34:55.915012 INFO: │   ├──initial_num_candidates: 1
1 day, 19:34:55.915032 INFO: │   ├──initial_ms1_tolerance: 30
1 day, 19:34:55.915050 INFO: │   ├──initial_ms2_tolerance: 30
1 day, 19:34:55.915068 INFO: │   ├──initial_mobility_tolerance: 0.1
1 day, 19:34:55.915089 INFO: │   └──initial_rt_tolerance: 0.5
1 day, 19:34:55.915107 INFO: ├──selection_config
1 day, 19:34:55.915126 INFO: │   ├──peak_len_rt: 10.0
1 day, 19:34:55.915148 INFO: │   ├──sigma_scale_rt: 0.5
1 day, 19:34:55.915166 INFO: │   ├──peak_len_mobility: 0.01
1 day, 19:34:55.915184 INFO: │   ├──sigma_scale_mobility: 1.0
1 day, 19:34:55.915206 INFO: │   ├──top_k_precursors: 3
1 day, 19:34:55.915224 INFO: │   ├──kernel_size: 30
1 day, 19:34:55.915244 INFO: │   ├──f_mobility: 1.0
1 day, 19:34:55.915263 INFO: │   ├──f_rt: 0.99
1 day, 19:34:55.915281 INFO: │   ├──center_fraction: 0.5
1 day, 19:34:55.915301 INFO: │   ├──min_size_mobility: 8
1 day, 19:34:55.915319 INFO: │   ├──min_size_rt: 3
1 day, 19:34:55.915336 INFO: │   ├──max_size_mobility: 20
1 day, 19:34:55.915355 INFO: │   ├──max_size_rt: 15
1 day, 19:34:55.915374 INFO: │   ├──group_channels: False
1 day, 19:34:55.915393 INFO: │   ├──use_weighted_score: True
1 day, 19:34:55.915413 INFO: │   ├──join_close_candidates: False
1 day, 19:34:55.915431 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
1 day, 19:34:55.915449 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
1 day, 19:34:55.915471 INFO: ├──scoring_config
1 day, 19:34:55.915489 INFO: │   ├──score_grouped: False
1 day, 19:34:55.915507 INFO: │   ├──top_k_isotopes: 3
1 day, 19:34:55.915528 INFO: │   ├──reference_channel: -1
1 day, 19:34:55.915545 INFO: │   ├──precursor_mz_tolerance: 10
1 day, 19:34:55.915564 INFO: │   └──fragment_mz_tolerance: 15
1 day, 19:34:55.915586 INFO: ├──library_multiplexing
1 day, 19:34:55.915604 INFO: │   ├──enabled: False
1 day, 19:34:55.915623 INFO: │   ├──input_channel: 0
1 day, 19:34:55.915649 INFO: │   └──multiplex_mapping:
1 day, 19:34:55.915668 INFO: ├──multiplexing
1 day, 19:34:55.915686 INFO: │   ├──enabled: False
1 day, 19:34:55.915706 INFO: │   ├──target_channels: 4,8
1 day, 19:34:55.915724 INFO: │   ├──decoy_channel: 12
1 day, 19:34:55.915742 INFO: │   ├──reference_channel: 0
1 day, 19:34:55.915763 INFO: │   └──competetive_scoring: True
1 day, 19:34:55.915781 INFO: ├──fdr
1 day, 19:34:55.915802 INFO: │   ├──fdr: 0.01
1 day, 19:34:55.915821 INFO: │   ├──group_level: proteins
1 day, 19:34:55.915841 INFO: │   [32;20m├──inference_strategy: library [multistep search, default: heuristic][0m
1 day, 19:34:55.915861 INFO: │   ├──competetive_scoring: True
1 day, 19:34:55.915882 INFO: │   ├──keep_decoys: False
1 day, 19:34:55.915901 INFO: │   ├──channel_wise_fdr: False
1 day, 19:34:55.915923 INFO: │   ├──enable_two_step_classifier: False
1 day, 19:34:55.915942 INFO: │   ├──two_step_classifier_max_iterations: 5
1 day, 19:34:55.915962 INFO: │   └──enable_nn_hyperparameter_tuning: False
1 day, 19:34:55.915981 INFO: ├──search_output
1 day, 19:34:55.916001 INFO: │   ├──file_format: tsv
1 day, 19:34:55.916019 INFO: │   ├──peptide_level_lfq: False
1 day, 19:34:55.916039 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
1 day, 19:34:55.916057 INFO: │   ├──min_k_fragments: 12
1 day, 19:34:55.916077 INFO: │   ├──min_correlation: 0.9
1 day, 19:34:55.916096 INFO: │   ├──num_samples_quadratic: 50
1 day, 19:34:55.916114 INFO: │   ├──min_nonnan: 3
1 day, 19:34:55.916136 INFO: │   ├──normalize_lfq: True
1 day, 19:34:55.916157 INFO: │   └──save_fragment_quant_matrix: False
1 day, 19:34:55.916176 INFO: ├──optimization
1 day, 19:34:55.916196 INFO: │   ├──order_of_optimization: None
1 day, 19:34:55.916216 INFO: │   ├──ms2_error
1 day, 19:34:55.916236 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1 day, 19:34:55.916257 INFO: │   │   ├──targeted_update_factor: 1.0
1 day, 19:34:55.916275 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1 day, 19:34:55.916294 INFO: │   │   ├──automatic_update_factor: 1.1
1 day, 19:34:55.916314 INFO: │   │   ├──try_narrower_values: True
1 day, 19:34:55.916332 INFO: │   │   ├──maximal_decrease: 0.5
1 day, 19:34:55.916352 INFO: │   │   ├──favour_narrower_optimum: False
1 day, 19:34:55.916373 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1 day, 19:34:55.916391 INFO: │   ├──ms1_error
1 day, 19:34:55.916410 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1 day, 19:34:55.916430 INFO: │   │   ├──targeted_update_factor: 1.0
1 day, 19:34:55.916448 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1 day, 19:34:55.916466 INFO: │   │   ├──automatic_update_factor: 1.1
1 day, 19:34:55.916485 INFO: │   │   ├──try_narrower_values: False
1 day, 19:34:55.916504 INFO: │   │   ├──maximal_decrease: 0.2
1 day, 19:34:55.916522 INFO: │   │   ├──favour_narrower_optimum: False
1 day, 19:34:55.916542 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1 day, 19:34:55.916560 INFO: │   ├──mobility_error
1 day, 19:34:55.916578 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1 day, 19:34:55.916598 INFO: │   │   ├──targeted_update_factor: 1.0
1 day, 19:34:55.916615 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1 day, 19:34:55.916634 INFO: │   │   ├──automatic_update_factor: 1.1
1 day, 19:34:55.916654 INFO: │   │   ├──try_narrower_values: False
1 day, 19:34:55.916672 INFO: │   │   ├──maximal_decrease: 0.2
1 day, 19:34:55.916694 INFO: │   │   ├──favour_narrower_optimum: False
1 day, 19:34:55.916713 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1 day, 19:34:55.916736 INFO: │   └──rt_error
1 day, 19:34:55.916757 INFO: │       ├──targeted_update_percentile_range: 0.95
1 day, 19:34:55.916777 INFO: │       ├──targeted_update_factor: 1.0
1 day, 19:34:55.916797 INFO: │       ├──automatic_update_percentile_range: 0.99
1 day, 19:34:55.916817 INFO: │       ├──automatic_update_factor: 1.1
1 day, 19:34:55.916834 INFO: │       ├──try_narrower_values: True
1 day, 19:34:55.916852 INFO: │       ├──maximal_decrease: 0.2
1 day, 19:34:55.916872 INFO: │       ├──favour_narrower_optimum: True
1 day, 19:34:55.916891 INFO: │       └──maximum_decrease_from_maximum: 0.1
1 day, 19:34:55.916909 INFO: ├──optimization_manager
1 day, 19:34:55.916929 INFO: │   ├──fwhm_rt: 5
1 day, 19:34:55.916948 INFO: │   ├──fwhm_mobility: 0.01
1 day, 19:34:55.916966 INFO: │   └──score_cutoff: 0
1 day, 19:34:55.916985 INFO: ├──transfer_library
1 day, 19:34:55.917004 INFO: │   ├──enabled: False
1 day, 19:34:55.917022 INFO: │   ├──fragment_types:
1 day, 19:34:55.917049 INFO: │   │   [32;20m- b[0m
1 day, 19:34:55.917067 INFO: │   │   [32;20m- y[0m
1 day, 19:34:55.917085 INFO: │   ├──max_charge: 2
1 day, 19:34:55.917105 INFO: │   ├──top_k_samples: 3
1 day, 19:34:55.917123 INFO: │   ├──norm_delta_max: True
1 day, 19:34:55.917141 INFO: │   ├──precursor_correlation_cutoff: 0.5
1 day, 19:34:55.917162 INFO: │   └──fragment_correlation_ratio: 0.75
1 day, 19:34:55.917181 INFO: └──transfer_learning
1 day, 19:34:55.917199 INFO:     ├──enabled: False
1 day, 19:34:55.917219 INFO:     ├──batch_size: 2000
1 day, 19:34:55.917238 INFO:     ├──max_lr: 0.0001
1 day, 19:34:55.917256 INFO:     ├──train_fraction: 0.7
1 day, 19:34:55.917276 INFO:     ├──validation_fraction: 0.2
1 day, 19:34:55.917296 INFO:     ├──test_fraction: 0.1
1 day, 19:34:55.917315 INFO:     ├──test_interval: 1
1 day, 19:34:55.917334 INFO:     ├──lr_patience: 3
1 day, 19:34:55.917353 INFO:     ├──epochs: 51
1 day, 19:34:55.917371 INFO:     ├──warmup_epochs: 5
1 day, 19:34:55.917390 INFO:     ├──nce: 25
1 day, 19:34:55.917409 INFO:     [32;20m└──instrument: timsTOF [user defined, default: Lumos][0m
1 day, 19:34:55.922755 INFO: Registering 7 custom modifications
1 day, 19:34:55.938542 INFO: Running DynamicLoader
1 day, 19:34:55.938639 INFO: Loading .hdf library from run_output/alphadia_1.10_defaultMBR/library/speclib.mbr.hdf
1 day, 19:34:56.325090 INFO: Running PrecursorInitializer
1 day, 19:34:56.325383 INFO: Running AnnotateFasta
1 day, 19:34:56.325723 INFO: Dropping decoys from input library before annotation
1 day, 19:34:56.341764 INFO: Running IsotopeGenerator
1 day, 19:34:56.342026 WARNING: Input library already contains isotope information. Skipping isotope generation. 
 Please note that isotope generation outside of alphabase is not supported.
1 day, 19:34:56.342068 INFO: Running RTNormalization
1 day, 19:34:56.345990 INFO: Saving library to run_output/alphadia_1.10_defaultMBR/speclib.hdf
1 day, 19:34:56.925797 INFO: Running DecoyGenerator
1 day, 19:35:11.791888 INFO: Running FlattenLibrary
1 day, 19:35:12.655309 INFO: Running InitFlatColumns
1 day, 19:35:12.659824 INFO: Running LogFlatLibraryStats
1 day, 19:35:12.659937 INFO: ============ Library Stats ============
1 day, 19:35:12.659969 INFO: Number of precursors: 164,063
1 day, 19:35:12.693861 INFO: 	thereof targets:82,039
1 day, 19:35:12.693999 INFO: 	thereof decoys: 82,024
1 day, 19:35:12.695463 INFO: Number of elution groups: 82,039
1 day, 19:35:12.695527 INFO: 	average size: 2.00
1 day, 19:35:12.704649 INFO: Number of proteins: 8,253
1 day, 19:35:12.705387 INFO: Number of channels: 1 ([0])
1 day, 19:35:12.705477 INFO: Isotopes Distribution for 4 isotopes
1 day, 19:35:12.705505 INFO: =======================================
1 day, 19:35:12.705614 INFO: Searching 6 files:
1 day, 19:35:12.705643 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 19:35:12.705678 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 19:35:12.705696 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 19:35:12.705715 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 19:35:12.705733 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 19:35:12.705750 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 19:35:12.705767 INFO: Using 0 fasta files:
1 day, 19:35:12.705786 INFO: Using library: run_output/alphadia_1.10_defaultMBR/library/speclib.mbr.hdf
1 day, 19:35:12.705805 INFO: Saving output to: run_output/alphadia_1.10_defaultMBR
1 day, 19:35:12.705837 PROGRESS: Starting Search Workflows
1 day, 19:35:12.705881 PROGRESS: Loading raw file 1/6: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 19:35:12.705932 INFO: Quantification results path: run_output/alphadia_1.10_defaultMBR/quant
1 day, 19:35:12.705987 INFO: Creating parent folder for workflows at run_output/alphadia_1.10_defaultMBR/quant
1 day, 19:35:12.706098 INFO: Creating workflow folder for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494 at run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 19:35:12.706488 INFO: Initializing RawFileManager
1 day, 19:35:12.706604 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 19:35:12.706651 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 19:35:12.706692 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 19:35:12.908470 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
1 day, 19:35:18.550457 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d...
1 day, 19:35:18.551442 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 19:35:18.553858 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 19:35:18.554080 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 19:35:18.554434 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 19:35:18.555900 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 19:35:18.563320 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 19:35:18.563511 INFO: Indexing quadrupole dimension
1 day, 19:35:19.023917 INFO: Transposing detector events
1 day, 19:35:28.106594 INFO: Finished transposing data
1 day, 19:35:28.143578 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 19:35:28.144693 INFO: RT (min)            : 0.0 - 70.0
1 day, 19:35:28.144786 INFO: RT duration (sec)   : 4199.9
1 day, 19:35:28.144840 INFO: RT duration (min)   : 70.0
1 day, 19:35:28.144889 INFO: Cycle len (scans)   : 9
1 day, 19:35:28.144934 INFO: Cycle len (sec)     : 0.97
1 day, 19:35:28.144979 INFO: Number of cycles    : 4347
1 day, 19:35:28.145037 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 19:35:28.164516 INFO: Initializing CalibrationManager
1 day, 19:35:28.164954 INFO: Loading calibration config
1 day, 19:35:28.165636 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'}]
1 day, 19:35:28.165804 INFO: Calibration group :fragment, found 1 estimator(s)
1 day, 19:35:28.165946 INFO: Calibration group :precursor, found 3 estimator(s)
1 day, 19:35:28.166133 INFO: Initializing OptimizationManager
1 day, 19:35:28.166368 INFO: initial parameter: ms1_error = 30
1 day, 19:35:28.166455 INFO: initial parameter: ms2_error = 30
1 day, 19:35:28.166548 INFO: initial parameter: rt_error = 2099.928159
1 day, 19:35:28.166631 INFO: initial parameter: mobility_error = 0.1
1 day, 19:35:28.166709 INFO: initial parameter: column_type = library
1 day, 19:35:28.166783 INFO: initial parameter: num_candidates = 1
1 day, 19:35:28.166852 INFO: initial parameter: classifier_version = -1
1 day, 19:35:28.166925 INFO: initial parameter: fwhm_rt = 5
1 day, 19:35:28.166997 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 19:35:28.167065 INFO: initial parameter: score_cutoff = 0
1 day, 19:35:28.167158 INFO: Initializing TimingManager
1 day, 19:35:28.167248 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 19:35:28.167386 INFO: FDRManager not loaded from disk.
1 day, 19:35:28.167425 INFO: Initializing FDRManager
1 day, 19:35:28.167480 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 19:35:28.195530 PROGRESS: 82,039 target precursors potentially observable (0 removed)
1 day, 19:35:28.232268 PROGRESS: Starting initial search for precursors.
1 day, 19:35:28.251213 INFO: Starting optimization step 0.
1 day, 19:35:28.251471 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:35:28.251551 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:35:28.254650 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:35:28.254706 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:35:28.254738 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 19:35:28.254762 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 19:35:28.258513 INFO: Starting candidate selection
1 day, 19:36:57.100953 INFO: Starting candidate scoring
1 day, 19:36:58.169969 INFO: Finished candidate processing
1 day, 19:36:58.170129 INFO: Collecting candidate features
1 day, 19:36:58.234171 INFO: Collecting fragment features
1 day, 19:36:58.249573 INFO: Finished candidate scoring
1 day, 19:36:58.259198 PROGRESS: === Extracted 15885 precursors and 175814 fragments ===
1 day, 19:36:58.259640 INFO: performing precursor FDR with 47 features
1 day, 19:36:58.259680 INFO: Decoy channel: -1
1 day, 19:36:58.259703 INFO: Competetive: True
1 day, 19:36:58.265234 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:36:58.446169 INFO: Test AUC: 0.801
1 day, 19:36:58.446294 INFO: Train AUC: 0.805
1 day, 19:36:58.446325 INFO: AUC difference: 0.50%
1 day, 19:36:58.548839 INFO: Resetting torch num_threads to 100
1 day, 19:36:58.550288 INFO: === FDR correction performed with classifier version -1 ===
1 day, 19:36:58.552384 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:36:58.552554 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:36:58.552662 PROGRESS: Target precursors: 6,547 (81.84%)
1 day, 19:36:58.552757 PROGRESS: Decoy precursors: 1,453 (18.16%)
1 day, 19:36:58.552845 PROGRESS: 
1 day, 19:36:58.552930 PROGRESS: Precursor Summary:
1 day, 19:36:58.555916 PROGRESS: Channel   0:	 0.05 FDR: 4,436; 0.01 FDR: 3,151; 0.001 FDR: 1,590
1 day, 19:36:58.556104 PROGRESS: 
1 day, 19:36:58.556205 PROGRESS: Protein Summary:
1 day, 19:36:58.559910 PROGRESS: Channel   0:	 0.05 FDR: 2,714; 0.01 FDR: 2,070; 0.001 FDR: 1,158
1 day, 19:36:58.560614 PROGRESS: =========================================================================
1 day, 19:36:58.573642 INFO: fragments_df_filtered: 5000
1 day, 19:36:58.591326 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:36:58.821963 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:36:59.060456 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:36:59.275424 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:36:59.691191 INFO: calibration group: precursor, predicting mz
1 day, 19:36:59.694117 INFO: calibration group: precursor, predicting rt
1 day, 19:36:59.703738 INFO: calibration group: precursor, predicting mobility
1 day, 19:36:59.706125 INFO: calibration group: fragment, predicting mz
1 day, 19:36:59.724176 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 19:36:59.724386 INFO: Starting optimization step 1.
1 day, 19:36:59.724467 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:36:59.724543 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:36:59.730234 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:36:59.730296 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:36:59.730345 INFO: FWHM in RT is 3.37 seconds, sigma is 0.74
1 day, 19:36:59.730375 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.33
1 day, 19:36:59.740526 INFO: Starting candidate selection
1 day, 19:38:36.310704 INFO: Starting candidate scoring
1 day, 19:38:38.335253 INFO: Finished candidate processing
1 day, 19:38:38.335399 INFO: Collecting candidate features
1 day, 19:38:38.394382 INFO: Collecting fragment features
1 day, 19:38:38.422580 INFO: Finished candidate scoring
1 day, 19:38:38.438566 PROGRESS: === Extracted 30416 precursors and 336567 fragments ===
1 day, 19:38:38.439045 INFO: performing precursor FDR with 47 features
1 day, 19:38:38.439085 INFO: Decoy channel: -1
1 day, 19:38:38.439110 INFO: Competetive: True
1 day, 19:38:38.451237 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:38:38.738583 INFO: Test AUC: 0.742
1 day, 19:38:38.738714 INFO: Train AUC: 0.747
1 day, 19:38:38.738744 INFO: AUC difference: 0.63%
1 day, 19:38:38.825428 INFO: Resetting torch num_threads to 100
1 day, 19:38:38.826716 INFO: === FDR correction performed with classifier version 0 ===
1 day, 19:38:38.828497 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:38:38.828601 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:38:38.828664 PROGRESS: Target precursors: 6,984 (87.30%)
1 day, 19:38:38.828721 PROGRESS: Decoy precursors: 1,016 (12.70%)
1 day, 19:38:38.828769 PROGRESS: 
1 day, 19:38:38.828819 PROGRESS: Precursor Summary:
1 day, 19:38:38.830967 PROGRESS: Channel   0:	 0.05 FDR: 5,722; 0.01 FDR: 3,894; 0.001 FDR: 1,056
1 day, 19:38:38.831079 PROGRESS: 
1 day, 19:38:38.831147 PROGRESS: Protein Summary:
1 day, 19:38:38.834029 PROGRESS: Channel   0:	 0.05 FDR: 3,270; 0.01 FDR: 2,415; 0.001 FDR:   778
1 day, 19:38:38.834139 PROGRESS: =========================================================================
1 day, 19:38:38.848934 INFO: fragments_df_filtered: 5000
1 day, 19:38:38.867275 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:38:39.164162 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:38:39.468775 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:38:39.762937 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:38:40.181383 INFO: calibration group: precursor, predicting mz
1 day, 19:38:40.184242 INFO: calibration group: precursor, predicting rt
1 day, 19:38:40.194098 INFO: calibration group: precursor, predicting mobility
1 day, 19:38:40.196461 INFO: calibration group: fragment, predicting mz
1 day, 19:38:40.214632 INFO: === checking if optimization conditions were reached ===
1 day, 19:38:40.216758 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 19:38:40.218496 PROGRESS: ❌ ms1_error      : 10.0000 > 10.0000 or insufficient steps taken.
1 day, 19:38:40.218557 INFO: ==============================================
1 day, 19:38:40.218667 INFO: Starting optimization step 2.
1 day, 19:38:40.218744 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:38:40.218817 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:38:40.224789 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:38:40.224856 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:38:40.224905 INFO: FWHM in RT is 3.14 seconds, sigma is 0.69
1 day, 19:38:40.224933 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.06
1 day, 19:38:40.226121 INFO: Starting candidate selection
1 day, 19:40:12.146936 INFO: Starting candidate scoring
1 day, 19:40:13.248697 INFO: Finished candidate processing
1 day, 19:40:13.248801 INFO: Collecting candidate features
1 day, 19:40:13.304849 INFO: Collecting fragment features
1 day, 19:40:13.325215 INFO: Finished candidate scoring
1 day, 19:40:13.339367 PROGRESS: === Extracted 30457 precursors and 332720 fragments ===
1 day, 19:40:13.339815 INFO: performing precursor FDR with 47 features
1 day, 19:40:13.339856 INFO: Decoy channel: -1
1 day, 19:40:13.339883 INFO: Competetive: True
1 day, 19:40:13.349332 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:40:13.731996 INFO: Test AUC: 0.796
1 day, 19:40:13.732127 INFO: Train AUC: 0.794
1 day, 19:40:13.732158 INFO: AUC difference: 0.31%
1 day, 19:40:13.820930 INFO: Resetting torch num_threads to 100
1 day, 19:40:13.822162 INFO: === FDR correction performed with classifier version 1 ===
1 day, 19:40:13.823684 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:40:13.823798 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:40:13.823859 PROGRESS: Target precursors: 7,460 (93.25%)
1 day, 19:40:13.823910 PROGRESS: Decoy precursors: 540 (6.75%)
1 day, 19:40:13.823964 PROGRESS: 
1 day, 19:40:13.824010 PROGRESS: Precursor Summary:
1 day, 19:40:13.826927 PROGRESS: Channel   0:	 0.05 FDR: 7,161; 0.01 FDR: 6,344; 0.001 FDR: 3,258
1 day, 19:40:13.827055 PROGRESS: 
1 day, 19:40:13.827116 PROGRESS: Protein Summary:
1 day, 19:40:13.830847 PROGRESS: Channel   0:	 0.05 FDR: 3,869; 0.01 FDR: 3,526; 0.001 FDR: 2,065
1 day, 19:40:13.830960 PROGRESS: =========================================================================
1 day, 19:40:13.853209 INFO: fragments_df_filtered: 5000
1 day, 19:40:13.872257 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:40:14.409264 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:40:14.968434 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:40:15.507056 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:40:15.860709 INFO: calibration group: precursor, predicting mz
1 day, 19:40:15.863507 INFO: calibration group: precursor, predicting rt
1 day, 19:40:15.872713 INFO: calibration group: precursor, predicting mobility
1 day, 19:40:15.874993 INFO: calibration group: fragment, predicting mz
1 day, 19:40:15.896977 INFO: === checking if optimization conditions were reached ===
1 day, 19:40:15.899795 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 19:40:15.901659 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
1 day, 19:40:15.901713 INFO: ==============================================
1 day, 19:40:15.901840 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 19:40:15.921079 INFO: calibration group: precursor, predicting mz
1 day, 19:40:15.924007 INFO: calibration group: precursor, predicting rt
1 day, 19:40:15.934054 INFO: calibration group: precursor, predicting mobility
1 day, 19:40:15.936403 INFO: calibration group: fragment, predicting mz
1 day, 19:40:15.958604 INFO: Starting optimization step 0.
1 day, 19:40:15.958780 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:40:15.958874 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:40:15.964280 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:40:15.964355 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:40:15.964413 INFO: FWHM in RT is 2.94 seconds, sigma is 0.65
1 day, 19:40:15.964437 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.12
1 day, 19:40:15.973623 INFO: Starting candidate selection
1 day, 19:41:44.126138 INFO: Starting candidate scoring
1 day, 19:41:45.251166 INFO: Finished candidate processing
1 day, 19:41:45.251292 INFO: Collecting candidate features
1 day, 19:41:45.309924 INFO: Collecting fragment features
1 day, 19:41:45.332429 INFO: Finished candidate scoring
1 day, 19:41:45.348111 PROGRESS: === Extracted 30386 precursors and 331681 fragments ===
1 day, 19:41:45.349281 INFO: performing precursor FDR with 47 features
1 day, 19:41:45.349323 INFO: Decoy channel: -1
1 day, 19:41:45.349347 INFO: Competetive: True
1 day, 19:41:45.359977 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:41:45.779636 INFO: Test AUC: 0.805
1 day, 19:41:45.779774 INFO: Train AUC: 0.807
1 day, 19:41:45.779805 INFO: AUC difference: 0.26%
1 day, 19:41:45.868924 INFO: Resetting torch num_threads to 100
1 day, 19:41:45.870426 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:41:45.872123 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:41:45.872235 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:41:45.872297 PROGRESS: Target precursors: 7,470 (93.38%)
1 day, 19:41:45.872351 PROGRESS: Decoy precursors: 530 (6.62%)
1 day, 19:41:45.872399 PROGRESS: 
1 day, 19:41:45.872445 PROGRESS: Precursor Summary:
1 day, 19:41:45.875182 PROGRESS: Channel   0:	 0.05 FDR: 7,202; 0.01 FDR: 6,495; 0.001 FDR: 3,631
1 day, 19:41:45.875302 PROGRESS: 
1 day, 19:41:45.875360 PROGRESS: Protein Summary:
1 day, 19:41:45.879395 PROGRESS: Channel   0:	 0.05 FDR: 3,874; 0.01 FDR: 3,586; 0.001 FDR: 2,290
1 day, 19:41:45.879501 PROGRESS: =========================================================================
1 day, 19:41:45.901818 INFO: fragments_df_filtered: 5000
1 day, 19:41:45.921316 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:41:46.551514 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:41:47.200429 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:41:47.829257 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:41:48.244609 INFO: calibration group: precursor, predicting mz
1 day, 19:41:48.247584 INFO: calibration group: precursor, predicting rt
1 day, 19:41:48.257007 INFO: calibration group: precursor, predicting mobility
1 day, 19:41:48.259404 INFO: calibration group: fragment, predicting mz
1 day, 19:41:48.278752 INFO: === checking if optimization conditions were reached ===
1 day, 19:41:48.278950 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 19:41:48.284098 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 176.2320.
1 day, 19:41:48.284156 INFO: ==============================================
1 day, 19:41:48.284274 INFO: Starting optimization step 1.
1 day, 19:41:48.284356 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:41:48.284438 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:41:48.289820 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:41:48.289884 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:41:48.289940 INFO: FWHM in RT is 2.92 seconds, sigma is 0.64
1 day, 19:41:48.289969 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.07
1 day, 19:41:48.291312 INFO: Starting candidate selection
1 day, 19:41:56.327924 INFO: Starting candidate scoring
1 day, 19:41:57.327756 INFO: Finished candidate processing
1 day, 19:41:57.327877 INFO: Collecting candidate features
1 day, 19:41:57.404020 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 30285)
1 day, 19:41:57.408447 INFO: Collecting fragment features
1 day, 19:41:57.427694 INFO: Finished candidate scoring
1 day, 19:41:57.443672 PROGRESS: === Extracted 30285 precursors and 325869 fragments ===
1 day, 19:41:57.444122 INFO: performing precursor FDR with 47 features
1 day, 19:41:57.444165 INFO: Decoy channel: -1
1 day, 19:41:57.444196 INFO: Competetive: True
1 day, 19:41:57.453020 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:41:57.457517 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 19:41:58.896163 INFO: Test AUC: 0.835
1 day, 19:41:58.896307 INFO: Train AUC: 0.838
1 day, 19:41:58.896344 INFO: AUC difference: 0.34%
1 day, 19:41:58.983686 INFO: Resetting torch num_threads to 100
1 day, 19:41:58.985170 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:41:58.986793 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:41:58.986907 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:41:58.986984 PROGRESS: Target precursors: 7,720 (96.50%)
1 day, 19:41:58.987051 PROGRESS: Decoy precursors: 280 (3.50%)
1 day, 19:41:58.987114 PROGRESS: 
1 day, 19:41:58.987172 PROGRESS: Precursor Summary:
1 day, 19:41:58.990207 PROGRESS: Channel   0:	 0.05 FDR: 7,720; 0.01 FDR: 7,241; 0.001 FDR: 5,649
1 day, 19:41:58.990343 PROGRESS: 
1 day, 19:41:58.990431 PROGRESS: Protein Summary:
1 day, 19:41:58.995008 PROGRESS: Channel   0:	 0.05 FDR: 4,106; 0.01 FDR: 3,891; 0.001 FDR: 3,252
1 day, 19:41:58.995133 PROGRESS: =========================================================================
1 day, 19:41:59.019713 INFO: fragments_df_filtered: 5000
1 day, 19:41:59.036084 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:41:59.790320 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:42:00.578723 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:42:01.335074 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:42:01.751364 INFO: calibration group: precursor, predicting mz
1 day, 19:42:01.754375 INFO: calibration group: precursor, predicting rt
1 day, 19:42:01.763700 INFO: calibration group: precursor, predicting mobility
1 day, 19:42:01.766077 INFO: calibration group: fragment, predicting mz
1 day, 19:42:01.784478 INFO: === checking if optimization conditions were reached ===
1 day, 19:42:01.784664 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 19:42:01.790835 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 50.1898.
1 day, 19:42:01.790899 INFO: ==============================================
1 day, 19:42:01.791013 INFO: Starting optimization step 2.
1 day, 19:42:01.791085 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:42:01.791152 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:42:01.798500 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:42:01.798574 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:42:01.798622 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 19:42:01.798651 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.98
1 day, 19:42:01.802398 INFO: Starting candidate selection
1 day, 19:42:04.758746 INFO: Starting candidate scoring
1 day, 19:42:05.785676 INFO: Finished candidate processing
1 day, 19:42:05.785799 INFO: Collecting candidate features
1 day, 19:42:05.833769 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 30262)
1 day, 19:42:05.840887 INFO: Collecting fragment features
1 day, 19:42:05.859812 INFO: Finished candidate scoring
1 day, 19:42:05.874477 PROGRESS: === Extracted 30262 precursors and 323112 fragments ===
1 day, 19:42:05.874892 INFO: performing precursor FDR with 47 features
1 day, 19:42:05.874931 INFO: Decoy channel: -1
1 day, 19:42:05.874955 INFO: Competetive: True
1 day, 19:42:05.883732 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:42:05.888016 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 19:42:06.269154 INFO: Test AUC: 0.845
1 day, 19:42:06.269297 INFO: Train AUC: 0.857
1 day, 19:42:06.269327 INFO: AUC difference: 1.34%
1 day, 19:42:07.903768 INFO: Resetting torch num_threads to 100
1 day, 19:42:07.905308 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:42:07.906988 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:42:07.907098 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:42:07.907163 PROGRESS: Target precursors: 7,814 (97.67%)
1 day, 19:42:07.907216 PROGRESS: Decoy precursors: 186 (2.33%)
1 day, 19:42:07.907277 PROGRESS: 
1 day, 19:42:07.907325 PROGRESS: Precursor Summary:
1 day, 19:42:07.910503 PROGRESS: Channel   0:	 0.05 FDR: 7,814; 0.01 FDR: 7,588; 0.001 FDR: 6,489
1 day, 19:42:07.910632 PROGRESS: 
1 day, 19:42:07.910702 PROGRESS: Protein Summary:
1 day, 19:42:07.915290 PROGRESS: Channel   0:	 0.05 FDR: 4,134; 0.01 FDR: 4,038; 0.001 FDR: 3,618
1 day, 19:42:07.915413 PROGRESS: =========================================================================
1 day, 19:42:07.940642 INFO: fragments_df_filtered: 5000
1 day, 19:42:07.956919 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:42:08.775994 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:42:09.628216 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:42:10.451949 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:42:10.867976 INFO: calibration group: precursor, predicting mz
1 day, 19:42:10.871054 INFO: calibration group: precursor, predicting rt
1 day, 19:42:10.880609 INFO: calibration group: precursor, predicting mobility
1 day, 19:42:10.883016 INFO: calibration group: fragment, predicting mz
1 day, 19:42:10.901489 INFO: === checking if optimization conditions were reached ===
1 day, 19:42:10.901677 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 19:42:10.908208 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 19.5672.
1 day, 19:42:10.908283 INFO: ==============================================
1 day, 19:42:10.908401 INFO: Starting optimization step 3.
1 day, 19:42:10.908481 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:42:10.908555 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:42:10.915754 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:42:10.915836 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:42:10.915882 INFO: FWHM in RT is 2.90 seconds, sigma is 0.64
1 day, 19:42:10.915910 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.94
1 day, 19:42:10.919929 INFO: Starting candidate selection
1 day, 19:42:12.740326 INFO: Starting candidate scoring
1 day, 19:42:13.709095 INFO: Finished candidate processing
1 day, 19:42:13.709220 INFO: Collecting candidate features
1 day, 19:42:13.758085 WARNING: intensity_correlation has 4 NaNs ( 0.01 % out of 30198)
1 day, 19:42:13.758351 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 30198)
1 day, 19:42:13.762537 INFO: Collecting fragment features
1 day, 19:42:13.781522 INFO: Finished candidate scoring
1 day, 19:42:13.797224 PROGRESS: === Extracted 30198 precursors and 320007 fragments ===
1 day, 19:42:13.797620 INFO: performing precursor FDR with 47 features
1 day, 19:42:13.797659 INFO: Decoy channel: -1
1 day, 19:42:13.797684 INFO: Competetive: True
1 day, 19:42:13.806230 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:42:13.811341 WARNING: dropped 1 target PSMs due to missing features
1 day, 19:42:13.811441 WARNING: dropped 4 decoy PSMs due to missing features
1 day, 19:42:14.209168 INFO: Test AUC: 0.872
1 day, 19:42:14.209304 INFO: Train AUC: 0.872
1 day, 19:42:14.209335 INFO: AUC difference: 0.02%
1 day, 19:42:14.294576 INFO: Resetting torch num_threads to 100
1 day, 19:42:14.296073 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:42:14.297721 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:42:14.297827 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:42:14.297889 PROGRESS: Target precursors: 7,857 (98.21%)
1 day, 19:42:14.297956 PROGRESS: Decoy precursors: 143 (1.79%)
1 day, 19:42:14.298769 PROGRESS: 
1 day, 19:42:14.298830 PROGRESS: Precursor Summary:
1 day, 19:42:14.302098 PROGRESS: Channel   0:	 0.05 FDR: 7,857; 0.01 FDR: 7,757; 0.001 FDR: 7,013
1 day, 19:42:14.302217 PROGRESS: 
1 day, 19:42:14.302275 PROGRESS: Protein Summary:
1 day, 19:42:14.306951 PROGRESS: Channel   0:	 0.05 FDR: 4,162; 0.01 FDR: 4,128; 0.001 FDR: 3,816
1 day, 19:42:14.307073 PROGRESS: =========================================================================
1 day, 19:42:14.333327 INFO: fragments_df_filtered: 5000
1 day, 19:42:14.349055 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:42:15.135782 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:42:15.935036 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:42:16.725132 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:42:17.078802 INFO: calibration group: precursor, predicting mz
1 day, 19:42:17.081889 INFO: calibration group: precursor, predicting rt
1 day, 19:42:17.091235 INFO: calibration group: precursor, predicting mobility
1 day, 19:42:17.093626 INFO: calibration group: fragment, predicting mz
1 day, 19:42:17.112250 INFO: === checking if optimization conditions were reached ===
1 day, 19:42:17.112433 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 19:42:17.119213 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 14.5289.
1 day, 19:42:17.119288 INFO: ==============================================
1 day, 19:42:17.119401 INFO: Starting optimization step 4.
1 day, 19:42:17.119478 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:42:17.119550 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:42:17.126266 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:42:17.126341 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:42:17.126386 INFO: FWHM in RT is 2.90 seconds, sigma is 0.64
1 day, 19:42:17.126414 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.92
1 day, 19:42:17.129827 INFO: Starting candidate selection
1 day, 19:42:18.670579 INFO: Starting candidate scoring
1 day, 19:42:19.639460 INFO: Finished candidate processing
1 day, 19:42:19.639576 INFO: Collecting candidate features
1 day, 19:42:19.710280 WARNING: intensity_correlation has 5 NaNs ( 0.02 % out of 30122)
1 day, 19:42:19.710619 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 30122)
1 day, 19:42:19.718204 INFO: Collecting fragment features
1 day, 19:42:19.737421 INFO: Finished candidate scoring
1 day, 19:42:19.753445 PROGRESS: === Extracted 30122 precursors and 317682 fragments ===
1 day, 19:42:19.753889 INFO: performing precursor FDR with 47 features
1 day, 19:42:19.753927 INFO: Decoy channel: -1
1 day, 19:42:19.753951 INFO: Competetive: True
1 day, 19:42:19.763218 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:42:19.767586 WARNING: dropped 6 decoy PSMs due to missing features
1 day, 19:42:20.217735 INFO: Test AUC: 0.888
1 day, 19:42:20.217883 INFO: Train AUC: 0.884
1 day, 19:42:20.217915 INFO: AUC difference: 0.49%
1 day, 19:42:20.304935 INFO: Resetting torch num_threads to 100
1 day, 19:42:20.306346 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:42:20.307945 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:42:20.308058 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:42:20.308122 PROGRESS: Target precursors: 7,850 (98.12%)
1 day, 19:42:20.308175 PROGRESS: Decoy precursors: 150 (1.88%)
1 day, 19:42:20.308225 PROGRESS: 
1 day, 19:42:20.308274 PROGRESS: Precursor Summary:
1 day, 19:42:20.311372 PROGRESS: Channel   0:	 0.05 FDR: 7,850; 0.01 FDR: 7,743; 0.001 FDR: 6,345
1 day, 19:42:20.311502 PROGRESS: 
1 day, 19:42:20.311562 PROGRESS: Protein Summary:
1 day, 19:42:20.316279 PROGRESS: Channel   0:	 0.05 FDR: 4,165; 0.01 FDR: 4,127; 0.001 FDR: 3,540
1 day, 19:42:20.316416 PROGRESS: =========================================================================
1 day, 19:42:20.343120 INFO: fragments_df_filtered: 5000
1 day, 19:42:20.360592 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:42:21.148325 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:42:21.957660 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:42:22.744326 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:42:23.094815 INFO: calibration group: precursor, predicting mz
1 day, 19:42:23.097889 INFO: calibration group: precursor, predicting rt
1 day, 19:42:23.107347 INFO: calibration group: precursor, predicting mobility
1 day, 19:42:23.109686 INFO: calibration group: fragment, predicting mz
1 day, 19:42:23.127714 INFO: === checking if optimization conditions were reached ===
1 day, 19:42:23.127897 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 19:42:23.133835 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 11.3656.
1 day, 19:42:23.133895 INFO: ==============================================
1 day, 19:42:23.133989 INFO: Starting optimization step 5.
1 day, 19:42:23.134055 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:42:23.134115 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:42:23.138410 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:42:23.138472 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:42:23.138509 INFO: FWHM in RT is 2.90 seconds, sigma is 0.64
1 day, 19:42:23.138532 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.90
1 day, 19:42:23.139597 INFO: Starting candidate selection
1 day, 19:42:24.734654 INFO: Starting candidate scoring
1 day, 19:42:25.720496 INFO: Finished candidate processing
1 day, 19:42:25.720615 INFO: Collecting candidate features
1 day, 19:42:25.800834 WARNING: intensity_correlation has 11 NaNs ( 0.04 % out of 30171)
1 day, 19:42:25.801132 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 30171)
1 day, 19:42:25.805420 INFO: Collecting fragment features
1 day, 19:42:25.828035 INFO: Finished candidate scoring
1 day, 19:42:25.849022 PROGRESS: === Extracted 30171 precursors and 318142 fragments ===
1 day, 19:42:25.849514 INFO: performing precursor FDR with 47 features
1 day, 19:42:25.849555 INFO: Decoy channel: -1
1 day, 19:42:25.849586 INFO: Competetive: True
1 day, 19:42:25.859356 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:42:25.864816 WARNING: dropped 1 target PSMs due to missing features
1 day, 19:42:25.864929 WARNING: dropped 11 decoy PSMs due to missing features
1 day, 19:42:26.170657 INFO: Test AUC: 0.882
1 day, 19:42:26.170802 INFO: Train AUC: 0.885
1 day, 19:42:26.170840 INFO: AUC difference: 0.31%
1 day, 19:42:26.258622 INFO: Resetting torch num_threads to 100
1 day, 19:42:26.260131 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:42:26.261759 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:42:26.261880 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:42:26.261960 PROGRESS: Target precursors: 7,867 (98.34%)
1 day, 19:42:26.262030 PROGRESS: Decoy precursors: 133 (1.66%)
1 day, 19:42:26.262100 PROGRESS: 
1 day, 19:42:26.262163 PROGRESS: Precursor Summary:
1 day, 19:42:26.265332 PROGRESS: Channel   0:	 0.05 FDR: 7,867; 0.01 FDR: 7,764; 0.001 FDR: 6,399
1 day, 19:42:26.265467 PROGRESS: 
1 day, 19:42:26.265542 PROGRESS: Protein Summary:
1 day, 19:42:26.270424 PROGRESS: Channel   0:	 0.05 FDR: 4,169; 0.01 FDR: 4,134; 0.001 FDR: 3,571
1 day, 19:42:26.270552 PROGRESS: =========================================================================
1 day, 19:42:26.295121 INFO: fragments_df_filtered: 5000
1 day, 19:42:26.311617 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:42:27.169955 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:42:28.023480 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:42:28.813138 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:42:29.169035 INFO: calibration group: precursor, predicting mz
1 day, 19:42:29.173253 INFO: calibration group: precursor, predicting rt
1 day, 19:42:29.183628 INFO: calibration group: precursor, predicting mobility
1 day, 19:42:29.186080 INFO: calibration group: fragment, predicting mz
1 day, 19:42:29.204790 INFO: === checking if optimization conditions were reached ===
1 day, 19:42:29.204998 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 19:42:29.211413 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 11.9054.
1 day, 19:42:29.211483 INFO: ==============================================
1 day, 19:42:29.211609 INFO: Starting optimization step 6.
1 day, 19:42:29.211688 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:42:29.211773 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:42:29.222203 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:42:29.222267 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:42:29.222325 INFO: FWHM in RT is 2.89 seconds, sigma is 0.64
1 day, 19:42:29.222349 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.90
1 day, 19:42:29.229433 INFO: Starting candidate selection
1 day, 19:42:30.757660 INFO: Starting candidate scoring
1 day, 19:42:31.738934 INFO: Finished candidate processing
1 day, 19:42:31.739055 INFO: Collecting candidate features
1 day, 19:42:31.793514 WARNING: intensity_correlation has 8 NaNs ( 0.03 % out of 30157)
1 day, 19:42:31.793775 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 30157)
1 day, 19:42:31.797925 INFO: Collecting fragment features
1 day, 19:42:31.820253 INFO: Finished candidate scoring
1 day, 19:42:31.834632 PROGRESS: === Extracted 30157 precursors and 317969 fragments ===
1 day, 19:42:31.835062 INFO: performing precursor FDR with 47 features
1 day, 19:42:31.835100 INFO: Decoy channel: -1
1 day, 19:42:31.835124 INFO: Competetive: True
1 day, 19:42:31.845967 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:42:31.851455 WARNING: dropped 1 target PSMs due to missing features
1 day, 19:42:31.851558 WARNING: dropped 8 decoy PSMs due to missing features
1 day, 19:42:32.139905 INFO: Test AUC: 0.882
1 day, 19:42:32.141176 INFO: Train AUC: 0.885
1 day, 19:42:32.141220 INFO: AUC difference: 0.35%
1 day, 19:42:32.228518 INFO: Resetting torch num_threads to 100
1 day, 19:42:32.230026 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:42:32.231746 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:42:32.231844 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:42:32.231908 PROGRESS: Target precursors: 7,860 (98.25%)
1 day, 19:42:32.231962 PROGRESS: Decoy precursors: 140 (1.75%)
1 day, 19:42:32.232011 PROGRESS: 
1 day, 19:42:32.232059 PROGRESS: Precursor Summary:
1 day, 19:42:32.235307 PROGRESS: Channel   0:	 0.05 FDR: 7,860; 0.01 FDR: 7,752; 0.001 FDR: 6,113
1 day, 19:42:32.235432 PROGRESS: 
1 day, 19:42:32.235492 PROGRESS: Protein Summary:
1 day, 19:42:32.240248 PROGRESS: Channel   0:	 0.05 FDR: 4,169; 0.01 FDR: 4,135; 0.001 FDR: 3,449
1 day, 19:42:32.240370 PROGRESS: =========================================================================
1 day, 19:42:32.266997 INFO: fragments_df_filtered: 5000
1 day, 19:42:32.285062 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:42:33.136139 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:42:33.998034 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:42:34.849710 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:42:35.265747 INFO: calibration group: precursor, predicting mz
1 day, 19:42:35.268758 INFO: calibration group: precursor, predicting rt
1 day, 19:42:35.277963 INFO: calibration group: precursor, predicting mobility
1 day, 19:42:35.280371 INFO: calibration group: fragment, predicting mz
1 day, 19:42:35.299192 INFO: === checking if optimization conditions were reached ===
1 day, 19:42:35.299399 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 19:42:35.300804 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 11.3656 found after 7 searches.
1 day, 19:42:35.300861 INFO: ==============================================
1 day, 19:42:35.300977 PROGRESS: Optimization finished for rt_error.
1 day, 19:42:35.321972 INFO: calibration group: precursor, predicting mz
1 day, 19:42:35.325354 INFO: calibration group: precursor, predicting rt
1 day, 19:42:35.335258 INFO: calibration group: precursor, predicting mobility
1 day, 19:42:35.337986 INFO: calibration group: fragment, predicting mz
1 day, 19:42:35.391200 INFO: Starting optimization step 0.
1 day, 19:42:35.391418 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:42:35.391498 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:42:35.398538 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:42:35.398617 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:42:35.398662 INFO: FWHM in RT is 2.89 seconds, sigma is 0.64
1 day, 19:42:35.398691 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.90
1 day, 19:42:35.407545 INFO: Starting candidate selection
1 day, 19:42:36.942238 INFO: Starting candidate scoring
1 day, 19:42:37.919724 INFO: Finished candidate processing
1 day, 19:42:37.919894 INFO: Collecting candidate features
1 day, 19:42:37.968817 WARNING: intensity_correlation has 9 NaNs ( 0.03 % out of 30181)
1 day, 19:42:37.969100 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 30181)
1 day, 19:42:37.973373 INFO: Collecting fragment features
1 day, 19:42:37.993489 INFO: Finished candidate scoring
1 day, 19:42:38.007921 PROGRESS: === Extracted 30181 precursors and 318203 fragments ===
1 day, 19:42:38.008316 INFO: performing precursor FDR with 47 features
1 day, 19:42:38.008354 INFO: Decoy channel: -1
1 day, 19:42:38.008378 INFO: Competetive: True
1 day, 19:42:38.017182 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:42:38.022164 WARNING: dropped 2 target PSMs due to missing features
1 day, 19:42:38.022259 WARNING: dropped 8 decoy PSMs due to missing features
1 day, 19:42:38.395575 INFO: Test AUC: 0.891
1 day, 19:42:38.395715 INFO: Train AUC: 0.891
1 day, 19:42:38.395746 INFO: AUC difference: 0.01%
1 day, 19:42:38.483232 INFO: Resetting torch num_threads to 100
1 day, 19:42:38.484701 INFO: === FDR correction performed with classifier version 8 ===
1 day, 19:42:38.486369 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:42:38.486468 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:42:38.486531 PROGRESS: Target precursors: 7,874 (98.42%)
1 day, 19:42:38.486584 PROGRESS: Decoy precursors: 126 (1.57%)
1 day, 19:42:38.486632 PROGRESS: 
1 day, 19:42:38.486679 PROGRESS: Precursor Summary:
1 day, 19:42:38.489883 PROGRESS: Channel   0:	 0.05 FDR: 7,874; 0.01 FDR: 7,782; 0.001 FDR: 7,199
1 day, 19:42:38.490000 PROGRESS: 
1 day, 19:42:38.490060 PROGRESS: Protein Summary:
1 day, 19:42:38.494982 PROGRESS: Channel   0:	 0.05 FDR: 4,169; 0.01 FDR: 4,144; 0.001 FDR: 3,910
1 day, 19:42:38.495093 PROGRESS: =========================================================================
1 day, 19:42:38.522864 INFO: fragments_df_filtered: 5000
1 day, 19:42:38.538447 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:42:39.331352 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:42:40.136283 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:42:40.928056 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:42:41.278484 INFO: calibration group: precursor, predicting mz
1 day, 19:42:41.282384 INFO: calibration group: precursor, predicting rt
1 day, 19:42:41.292520 INFO: calibration group: precursor, predicting mobility
1 day, 19:42:41.295842 INFO: calibration group: fragment, predicting mz
1 day, 19:42:41.314322 INFO: === checking if optimization conditions were reached ===
1 day, 19:42:41.314500 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 19:42:41.317693 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0571.
1 day, 19:42:41.317756 INFO: ==============================================
1 day, 19:42:41.317864 INFO: Starting optimization step 1.
1 day, 19:42:41.317942 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:42:41.318012 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:42:41.325859 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:42:41.325930 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:42:41.325975 INFO: FWHM in RT is 2.89 seconds, sigma is 0.64
1 day, 19:42:41.326003 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.90
1 day, 19:42:41.327193 INFO: Starting candidate selection
1 day, 19:42:42.645951 INFO: Starting candidate scoring
1 day, 19:42:43.590587 INFO: Finished candidate processing
1 day, 19:42:43.590709 INFO: Collecting candidate features
1 day, 19:42:43.638951 WARNING: intensity_correlation has 15 NaNs ( 0.05 % out of 30097)
1 day, 19:42:43.639315 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 30097)
1 day, 19:42:43.646214 INFO: Collecting fragment features
1 day, 19:42:43.665369 INFO: Finished candidate scoring
1 day, 19:42:43.679556 PROGRESS: === Extracted 30097 precursors and 314231 fragments ===
1 day, 19:42:43.680018 INFO: performing precursor FDR with 47 features
1 day, 19:42:43.680060 INFO: Decoy channel: -1
1 day, 19:42:43.680093 INFO: Competetive: True
1 day, 19:42:43.688628 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:42:43.694063 WARNING: dropped 1 target PSMs due to missing features
1 day, 19:42:43.694175 WARNING: dropped 15 decoy PSMs due to missing features
1 day, 19:42:43.959950 INFO: Test AUC: 0.890
1 day, 19:42:43.960091 INFO: Train AUC: 0.894
1 day, 19:42:43.960126 INFO: AUC difference: 0.38%
1 day, 19:42:44.047823 INFO: Resetting torch num_threads to 100
1 day, 19:42:44.049359 INFO: === FDR correction performed with classifier version 8 ===
1 day, 19:42:44.051055 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:42:44.051181 PROGRESS: Total precursors accumulated: 7,998
1 day, 19:42:44.051264 PROGRESS: Target precursors: 7,887 (98.61%)
1 day, 19:42:44.051339 PROGRESS: Decoy precursors: 111 (1.39%)
1 day, 19:42:44.051399 PROGRESS: 
1 day, 19:42:44.051457 PROGRESS: Precursor Summary:
1 day, 19:42:44.054774 PROGRESS: Channel   0:	 0.05 FDR: 7,887; 0.01 FDR: 7,823; 0.001 FDR: 7,397
1 day, 19:42:44.054905 PROGRESS: 
1 day, 19:42:44.054986 PROGRESS: Protein Summary:
1 day, 19:42:44.060019 PROGRESS: Channel   0:	 0.05 FDR: 4,174; 0.01 FDR: 4,158; 0.001 FDR: 3,985
1 day, 19:42:44.060161 PROGRESS: =========================================================================
1 day, 19:42:44.086037 INFO: fragments_df_filtered: 5000
1 day, 19:42:44.101622 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:42:44.966923 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:42:45.844879 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:42:46.708963 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:42:47.128704 INFO: calibration group: precursor, predicting mz
1 day, 19:42:47.131669 INFO: calibration group: precursor, predicting rt
1 day, 19:42:47.140852 INFO: calibration group: precursor, predicting mobility
1 day, 19:42:47.143155 INFO: calibration group: fragment, predicting mz
1 day, 19:42:47.161361 INFO: === checking if optimization conditions were reached ===
1 day, 19:42:47.161548 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 19:42:47.164199 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0509.
1 day, 19:42:47.164254 INFO: ==============================================
1 day, 19:42:47.164387 INFO: Starting optimization step 2.
1 day, 19:42:47.164474 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:42:47.164549 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:42:47.170072 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:42:47.170137 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:42:47.170184 INFO: FWHM in RT is 2.89 seconds, sigma is 0.64
1 day, 19:42:47.170212 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.87
1 day, 19:42:47.171291 INFO: Starting candidate selection
1 day, 19:42:48.519310 INFO: Starting candidate scoring
1 day, 19:42:49.483796 INFO: Finished candidate processing
1 day, 19:42:49.483917 INFO: Collecting candidate features
1 day, 19:42:49.531811 WARNING: intensity_correlation has 15 NaNs ( 0.05 % out of 30078)
1 day, 19:42:49.532132 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 30078)
1 day, 19:42:49.538951 INFO: Collecting fragment features
1 day, 19:42:49.557559 INFO: Finished candidate scoring
1 day, 19:42:49.571160 PROGRESS: === Extracted 30078 precursors and 312617 fragments ===
1 day, 19:42:49.571553 INFO: performing precursor FDR with 47 features
1 day, 19:42:49.571591 INFO: Decoy channel: -1
1 day, 19:42:49.571615 INFO: Competetive: True
1 day, 19:42:49.579835 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:42:49.584921 WARNING: dropped 1 target PSMs due to missing features
1 day, 19:42:49.585035 WARNING: dropped 15 decoy PSMs due to missing features
1 day, 19:42:49.860184 INFO: Test AUC: 0.887
1 day, 19:42:49.860326 INFO: Train AUC: 0.892
1 day, 19:42:49.860355 INFO: AUC difference: 0.64%
1 day, 19:42:49.948790 INFO: Resetting torch num_threads to 100
1 day, 19:42:49.950224 INFO: === FDR correction performed with classifier version 8 ===
1 day, 19:42:49.951818 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:42:49.951916 PROGRESS: Total precursors accumulated: 7,998
1 day, 19:42:49.951976 PROGRESS: Target precursors: 7,880 (98.52%)
1 day, 19:42:49.952029 PROGRESS: Decoy precursors: 118 (1.48%)
1 day, 19:42:49.952076 PROGRESS: 
1 day, 19:42:49.952122 PROGRESS: Precursor Summary:
1 day, 19:42:49.955212 PROGRESS: Channel   0:	 0.05 FDR: 7,880; 0.01 FDR: 7,814; 0.001 FDR: 7,357
1 day, 19:42:49.955333 PROGRESS: 
1 day, 19:42:49.955390 PROGRESS: Protein Summary:
1 day, 19:42:49.960104 PROGRESS: Channel   0:	 0.05 FDR: 4,173; 0.01 FDR: 4,156; 0.001 FDR: 3,975
1 day, 19:42:49.960222 PROGRESS: =========================================================================
1 day, 19:42:49.985463 INFO: fragments_df_filtered: 5000
1 day, 19:42:50.000900 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:42:50.866476 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:42:51.743545 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:42:52.601643 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:42:53.017951 INFO: calibration group: precursor, predicting mz
1 day, 19:42:53.020919 INFO: calibration group: precursor, predicting rt
1 day, 19:42:53.030201 INFO: calibration group: precursor, predicting mobility
1 day, 19:42:53.032537 INFO: calibration group: fragment, predicting mz
1 day, 19:42:53.051016 INFO: === checking if optimization conditions were reached ===
1 day, 19:42:53.051177 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 19:42:53.052061 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.0571 found after 3 searches.
1 day, 19:42:53.052109 INFO: ==============================================
1 day, 19:42:53.052198 PROGRESS: Optimization finished for mobility_error.
1 day, 19:42:53.067881 INFO: calibration group: precursor, predicting mz
1 day, 19:42:53.070791 INFO: calibration group: precursor, predicting rt
1 day, 19:42:53.079907 INFO: calibration group: precursor, predicting mobility
1 day, 19:42:53.082272 INFO: calibration group: fragment, predicting mz
1 day, 19:42:53.125777 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 19:42:53.125959 PROGRESS: ==============================================
1 day, 19:42:53.126055 PROGRESS: ms2_error      : 15.0000
1 day, 19:42:53.126128 PROGRESS: ms1_error      : 10.0000
1 day, 19:42:53.126185 PROGRESS: rt_error       : 11.3656
1 day, 19:42:53.126233 PROGRESS: mobility_error : 0.0571
1 day, 19:42:53.126279 PROGRESS: ==============================================
1 day, 19:42:53.127512 INFO: calibration group: precursor, predicting mz
1 day, 19:42:53.146537 INFO: calibration group: precursor, predicting rt
1 day, 19:42:53.235409 INFO: calibration group: precursor, predicting mobility
1 day, 19:42:53.255649 INFO: calibration group: fragment, predicting mz
1 day, 19:42:53.473689 PROGRESS: Extracting batch of 162861 precursors
1 day, 19:42:53.521444 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:42:53.521596 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:42:53.521645 INFO: FWHM in RT is 2.89 seconds, sigma is 0.64
1 day, 19:42:53.521669 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.87
1 day, 19:42:53.522585 INFO: Starting candidate selection
1 day, 19:43:02.578666 INFO: Applying score cutoff of 25.36326449584961
1 day, 19:43:02.584977 INFO: Removed 20746 precursors with score below cutoff
1 day, 19:43:02.901639 INFO: Starting candidate scoring
1 day, 19:43:11.563314 INFO: Finished candidate processing
1 day, 19:43:11.563492 INFO: Collecting candidate features
1 day, 19:43:12.074491 WARNING: intensity_correlation has 10 NaNs ( 0.00 % out of 289026)
1 day, 19:43:12.091479 INFO: Collecting fragment features
1 day, 19:43:12.266765 INFO: Finished candidate scoring
1 day, 19:43:12.463909 INFO: === FDR correction performed with classifier version 11 ===
1 day, 19:43:12.464751 INFO: performing precursor FDR with 47 features
1 day, 19:43:12.464786 INFO: Decoy channel: -1
1 day, 19:43:12.464809 INFO: Competetive: True
1 day, 19:43:12.569192 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:43:12.620833 WARNING: dropped 1 target PSMs due to missing features
1 day, 19:43:12.620992 WARNING: dropped 9 decoy PSMs due to missing features
1 day, 19:43:12.621057 WARNING: FDR calculation for 153262 target and 135754 decoy PSMs
1 day, 19:43:12.621086 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1 day, 19:43:17.630882 INFO: Test AUC: 0.905
1 day, 19:43:17.631024 INFO: Train AUC: 0.907
1 day, 19:43:17.631056 INFO: AUC difference: 0.21%
1 day, 19:43:17.732209 INFO: Resetting torch num_threads to 100
1 day, 19:43:17.755119 INFO: Removing fragments below FDR threshold
1 day, 19:43:17.810823 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:43:17.811107 PROGRESS: Total precursors accumulated: 81,604
1 day, 19:43:17.811177 PROGRESS: Target precursors: 80,797 (99.01%)
1 day, 19:43:17.811245 PROGRESS: Decoy precursors: 807 (0.99%)
1 day, 19:43:17.811299 PROGRESS: 
1 day, 19:43:17.811347 PROGRESS: Precursor Summary:
1 day, 19:43:17.854199 PROGRESS: Channel   0:	 0.05 FDR: 80,797; 0.01 FDR: 80,797; 0.001 FDR: 78,233
1 day, 19:43:17.854528 PROGRESS: 
1 day, 19:43:17.854595 PROGRESS: Protein Summary:
1 day, 19:43:17.918529 PROGRESS: Channel   0:	 0.05 FDR: 8,247; 0.01 FDR: 8,247; 0.001 FDR: 8,212
1 day, 19:43:17.918815 PROGRESS: =========================================================================
1 day, 19:43:18.615366 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 19:43:18.663681 PROGRESS: Loading raw file 2/6: ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 19:43:18.663864 INFO: Quantification results path: run_output/alphadia_1.10_defaultMBR/quant
1 day, 19:43:18.663948 INFO: Creating workflow folder for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500 at run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 19:43:18.664663 INFO: Initializing RawFileManager
1 day, 19:43:18.664791 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 19:43:18.664853 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 19:43:18.664895 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 19:43:18.869838 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
1 day, 19:43:25.625040 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d...
1 day, 19:43:25.629816 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 19:43:25.635442 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 19:43:25.635767 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 19:43:25.636282 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 19:43:25.637977 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 19:43:25.657277 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 19:43:25.657516 INFO: Indexing quadrupole dimension
1 day, 19:43:26.162271 INFO: Transposing detector events
1 day, 19:43:35.051303 INFO: Finished transposing data
1 day, 19:43:35.078511 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 19:43:35.079328 INFO: RT (min)            : 0.0 - 70.0
1 day, 19:43:35.079371 INFO: RT duration (sec)   : 4199.8
1 day, 19:43:35.079399 INFO: RT duration (min)   : 70.0
1 day, 19:43:35.079426 INFO: Cycle len (scans)   : 9
1 day, 19:43:35.079448 INFO: Cycle len (sec)     : 0.97
1 day, 19:43:35.079467 INFO: Number of cycles    : 4347
1 day, 19:43:35.079486 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 19:43:35.158923 INFO: Initializing CalibrationManager
1 day, 19:43:35.159286 INFO: Loading calibration config
1 day, 19:43:35.160158 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'}]
1 day, 19:43:35.160252 INFO: Calibration group :fragment, found 1 estimator(s)
1 day, 19:43:35.160349 INFO: Calibration group :precursor, found 3 estimator(s)
1 day, 19:43:35.160541 INFO: Initializing OptimizationManager
1 day, 19:43:35.160659 INFO: initial parameter: ms1_error = 30
1 day, 19:43:35.160717 INFO: initial parameter: ms2_error = 30
1 day, 19:43:35.160787 INFO: initial parameter: rt_error = 2099.894844
1 day, 19:43:35.160838 INFO: initial parameter: mobility_error = 0.1
1 day, 19:43:35.160888 INFO: initial parameter: column_type = library
1 day, 19:43:35.160932 INFO: initial parameter: num_candidates = 1
1 day, 19:43:35.160978 INFO: initial parameter: classifier_version = -1
1 day, 19:43:35.161034 INFO: initial parameter: fwhm_rt = 5
1 day, 19:43:35.161093 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 19:43:35.161141 INFO: initial parameter: score_cutoff = 0
1 day, 19:43:35.161208 INFO: Initializing TimingManager
1 day, 19:43:35.161269 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 19:43:35.161427 INFO: FDRManager not loaded from disk.
1 day, 19:43:35.161455 INFO: Initializing FDRManager
1 day, 19:43:35.161494 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 19:43:35.193842 PROGRESS: 82,039 target precursors potentially observable (0 removed)
1 day, 19:43:35.234039 PROGRESS: Starting initial search for precursors.
1 day, 19:43:35.254699 INFO: Starting optimization step 0.
1 day, 19:43:35.254951 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:43:35.255054 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:43:35.258892 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:43:35.258952 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:43:35.259000 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 19:43:35.259024 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 19:43:35.260126 INFO: Starting candidate selection
1 day, 19:45:01.549274 INFO: Starting candidate scoring
1 day, 19:45:02.623966 INFO: Finished candidate processing
1 day, 19:45:02.624081 INFO: Collecting candidate features
1 day, 19:45:02.660699 INFO: Collecting fragment features
1 day, 19:45:02.676514 INFO: Finished candidate scoring
1 day, 19:45:02.684964 PROGRESS: === Extracted 15885 precursors and 175846 fragments ===
1 day, 19:45:02.685401 INFO: performing precursor FDR with 47 features
1 day, 19:45:02.685443 INFO: Decoy channel: -1
1 day, 19:45:02.685468 INFO: Competetive: True
1 day, 19:45:02.690395 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:45:02.822764 INFO: Test AUC: 0.821
1 day, 19:45:02.822888 INFO: Train AUC: 0.828
1 day, 19:45:02.822918 INFO: AUC difference: 0.86%
1 day, 19:45:02.906199 INFO: Resetting torch num_threads to 100
1 day, 19:45:02.907225 INFO: === FDR correction performed with classifier version -1 ===
1 day, 19:45:02.908670 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:45:02.908772 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:45:02.908833 PROGRESS: Target precursors: 6,637 (82.96%)
1 day, 19:45:02.908886 PROGRESS: Decoy precursors: 1,363 (17.04%)
1 day, 19:45:02.908932 PROGRESS: 
1 day, 19:45:02.908978 PROGRESS: Precursor Summary:
1 day, 19:45:02.911263 PROGRESS: Channel   0:	 0.05 FDR: 5,247; 0.01 FDR: 3,919; 0.001 FDR: 2,205
1 day, 19:45:02.911367 PROGRESS: 
1 day, 19:45:02.911425 PROGRESS: Protein Summary:
1 day, 19:45:02.914271 PROGRESS: Channel   0:	 0.05 FDR: 3,079; 0.01 FDR: 2,457; 0.001 FDR: 1,540
1 day, 19:45:02.914372 PROGRESS: =========================================================================
1 day, 19:45:02.923214 INFO: fragments_df_filtered: 5000
1 day, 19:45:02.939944 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:45:03.240901 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:45:03.548913 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:45:03.846838 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:45:04.264689 INFO: calibration group: precursor, predicting mz
1 day, 19:45:04.267421 INFO: calibration group: precursor, predicting rt
1 day, 19:45:04.277182 INFO: calibration group: precursor, predicting mobility
1 day, 19:45:04.279437 INFO: calibration group: fragment, predicting mz
1 day, 19:45:04.299105 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 19:45:04.299302 INFO: Starting optimization step 1.
1 day, 19:45:04.299387 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:45:04.299463 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:45:04.304954 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:45:04.305056 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:45:04.305110 INFO: FWHM in RT is 3.24 seconds, sigma is 0.71
1 day, 19:45:04.305143 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.13
1 day, 19:45:04.306312 INFO: Starting candidate selection
1 day, 19:46:40.406615 INFO: Starting candidate scoring
1 day, 19:46:42.439935 INFO: Finished candidate processing
1 day, 19:46:42.440048 INFO: Collecting candidate features
1 day, 19:46:42.496647 INFO: Collecting fragment features
1 day, 19:46:42.516400 INFO: Finished candidate scoring
1 day, 19:46:42.533114 PROGRESS: === Extracted 30469 precursors and 337367 fragments ===
1 day, 19:46:42.533591 INFO: performing precursor FDR with 47 features
1 day, 19:46:42.533633 INFO: Decoy channel: -1
1 day, 19:46:42.533659 INFO: Competetive: True
1 day, 19:46:42.544627 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:46:42.930736 INFO: Test AUC: 0.749
1 day, 19:46:42.930855 INFO: Train AUC: 0.746
1 day, 19:46:42.930887 INFO: AUC difference: 0.43%
1 day, 19:46:43.019552 INFO: Resetting torch num_threads to 100
1 day, 19:46:43.020799 INFO: === FDR correction performed with classifier version 0 ===
1 day, 19:46:43.022444 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:46:43.022553 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:46:43.022614 PROGRESS: Target precursors: 7,020 (87.75%)
1 day, 19:46:43.022672 PROGRESS: Decoy precursors: 980 (12.25%)
1 day, 19:46:43.022725 PROGRESS: 
1 day, 19:46:43.022801 PROGRESS: Precursor Summary:
1 day, 19:46:43.025235 PROGRESS: Channel   0:	 0.05 FDR: 6,085; 0.01 FDR: 5,072; 0.001 FDR: 3,205
1 day, 19:46:43.025355 PROGRESS: 
1 day, 19:46:43.025425 PROGRESS: Protein Summary:
1 day, 19:46:43.028938 PROGRESS: Channel   0:	 0.05 FDR: 3,422; 0.01 FDR: 2,990; 0.001 FDR: 2,105
1 day, 19:46:43.029063 PROGRESS: =========================================================================
1 day, 19:46:43.047981 INFO: fragments_df_filtered: 5000
1 day, 19:46:43.066697 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:46:43.496310 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:46:43.936011 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:46:44.359269 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:46:44.778126 INFO: calibration group: precursor, predicting mz
1 day, 19:46:44.780864 INFO: calibration group: precursor, predicting rt
1 day, 19:46:44.790557 INFO: calibration group: precursor, predicting mobility
1 day, 19:46:44.792830 INFO: calibration group: fragment, predicting mz
1 day, 19:46:44.811310 INFO: === checking if optimization conditions were reached ===
1 day, 19:46:44.813137 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 19:46:44.814749 PROGRESS: ❌ ms1_error      : 10.0000 > 10.0000 or insufficient steps taken.
1 day, 19:46:44.814799 INFO: ==============================================
1 day, 19:46:44.814896 INFO: Starting optimization step 2.
1 day, 19:46:44.814965 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:46:44.815031 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:46:44.819182 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:46:44.819248 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:46:44.819289 INFO: FWHM in RT is 3.22 seconds, sigma is 0.71
1 day, 19:46:44.819313 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.99
1 day, 19:46:44.820331 INFO: Starting candidate selection
1 day, 19:48:10.388332 INFO: Starting candidate scoring
1 day, 19:48:11.501992 INFO: Finished candidate processing
1 day, 19:48:11.502133 INFO: Collecting candidate features
1 day, 19:48:11.557697 INFO: Collecting fragment features
1 day, 19:48:11.580420 INFO: Finished candidate scoring
1 day, 19:48:11.593581 PROGRESS: === Extracted 30551 precursors and 333891 fragments ===
1 day, 19:48:11.594040 INFO: performing precursor FDR with 47 features
1 day, 19:48:11.594082 INFO: Decoy channel: -1
1 day, 19:48:11.594122 INFO: Competetive: True
1 day, 19:48:11.605048 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:48:11.880777 INFO: Test AUC: 0.791
1 day, 19:48:11.880900 INFO: Train AUC: 0.798
1 day, 19:48:11.880931 INFO: AUC difference: 0.86%
1 day, 19:48:11.967194 INFO: Resetting torch num_threads to 100
1 day, 19:48:11.968360 INFO: === FDR correction performed with classifier version 1 ===
1 day, 19:48:11.969878 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:48:11.969980 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:48:11.970043 PROGRESS: Target precursors: 7,529 (94.11%)
1 day, 19:48:11.970098 PROGRESS: Decoy precursors: 471 (5.89%)
1 day, 19:48:11.970145 PROGRESS: 
1 day, 19:48:11.970191 PROGRESS: Precursor Summary:
1 day, 19:48:11.973081 PROGRESS: Channel   0:	 0.05 FDR: 7,342; 0.01 FDR: 6,741; 0.001 FDR: 5,426
1 day, 19:48:11.973198 PROGRESS: 
1 day, 19:48:11.973256 PROGRESS: Protein Summary:
1 day, 19:48:11.977252 PROGRESS: Channel   0:	 0.05 FDR: 3,961; 0.01 FDR: 3,713; 0.001 FDR: 3,172
1 day, 19:48:11.977363 PROGRESS: =========================================================================
1 day, 19:48:12.000386 INFO: fragments_df_filtered: 5000
1 day, 19:48:12.018417 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:48:12.619684 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:48:13.249279 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:48:15.520206 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:48:15.872208 INFO: calibration group: precursor, predicting mz
1 day, 19:48:15.875297 INFO: calibration group: precursor, predicting rt
1 day, 19:48:15.884510 INFO: calibration group: precursor, predicting mobility
1 day, 19:48:15.886845 INFO: calibration group: fragment, predicting mz
1 day, 19:48:15.905740 INFO: === checking if optimization conditions were reached ===
1 day, 19:48:15.907859 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 19:48:15.910247 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
1 day, 19:48:15.910309 INFO: ==============================================
1 day, 19:48:15.910440 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 19:48:15.930263 INFO: calibration group: precursor, predicting mz
1 day, 19:48:15.933086 INFO: calibration group: precursor, predicting rt
1 day, 19:48:15.942193 INFO: calibration group: precursor, predicting mobility
1 day, 19:48:15.944474 INFO: calibration group: fragment, predicting mz
1 day, 19:48:15.964288 INFO: Starting optimization step 0.
1 day, 19:48:15.964442 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:48:15.964512 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:48:15.970640 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:48:15.970702 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:48:15.970745 INFO: FWHM in RT is 2.92 seconds, sigma is 0.64
1 day, 19:48:15.970770 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.08
1 day, 19:48:15.976480 INFO: Starting candidate selection
1 day, 19:49:49.520582 INFO: Starting candidate scoring
1 day, 19:49:50.618755 INFO: Finished candidate processing
1 day, 19:49:50.618858 INFO: Collecting candidate features
1 day, 19:49:50.673580 INFO: Collecting fragment features
1 day, 19:49:50.697869 INFO: Finished candidate scoring
1 day, 19:49:50.719559 PROGRESS: === Extracted 30471 precursors and 332702 fragments ===
1 day, 19:49:50.720011 INFO: performing precursor FDR with 47 features
1 day, 19:49:50.720050 INFO: Decoy channel: -1
1 day, 19:49:50.720074 INFO: Competetive: True
1 day, 19:49:50.730242 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:49:51.042014 INFO: Test AUC: 0.805
1 day, 19:49:51.042144 INFO: Train AUC: 0.815
1 day, 19:49:51.042173 INFO: AUC difference: 1.25%
1 day, 19:49:51.129874 INFO: Resetting torch num_threads to 100
1 day, 19:49:51.131039 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:49:51.132744 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:49:51.132864 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:49:51.132926 PROGRESS: Target precursors: 7,571 (94.64%)
1 day, 19:49:51.132978 PROGRESS: Decoy precursors: 429 (5.36%)
1 day, 19:49:51.133034 PROGRESS: 
1 day, 19:49:51.133085 PROGRESS: Precursor Summary:
1 day, 19:49:51.136004 PROGRESS: Channel   0:	 0.05 FDR: 7,493; 0.01 FDR: 6,909; 0.001 FDR: 6,177
1 day, 19:49:51.136128 PROGRESS: 
1 day, 19:49:51.136187 PROGRESS: Protein Summary:
1 day, 19:49:51.140500 PROGRESS: Channel   0:	 0.05 FDR: 4,022; 0.01 FDR: 3,764; 0.001 FDR: 3,490
1 day, 19:49:51.140617 PROGRESS: =========================================================================
1 day, 19:49:51.164426 INFO: fragments_df_filtered: 5000
1 day, 19:49:51.182726 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:49:51.878927 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:49:52.604583 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:49:53.300536 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:49:53.717909 INFO: calibration group: precursor, predicting mz
1 day, 19:49:53.720790 INFO: calibration group: precursor, predicting rt
1 day, 19:49:53.730187 INFO: calibration group: precursor, predicting mobility
1 day, 19:49:53.732553 INFO: calibration group: fragment, predicting mz
1 day, 19:49:53.751952 INFO: === checking if optimization conditions were reached ===
1 day, 19:49:53.752134 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 19:49:53.757436 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 183.3551.
1 day, 19:49:53.757493 INFO: ==============================================
1 day, 19:49:53.757597 INFO: Starting optimization step 1.
1 day, 19:49:53.757667 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:49:53.757731 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:49:53.762093 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:49:53.762151 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:49:53.762193 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 19:49:53.762217 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.03
1 day, 19:49:53.763314 INFO: Starting candidate selection
1 day, 19:50:02.124597 INFO: Starting candidate scoring
1 day, 19:50:03.131865 INFO: Finished candidate processing
1 day, 19:50:03.132017 INFO: Collecting candidate features
1 day, 19:50:03.179639 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 30354)
1 day, 19:50:03.184124 INFO: Collecting fragment features
1 day, 19:50:03.203523 INFO: Finished candidate scoring
1 day, 19:50:03.218607 PROGRESS: === Extracted 30354 precursors and 326954 fragments ===
1 day, 19:50:03.218980 INFO: performing precursor FDR with 47 features
1 day, 19:50:03.219023 INFO: Decoy channel: -1
1 day, 19:50:03.219050 INFO: Competetive: True
1 day, 19:50:03.227369 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:50:03.231389 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 19:50:03.499982 INFO: Test AUC: 0.837
1 day, 19:50:03.500114 INFO: Train AUC: 0.839
1 day, 19:50:03.500145 INFO: AUC difference: 0.25%
1 day, 19:50:03.587516 INFO: Resetting torch num_threads to 100
1 day, 19:50:03.588699 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:50:03.590304 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:50:03.590408 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:50:03.590470 PROGRESS: Target precursors: 7,774 (97.17%)
1 day, 19:50:03.590525 PROGRESS: Decoy precursors: 226 (2.83%)
1 day, 19:50:03.590572 PROGRESS: 
1 day, 19:50:03.590619 PROGRESS: Precursor Summary:
1 day, 19:50:03.593584 PROGRESS: Channel   0:	 0.05 FDR: 7,774; 0.01 FDR: 7,508; 0.001 FDR: 6,559
1 day, 19:50:03.593707 PROGRESS: 
1 day, 19:50:03.593785 PROGRESS: Protein Summary:
1 day, 19:50:03.598367 PROGRESS: Channel   0:	 0.05 FDR: 4,127; 0.01 FDR: 4,015; 0.001 FDR: 3,653
1 day, 19:50:03.598492 PROGRESS: =========================================================================
1 day, 19:50:03.623771 INFO: fragments_df_filtered: 5000
1 day, 19:50:03.638350 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:50:04.442998 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:50:05.289361 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:50:06.094263 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:50:06.513697 INFO: calibration group: precursor, predicting mz
1 day, 19:50:06.516596 INFO: calibration group: precursor, predicting rt
1 day, 19:50:06.525851 INFO: calibration group: precursor, predicting mobility
1 day, 19:50:06.528196 INFO: calibration group: fragment, predicting mz
1 day, 19:50:06.548970 INFO: === checking if optimization conditions were reached ===
1 day, 19:50:06.549139 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 19:50:06.554739 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 55.4757.
1 day, 19:50:06.554798 INFO: ==============================================
1 day, 19:50:06.554890 INFO: Starting optimization step 2.
1 day, 19:50:06.554955 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:50:06.555012 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:50:06.559033 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:50:06.559098 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:50:06.559137 INFO: FWHM in RT is 2.90 seconds, sigma is 0.64
1 day, 19:50:06.559160 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.95
1 day, 19:50:06.560194 INFO: Starting candidate selection
1 day, 19:50:09.987046 INFO: Starting candidate scoring
1 day, 19:50:10.981647 INFO: Finished candidate processing
1 day, 19:50:10.981769 INFO: Collecting candidate features
1 day, 19:50:11.032292 WARNING: intensity_correlation has 2 NaNs ( 0.01 % out of 30301)
1 day, 19:50:11.039403 INFO: Collecting fragment features
1 day, 19:50:11.061596 INFO: Finished candidate scoring
1 day, 19:50:11.078134 PROGRESS: === Extracted 30301 precursors and 324028 fragments ===
1 day, 19:50:11.078547 INFO: performing precursor FDR with 47 features
1 day, 19:50:11.078587 INFO: Decoy channel: -1
1 day, 19:50:11.078610 INFO: Competetive: True
1 day, 19:50:11.088213 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:50:11.092233 WARNING: dropped 2 decoy PSMs due to missing features
1 day, 19:50:11.368657 INFO: Test AUC: 0.854
1 day, 19:50:11.368787 INFO: Train AUC: 0.853
1 day, 19:50:11.368818 INFO: AUC difference: 0.12%
1 day, 19:50:11.459030 INFO: Resetting torch num_threads to 100
1 day, 19:50:11.460233 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:50:11.461823 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:50:11.461927 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:50:11.461987 PROGRESS: Target precursors: 7,849 (98.11%)
1 day, 19:50:11.462040 PROGRESS: Decoy precursors: 151 (1.89%)
1 day, 19:50:11.462086 PROGRESS: 
1 day, 19:50:11.462133 PROGRESS: Precursor Summary:
1 day, 19:50:11.465305 PROGRESS: Channel   0:	 0.05 FDR: 7,849; 0.01 FDR: 7,735; 0.001 FDR: 7,246
1 day, 19:50:11.465427 PROGRESS: 
1 day, 19:50:11.465486 PROGRESS: Protein Summary:
1 day, 19:50:11.470068 PROGRESS: Channel   0:	 0.05 FDR: 4,161; 0.01 FDR: 4,116; 0.001 FDR: 3,929
1 day, 19:50:11.470177 PROGRESS: =========================================================================
1 day, 19:50:11.494809 INFO: fragments_df_filtered: 5000
1 day, 19:50:11.510464 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:50:12.355693 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:50:13.243290 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:50:14.091320 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:50:14.514210 INFO: calibration group: precursor, predicting mz
1 day, 19:50:14.517559 INFO: calibration group: precursor, predicting rt
1 day, 19:50:14.527352 INFO: calibration group: precursor, predicting mobility
1 day, 19:50:14.529684 INFO: calibration group: fragment, predicting mz
1 day, 19:50:14.551019 INFO: === checking if optimization conditions were reached ===
1 day, 19:50:14.551195 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 19:50:14.557425 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 18.9435.
1 day, 19:50:14.557489 INFO: ==============================================
1 day, 19:50:14.557599 INFO: Starting optimization step 3.
1 day, 19:50:14.557673 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:50:14.557742 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:50:14.562875 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:50:14.562942 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:50:14.562984 INFO: FWHM in RT is 2.89 seconds, sigma is 0.64
1 day, 19:50:14.563007 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.92
1 day, 19:50:14.577513 INFO: Starting candidate selection
1 day, 19:50:16.517345 INFO: Starting candidate scoring
1 day, 19:50:17.519821 INFO: Finished candidate processing
1 day, 19:50:17.520020 INFO: Collecting candidate features
1 day, 19:50:17.579215 WARNING: intensity_correlation has 5 NaNs ( 0.02 % out of 30268)
1 day, 19:50:17.586422 INFO: Collecting fragment features
1 day, 19:50:17.609660 INFO: Finished candidate scoring
1 day, 19:50:17.623135 PROGRESS: === Extracted 30268 precursors and 320814 fragments ===
1 day, 19:50:17.623511 INFO: performing precursor FDR with 47 features
1 day, 19:50:17.623549 INFO: Decoy channel: -1
1 day, 19:50:17.623573 INFO: Competetive: True
1 day, 19:50:17.635108 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:50:17.640001 WARNING: dropped 1 target PSMs due to missing features
1 day, 19:50:17.640091 WARNING: dropped 4 decoy PSMs due to missing features
1 day, 19:50:17.912992 INFO: Test AUC: 0.872
1 day, 19:50:17.913126 INFO: Train AUC: 0.869
1 day, 19:50:17.913156 INFO: AUC difference: 0.36%
1 day, 19:50:18.002370 INFO: Resetting torch num_threads to 100
1 day, 19:50:18.003565 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:50:18.005040 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:50:18.005142 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:50:18.005204 PROGRESS: Target precursors: 7,895 (98.69%)
1 day, 19:50:18.005258 PROGRESS: Decoy precursors: 105 (1.31%)
1 day, 19:50:18.005316 PROGRESS: 
1 day, 19:50:18.005366 PROGRESS: Precursor Summary:
1 day, 19:50:18.008543 PROGRESS: Channel   0:	 0.05 FDR: 7,895; 0.01 FDR: 7,864; 0.001 FDR: 7,308
1 day, 19:50:18.008664 PROGRESS: 
1 day, 19:50:18.008723 PROGRESS: Protein Summary:
1 day, 19:50:18.013309 PROGRESS: Channel   0:	 0.05 FDR: 4,178; 0.01 FDR: 4,173; 0.001 FDR: 3,960
1 day, 19:50:18.013419 PROGRESS: =========================================================================
1 day, 19:50:18.039157 INFO: fragments_df_filtered: 5000
1 day, 19:50:18.055658 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:50:18.926891 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:50:19.809136 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:50:20.679964 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:50:21.098227 INFO: calibration group: precursor, predicting mz
1 day, 19:50:21.101094 INFO: calibration group: precursor, predicting rt
1 day, 19:50:21.110212 INFO: calibration group: precursor, predicting mobility
1 day, 19:50:21.112535 INFO: calibration group: fragment, predicting mz
1 day, 19:50:21.131135 INFO: === checking if optimization conditions were reached ===
1 day, 19:50:21.131292 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 19:50:21.137061 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 11.8288.
1 day, 19:50:21.137122 INFO: ==============================================
1 day, 19:50:21.137221 INFO: Starting optimization step 4.
1 day, 19:50:21.137287 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:50:21.137344 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:50:21.141418 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:50:21.141480 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:50:21.141515 INFO: FWHM in RT is 2.89 seconds, sigma is 0.63
1 day, 19:50:21.141537 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.90
1 day, 19:50:21.142616 INFO: Starting candidate selection
1 day, 19:50:22.768965 INFO: Starting candidate scoring
1 day, 19:50:23.726295 INFO: Finished candidate processing
1 day, 19:50:23.727926 INFO: Collecting candidate features
1 day, 19:50:23.777644 WARNING: intensity_correlation has 6 NaNs ( 0.02 % out of 30182)
1 day, 19:50:23.782053 INFO: Collecting fragment features
1 day, 19:50:23.800537 INFO: Finished candidate scoring
1 day, 19:50:23.813677 PROGRESS: === Extracted 30182 precursors and 318310 fragments ===
1 day, 19:50:23.814052 INFO: performing precursor FDR with 47 features
1 day, 19:50:23.814091 INFO: Decoy channel: -1
1 day, 19:50:23.814114 INFO: Competetive: True
1 day, 19:50:23.822991 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:50:23.827249 WARNING: dropped 6 decoy PSMs due to missing features
1 day, 19:50:24.095430 INFO: Test AUC: 0.882
1 day, 19:50:24.095557 INFO: Train AUC: 0.878
1 day, 19:50:24.095587 INFO: AUC difference: 0.37%
1 day, 19:50:24.181669 INFO: Resetting torch num_threads to 100
1 day, 19:50:24.182837 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:50:24.184274 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:50:24.184372 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:50:24.184433 PROGRESS: Target precursors: 7,903 (98.79%)
1 day, 19:50:24.184486 PROGRESS: Decoy precursors: 97 (1.21%)
1 day, 19:50:24.184533 PROGRESS: 
1 day, 19:50:24.184580 PROGRESS: Precursor Summary:
1 day, 19:50:24.187727 PROGRESS: Channel   0:	 0.05 FDR: 7,903; 0.01 FDR: 7,876; 0.001 FDR: 7,556
1 day, 19:50:24.187848 PROGRESS: 
1 day, 19:50:24.187907 PROGRESS: Protein Summary:
1 day, 19:50:24.192524 PROGRESS: Channel   0:	 0.05 FDR: 4,188; 0.01 FDR: 4,182; 0.001 FDR: 4,047
1 day, 19:50:24.192642 PROGRESS: =========================================================================
1 day, 19:50:24.217430 INFO: fragments_df_filtered: 5000
1 day, 19:50:24.231861 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:50:25.039074 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:50:25.860068 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:50:26.668022 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:50:27.024596 INFO: calibration group: precursor, predicting mz
1 day, 19:50:27.027486 INFO: calibration group: precursor, predicting rt
1 day, 19:50:27.036606 INFO: calibration group: precursor, predicting mobility
1 day, 19:50:27.038954 INFO: calibration group: fragment, predicting mz
1 day, 19:50:27.057880 INFO: === checking if optimization conditions were reached ===
1 day, 19:50:27.058067 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 19:50:27.064511 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 9.6661.
1 day, 19:50:27.064583 INFO: ==============================================
1 day, 19:50:27.064691 INFO: Starting optimization step 5.
1 day, 19:50:27.064766 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:50:27.064833 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:50:27.069938 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:50:27.070022 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:50:27.070065 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
1 day, 19:50:27.070092 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.90
1 day, 19:50:27.072074 INFO: Starting candidate selection
1 day, 19:50:28.705667 INFO: Starting candidate scoring
1 day, 19:50:29.676326 INFO: Finished candidate processing
1 day, 19:50:29.676518 INFO: Collecting candidate features
1 day, 19:50:29.726532 WARNING: intensity_correlation has 7 NaNs ( 0.02 % out of 30191)
1 day, 19:50:29.733696 INFO: Collecting fragment features
1 day, 19:50:29.751966 INFO: Finished candidate scoring
1 day, 19:50:29.764927 PROGRESS: === Extracted 30191 precursors and 318183 fragments ===
1 day, 19:50:29.765311 INFO: performing precursor FDR with 47 features
1 day, 19:50:29.765350 INFO: Decoy channel: -1
1 day, 19:50:29.765375 INFO: Competetive: True
1 day, 19:50:29.773187 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:50:29.777179 WARNING: dropped 7 decoy PSMs due to missing features
1 day, 19:50:30.042670 INFO: Test AUC: 0.877
1 day, 19:50:30.042797 INFO: Train AUC: 0.878
1 day, 19:50:30.042828 INFO: AUC difference: 0.15%
1 day, 19:50:30.129590 INFO: Resetting torch num_threads to 100
1 day, 19:50:30.130744 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:50:30.132206 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:50:30.132313 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:50:30.132380 PROGRESS: Target precursors: 7,878 (98.47%)
1 day, 19:50:30.132434 PROGRESS: Decoy precursors: 122 (1.52%)
1 day, 19:50:30.132483 PROGRESS: 
1 day, 19:50:30.132531 PROGRESS: Precursor Summary:
1 day, 19:50:30.135540 PROGRESS: Channel   0:	 0.05 FDR: 7,878; 0.01 FDR: 7,796; 0.001 FDR: 7,403
1 day, 19:50:30.135666 PROGRESS: 
1 day, 19:50:30.135727 PROGRESS: Protein Summary:
1 day, 19:50:30.140280 PROGRESS: Channel   0:	 0.05 FDR: 4,175; 0.01 FDR: 4,153; 0.001 FDR: 3,984
1 day, 19:50:30.140393 PROGRESS: =========================================================================
1 day, 19:50:30.164766 INFO: fragments_df_filtered: 5000
1 day, 19:50:30.179212 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:50:30.970525 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:50:31.773963 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:50:32.569216 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:50:32.920795 INFO: calibration group: precursor, predicting mz
1 day, 19:50:32.923536 INFO: calibration group: precursor, predicting rt
1 day, 19:50:32.932684 INFO: calibration group: precursor, predicting mobility
1 day, 19:50:32.934953 INFO: calibration group: fragment, predicting mz
1 day, 19:50:32.952922 INFO: === checking if optimization conditions were reached ===
1 day, 19:50:32.953101 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 19:50:32.959520 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 9.1265.
1 day, 19:50:32.959592 INFO: ==============================================
1 day, 19:50:32.959716 INFO: Starting optimization step 6.
1 day, 19:50:32.959796 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:50:32.959868 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:50:32.965322 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:50:32.965396 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:50:32.965440 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
1 day, 19:50:32.965469 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.88
1 day, 19:50:32.967454 INFO: Starting candidate selection
1 day, 19:50:34.611929 INFO: Starting candidate scoring
1 day, 19:50:35.603914 INFO: Finished candidate processing
1 day, 19:50:35.604100 INFO: Collecting candidate features
1 day, 19:50:35.685384 WARNING: intensity_correlation has 10 NaNs ( 0.03 % out of 30182)
1 day, 19:50:35.690003 INFO: Collecting fragment features
1 day, 19:50:35.709013 INFO: Finished candidate scoring
1 day, 19:50:35.724315 PROGRESS: === Extracted 30182 precursors and 318100 fragments ===
1 day, 19:50:35.724795 INFO: performing precursor FDR with 47 features
1 day, 19:50:35.724832 INFO: Decoy channel: -1
1 day, 19:50:35.724855 INFO: Competetive: True
1 day, 19:50:35.735358 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:50:35.741560 WARNING: dropped 1 target PSMs due to missing features
1 day, 19:50:35.741689 WARNING: dropped 9 decoy PSMs due to missing features
1 day, 19:50:36.176043 INFO: Test AUC: 0.875
1 day, 19:50:36.176191 INFO: Train AUC: 0.878
1 day, 19:50:36.176222 INFO: AUC difference: 0.36%
1 day, 19:50:36.267646 INFO: Resetting torch num_threads to 100
1 day, 19:50:36.269358 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:50:36.271047 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:50:36.271152 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:50:36.271213 PROGRESS: Target precursors: 7,864 (98.30%)
1 day, 19:50:36.271269 PROGRESS: Decoy precursors: 136 (1.70%)
1 day, 19:50:36.271317 PROGRESS: 
1 day, 19:50:36.271368 PROGRESS: Precursor Summary:
1 day, 19:50:36.274713 PROGRESS: Channel   0:	 0.05 FDR: 7,864; 0.01 FDR: 7,773; 0.001 FDR: 7,472
1 day, 19:50:36.274847 PROGRESS: 
1 day, 19:50:36.274904 PROGRESS: Protein Summary:
1 day, 19:50:36.279759 PROGRESS: Channel   0:	 0.05 FDR: 4,175; 0.01 FDR: 4,143; 0.001 FDR: 4,016
1 day, 19:50:36.279891 PROGRESS: =========================================================================
1 day, 19:50:36.305817 INFO: fragments_df_filtered: 5000
1 day, 19:50:36.324420 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:50:37.130960 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:50:37.934793 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:50:38.727971 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:50:39.082685 INFO: calibration group: precursor, predicting mz
1 day, 19:50:39.085861 INFO: calibration group: precursor, predicting rt
1 day, 19:50:39.095397 INFO: calibration group: precursor, predicting mobility
1 day, 19:50:39.097803 INFO: calibration group: fragment, predicting mz
1 day, 19:50:39.116975 INFO: === checking if optimization conditions were reached ===
1 day, 19:50:39.117156 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 19:50:39.123246 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 9.8691.
1 day, 19:50:39.123312 INFO: ==============================================
1 day, 19:50:39.123410 INFO: Starting optimization step 7.
1 day, 19:50:39.123477 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:50:39.123540 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:50:39.129758 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:50:39.129834 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:50:39.129874 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 19:50:39.129895 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.88
1 day, 19:50:39.131897 INFO: Starting candidate selection
1 day, 19:50:40.788574 INFO: Starting candidate scoring
1 day, 19:50:41.776919 INFO: Finished candidate processing
1 day, 19:50:41.777040 INFO: Collecting candidate features
1 day, 19:50:41.826284 WARNING: intensity_correlation has 9 NaNs ( 0.03 % out of 30189)
1 day, 19:50:41.833348 INFO: Collecting fragment features
1 day, 19:50:41.851540 INFO: Finished candidate scoring
1 day, 19:50:41.864722 PROGRESS: === Extracted 30189 precursors and 318083 fragments ===
1 day, 19:50:41.865113 INFO: performing precursor FDR with 47 features
1 day, 19:50:41.865152 INFO: Decoy channel: -1
1 day, 19:50:41.865177 INFO: Competetive: True
1 day, 19:50:41.873084 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:50:41.878031 WARNING: dropped 1 target PSMs due to missing features
1 day, 19:50:41.878134 WARNING: dropped 8 decoy PSMs due to missing features
1 day, 19:50:42.143552 INFO: Test AUC: 0.874
1 day, 19:50:42.143678 INFO: Train AUC: 0.879
1 day, 19:50:42.143713 INFO: AUC difference: 0.56%
1 day, 19:50:42.230063 INFO: Resetting torch num_threads to 100
1 day, 19:50:42.231183 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:50:42.232625 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:50:42.232724 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:50:42.232789 PROGRESS: Target precursors: 7,875 (98.44%)
1 day, 19:50:42.232845 PROGRESS: Decoy precursors: 125 (1.56%)
1 day, 19:50:42.232894 PROGRESS: 
1 day, 19:50:42.232944 PROGRESS: Precursor Summary:
1 day, 19:50:42.235955 PROGRESS: Channel   0:	 0.05 FDR: 7,875; 0.01 FDR: 7,783; 0.001 FDR: 7,507
1 day, 19:50:42.236080 PROGRESS: 
1 day, 19:50:42.236141 PROGRESS: Protein Summary:
1 day, 19:50:42.240685 PROGRESS: Channel   0:	 0.05 FDR: 4,179; 0.01 FDR: 4,150; 0.001 FDR: 4,031
1 day, 19:50:42.240807 PROGRESS: =========================================================================
1 day, 19:50:42.264311 INFO: fragments_df_filtered: 5000
1 day, 19:50:42.278630 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:50:43.135367 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:50:44.006860 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:50:44.861576 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:50:45.278763 INFO: calibration group: precursor, predicting mz
1 day, 19:50:45.281594 INFO: calibration group: precursor, predicting rt
1 day, 19:50:45.290730 INFO: calibration group: precursor, predicting mobility
1 day, 19:50:45.293083 INFO: calibration group: fragment, predicting mz
1 day, 19:50:45.312284 INFO: === checking if optimization conditions were reached ===
1 day, 19:50:45.312454 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
1 day, 19:50:45.318868 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 10.1362.
1 day, 19:50:45.318937 INFO: ==============================================
1 day, 19:50:45.319047 INFO: Starting optimization step 8.
1 day, 19:50:45.319126 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:50:45.319197 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:50:45.325912 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:50:45.325987 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:50:45.326030 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 19:50:45.326059 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.88
1 day, 19:50:45.329316 INFO: Starting candidate selection
1 day, 19:50:46.950712 INFO: Starting candidate scoring
1 day, 19:50:47.931984 INFO: Finished candidate processing
1 day, 19:50:47.932118 INFO: Collecting candidate features
1 day, 19:50:47.986006 WARNING: intensity_correlation has 8 NaNs ( 0.03 % out of 30194)
1 day, 19:50:47.990741 INFO: Collecting fragment features
1 day, 19:50:48.010271 INFO: Finished candidate scoring
1 day, 19:50:48.025697 PROGRESS: === Extracted 30194 precursors and 318227 fragments ===
1 day, 19:50:48.026166 INFO: performing precursor FDR with 47 features
1 day, 19:50:48.026205 INFO: Decoy channel: -1
1 day, 19:50:48.026229 INFO: Competetive: True
1 day, 19:50:48.036963 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:50:48.043071 WARNING: dropped 1 target PSMs due to missing features
1 day, 19:50:48.043196 WARNING: dropped 7 decoy PSMs due to missing features
1 day, 19:50:48.483577 INFO: Test AUC: 0.878
1 day, 19:50:48.483737 INFO: Train AUC: 0.878
1 day, 19:50:48.483767 INFO: AUC difference: 0.00%
1 day, 19:50:48.575533 INFO: Resetting torch num_threads to 100
1 day, 19:50:48.577220 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:50:48.578874 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:50:48.578983 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:50:48.579045 PROGRESS: Target precursors: 7,878 (98.47%)
1 day, 19:50:48.579098 PROGRESS: Decoy precursors: 122 (1.52%)
1 day, 19:50:48.579149 PROGRESS: 
1 day, 19:50:48.579197 PROGRESS: Precursor Summary:
1 day, 19:50:48.582463 PROGRESS: Channel   0:	 0.05 FDR: 7,878; 0.01 FDR: 7,783; 0.001 FDR: 7,485
1 day, 19:50:48.582605 PROGRESS: 
1 day, 19:50:48.582664 PROGRESS: Protein Summary:
1 day, 19:50:48.587537 PROGRESS: Channel   0:	 0.05 FDR: 4,176; 0.01 FDR: 4,149; 0.001 FDR: 4,019
1 day, 19:50:48.587651 PROGRESS: =========================================================================
1 day, 19:50:48.614114 INFO: fragments_df_filtered: 5000
1 day, 19:50:48.634739 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:50:49.428640 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:50:50.233302 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:50:51.077490 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:50:51.431404 INFO: calibration group: precursor, predicting mz
1 day, 19:50:51.435629 INFO: calibration group: precursor, predicting rt
1 day, 19:50:51.446175 INFO: calibration group: precursor, predicting mobility
1 day, 19:50:51.449629 INFO: calibration group: fragment, predicting mz
1 day, 19:50:51.468088 INFO: === checking if optimization conditions were reached ===
1 day, 19:50:51.468280 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
1 day, 19:50:51.469567 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 9.1265 found after 9 searches.
1 day, 19:50:51.469622 INFO: ==============================================
1 day, 19:50:51.469723 PROGRESS: Optimization finished for rt_error.
1 day, 19:50:51.488660 INFO: calibration group: precursor, predicting mz
1 day, 19:50:51.491689 INFO: calibration group: precursor, predicting rt
1 day, 19:50:51.500975 INFO: calibration group: precursor, predicting mobility
1 day, 19:50:51.503350 INFO: calibration group: fragment, predicting mz
1 day, 19:50:51.549114 INFO: Starting optimization step 0.
1 day, 19:50:51.549327 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:50:51.549400 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:50:51.555964 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:50:51.556036 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:50:51.556075 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 19:50:51.556098 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.88
1 day, 19:50:51.565057 INFO: Starting candidate selection
1 day, 19:50:53.208586 INFO: Starting candidate scoring
1 day, 19:50:54.195127 INFO: Finished candidate processing
1 day, 19:50:54.195234 INFO: Collecting candidate features
1 day, 19:50:54.243560 WARNING: intensity_correlation has 8 NaNs ( 0.03 % out of 30176)
1 day, 19:50:54.247947 INFO: Collecting fragment features
1 day, 19:50:54.266649 INFO: Finished candidate scoring
1 day, 19:50:54.279831 PROGRESS: === Extracted 30176 precursors and 318081 fragments ===
1 day, 19:50:54.280202 INFO: performing precursor FDR with 47 features
1 day, 19:50:54.280240 INFO: Decoy channel: -1
1 day, 19:50:54.280265 INFO: Competetive: True
1 day, 19:50:54.288108 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:50:54.292889 WARNING: dropped 1 target PSMs due to missing features
1 day, 19:50:54.292985 WARNING: dropped 7 decoy PSMs due to missing features
1 day, 19:50:54.658222 INFO: Test AUC: 0.884
1 day, 19:50:54.658345 INFO: Train AUC: 0.887
1 day, 19:50:54.658374 INFO: AUC difference: 0.36%
1 day, 19:50:54.744843 INFO: Resetting torch num_threads to 100
1 day, 19:50:54.746023 INFO: === FDR correction performed with classifier version 9 ===
1 day, 19:50:54.747460 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:50:54.747568 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:50:54.747630 PROGRESS: Target precursors: 7,870 (98.38%)
1 day, 19:50:54.747684 PROGRESS: Decoy precursors: 130 (1.62%)
1 day, 19:50:54.747729 PROGRESS: 
1 day, 19:50:54.747777 PROGRESS: Precursor Summary:
1 day, 19:50:54.750779 PROGRESS: Channel   0:	 0.05 FDR: 7,870; 0.01 FDR: 7,773; 0.001 FDR: 7,500
1 day, 19:50:54.750900 PROGRESS: 
1 day, 19:50:54.750959 PROGRESS: Protein Summary:
1 day, 19:50:54.755492 PROGRESS: Channel   0:	 0.05 FDR: 4,175; 0.01 FDR: 4,136; 0.001 FDR: 4,029
1 day, 19:50:54.755608 PROGRESS: =========================================================================
1 day, 19:50:54.780379 INFO: fragments_df_filtered: 5000
1 day, 19:50:54.795511 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:50:55.646453 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:50:56.488163 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:50:57.275957 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:50:57.626155 INFO: calibration group: precursor, predicting mz
1 day, 19:50:57.628988 INFO: calibration group: precursor, predicting rt
1 day, 19:50:57.639149 INFO: calibration group: precursor, predicting mobility
1 day, 19:50:57.641800 INFO: calibration group: fragment, predicting mz
1 day, 19:50:57.660379 INFO: === checking if optimization conditions were reached ===
1 day, 19:50:57.660548 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 19:50:57.663521 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0580.
1 day, 19:50:57.663587 INFO: ==============================================
1 day, 19:50:57.663694 INFO: Starting optimization step 1.
1 day, 19:50:57.663767 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:50:57.663833 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:50:57.670792 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:50:57.670872 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:50:57.670915 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 19:50:57.670942 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.87
1 day, 19:50:57.672138 INFO: Starting candidate selection
1 day, 19:50:59.053768 INFO: Starting candidate scoring
1 day, 19:51:00.035157 INFO: Finished candidate processing
1 day, 19:51:00.036549 INFO: Collecting candidate features
1 day, 19:51:00.086296 WARNING: intensity_correlation has 12 NaNs ( 0.04 % out of 30152)
1 day, 19:51:00.093353 INFO: Collecting fragment features
1 day, 19:51:00.112661 INFO: Finished candidate scoring
1 day, 19:51:00.125255 PROGRESS: === Extracted 30152 precursors and 314870 fragments ===
1 day, 19:51:00.125642 INFO: performing precursor FDR with 47 features
1 day, 19:51:00.125685 INFO: Decoy channel: -1
1 day, 19:51:00.125712 INFO: Competetive: True
1 day, 19:51:00.134008 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:51:00.138681 WARNING: dropped 2 target PSMs due to missing features
1 day, 19:51:00.138773 WARNING: dropped 10 decoy PSMs due to missing features
1 day, 19:51:00.404924 INFO: Test AUC: 0.880
1 day, 19:51:00.405058 INFO: Train AUC: 0.889
1 day, 19:51:00.405090 INFO: AUC difference: 1.01%
1 day, 19:51:00.490184 INFO: Resetting torch num_threads to 100
1 day, 19:51:00.491295 INFO: === FDR correction performed with classifier version 9 ===
1 day, 19:51:00.492609 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:51:00.492705 PROGRESS: Total precursors accumulated: 7,998
1 day, 19:51:00.492767 PROGRESS: Target precursors: 7,870 (98.40%)
1 day, 19:51:00.492822 PROGRESS: Decoy precursors: 128 (1.60%)
1 day, 19:51:00.492870 PROGRESS: 
1 day, 19:51:00.492917 PROGRESS: Precursor Summary:
1 day, 19:51:00.495884 PROGRESS: Channel   0:	 0.05 FDR: 7,870; 0.01 FDR: 7,773; 0.001 FDR: 7,557
1 day, 19:51:00.495999 PROGRESS: 
1 day, 19:51:00.496070 PROGRESS: Protein Summary:
1 day, 19:51:00.500528 PROGRESS: Channel   0:	 0.05 FDR: 4,180; 0.01 FDR: 4,143; 0.001 FDR: 4,056
1 day, 19:51:00.500633 PROGRESS: =========================================================================
1 day, 19:51:00.525269 INFO: fragments_df_filtered: 5000
1 day, 19:51:00.540111 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:51:01.328296 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:51:02.137085 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:51:02.928044 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:51:03.279823 INFO: calibration group: precursor, predicting mz
1 day, 19:51:03.283716 INFO: calibration group: precursor, predicting rt
1 day, 19:51:03.294012 INFO: calibration group: precursor, predicting mobility
1 day, 19:51:03.297488 INFO: calibration group: fragment, predicting mz
1 day, 19:51:03.315891 INFO: === checking if optimization conditions were reached ===
1 day, 19:51:03.316069 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 19:51:03.319624 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0511.
1 day, 19:51:03.319689 INFO: ==============================================
1 day, 19:51:03.319797 INFO: Starting optimization step 2.
1 day, 19:51:03.319880 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:51:03.319952 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:51:03.325833 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:51:03.325903 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:51:03.325947 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 19:51:03.325974 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.85
1 day, 19:51:03.327065 INFO: Starting candidate selection
1 day, 19:51:04.657076 INFO: Starting candidate scoring
1 day, 19:51:05.649836 INFO: Finished candidate processing
1 day, 19:51:05.649940 INFO: Collecting candidate features
1 day, 19:51:05.697861 WARNING: intensity_correlation has 14 NaNs ( 0.05 % out of 30129)
1 day, 19:51:05.702177 INFO: Collecting fragment features
1 day, 19:51:05.720438 INFO: Finished candidate scoring
1 day, 19:51:05.733235 PROGRESS: === Extracted 30129 precursors and 313341 fragments ===
1 day, 19:51:05.733608 INFO: performing precursor FDR with 47 features
1 day, 19:51:05.733646 INFO: Decoy channel: -1
1 day, 19:51:05.733669 INFO: Competetive: True
1 day, 19:51:05.741474 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:51:05.746376 WARNING: dropped 3 target PSMs due to missing features
1 day, 19:51:05.746474 WARNING: dropped 11 decoy PSMs due to missing features
1 day, 19:51:06.009642 INFO: Test AUC: 0.881
1 day, 19:51:06.009767 INFO: Train AUC: 0.888
1 day, 19:51:06.009797 INFO: AUC difference: 0.79%
1 day, 19:51:06.094427 INFO: Resetting torch num_threads to 100
1 day, 19:51:06.095534 INFO: === FDR correction performed with classifier version 9 ===
1 day, 19:51:06.096934 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:51:06.097046 PROGRESS: Total precursors accumulated: 7,998
1 day, 19:51:06.097111 PROGRESS: Target precursors: 7,867 (98.36%)
1 day, 19:51:06.097165 PROGRESS: Decoy precursors: 131 (1.64%)
1 day, 19:51:06.097212 PROGRESS: 
1 day, 19:51:06.097258 PROGRESS: Precursor Summary:
1 day, 19:51:06.100744 PROGRESS: Channel   0:	 0.05 FDR: 7,867; 0.01 FDR: 7,764; 0.001 FDR: 7,527
1 day, 19:51:06.100874 PROGRESS: 
1 day, 19:51:06.100932 PROGRESS: Protein Summary:
1 day, 19:51:06.105485 PROGRESS: Channel   0:	 0.05 FDR: 4,174; 0.01 FDR: 4,143; 0.001 FDR: 4,048
1 day, 19:51:06.105604 PROGRESS: =========================================================================
1 day, 19:51:06.129880 INFO: fragments_df_filtered: 5000
1 day, 19:51:06.145095 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:51:06.942702 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:51:07.744137 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:51:08.527849 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:51:08.881593 INFO: calibration group: precursor, predicting mz
1 day, 19:51:08.885730 INFO: calibration group: precursor, predicting rt
1 day, 19:51:08.896113 INFO: calibration group: precursor, predicting mobility
1 day, 19:51:08.899573 INFO: calibration group: fragment, predicting mz
1 day, 19:51:08.918859 INFO: === checking if optimization conditions were reached ===
1 day, 19:51:08.919032 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 19:51:08.919810 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.0580 found after 3 searches.
1 day, 19:51:08.919860 INFO: ==============================================
1 day, 19:51:08.919948 PROGRESS: Optimization finished for mobility_error.
1 day, 19:51:08.935481 INFO: calibration group: precursor, predicting mz
1 day, 19:51:08.938257 INFO: calibration group: precursor, predicting rt
1 day, 19:51:08.947403 INFO: calibration group: precursor, predicting mobility
1 day, 19:51:08.949810 INFO: calibration group: fragment, predicting mz
1 day, 19:51:08.994758 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 19:51:08.994928 PROGRESS: ==============================================
1 day, 19:51:08.995004 PROGRESS: ms2_error      : 15.0000
1 day, 19:51:08.995065 PROGRESS: ms1_error      : 10.0000
1 day, 19:51:08.995116 PROGRESS: rt_error       : 9.1265
1 day, 19:51:08.995170 PROGRESS: mobility_error : 0.0580
1 day, 19:51:08.995217 PROGRESS: ==============================================
1 day, 19:51:08.996144 INFO: calibration group: precursor, predicting mz
1 day, 19:51:09.015337 INFO: calibration group: precursor, predicting rt
1 day, 19:51:09.101366 INFO: calibration group: precursor, predicting mobility
1 day, 19:51:09.121948 INFO: calibration group: fragment, predicting mz
1 day, 19:51:09.350402 PROGRESS: Extracting batch of 162861 precursors
1 day, 19:51:09.386825 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:51:09.386959 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:51:09.387006 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 19:51:09.387031 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.85
1 day, 19:51:09.387826 INFO: Starting candidate selection
1 day, 19:51:18.309169 INFO: Applying score cutoff of 26.016138496398927
1 day, 19:51:18.314803 INFO: Removed 22862 precursors with score below cutoff
1 day, 19:51:18.629242 INFO: Starting candidate scoring
1 day, 19:51:27.342467 INFO: Finished candidate processing
1 day, 19:51:27.342679 INFO: Collecting candidate features
1 day, 19:51:27.951005 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 286815)
1 day, 19:51:27.971844 INFO: Collecting fragment features
1 day, 19:51:28.172430 INFO: Finished candidate scoring
1 day, 19:51:28.375979 INFO: === FDR correction performed with classifier version 13 ===
1 day, 19:51:28.376985 INFO: performing precursor FDR with 47 features
1 day, 19:51:28.377038 INFO: Decoy channel: -1
1 day, 19:51:28.377070 INFO: Competetive: True
1 day, 19:51:28.494842 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:51:28.545151 WARNING: dropped 2 target PSMs due to missing features
1 day, 19:51:28.545320 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 19:51:28.545374 WARNING: FDR calculation for 152687 target and 134125 decoy PSMs
1 day, 19:51:28.545409 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1 day, 19:51:34.485090 INFO: Test AUC: 0.902
1 day, 19:51:34.485319 INFO: Train AUC: 0.906
1 day, 19:51:34.485353 INFO: AUC difference: 0.41%
1 day, 19:51:36.443337 INFO: Resetting torch num_threads to 100
1 day, 19:51:36.463793 INFO: Removing fragments below FDR threshold
1 day, 19:51:36.521595 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:51:36.521901 PROGRESS: Total precursors accumulated: 80,613
1 day, 19:51:36.521970 PROGRESS: Target precursors: 79,815 (99.01%)
1 day, 19:51:36.522025 PROGRESS: Decoy precursors: 798 (0.99%)
1 day, 19:51:36.522078 PROGRESS: 
1 day, 19:51:36.522126 PROGRESS: Precursor Summary:
1 day, 19:51:36.568316 PROGRESS: Channel   0:	 0.05 FDR: 79,815; 0.01 FDR: 79,815; 0.001 FDR: 78,057
1 day, 19:51:36.568643 PROGRESS: 
1 day, 19:51:36.568710 PROGRESS: Protein Summary:
1 day, 19:51:36.626976 PROGRESS: Channel   0:	 0.05 FDR: 8,243; 0.01 FDR: 8,243; 0.001 FDR: 8,214
1 day, 19:51:36.627243 PROGRESS: =========================================================================
1 day, 19:51:37.307483 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 19:51:37.350827 PROGRESS: Loading raw file 3/6: ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 19:51:37.350972 INFO: Quantification results path: run_output/alphadia_1.10_defaultMBR/quant
1 day, 19:51:37.351050 INFO: Creating workflow folder for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506 at run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 19:51:37.351933 INFO: Initializing RawFileManager
1 day, 19:51:37.352131 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 19:51:37.352176 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 19:51:37.352207 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 19:51:37.564970 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
1 day, 19:51:44.490737 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d...
1 day, 19:51:44.493387 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 19:51:44.496752 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 19:51:44.496971 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 19:51:44.497339 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 19:51:44.499176 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 19:51:44.514564 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 19:51:44.514833 INFO: Indexing quadrupole dimension
1 day, 19:51:45.000812 INFO: Transposing detector events
1 day, 19:51:55.370965 INFO: Finished transposing data
1 day, 19:51:55.412190 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 19:51:55.413164 INFO: RT (min)            : 0.0 - 70.0
1 day, 19:51:55.413265 INFO: RT duration (sec)   : 4199.8
1 day, 19:51:55.413325 INFO: RT duration (min)   : 70.0
1 day, 19:51:55.413375 INFO: Cycle len (scans)   : 9
1 day, 19:51:55.413422 INFO: Cycle len (sec)     : 0.97
1 day, 19:51:55.413466 INFO: Number of cycles    : 4347
1 day, 19:51:55.413510 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 19:51:55.445507 INFO: Initializing CalibrationManager
1 day, 19:51:55.445873 INFO: Loading calibration config
1 day, 19:51:55.446307 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'}]
1 day, 19:51:55.446411 INFO: Calibration group :fragment, found 1 estimator(s)
1 day, 19:51:55.446484 INFO: Calibration group :precursor, found 3 estimator(s)
1 day, 19:51:55.446606 INFO: Initializing OptimizationManager
1 day, 19:51:55.446816 INFO: initial parameter: ms1_error = 30
1 day, 19:51:55.446867 INFO: initial parameter: ms2_error = 30
1 day, 19:51:55.446925 INFO: initial parameter: rt_error = 2099.8992935
1 day, 19:51:55.446973 INFO: initial parameter: mobility_error = 0.1
1 day, 19:51:55.447019 INFO: initial parameter: column_type = library
1 day, 19:51:55.447065 INFO: initial parameter: num_candidates = 1
1 day, 19:51:55.447109 INFO: initial parameter: classifier_version = -1
1 day, 19:51:55.447150 INFO: initial parameter: fwhm_rt = 5
1 day, 19:51:55.447193 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 19:51:55.447238 INFO: initial parameter: score_cutoff = 0
1 day, 19:51:55.447293 INFO: Initializing TimingManager
1 day, 19:51:55.447344 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 19:51:55.447410 INFO: FDRManager not loaded from disk.
1 day, 19:51:55.447433 INFO: Initializing FDRManager
1 day, 19:51:55.447461 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 19:51:55.478938 PROGRESS: 82,039 target precursors potentially observable (0 removed)
1 day, 19:51:55.524686 PROGRESS: Starting initial search for precursors.
1 day, 19:51:55.545438 INFO: Starting optimization step 0.
1 day, 19:51:55.545687 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:51:55.545758 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:51:55.549128 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:51:55.549187 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:51:55.549218 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 19:51:55.549240 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 19:51:55.550279 INFO: Starting candidate selection
1 day, 19:53:21.408617 INFO: Starting candidate scoring
1 day, 19:53:22.496296 INFO: Finished candidate processing
1 day, 19:53:22.496400 INFO: Collecting candidate features
1 day, 19:53:22.538127 INFO: Collecting fragment features
1 day, 19:53:22.555557 INFO: Finished candidate scoring
1 day, 19:53:22.565518 PROGRESS: === Extracted 15886 precursors and 175807 fragments ===
1 day, 19:53:22.565955 INFO: performing precursor FDR with 47 features
1 day, 19:53:22.565994 INFO: Decoy channel: -1
1 day, 19:53:22.566017 INFO: Competetive: True
1 day, 19:53:22.572173 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:53:22.749400 INFO: Test AUC: 0.827
1 day, 19:53:22.749505 INFO: Train AUC: 0.828
1 day, 19:53:22.749535 INFO: AUC difference: 0.15%
1 day, 19:53:22.836945 INFO: Resetting torch num_threads to 100
1 day, 19:53:22.838094 INFO: === FDR correction performed with classifier version -1 ===
1 day, 19:53:22.839724 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:53:22.839846 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:53:22.839931 PROGRESS: Target precursors: 6,638 (82.97%)
1 day, 19:53:22.839997 PROGRESS: Decoy precursors: 1,362 (17.03%)
1 day, 19:53:22.840049 PROGRESS: 
1 day, 19:53:22.840110 PROGRESS: Precursor Summary:
1 day, 19:53:22.842792 PROGRESS: Channel   0:	 0.05 FDR: 5,248; 0.01 FDR: 3,683; 0.001 FDR: 1,694
1 day, 19:53:22.842919 PROGRESS: 
1 day, 19:53:22.842981 PROGRESS: Protein Summary:
1 day, 19:53:22.845938 PROGRESS: Channel   0:	 0.05 FDR: 3,051; 0.01 FDR: 2,306; 0.001 FDR: 1,195
1 day, 19:53:22.846070 PROGRESS: =========================================================================
1 day, 19:53:22.854603 INFO: fragments_df_filtered: 5000
1 day, 19:53:22.876797 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:53:23.156697 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:53:23.446328 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:53:23.722043 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:53:24.087529 INFO: calibration group: precursor, predicting mz
1 day, 19:53:24.090389 INFO: calibration group: precursor, predicting rt
1 day, 19:53:24.100187 INFO: calibration group: precursor, predicting mobility
1 day, 19:53:24.102560 INFO: calibration group: fragment, predicting mz
1 day, 19:53:24.121323 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 19:53:24.121510 INFO: Starting optimization step 1.
1 day, 19:53:24.121594 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:53:24.121669 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:53:24.127301 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:53:24.127365 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:53:24.127414 INFO: FWHM in RT is 3.32 seconds, sigma is 0.73
1 day, 19:53:24.127443 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.22
1 day, 19:53:24.128702 INFO: Starting candidate selection
1 day, 19:55:00.061119 INFO: Starting candidate scoring
1 day, 19:55:02.074783 INFO: Finished candidate processing
1 day, 19:55:02.074890 INFO: Collecting candidate features
1 day, 19:55:02.133122 INFO: Collecting fragment features
1 day, 19:55:02.154878 INFO: Finished candidate scoring
1 day, 19:55:02.169922 PROGRESS: === Extracted 30475 precursors and 337252 fragments ===
1 day, 19:55:02.170378 INFO: performing precursor FDR with 47 features
1 day, 19:55:02.170418 INFO: Decoy channel: -1
1 day, 19:55:02.170442 INFO: Competetive: True
1 day, 19:55:02.181816 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:55:02.562007 INFO: Test AUC: 0.745
1 day, 19:55:02.562133 INFO: Train AUC: 0.745
1 day, 19:55:02.562162 INFO: AUC difference: 0.05%
1 day, 19:55:02.652434 INFO: Resetting torch num_threads to 100
1 day, 19:55:02.653721 INFO: === FDR correction performed with classifier version 0 ===
1 day, 19:55:02.655179 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:55:02.655288 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:55:02.655351 PROGRESS: Target precursors: 6,985 (87.31%)
1 day, 19:55:02.655403 PROGRESS: Decoy precursors: 1,015 (12.69%)
1 day, 19:55:02.655448 PROGRESS: 
1 day, 19:55:02.655493 PROGRESS: Precursor Summary:
1 day, 19:55:02.657863 PROGRESS: Channel   0:	 0.05 FDR: 5,907; 0.01 FDR: 4,585; 0.001 FDR: 2,430
1 day, 19:55:02.657986 PROGRESS: 
1 day, 19:55:02.658053 PROGRESS: Protein Summary:
1 day, 19:55:02.661252 PROGRESS: Channel   0:	 0.05 FDR: 3,365; 0.01 FDR: 2,740; 0.001 FDR: 1,638
1 day, 19:55:02.661367 PROGRESS: =========================================================================
1 day, 19:55:02.678955 INFO: fragments_df_filtered: 5000
1 day, 19:55:02.702290 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:55:03.073377 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:55:03.453094 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:55:03.822122 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:55:04.242718 INFO: calibration group: precursor, predicting mz
1 day, 19:55:04.245491 INFO: calibration group: precursor, predicting rt
1 day, 19:55:04.255255 INFO: calibration group: precursor, predicting mobility
1 day, 19:55:04.257522 INFO: calibration group: fragment, predicting mz
1 day, 19:55:04.275270 INFO: === checking if optimization conditions were reached ===
1 day, 19:55:04.277071 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 19:55:04.278632 PROGRESS: ❌ ms1_error      : 10.0000 > 10.0000 or insufficient steps taken.
1 day, 19:55:04.278683 INFO: ==============================================
1 day, 19:55:04.278776 INFO: Starting optimization step 2.
1 day, 19:55:04.278842 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:55:04.278906 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:55:04.282852 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:55:04.282914 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:55:04.282957 INFO: FWHM in RT is 3.21 seconds, sigma is 0.71
1 day, 19:55:04.282982 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.03
1 day, 19:55:04.284146 INFO: Starting candidate selection
1 day, 19:56:31.967296 INFO: Starting candidate scoring
1 day, 19:56:33.059349 INFO: Finished candidate processing
1 day, 19:56:33.059452 INFO: Collecting candidate features
1 day, 19:56:33.114378 INFO: Collecting fragment features
1 day, 19:56:33.136556 INFO: Finished candidate scoring
1 day, 19:56:33.151942 PROGRESS: === Extracted 30536 precursors and 333655 fragments ===
1 day, 19:56:33.152391 INFO: performing precursor FDR with 47 features
1 day, 19:56:33.152429 INFO: Decoy channel: -1
1 day, 19:56:33.152452 INFO: Competetive: True
1 day, 19:56:33.162849 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:56:33.475858 INFO: Test AUC: 0.792
1 day, 19:56:33.475981 INFO: Train AUC: 0.794
1 day, 19:56:33.476011 INFO: AUC difference: 0.30%
1 day, 19:56:33.564693 INFO: Resetting torch num_threads to 100
1 day, 19:56:33.565971 INFO: === FDR correction performed with classifier version 1 ===
1 day, 19:56:33.567437 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:56:33.567557 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:56:33.567620 PROGRESS: Target precursors: 7,477 (93.46%)
1 day, 19:56:33.567675 PROGRESS: Decoy precursors: 523 (6.54%)
1 day, 19:56:33.567726 PROGRESS: 
1 day, 19:56:33.567773 PROGRESS: Precursor Summary:
1 day, 19:56:33.570680 PROGRESS: Channel   0:	 0.05 FDR: 7,243; 0.01 FDR: 6,660; 0.001 FDR: 5,341
1 day, 19:56:33.570815 PROGRESS: 
1 day, 19:56:33.570877 PROGRESS: Protein Summary:
1 day, 19:56:33.574981 PROGRESS: Channel   0:	 0.05 FDR: 3,916; 0.01 FDR: 3,643; 0.001 FDR: 3,122
1 day, 19:56:33.575106 PROGRESS: =========================================================================
1 day, 19:56:33.597773 INFO: fragments_df_filtered: 5000
1 day, 19:56:33.616789 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:56:34.275874 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:56:34.956814 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:56:35.610902 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:56:36.026573 INFO: calibration group: precursor, predicting mz
1 day, 19:56:36.029413 INFO: calibration group: precursor, predicting rt
1 day, 19:56:36.038828 INFO: calibration group: precursor, predicting mobility
1 day, 19:56:36.041124 INFO: calibration group: fragment, predicting mz
1 day, 19:56:36.060025 INFO: === checking if optimization conditions were reached ===
1 day, 19:56:36.061767 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 19:56:36.063607 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
1 day, 19:56:36.063658 INFO: ==============================================
1 day, 19:56:36.063758 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 19:56:36.078198 INFO: calibration group: precursor, predicting mz
1 day, 19:56:36.080988 INFO: calibration group: precursor, predicting rt
1 day, 19:56:36.090153 INFO: calibration group: precursor, predicting mobility
1 day, 19:56:36.092447 INFO: calibration group: fragment, predicting mz
1 day, 19:56:36.112276 INFO: Starting optimization step 0.
1 day, 19:56:36.112426 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:56:36.112500 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:56:36.116360 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:56:36.117711 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:56:36.117772 INFO: FWHM in RT is 2.92 seconds, sigma is 0.64
1 day, 19:56:36.117798 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.07
1 day, 19:56:36.126810 INFO: Starting candidate selection
1 day, 19:58:01.277847 INFO: Starting candidate scoring
1 day, 19:58:02.377483 INFO: Finished candidate processing
1 day, 19:58:02.377587 INFO: Collecting candidate features
1 day, 19:58:02.437191 INFO: Collecting fragment features
1 day, 19:58:02.459579 INFO: Finished candidate scoring
1 day, 19:58:02.473660 PROGRESS: === Extracted 30459 precursors and 332453 fragments ===
1 day, 19:58:02.474121 INFO: performing precursor FDR with 47 features
1 day, 19:58:02.474161 INFO: Decoy channel: -1
1 day, 19:58:02.474184 INFO: Competetive: True
1 day, 19:58:02.484531 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:58:02.856808 INFO: Test AUC: 0.797
1 day, 19:58:02.856934 INFO: Train AUC: 0.808
1 day, 19:58:02.856965 INFO: AUC difference: 1.40%
1 day, 19:58:02.947270 INFO: Resetting torch num_threads to 100
1 day, 19:58:02.948512 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:58:02.949950 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:58:02.950059 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:58:02.950125 PROGRESS: Target precursors: 7,506 (93.83%)
1 day, 19:58:02.950179 PROGRESS: Decoy precursors: 494 (6.17%)
1 day, 19:58:02.950229 PROGRESS: 
1 day, 19:58:02.950277 PROGRESS: Precursor Summary:
1 day, 19:58:02.953202 PROGRESS: Channel   0:	 0.05 FDR: 7,301; 0.01 FDR: 6,742; 0.001 FDR: 5,953
1 day, 19:58:02.953329 PROGRESS: 
1 day, 19:58:02.953389 PROGRESS: Protein Summary:
1 day, 19:58:02.957594 PROGRESS: Channel   0:	 0.05 FDR: 3,949; 0.01 FDR: 3,687; 0.001 FDR: 3,381
1 day, 19:58:02.957714 PROGRESS: =========================================================================
1 day, 19:58:02.980383 INFO: fragments_df_filtered: 5000
1 day, 19:58:02.999989 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:58:03.615565 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:58:04.249746 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:58:04.920560 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:58:05.338067 INFO: calibration group: precursor, predicting mz
1 day, 19:58:05.340897 INFO: calibration group: precursor, predicting rt
1 day, 19:58:05.350104 INFO: calibration group: precursor, predicting mobility
1 day, 19:58:05.352399 INFO: calibration group: fragment, predicting mz
1 day, 19:58:05.371139 INFO: === checking if optimization conditions were reached ===
1 day, 19:58:05.371307 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 19:58:05.376450 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 175.4556.
1 day, 19:58:05.376512 INFO: ==============================================
1 day, 19:58:05.376624 INFO: Starting optimization step 1.
1 day, 19:58:05.376703 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:58:05.376781 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:58:05.381019 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:58:05.381099 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:58:05.381148 INFO: FWHM in RT is 2.90 seconds, sigma is 0.64
1 day, 19:58:05.381178 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.04
1 day, 19:58:05.382350 INFO: Starting candidate selection
1 day, 19:58:13.707395 INFO: Starting candidate scoring
1 day, 19:58:14.705848 INFO: Finished candidate processing
1 day, 19:58:14.705954 INFO: Collecting candidate features
1 day, 19:58:14.755768 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 30390)
1 day, 19:58:14.760307 INFO: Collecting fragment features
1 day, 19:58:14.779109 INFO: Finished candidate scoring
1 day, 19:58:14.793765 PROGRESS: === Extracted 30390 precursors and 327013 fragments ===
1 day, 19:58:14.794137 INFO: performing precursor FDR with 47 features
1 day, 19:58:14.794181 INFO: Decoy channel: -1
1 day, 19:58:14.794209 INFO: Competetive: True
1 day, 19:58:14.802740 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:58:14.806727 WARNING: dropped 3 decoy PSMs due to missing features
1 day, 19:58:15.177042 INFO: Test AUC: 0.833
1 day, 19:58:15.177171 INFO: Train AUC: 0.835
1 day, 19:58:15.177205 INFO: AUC difference: 0.23%
1 day, 19:58:15.266223 INFO: Resetting torch num_threads to 100
1 day, 19:58:15.267396 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:58:15.268946 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:58:15.269054 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:58:15.269128 PROGRESS: Target precursors: 7,755 (96.94%)
1 day, 19:58:15.269190 PROGRESS: Decoy precursors: 245 (3.06%)
1 day, 19:58:15.269246 PROGRESS: 
1 day, 19:58:15.269303 PROGRESS: Precursor Summary:
1 day, 19:58:15.272305 PROGRESS: Channel   0:	 0.05 FDR: 7,755; 0.01 FDR: 7,452; 0.001 FDR: 6,354
1 day, 19:58:15.272431 PROGRESS: 
1 day, 19:58:15.272506 PROGRESS: Protein Summary:
1 day, 19:58:15.276917 PROGRESS: Channel   0:	 0.05 FDR: 4,125; 0.01 FDR: 4,001; 0.001 FDR: 3,573
1 day, 19:58:15.277045 PROGRESS: =========================================================================
1 day, 19:58:15.303449 INFO: fragments_df_filtered: 5000
1 day, 19:58:15.318419 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:58:16.112161 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:58:16.934922 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:58:17.727498 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:58:18.144411 INFO: calibration group: precursor, predicting mz
1 day, 19:58:18.147346 INFO: calibration group: precursor, predicting rt
1 day, 19:58:18.156600 INFO: calibration group: precursor, predicting mobility
1 day, 19:58:18.158972 INFO: calibration group: fragment, predicting mz
1 day, 19:58:18.178075 INFO: === checking if optimization conditions were reached ===
1 day, 19:58:18.178231 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 19:58:18.183799 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 49.7477.
1 day, 19:58:18.183865 INFO: ==============================================
1 day, 19:58:18.183967 INFO: Starting optimization step 2.
1 day, 19:58:18.184041 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:58:18.184105 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:58:18.188192 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:58:18.188256 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:58:18.188296 INFO: FWHM in RT is 2.89 seconds, sigma is 0.63
1 day, 19:58:18.188322 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.96
1 day, 19:58:18.189599 INFO: Starting candidate selection
1 day, 19:58:21.408197 INFO: Starting candidate scoring
1 day, 19:58:22.393254 INFO: Finished candidate processing
1 day, 19:58:22.393389 INFO: Collecting candidate features
1 day, 19:58:22.454340 WARNING: intensity_correlation has 5 NaNs ( 0.02 % out of 30341)
1 day, 19:58:22.465133 INFO: Collecting fragment features
1 day, 19:58:22.485609 INFO: Finished candidate scoring
1 day, 19:58:22.501759 PROGRESS: === Extracted 30341 precursors and 323951 fragments ===
1 day, 19:58:22.502199 INFO: performing precursor FDR with 47 features
1 day, 19:58:22.502235 INFO: Decoy channel: -1
1 day, 19:58:22.502257 INFO: Competetive: True
1 day, 19:58:22.512646 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:58:22.517538 WARNING: dropped 5 decoy PSMs due to missing features
1 day, 19:58:22.955278 INFO: Test AUC: 0.856
1 day, 19:58:22.955437 INFO: Train AUC: 0.852
1 day, 19:58:22.955468 INFO: AUC difference: 0.45%
1 day, 19:58:23.053991 INFO: Resetting torch num_threads to 100
1 day, 19:58:23.055728 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:58:23.058464 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:58:23.058585 PROGRESS: Total precursors accumulated: 8,000
1 day, 19:58:23.058652 PROGRESS: Target precursors: 7,846 (98.08%)
1 day, 19:58:23.058709 PROGRESS: Decoy precursors: 154 (1.93%)
1 day, 19:58:23.058757 PROGRESS: 
1 day, 19:58:23.058803 PROGRESS: Precursor Summary:
1 day, 19:58:23.062355 PROGRESS: Channel   0:	 0.05 FDR: 7,846; 0.01 FDR: 7,698; 0.001 FDR: 7,130
1 day, 19:58:23.062485 PROGRESS: 
1 day, 19:58:23.062542 PROGRESS: Protein Summary:
1 day, 19:58:23.067459 PROGRESS: Channel   0:	 0.05 FDR: 4,158; 0.01 FDR: 4,103; 0.001 FDR: 3,867
1 day, 19:58:23.067579 PROGRESS: =========================================================================
1 day, 19:58:23.096482 INFO: fragments_df_filtered: 5000
1 day, 19:58:23.115934 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:58:23.894653 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:58:24.709196 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:58:25.489088 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:58:25.844413 INFO: calibration group: precursor, predicting mz
1 day, 19:58:25.847649 INFO: calibration group: precursor, predicting rt
1 day, 19:58:25.857297 INFO: calibration group: precursor, predicting mobility
1 day, 19:58:25.859727 INFO: calibration group: fragment, predicting mz
1 day, 19:58:25.879464 INFO: === checking if optimization conditions were reached ===
1 day, 19:58:25.879652 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 19:58:25.886327 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 20.6882.
1 day, 19:58:25.886405 INFO: ==============================================
1 day, 19:58:25.886528 INFO: Starting optimization step 3.
1 day, 19:58:25.886604 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:58:25.886673 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:58:25.895401 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:58:25.895480 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:58:25.895526 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
1 day, 19:58:25.895554 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.92
1 day, 19:58:25.901365 INFO: Starting candidate selection
1 day, 19:58:27.806497 INFO: Starting candidate scoring
1 day, 19:58:28.770272 INFO: Finished candidate processing
1 day, 19:58:28.770379 INFO: Collecting candidate features
1 day, 19:58:28.820620 WARNING: intensity_correlation has 5 NaNs ( 0.02 % out of 30278)
1 day, 19:58:28.825135 INFO: Collecting fragment features
1 day, 19:58:28.843929 INFO: Finished candidate scoring
1 day, 19:58:28.857480 PROGRESS: === Extracted 30278 precursors and 320733 fragments ===
1 day, 19:58:28.857858 INFO: performing precursor FDR with 47 features
1 day, 19:58:28.857897 INFO: Decoy channel: -1
1 day, 19:58:28.857921 INFO: Competetive: True
1 day, 19:58:28.866240 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:58:28.870266 WARNING: dropped 5 decoy PSMs due to missing features
1 day, 19:58:29.233773 INFO: Test AUC: 0.867
1 day, 19:58:29.233900 INFO: Train AUC: 0.869
1 day, 19:58:29.233930 INFO: AUC difference: 0.26%
1 day, 19:58:29.322817 INFO: Resetting torch num_threads to 100
1 day, 19:58:29.323966 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:58:29.325398 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:58:29.325498 PROGRESS: Total precursors accumulated: 7,999
1 day, 19:58:29.325563 PROGRESS: Target precursors: 7,895 (98.70%)
1 day, 19:58:29.325619 PROGRESS: Decoy precursors: 104 (1.30%)
1 day, 19:58:29.325680 PROGRESS: 
1 day, 19:58:29.325731 PROGRESS: Precursor Summary:
1 day, 19:58:29.328780 PROGRESS: Channel   0:	 0.05 FDR: 7,895; 0.01 FDR: 7,834; 0.001 FDR: 7,383
1 day, 19:58:29.328907 PROGRESS: 
1 day, 19:58:29.328969 PROGRESS: Protein Summary:
1 day, 19:58:29.333612 PROGRESS: Channel   0:	 0.05 FDR: 4,179; 0.01 FDR: 4,157; 0.001 FDR: 3,971
1 day, 19:58:29.333732 PROGRESS: =========================================================================
1 day, 19:58:29.359095 INFO: fragments_df_filtered: 5000
1 day, 19:58:29.373825 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:58:30.171364 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:58:30.982795 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:58:31.787204 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:58:32.137752 INFO: calibration group: precursor, predicting mz
1 day, 19:58:32.140555 INFO: calibration group: precursor, predicting rt
1 day, 19:58:32.149903 INFO: calibration group: precursor, predicting mobility
1 day, 19:58:32.152224 INFO: calibration group: fragment, predicting mz
1 day, 19:58:32.171060 INFO: === checking if optimization conditions were reached ===
1 day, 19:58:32.171230 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 19:58:32.177677 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 12.8442.
1 day, 19:58:32.177744 INFO: ==============================================
1 day, 19:58:32.177853 INFO: Starting optimization step 4.
1 day, 19:58:32.177930 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:58:32.177999 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:58:32.183678 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:58:32.183756 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:58:32.183799 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 19:58:32.183829 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.89
1 day, 19:58:32.185934 INFO: Starting candidate selection
1 day, 19:58:33.810374 INFO: Starting candidate scoring
1 day, 19:58:34.814022 INFO: Finished candidate processing
1 day, 19:58:34.814124 INFO: Collecting candidate features
1 day, 19:58:34.864514 WARNING: intensity_correlation has 8 NaNs ( 0.03 % out of 30262)
1 day, 19:58:34.868926 INFO: Collecting fragment features
1 day, 19:58:34.887527 INFO: Finished candidate scoring
1 day, 19:58:34.900395 PROGRESS: === Extracted 30262 precursors and 318638 fragments ===
1 day, 19:58:34.900767 INFO: performing precursor FDR with 47 features
1 day, 19:58:34.900805 INFO: Decoy channel: -1
1 day, 19:58:34.900826 INFO: Competetive: True
1 day, 19:58:34.908716 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:58:34.913656 WARNING: dropped 1 target PSMs due to missing features
1 day, 19:58:34.913750 WARNING: dropped 7 decoy PSMs due to missing features
1 day, 19:58:35.282551 INFO: Test AUC: 0.875
1 day, 19:58:35.282677 INFO: Train AUC: 0.880
1 day, 19:58:35.282707 INFO: AUC difference: 0.53%
1 day, 19:58:35.372331 INFO: Resetting torch num_threads to 100
1 day, 19:58:35.373495 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:58:35.374953 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:58:35.375048 PROGRESS: Total precursors accumulated: 7,998
1 day, 19:58:35.375110 PROGRESS: Target precursors: 7,909 (98.89%)
1 day, 19:58:35.375165 PROGRESS: Decoy precursors: 89 (1.11%)
1 day, 19:58:35.375214 PROGRESS: 
1 day, 19:58:35.375261 PROGRESS: Precursor Summary:
1 day, 19:58:35.378261 PROGRESS: Channel   0:	 0.05 FDR: 7,909; 0.01 FDR: 7,891; 0.001 FDR: 7,456
1 day, 19:58:35.378399 PROGRESS: 
1 day, 19:58:35.378463 PROGRESS: Protein Summary:
1 day, 19:58:35.383058 PROGRESS: Channel   0:	 0.05 FDR: 4,187; 0.01 FDR: 4,182; 0.001 FDR: 4,003
1 day, 19:58:35.383176 PROGRESS: =========================================================================
1 day, 19:58:35.408319 INFO: fragments_df_filtered: 5000
1 day, 19:58:35.422666 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:58:36.236407 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:58:37.062000 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:58:37.876781 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:58:38.227744 INFO: calibration group: precursor, predicting mz
1 day, 19:58:38.230625 INFO: calibration group: precursor, predicting rt
1 day, 19:58:38.239822 INFO: calibration group: precursor, predicting mobility
1 day, 19:58:38.242188 INFO: calibration group: fragment, predicting mz
1 day, 19:58:38.260725 INFO: === checking if optimization conditions were reached ===
1 day, 19:58:38.260889 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 19:58:38.267398 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 11.3611.
1 day, 19:58:38.267469 INFO: ==============================================
1 day, 19:58:38.267585 INFO: Starting optimization step 5.
1 day, 19:58:38.267661 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:58:38.267727 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:58:38.272724 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:58:38.272795 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:58:38.272839 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 19:58:38.272869 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.87
1 day, 19:58:38.274074 INFO: Starting candidate selection
1 day, 19:58:39.909180 INFO: Starting candidate scoring
1 day, 19:58:40.891133 INFO: Finished candidate processing
1 day, 19:58:40.891269 INFO: Collecting candidate features
1 day, 19:58:40.943188 WARNING: intensity_correlation has 9 NaNs ( 0.03 % out of 30267)
1 day, 19:58:40.943447 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 30267)
1 day, 19:58:40.947639 INFO: Collecting fragment features
1 day, 19:58:40.967300 INFO: Finished candidate scoring
1 day, 19:58:40.980199 PROGRESS: === Extracted 30267 precursors and 318665 fragments ===
1 day, 19:58:40.980572 INFO: performing precursor FDR with 47 features
1 day, 19:58:40.980611 INFO: Decoy channel: -1
1 day, 19:58:40.980634 INFO: Competetive: True
1 day, 19:58:40.989289 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:58:40.994228 WARNING: dropped 1 target PSMs due to missing features
1 day, 19:58:40.994317 WARNING: dropped 9 decoy PSMs due to missing features
1 day, 19:58:41.370378 INFO: Test AUC: 0.878
1 day, 19:58:41.370503 INFO: Train AUC: 0.877
1 day, 19:58:41.370534 INFO: AUC difference: 0.06%
1 day, 19:58:41.459011 INFO: Resetting torch num_threads to 100
1 day, 19:58:41.460188 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:58:41.461566 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:58:41.461675 PROGRESS: Total precursors accumulated: 7,999
1 day, 19:58:41.461740 PROGRESS: Target precursors: 7,901 (98.77%)
1 day, 19:58:41.461794 PROGRESS: Decoy precursors: 98 (1.23%)
1 day, 19:58:41.461843 PROGRESS: 
1 day, 19:58:41.461888 PROGRESS: Precursor Summary:
1 day, 19:58:41.464840 PROGRESS: Channel   0:	 0.05 FDR: 7,901; 0.01 FDR: 7,861; 0.001 FDR: 7,512
1 day, 19:58:41.464962 PROGRESS: 
1 day, 19:58:41.465030 PROGRESS: Protein Summary:
1 day, 19:58:41.469555 PROGRESS: Channel   0:	 0.05 FDR: 4,181; 0.01 FDR: 4,174; 0.001 FDR: 4,032
1 day, 19:58:41.469665 PROGRESS: =========================================================================
1 day, 19:58:41.493980 INFO: fragments_df_filtered: 5000
1 day, 19:58:41.508430 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:58:42.349201 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:58:43.168699 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:58:43.973001 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:58:44.331483 INFO: calibration group: precursor, predicting mz
1 day, 19:58:44.334818 INFO: calibration group: precursor, predicting rt
1 day, 19:58:44.344295 INFO: calibration group: precursor, predicting mobility
1 day, 19:58:44.346678 INFO: calibration group: fragment, predicting mz
1 day, 19:58:44.365927 INFO: === checking if optimization conditions were reached ===
1 day, 19:58:44.366123 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 19:58:44.372714 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 10.7725.
1 day, 19:58:44.372785 INFO: ==============================================
1 day, 19:58:44.372912 INFO: Starting optimization step 6.
1 day, 19:58:44.372999 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:58:44.373097 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:58:44.391311 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:58:44.391397 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:58:44.391447 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 19:58:44.391475 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.87
1 day, 19:58:44.400517 INFO: Starting candidate selection
1 day, 19:58:45.947974 INFO: Starting candidate scoring
1 day, 19:58:46.930168 INFO: Finished candidate processing
1 day, 19:58:46.930360 INFO: Collecting candidate features
1 day, 19:58:46.991089 WARNING: intensity_correlation has 9 NaNs ( 0.03 % out of 30257)
1 day, 19:58:46.991361 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 30257)
1 day, 19:58:46.995672 INFO: Collecting fragment features
1 day, 19:58:47.019163 INFO: Finished candidate scoring
1 day, 19:58:47.032768 PROGRESS: === Extracted 30257 precursors and 318548 fragments ===
1 day, 19:58:47.033208 INFO: performing precursor FDR with 47 features
1 day, 19:58:47.033250 INFO: Decoy channel: -1
1 day, 19:58:47.033274 INFO: Competetive: True
1 day, 19:58:47.044747 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:58:47.049845 WARNING: dropped 2 target PSMs due to missing features
1 day, 19:58:47.049928 WARNING: dropped 8 decoy PSMs due to missing features
1 day, 19:58:47.417100 INFO: Test AUC: 0.874
1 day, 19:58:47.417222 INFO: Train AUC: 0.877
1 day, 19:58:47.417253 INFO: AUC difference: 0.34%
1 day, 19:58:47.506007 INFO: Resetting torch num_threads to 100
1 day, 19:58:47.507157 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:58:47.508826 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:58:47.508925 PROGRESS: Total precursors accumulated: 7,999
1 day, 19:58:47.508986 PROGRESS: Target precursors: 7,893 (98.67%)
1 day, 19:58:47.509053 PROGRESS: Decoy precursors: 106 (1.33%)
1 day, 19:58:47.509103 PROGRESS: 
1 day, 19:58:47.509148 PROGRESS: Precursor Summary:
1 day, 19:58:47.512136 PROGRESS: Channel   0:	 0.05 FDR: 7,893; 0.01 FDR: 7,843; 0.001 FDR: 7,356
1 day, 19:58:47.512248 PROGRESS: 
1 day, 19:58:47.512306 PROGRESS: Protein Summary:
1 day, 19:58:47.516864 PROGRESS: Channel   0:	 0.05 FDR: 4,178; 0.01 FDR: 4,166; 0.001 FDR: 3,972
1 day, 19:58:47.516983 PROGRESS: =========================================================================
1 day, 19:58:47.542631 INFO: fragments_df_filtered: 5000
1 day, 19:58:47.560756 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:58:48.361115 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:58:49.173265 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:58:49.974937 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:58:50.325652 INFO: calibration group: precursor, predicting mz
1 day, 19:58:50.328431 INFO: calibration group: precursor, predicting rt
1 day, 19:58:50.337554 INFO: calibration group: precursor, predicting mobility
1 day, 19:58:50.339830 INFO: calibration group: fragment, predicting mz
1 day, 19:58:50.358408 INFO: === checking if optimization conditions were reached ===
1 day, 19:58:50.358593 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 19:58:50.365105 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 10.4040.
1 day, 19:58:50.365171 INFO: ==============================================
1 day, 19:58:50.365283 INFO: Starting optimization step 7.
1 day, 19:58:50.365362 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:58:50.365433 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:58:50.371683 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:58:50.371755 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:58:50.371807 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 19:58:50.371836 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.88
1 day, 19:58:50.374623 INFO: Starting candidate selection
1 day, 19:58:52.015654 INFO: Starting candidate scoring
1 day, 19:58:53.014064 INFO: Finished candidate processing
1 day, 19:58:53.014279 INFO: Collecting candidate features
1 day, 19:58:53.065585 WARNING: intensity_correlation has 10 NaNs ( 0.03 % out of 30268)
1 day, 19:58:53.065846 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 30268)
1 day, 19:58:53.070034 INFO: Collecting fragment features
1 day, 19:58:53.089168 INFO: Finished candidate scoring
1 day, 19:58:53.102064 PROGRESS: === Extracted 30268 precursors and 318622 fragments ===
1 day, 19:58:53.102434 INFO: performing precursor FDR with 47 features
1 day, 19:58:53.102472 INFO: Decoy channel: -1
1 day, 19:58:53.102496 INFO: Competetive: True
1 day, 19:58:53.110492 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:58:53.115137 WARNING: dropped 2 target PSMs due to missing features
1 day, 19:58:53.115219 WARNING: dropped 9 decoy PSMs due to missing features
1 day, 19:58:53.471301 INFO: Test AUC: 0.865
1 day, 19:58:53.471426 INFO: Train AUC: 0.880
1 day, 19:58:53.471456 INFO: AUC difference: 1.73%
1 day, 19:58:53.558673 INFO: Resetting torch num_threads to 100
1 day, 19:58:53.559837 INFO: === FDR correction performed with classifier version 2 ===
1 day, 19:58:53.561217 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:58:53.561317 PROGRESS: Total precursors accumulated: 7,999
1 day, 19:58:53.561382 PROGRESS: Target precursors: 7,888 (98.61%)
1 day, 19:58:53.561437 PROGRESS: Decoy precursors: 111 (1.39%)
1 day, 19:58:53.561488 PROGRESS: 
1 day, 19:58:53.561538 PROGRESS: Precursor Summary:
1 day, 19:58:53.564656 PROGRESS: Channel   0:	 0.05 FDR: 7,888; 0.01 FDR: 7,842; 0.001 FDR: 7,437
1 day, 19:58:53.564774 PROGRESS: 
1 day, 19:58:53.564835 PROGRESS: Protein Summary:
1 day, 19:58:53.569348 PROGRESS: Channel   0:	 0.05 FDR: 4,178; 0.01 FDR: 4,163; 0.001 FDR: 4,000
1 day, 19:58:53.569461 PROGRESS: =========================================================================
1 day, 19:58:53.593563 INFO: fragments_df_filtered: 5000
1 day, 19:58:53.607920 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:58:54.409505 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:58:55.221259 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:58:56.020138 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:58:56.370557 INFO: calibration group: precursor, predicting mz
1 day, 19:58:56.373322 INFO: calibration group: precursor, predicting rt
1 day, 19:58:56.382484 INFO: calibration group: precursor, predicting mobility
1 day, 19:58:56.384751 INFO: calibration group: fragment, predicting mz
1 day, 19:58:56.403079 INFO: === checking if optimization conditions were reached ===
1 day, 19:58:56.403250 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
1 day, 19:58:56.404505 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 10.4040 found after 8 searches.
1 day, 19:58:56.404562 INFO: ==============================================
1 day, 19:58:56.404667 PROGRESS: Optimization finished for rt_error.
1 day, 19:58:56.423105 INFO: calibration group: precursor, predicting mz
1 day, 19:58:56.426297 INFO: calibration group: precursor, predicting rt
1 day, 19:58:56.436043 INFO: calibration group: precursor, predicting mobility
1 day, 19:58:56.438702 INFO: calibration group: fragment, predicting mz
1 day, 19:58:56.490852 INFO: Starting optimization step 0.
1 day, 19:58:56.491059 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:58:56.491140 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:58:56.496181 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:58:56.496258 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:58:56.496303 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 19:58:56.496332 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.87
1 day, 19:58:56.505307 INFO: Starting candidate selection
1 day, 19:58:58.111847 INFO: Starting candidate scoring
1 day, 19:58:59.102549 INFO: Finished candidate processing
1 day, 19:58:59.102681 INFO: Collecting candidate features
1 day, 19:58:59.153313 WARNING: intensity_correlation has 8 NaNs ( 0.03 % out of 30264)
1 day, 19:58:59.153669 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 30264)
1 day, 19:58:59.161174 INFO: Collecting fragment features
1 day, 19:58:59.180229 INFO: Finished candidate scoring
1 day, 19:58:59.193265 PROGRESS: === Extracted 30264 precursors and 318587 fragments ===
1 day, 19:58:59.193647 INFO: performing precursor FDR with 47 features
1 day, 19:58:59.193691 INFO: Decoy channel: -1
1 day, 19:58:59.193720 INFO: Competetive: True
1 day, 19:58:59.201457 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:58:59.206392 WARNING: dropped 2 target PSMs due to missing features
1 day, 19:58:59.206496 WARNING: dropped 7 decoy PSMs due to missing features
1 day, 19:58:59.553746 INFO: Test AUC: 0.881
1 day, 19:58:59.553877 INFO: Train AUC: 0.887
1 day, 19:58:59.553913 INFO: AUC difference: 0.70%
1 day, 19:58:59.638649 INFO: Resetting torch num_threads to 100
1 day, 19:58:59.639818 INFO: === FDR correction performed with classifier version 10 ===
1 day, 19:58:59.641243 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:58:59.641582 PROGRESS: Total precursors accumulated: 7,999
1 day, 19:58:59.641656 PROGRESS: Target precursors: 7,881 (98.52%)
1 day, 19:58:59.641715 PROGRESS: Decoy precursors: 118 (1.48%)
1 day, 19:58:59.641772 PROGRESS: 
1 day, 19:58:59.641826 PROGRESS: Precursor Summary:
1 day, 19:58:59.644973 PROGRESS: Channel   0:	 0.05 FDR: 7,881; 0.01 FDR: 7,828; 0.001 FDR: 7,442
1 day, 19:58:59.645100 PROGRESS: 
1 day, 19:58:59.645166 PROGRESS: Protein Summary:
1 day, 19:58:59.649653 PROGRESS: Channel   0:	 0.05 FDR: 4,177; 0.01 FDR: 4,163; 0.001 FDR: 4,001
1 day, 19:58:59.649770 PROGRESS: =========================================================================
1 day, 19:58:59.674903 INFO: fragments_df_filtered: 5000
1 day, 19:58:59.689239 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:59:00.489396 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:59:01.299498 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:59:02.099787 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:59:02.449323 INFO: calibration group: precursor, predicting mz
1 day, 19:59:02.452208 INFO: calibration group: precursor, predicting rt
1 day, 19:59:02.461910 INFO: calibration group: precursor, predicting mobility
1 day, 19:59:02.464270 INFO: calibration group: fragment, predicting mz
1 day, 19:59:02.481983 INFO: === checking if optimization conditions were reached ===
1 day, 19:59:02.482177 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 19:59:02.485187 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0580.
1 day, 19:59:02.485251 INFO: ==============================================
1 day, 19:59:02.485366 INFO: Starting optimization step 1.
1 day, 19:59:02.485443 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:59:02.485512 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:59:02.491127 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:59:02.491197 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:59:02.491241 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 19:59:02.491269 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.88
1 day, 19:59:02.492438 INFO: Starting candidate selection
1 day, 19:59:03.858094 INFO: Starting candidate scoring
1 day, 19:59:04.832772 INFO: Finished candidate processing
1 day, 19:59:04.832910 INFO: Collecting candidate features
1 day, 19:59:04.889349 WARNING: intensity_correlation has 9 NaNs ( 0.03 % out of 30211)
1 day, 19:59:04.889632 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 30211)
1 day, 19:59:04.893979 INFO: Collecting fragment features
1 day, 19:59:04.913708 INFO: Finished candidate scoring
1 day, 19:59:04.928962 PROGRESS: === Extracted 30211 precursors and 314996 fragments ===
1 day, 19:59:04.929422 INFO: performing precursor FDR with 47 features
1 day, 19:59:04.929462 INFO: Decoy channel: -1
1 day, 19:59:04.929493 INFO: Competetive: True
1 day, 19:59:04.938923 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:59:04.944810 WARNING: dropped 2 target PSMs due to missing features
1 day, 19:59:04.944927 WARNING: dropped 8 decoy PSMs due to missing features
1 day, 19:59:05.379023 INFO: Test AUC: 0.894
1 day, 19:59:05.379186 INFO: Train AUC: 0.883
1 day, 19:59:05.379221 INFO: AUC difference: 1.27%
1 day, 19:59:08.078281 INFO: Resetting torch num_threads to 100
1 day, 19:59:08.080122 INFO: === FDR correction performed with classifier version 10 ===
1 day, 19:59:08.083010 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:59:08.083154 PROGRESS: Total precursors accumulated: 7,998
1 day, 19:59:08.083220 PROGRESS: Target precursors: 7,883 (98.56%)
1 day, 19:59:08.083274 PROGRESS: Decoy precursors: 115 (1.44%)
1 day, 19:59:08.083321 PROGRESS: 
1 day, 19:59:08.083368 PROGRESS: Precursor Summary:
1 day, 19:59:08.087955 PROGRESS: Channel   0:	 0.05 FDR: 7,883; 0.01 FDR: 7,821; 0.001 FDR: 7,500
1 day, 19:59:08.088117 PROGRESS: 
1 day, 19:59:08.088181 PROGRESS: Protein Summary:
1 day, 19:59:08.093364 PROGRESS: Channel   0:	 0.05 FDR: 4,178; 0.01 FDR: 4,153; 0.001 FDR: 4,024
1 day, 19:59:08.093505 PROGRESS: =========================================================================
1 day, 19:59:08.122195 INFO: fragments_df_filtered: 5000
1 day, 19:59:08.142887 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:59:08.958417 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:59:09.773951 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:59:10.570837 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:59:10.921928 INFO: calibration group: precursor, predicting mz
1 day, 19:59:10.924870 INFO: calibration group: precursor, predicting rt
1 day, 19:59:10.934061 INFO: calibration group: precursor, predicting mobility
1 day, 19:59:10.936408 INFO: calibration group: fragment, predicting mz
1 day, 19:59:10.954587 INFO: === checking if optimization conditions were reached ===
1 day, 19:59:10.954756 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 19:59:10.957288 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0514.
1 day, 19:59:10.957345 INFO: ==============================================
1 day, 19:59:10.957443 INFO: Starting optimization step 2.
1 day, 19:59:10.957511 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 19:59:10.957570 PROGRESS: Extracting batch of 15886 precursors
1 day, 19:59:10.961718 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:59:10.961780 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:59:10.961817 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 19:59:10.961839 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.86
1 day, 19:59:10.970666 INFO: Starting candidate selection
1 day, 19:59:12.338054 INFO: Starting candidate scoring
1 day, 19:59:13.300756 INFO: Finished candidate processing
1 day, 19:59:13.300897 INFO: Collecting candidate features
1 day, 19:59:13.352106 WARNING: intensity_correlation has 9 NaNs ( 0.03 % out of 30160)
1 day, 19:59:13.352387 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 30160)
1 day, 19:59:13.356585 INFO: Collecting fragment features
1 day, 19:59:13.375623 INFO: Finished candidate scoring
1 day, 19:59:13.391952 PROGRESS: === Extracted 30160 precursors and 313842 fragments ===
1 day, 19:59:13.392342 INFO: performing precursor FDR with 47 features
1 day, 19:59:13.392385 INFO: Decoy channel: -1
1 day, 19:59:13.392411 INFO: Competetive: True
1 day, 19:59:13.401197 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:59:13.406194 WARNING: dropped 2 target PSMs due to missing features
1 day, 19:59:13.406295 WARNING: dropped 8 decoy PSMs due to missing features
1 day, 19:59:13.769227 INFO: Test AUC: 0.886
1 day, 19:59:13.769354 INFO: Train AUC: 0.885
1 day, 19:59:13.769385 INFO: AUC difference: 0.09%
1 day, 19:59:13.854196 INFO: Resetting torch num_threads to 100
1 day, 19:59:13.855421 INFO: === FDR correction performed with classifier version 10 ===
1 day, 19:59:13.856911 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:59:13.857012 PROGRESS: Total precursors accumulated: 7,998
1 day, 19:59:13.857088 PROGRESS: Target precursors: 7,883 (98.56%)
1 day, 19:59:13.857141 PROGRESS: Decoy precursors: 115 (1.44%)
1 day, 19:59:13.857191 PROGRESS: 
1 day, 19:59:13.857236 PROGRESS: Precursor Summary:
1 day, 19:59:13.860381 PROGRESS: Channel   0:	 0.05 FDR: 7,883; 0.01 FDR: 7,814; 0.001 FDR: 7,562
1 day, 19:59:13.860505 PROGRESS: 
1 day, 19:59:13.860566 PROGRESS: Protein Summary:
1 day, 19:59:13.865277 PROGRESS: Channel   0:	 0.05 FDR: 4,177; 0.01 FDR: 4,148; 0.001 FDR: 4,049
1 day, 19:59:13.865388 PROGRESS: =========================================================================
1 day, 19:59:13.889693 INFO: fragments_df_filtered: 5000
1 day, 19:59:13.904287 INFO: calibration group: precursor, fitting mz estimator 
1 day, 19:59:14.702199 INFO: calibration group: precursor, fitting rt estimator 
1 day, 19:59:15.512161 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 19:59:16.305140 INFO: calibration group: fragment, fitting mz estimator 
1 day, 19:59:16.655405 INFO: calibration group: precursor, predicting mz
1 day, 19:59:16.658410 INFO: calibration group: precursor, predicting rt
1 day, 19:59:16.667726 INFO: calibration group: precursor, predicting mobility
1 day, 19:59:16.670104 INFO: calibration group: fragment, predicting mz
1 day, 19:59:16.689315 INFO: === checking if optimization conditions were reached ===
1 day, 19:59:16.689479 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 19:59:16.690249 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.1000 found after 3 searches.
1 day, 19:59:16.690300 INFO: ==============================================
1 day, 19:59:16.690389 PROGRESS: Optimization finished for mobility_error.
1 day, 19:59:16.704903 INFO: calibration group: precursor, predicting mz
1 day, 19:59:16.707772 INFO: calibration group: precursor, predicting rt
1 day, 19:59:16.717537 INFO: calibration group: precursor, predicting mobility
1 day, 19:59:16.719895 INFO: calibration group: fragment, predicting mz
1 day, 19:59:16.763330 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 19:59:16.763501 PROGRESS: ==============================================
1 day, 19:59:16.763572 PROGRESS: ms2_error      : 15.0000
1 day, 19:59:16.763632 PROGRESS: ms1_error      : 10.0000
1 day, 19:59:16.763685 PROGRESS: rt_error       : 10.4040
1 day, 19:59:16.763736 PROGRESS: mobility_error : 0.1000
1 day, 19:59:16.763785 PROGRESS: ==============================================
1 day, 19:59:16.764616 INFO: calibration group: precursor, predicting mz
1 day, 19:59:16.783977 INFO: calibration group: precursor, predicting rt
1 day, 19:59:16.873203 INFO: calibration group: precursor, predicting mobility
1 day, 19:59:16.893977 INFO: calibration group: fragment, predicting mz
1 day, 19:59:17.129651 PROGRESS: Extracting batch of 162861 precursors
1 day, 19:59:17.167723 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 19:59:17.167853 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 19:59:17.167900 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 19:59:17.167926 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.88
1 day, 19:59:17.168805 INFO: Starting candidate selection
1 day, 19:59:28.478506 INFO: Applying score cutoff of 28.377387195587158
1 day, 19:59:28.484571 INFO: Removed 24541 precursors with score below cutoff
1 day, 19:59:28.819656 INFO: Starting candidate scoring
1 day, 19:59:37.597186 INFO: Finished candidate processing
1 day, 19:59:37.597289 INFO: Collecting candidate features
1 day, 19:59:38.074690 INFO: Collecting fragment features
1 day, 19:59:38.264215 INFO: Finished candidate scoring
1 day, 19:59:38.418637 INFO: === FDR correction performed with classifier version 11 ===
1 day, 19:59:38.420095 INFO: performing precursor FDR with 47 features
1 day, 19:59:38.420146 INFO: Decoy channel: -1
1 day, 19:59:38.420173 INFO: Competetive: True
1 day, 19:59:38.519426 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 19:59:38.550274 WARNING: FDR calculation for 152364 target and 133215 decoy PSMs
1 day, 19:59:38.550415 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1 day, 19:59:43.370150 INFO: Test AUC: 0.899
1 day, 19:59:43.370280 INFO: Train AUC: 0.901
1 day, 19:59:43.370312 INFO: AUC difference: 0.24%
1 day, 19:59:43.473480 INFO: Resetting torch num_threads to 100
1 day, 19:59:43.491549 INFO: Removing fragments below FDR threshold
1 day, 19:59:43.544333 PROGRESS: ============================= Precursor FDR =============================
1 day, 19:59:43.544658 PROGRESS: Total precursors accumulated: 80,959
1 day, 19:59:43.544728 PROGRESS: Target precursors: 80,158 (99.01%)
1 day, 19:59:43.544784 PROGRESS: Decoy precursors: 801 (0.99%)
1 day, 19:59:43.544836 PROGRESS: 
1 day, 19:59:43.544885 PROGRESS: Precursor Summary:
1 day, 19:59:43.580607 PROGRESS: Channel   0:	 0.05 FDR: 80,158; 0.01 FDR: 80,158; 0.001 FDR: 77,623
1 day, 19:59:43.580943 PROGRESS: 
1 day, 19:59:43.581011 PROGRESS: Protein Summary:
1 day, 19:59:43.631490 PROGRESS: Channel   0:	 0.05 FDR: 8,244; 0.01 FDR: 8,244; 0.001 FDR: 8,212
1 day, 19:59:43.631799 PROGRESS: =========================================================================
1 day, 19:59:44.306578 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 19:59:44.347911 PROGRESS: Loading raw file 4/6: ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 19:59:44.348063 INFO: Quantification results path: run_output/alphadia_1.10_defaultMBR/quant
1 day, 19:59:44.348140 INFO: Creating workflow folder for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496 at run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 19:59:44.349014 INFO: Initializing RawFileManager
1 day, 19:59:44.349124 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 19:59:44.349168 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 19:59:44.349196 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 19:59:44.561163 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
1 day, 19:59:51.943853 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d...
1 day, 19:59:51.946622 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 19:59:51.951318 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 19:59:51.951611 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 19:59:51.952056 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 19:59:51.953850 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 19:59:51.976537 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 19:59:51.976875 INFO: Indexing quadrupole dimension
1 day, 19:59:52.444649 INFO: Transposing detector events
1 day, 20:00:02.186134 INFO: Finished transposing data
1 day, 20:00:02.222182 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 20:00:02.223200 INFO: RT (min)            : 0.0 - 70.0
1 day, 20:00:02.223295 INFO: RT duration (sec)   : 4199.8
1 day, 20:00:02.223355 INFO: RT duration (min)   : 70.0
1 day, 20:00:02.223408 INFO: Cycle len (scans)   : 9
1 day, 20:00:02.223454 INFO: Cycle len (sec)     : 0.97
1 day, 20:00:02.223502 INFO: Number of cycles    : 4347
1 day, 20:00:02.223549 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 20:00:02.279989 INFO: Initializing CalibrationManager
1 day, 20:00:02.280354 INFO: Loading calibration config
1 day, 20:00:02.281045 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'}]
1 day, 20:00:02.281147 INFO: Calibration group :fragment, found 1 estimator(s)
1 day, 20:00:02.281245 INFO: Calibration group :precursor, found 3 estimator(s)
1 day, 20:00:02.281401 INFO: Initializing OptimizationManager
1 day, 20:00:02.281529 INFO: initial parameter: ms1_error = 30
1 day, 20:00:02.281588 INFO: initial parameter: ms2_error = 30
1 day, 20:00:02.281656 INFO: initial parameter: rt_error = 2099.891532
1 day, 20:00:02.281709 INFO: initial parameter: mobility_error = 0.1
1 day, 20:00:02.281756 INFO: initial parameter: column_type = library
1 day, 20:00:02.281802 INFO: initial parameter: num_candidates = 1
1 day, 20:00:02.281850 INFO: initial parameter: classifier_version = -1
1 day, 20:00:02.281894 INFO: initial parameter: fwhm_rt = 5
1 day, 20:00:02.281939 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 20:00:02.281981 INFO: initial parameter: score_cutoff = 0
1 day, 20:00:02.282045 INFO: Initializing TimingManager
1 day, 20:00:02.282104 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 20:00:02.282203 INFO: FDRManager not loaded from disk.
1 day, 20:00:02.282228 INFO: Initializing FDRManager
1 day, 20:00:02.282264 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 20:00:02.311843 PROGRESS: 82,039 target precursors potentially observable (0 removed)
1 day, 20:00:02.357666 PROGRESS: Starting initial search for precursors.
1 day, 20:00:02.375884 INFO: Starting optimization step 0.
1 day, 20:00:02.376139 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:00:02.376237 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:00:02.379470 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:00:02.379524 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:00:02.379562 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 20:00:02.379586 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 20:00:02.381478 INFO: Starting candidate selection
1 day, 20:01:28.330160 INFO: Starting candidate scoring
1 day, 20:01:29.362635 INFO: Finished candidate processing
1 day, 20:01:29.362775 INFO: Collecting candidate features
1 day, 20:01:29.400160 INFO: Collecting fragment features
1 day, 20:01:29.417243 INFO: Finished candidate scoring
1 day, 20:01:29.427420 PROGRESS: === Extracted 15885 precursors and 175826 fragments ===
1 day, 20:01:29.427866 INFO: performing precursor FDR with 47 features
1 day, 20:01:29.427903 INFO: Decoy channel: -1
1 day, 20:01:29.427926 INFO: Competetive: True
1 day, 20:01:29.433092 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:01:29.605303 INFO: Test AUC: 0.807
1 day, 20:01:29.605424 INFO: Train AUC: 0.818
1 day, 20:01:29.605455 INFO: AUC difference: 1.38%
1 day, 20:01:29.695739 INFO: Resetting torch num_threads to 100
1 day, 20:01:29.696883 INFO: === FDR correction performed with classifier version -1 ===
1 day, 20:01:29.698864 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:01:29.698994 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:01:29.699056 PROGRESS: Target precursors: 6,641 (83.01%)
1 day, 20:01:29.699108 PROGRESS: Decoy precursors: 1,359 (16.99%)
1 day, 20:01:29.699154 PROGRESS: 
1 day, 20:01:29.699200 PROGRESS: Precursor Summary:
1 day, 20:01:29.701892 PROGRESS: Channel   0:	 0.05 FDR: 5,213; 0.01 FDR: 4,351; 0.001 FDR: 3,271
1 day, 20:01:29.702033 PROGRESS: 
1 day, 20:01:29.702091 PROGRESS: Protein Summary:
1 day, 20:01:29.705432 PROGRESS: Channel   0:	 0.05 FDR: 3,052; 0.01 FDR: 2,653; 0.001 FDR: 2,116
1 day, 20:01:29.705554 PROGRESS: =========================================================================
1 day, 20:01:29.715020 INFO: fragments_df_filtered: 5000
1 day, 20:01:29.732028 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:01:30.011580 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:01:30.361932 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:01:30.640403 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:01:30.997299 INFO: calibration group: precursor, predicting mz
1 day, 20:01:31.000178 INFO: calibration group: precursor, predicting rt
1 day, 20:01:31.009896 INFO: calibration group: precursor, predicting mobility
1 day, 20:01:31.012281 INFO: calibration group: fragment, predicting mz
1 day, 20:01:31.031434 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 20:01:31.031606 INFO: Starting optimization step 1.
1 day, 20:01:31.031688 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:01:31.031754 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:01:31.035961 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:01:31.036022 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:01:31.036065 INFO: FWHM in RT is 3.25 seconds, sigma is 0.72
1 day, 20:01:31.036088 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.08
1 day, 20:01:31.044882 INFO: Starting candidate selection
1 day, 20:03:07.042625 INFO: Starting candidate scoring
1 day, 20:03:08.955820 INFO: Finished candidate processing
1 day, 20:03:08.955994 INFO: Collecting candidate features
1 day, 20:03:09.033324 INFO: Collecting fragment features
1 day, 20:03:09.058792 INFO: Finished candidate scoring
1 day, 20:03:09.079005 PROGRESS: === Extracted 30459 precursors and 336997 fragments ===
1 day, 20:03:09.079506 INFO: performing precursor FDR with 47 features
1 day, 20:03:09.079546 INFO: Decoy channel: -1
1 day, 20:03:09.079571 INFO: Competetive: True
1 day, 20:03:09.093698 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:03:09.455479 INFO: Test AUC: 0.756
1 day, 20:03:09.455605 INFO: Train AUC: 0.749
1 day, 20:03:09.455639 INFO: AUC difference: 0.92%
1 day, 20:03:09.546839 INFO: Resetting torch num_threads to 100
1 day, 20:03:09.548114 INFO: === FDR correction performed with classifier version 0 ===
1 day, 20:03:09.549660 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:03:09.549778 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:03:09.549848 PROGRESS: Target precursors: 6,837 (85.46%)
1 day, 20:03:09.549908 PROGRESS: Decoy precursors: 1,163 (14.54%)
1 day, 20:03:09.549962 PROGRESS: 
1 day, 20:03:09.550017 PROGRESS: Precursor Summary:
1 day, 20:03:09.550961 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1 day, 20:03:09.551062 PROGRESS: 
1 day, 20:03:09.551134 PROGRESS: Protein Summary:
1 day, 20:03:09.552145 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1 day, 20:03:09.552240 PROGRESS: =========================================================================
1 day, 20:03:09.585230 INFO: calibration group: precursor, predicting mz
1 day, 20:03:09.590431 INFO: calibration group: precursor, predicting rt
1 day, 20:03:09.607512 INFO: calibration group: precursor, predicting mobility
1 day, 20:03:09.611775 INFO: calibration group: fragment, predicting mz
1 day, 20:03:09.650427 INFO: === skipping optimization until target number of precursors are found ===
1 day, 20:03:09.650735 INFO: Starting optimization step 2.
1 day, 20:03:09.650829 PROGRESS: === Extracting elution groups 8000 to 24000 ===
1 day, 20:03:09.650912 PROGRESS: Extracting batch of 31769 precursors
1 day, 20:03:09.662281 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:03:09.662392 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:03:09.662450 INFO: FWHM in RT is 3.25 seconds, sigma is 0.72
1 day, 20:03:09.662480 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.08
1 day, 20:03:09.671640 INFO: Starting candidate selection
1 day, 20:06:15.330148 INFO: Starting candidate scoring
1 day, 20:06:18.760807 INFO: Finished candidate processing
1 day, 20:06:18.761175 INFO: Collecting candidate features
1 day, 20:06:18.900922 INFO: Collecting fragment features
1 day, 20:06:18.945728 INFO: Finished candidate scoring
1 day, 20:06:19.002616 PROGRESS: === Extracted 91375 precursors and 1013371 fragments ===
1 day, 20:06:19.016812 INFO: performing precursor FDR with 47 features
1 day, 20:06:19.016952 INFO: Decoy channel: -1
1 day, 20:06:19.016978 INFO: Competetive: True
1 day, 20:06:19.055216 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:06:20.615819 INFO: Test AUC: 0.771
1 day, 20:06:20.615959 INFO: Train AUC: 0.768
1 day, 20:06:20.615989 INFO: AUC difference: 0.38%
1 day, 20:06:20.718529 INFO: Resetting torch num_threads to 100
1 day, 20:06:20.722324 INFO: === FDR correction performed with classifier version 0 ===
1 day, 20:06:20.726370 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:06:20.726541 PROGRESS: Total precursors accumulated: 24,000
1 day, 20:06:20.726617 PROGRESS: Target precursors: 21,427 (89.28%)
1 day, 20:06:20.726669 PROGRESS: Decoy precursors: 2,573 (10.72%)
1 day, 20:06:20.726720 PROGRESS: 
1 day, 20:06:20.726769 PROGRESS: Precursor Summary:
1 day, 20:06:20.733182 PROGRESS: Channel   0:	 0.05 FDR: 18,636; 0.01 FDR: 16,806; 0.001 FDR: 13,683
1 day, 20:06:20.733375 PROGRESS: 
1 day, 20:06:20.733437 PROGRESS: Protein Summary:
1 day, 20:06:20.742935 PROGRESS: Channel   0:	 0.05 FDR: 5,823; 0.01 FDR: 5,439; 0.001 FDR: 4,809
1 day, 20:06:20.743134 PROGRESS: =========================================================================
1 day, 20:06:20.814917 INFO: fragments_df_filtered: 5000
1 day, 20:06:20.838714 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:06:24.383943 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:06:28.036377 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:06:31.575169 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:06:31.933180 INFO: calibration group: precursor, predicting mz
1 day, 20:06:31.936194 INFO: calibration group: precursor, predicting rt
1 day, 20:06:31.945434 INFO: calibration group: precursor, predicting mobility
1 day, 20:06:31.947805 INFO: calibration group: fragment, predicting mz
1 day, 20:06:31.967588 INFO: === checking if optimization conditions were reached ===
1 day, 20:06:31.969481 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 20:06:31.973064 PROGRESS: ❌ ms1_error      : 10.0000 > 10.0000 or insufficient steps taken.
1 day, 20:06:31.973119 INFO: ==============================================
1 day, 20:06:31.973236 INFO: Starting optimization step 3.
1 day, 20:06:31.973305 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:06:31.973369 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:06:31.978120 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:06:31.978187 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:06:31.978228 INFO: FWHM in RT is 3.24 seconds, sigma is 0.71
1 day, 20:06:31.978251 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.92
1 day, 20:06:31.979156 INFO: Starting candidate selection
1 day, 20:07:58.836591 INFO: Starting candidate scoring
1 day, 20:07:59.881614 INFO: Finished candidate processing
1 day, 20:07:59.881724 INFO: Collecting candidate features
1 day, 20:07:59.939421 INFO: Collecting fragment features
1 day, 20:07:59.960424 INFO: Finished candidate scoring
1 day, 20:07:59.975824 PROGRESS: === Extracted 30520 precursors and 333204 fragments ===
1 day, 20:07:59.976279 INFO: performing precursor FDR with 47 features
1 day, 20:07:59.976318 INFO: Decoy channel: -1
1 day, 20:07:59.976341 INFO: Competetive: True
1 day, 20:07:59.987932 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:08:00.377360 INFO: Test AUC: 0.799
1 day, 20:08:00.377485 INFO: Train AUC: 0.803
1 day, 20:08:00.377516 INFO: AUC difference: 0.42%
1 day, 20:08:00.471248 INFO: Resetting torch num_threads to 100
1 day, 20:08:00.472632 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:08:00.474164 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:08:00.474270 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:08:00.474332 PROGRESS: Target precursors: 7,538 (94.23%)
1 day, 20:08:00.474385 PROGRESS: Decoy precursors: 462 (5.78%)
1 day, 20:08:00.474432 PROGRESS: 
1 day, 20:08:00.474478 PROGRESS: Precursor Summary:
1 day, 20:08:00.477587 PROGRESS: Channel   0:	 0.05 FDR: 7,374; 0.01 FDR: 6,870; 0.001 FDR: 5,724
1 day, 20:08:00.477716 PROGRESS: 
1 day, 20:08:00.477780 PROGRESS: Protein Summary:
1 day, 20:08:00.482237 PROGRESS: Channel   0:	 0.05 FDR: 3,987; 0.01 FDR: 3,768; 0.001 FDR: 3,263
1 day, 20:08:00.482355 PROGRESS: =========================================================================
1 day, 20:08:00.506926 INFO: fragments_df_filtered: 5000
1 day, 20:08:00.527401 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:08:01.153907 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:08:01.810647 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:08:02.440107 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:08:02.797113 INFO: calibration group: precursor, predicting mz
1 day, 20:08:02.800164 INFO: calibration group: precursor, predicting rt
1 day, 20:08:02.809905 INFO: calibration group: precursor, predicting mobility
1 day, 20:08:02.812366 INFO: calibration group: fragment, predicting mz
1 day, 20:08:02.832389 INFO: === checking if optimization conditions were reached ===
1 day, 20:08:02.834550 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 20:08:02.836766 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
1 day, 20:08:02.836824 INFO: ==============================================
1 day, 20:08:02.836958 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 20:08:02.857334 INFO: calibration group: precursor, predicting mz
1 day, 20:08:02.860611 INFO: calibration group: precursor, predicting rt
1 day, 20:08:02.870553 INFO: calibration group: precursor, predicting mobility
1 day, 20:08:02.873289 INFO: calibration group: fragment, predicting mz
1 day, 20:08:02.895175 INFO: Starting optimization step 0.
1 day, 20:08:02.895365 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:08:02.895459 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:08:02.901907 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:08:02.901990 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:08:02.902041 INFO: FWHM in RT is 2.93 seconds, sigma is 0.64
1 day, 20:08:02.902071 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.06
1 day, 20:08:02.910975 INFO: Starting candidate selection
1 day, 20:09:33.681853 INFO: Starting candidate scoring
1 day, 20:09:34.752291 INFO: Finished candidate processing
1 day, 20:09:34.752396 INFO: Collecting candidate features
1 day, 20:09:34.813552 INFO: Collecting fragment features
1 day, 20:09:34.839872 INFO: Finished candidate scoring
1 day, 20:09:34.853594 PROGRESS: === Extracted 30467 precursors and 332256 fragments ===
1 day, 20:09:34.854062 INFO: performing precursor FDR with 47 features
1 day, 20:09:34.854103 INFO: Decoy channel: -1
1 day, 20:09:34.854126 INFO: Competetive: True
1 day, 20:09:34.868194 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:09:35.247925 INFO: Test AUC: 0.812
1 day, 20:09:35.248049 INFO: Train AUC: 0.816
1 day, 20:09:35.248080 INFO: AUC difference: 0.51%
1 day, 20:09:35.340574 INFO: Resetting torch num_threads to 100
1 day, 20:09:35.341785 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:09:35.343178 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:09:35.343289 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:09:35.343355 PROGRESS: Target precursors: 7,574 (94.67%)
1 day, 20:09:35.343410 PROGRESS: Decoy precursors: 426 (5.33%)
1 day, 20:09:35.343458 PROGRESS: 
1 day, 20:09:35.343503 PROGRESS: Precursor Summary:
1 day, 20:09:35.346471 PROGRESS: Channel   0:	 0.05 FDR: 7,517; 0.01 FDR: 6,938; 0.001 FDR: 5,720
1 day, 20:09:35.346604 PROGRESS: 
1 day, 20:09:35.346663 PROGRESS: Protein Summary:
1 day, 20:09:35.350828 PROGRESS: Channel   0:	 0.05 FDR: 4,027; 0.01 FDR: 3,784; 0.001 FDR: 3,275
1 day, 20:09:35.350946 PROGRESS: =========================================================================
1 day, 20:09:35.373839 INFO: fragments_df_filtered: 5000
1 day, 20:09:35.393106 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:09:36.041880 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:09:36.713943 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:09:37.352704 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:09:37.708659 INFO: calibration group: precursor, predicting mz
1 day, 20:09:37.711629 INFO: calibration group: precursor, predicting rt
1 day, 20:09:37.721303 INFO: calibration group: precursor, predicting mobility
1 day, 20:09:37.723769 INFO: calibration group: fragment, predicting mz
1 day, 20:09:37.744513 INFO: === checking if optimization conditions were reached ===
1 day, 20:09:37.744687 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 20:09:37.750167 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 296.3653.
1 day, 20:09:37.750226 INFO: ==============================================
1 day, 20:09:37.750331 INFO: Starting optimization step 1.
1 day, 20:09:37.750402 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:09:37.750467 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:09:37.754809 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:09:37.754869 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:09:37.754925 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 20:09:37.754951 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.02
1 day, 20:09:37.756071 INFO: Starting candidate selection
1 day, 20:09:51.160058 INFO: Starting candidate scoring
1 day, 20:09:52.141514 INFO: Finished candidate processing
1 day, 20:09:52.141650 INFO: Collecting candidate features
1 day, 20:09:52.203640 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 30387)
1 day, 20:09:52.212644 INFO: Collecting fragment features
1 day, 20:09:52.234589 INFO: Finished candidate scoring
1 day, 20:09:52.250532 PROGRESS: === Extracted 30387 precursors and 328022 fragments ===
1 day, 20:09:52.250996 INFO: performing precursor FDR with 47 features
1 day, 20:09:52.251036 INFO: Decoy channel: -1
1 day, 20:09:52.251059 INFO: Competetive: True
1 day, 20:09:52.261807 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:09:52.266671 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 20:09:52.710986 INFO: Test AUC: 0.832
1 day, 20:09:52.711151 INFO: Train AUC: 0.838
1 day, 20:09:52.711181 INFO: AUC difference: 0.65%
1 day, 20:09:52.803566 INFO: Resetting torch num_threads to 100
1 day, 20:09:52.805215 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:09:52.806791 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:09:52.806890 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:09:52.806963 PROGRESS: Target precursors: 7,743 (96.79%)
1 day, 20:09:52.807026 PROGRESS: Decoy precursors: 257 (3.21%)
1 day, 20:09:52.807074 PROGRESS: 
1 day, 20:09:52.807121 PROGRESS: Precursor Summary:
1 day, 20:09:52.810422 PROGRESS: Channel   0:	 0.05 FDR: 7,743; 0.01 FDR: 7,449; 0.001 FDR: 6,830
1 day, 20:09:52.810544 PROGRESS: 
1 day, 20:09:52.810604 PROGRESS: Protein Summary:
1 day, 20:09:52.815252 PROGRESS: Channel   0:	 0.05 FDR: 4,124; 0.01 FDR: 3,996; 0.001 FDR: 3,758
1 day, 20:09:52.815374 PROGRESS: =========================================================================
1 day, 20:09:52.844832 INFO: fragments_df_filtered: 5000
1 day, 20:09:52.863660 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:09:53.611606 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:09:54.448205 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:09:55.243237 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:09:55.662258 INFO: calibration group: precursor, predicting mz
1 day, 20:09:55.665657 INFO: calibration group: precursor, predicting rt
1 day, 20:09:55.675492 INFO: calibration group: precursor, predicting mobility
1 day, 20:09:55.677948 INFO: calibration group: fragment, predicting mz
1 day, 20:09:55.698656 INFO: === checking if optimization conditions were reached ===
1 day, 20:09:55.698841 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 20:09:55.704812 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 119.0359.
1 day, 20:09:55.704877 INFO: ==============================================
1 day, 20:09:55.704978 INFO: Starting optimization step 2.
1 day, 20:09:55.705074 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:09:55.705140 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:09:55.712078 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:09:55.712156 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:09:55.712196 INFO: FWHM in RT is 2.89 seconds, sigma is 0.64
1 day, 20:09:55.712222 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.92
1 day, 20:09:55.714914 INFO: Starting candidate selection
1 day, 20:10:01.485990 INFO: Starting candidate scoring
1 day, 20:10:03.228136 INFO: Finished candidate processing
1 day, 20:10:03.228232 INFO: Collecting candidate features
1 day, 20:10:03.281601 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 30340)
1 day, 20:10:03.281942 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 30340)
1 day, 20:10:03.289091 INFO: Collecting fragment features
1 day, 20:10:03.307910 INFO: Finished candidate scoring
1 day, 20:10:03.322294 PROGRESS: === Extracted 30340 precursors and 325010 fragments ===
1 day, 20:10:03.322660 INFO: performing precursor FDR with 47 features
1 day, 20:10:03.322696 INFO: Decoy channel: -1
1 day, 20:10:03.322718 INFO: Competetive: True
1 day, 20:10:03.331284 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:10:03.335526 WARNING: dropped 2 decoy PSMs due to missing features
1 day, 20:10:03.712118 INFO: Test AUC: 0.851
1 day, 20:10:03.712246 INFO: Train AUC: 0.854
1 day, 20:10:03.712276 INFO: AUC difference: 0.38%
1 day, 20:10:03.802174 INFO: Resetting torch num_threads to 100
1 day, 20:10:03.803356 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:10:03.804734 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:10:03.804826 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:10:03.804888 PROGRESS: Target precursors: 7,830 (97.88%)
1 day, 20:10:03.804939 PROGRESS: Decoy precursors: 170 (2.12%)
1 day, 20:10:03.804988 PROGRESS: 
1 day, 20:10:03.805046 PROGRESS: Precursor Summary:
1 day, 20:10:03.808034 PROGRESS: Channel   0:	 0.05 FDR: 7,830; 0.01 FDR: 7,730; 0.001 FDR: 7,248
1 day, 20:10:03.808150 PROGRESS: 
1 day, 20:10:03.808208 PROGRESS: Protein Summary:
1 day, 20:10:03.812725 PROGRESS: Channel   0:	 0.05 FDR: 4,162; 0.01 FDR: 4,121; 0.001 FDR: 3,933
1 day, 20:10:03.812832 PROGRESS: =========================================================================
1 day, 20:10:03.838376 INFO: fragments_df_filtered: 5000
1 day, 20:10:03.853396 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:10:04.699908 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:10:05.589101 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:10:06.436806 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:10:06.855260 INFO: calibration group: precursor, predicting mz
1 day, 20:10:06.858160 INFO: calibration group: precursor, predicting rt
1 day, 20:10:06.867768 INFO: calibration group: precursor, predicting mobility
1 day, 20:10:06.870201 INFO: calibration group: fragment, predicting mz
1 day, 20:10:06.889843 INFO: === checking if optimization conditions were reached ===
1 day, 20:10:06.890068 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 20:10:06.896651 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 50.3024.
1 day, 20:10:06.896723 INFO: ==============================================
1 day, 20:10:06.896832 INFO: Starting optimization step 3.
1 day, 20:10:06.896907 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:10:06.896975 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:10:06.903065 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:10:06.903132 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:10:06.903174 INFO: FWHM in RT is 2.89 seconds, sigma is 0.64
1 day, 20:10:06.903203 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.88
1 day, 20:10:06.905602 INFO: Starting candidate selection
1 day, 20:10:10.121567 INFO: Starting candidate scoring
1 day, 20:10:11.051330 INFO: Finished candidate processing
1 day, 20:10:11.051486 INFO: Collecting candidate features
1 day, 20:10:11.100952 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 30298)
1 day, 20:10:11.105432 INFO: Collecting fragment features
1 day, 20:10:11.123535 INFO: Finished candidate scoring
1 day, 20:10:11.136469 PROGRESS: === Extracted 30298 precursors and 322651 fragments ===
1 day, 20:10:11.136860 INFO: performing precursor FDR with 47 features
1 day, 20:10:11.136897 INFO: Decoy channel: -1
1 day, 20:10:11.136919 INFO: Competetive: True
1 day, 20:10:11.145159 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:10:11.149156 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 20:10:11.529068 INFO: Test AUC: 0.854
1 day, 20:10:11.529190 INFO: Train AUC: 0.865
1 day, 20:10:11.529221 INFO: AUC difference: 1.18%
1 day, 20:10:11.618023 INFO: Resetting torch num_threads to 100
1 day, 20:10:11.619187 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:10:11.620585 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:10:11.620684 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:10:11.620747 PROGRESS: Target precursors: 7,904 (98.80%)
1 day, 20:10:11.620799 PROGRESS: Decoy precursors: 96 (1.20%)
1 day, 20:10:11.620848 PROGRESS: 
1 day, 20:10:11.620894 PROGRESS: Precursor Summary:
1 day, 20:10:11.623916 PROGRESS: Channel   0:	 0.05 FDR: 7,904; 0.01 FDR: 7,869; 0.001 FDR: 7,566
1 day, 20:10:11.624037 PROGRESS: 
1 day, 20:10:11.624099 PROGRESS: Protein Summary:
1 day, 20:10:11.628678 PROGRESS: Channel   0:	 0.05 FDR: 4,188; 0.01 FDR: 4,175; 0.001 FDR: 4,056
1 day, 20:10:11.628790 PROGRESS: =========================================================================
1 day, 20:10:11.653700 INFO: fragments_df_filtered: 5000
1 day, 20:10:11.668119 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:10:12.534714 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:10:13.387869 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:10:14.211335 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:10:14.564512 INFO: calibration group: precursor, predicting mz
1 day, 20:10:14.567439 INFO: calibration group: precursor, predicting rt
1 day, 20:10:14.577190 INFO: calibration group: precursor, predicting mobility
1 day, 20:10:14.579604 INFO: calibration group: fragment, predicting mz
1 day, 20:10:14.600419 INFO: === checking if optimization conditions were reached ===
1 day, 20:10:14.600587 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 20:10:14.607230 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 26.4911.
1 day, 20:10:14.607302 INFO: ==============================================
1 day, 20:10:14.607414 INFO: Starting optimization step 4.
1 day, 20:10:14.607492 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:10:14.607562 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:10:14.613604 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:10:14.613676 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:10:14.613720 INFO: FWHM in RT is 2.89 seconds, sigma is 0.63
1 day, 20:10:14.613748 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.86
1 day, 20:10:14.616330 INFO: Starting candidate selection
1 day, 20:10:16.910006 INFO: Starting candidate scoring
1 day, 20:10:17.833960 INFO: Finished candidate processing
1 day, 20:10:17.834091 INFO: Collecting candidate features
1 day, 20:10:17.885040 WARNING: intensity_correlation has 7 NaNs ( 0.02 % out of 30257)
1 day, 20:10:17.892233 INFO: Collecting fragment features
1 day, 20:10:17.910696 INFO: Finished candidate scoring
1 day, 20:10:17.923475 PROGRESS: === Extracted 30257 precursors and 320268 fragments ===
1 day, 20:10:17.923845 INFO: performing precursor FDR with 47 features
1 day, 20:10:17.923885 INFO: Decoy channel: -1
1 day, 20:10:17.923912 INFO: Competetive: True
1 day, 20:10:17.931786 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:10:17.936522 WARNING: dropped 1 target PSMs due to missing features
1 day, 20:10:17.936605 WARNING: dropped 6 decoy PSMs due to missing features
1 day, 20:10:18.315534 INFO: Test AUC: 0.871
1 day, 20:10:18.315661 INFO: Train AUC: 0.871
1 day, 20:10:18.315691 INFO: AUC difference: 0.02%
1 day, 20:10:18.416094 INFO: Resetting torch num_threads to 100
1 day, 20:10:18.417331 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:10:18.418740 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:10:18.418845 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:10:18.418908 PROGRESS: Target precursors: 7,927 (99.09%)
1 day, 20:10:18.418962 PROGRESS: Decoy precursors: 73 (0.91%)
1 day, 20:10:18.419008 PROGRESS: 
1 day, 20:10:18.419053 PROGRESS: Precursor Summary:
1 day, 20:10:18.422045 PROGRESS: Channel   0:	 0.05 FDR: 7,927; 0.01 FDR: 7,927; 0.001 FDR: 7,738
1 day, 20:10:18.422169 PROGRESS: 
1 day, 20:10:18.422229 PROGRESS: Protein Summary:
1 day, 20:10:18.426823 PROGRESS: Channel   0:	 0.05 FDR: 4,194; 0.01 FDR: 4,194; 0.001 FDR: 4,125
1 day, 20:10:18.426941 PROGRESS: =========================================================================
1 day, 20:10:18.452089 INFO: fragments_df_filtered: 5000
1 day, 20:10:18.466449 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:10:19.284271 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:10:20.130194 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:10:20.951383 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:10:21.303484 INFO: calibration group: precursor, predicting mz
1 day, 20:10:21.306361 INFO: calibration group: precursor, predicting rt
1 day, 20:10:21.315903 INFO: calibration group: precursor, predicting mobility
1 day, 20:10:21.318260 INFO: calibration group: fragment, predicting mz
1 day, 20:10:21.336580 INFO: === checking if optimization conditions were reached ===
1 day, 20:10:21.336760 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 20:10:21.343377 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 16.3476.
1 day, 20:10:21.343444 INFO: ==============================================
1 day, 20:10:21.343552 INFO: Starting optimization step 5.
1 day, 20:10:21.343627 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:10:21.343693 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:10:21.349687 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:10:21.349757 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:10:21.349800 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 20:10:21.349827 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.85
1 day, 20:10:21.352230 INFO: Starting candidate selection
1 day, 20:10:23.217619 INFO: Starting candidate scoring
1 day, 20:10:24.139600 INFO: Finished candidate processing
1 day, 20:10:24.139703 INFO: Collecting candidate features
1 day, 20:10:24.212894 WARNING: intensity_correlation has 6 NaNs ( 0.02 % out of 30227)
1 day, 20:10:24.218201 INFO: Collecting fragment features
1 day, 20:10:24.236228 INFO: Finished candidate scoring
1 day, 20:10:24.248613 PROGRESS: === Extracted 30227 precursors and 319071 fragments ===
1 day, 20:10:24.248981 INFO: performing precursor FDR with 47 features
1 day, 20:10:24.249019 INFO: Decoy channel: -1
1 day, 20:10:24.249057 INFO: Competetive: True
1 day, 20:10:24.256967 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:10:24.260943 WARNING: dropped 6 decoy PSMs due to missing features
1 day, 20:10:24.634434 INFO: Test AUC: 0.876
1 day, 20:10:24.634560 INFO: Train AUC: 0.880
1 day, 20:10:24.634590 INFO: AUC difference: 0.50%
1 day, 20:10:24.720528 INFO: Resetting torch num_threads to 100
1 day, 20:10:24.721714 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:10:24.723062 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:10:24.723163 PROGRESS: Total precursors accumulated: 7,999
1 day, 20:10:24.723225 PROGRESS: Target precursors: 7,935 (99.20%)
1 day, 20:10:24.723277 PROGRESS: Decoy precursors: 64 (0.80%)
1 day, 20:10:24.723324 PROGRESS: 
1 day, 20:10:24.723371 PROGRESS: Precursor Summary:
1 day, 20:10:24.726362 PROGRESS: Channel   0:	 0.05 FDR: 7,935; 0.01 FDR: 7,935; 0.001 FDR: 7,802
1 day, 20:10:24.726477 PROGRESS: 
1 day, 20:10:24.726534 PROGRESS: Protein Summary:
1 day, 20:10:24.731109 PROGRESS: Channel   0:	 0.05 FDR: 4,199; 0.01 FDR: 4,199; 0.001 FDR: 4,144
1 day, 20:10:24.731224 PROGRESS: =========================================================================
1 day, 20:10:24.756187 INFO: fragments_df_filtered: 5000
1 day, 20:10:24.770384 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:10:25.588043 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:10:26.425530 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:10:27.249322 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:10:27.599456 INFO: calibration group: precursor, predicting mz
1 day, 20:10:27.602319 INFO: calibration group: precursor, predicting rt
1 day, 20:10:27.611917 INFO: calibration group: precursor, predicting mobility
1 day, 20:10:27.614380 INFO: calibration group: fragment, predicting mz
1 day, 20:10:27.633947 INFO: === checking if optimization conditions were reached ===
1 day, 20:10:27.634122 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 20:10:27.640705 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 13.1899.
1 day, 20:10:27.640774 INFO: ==============================================
1 day, 20:10:27.640890 INFO: Starting optimization step 6.
1 day, 20:10:27.640969 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:10:27.641052 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:10:27.646009 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:10:27.646079 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:10:27.646122 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 20:10:27.646152 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.84
1 day, 20:10:27.647696 INFO: Starting candidate selection
1 day, 20:10:29.217949 INFO: Starting candidate scoring
1 day, 20:10:30.139586 INFO: Finished candidate processing
1 day, 20:10:30.139689 INFO: Collecting candidate features
1 day, 20:10:30.189836 WARNING: intensity_correlation has 9 NaNs ( 0.03 % out of 30184)
1 day, 20:10:30.198141 INFO: Collecting fragment features
1 day, 20:10:30.216049 INFO: Finished candidate scoring
1 day, 20:10:30.228493 PROGRESS: === Extracted 30184 precursors and 317070 fragments ===
1 day, 20:10:30.228862 INFO: performing precursor FDR with 47 features
1 day, 20:10:30.228900 INFO: Decoy channel: -1
1 day, 20:10:30.228925 INFO: Competetive: True
1 day, 20:10:30.237056 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:10:30.240993 WARNING: dropped 9 decoy PSMs due to missing features
1 day, 20:10:30.626424 INFO: Test AUC: 0.891
1 day, 20:10:30.626548 INFO: Train AUC: 0.885
1 day, 20:10:30.626579 INFO: AUC difference: 0.70%
1 day, 20:10:30.712810 INFO: Resetting torch num_threads to 100
1 day, 20:10:30.713917 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:10:30.715273 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:10:30.715369 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:10:30.715429 PROGRESS: Target precursors: 7,941 (99.26%)
1 day, 20:10:30.715483 PROGRESS: Decoy precursors: 59 (0.74%)
1 day, 20:10:30.715540 PROGRESS: 
1 day, 20:10:30.715590 PROGRESS: Precursor Summary:
1 day, 20:10:30.718597 PROGRESS: Channel   0:	 0.05 FDR: 7,941; 0.01 FDR: 7,941; 0.001 FDR: 7,742
1 day, 20:10:30.718722 PROGRESS: 
1 day, 20:10:30.718786 PROGRESS: Protein Summary:
1 day, 20:10:30.723451 PROGRESS: Channel   0:	 0.05 FDR: 4,196; 0.01 FDR: 4,196; 0.001 FDR: 4,122
1 day, 20:10:30.723565 PROGRESS: =========================================================================
1 day, 20:10:30.748899 INFO: fragments_df_filtered: 5000
1 day, 20:10:30.763085 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:10:31.658442 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:10:32.552308 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:10:33.375257 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:10:33.728811 INFO: calibration group: precursor, predicting mz
1 day, 20:10:33.731779 INFO: calibration group: precursor, predicting rt
1 day, 20:10:33.741434 INFO: calibration group: precursor, predicting mobility
1 day, 20:10:33.743890 INFO: calibration group: fragment, predicting mz
1 day, 20:10:33.762721 INFO: === checking if optimization conditions were reached ===
1 day, 20:10:33.762867 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 20:10:33.768956 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 10.6216.
1 day, 20:10:33.769018 INFO: ==============================================
1 day, 20:10:33.769127 INFO: Starting optimization step 7.
1 day, 20:10:33.769196 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:10:33.769264 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:10:33.773728 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:10:33.773787 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:10:33.773825 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 20:10:33.773850 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.83
1 day, 20:10:33.774806 INFO: Starting candidate selection
1 day, 20:10:35.371916 INFO: Starting candidate scoring
1 day, 20:10:36.299673 INFO: Finished candidate processing
1 day, 20:10:36.300782 INFO: Collecting candidate features
1 day, 20:10:36.350917 WARNING: intensity_correlation has 9 NaNs ( 0.03 % out of 30191)
1 day, 20:10:36.358044 INFO: Collecting fragment features
1 day, 20:10:36.376036 INFO: Finished candidate scoring
1 day, 20:10:36.388384 PROGRESS: === Extracted 30191 precursors and 317226 fragments ===
1 day, 20:10:36.388762 INFO: performing precursor FDR with 47 features
1 day, 20:10:36.388800 INFO: Decoy channel: -1
1 day, 20:10:36.388824 INFO: Competetive: True
1 day, 20:10:36.396903 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:10:36.400840 WARNING: dropped 9 decoy PSMs due to missing features
1 day, 20:10:36.769491 INFO: Test AUC: 0.889
1 day, 20:10:36.769612 INFO: Train AUC: 0.890
1 day, 20:10:36.769642 INFO: AUC difference: 0.17%
1 day, 20:10:36.856005 INFO: Resetting torch num_threads to 100
1 day, 20:10:36.857162 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:10:36.858589 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:10:36.858684 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:10:36.858745 PROGRESS: Target precursors: 7,947 (99.34%)
1 day, 20:10:36.858796 PROGRESS: Decoy precursors: 53 (0.66%)
1 day, 20:10:36.858846 PROGRESS: 
1 day, 20:10:36.858891 PROGRESS: Precursor Summary:
1 day, 20:10:36.861884 PROGRESS: Channel   0:	 0.05 FDR: 7,947; 0.01 FDR: 7,947; 0.001 FDR: 7,619
1 day, 20:10:36.862004 PROGRESS: 
1 day, 20:10:36.862064 PROGRESS: Protein Summary:
1 day, 20:10:36.866600 PROGRESS: Channel   0:	 0.05 FDR: 4,197; 0.01 FDR: 4,197; 0.001 FDR: 4,072
1 day, 20:10:36.866713 PROGRESS: =========================================================================
1 day, 20:10:36.891561 INFO: fragments_df_filtered: 5000
1 day, 20:10:36.905816 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:10:37.792427 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:10:38.630800 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:10:42.067949 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:10:42.426286 INFO: calibration group: precursor, predicting mz
1 day, 20:10:42.429572 INFO: calibration group: precursor, predicting rt
1 day, 20:10:42.439661 INFO: calibration group: precursor, predicting mobility
1 day, 20:10:42.442081 INFO: calibration group: fragment, predicting mz
1 day, 20:10:42.461078 INFO: === checking if optimization conditions were reached ===
1 day, 20:10:42.461242 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
1 day, 20:10:42.467555 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 11.1908.
1 day, 20:10:42.467630 INFO: ==============================================
1 day, 20:10:42.467737 INFO: Starting optimization step 8.
1 day, 20:10:42.467805 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:10:42.467868 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:10:42.472342 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:10:42.472406 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:10:42.472442 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 20:10:42.472466 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.81
1 day, 20:10:42.473508 INFO: Starting candidate selection
1 day, 20:10:44.089671 INFO: Starting candidate scoring
1 day, 20:10:45.006548 INFO: Finished candidate processing
1 day, 20:10:45.006743 INFO: Collecting candidate features
1 day, 20:10:45.057618 WARNING: intensity_correlation has 10 NaNs ( 0.03 % out of 30186)
1 day, 20:10:45.061972 INFO: Collecting fragment features
1 day, 20:10:45.081537 INFO: Finished candidate scoring
1 day, 20:10:45.097539 PROGRESS: === Extracted 30186 precursors and 317173 fragments ===
1 day, 20:10:45.097909 INFO: performing precursor FDR with 47 features
1 day, 20:10:45.097947 INFO: Decoy channel: -1
1 day, 20:10:45.097970 INFO: Competetive: True
1 day, 20:10:45.106620 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:10:45.110676 WARNING: dropped 10 decoy PSMs due to missing features
1 day, 20:10:45.470014 INFO: Test AUC: 0.890
1 day, 20:10:45.470137 INFO: Train AUC: 0.891
1 day, 20:10:45.470166 INFO: AUC difference: 0.20%
1 day, 20:10:45.555347 INFO: Resetting torch num_threads to 100
1 day, 20:10:45.556580 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:10:45.558123 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:10:45.558234 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:10:45.558303 PROGRESS: Target precursors: 7,949 (99.36%)
1 day, 20:10:45.558358 PROGRESS: Decoy precursors: 51 (0.64%)
1 day, 20:10:45.558409 PROGRESS: 
1 day, 20:10:45.558457 PROGRESS: Precursor Summary:
1 day, 20:10:45.561565 PROGRESS: Channel   0:	 0.05 FDR: 7,949; 0.01 FDR: 7,949; 0.001 FDR: 7,648
1 day, 20:10:45.561694 PROGRESS: 
1 day, 20:10:45.561755 PROGRESS: Protein Summary:
1 day, 20:10:45.566473 PROGRESS: Channel   0:	 0.05 FDR: 4,200; 0.01 FDR: 4,200; 0.001 FDR: 4,082
1 day, 20:10:45.566595 PROGRESS: =========================================================================
1 day, 20:10:45.591290 INFO: fragments_df_filtered: 5000
1 day, 20:10:45.605979 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:10:46.494137 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:10:47.396274 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:10:48.287997 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:10:48.704198 INFO: calibration group: precursor, predicting mz
1 day, 20:10:48.707144 INFO: calibration group: precursor, predicting rt
1 day, 20:10:48.716743 INFO: calibration group: precursor, predicting mobility
1 day, 20:10:48.719129 INFO: calibration group: fragment, predicting mz
1 day, 20:10:48.737985 INFO: === checking if optimization conditions were reached ===
1 day, 20:10:48.738147 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
1 day, 20:10:48.744311 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 11.2067.
1 day, 20:10:48.744370 INFO: ==============================================
1 day, 20:10:48.744465 INFO: Starting optimization step 9.
1 day, 20:10:48.744532 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:10:48.744591 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:10:48.748970 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:10:48.749047 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:10:48.749087 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 20:10:48.749120 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 20:10:48.750012 INFO: Starting candidate selection
1 day, 20:10:50.352818 INFO: Starting candidate scoring
1 day, 20:10:51.261425 INFO: Finished candidate processing
1 day, 20:10:51.261617 INFO: Collecting candidate features
1 day, 20:10:51.322427 WARNING: intensity_correlation has 9 NaNs ( 0.03 % out of 30183)
1 day, 20:10:51.326985 INFO: Collecting fragment features
1 day, 20:10:51.344386 INFO: Finished candidate scoring
1 day, 20:10:51.359729 PROGRESS: === Extracted 30183 precursors and 317133 fragments ===
1 day, 20:10:51.360109 INFO: performing precursor FDR with 47 features
1 day, 20:10:51.360147 INFO: Decoy channel: -1
1 day, 20:10:51.360171 INFO: Competetive: True
1 day, 20:10:51.368283 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:10:51.372351 WARNING: dropped 9 decoy PSMs due to missing features
1 day, 20:10:51.731597 INFO: Test AUC: 0.893
1 day, 20:10:51.731741 INFO: Train AUC: 0.891
1 day, 20:10:51.731772 INFO: AUC difference: 0.30%
1 day, 20:10:51.817366 INFO: Resetting torch num_threads to 100
1 day, 20:10:51.818587 INFO: === FDR correction performed with classifier version 3 ===
1 day, 20:10:51.819972 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:10:51.820068 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:10:51.820132 PROGRESS: Target precursors: 7,949 (99.36%)
1 day, 20:10:51.820185 PROGRESS: Decoy precursors: 51 (0.64%)
1 day, 20:10:51.820237 PROGRESS: 
1 day, 20:10:51.820286 PROGRESS: Precursor Summary:
1 day, 20:10:51.823333 PROGRESS: Channel   0:	 0.05 FDR: 7,949; 0.01 FDR: 7,949; 0.001 FDR: 7,677
1 day, 20:10:51.823457 PROGRESS: 
1 day, 20:10:51.823518 PROGRESS: Protein Summary:
1 day, 20:10:51.828175 PROGRESS: Channel   0:	 0.05 FDR: 4,201; 0.01 FDR: 4,201; 0.001 FDR: 4,095
1 day, 20:10:51.828296 PROGRESS: =========================================================================
1 day, 20:10:51.853918 INFO: fragments_df_filtered: 5000
1 day, 20:10:51.868542 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:10:52.755543 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:10:53.634881 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:10:54.456467 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:10:54.808156 INFO: calibration group: precursor, predicting mz
1 day, 20:10:54.811445 INFO: calibration group: precursor, predicting rt
1 day, 20:10:54.821220 INFO: calibration group: precursor, predicting mobility
1 day, 20:10:54.823649 INFO: calibration group: fragment, predicting mz
1 day, 20:10:54.843061 INFO: === checking if optimization conditions were reached ===
1 day, 20:10:54.843224 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
1 day, 20:10:54.844294 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 10.6216 found after 10 searches.
1 day, 20:10:54.844349 INFO: ==============================================
1 day, 20:10:54.844442 PROGRESS: Optimization finished for rt_error.
1 day, 20:10:54.860938 INFO: calibration group: precursor, predicting mz
1 day, 20:10:54.863880 INFO: calibration group: precursor, predicting rt
1 day, 20:10:54.873394 INFO: calibration group: precursor, predicting mobility
1 day, 20:10:54.875822 INFO: calibration group: fragment, predicting mz
1 day, 20:10:54.920324 INFO: Starting optimization step 0.
1 day, 20:10:54.920498 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:10:54.920569 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:10:54.925103 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:10:54.925166 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:10:54.925203 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 20:10:54.925227 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.81
1 day, 20:10:54.926163 INFO: Starting candidate selection
1 day, 20:10:56.556741 INFO: Starting candidate scoring
1 day, 20:10:57.478440 INFO: Finished candidate processing
1 day, 20:10:57.478556 INFO: Collecting candidate features
1 day, 20:10:57.536896 WARNING: intensity_correlation has 10 NaNs ( 0.03 % out of 30180)
1 day, 20:10:57.542326 INFO: Collecting fragment features
1 day, 20:10:57.569472 INFO: Finished candidate scoring
1 day, 20:10:57.585742 PROGRESS: === Extracted 30180 precursors and 317038 fragments ===
1 day, 20:10:57.586154 INFO: performing precursor FDR with 47 features
1 day, 20:10:57.586192 INFO: Decoy channel: -1
1 day, 20:10:57.586216 INFO: Competetive: True
1 day, 20:10:57.599572 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:10:57.603794 WARNING: dropped 10 decoy PSMs due to missing features
1 day, 20:10:57.971177 INFO: Test AUC: 0.898
1 day, 20:10:57.971297 INFO: Train AUC: 0.900
1 day, 20:10:57.971327 INFO: AUC difference: 0.26%
1 day, 20:10:58.061506 INFO: Resetting torch num_threads to 100
1 day, 20:10:58.062756 INFO: === FDR correction performed with classifier version 11 ===
1 day, 20:10:58.064243 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:10:58.064345 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:10:58.064406 PROGRESS: Target precursors: 7,953 (99.41%)
1 day, 20:10:58.064460 PROGRESS: Decoy precursors: 47 (0.59%)
1 day, 20:10:58.064508 PROGRESS: 
1 day, 20:10:58.064554 PROGRESS: Precursor Summary:
1 day, 20:10:58.067792 PROGRESS: Channel   0:	 0.05 FDR: 7,953; 0.01 FDR: 7,953; 0.001 FDR: 7,766
1 day, 20:10:58.067919 PROGRESS: 
1 day, 20:10:58.067978 PROGRESS: Protein Summary:
1 day, 20:10:58.076361 PROGRESS: Channel   0:	 0.05 FDR: 4,199; 0.01 FDR: 4,199; 0.001 FDR: 4,127
1 day, 20:10:58.076662 PROGRESS: =========================================================================
1 day, 20:10:58.106336 INFO: fragments_df_filtered: 5000
1 day, 20:10:58.125233 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:10:59.020820 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:10:59.869413 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:11:00.694675 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:11:01.048439 INFO: calibration group: precursor, predicting mz
1 day, 20:11:01.051438 INFO: calibration group: precursor, predicting rt
1 day, 20:11:01.061160 INFO: calibration group: precursor, predicting mobility
1 day, 20:11:01.063572 INFO: calibration group: fragment, predicting mz
1 day, 20:11:01.083861 INFO: === checking if optimization conditions were reached ===
1 day, 20:11:01.084064 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 20:11:01.087065 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0600.
1 day, 20:11:01.087131 INFO: ==============================================
1 day, 20:11:01.087242 INFO: Starting optimization step 1.
1 day, 20:11:01.087323 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:11:01.087398 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:11:01.093472 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:11:01.093547 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:11:01.093596 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 20:11:01.093627 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 20:11:01.100365 INFO: Starting candidate selection
1 day, 20:11:02.483902 INFO: Starting candidate scoring
1 day, 20:11:03.393177 INFO: Finished candidate processing
1 day, 20:11:03.393382 INFO: Collecting candidate features
1 day, 20:11:03.478110 WARNING: intensity_correlation has 12 NaNs ( 0.04 % out of 30129)
1 day, 20:11:03.482787 INFO: Collecting fragment features
1 day, 20:11:03.504670 INFO: Finished candidate scoring
1 day, 20:11:03.521961 PROGRESS: === Extracted 30129 precursors and 314144 fragments ===
1 day, 20:11:03.522412 INFO: performing precursor FDR with 47 features
1 day, 20:11:03.522460 INFO: Decoy channel: -1
1 day, 20:11:03.522501 INFO: Competetive: True
1 day, 20:11:03.535456 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:11:03.540405 WARNING: dropped 12 decoy PSMs due to missing features
1 day, 20:11:03.998979 INFO: Test AUC: 0.895
1 day, 20:11:03.999141 INFO: Train AUC: 0.901
1 day, 20:11:03.999173 INFO: AUC difference: 0.71%
1 day, 20:11:04.091208 INFO: Resetting torch num_threads to 100
1 day, 20:11:04.092936 INFO: === FDR correction performed with classifier version 11 ===
1 day, 20:11:04.094618 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:11:04.094735 PROGRESS: Total precursors accumulated: 7,998
1 day, 20:11:04.094808 PROGRESS: Target precursors: 7,958 (99.50%)
1 day, 20:11:04.094872 PROGRESS: Decoy precursors: 40 (0.50%)
1 day, 20:11:04.094929 PROGRESS: 
1 day, 20:11:04.094982 PROGRESS: Precursor Summary:
1 day, 20:11:04.098362 PROGRESS: Channel   0:	 0.05 FDR: 7,958; 0.01 FDR: 7,958; 0.001 FDR: 7,797
1 day, 20:11:04.098504 PROGRESS: 
1 day, 20:11:04.098573 PROGRESS: Protein Summary:
1 day, 20:11:04.103609 PROGRESS: Channel   0:	 0.05 FDR: 4,205; 0.01 FDR: 4,205; 0.001 FDR: 4,143
1 day, 20:11:04.103735 PROGRESS: =========================================================================
1 day, 20:11:04.129955 INFO: fragments_df_filtered: 5000
1 day, 20:11:04.149862 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:11:04.976893 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:11:05.886707 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:11:06.780040 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:11:07.200039 INFO: calibration group: precursor, predicting mz
1 day, 20:11:07.203277 INFO: calibration group: precursor, predicting rt
1 day, 20:11:07.213192 INFO: calibration group: precursor, predicting mobility
1 day, 20:11:07.215621 INFO: calibration group: fragment, predicting mz
1 day, 20:11:07.235104 INFO: === checking if optimization conditions were reached ===
1 day, 20:11:07.235306 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 20:11:07.238498 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0542.
1 day, 20:11:07.238565 INFO: ==============================================
1 day, 20:11:07.238689 INFO: Starting optimization step 2.
1 day, 20:11:07.238770 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:11:07.238844 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:11:07.245998 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:11:07.246078 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:11:07.246125 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 20:11:07.246154 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 20:11:07.247301 INFO: Starting candidate selection
1 day, 20:11:08.610744 INFO: Starting candidate scoring
1 day, 20:11:09.529863 INFO: Finished candidate processing
1 day, 20:11:09.529965 INFO: Collecting candidate features
1 day, 20:11:09.590934 WARNING: intensity_correlation has 13 NaNs ( 0.04 % out of 30109)
1 day, 20:11:09.598114 INFO: Collecting fragment features
1 day, 20:11:09.620300 INFO: Finished candidate scoring
1 day, 20:11:09.634356 PROGRESS: === Extracted 30109 precursors and 312978 fragments ===
1 day, 20:11:09.634725 INFO: performing precursor FDR with 47 features
1 day, 20:11:09.634764 INFO: Decoy channel: -1
1 day, 20:11:09.634789 INFO: Competetive: True
1 day, 20:11:09.642900 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:11:09.646880 WARNING: dropped 13 decoy PSMs due to missing features
1 day, 20:11:10.010388 INFO: Test AUC: 0.899
1 day, 20:11:10.010514 INFO: Train AUC: 0.899
1 day, 20:11:10.010545 INFO: AUC difference: 0.02%
1 day, 20:11:10.099850 INFO: Resetting torch num_threads to 100
1 day, 20:11:10.101109 INFO: === FDR correction performed with classifier version 11 ===
1 day, 20:11:10.102618 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:11:10.102729 PROGRESS: Total precursors accumulated: 7,998
1 day, 20:11:10.102792 PROGRESS: Target precursors: 7,955 (99.46%)
1 day, 20:11:10.102847 PROGRESS: Decoy precursors: 43 (0.54%)
1 day, 20:11:10.102899 PROGRESS: 
1 day, 20:11:10.102947 PROGRESS: Precursor Summary:
1 day, 20:11:10.106191 PROGRESS: Channel   0:	 0.05 FDR: 7,955; 0.01 FDR: 7,955; 0.001 FDR: 7,719
1 day, 20:11:10.106322 PROGRESS: 
1 day, 20:11:10.106383 PROGRESS: Protein Summary:
1 day, 20:11:10.111140 PROGRESS: Channel   0:	 0.05 FDR: 4,203; 0.01 FDR: 4,203; 0.001 FDR: 4,111
1 day, 20:11:10.111258 PROGRESS: =========================================================================
1 day, 20:11:10.135921 INFO: fragments_df_filtered: 5000
1 day, 20:11:10.150520 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:11:10.976816 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:11:11.815116 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:11:12.641378 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:11:12.991558 INFO: calibration group: precursor, predicting mz
1 day, 20:11:12.994526 INFO: calibration group: precursor, predicting rt
1 day, 20:11:13.004234 INFO: calibration group: precursor, predicting mobility
1 day, 20:11:13.006685 INFO: calibration group: fragment, predicting mz
1 day, 20:11:13.025825 INFO: === checking if optimization conditions were reached ===
1 day, 20:11:13.025996 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 20:11:13.026961 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.0600 found after 3 searches.
1 day, 20:11:13.027018 INFO: ==============================================
1 day, 20:11:13.027122 PROGRESS: Optimization finished for mobility_error.
1 day, 20:11:13.046700 INFO: calibration group: precursor, predicting mz
1 day, 20:11:13.049977 INFO: calibration group: precursor, predicting rt
1 day, 20:11:13.059964 INFO: calibration group: precursor, predicting mobility
1 day, 20:11:13.062697 INFO: calibration group: fragment, predicting mz
1 day, 20:11:13.114914 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 20:11:13.115117 PROGRESS: ==============================================
1 day, 20:11:13.115201 PROGRESS: ms2_error      : 15.0000
1 day, 20:11:13.115286 PROGRESS: ms1_error      : 10.0000
1 day, 20:11:13.115353 PROGRESS: rt_error       : 10.6216
1 day, 20:11:13.115410 PROGRESS: mobility_error : 0.0600
1 day, 20:11:13.115464 PROGRESS: ==============================================
1 day, 20:11:13.117102 INFO: calibration group: precursor, predicting mz
1 day, 20:11:13.138653 INFO: calibration group: precursor, predicting rt
1 day, 20:11:13.232577 INFO: calibration group: precursor, predicting mobility
1 day, 20:11:13.255337 INFO: calibration group: fragment, predicting mz
1 day, 20:11:13.487196 PROGRESS: Extracting batch of 162861 precursors
1 day, 20:11:13.532449 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:11:13.532582 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:11:13.532628 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 20:11:13.532653 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 20:11:13.533431 INFO: Starting candidate selection
1 day, 20:11:22.577647 INFO: Applying score cutoff of 19.506486516952513
1 day, 20:11:22.585441 INFO: Removed 8424 precursors with score below cutoff
1 day, 20:11:22.900509 INFO: Starting candidate scoring
1 day, 20:11:31.443998 INFO: Finished candidate processing
1 day, 20:11:31.444103 INFO: Collecting candidate features
1 day, 20:11:31.936143 WARNING: intensity_correlation has 24 NaNs ( 0.01 % out of 301317)
1 day, 20:11:31.949656 INFO: Collecting fragment features
1 day, 20:11:32.154980 INFO: Finished candidate scoring
1 day, 20:11:32.309503 INFO: === FDR correction performed with classifier version 15 ===
1 day, 20:11:32.310489 INFO: performing precursor FDR with 47 features
1 day, 20:11:32.310536 INFO: Decoy channel: -1
1 day, 20:11:32.310561 INFO: Competetive: True
1 day, 20:11:32.395037 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:11:32.438454 WARNING: dropped 1 target PSMs due to missing features
1 day, 20:11:32.438591 WARNING: dropped 23 decoy PSMs due to missing features
1 day, 20:11:37.651629 INFO: Test AUC: 0.911
1 day, 20:11:37.651755 INFO: Train AUC: 0.915
1 day, 20:11:37.651787 INFO: AUC difference: 0.46%
1 day, 20:11:37.756048 INFO: Resetting torch num_threads to 100
1 day, 20:11:37.769036 INFO: Removing fragments below FDR threshold
1 day, 20:11:37.822397 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:11:37.822670 PROGRESS: Total precursors accumulated: 81,941
1 day, 20:11:37.822738 PROGRESS: Target precursors: 81,465 (99.42%)
1 day, 20:11:37.822803 PROGRESS: Decoy precursors: 476 (0.58%)
1 day, 20:11:37.822852 PROGRESS: 
1 day, 20:11:37.822897 PROGRESS: Precursor Summary:
1 day, 20:11:37.858388 PROGRESS: Channel   0:	 0.05 FDR: 81,465; 0.01 FDR: 81,465; 0.001 FDR: 80,430
1 day, 20:11:37.858730 PROGRESS: 
1 day, 20:11:37.858798 PROGRESS: Protein Summary:
1 day, 20:11:37.906696 PROGRESS: Channel   0:	 0.05 FDR: 8,249; 0.01 FDR: 8,249; 0.001 FDR: 8,241
1 day, 20:11:37.906977 PROGRESS: =========================================================================
1 day, 20:11:38.585119 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 20:11:38.628867 PROGRESS: Loading raw file 5/6: ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 20:11:38.629058 INFO: Quantification results path: run_output/alphadia_1.10_defaultMBR/quant
1 day, 20:11:38.629139 INFO: Creating workflow folder for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502 at run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 20:11:38.629936 INFO: Initializing RawFileManager
1 day, 20:11:38.630054 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:11:38.630107 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:11:38.630165 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:11:38.841612 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
1 day, 20:11:45.860468 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d...
1 day, 20:11:45.862052 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:11:45.864497 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:11:45.864719 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:11:45.865213 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:11:45.866647 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:11:45.880411 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:11:45.880798 INFO: Indexing quadrupole dimension
1 day, 20:11:46.346634 INFO: Transposing detector events
1 day, 20:11:54.989460 INFO: Finished transposing data
1 day, 20:11:55.015359 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 20:11:55.017896 INFO: RT (min)            : 0.0 - 70.0
1 day, 20:11:55.017944 INFO: RT duration (sec)   : 4199.9
1 day, 20:11:55.017968 INFO: RT duration (min)   : 70.0
1 day, 20:11:55.017991 INFO: Cycle len (scans)   : 9
1 day, 20:11:55.018009 INFO: Cycle len (sec)     : 0.97
1 day, 20:11:55.018029 INFO: Number of cycles    : 4347
1 day, 20:11:55.018047 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 20:11:55.066081 INFO: Initializing CalibrationManager
1 day, 20:11:55.066442 INFO: Loading calibration config
1 day, 20:11:55.067205 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'}]
1 day, 20:11:55.067311 INFO: Calibration group :fragment, found 1 estimator(s)
1 day, 20:11:55.067411 INFO: Calibration group :precursor, found 3 estimator(s)
1 day, 20:11:55.067593 INFO: Initializing OptimizationManager
1 day, 20:11:55.067723 INFO: initial parameter: ms1_error = 30
1 day, 20:11:55.067789 INFO: initial parameter: ms2_error = 30
1 day, 20:11:55.067857 INFO: initial parameter: rt_error = 2099.9331315
1 day, 20:11:55.067909 INFO: initial parameter: mobility_error = 0.1
1 day, 20:11:55.067958 INFO: initial parameter: column_type = library
1 day, 20:11:55.068003 INFO: initial parameter: num_candidates = 1
1 day, 20:11:55.068047 INFO: initial parameter: classifier_version = -1
1 day, 20:11:55.068090 INFO: initial parameter: fwhm_rt = 5
1 day, 20:11:55.068144 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 20:11:55.068190 INFO: initial parameter: score_cutoff = 0
1 day, 20:11:55.068259 INFO: Initializing TimingManager
1 day, 20:11:55.068320 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 20:11:55.068419 INFO: FDRManager not loaded from disk.
1 day, 20:11:55.068446 INFO: Initializing FDRManager
1 day, 20:11:55.068484 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 20:11:55.099908 PROGRESS: 82,039 target precursors potentially observable (0 removed)
1 day, 20:11:55.140842 PROGRESS: Starting initial search for precursors.
1 day, 20:11:55.162049 INFO: Starting optimization step 0.
1 day, 20:11:55.162284 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:11:55.162364 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:11:55.166134 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:11:55.166190 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:11:55.166227 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 20:11:55.166250 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 20:11:55.167188 INFO: Starting candidate selection
1 day, 20:13:20.395290 INFO: Starting candidate scoring
1 day, 20:13:21.413963 INFO: Finished candidate processing
1 day, 20:13:21.414071 INFO: Collecting candidate features
1 day, 20:13:21.449005 INFO: Collecting fragment features
1 day, 20:13:21.463222 INFO: Finished candidate scoring
1 day, 20:13:21.472211 PROGRESS: === Extracted 15885 precursors and 175780 fragments ===
1 day, 20:13:21.472651 INFO: performing precursor FDR with 47 features
1 day, 20:13:21.472692 INFO: Decoy channel: -1
1 day, 20:13:21.472726 INFO: Competetive: True
1 day, 20:13:21.477400 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:13:21.638344 INFO: Test AUC: 0.828
1 day, 20:13:21.638466 INFO: Train AUC: 0.827
1 day, 20:13:21.638498 INFO: AUC difference: 0.05%
1 day, 20:13:21.728357 INFO: Resetting torch num_threads to 100
1 day, 20:13:21.730260 INFO: === FDR correction performed with classifier version -1 ===
1 day, 20:13:21.731756 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:13:21.731860 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:13:21.731924 PROGRESS: Target precursors: 6,634 (82.93%)
1 day, 20:13:21.731976 PROGRESS: Decoy precursors: 1,366 (17.08%)
1 day, 20:13:21.732021 PROGRESS: 
1 day, 20:13:21.732066 PROGRESS: Precursor Summary:
1 day, 20:13:21.734378 PROGRESS: Channel   0:	 0.05 FDR: 5,234; 0.01 FDR: 3,641; 0.001 FDR: 2,217
1 day, 20:13:21.734491 PROGRESS: 
1 day, 20:13:21.734554 PROGRESS: Protein Summary:
1 day, 20:13:21.737489 PROGRESS: Channel   0:	 0.05 FDR: 3,026; 0.01 FDR: 2,280; 0.001 FDR: 1,482
1 day, 20:13:21.737595 PROGRESS: =========================================================================
1 day, 20:13:21.746327 INFO: fragments_df_filtered: 5000
1 day, 20:13:21.764049 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:13:21.970504 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:13:22.189926 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:13:22.397737 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:13:22.751724 INFO: calibration group: precursor, predicting mz
1 day, 20:13:22.754649 INFO: calibration group: precursor, predicting rt
1 day, 20:13:22.764708 INFO: calibration group: precursor, predicting mobility
1 day, 20:13:22.767194 INFO: calibration group: fragment, predicting mz
1 day, 20:13:22.786798 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 20:13:22.787014 INFO: Starting optimization step 1.
1 day, 20:13:22.787097 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:13:22.787170 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:13:22.792831 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:13:22.792902 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:13:22.792952 INFO: FWHM in RT is 3.32 seconds, sigma is 0.73
1 day, 20:13:22.792981 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.28
1 day, 20:13:22.794123 INFO: Starting candidate selection
1 day, 20:14:56.823112 INFO: Starting candidate scoring
1 day, 20:14:58.719117 INFO: Finished candidate processing
1 day, 20:14:58.719227 INFO: Collecting candidate features
1 day, 20:14:58.780572 INFO: Collecting fragment features
1 day, 20:14:58.800712 INFO: Finished candidate scoring
1 day, 20:14:58.814211 PROGRESS: === Extracted 30442 precursors and 336817 fragments ===
1 day, 20:14:58.814667 INFO: performing precursor FDR with 47 features
1 day, 20:14:58.814706 INFO: Decoy channel: -1
1 day, 20:14:58.814731 INFO: Competetive: True
1 day, 20:14:58.824710 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:14:59.193181 INFO: Test AUC: 0.716
1 day, 20:14:59.193300 INFO: Train AUC: 0.726
1 day, 20:14:59.193330 INFO: AUC difference: 1.26%
1 day, 20:14:59.282863 INFO: Resetting torch num_threads to 100
1 day, 20:14:59.284061 INFO: === FDR correction performed with classifier version 0 ===
1 day, 20:14:59.285677 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:14:59.285797 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:14:59.285861 PROGRESS: Target precursors: 7,204 (90.05%)
1 day, 20:14:59.285914 PROGRESS: Decoy precursors: 796 (9.95%)
1 day, 20:14:59.285961 PROGRESS: 
1 day, 20:14:59.286008 PROGRESS: Precursor Summary:
1 day, 20:14:59.288899 PROGRESS: Channel   0:	 0.05 FDR: 6,022; 0.01 FDR: 5,071; 0.001 FDR: 2,552
1 day, 20:14:59.289019 PROGRESS: 
1 day, 20:14:59.289103 PROGRESS: Protein Summary:
1 day, 20:14:59.292352 PROGRESS: Channel   0:	 0.05 FDR: 3,392; 0.01 FDR: 2,949; 0.001 FDR: 1,703
1 day, 20:14:59.292465 PROGRESS: =========================================================================
1 day, 20:14:59.310642 INFO: fragments_df_filtered: 5000
1 day, 20:14:59.329352 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:14:59.692460 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:15:00.076452 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:15:00.438072 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:15:00.787388 INFO: calibration group: precursor, predicting mz
1 day, 20:15:00.790295 INFO: calibration group: precursor, predicting rt
1 day, 20:15:00.800467 INFO: calibration group: precursor, predicting mobility
1 day, 20:15:00.802912 INFO: calibration group: fragment, predicting mz
1 day, 20:15:00.822855 INFO: === checking if optimization conditions were reached ===
1 day, 20:15:00.824659 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 20:15:00.826431 PROGRESS: ❌ ms1_error      : 10.0000 > 10.0000 or insufficient steps taken.
1 day, 20:15:00.826484 INFO: ==============================================
1 day, 20:15:00.826578 INFO: Starting optimization step 2.
1 day, 20:15:00.826646 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:15:00.826710 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:15:00.830683 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:15:00.830748 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:15:00.830790 INFO: FWHM in RT is 3.20 seconds, sigma is 0.70
1 day, 20:15:00.830815 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.99
1 day, 20:15:00.831806 INFO: Starting candidate selection
1 day, 20:16:32.370714 INFO: Starting candidate scoring
1 day, 20:16:33.410882 INFO: Finished candidate processing
1 day, 20:16:33.410986 INFO: Collecting candidate features
1 day, 20:16:33.473485 INFO: Collecting fragment features
1 day, 20:16:33.493209 INFO: Finished candidate scoring
1 day, 20:16:33.506716 PROGRESS: === Extracted 30467 precursors and 332826 fragments ===
1 day, 20:16:33.507169 INFO: performing precursor FDR with 47 features
1 day, 20:16:33.507209 INFO: Decoy channel: -1
1 day, 20:16:33.507233 INFO: Competetive: True
1 day, 20:16:33.517236 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:16:33.886764 INFO: Test AUC: 0.766
1 day, 20:16:33.886883 INFO: Train AUC: 0.768
1 day, 20:16:33.886912 INFO: AUC difference: 0.25%
1 day, 20:16:33.976543 INFO: Resetting torch num_threads to 100
1 day, 20:16:33.977786 INFO: === FDR correction performed with classifier version 1 ===
1 day, 20:16:33.979367 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:16:33.979469 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:16:33.979534 PROGRESS: Target precursors: 7,811 (97.64%)
1 day, 20:16:33.979587 PROGRESS: Decoy precursors: 189 (2.36%)
1 day, 20:16:33.979637 PROGRESS: 
1 day, 20:16:33.979685 PROGRESS: Precursor Summary:
1 day, 20:16:33.982579 PROGRESS: Channel   0:	 0.05 FDR: 7,811; 0.01 FDR: 6,884; 0.001 FDR: 6,036
1 day, 20:16:33.982710 PROGRESS: 
1 day, 20:16:33.982770 PROGRESS: Protein Summary:
1 day, 20:16:33.987083 PROGRESS: Channel   0:	 0.05 FDR: 4,139; 0.01 FDR: 3,742; 0.001 FDR: 3,388
1 day, 20:16:33.987197 PROGRESS: =========================================================================
1 day, 20:16:34.011002 INFO: fragments_df_filtered: 5000
1 day, 20:16:34.029583 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:16:34.659708 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:16:35.315391 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:16:35.943562 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:16:36.295160 INFO: calibration group: precursor, predicting mz
1 day, 20:16:36.298166 INFO: calibration group: precursor, predicting rt
1 day, 20:16:36.307913 INFO: calibration group: precursor, predicting mobility
1 day, 20:16:36.310404 INFO: calibration group: fragment, predicting mz
1 day, 20:16:36.331019 INFO: === checking if optimization conditions were reached ===
1 day, 20:16:36.333100 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 20:16:36.335276 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
1 day, 20:16:36.335979 INFO: ==============================================
1 day, 20:16:36.336105 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 20:16:36.355244 INFO: calibration group: precursor, predicting mz
1 day, 20:16:36.358117 INFO: calibration group: precursor, predicting rt
1 day, 20:16:36.367602 INFO: calibration group: precursor, predicting mobility
1 day, 20:16:36.370033 INFO: calibration group: fragment, predicting mz
1 day, 20:16:36.391255 INFO: Starting optimization step 0.
1 day, 20:16:36.391415 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:16:36.391489 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:16:36.395633 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:16:36.395687 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:16:36.395730 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 20:16:36.395754 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.00
1 day, 20:16:36.404801 INFO: Starting candidate selection
1 day, 20:18:04.379953 INFO: Starting candidate scoring
1 day, 20:18:05.418231 INFO: Finished candidate processing
1 day, 20:18:05.418337 INFO: Collecting candidate features
1 day, 20:18:05.483882 INFO: Collecting fragment features
1 day, 20:18:05.507390 INFO: Finished candidate scoring
1 day, 20:18:05.520710 PROGRESS: === Extracted 30455 precursors and 332185 fragments ===
1 day, 20:18:05.521187 INFO: performing precursor FDR with 47 features
1 day, 20:18:05.521228 INFO: Decoy channel: -1
1 day, 20:18:05.521252 INFO: Competetive: True
1 day, 20:18:05.531406 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:18:05.904896 INFO: Test AUC: 0.771
1 day, 20:18:05.905020 INFO: Train AUC: 0.775
1 day, 20:18:05.905061 INFO: AUC difference: 0.61%
1 day, 20:18:05.994035 INFO: Resetting torch num_threads to 100
1 day, 20:18:05.995247 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:18:05.996809 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:18:05.996904 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:18:05.996964 PROGRESS: Target precursors: 7,860 (98.25%)
1 day, 20:18:05.997017 PROGRESS: Decoy precursors: 140 (1.75%)
1 day, 20:18:05.997078 PROGRESS: 
1 day, 20:18:05.997123 PROGRESS: Precursor Summary:
1 day, 20:18:06.000030 PROGRESS: Channel   0:	 0.05 FDR: 7,860; 0.01 FDR: 7,846; 0.001 FDR: 6,248
1 day, 20:18:06.000157 PROGRESS: 
1 day, 20:18:06.000216 PROGRESS: Protein Summary:
1 day, 20:18:06.004633 PROGRESS: Channel   0:	 0.05 FDR: 4,170; 0.01 FDR: 4,163; 0.001 FDR: 3,477
1 day, 20:18:06.004749 PROGRESS: =========================================================================
1 day, 20:18:06.030975 INFO: fragments_df_filtered: 5000
1 day, 20:18:06.050930 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:18:06.866266 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:18:07.694966 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:18:08.498230 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:18:08.849941 INFO: calibration group: precursor, predicting mz
1 day, 20:18:08.852873 INFO: calibration group: precursor, predicting rt
1 day, 20:18:08.862497 INFO: calibration group: precursor, predicting mobility
1 day, 20:18:08.864904 INFO: calibration group: fragment, predicting mz
1 day, 20:18:08.885442 INFO: === checking if optimization conditions were reached ===
1 day, 20:18:08.885618 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 20:18:08.891654 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 1031.1060.
1 day, 20:18:08.891717 INFO: ==============================================
1 day, 20:18:08.891826 INFO: Starting optimization step 1.
1 day, 20:18:08.891904 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:18:08.891977 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:18:08.895847 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:18:08.895929 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:18:08.895980 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 20:18:08.896010 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.84
1 day, 20:18:08.897184 INFO: Starting candidate selection
1 day, 20:18:55.062660 INFO: Starting candidate scoring
1 day, 20:18:56.099849 INFO: Finished candidate processing
1 day, 20:18:56.099956 INFO: Collecting candidate features
1 day, 20:18:56.154335 INFO: Collecting fragment features
1 day, 20:18:56.173475 INFO: Finished candidate scoring
1 day, 20:18:56.186566 PROGRESS: === Extracted 30422 precursors and 331751 fragments ===
1 day, 20:18:56.186947 INFO: performing precursor FDR with 47 features
1 day, 20:18:56.186988 INFO: Decoy channel: -1
1 day, 20:18:56.187012 INFO: Competetive: True
1 day, 20:18:56.196063 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:18:56.552006 INFO: Test AUC: 0.784
1 day, 20:18:56.552129 INFO: Train AUC: 0.777
1 day, 20:18:56.552159 INFO: AUC difference: 0.93%
1 day, 20:18:56.639782 INFO: Resetting torch num_threads to 100
1 day, 20:18:56.640914 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:18:56.643817 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:18:56.643928 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:18:56.643993 PROGRESS: Target precursors: 7,849 (98.11%)
1 day, 20:18:56.644049 PROGRESS: Decoy precursors: 151 (1.89%)
1 day, 20:18:56.644102 PROGRESS: 
1 day, 20:18:56.644152 PROGRESS: Precursor Summary:
1 day, 20:18:56.647092 PROGRESS: Channel   0:	 0.05 FDR: 7,849; 0.01 FDR: 7,836; 0.001 FDR: 6,190
1 day, 20:18:56.647216 PROGRESS: 
1 day, 20:18:56.647290 PROGRESS: Protein Summary:
1 day, 20:18:56.651723 PROGRESS: Channel   0:	 0.05 FDR: 4,165; 0.01 FDR: 4,162; 0.001 FDR: 3,464
1 day, 20:18:56.651838 PROGRESS: =========================================================================
1 day, 20:18:56.678464 INFO: fragments_df_filtered: 5000
1 day, 20:18:56.695603 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:18:57.505904 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:18:58.320225 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:18:59.120299 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:18:59.470637 INFO: calibration group: precursor, predicting mz
1 day, 20:18:59.473593 INFO: calibration group: precursor, predicting rt
1 day, 20:18:59.483239 INFO: calibration group: precursor, predicting mobility
1 day, 20:18:59.485664 INFO: calibration group: fragment, predicting mz
1 day, 20:18:59.505973 INFO: === checking if optimization conditions were reached ===
1 day, 20:18:59.506166 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 20:18:59.512681 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 892.1751.
1 day, 20:18:59.512756 INFO: ==============================================
1 day, 20:18:59.512874 INFO: Starting optimization step 2.
1 day, 20:18:59.512954 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:18:59.513022 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:18:59.518975 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:18:59.519042 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:18:59.519083 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 20:18:59.519111 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.84
1 day, 20:18:59.521639 INFO: Starting candidate selection
1 day, 20:19:37.383161 INFO: Starting candidate scoring
1 day, 20:19:38.425485 INFO: Finished candidate processing
1 day, 20:19:38.425593 INFO: Collecting candidate features
1 day, 20:19:38.484386 INFO: Collecting fragment features
1 day, 20:19:38.511376 INFO: Finished candidate scoring
1 day, 20:19:38.524308 PROGRESS: === Extracted 30421 precursors and 331549 fragments ===
1 day, 20:19:38.524765 INFO: performing precursor FDR with 47 features
1 day, 20:19:38.524805 INFO: Decoy channel: -1
1 day, 20:19:38.524831 INFO: Competetive: True
1 day, 20:19:38.535328 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:19:38.910869 INFO: Test AUC: 0.778
1 day, 20:19:38.910985 INFO: Train AUC: 0.780
1 day, 20:19:38.911015 INFO: AUC difference: 0.25%
1 day, 20:19:38.998903 INFO: Resetting torch num_threads to 100
1 day, 20:19:39.000106 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:19:39.001497 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:19:39.001594 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:19:39.001659 PROGRESS: Target precursors: 7,851 (98.14%)
1 day, 20:19:39.001713 PROGRESS: Decoy precursors: 149 (1.86%)
1 day, 20:19:39.001763 PROGRESS: 
1 day, 20:19:39.001812 PROGRESS: Precursor Summary:
1 day, 20:19:39.004818 PROGRESS: Channel   0:	 0.05 FDR: 7,851; 0.01 FDR: 7,839; 0.001 FDR: 6,451
1 day, 20:19:39.004933 PROGRESS: 
1 day, 20:19:39.004994 PROGRESS: Protein Summary:
1 day, 20:19:39.009426 PROGRESS: Channel   0:	 0.05 FDR: 4,165; 0.01 FDR: 4,163; 0.001 FDR: 3,557
1 day, 20:19:39.009538 PROGRESS: =========================================================================
1 day, 20:19:39.035773 INFO: fragments_df_filtered: 5000
1 day, 20:19:39.054664 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:19:39.855802 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:19:40.674818 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:19:41.477209 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:19:41.827121 INFO: calibration group: precursor, predicting mz
1 day, 20:19:41.830643 INFO: calibration group: precursor, predicting rt
1 day, 20:19:41.840178 INFO: calibration group: precursor, predicting mobility
1 day, 20:19:41.842575 INFO: calibration group: fragment, predicting mz
1 day, 20:19:41.863837 INFO: === checking if optimization conditions were reached ===
1 day, 20:19:41.864025 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 20:19:41.870741 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 787.8072.
1 day, 20:19:41.870817 INFO: ==============================================
1 day, 20:19:41.870938 INFO: Starting optimization step 3.
1 day, 20:19:41.871020 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:19:41.871096 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:19:41.876959 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:19:41.877038 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:19:41.877089 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 20:19:41.877119 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.84
1 day, 20:19:41.879806 INFO: Starting candidate selection
1 day, 20:20:14.590038 INFO: Starting candidate scoring
1 day, 20:20:15.664352 INFO: Finished candidate processing
1 day, 20:20:15.664527 INFO: Collecting candidate features
1 day, 20:20:15.749988 INFO: Collecting fragment features
1 day, 20:20:15.772627 INFO: Finished candidate scoring
1 day, 20:20:15.787442 PROGRESS: === Extracted 30387 precursors and 330998 fragments ===
1 day, 20:20:15.787935 INFO: performing precursor FDR with 47 features
1 day, 20:20:15.787975 INFO: Decoy channel: -1
1 day, 20:20:15.788005 INFO: Competetive: True
1 day, 20:20:15.798440 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:20:16.169790 INFO: Test AUC: 0.782
1 day, 20:20:16.169915 INFO: Train AUC: 0.783
1 day, 20:20:16.169951 INFO: AUC difference: 0.14%
1 day, 20:20:16.258286 INFO: Resetting torch num_threads to 100
1 day, 20:20:16.259639 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:20:16.261172 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:20:16.261279 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:20:16.261367 PROGRESS: Target precursors: 7,852 (98.15%)
1 day, 20:20:16.261435 PROGRESS: Decoy precursors: 148 (1.85%)
1 day, 20:20:16.261512 PROGRESS: 
1 day, 20:20:16.261575 PROGRESS: Precursor Summary:
1 day, 20:20:16.264586 PROGRESS: Channel   0:	 0.05 FDR: 7,852; 0.01 FDR: 7,840; 0.001 FDR: 6,365
1 day, 20:20:16.264711 PROGRESS: 
1 day, 20:20:16.264781 PROGRESS: Protein Summary:
1 day, 20:20:16.269304 PROGRESS: Channel   0:	 0.05 FDR: 4,169; 0.01 FDR: 4,166; 0.001 FDR: 3,529
1 day, 20:20:16.269431 PROGRESS: =========================================================================
1 day, 20:20:16.295497 INFO: fragments_df_filtered: 5000
1 day, 20:20:16.314757 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:20:17.117392 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:20:17.936183 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:20:18.739216 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:20:19.087530 INFO: calibration group: precursor, predicting mz
1 day, 20:20:19.090554 INFO: calibration group: precursor, predicting rt
1 day, 20:20:19.100259 INFO: calibration group: precursor, predicting mobility
1 day, 20:20:19.102652 INFO: calibration group: fragment, predicting mz
1 day, 20:20:19.123930 INFO: === checking if optimization conditions were reached ===
1 day, 20:20:19.124136 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 20:20:19.130811 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 721.5405.
1 day, 20:20:19.130879 INFO: ==============================================
1 day, 20:20:19.130998 INFO: Starting optimization step 4.
1 day, 20:20:19.131072 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:20:19.131144 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:20:19.136921 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:20:19.136987 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:20:19.137052 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 20:20:19.137083 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.84
1 day, 20:20:19.139707 INFO: Starting candidate selection
1 day, 20:20:51.438925 INFO: Starting candidate scoring
1 day, 20:20:52.504460 INFO: Finished candidate processing
1 day, 20:20:52.504640 INFO: Collecting candidate features
1 day, 20:20:52.595088 INFO: Collecting fragment features
1 day, 20:20:52.618803 INFO: Finished candidate scoring
1 day, 20:20:52.634033 PROGRESS: === Extracted 30390 precursors and 330818 fragments ===
1 day, 20:20:52.634513 INFO: performing precursor FDR with 47 features
1 day, 20:20:52.634566 INFO: Decoy channel: -1
1 day, 20:20:52.634592 INFO: Competetive: True
1 day, 20:20:52.646818 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:20:53.023814 INFO: Test AUC: 0.784
1 day, 20:20:53.023956 INFO: Train AUC: 0.783
1 day, 20:20:53.023986 INFO: AUC difference: 0.06%
1 day, 20:20:53.112687 INFO: Resetting torch num_threads to 100
1 day, 20:20:53.114231 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:20:53.115688 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:20:53.115783 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:20:53.115846 PROGRESS: Target precursors: 7,845 (98.06%)
1 day, 20:20:53.115899 PROGRESS: Decoy precursors: 155 (1.94%)
1 day, 20:20:53.115948 PROGRESS: 
1 day, 20:20:53.115993 PROGRESS: Precursor Summary:
1 day, 20:20:53.119257 PROGRESS: Channel   0:	 0.05 FDR: 7,845; 0.01 FDR: 7,835; 0.001 FDR: 6,274
1 day, 20:20:53.119375 PROGRESS: 
1 day, 20:20:53.119434 PROGRESS: Protein Summary:
1 day, 20:20:53.124041 PROGRESS: Channel   0:	 0.05 FDR: 4,164; 0.01 FDR: 4,162; 0.001 FDR: 3,479
1 day, 20:20:53.124151 PROGRESS: =========================================================================
1 day, 20:20:53.149960 INFO: fragments_df_filtered: 5000
1 day, 20:20:53.170136 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:20:54.036679 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:20:54.918314 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:20:55.786643 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:20:56.203186 INFO: calibration group: precursor, predicting mz
1 day, 20:20:56.206154 INFO: calibration group: precursor, predicting rt
1 day, 20:20:56.215526 INFO: calibration group: precursor, predicting mobility
1 day, 20:20:56.217909 INFO: calibration group: fragment, predicting mz
1 day, 20:20:56.238745 INFO: === checking if optimization conditions were reached ===
1 day, 20:20:56.238953 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 20:20:56.245613 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 669.2799.
1 day, 20:20:56.245682 INFO: ==============================================
1 day, 20:20:56.245800 INFO: Starting optimization step 5.
1 day, 20:20:56.245878 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:20:56.245954 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:20:56.252149 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:20:56.252214 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:20:56.252263 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 20:20:56.252294 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.84
1 day, 20:20:56.255611 INFO: Starting candidate selection
1 day, 20:21:24.883166 INFO: Starting candidate scoring
1 day, 20:21:25.902302 INFO: Finished candidate processing
1 day, 20:21:25.902470 INFO: Collecting candidate features
1 day, 20:21:25.954091 INFO: Collecting fragment features
1 day, 20:21:25.972169 INFO: Finished candidate scoring
1 day, 20:21:25.985776 PROGRESS: === Extracted 30398 precursors and 330740 fragments ===
1 day, 20:21:25.986181 INFO: performing precursor FDR with 47 features
1 day, 20:21:25.986219 INFO: Decoy channel: -1
1 day, 20:21:25.986243 INFO: Competetive: True
1 day, 20:21:25.994914 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:21:26.358745 INFO: Test AUC: 0.794
1 day, 20:21:26.358884 INFO: Train AUC: 0.782
1 day, 20:21:26.358915 INFO: AUC difference: 1.50%
1 day, 20:21:28.884447 INFO: Resetting torch num_threads to 100
1 day, 20:21:28.885986 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:21:28.887831 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:21:28.887943 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:21:28.888005 PROGRESS: Target precursors: 7,848 (98.10%)
1 day, 20:21:28.888057 PROGRESS: Decoy precursors: 152 (1.90%)
1 day, 20:21:28.888106 PROGRESS: 
1 day, 20:21:28.888152 PROGRESS: Precursor Summary:
1 day, 20:21:28.891335 PROGRESS: Channel   0:	 0.05 FDR: 7,848; 0.01 FDR: 7,838; 0.001 FDR: 6,160
1 day, 20:21:28.891465 PROGRESS: 
1 day, 20:21:28.891524 PROGRESS: Protein Summary:
1 day, 20:21:28.896253 PROGRESS: Channel   0:	 0.05 FDR: 4,164; 0.01 FDR: 4,162; 0.001 FDR: 3,445
1 day, 20:21:28.896363 PROGRESS: =========================================================================
1 day, 20:21:28.921973 INFO: fragments_df_filtered: 5000
1 day, 20:21:28.938976 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:21:29.809752 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:21:30.692317 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:21:31.560473 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:21:31.977618 INFO: calibration group: precursor, predicting mz
1 day, 20:21:31.980784 INFO: calibration group: precursor, predicting rt
1 day, 20:21:31.990121 INFO: calibration group: precursor, predicting mobility
1 day, 20:21:31.992505 INFO: calibration group: fragment, predicting mz
1 day, 20:21:32.011919 INFO: === checking if optimization conditions were reached ===
1 day, 20:21:32.012088 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 20:21:32.018198 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 639.0316.
1 day, 20:21:32.018266 INFO: ==============================================
1 day, 20:21:32.018378 INFO: Starting optimization step 6.
1 day, 20:21:32.018448 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:21:32.018508 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:21:32.023731 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:21:32.023799 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:21:32.023838 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 20:21:32.023861 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.84
1 day, 20:21:32.032447 INFO: Starting candidate selection
1 day, 20:22:03.201230 INFO: Starting candidate scoring
1 day, 20:22:04.240734 INFO: Finished candidate processing
1 day, 20:22:04.240927 INFO: Collecting candidate features
1 day, 20:22:04.327765 INFO: Collecting fragment features
1 day, 20:22:04.352329 INFO: Finished candidate scoring
1 day, 20:22:04.369682 PROGRESS: === Extracted 30389 precursors and 330593 fragments ===
1 day, 20:22:04.370146 INFO: performing precursor FDR with 47 features
1 day, 20:22:04.370187 INFO: Decoy channel: -1
1 day, 20:22:04.370212 INFO: Competetive: True
1 day, 20:22:04.383662 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:22:04.765932 INFO: Test AUC: 0.779
1 day, 20:22:04.766071 INFO: Train AUC: 0.786
1 day, 20:22:04.766101 INFO: AUC difference: 0.81%
1 day, 20:22:04.855167 INFO: Resetting torch num_threads to 100
1 day, 20:22:04.856738 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:22:04.858446 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:22:04.858555 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:22:04.858619 PROGRESS: Target precursors: 7,870 (98.38%)
1 day, 20:22:04.858674 PROGRESS: Decoy precursors: 130 (1.62%)
1 day, 20:22:04.858721 PROGRESS: 
1 day, 20:22:04.858767 PROGRESS: Precursor Summary:
1 day, 20:22:04.861871 PROGRESS: Channel   0:	 0.05 FDR: 7,870; 0.01 FDR: 7,855; 0.001 FDR: 6,235
1 day, 20:22:04.862001 PROGRESS: 
1 day, 20:22:04.862061 PROGRESS: Protein Summary:
1 day, 20:22:04.866774 PROGRESS: Channel   0:	 0.05 FDR: 4,169; 0.01 FDR: 4,164; 0.001 FDR: 3,475
1 day, 20:22:04.868265 PROGRESS: =========================================================================
1 day, 20:22:04.894504 INFO: fragments_df_filtered: 5000
1 day, 20:22:04.914240 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:22:05.789635 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:22:06.674764 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:22:07.545571 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:22:07.923263 INFO: calibration group: precursor, predicting mz
1 day, 20:22:07.926443 INFO: calibration group: precursor, predicting rt
1 day, 20:22:07.935854 INFO: calibration group: precursor, predicting mobility
1 day, 20:22:07.938277 INFO: calibration group: fragment, predicting mz
1 day, 20:22:07.958226 INFO: === checking if optimization conditions were reached ===
1 day, 20:22:07.958423 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 20:22:07.959988 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 639.0316 found after 7 searches.
1 day, 20:22:07.960047 INFO: ==============================================
1 day, 20:22:07.960160 PROGRESS: Optimization finished for rt_error.
1 day, 20:22:07.981650 INFO: calibration group: precursor, predicting mz
1 day, 20:22:07.985062 INFO: calibration group: precursor, predicting rt
1 day, 20:22:07.994909 INFO: calibration group: precursor, predicting mobility
1 day, 20:22:07.997650 INFO: calibration group: fragment, predicting mz
1 day, 20:22:08.052311 INFO: Starting optimization step 0.
1 day, 20:22:08.052560 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:22:08.052653 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:22:08.059418 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:22:08.059488 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:22:08.059538 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 20:22:08.059566 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.84
1 day, 20:22:08.068584 INFO: Starting candidate selection
1 day, 20:22:39.831369 INFO: Starting candidate scoring
1 day, 20:22:40.869587 INFO: Finished candidate processing
1 day, 20:22:40.869709 INFO: Collecting candidate features
1 day, 20:22:40.922008 INFO: Collecting fragment features
1 day, 20:22:40.941611 INFO: Finished candidate scoring
1 day, 20:22:40.959051 PROGRESS: === Extracted 30393 precursors and 330658 fragments ===
1 day, 20:22:40.959483 INFO: performing precursor FDR with 47 features
1 day, 20:22:40.959524 INFO: Decoy channel: -1
1 day, 20:22:40.959552 INFO: Competetive: True
1 day, 20:22:40.969934 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:22:41.244137 INFO: Test AUC: 0.788
1 day, 20:22:41.244282 INFO: Train AUC: 0.786
1 day, 20:22:41.244312 INFO: AUC difference: 0.26%
1 day, 20:22:41.332439 INFO: Resetting torch num_threads to 100
1 day, 20:22:41.334016 INFO: === FDR correction performed with classifier version 9 ===
1 day, 20:22:41.335625 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:22:41.335725 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:22:41.335785 PROGRESS: Target precursors: 7,853 (98.16%)
1 day, 20:22:41.335839 PROGRESS: Decoy precursors: 147 (1.84%)
1 day, 20:22:41.335886 PROGRESS: 
1 day, 20:22:41.335932 PROGRESS: Precursor Summary:
1 day, 20:22:41.339016 PROGRESS: Channel   0:	 0.05 FDR: 7,853; 0.01 FDR: 7,844; 0.001 FDR: 6,340
1 day, 20:22:41.339146 PROGRESS: 
1 day, 20:22:41.339204 PROGRESS: Protein Summary:
1 day, 20:22:41.343856 PROGRESS: Channel   0:	 0.05 FDR: 4,166; 0.01 FDR: 4,164; 0.001 FDR: 3,507
1 day, 20:22:41.343971 PROGRESS: =========================================================================
1 day, 20:22:41.370062 INFO: fragments_df_filtered: 5000
1 day, 20:22:41.387602 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:22:42.188076 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:22:43.006305 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:22:43.809350 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:22:44.161148 INFO: calibration group: precursor, predicting mz
1 day, 20:22:44.164175 INFO: calibration group: precursor, predicting rt
1 day, 20:22:44.173601 INFO: calibration group: precursor, predicting mobility
1 day, 20:22:44.175920 INFO: calibration group: fragment, predicting mz
1 day, 20:22:44.194033 INFO: === checking if optimization conditions were reached ===
1 day, 20:22:44.194212 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 20:22:44.196855 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0703.
1 day, 20:22:44.196913 INFO: ==============================================
1 day, 20:22:44.197012 INFO: Starting optimization step 1.
1 day, 20:22:44.197111 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:22:44.197180 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:22:44.202784 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:22:44.202843 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:22:44.202886 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 20:22:44.202910 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.84
1 day, 20:22:44.203913 INFO: Starting candidate selection
1 day, 20:23:05.937109 INFO: Starting candidate scoring
1 day, 20:23:06.931257 INFO: Finished candidate processing
1 day, 20:23:06.931429 INFO: Collecting candidate features
1 day, 20:23:06.982204 INFO: Collecting fragment features
1 day, 20:23:07.002141 INFO: Finished candidate scoring
1 day, 20:23:07.018776 PROGRESS: === Extracted 30400 precursors and 329938 fragments ===
1 day, 20:23:07.019185 INFO: performing precursor FDR with 47 features
1 day, 20:23:07.019224 INFO: Decoy channel: -1
1 day, 20:23:07.019248 INFO: Competetive: True
1 day, 20:23:07.028025 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:23:07.389259 INFO: Test AUC: 0.788
1 day, 20:23:07.389394 INFO: Train AUC: 0.786
1 day, 20:23:07.389425 INFO: AUC difference: 0.20%
1 day, 20:23:07.477542 INFO: Resetting torch num_threads to 100
1 day, 20:23:07.479086 INFO: === FDR correction performed with classifier version 9 ===
1 day, 20:23:07.480648 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:23:07.480869 PROGRESS: Total precursors accumulated: 7,998
1 day, 20:23:07.480943 PROGRESS: Target precursors: 7,864 (98.32%)
1 day, 20:23:07.480996 PROGRESS: Decoy precursors: 134 (1.68%)
1 day, 20:23:07.481058 PROGRESS: 
1 day, 20:23:07.481108 PROGRESS: Precursor Summary:
1 day, 20:23:07.484515 PROGRESS: Channel   0:	 0.05 FDR: 7,864; 0.01 FDR: 7,853; 0.001 FDR: 6,586
1 day, 20:23:07.484640 PROGRESS: 
1 day, 20:23:07.484699 PROGRESS: Protein Summary:
1 day, 20:23:07.489451 PROGRESS: Channel   0:	 0.05 FDR: 4,175; 0.01 FDR: 4,169; 0.001 FDR: 3,607
1 day, 20:23:07.489571 PROGRESS: =========================================================================
1 day, 20:23:07.515311 INFO: fragments_df_filtered: 5000
1 day, 20:23:07.531578 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:23:08.408142 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:23:09.293260 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:23:10.163976 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:23:10.581316 INFO: calibration group: precursor, predicting mz
1 day, 20:23:10.584456 INFO: calibration group: precursor, predicting rt
1 day, 20:23:10.594095 INFO: calibration group: precursor, predicting mobility
1 day, 20:23:10.596492 INFO: calibration group: fragment, predicting mz
1 day, 20:23:10.616468 INFO: === checking if optimization conditions were reached ===
1 day, 20:23:10.616658 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 20:23:10.619326 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0583.
1 day, 20:23:10.619382 INFO: ==============================================
1 day, 20:23:10.619484 INFO: Starting optimization step 2.
1 day, 20:23:10.619553 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:23:10.619612 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:23:10.624453 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:23:10.624510 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:23:10.624547 INFO: FWHM in RT is 2.90 seconds, sigma is 0.64
1 day, 20:23:10.624570 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.85
1 day, 20:23:10.625637 INFO: Starting candidate selection
1 day, 20:23:28.076441 INFO: Starting candidate scoring
1 day, 20:23:29.085725 INFO: Finished candidate processing
1 day, 20:23:29.085849 INFO: Collecting candidate features
1 day, 20:23:29.139993 WARNING: intensity_correlation has 2 NaNs ( 0.01 % out of 30391)
1 day, 20:23:29.144610 INFO: Collecting fragment features
1 day, 20:23:29.167470 INFO: Finished candidate scoring
1 day, 20:23:29.184172 PROGRESS: === Extracted 30391 precursors and 329015 fragments ===
1 day, 20:23:29.184657 INFO: performing precursor FDR with 47 features
1 day, 20:23:29.184697 INFO: Decoy channel: -1
1 day, 20:23:29.184726 INFO: Competetive: True
1 day, 20:23:29.197597 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:23:29.202280 WARNING: dropped 2 decoy PSMs due to missing features
1 day, 20:23:29.584356 INFO: Test AUC: 0.785
1 day, 20:23:29.584490 INFO: Train AUC: 0.788
1 day, 20:23:29.584533 INFO: AUC difference: 0.31%
1 day, 20:23:29.675829 INFO: Resetting torch num_threads to 100
1 day, 20:23:29.677432 INFO: === FDR correction performed with classifier version 9 ===
1 day, 20:23:29.679058 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:23:29.679173 PROGRESS: Total precursors accumulated: 7,998
1 day, 20:23:29.679244 PROGRESS: Target precursors: 7,872 (98.42%)
1 day, 20:23:29.679306 PROGRESS: Decoy precursors: 126 (1.58%)
1 day, 20:23:29.679362 PROGRESS: 
1 day, 20:23:29.679418 PROGRESS: Precursor Summary:
1 day, 20:23:29.682896 PROGRESS: Channel   0:	 0.05 FDR: 7,872; 0.01 FDR: 7,863; 0.001 FDR: 6,567
1 day, 20:23:29.683034 PROGRESS: 
1 day, 20:23:29.683103 PROGRESS: Protein Summary:
1 day, 20:23:29.687874 PROGRESS: Channel   0:	 0.05 FDR: 4,172; 0.01 FDR: 4,168; 0.001 FDR: 3,599
1 day, 20:23:29.688012 PROGRESS: =========================================================================
1 day, 20:23:29.715436 INFO: fragments_df_filtered: 5000
1 day, 20:23:29.735391 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:23:30.567523 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:23:31.391241 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:23:32.196960 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:23:32.551267 INFO: calibration group: precursor, predicting mz
1 day, 20:23:32.554364 INFO: calibration group: precursor, predicting rt
1 day, 20:23:32.563720 INFO: calibration group: precursor, predicting mobility
1 day, 20:23:32.566156 INFO: calibration group: fragment, predicting mz
1 day, 20:23:32.585899 INFO: === checking if optimization conditions were reached ===
1 day, 20:23:32.586131 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 20:23:32.587236 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.0583 found after 3 searches.
1 day, 20:23:32.587294 INFO: ==============================================
1 day, 20:23:32.587406 PROGRESS: Optimization finished for mobility_error.
1 day, 20:23:32.608770 INFO: calibration group: precursor, predicting mz
1 day, 20:23:32.612164 INFO: calibration group: precursor, predicting rt
1 day, 20:23:32.622036 INFO: calibration group: precursor, predicting mobility
1 day, 20:23:32.624751 INFO: calibration group: fragment, predicting mz
1 day, 20:23:32.678603 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 20:23:32.678830 PROGRESS: ==============================================
1 day, 20:23:32.678921 PROGRESS: ms2_error      : 15.0000
1 day, 20:23:32.678994 PROGRESS: ms1_error      : 10.0000
1 day, 20:23:32.679074 PROGRESS: rt_error       : 639.0316
1 day, 20:23:32.679136 PROGRESS: mobility_error : 0.0583
1 day, 20:23:32.679189 PROGRESS: ==============================================
1 day, 20:23:32.680922 INFO: calibration group: precursor, predicting mz
1 day, 20:23:32.702813 INFO: calibration group: precursor, predicting rt
1 day, 20:23:32.792892 INFO: calibration group: precursor, predicting mobility
1 day, 20:23:32.815324 INFO: calibration group: fragment, predicting mz
1 day, 20:23:33.053500 PROGRESS: Extracting batch of 162861 precursors
1 day, 20:23:33.106335 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:23:33.106486 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:23:33.106545 INFO: FWHM in RT is 2.90 seconds, sigma is 0.64
1 day, 20:23:33.106570 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 20:23:33.107466 INFO: Starting candidate selection
1 day, 20:26:20.226229 INFO: Applying score cutoff of 31.170629611968995
1 day, 20:26:20.232631 INFO: Removed 4778 precursors with score below cutoff
1 day, 20:26:20.578274 INFO: Starting candidate scoring
1 day, 20:26:29.801122 INFO: Finished candidate processing
1 day, 20:26:29.801294 INFO: Collecting candidate features
1 day, 20:26:30.346121 INFO: Collecting fragment features
1 day, 20:26:30.544167 INFO: Finished candidate scoring
1 day, 20:26:30.803912 INFO: === FDR correction performed with classifier version 12 ===
1 day, 20:26:30.805223 INFO: performing precursor FDR with 47 features
1 day, 20:26:30.805283 INFO: Decoy channel: -1
1 day, 20:26:30.805309 INFO: Competetive: True
1 day, 20:26:30.912537 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:26:36.154163 INFO: Test AUC: 0.817
1 day, 20:26:36.154304 INFO: Train AUC: 0.820
1 day, 20:26:36.154336 INFO: AUC difference: 0.36%
1 day, 20:26:36.268078 INFO: Resetting torch num_threads to 100
1 day, 20:26:36.291068 INFO: Removing fragments below FDR threshold
1 day, 20:26:36.355765 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:26:36.356106 PROGRESS: Total precursors accumulated: 73,542
1 day, 20:26:36.356175 PROGRESS: Target precursors: 72,814 (99.01%)
1 day, 20:26:36.356230 PROGRESS: Decoy precursors: 728 (0.99%)
1 day, 20:26:36.356290 PROGRESS: 
1 day, 20:26:36.356339 PROGRESS: Precursor Summary:
1 day, 20:26:36.400597 PROGRESS: Channel   0:	 0.05 FDR: 72,814; 0.01 FDR: 72,814; 0.001 FDR: 70,132
1 day, 20:26:36.400939 PROGRESS: 
1 day, 20:26:36.401015 PROGRESS: Protein Summary:
1 day, 20:26:36.455656 PROGRESS: Channel   0:	 0.05 FDR: 8,127; 0.01 FDR: 8,127; 0.001 FDR: 8,061
1 day, 20:26:36.455944 PROGRESS: =========================================================================
1 day, 20:26:37.113530 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 20:26:37.163259 PROGRESS: Loading raw file 6/6: ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 20:26:37.163435 INFO: Quantification results path: run_output/alphadia_1.10_defaultMBR/quant
1 day, 20:26:37.163515 INFO: Creating workflow folder for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508 at run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 20:26:37.164471 INFO: Initializing RawFileManager
1 day, 20:26:37.164581 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:26:37.164635 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:26:37.164671 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:26:37.381802 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
1 day, 20:26:43.888838 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d...
1 day, 20:26:43.890657 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:26:43.893836 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:26:43.894104 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:26:43.894504 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:26:43.896034 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:26:43.910313 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:26:43.910588 INFO: Indexing quadrupole dimension
1 day, 20:26:44.400709 INFO: Transposing detector events
1 day, 20:26:53.333417 INFO: Finished transposing data
1 day, 20:26:53.372956 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 20:26:53.375401 INFO: RT (min)            : 0.0 - 70.0
1 day, 20:26:53.375521 INFO: RT duration (sec)   : 4199.8
1 day, 20:26:53.375589 INFO: RT duration (min)   : 70.0
1 day, 20:26:53.375652 INFO: Cycle len (scans)   : 9
1 day, 20:26:53.375701 INFO: Cycle len (sec)     : 0.97
1 day, 20:26:53.375746 INFO: Number of cycles    : 4347
1 day, 20:26:53.375793 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 20:26:53.467479 INFO: Initializing CalibrationManager
1 day, 20:26:53.467866 INFO: Loading calibration config
1 day, 20:26:53.468810 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'}]
1 day, 20:26:53.468909 INFO: Calibration group :fragment, found 1 estimator(s)
1 day, 20:26:53.469016 INFO: Calibration group :precursor, found 3 estimator(s)
1 day, 20:26:53.469246 INFO: Initializing OptimizationManager
1 day, 20:26:53.469356 INFO: initial parameter: ms1_error = 30
1 day, 20:26:53.469413 INFO: initial parameter: ms2_error = 30
1 day, 20:26:53.469477 INFO: initial parameter: rt_error = 2099.9231665
1 day, 20:26:53.469536 INFO: initial parameter: mobility_error = 0.1
1 day, 20:26:53.469590 INFO: initial parameter: column_type = library
1 day, 20:26:53.469635 INFO: initial parameter: num_candidates = 1
1 day, 20:26:53.469681 INFO: initial parameter: classifier_version = -1
1 day, 20:26:53.469723 INFO: initial parameter: fwhm_rt = 5
1 day, 20:26:53.469769 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 20:26:53.469812 INFO: initial parameter: score_cutoff = 0
1 day, 20:26:53.469876 INFO: Initializing TimingManager
1 day, 20:26:53.469937 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 20:26:53.470063 INFO: FDRManager not loaded from disk.
1 day, 20:26:53.470089 INFO: Initializing FDRManager
1 day, 20:26:53.470124 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 20:26:53.503844 PROGRESS: 82,039 target precursors potentially observable (0 removed)
1 day, 20:26:53.546368 PROGRESS: Starting initial search for precursors.
1 day, 20:26:53.570310 INFO: Starting optimization step 0.
1 day, 20:26:53.570561 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:26:53.570657 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:26:53.575041 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:26:53.575094 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:26:53.575136 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 20:26:53.575161 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 20:26:53.576294 INFO: Starting candidate selection
1 day, 20:28:18.994278 INFO: Starting candidate scoring
1 day, 20:28:20.016850 INFO: Finished candidate processing
1 day, 20:28:20.016952 INFO: Collecting candidate features
1 day, 20:28:20.051309 INFO: Collecting fragment features
1 day, 20:28:20.068236 INFO: Finished candidate scoring
1 day, 20:28:20.078393 PROGRESS: === Extracted 15886 precursors and 175801 fragments ===
1 day, 20:28:20.078830 INFO: performing precursor FDR with 47 features
1 day, 20:28:20.078870 INFO: Decoy channel: -1
1 day, 20:28:20.078894 INFO: Competetive: True
1 day, 20:28:20.083638 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:28:20.249540 INFO: Test AUC: 0.817
1 day, 20:28:20.249658 INFO: Train AUC: 0.826
1 day, 20:28:20.249689 INFO: AUC difference: 1.13%
1 day, 20:28:20.338838 INFO: Resetting torch num_threads to 100
1 day, 20:28:20.339883 INFO: === FDR correction performed with classifier version -1 ===
1 day, 20:28:20.341470 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:28:20.341581 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:28:20.341643 PROGRESS: Target precursors: 6,611 (82.64%)
1 day, 20:28:20.341698 PROGRESS: Decoy precursors: 1,389 (17.36%)
1 day, 20:28:20.341744 PROGRESS: 
1 day, 20:28:20.341792 PROGRESS: Precursor Summary:
1 day, 20:28:20.344081 PROGRESS: Channel   0:	 0.05 FDR: 5,194; 0.01 FDR: 4,073; 0.001 FDR: 2,210
1 day, 20:28:20.344182 PROGRESS: 
1 day, 20:28:20.344239 PROGRESS: Protein Summary:
1 day, 20:28:20.347196 PROGRESS: Channel   0:	 0.05 FDR: 3,006; 0.01 FDR: 2,474; 0.001 FDR: 1,479
1 day, 20:28:20.347303 PROGRESS: =========================================================================
1 day, 20:28:20.356810 INFO: fragments_df_filtered: 5000
1 day, 20:28:20.375789 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:28:20.692599 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:28:21.016096 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:28:21.333637 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:28:21.734486 INFO: calibration group: precursor, predicting mz
1 day, 20:28:21.737417 INFO: calibration group: precursor, predicting rt
1 day, 20:28:21.747190 INFO: calibration group: precursor, predicting mobility
1 day, 20:28:21.749564 INFO: calibration group: fragment, predicting mz
1 day, 20:28:21.768591 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 20:28:21.768824 INFO: Starting optimization step 1.
1 day, 20:28:21.768911 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:28:21.768991 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:28:21.774294 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:28:21.774361 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:28:21.774414 INFO: FWHM in RT is 3.28 seconds, sigma is 0.72
1 day, 20:28:21.774444 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.22
1 day, 20:28:21.775659 INFO: Starting candidate selection
1 day, 20:29:58.293572 INFO: Starting candidate scoring
1 day, 20:30:00.257674 INFO: Finished candidate processing
1 day, 20:30:00.257817 INFO: Collecting candidate features
1 day, 20:30:00.326447 INFO: Collecting fragment features
1 day, 20:30:00.352458 INFO: Finished candidate scoring
1 day, 20:30:00.383160 PROGRESS: === Extracted 30497 precursors and 337597 fragments ===
1 day, 20:30:00.383919 INFO: performing precursor FDR with 47 features
1 day, 20:30:00.383963 INFO: Decoy channel: -1
1 day, 20:30:00.383988 INFO: Competetive: True
1 day, 20:30:00.399740 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:30:00.846780 INFO: Test AUC: 0.721
1 day, 20:30:00.846935 INFO: Train AUC: 0.725
1 day, 20:30:00.846968 INFO: AUC difference: 0.54%
1 day, 20:30:00.942545 INFO: Resetting torch num_threads to 100
1 day, 20:30:00.944273 INFO: === FDR correction performed with classifier version 0 ===
1 day, 20:30:00.946092 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:30:00.946218 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:30:00.946281 PROGRESS: Target precursors: 7,224 (90.30%)
1 day, 20:30:00.946336 PROGRESS: Decoy precursors: 776 (9.70%)
1 day, 20:30:00.946385 PROGRESS: 
1 day, 20:30:00.946432 PROGRESS: Precursor Summary:
1 day, 20:30:00.948960 PROGRESS: Channel   0:	 0.05 FDR: 6,009; 0.01 FDR: 4,872; 0.001 FDR: 2,514
1 day, 20:30:00.949096 PROGRESS: 
1 day, 20:30:00.949171 PROGRESS: Protein Summary:
1 day, 20:30:00.952532 PROGRESS: Channel   0:	 0.05 FDR: 3,379; 0.01 FDR: 2,862; 0.001 FDR: 1,662
1 day, 20:30:00.952646 PROGRESS: =========================================================================
1 day, 20:30:00.973018 INFO: fragments_df_filtered: 5000
1 day, 20:30:01.009246 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:30:01.352759 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:30:01.708167 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:30:02.047400 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:30:02.399465 INFO: calibration group: precursor, predicting mz
1 day, 20:30:02.402660 INFO: calibration group: precursor, predicting rt
1 day, 20:30:02.416809 INFO: calibration group: precursor, predicting mobility
1 day, 20:30:02.419313 INFO: calibration group: fragment, predicting mz
1 day, 20:30:02.439612 INFO: === checking if optimization conditions were reached ===
1 day, 20:30:02.441996 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 20:30:02.443844 PROGRESS: ❌ ms1_error      : 10.0000 > 10.0000 or insufficient steps taken.
1 day, 20:30:02.443902 INFO: ==============================================
1 day, 20:30:02.444026 INFO: Starting optimization step 2.
1 day, 20:30:02.444108 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:30:02.444186 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:30:02.451741 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:30:02.451810 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:30:02.451861 INFO: FWHM in RT is 3.19 seconds, sigma is 0.70
1 day, 20:30:02.451890 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.02
1 day, 20:30:02.457583 INFO: Starting candidate selection
1 day, 20:31:30.982071 INFO: Starting candidate scoring
1 day, 20:31:32.035760 INFO: Finished candidate processing
1 day, 20:31:32.035865 INFO: Collecting candidate features
1 day, 20:31:32.093264 INFO: Collecting fragment features
1 day, 20:31:32.117069 INFO: Finished candidate scoring
1 day, 20:31:32.131527 PROGRESS: === Extracted 30522 precursors and 333498 fragments ===
1 day, 20:31:32.132008 INFO: performing precursor FDR with 47 features
1 day, 20:31:32.132048 INFO: Decoy channel: -1
1 day, 20:31:32.132071 INFO: Competetive: True
1 day, 20:31:32.144422 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:31:32.520346 INFO: Test AUC: 0.759
1 day, 20:31:32.520473 INFO: Train AUC: 0.765
1 day, 20:31:32.520503 INFO: AUC difference: 0.85%
1 day, 20:31:32.608974 INFO: Resetting torch num_threads to 100
1 day, 20:31:32.610256 INFO: === FDR correction performed with classifier version 1 ===
1 day, 20:31:32.611807 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:31:32.611913 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:31:32.611978 PROGRESS: Target precursors: 7,787 (97.34%)
1 day, 20:31:32.612034 PROGRESS: Decoy precursors: 213 (2.66%)
1 day, 20:31:32.612092 PROGRESS: 
1 day, 20:31:32.612140 PROGRESS: Precursor Summary:
1 day, 20:31:32.615096 PROGRESS: Channel   0:	 0.05 FDR: 7,787; 0.01 FDR: 6,719; 0.001 FDR: 5,470
1 day, 20:31:32.615237 PROGRESS: 
1 day, 20:31:32.615298 PROGRESS: Protein Summary:
1 day, 20:31:32.619464 PROGRESS: Channel   0:	 0.05 FDR: 4,132; 0.01 FDR: 3,664; 0.001 FDR: 3,142
1 day, 20:31:32.619582 PROGRESS: =========================================================================
1 day, 20:31:32.642833 INFO: fragments_df_filtered: 5000
1 day, 20:31:32.663595 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:31:33.262034 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:31:33.888433 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:31:34.490533 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:31:34.841053 INFO: calibration group: precursor, predicting mz
1 day, 20:31:34.843876 INFO: calibration group: precursor, predicting rt
1 day, 20:31:34.853006 INFO: calibration group: precursor, predicting mobility
1 day, 20:31:34.855266 INFO: calibration group: fragment, predicting mz
1 day, 20:31:34.873250 INFO: === checking if optimization conditions were reached ===
1 day, 20:31:34.875339 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 20:31:34.877495 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
1 day, 20:31:34.877570 INFO: ==============================================
1 day, 20:31:34.877702 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 20:31:34.899581 INFO: calibration group: precursor, predicting mz
1 day, 20:31:34.902600 INFO: calibration group: precursor, predicting rt
1 day, 20:31:34.914872 INFO: calibration group: precursor, predicting mobility
1 day, 20:31:34.917184 INFO: calibration group: fragment, predicting mz
1 day, 20:31:34.935962 INFO: Starting optimization step 0.
1 day, 20:31:34.936119 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:31:34.936202 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:31:34.940060 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:31:34.940118 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:31:34.940164 INFO: FWHM in RT is 2.90 seconds, sigma is 0.64
1 day, 20:31:34.940193 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.07
1 day, 20:31:34.949162 INFO: Starting candidate selection
1 day, 20:33:05.979743 INFO: Starting candidate scoring
1 day, 20:33:07.042474 INFO: Finished candidate processing
1 day, 20:33:07.042622 INFO: Collecting candidate features
1 day, 20:33:07.118674 INFO: Collecting fragment features
1 day, 20:33:07.145252 INFO: Finished candidate scoring
1 day, 20:33:07.164063 PROGRESS: === Extracted 30444 precursors and 332292 fragments ===
1 day, 20:33:07.164783 INFO: performing precursor FDR with 47 features
1 day, 20:33:07.164824 INFO: Decoy channel: -1
1 day, 20:33:07.164850 INFO: Competetive: True
1 day, 20:33:07.177704 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:33:07.553905 INFO: Test AUC: 0.780
1 day, 20:33:07.554026 INFO: Train AUC: 0.771
1 day, 20:33:07.554058 INFO: AUC difference: 1.20%
1 day, 20:33:07.646134 INFO: Resetting torch num_threads to 100
1 day, 20:33:07.647415 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:33:07.648843 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:33:07.648942 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:33:07.649002 PROGRESS: Target precursors: 7,828 (97.85%)
1 day, 20:33:07.649068 PROGRESS: Decoy precursors: 172 (2.15%)
1 day, 20:33:07.649119 PROGRESS: 
1 day, 20:33:07.649167 PROGRESS: Precursor Summary:
1 day, 20:33:07.652253 PROGRESS: Channel   0:	 0.05 FDR: 7,828; 0.01 FDR: 6,780; 0.001 FDR: 5,860
1 day, 20:33:07.652383 PROGRESS: 
1 day, 20:33:07.652446 PROGRESS: Protein Summary:
1 day, 20:33:07.656709 PROGRESS: Channel   0:	 0.05 FDR: 4,145; 0.01 FDR: 3,694; 0.001 FDR: 3,313
1 day, 20:33:07.656830 PROGRESS: =========================================================================
1 day, 20:33:07.680458 INFO: fragments_df_filtered: 5000
1 day, 20:33:07.710747 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:33:08.334974 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:33:08.972678 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:33:09.583019 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:33:09.934753 INFO: calibration group: precursor, predicting mz
1 day, 20:33:09.937625 INFO: calibration group: precursor, predicting rt
1 day, 20:33:09.947170 INFO: calibration group: precursor, predicting mobility
1 day, 20:33:09.949546 INFO: calibration group: fragment, predicting mz
1 day, 20:33:09.969054 INFO: === checking if optimization conditions were reached ===
1 day, 20:33:09.969252 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 20:33:09.974469 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 178.7724.
1 day, 20:33:09.974529 INFO: ==============================================
1 day, 20:33:09.974640 INFO: Starting optimization step 1.
1 day, 20:33:09.974711 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:33:09.974779 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:33:09.979342 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:33:09.979407 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:33:09.979451 INFO: FWHM in RT is 2.89 seconds, sigma is 0.64
1 day, 20:33:09.979473 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.03
1 day, 20:33:09.985120 INFO: Starting candidate selection
1 day, 20:33:18.225731 INFO: Starting candidate scoring
1 day, 20:33:19.199183 INFO: Finished candidate processing
1 day, 20:33:19.200602 INFO: Collecting candidate features
1 day, 20:33:19.251660 INFO: Collecting fragment features
1 day, 20:33:19.269944 INFO: Finished candidate scoring
1 day, 20:33:19.282583 PROGRESS: === Extracted 30352 precursors and 326267 fragments ===
1 day, 20:33:19.282967 INFO: performing precursor FDR with 47 features
1 day, 20:33:19.283003 INFO: Decoy channel: -1
1 day, 20:33:19.283026 INFO: Competetive: True
1 day, 20:33:19.293543 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:33:19.650242 INFO: Test AUC: 0.806
1 day, 20:33:19.650363 INFO: Train AUC: 0.807
1 day, 20:33:19.650393 INFO: AUC difference: 0.13%
1 day, 20:33:19.735885 INFO: Resetting torch num_threads to 100
1 day, 20:33:19.737072 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:33:19.738634 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:33:19.738732 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:33:19.738794 PROGRESS: Target precursors: 7,913 (98.91%)
1 day, 20:33:19.738846 PROGRESS: Decoy precursors: 87 (1.09%)
1 day, 20:33:19.738894 PROGRESS: 
1 day, 20:33:19.738940 PROGRESS: Precursor Summary:
1 day, 20:33:19.741992 PROGRESS: Channel   0:	 0.05 FDR: 7,913; 0.01 FDR: 7,904; 0.001 FDR: 6,632
1 day, 20:33:19.742110 PROGRESS: 
1 day, 20:33:19.742179 PROGRESS: Protein Summary:
1 day, 20:33:19.746665 PROGRESS: Channel   0:	 0.05 FDR: 4,179; 0.01 FDR: 4,176; 0.001 FDR: 3,662
1 day, 20:33:19.746781 PROGRESS: =========================================================================
1 day, 20:33:19.773396 INFO: fragments_df_filtered: 5000
1 day, 20:33:19.787785 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:33:20.665272 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:33:21.564571 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:33:22.442393 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:33:22.857682 INFO: calibration group: precursor, predicting mz
1 day, 20:33:22.860507 INFO: calibration group: precursor, predicting rt
1 day, 20:33:22.869627 INFO: calibration group: precursor, predicting mobility
1 day, 20:33:22.871970 INFO: calibration group: fragment, predicting mz
1 day, 20:33:22.890652 INFO: === checking if optimization conditions were reached ===
1 day, 20:33:22.890830 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 20:33:22.897202 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 161.9899.
1 day, 20:33:22.897269 INFO: ==============================================
1 day, 20:33:22.897380 INFO: Starting optimization step 2.
1 day, 20:33:22.897458 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:33:22.897532 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:33:22.902283 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:33:22.902345 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:33:22.902388 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 20:33:22.902416 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.84
1 day, 20:33:22.903514 INFO: Starting candidate selection
1 day, 20:33:30.189006 INFO: Starting candidate scoring
1 day, 20:33:31.139056 INFO: Finished candidate processing
1 day, 20:33:31.139189 INFO: Collecting candidate features
1 day, 20:33:31.184152 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 30361)
1 day, 20:33:31.188607 INFO: Collecting fragment features
1 day, 20:33:31.208983 INFO: Finished candidate scoring
1 day, 20:33:31.221798 PROGRESS: === Extracted 30361 precursors and 325669 fragments ===
1 day, 20:33:31.222179 INFO: performing precursor FDR with 47 features
1 day, 20:33:31.222220 INFO: Decoy channel: -1
1 day, 20:33:31.222248 INFO: Competetive: True
1 day, 20:33:31.231061 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:33:31.234998 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 20:33:31.570404 INFO: Test AUC: 0.814
1 day, 20:33:31.570534 INFO: Train AUC: 0.811
1 day, 20:33:31.570567 INFO: AUC difference: 0.37%
1 day, 20:33:31.656082 INFO: Resetting torch num_threads to 100
1 day, 20:33:31.657258 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:33:31.658628 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:33:31.658730 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:33:31.658798 PROGRESS: Target precursors: 7,911 (98.89%)
1 day, 20:33:31.658855 PROGRESS: Decoy precursors: 89 (1.11%)
1 day, 20:33:31.658908 PROGRESS: 
1 day, 20:33:31.658961 PROGRESS: Precursor Summary:
1 day, 20:33:31.661931 PROGRESS: Channel   0:	 0.05 FDR: 7,911; 0.01 FDR: 7,907; 0.001 FDR: 7,095
1 day, 20:33:31.662058 PROGRESS: 
1 day, 20:33:31.662123 PROGRESS: Protein Summary:
1 day, 20:33:31.666605 PROGRESS: Channel   0:	 0.05 FDR: 4,180; 0.01 FDR: 4,177; 0.001 FDR: 3,846
1 day, 20:33:31.666718 PROGRESS: =========================================================================
1 day, 20:33:31.691952 INFO: fragments_df_filtered: 5000
1 day, 20:33:31.706799 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:33:32.525208 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:33:33.423300 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:33:34.304282 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:33:34.720894 INFO: calibration group: precursor, predicting mz
1 day, 20:33:34.723753 INFO: calibration group: precursor, predicting rt
1 day, 20:33:34.732837 INFO: calibration group: precursor, predicting mobility
1 day, 20:33:34.735165 INFO: calibration group: fragment, predicting mz
1 day, 20:33:34.752934 INFO: === checking if optimization conditions were reached ===
1 day, 20:33:34.753119 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 20:33:34.759109 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 140.4229.
1 day, 20:33:34.759172 INFO: ==============================================
1 day, 20:33:34.759271 INFO: Starting optimization step 3.
1 day, 20:33:34.759339 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:33:34.759400 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:33:34.763315 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:33:34.763372 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:33:34.763407 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
1 day, 20:33:34.763430 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.84
1 day, 20:33:34.764236 INFO: Starting candidate selection
1 day, 20:33:41.553936 INFO: Starting candidate scoring
1 day, 20:33:42.490649 INFO: Finished candidate processing
1 day, 20:33:42.490786 INFO: Collecting candidate features
1 day, 20:33:42.539033 INFO: Collecting fragment features
1 day, 20:33:42.558349 INFO: Finished candidate scoring
1 day, 20:33:42.570965 PROGRESS: === Extracted 30351 precursors and 325410 fragments ===
1 day, 20:33:42.572101 INFO: performing precursor FDR with 47 features
1 day, 20:33:42.572141 INFO: Decoy channel: -1
1 day, 20:33:42.572165 INFO: Competetive: True
1 day, 20:33:42.580000 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:33:42.936572 INFO: Test AUC: 0.814
1 day, 20:33:42.936697 INFO: Train AUC: 0.814
1 day, 20:33:42.936727 INFO: AUC difference: 0.08%
1 day, 20:33:43.021406 INFO: Resetting torch num_threads to 100
1 day, 20:33:43.022575 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:33:43.024015 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:33:43.024108 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:33:43.024170 PROGRESS: Target precursors: 7,908 (98.85%)
1 day, 20:33:43.024220 PROGRESS: Decoy precursors: 92 (1.15%)
1 day, 20:33:43.024267 PROGRESS: 
1 day, 20:33:43.024319 PROGRESS: Precursor Summary:
1 day, 20:33:43.027288 PROGRESS: Channel   0:	 0.05 FDR: 7,908; 0.01 FDR: 7,896; 0.001 FDR: 6,925
1 day, 20:33:43.027405 PROGRESS: 
1 day, 20:33:43.027462 PROGRESS: Protein Summary:
1 day, 20:33:43.031945 PROGRESS: Channel   0:	 0.05 FDR: 4,178; 0.01 FDR: 4,174; 0.001 FDR: 3,787
1 day, 20:33:43.032052 PROGRESS: =========================================================================
1 day, 20:33:43.057253 INFO: fragments_df_filtered: 5000
1 day, 20:33:43.071735 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:33:43.947516 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:33:44.848670 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:33:45.723674 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:33:46.121697 INFO: calibration group: precursor, predicting mz
1 day, 20:33:46.125293 INFO: calibration group: precursor, predicting rt
1 day, 20:33:46.134570 INFO: calibration group: precursor, predicting mobility
1 day, 20:33:46.136961 INFO: calibration group: fragment, predicting mz
1 day, 20:33:46.156393 INFO: === checking if optimization conditions were reached ===
1 day, 20:33:46.156539 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 20:33:46.162421 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 118.2421.
1 day, 20:33:46.162485 INFO: ==============================================
1 day, 20:33:46.162578 INFO: Starting optimization step 4.
1 day, 20:33:46.162645 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:33:46.162713 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:33:46.166499 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:33:46.166550 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:33:46.166585 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 20:33:46.166607 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.83
1 day, 20:33:46.167489 INFO: Starting candidate selection
1 day, 20:33:51.972813 INFO: Starting candidate scoring
1 day, 20:33:52.926017 INFO: Finished candidate processing
1 day, 20:33:52.926163 INFO: Collecting candidate features
1 day, 20:33:52.970792 WARNING: intensity_correlation has 2 NaNs ( 0.01 % out of 30369)
1 day, 20:33:52.975113 INFO: Collecting fragment features
1 day, 20:33:52.993572 INFO: Finished candidate scoring
1 day, 20:33:53.006252 PROGRESS: === Extracted 30369 precursors and 325210 fragments ===
1 day, 20:33:53.006611 INFO: performing precursor FDR with 47 features
1 day, 20:33:53.006647 INFO: Decoy channel: -1
1 day, 20:33:53.006668 INFO: Competetive: True
1 day, 20:33:53.014422 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:33:53.018232 WARNING: dropped 2 decoy PSMs due to missing features
1 day, 20:33:53.364511 INFO: Test AUC: 0.818
1 day, 20:33:53.364644 INFO: Train AUC: 0.817
1 day, 20:33:53.364673 INFO: AUC difference: 0.16%
1 day, 20:33:53.448828 INFO: Resetting torch num_threads to 100
1 day, 20:33:53.450042 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:33:53.451473 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:33:53.451570 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:33:53.451630 PROGRESS: Target precursors: 7,910 (98.88%)
1 day, 20:33:53.451681 PROGRESS: Decoy precursors: 90 (1.12%)
1 day, 20:33:53.451728 PROGRESS: 
1 day, 20:33:53.451773 PROGRESS: Precursor Summary:
1 day, 20:33:53.454703 PROGRESS: Channel   0:	 0.05 FDR: 7,910; 0.01 FDR: 7,905; 0.001 FDR: 6,800
1 day, 20:33:53.454812 PROGRESS: 
1 day, 20:33:53.454870 PROGRESS: Protein Summary:
1 day, 20:33:53.459291 PROGRESS: Channel   0:	 0.05 FDR: 4,181; 0.01 FDR: 4,178; 0.001 FDR: 3,736
1 day, 20:33:53.459404 PROGRESS: =========================================================================
1 day, 20:33:53.484443 INFO: fragments_df_filtered: 5000
1 day, 20:33:53.498789 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:33:54.309015 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:33:55.149048 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:33:55.957978 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:33:56.310584 INFO: calibration group: precursor, predicting mz
1 day, 20:33:56.313385 INFO: calibration group: precursor, predicting rt
1 day, 20:33:56.322590 INFO: calibration group: precursor, predicting mobility
1 day, 20:33:56.324915 INFO: calibration group: fragment, predicting mz
1 day, 20:33:56.343425 INFO: === checking if optimization conditions were reached ===
1 day, 20:33:56.343578 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 20:33:56.349494 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 100.6859.
1 day, 20:33:56.349552 INFO: ==============================================
1 day, 20:33:56.349647 INFO: Starting optimization step 5.
1 day, 20:33:56.349717 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:33:56.349777 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:33:56.353329 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:33:56.353384 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:33:56.353420 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 20:33:56.353444 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.83
1 day, 20:33:56.354342 INFO: Starting candidate selection
1 day, 20:34:01.537211 INFO: Starting candidate scoring
1 day, 20:34:02.494940 INFO: Finished candidate processing
1 day, 20:34:02.495077 INFO: Collecting candidate features
1 day, 20:34:02.543472 INFO: Collecting fragment features
1 day, 20:34:02.566247 INFO: Finished candidate scoring
1 day, 20:34:02.579684 PROGRESS: === Extracted 30384 precursors and 325044 fragments ===
1 day, 20:34:02.580060 INFO: performing precursor FDR with 47 features
1 day, 20:34:02.580096 INFO: Decoy channel: -1
1 day, 20:34:02.580121 INFO: Competetive: True
1 day, 20:34:02.588122 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:34:02.929185 INFO: Test AUC: 0.817
1 day, 20:34:02.929310 INFO: Train AUC: 0.822
1 day, 20:34:02.929342 INFO: AUC difference: 0.64%
1 day, 20:34:03.014591 INFO: Resetting torch num_threads to 100
1 day, 20:34:03.015705 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:34:03.017149 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:34:03.017253 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:34:03.017315 PROGRESS: Target precursors: 7,907 (98.84%)
1 day, 20:34:03.017367 PROGRESS: Decoy precursors: 93 (1.16%)
1 day, 20:34:03.017415 PROGRESS: 
1 day, 20:34:03.017460 PROGRESS: Precursor Summary:
1 day, 20:34:03.020379 PROGRESS: Channel   0:	 0.05 FDR: 7,907; 0.01 FDR: 7,901; 0.001 FDR: 6,916
1 day, 20:34:03.020489 PROGRESS: 
1 day, 20:34:03.020545 PROGRESS: Protein Summary:
1 day, 20:34:03.024938 PROGRESS: Channel   0:	 0.05 FDR: 4,179; 0.01 FDR: 4,176; 0.001 FDR: 3,781
1 day, 20:34:03.025054 PROGRESS: =========================================================================
1 day, 20:34:03.050561 INFO: fragments_df_filtered: 5000
1 day, 20:34:03.064823 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:34:03.873540 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:34:04.715664 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:34:05.528969 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:34:05.881334 INFO: calibration group: precursor, predicting mz
1 day, 20:34:05.884735 INFO: calibration group: precursor, predicting rt
1 day, 20:34:05.894148 INFO: calibration group: precursor, predicting mobility
1 day, 20:34:05.896490 INFO: calibration group: fragment, predicting mz
1 day, 20:34:05.916420 INFO: === checking if optimization conditions were reached ===
1 day, 20:34:05.916605 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 20:34:05.923300 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 82.9194.
1 day, 20:34:05.923382 INFO: ==============================================
1 day, 20:34:05.923515 INFO: Starting optimization step 6.
1 day, 20:34:05.923603 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:34:05.923685 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:34:05.943282 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:34:05.943360 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:34:05.943411 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 20:34:05.943440 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.83
1 day, 20:34:05.952202 INFO: Starting candidate selection
1 day, 20:34:10.087809 INFO: Starting candidate scoring
1 day, 20:34:11.068821 INFO: Finished candidate processing
1 day, 20:34:11.068969 INFO: Collecting candidate features
1 day, 20:34:11.123191 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 30360)
1 day, 20:34:11.130345 INFO: Collecting fragment features
1 day, 20:34:11.151755 INFO: Finished candidate scoring
1 day, 20:34:11.164938 PROGRESS: === Extracted 30360 precursors and 324285 fragments ===
1 day, 20:34:11.165378 INFO: performing precursor FDR with 47 features
1 day, 20:34:11.165415 INFO: Decoy channel: -1
1 day, 20:34:11.165438 INFO: Competetive: True
1 day, 20:34:11.175322 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:34:11.179526 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 20:34:11.521130 INFO: Test AUC: 0.824
1 day, 20:34:11.521253 INFO: Train AUC: 0.823
1 day, 20:34:11.521283 INFO: AUC difference: 0.05%
1 day, 20:34:13.827120 INFO: Resetting torch num_threads to 100
1 day, 20:34:13.828335 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:34:13.829905 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:34:13.830012 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:34:13.830075 PROGRESS: Target precursors: 7,926 (99.08%)
1 day, 20:34:13.830126 PROGRESS: Decoy precursors: 74 (0.92%)
1 day, 20:34:13.830178 PROGRESS: 
1 day, 20:34:13.830225 PROGRESS: Precursor Summary:
1 day, 20:34:13.833548 PROGRESS: Channel   0:	 0.05 FDR: 7,926; 0.01 FDR: 7,926; 0.001 FDR: 7,032
1 day, 20:34:13.833670 PROGRESS: 
1 day, 20:34:13.833728 PROGRESS: Protein Summary:
1 day, 20:34:13.838360 PROGRESS: Channel   0:	 0.05 FDR: 4,188; 0.01 FDR: 4,188; 0.001 FDR: 3,827
1 day, 20:34:13.838484 PROGRESS: =========================================================================
1 day, 20:34:13.864124 INFO: fragments_df_filtered: 5000
1 day, 20:34:13.882365 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:34:14.698293 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:34:15.546650 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:34:16.366014 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:34:16.718205 INFO: calibration group: precursor, predicting mz
1 day, 20:34:16.721206 INFO: calibration group: precursor, predicting rt
1 day, 20:34:16.730649 INFO: calibration group: precursor, predicting mobility
1 day, 20:34:16.733055 INFO: calibration group: fragment, predicting mz
1 day, 20:34:16.752784 INFO: === checking if optimization conditions were reached ===
1 day, 20:34:16.752942 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 20:34:16.758922 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 68.6647.
1 day, 20:34:16.759002 INFO: ==============================================
1 day, 20:34:16.759104 INFO: Starting optimization step 7.
1 day, 20:34:16.759175 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:34:16.759236 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:34:16.763715 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:34:16.763772 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:34:16.763815 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 20:34:16.763842 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.83
1 day, 20:34:16.766497 INFO: Starting candidate selection
1 day, 20:34:20.427404 INFO: Starting candidate scoring
1 day, 20:34:21.378287 INFO: Finished candidate processing
1 day, 20:34:21.378425 INFO: Collecting candidate features
1 day, 20:34:21.425292 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 30357)
1 day, 20:34:21.429644 INFO: Collecting fragment features
1 day, 20:34:21.450766 INFO: Finished candidate scoring
1 day, 20:34:21.467208 PROGRESS: === Extracted 30357 precursors and 323663 fragments ===
1 day, 20:34:21.467631 INFO: performing precursor FDR with 47 features
1 day, 20:34:21.467676 INFO: Decoy channel: -1
1 day, 20:34:21.467708 INFO: Competetive: True
1 day, 20:34:21.476979 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:34:21.481105 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 20:34:21.818142 INFO: Test AUC: 0.829
1 day, 20:34:21.818265 INFO: Train AUC: 0.826
1 day, 20:34:21.818295 INFO: AUC difference: 0.29%
1 day, 20:34:21.901964 INFO: Resetting torch num_threads to 100
1 day, 20:34:21.903201 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:34:21.904631 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:34:21.904746 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:34:21.904809 PROGRESS: Target precursors: 7,930 (99.12%)
1 day, 20:34:21.904861 PROGRESS: Decoy precursors: 70 (0.88%)
1 day, 20:34:21.904910 PROGRESS: 
1 day, 20:34:21.904956 PROGRESS: Precursor Summary:
1 day, 20:34:21.908038 PROGRESS: Channel   0:	 0.05 FDR: 7,930; 0.01 FDR: 7,930; 0.001 FDR: 6,935
1 day, 20:34:21.908161 PROGRESS: 
1 day, 20:34:21.908218 PROGRESS: Protein Summary:
1 day, 20:34:21.912814 PROGRESS: Channel   0:	 0.05 FDR: 4,195; 0.01 FDR: 4,195; 0.001 FDR: 3,786
1 day, 20:34:21.912930 PROGRESS: =========================================================================
1 day, 20:34:21.938098 INFO: fragments_df_filtered: 5000
1 day, 20:34:21.952734 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:34:22.769696 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:34:23.681357 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:34:24.563732 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:34:24.930063 INFO: calibration group: precursor, predicting mz
1 day, 20:34:24.933008 INFO: calibration group: precursor, predicting rt
1 day, 20:34:24.942232 INFO: calibration group: precursor, predicting mobility
1 day, 20:34:24.944537 INFO: calibration group: fragment, predicting mz
1 day, 20:34:24.962237 INFO: === checking if optimization conditions were reached ===
1 day, 20:34:24.962399 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
1 day, 20:34:24.968337 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 56.5468.
1 day, 20:34:24.968402 INFO: ==============================================
1 day, 20:34:24.968500 INFO: Starting optimization step 8.
1 day, 20:34:24.968568 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:34:24.968625 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:34:24.972480 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:34:24.972532 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:34:24.972569 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 20:34:24.972591 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 20:34:24.973713 INFO: Starting candidate selection
1 day, 20:34:28.443144 INFO: Starting candidate scoring
1 day, 20:34:29.376381 INFO: Finished candidate processing
1 day, 20:34:29.376563 INFO: Collecting candidate features
1 day, 20:34:29.424389 WARNING: intensity_correlation has 4 NaNs ( 0.01 % out of 30330)
1 day, 20:34:29.428761 INFO: Collecting fragment features
1 day, 20:34:29.446675 INFO: Finished candidate scoring
1 day, 20:34:29.462608 PROGRESS: === Extracted 30330 precursors and 323205 fragments ===
1 day, 20:34:29.462997 INFO: performing precursor FDR with 47 features
1 day, 20:34:29.463037 INFO: Decoy channel: -1
1 day, 20:34:29.463063 INFO: Competetive: True
1 day, 20:34:29.471545 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:34:29.475781 WARNING: dropped 4 decoy PSMs due to missing features
1 day, 20:34:29.813524 INFO: Test AUC: 0.828
1 day, 20:34:29.813656 INFO: Train AUC: 0.828
1 day, 20:34:29.813690 INFO: AUC difference: 0.00%
1 day, 20:34:29.897237 INFO: Resetting torch num_threads to 100
1 day, 20:34:29.898458 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:34:29.899904 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:34:29.900016 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:34:29.900081 PROGRESS: Target precursors: 7,930 (99.12%)
1 day, 20:34:29.900136 PROGRESS: Decoy precursors: 70 (0.88%)
1 day, 20:34:29.900189 PROGRESS: 
1 day, 20:34:29.900238 PROGRESS: Precursor Summary:
1 day, 20:34:29.903270 PROGRESS: Channel   0:	 0.05 FDR: 7,930; 0.01 FDR: 7,930; 0.001 FDR: 6,801
1 day, 20:34:29.903410 PROGRESS: 
1 day, 20:34:29.903475 PROGRESS: Protein Summary:
1 day, 20:34:29.908116 PROGRESS: Channel   0:	 0.05 FDR: 4,195; 0.01 FDR: 4,195; 0.001 FDR: 3,731
1 day, 20:34:29.908226 PROGRESS: =========================================================================
1 day, 20:34:29.933521 INFO: fragments_df_filtered: 5000
1 day, 20:34:29.948117 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:34:30.776544 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:34:31.625338 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:34:32.447856 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:34:32.798517 INFO: calibration group: precursor, predicting mz
1 day, 20:34:32.801499 INFO: calibration group: precursor, predicting rt
1 day, 20:34:32.810819 INFO: calibration group: precursor, predicting mobility
1 day, 20:34:32.813217 INFO: calibration group: fragment, predicting mz
1 day, 20:34:32.832279 INFO: === checking if optimization conditions were reached ===
1 day, 20:34:32.832463 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
1 day, 20:34:32.838997 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 48.1562.
1 day, 20:34:32.839067 INFO: ==============================================
1 day, 20:34:32.839174 INFO: Starting optimization step 9.
1 day, 20:34:32.839247 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:34:32.839314 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:34:32.844860 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:34:32.844921 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:34:32.844966 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 20:34:32.844993 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 20:34:32.847130 INFO: Starting candidate selection
1 day, 20:34:36.041940 INFO: Starting candidate scoring
1 day, 20:34:36.972137 INFO: Finished candidate processing
1 day, 20:34:36.972274 INFO: Collecting candidate features
1 day, 20:34:37.018229 WARNING: intensity_correlation has 4 NaNs ( 0.01 % out of 30318)
1 day, 20:34:37.022713 INFO: Collecting fragment features
1 day, 20:34:37.040277 INFO: Finished candidate scoring
1 day, 20:34:37.055927 PROGRESS: === Extracted 30318 precursors and 322738 fragments ===
1 day, 20:34:37.056365 INFO: performing precursor FDR with 47 features
1 day, 20:34:37.056412 INFO: Decoy channel: -1
1 day, 20:34:37.056443 INFO: Competetive: True
1 day, 20:34:37.064522 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:34:37.068627 WARNING: dropped 4 decoy PSMs due to missing features
1 day, 20:34:37.400748 INFO: Test AUC: 0.828
1 day, 20:34:37.400878 INFO: Train AUC: 0.831
1 day, 20:34:37.400914 INFO: AUC difference: 0.37%
1 day, 20:34:37.485185 INFO: Resetting torch num_threads to 100
1 day, 20:34:37.486455 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:34:37.487949 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:34:37.488059 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:34:37.488138 PROGRESS: Target precursors: 7,938 (99.22%)
1 day, 20:34:37.488211 PROGRESS: Decoy precursors: 62 (0.78%)
1 day, 20:34:37.488271 PROGRESS: 
1 day, 20:34:37.488329 PROGRESS: Precursor Summary:
1 day, 20:34:37.491525 PROGRESS: Channel   0:	 0.05 FDR: 7,938; 0.01 FDR: 7,938; 0.001 FDR: 7,114
1 day, 20:34:37.491671 PROGRESS: 
1 day, 20:34:37.491755 PROGRESS: Protein Summary:
1 day, 20:34:37.496487 PROGRESS: Channel   0:	 0.05 FDR: 4,194; 0.01 FDR: 4,194; 0.001 FDR: 3,858
1 day, 20:34:37.496615 PROGRESS: =========================================================================
1 day, 20:34:37.521271 INFO: fragments_df_filtered: 5000
1 day, 20:34:37.535935 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:34:38.420418 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:34:39.338068 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:34:40.223213 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:34:40.640688 INFO: calibration group: precursor, predicting mz
1 day, 20:34:40.643647 INFO: calibration group: precursor, predicting rt
1 day, 20:34:40.653034 INFO: calibration group: precursor, predicting mobility
1 day, 20:34:40.655374 INFO: calibration group: fragment, predicting mz
1 day, 20:34:40.674743 INFO: === checking if optimization conditions were reached ===
1 day, 20:34:40.674908 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
1 day, 20:34:40.680907 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 42.0282.
1 day, 20:34:40.680967 INFO: ==============================================
1 day, 20:34:40.681075 INFO: Starting optimization step 10.
1 day, 20:34:40.681149 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:34:40.681208 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:34:40.685748 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:34:40.685802 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:34:40.685837 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 20:34:40.685858 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 20:34:40.686871 INFO: Starting candidate selection
1 day, 20:34:43.514672 INFO: Starting candidate scoring
1 day, 20:34:44.443527 INFO: Finished candidate processing
1 day, 20:34:44.444138 INFO: Collecting candidate features
1 day, 20:34:44.487504 WARNING: intensity_correlation has 4 NaNs ( 0.01 % out of 30300)
1 day, 20:34:44.491853 INFO: Collecting fragment features
1 day, 20:34:44.509425 INFO: Finished candidate scoring
1 day, 20:34:44.524456 PROGRESS: === Extracted 30300 precursors and 322091 fragments ===
1 day, 20:34:44.524837 INFO: performing precursor FDR with 47 features
1 day, 20:34:44.524874 INFO: Decoy channel: -1
1 day, 20:34:44.524898 INFO: Competetive: True
1 day, 20:34:44.533123 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:34:44.537991 WARNING: dropped 1 target PSMs due to missing features
1 day, 20:34:44.538083 WARNING: dropped 3 decoy PSMs due to missing features
1 day, 20:34:44.867384 INFO: Test AUC: 0.833
1 day, 20:34:44.867510 INFO: Train AUC: 0.832
1 day, 20:34:44.867542 INFO: AUC difference: 0.16%
1 day, 20:34:44.951283 INFO: Resetting torch num_threads to 100
1 day, 20:34:44.952499 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:34:44.953945 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:34:44.954048 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:34:44.954108 PROGRESS: Target precursors: 7,942 (99.28%)
1 day, 20:34:44.954438 PROGRESS: Decoy precursors: 58 (0.73%)
1 day, 20:34:44.954496 PROGRESS: 
1 day, 20:34:44.954543 PROGRESS: Precursor Summary:
1 day, 20:34:44.957603 PROGRESS: Channel   0:	 0.05 FDR: 7,942; 0.01 FDR: 7,942; 0.001 FDR: 7,095
1 day, 20:34:44.957728 PROGRESS: 
1 day, 20:34:44.957787 PROGRESS: Protein Summary:
1 day, 20:34:44.962376 PROGRESS: Channel   0:	 0.05 FDR: 4,197; 0.01 FDR: 4,197; 0.001 FDR: 3,854
1 day, 20:34:44.962487 PROGRESS: =========================================================================
1 day, 20:34:44.987042 INFO: fragments_df_filtered: 5000
1 day, 20:34:45.002126 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:34:45.885891 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:34:46.793742 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:34:47.637236 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:34:47.988086 INFO: calibration group: precursor, predicting mz
1 day, 20:34:47.991034 INFO: calibration group: precursor, predicting rt
1 day, 20:34:48.000320 INFO: calibration group: precursor, predicting mobility
1 day, 20:34:48.002687 INFO: calibration group: fragment, predicting mz
1 day, 20:34:48.021899 INFO: === checking if optimization conditions were reached ===
1 day, 20:34:48.022070 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 2 ===
1 day, 20:34:48.028052 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 33.5393.
1 day, 20:34:48.028112 INFO: ==============================================
1 day, 20:34:48.028203 INFO: Starting optimization step 11.
1 day, 20:34:48.028270 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:34:48.029147 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:34:48.032822 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:34:48.032871 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:34:48.032905 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 20:34:48.032928 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 20:34:48.034021 INFO: Starting candidate selection
1 day, 20:34:50.668639 INFO: Starting candidate scoring
1 day, 20:34:51.603460 INFO: Finished candidate processing
1 day, 20:34:51.603612 INFO: Collecting candidate features
1 day, 20:34:51.646500 WARNING: intensity_correlation has 5 NaNs ( 0.02 % out of 30321)
1 day, 20:34:51.650808 INFO: Collecting fragment features
1 day, 20:34:51.670337 INFO: Finished candidate scoring
1 day, 20:34:51.684680 PROGRESS: === Extracted 30321 precursors and 321803 fragments ===
1 day, 20:34:51.685068 INFO: performing precursor FDR with 47 features
1 day, 20:34:51.685109 INFO: Decoy channel: -1
1 day, 20:34:51.685133 INFO: Competetive: True
1 day, 20:34:51.692949 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:34:51.696922 WARNING: dropped 5 decoy PSMs due to missing features
1 day, 20:34:52.026234 INFO: Test AUC: 0.833
1 day, 20:34:52.026357 INFO: Train AUC: 0.837
1 day, 20:34:52.026387 INFO: AUC difference: 0.44%
1 day, 20:34:52.110593 INFO: Resetting torch num_threads to 100
1 day, 20:34:52.111794 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:34:52.113283 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:34:52.113383 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:34:52.113445 PROGRESS: Target precursors: 7,940 (99.25%)
1 day, 20:34:52.113498 PROGRESS: Decoy precursors: 60 (0.75%)
1 day, 20:34:52.113545 PROGRESS: 
1 day, 20:34:52.113596 PROGRESS: Precursor Summary:
1 day, 20:34:52.116676 PROGRESS: Channel   0:	 0.05 FDR: 7,940; 0.01 FDR: 7,940; 0.001 FDR: 7,186
1 day, 20:34:52.116800 PROGRESS: 
1 day, 20:34:52.116860 PROGRESS: Protein Summary:
1 day, 20:34:52.121521 PROGRESS: Channel   0:	 0.05 FDR: 4,195; 0.01 FDR: 4,195; 0.001 FDR: 3,894
1 day, 20:34:52.121639 PROGRESS: =========================================================================
1 day, 20:34:52.146031 INFO: fragments_df_filtered: 5000
1 day, 20:34:52.160522 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:34:52.978605 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:34:53.829548 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:34:54.647011 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:34:54.997998 INFO: calibration group: precursor, predicting mz
1 day, 20:34:55.000915 INFO: calibration group: precursor, predicting rt
1 day, 20:34:55.010194 INFO: calibration group: precursor, predicting mobility
1 day, 20:34:55.012541 INFO: calibration group: fragment, predicting mz
1 day, 20:34:55.032465 INFO: === checking if optimization conditions were reached ===
1 day, 20:34:55.032621 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 2 ===
1 day, 20:34:55.038604 PROGRESS: ❌ rt_error       : optimization incomplete after 12 search(es). Will search with parameter 24.6929.
1 day, 20:34:55.038663 INFO: ==============================================
1 day, 20:34:55.038754 INFO: Starting optimization step 12.
1 day, 20:34:55.038821 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:34:55.038879 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:34:55.042817 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:34:55.042871 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:34:55.042906 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 20:34:55.042929 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 20:34:55.043973 INFO: Starting candidate selection
1 day, 20:34:57.213339 INFO: Starting candidate scoring
1 day, 20:34:58.142167 INFO: Finished candidate processing
1 day, 20:34:58.142300 INFO: Collecting candidate features
1 day, 20:34:58.185673 WARNING: intensity_correlation has 4 NaNs ( 0.01 % out of 30315)
1 day, 20:34:58.189999 INFO: Collecting fragment features
1 day, 20:34:58.208805 INFO: Finished candidate scoring
1 day, 20:34:58.222909 PROGRESS: === Extracted 30315 precursors and 321119 fragments ===
1 day, 20:34:58.223290 INFO: performing precursor FDR with 47 features
1 day, 20:34:58.223330 INFO: Decoy channel: -1
1 day, 20:34:58.223354 INFO: Competetive: True
1 day, 20:34:58.231144 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:34:58.235073 WARNING: dropped 4 decoy PSMs due to missing features
1 day, 20:34:58.565059 INFO: Test AUC: 0.846
1 day, 20:34:58.565183 INFO: Train AUC: 0.841
1 day, 20:34:58.565215 INFO: AUC difference: 0.51%
1 day, 20:34:58.650485 INFO: Resetting torch num_threads to 100
1 day, 20:34:58.651629 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:34:58.653099 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:34:58.653199 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:34:58.653260 PROGRESS: Target precursors: 7,946 (99.33%)
1 day, 20:34:58.653313 PROGRESS: Decoy precursors: 54 (0.68%)
1 day, 20:34:58.653360 PROGRESS: 
1 day, 20:34:58.653404 PROGRESS: Precursor Summary:
1 day, 20:34:58.656432 PROGRESS: Channel   0:	 0.05 FDR: 7,946; 0.01 FDR: 7,946; 0.001 FDR: 7,375
1 day, 20:34:58.656550 PROGRESS: 
1 day, 20:34:58.656607 PROGRESS: Protein Summary:
1 day, 20:34:58.661261 PROGRESS: Channel   0:	 0.05 FDR: 4,202; 0.01 FDR: 4,202; 0.001 FDR: 3,980
1 day, 20:34:58.661376 PROGRESS: =========================================================================
1 day, 20:34:58.686248 INFO: fragments_df_filtered: 5000
1 day, 20:34:58.700810 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:34:59.520034 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:35:00.360158 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:35:01.185464 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:35:01.537577 INFO: calibration group: precursor, predicting mz
1 day, 20:35:01.540583 INFO: calibration group: precursor, predicting rt
1 day, 20:35:01.549942 INFO: calibration group: precursor, predicting mobility
1 day, 20:35:01.552317 INFO: calibration group: fragment, predicting mz
1 day, 20:35:01.571723 INFO: === checking if optimization conditions were reached ===
1 day, 20:35:01.571887 PROGRESS: === Optimization of rt_error has been performed 13 time(s); minimum number is 2 ===
1 day, 20:35:01.577927 PROGRESS: ❌ rt_error       : optimization incomplete after 13 search(es). Will search with parameter 19.9764.
1 day, 20:35:01.577987 INFO: ==============================================
1 day, 20:35:01.578081 INFO: Starting optimization step 13.
1 day, 20:35:01.578147 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:35:01.578204 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:35:01.582358 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:35:01.582413 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:35:01.582449 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
1 day, 20:35:01.582473 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 20:35:01.583477 INFO: Starting candidate selection
1 day, 20:35:03.503894 INFO: Starting candidate scoring
1 day, 20:35:04.418536 INFO: Finished candidate processing
1 day, 20:35:04.418641 INFO: Collecting candidate features
1 day, 20:35:04.462625 WARNING: intensity_correlation has 7 NaNs ( 0.02 % out of 30270)
1 day, 20:35:04.466971 INFO: Collecting fragment features
1 day, 20:35:04.484897 INFO: Finished candidate scoring
1 day, 20:35:04.498411 PROGRESS: === Extracted 30270 precursors and 319583 fragments ===
1 day, 20:35:04.498785 INFO: performing precursor FDR with 47 features
1 day, 20:35:04.498824 INFO: Decoy channel: -1
1 day, 20:35:04.498848 INFO: Competetive: True
1 day, 20:35:04.506685 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:35:04.511406 WARNING: dropped 1 target PSMs due to missing features
1 day, 20:35:04.511494 WARNING: dropped 6 decoy PSMs due to missing features
1 day, 20:35:04.836603 INFO: Test AUC: 0.845
1 day, 20:35:04.836730 INFO: Train AUC: 0.847
1 day, 20:35:04.836759 INFO: AUC difference: 0.16%
1 day, 20:35:04.921574 INFO: Resetting torch num_threads to 100
1 day, 20:35:04.922791 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:35:04.924346 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:35:04.924444 PROGRESS: Total precursors accumulated: 7,999
1 day, 20:35:04.924508 PROGRESS: Target precursors: 7,950 (99.39%)
1 day, 20:35:04.924565 PROGRESS: Decoy precursors: 49 (0.61%)
1 day, 20:35:04.924614 PROGRESS: 
1 day, 20:35:04.924663 PROGRESS: Precursor Summary:
1 day, 20:35:04.927813 PROGRESS: Channel   0:	 0.05 FDR: 7,950; 0.01 FDR: 7,950; 0.001 FDR: 7,401
1 day, 20:35:04.927936 PROGRESS: 
1 day, 20:35:04.928008 PROGRESS: Protein Summary:
1 day, 20:35:04.932722 PROGRESS: Channel   0:	 0.05 FDR: 4,202; 0.01 FDR: 4,202; 0.001 FDR: 3,984
1 day, 20:35:04.932830 PROGRESS: =========================================================================
1 day, 20:35:04.957594 INFO: fragments_df_filtered: 5000
1 day, 20:35:04.972233 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:35:05.795460 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:35:06.628336 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:35:07.452673 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:35:07.802119 INFO: calibration group: precursor, predicting mz
1 day, 20:35:07.805021 INFO: calibration group: precursor, predicting rt
1 day, 20:35:07.814280 INFO: calibration group: precursor, predicting mobility
1 day, 20:35:07.816643 INFO: calibration group: fragment, predicting mz
1 day, 20:35:07.835678 INFO: === checking if optimization conditions were reached ===
1 day, 20:35:07.835831 PROGRESS: === Optimization of rt_error has been performed 14 time(s); minimum number is 2 ===
1 day, 20:35:07.841816 PROGRESS: ❌ rt_error       : optimization incomplete after 14 search(es). Will search with parameter 15.7169.
1 day, 20:35:07.841877 INFO: ==============================================
1 day, 20:35:07.841970 INFO: Starting optimization step 14.
1 day, 20:35:07.842035 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:35:07.842094 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:35:07.846231 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:35:07.846284 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:35:07.846319 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 20:35:07.846343 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 20:35:07.847297 INFO: Starting candidate selection
1 day, 20:35:09.585294 INFO: Starting candidate scoring
1 day, 20:35:10.496430 INFO: Finished candidate processing
1 day, 20:35:10.496610 INFO: Collecting candidate features
1 day, 20:35:10.569103 WARNING: intensity_correlation has 7 NaNs ( 0.02 % out of 30263)
1 day, 20:35:10.573436 INFO: Collecting fragment features
1 day, 20:35:10.591379 INFO: Finished candidate scoring
1 day, 20:35:10.604683 PROGRESS: === Extracted 30263 precursors and 318736 fragments ===
1 day, 20:35:10.605062 INFO: performing precursor FDR with 47 features
1 day, 20:35:10.605101 INFO: Decoy channel: -1
1 day, 20:35:10.605124 INFO: Competetive: True
1 day, 20:35:10.613001 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:35:10.616858 WARNING: dropped 7 decoy PSMs due to missing features
1 day, 20:35:10.946198 INFO: Test AUC: 0.850
1 day, 20:35:10.946326 INFO: Train AUC: 0.850
1 day, 20:35:10.946356 INFO: AUC difference: 0.02%
1 day, 20:35:11.030322 INFO: Resetting torch num_threads to 100
1 day, 20:35:11.031540 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:35:11.032927 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:35:11.033034 PROGRESS: Total precursors accumulated: 8,000
1 day, 20:35:11.033099 PROGRESS: Target precursors: 7,954 (99.42%)
1 day, 20:35:11.033154 PROGRESS: Decoy precursors: 46 (0.57%)
1 day, 20:35:11.033204 PROGRESS: 
1 day, 20:35:11.033251 PROGRESS: Precursor Summary:
1 day, 20:35:11.036249 PROGRESS: Channel   0:	 0.05 FDR: 7,954; 0.01 FDR: 7,954; 0.001 FDR: 7,397
1 day, 20:35:11.036374 PROGRESS: 
1 day, 20:35:11.036433 PROGRESS: Protein Summary:
1 day, 20:35:11.040997 PROGRESS: Channel   0:	 0.05 FDR: 4,205; 0.01 FDR: 4,205; 0.001 FDR: 3,976
1 day, 20:35:11.041125 PROGRESS: =========================================================================
1 day, 20:35:11.065741 INFO: fragments_df_filtered: 5000
1 day, 20:35:11.080071 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:35:11.914023 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:35:12.755286 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:35:13.577898 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:35:13.928905 INFO: calibration group: precursor, predicting mz
1 day, 20:35:13.931901 INFO: calibration group: precursor, predicting rt
1 day, 20:35:13.941226 INFO: calibration group: precursor, predicting mobility
1 day, 20:35:13.943634 INFO: calibration group: fragment, predicting mz
1 day, 20:35:13.963288 INFO: === checking if optimization conditions were reached ===
1 day, 20:35:13.963466 PROGRESS: === Optimization of rt_error has been performed 15 time(s); minimum number is 2 ===
1 day, 20:35:13.970047 PROGRESS: ❌ rt_error       : optimization incomplete after 15 search(es). Will search with parameter 14.5561.
1 day, 20:35:13.970118 INFO: ==============================================
1 day, 20:35:13.970228 INFO: Starting optimization step 15.
1 day, 20:35:13.970315 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:35:13.970382 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:35:13.975757 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:35:13.975821 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:35:13.975865 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 20:35:13.975892 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 20:35:13.977736 INFO: Starting candidate selection
1 day, 20:35:15.531713 INFO: Starting candidate scoring
1 day, 20:35:16.459107 INFO: Finished candidate processing
1 day, 20:35:16.459289 INFO: Collecting candidate features
1 day, 20:35:16.507441 WARNING: intensity_correlation has 8 NaNs ( 0.03 % out of 30224)
1 day, 20:35:16.511774 INFO: Collecting fragment features
1 day, 20:35:16.531534 INFO: Finished candidate scoring
1 day, 20:35:16.544713 PROGRESS: === Extracted 30224 precursors and 317425 fragments ===
1 day, 20:35:16.545102 INFO: performing precursor FDR with 47 features
1 day, 20:35:16.545143 INFO: Decoy channel: -1
1 day, 20:35:16.545166 INFO: Competetive: True
1 day, 20:35:16.552896 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:35:16.556703 WARNING: dropped 8 decoy PSMs due to missing features
1 day, 20:35:16.889282 INFO: Test AUC: 0.859
1 day, 20:35:16.889410 INFO: Train AUC: 0.855
1 day, 20:35:16.889439 INFO: AUC difference: 0.49%
1 day, 20:35:16.975426 INFO: Resetting torch num_threads to 100
1 day, 20:35:16.976671 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:35:16.978055 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:35:16.978152 PROGRESS: Total precursors accumulated: 7,999
1 day, 20:35:16.978213 PROGRESS: Target precursors: 7,958 (99.49%)
1 day, 20:35:16.978266 PROGRESS: Decoy precursors: 41 (0.51%)
1 day, 20:35:16.978314 PROGRESS: 
1 day, 20:35:16.978373 PROGRESS: Precursor Summary:
1 day, 20:35:16.981347 PROGRESS: Channel   0:	 0.05 FDR: 7,958; 0.01 FDR: 7,958; 0.001 FDR: 7,122
1 day, 20:35:16.981469 PROGRESS: 
1 day, 20:35:16.981534 PROGRESS: Protein Summary:
1 day, 20:35:16.986088 PROGRESS: Channel   0:	 0.05 FDR: 4,208; 0.01 FDR: 4,208; 0.001 FDR: 3,867
1 day, 20:35:16.986202 PROGRESS: =========================================================================
1 day, 20:35:17.010375 INFO: fragments_df_filtered: 5000
1 day, 20:35:17.024904 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:35:17.847284 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:35:18.680979 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:35:19.507092 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:35:19.857945 INFO: calibration group: precursor, predicting mz
1 day, 20:35:19.860819 INFO: calibration group: precursor, predicting rt
1 day, 20:35:19.869991 INFO: calibration group: precursor, predicting mobility
1 day, 20:35:19.872359 INFO: calibration group: fragment, predicting mz
1 day, 20:35:19.890928 INFO: === checking if optimization conditions were reached ===
1 day, 20:35:19.891083 PROGRESS: === Optimization of rt_error has been performed 16 time(s); minimum number is 2 ===
1 day, 20:35:19.897076 PROGRESS: ❌ rt_error       : optimization incomplete after 16 search(es). Will search with parameter 12.5333.
1 day, 20:35:19.897135 INFO: ==============================================
1 day, 20:35:19.897231 INFO: Starting optimization step 16.
1 day, 20:35:19.897299 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:35:19.897361 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:35:19.901091 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:35:19.901149 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:35:19.901185 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 20:35:19.901209 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 20:35:19.902129 INFO: Starting candidate selection
1 day, 20:35:21.454183 INFO: Starting candidate scoring
1 day, 20:35:22.378598 INFO: Finished candidate processing
1 day, 20:35:22.378784 INFO: Collecting candidate features
1 day, 20:35:22.423138 WARNING: intensity_correlation has 7 NaNs ( 0.02 % out of 30206)
1 day, 20:35:22.427478 INFO: Collecting fragment features
1 day, 20:35:22.445172 INFO: Finished candidate scoring
1 day, 20:35:22.458340 PROGRESS: === Extracted 30206 precursors and 317218 fragments ===
1 day, 20:35:22.458718 INFO: performing precursor FDR with 47 features
1 day, 20:35:22.458757 INFO: Decoy channel: -1
1 day, 20:35:22.458781 INFO: Competetive: True
1 day, 20:35:22.466480 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:35:22.471168 WARNING: dropped 2 target PSMs due to missing features
1 day, 20:35:22.471254 WARNING: dropped 5 decoy PSMs due to missing features
1 day, 20:35:22.797191 INFO: Test AUC: 0.864
1 day, 20:35:22.797314 INFO: Train AUC: 0.854
1 day, 20:35:22.797344 INFO: AUC difference: 1.12%
1 day, 20:35:22.881080 INFO: Resetting torch num_threads to 100
1 day, 20:35:22.882289 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:35:22.883667 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:35:22.883762 PROGRESS: Total precursors accumulated: 7,998
1 day, 20:35:22.883822 PROGRESS: Target precursors: 7,959 (99.51%)
1 day, 20:35:22.883874 PROGRESS: Decoy precursors: 39 (0.49%)
1 day, 20:35:22.883922 PROGRESS: 
1 day, 20:35:22.883966 PROGRESS: Precursor Summary:
1 day, 20:35:22.886988 PROGRESS: Channel   0:	 0.05 FDR: 7,959; 0.01 FDR: 7,959; 0.001 FDR: 7,528
1 day, 20:35:22.887114 PROGRESS: 
1 day, 20:35:22.887173 PROGRESS: Protein Summary:
1 day, 20:35:22.891800 PROGRESS: Channel   0:	 0.05 FDR: 4,207; 0.01 FDR: 4,207; 0.001 FDR: 4,038
1 day, 20:35:22.891909 PROGRESS: =========================================================================
1 day, 20:35:22.916548 INFO: fragments_df_filtered: 5000
1 day, 20:35:22.930860 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:35:23.819273 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:35:24.726310 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:35:25.616693 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:35:26.033334 INFO: calibration group: precursor, predicting mz
1 day, 20:35:26.036116 INFO: calibration group: precursor, predicting rt
1 day, 20:35:26.045385 INFO: calibration group: precursor, predicting mobility
1 day, 20:35:26.047629 INFO: calibration group: fragment, predicting mz
1 day, 20:35:26.065127 INFO: === checking if optimization conditions were reached ===
1 day, 20:35:26.065291 PROGRESS: === Optimization of rt_error has been performed 17 time(s); minimum number is 2 ===
1 day, 20:35:26.071124 PROGRESS: ❌ rt_error       : optimization incomplete after 17 search(es). Will search with parameter 12.0108.
1 day, 20:35:26.071183 INFO: ==============================================
1 day, 20:35:26.071275 INFO: Starting optimization step 17.
1 day, 20:35:26.071345 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:35:26.071403 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:35:26.075561 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:35:26.075618 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:35:26.075653 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 20:35:26.075677 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.81
1 day, 20:35:26.076845 INFO: Starting candidate selection
1 day, 20:35:27.611315 INFO: Starting candidate scoring
1 day, 20:35:28.527710 INFO: Finished candidate processing
1 day, 20:35:28.527812 INFO: Collecting candidate features
1 day, 20:35:28.571355 WARNING: intensity_correlation has 11 NaNs ( 0.04 % out of 30214)
1 day, 20:35:28.575636 INFO: Collecting fragment features
1 day, 20:35:28.593283 INFO: Finished candidate scoring
1 day, 20:35:28.605875 PROGRESS: === Extracted 30214 precursors and 317276 fragments ===
1 day, 20:35:28.606257 INFO: performing precursor FDR with 47 features
1 day, 20:35:28.606295 INFO: Decoy channel: -1
1 day, 20:35:28.606319 INFO: Competetive: True
1 day, 20:35:28.614309 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:35:28.619223 WARNING: dropped 4 target PSMs due to missing features
1 day, 20:35:28.619308 WARNING: dropped 7 decoy PSMs due to missing features
1 day, 20:35:28.946068 INFO: Test AUC: 0.859
1 day, 20:35:28.946189 INFO: Train AUC: 0.854
1 day, 20:35:28.946221 INFO: AUC difference: 0.55%
1 day, 20:35:29.029932 INFO: Resetting torch num_threads to 100
1 day, 20:35:29.031129 INFO: === FDR correction performed with classifier version 2 ===
1 day, 20:35:29.032524 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:35:29.032640 PROGRESS: Total precursors accumulated: 7,998
1 day, 20:35:29.032707 PROGRESS: Target precursors: 7,962 (99.55%)
1 day, 20:35:29.032761 PROGRESS: Decoy precursors: 36 (0.45%)
1 day, 20:35:29.032807 PROGRESS: 
1 day, 20:35:29.032853 PROGRESS: Precursor Summary:
1 day, 20:35:29.035862 PROGRESS: Channel   0:	 0.05 FDR: 7,962; 0.01 FDR: 7,962; 0.001 FDR: 7,544
1 day, 20:35:29.035991 PROGRESS: 
1 day, 20:35:29.036049 PROGRESS: Protein Summary:
1 day, 20:35:29.040610 PROGRESS: Channel   0:	 0.05 FDR: 4,208; 0.01 FDR: 4,208; 0.001 FDR: 4,046
1 day, 20:35:29.040727 PROGRESS: =========================================================================
1 day, 20:35:29.065094 INFO: fragments_df_filtered: 5000
1 day, 20:35:29.079643 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:35:29.906357 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:35:30.742179 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:35:31.569019 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:35:31.918186 INFO: calibration group: precursor, predicting mz
1 day, 20:35:31.921045 INFO: calibration group: precursor, predicting rt
1 day, 20:35:31.930256 INFO: calibration group: precursor, predicting mobility
1 day, 20:35:31.932599 INFO: calibration group: fragment, predicting mz
1 day, 20:35:31.950703 INFO: === checking if optimization conditions were reached ===
1 day, 20:35:31.950855 PROGRESS: === Optimization of rt_error has been performed 18 time(s); minimum number is 2 ===
1 day, 20:35:31.951865 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 12.0108 found after 18 searches.
1 day, 20:35:31.951914 INFO: ==============================================
1 day, 20:35:31.952015 PROGRESS: Optimization finished for rt_error.
1 day, 20:35:31.966295 INFO: calibration group: precursor, predicting mz
1 day, 20:35:31.969123 INFO: calibration group: precursor, predicting rt
1 day, 20:35:31.978326 INFO: calibration group: precursor, predicting mobility
1 day, 20:35:31.980700 INFO: calibration group: fragment, predicting mz
1 day, 20:35:32.024396 INFO: Starting optimization step 0.
1 day, 20:35:32.024577 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:35:32.024643 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:35:32.028457 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:35:32.028514 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:35:32.028549 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
1 day, 20:35:32.028571 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 20:35:32.037405 INFO: Starting candidate selection
1 day, 20:35:33.617319 INFO: Starting candidate scoring
1 day, 20:35:34.540856 INFO: Finished candidate processing
1 day, 20:35:34.541067 INFO: Collecting candidate features
1 day, 20:35:34.585119 WARNING: intensity_correlation has 11 NaNs ( 0.04 % out of 30198)
1 day, 20:35:34.589459 INFO: Collecting fragment features
1 day, 20:35:34.607090 INFO: Finished candidate scoring
1 day, 20:35:34.619816 PROGRESS: === Extracted 30198 precursors and 317110 fragments ===
1 day, 20:35:34.620187 INFO: performing precursor FDR with 47 features
1 day, 20:35:34.620225 INFO: Decoy channel: -1
1 day, 20:35:34.620260 INFO: Competetive: True
1 day, 20:35:34.628030 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:35:34.632819 WARNING: dropped 4 target PSMs due to missing features
1 day, 20:35:34.632910 WARNING: dropped 7 decoy PSMs due to missing features
1 day, 20:35:34.961013 INFO: Test AUC: 0.856
1 day, 20:35:34.961152 INFO: Train AUC: 0.857
1 day, 20:35:34.961185 INFO: AUC difference: 0.20%
1 day, 20:35:35.045229 INFO: Resetting torch num_threads to 100
1 day, 20:35:35.046420 INFO: === FDR correction performed with classifier version 20 ===
1 day, 20:35:35.047805 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:35:35.047900 PROGRESS: Total precursors accumulated: 7,998
1 day, 20:35:35.047961 PROGRESS: Target precursors: 7,958 (99.50%)
1 day, 20:35:35.048014 PROGRESS: Decoy precursors: 40 (0.50%)
1 day, 20:35:35.048062 PROGRESS: 
1 day, 20:35:35.048123 PROGRESS: Precursor Summary:
1 day, 20:35:35.051115 PROGRESS: Channel   0:	 0.05 FDR: 7,958; 0.01 FDR: 7,958; 0.001 FDR: 7,436
1 day, 20:35:35.051241 PROGRESS: 
1 day, 20:35:35.051301 PROGRESS: Protein Summary:
1 day, 20:35:35.055853 PROGRESS: Channel   0:	 0.05 FDR: 4,208; 0.01 FDR: 4,208; 0.001 FDR: 3,999
1 day, 20:35:35.055962 PROGRESS: =========================================================================
1 day, 20:35:35.080048 INFO: fragments_df_filtered: 5000
1 day, 20:35:35.094392 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:35:35.928955 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:35:36.762755 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:35:37.589961 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:35:37.959890 INFO: calibration group: precursor, predicting mz
1 day, 20:35:37.962732 INFO: calibration group: precursor, predicting rt
1 day, 20:35:37.972022 INFO: calibration group: precursor, predicting mobility
1 day, 20:35:37.974360 INFO: calibration group: fragment, predicting mz
1 day, 20:35:37.993357 INFO: === checking if optimization conditions were reached ===
1 day, 20:35:37.993509 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 20:35:37.996155 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0609.
1 day, 20:35:37.996208 INFO: ==============================================
1 day, 20:35:37.996298 INFO: Starting optimization step 1.
1 day, 20:35:37.996367 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:35:37.996426 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:35:38.000022 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:35:38.000076 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:35:38.000113 INFO: FWHM in RT is 2.84 seconds, sigma is 0.63
1 day, 20:35:38.000136 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.81
1 day, 20:35:38.001161 INFO: Starting candidate selection
1 day, 20:35:39.347291 INFO: Starting candidate scoring
1 day, 20:35:40.295900 INFO: Finished candidate processing
1 day, 20:35:40.296089 INFO: Collecting candidate features
1 day, 20:35:40.339447 WARNING: intensity_correlation has 11 NaNs ( 0.04 % out of 30160)
1 day, 20:35:40.343771 INFO: Collecting fragment features
1 day, 20:35:40.361372 INFO: Finished candidate scoring
1 day, 20:35:40.374212 PROGRESS: === Extracted 30160 precursors and 314586 fragments ===
1 day, 20:35:40.374580 INFO: performing precursor FDR with 47 features
1 day, 20:35:40.374619 INFO: Decoy channel: -1
1 day, 20:35:40.374642 INFO: Competetive: True
1 day, 20:35:40.382263 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:35:40.386954 WARNING: dropped 3 target PSMs due to missing features
1 day, 20:35:40.387045 WARNING: dropped 8 decoy PSMs due to missing features
1 day, 20:35:40.714408 INFO: Test AUC: 0.856
1 day, 20:35:40.714535 INFO: Train AUC: 0.859
1 day, 20:35:40.714565 INFO: AUC difference: 0.30%
1 day, 20:35:40.798172 INFO: Resetting torch num_threads to 100
1 day, 20:35:40.799381 INFO: === FDR correction performed with classifier version 20 ===
1 day, 20:35:40.800745 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:35:40.800838 PROGRESS: Total precursors accumulated: 7,996
1 day, 20:35:40.800901 PROGRESS: Target precursors: 7,963 (99.59%)
1 day, 20:35:40.800955 PROGRESS: Decoy precursors: 33 (0.41%)
1 day, 20:35:40.801004 PROGRESS: 
1 day, 20:35:40.801058 PROGRESS: Precursor Summary:
1 day, 20:35:40.804027 PROGRESS: Channel   0:	 0.05 FDR: 7,963; 0.01 FDR: 7,963; 0.001 FDR: 7,590
1 day, 20:35:40.804145 PROGRESS: 
1 day, 20:35:40.804205 PROGRESS: Protein Summary:
1 day, 20:35:40.808739 PROGRESS: Channel   0:	 0.05 FDR: 4,206; 0.01 FDR: 4,206; 0.001 FDR: 4,066
1 day, 20:35:40.808851 PROGRESS: =========================================================================
1 day, 20:35:40.832874 INFO: fragments_df_filtered: 5000
1 day, 20:35:40.847243 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:35:41.684230 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:35:42.522515 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:35:43.350733 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:35:43.701680 INFO: calibration group: precursor, predicting mz
1 day, 20:35:43.704440 INFO: calibration group: precursor, predicting rt
1 day, 20:35:43.713500 INFO: calibration group: precursor, predicting mobility
1 day, 20:35:43.715811 INFO: calibration group: fragment, predicting mz
1 day, 20:35:43.734342 INFO: === checking if optimization conditions were reached ===
1 day, 20:35:43.734525 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 20:35:43.737403 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0534.
1 day, 20:35:43.737466 INFO: ==============================================
1 day, 20:35:43.737571 INFO: Starting optimization step 2.
1 day, 20:35:43.737650 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 20:35:43.737721 PROGRESS: Extracting batch of 15886 precursors
1 day, 20:35:43.742616 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:35:43.742678 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:35:43.742720 INFO: FWHM in RT is 2.84 seconds, sigma is 0.62
1 day, 20:35:43.742747 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.80
1 day, 20:35:43.743905 INFO: Starting candidate selection
1 day, 20:35:45.017729 INFO: Starting candidate scoring
1 day, 20:35:45.936660 INFO: Finished candidate processing
1 day, 20:35:45.936850 INFO: Collecting candidate features
1 day, 20:35:45.982225 WARNING: intensity_correlation has 12 NaNs ( 0.04 % out of 30132)
1 day, 20:35:45.989523 INFO: Collecting fragment features
1 day, 20:35:46.009090 INFO: Finished candidate scoring
1 day, 20:35:46.021737 PROGRESS: === Extracted 30132 precursors and 313099 fragments ===
1 day, 20:35:46.022109 INFO: performing precursor FDR with 47 features
1 day, 20:35:46.022148 INFO: Decoy channel: -1
1 day, 20:35:46.022172 INFO: Competetive: True
1 day, 20:35:46.030301 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:35:46.035004 WARNING: dropped 3 target PSMs due to missing features
1 day, 20:35:46.035092 WARNING: dropped 9 decoy PSMs due to missing features
1 day, 20:35:46.360970 INFO: Test AUC: 0.848
1 day, 20:35:46.361101 INFO: Train AUC: 0.856
1 day, 20:35:46.361131 INFO: AUC difference: 0.95%
1 day, 20:35:46.444968 INFO: Resetting torch num_threads to 100
1 day, 20:35:46.446154 INFO: === FDR correction performed with classifier version 20 ===
1 day, 20:35:46.447547 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:35:46.447655 PROGRESS: Total precursors accumulated: 7,997
1 day, 20:35:46.447720 PROGRESS: Target precursors: 7,967 (99.62%)
1 day, 20:35:46.447773 PROGRESS: Decoy precursors: 30 (0.38%)
1 day, 20:35:46.447822 PROGRESS: 
1 day, 20:35:46.447878 PROGRESS: Precursor Summary:
1 day, 20:35:46.450934 PROGRESS: Channel   0:	 0.05 FDR: 7,967; 0.01 FDR: 7,967; 0.001 FDR: 7,586
1 day, 20:35:46.451066 PROGRESS: 
1 day, 20:35:46.451126 PROGRESS: Protein Summary:
1 day, 20:35:46.455680 PROGRESS: Channel   0:	 0.05 FDR: 4,206; 0.01 FDR: 4,206; 0.001 FDR: 4,064
1 day, 20:35:46.455795 PROGRESS: =========================================================================
1 day, 20:35:46.480229 INFO: fragments_df_filtered: 5000
1 day, 20:35:46.494404 INFO: calibration group: precursor, fitting mz estimator 
1 day, 20:35:47.385721 INFO: calibration group: precursor, fitting rt estimator 
1 day, 20:35:48.287401 INFO: calibration group: precursor, fitting mobility estimator 
1 day, 20:35:49.169440 INFO: calibration group: fragment, fitting mz estimator 
1 day, 20:35:49.520245 INFO: calibration group: precursor, predicting mz
1 day, 20:35:49.522994 INFO: calibration group: precursor, predicting rt
1 day, 20:35:49.532112 INFO: calibration group: precursor, predicting mobility
1 day, 20:35:49.534400 INFO: calibration group: fragment, predicting mz
1 day, 20:35:49.552493 INFO: === checking if optimization conditions were reached ===
1 day, 20:35:49.552655 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 20:35:49.553429 PROGRESS: ✅ mobility_error : optimization complete. Optimal parameter 0.0534 found after 3 searches.
1 day, 20:35:49.553482 INFO: ==============================================
1 day, 20:35:49.554630 PROGRESS: Optimization finished for mobility_error.
1 day, 20:35:49.568734 INFO: calibration group: precursor, predicting mz
1 day, 20:35:49.571445 INFO: calibration group: precursor, predicting rt
1 day, 20:35:49.580428 INFO: calibration group: precursor, predicting mobility
1 day, 20:35:49.582752 INFO: calibration group: fragment, predicting mz
1 day, 20:35:49.625036 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 20:35:49.625204 PROGRESS: ==============================================
1 day, 20:35:49.625281 PROGRESS: ms2_error      : 15.0000
1 day, 20:35:49.625339 PROGRESS: ms1_error      : 10.0000
1 day, 20:35:49.625390 PROGRESS: rt_error       : 12.0108
1 day, 20:35:49.625441 PROGRESS: mobility_error : 0.0534
1 day, 20:35:49.625492 PROGRESS: ==============================================
1 day, 20:35:49.626298 INFO: calibration group: precursor, predicting mz
1 day, 20:35:49.645486 INFO: calibration group: precursor, predicting rt
1 day, 20:35:49.731818 INFO: calibration group: precursor, predicting mobility
1 day, 20:35:49.751323 INFO: calibration group: fragment, predicting mz
1 day, 20:35:49.965779 PROGRESS: Extracting batch of 162861 precursors
1 day, 20:35:50.000490 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 20:35:50.000623 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 20:35:50.000669 INFO: FWHM in RT is 2.84 seconds, sigma is 0.62
1 day, 20:35:50.000694 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
1 day, 20:35:50.001477 INFO: Starting candidate selection
1 day, 20:35:58.065130 INFO: Applying score cutoff of 18.31161153793335
1 day, 20:35:58.072954 INFO: Removed 7714 precursors with score below cutoff
1 day, 20:35:58.404373 INFO: Starting candidate scoring
1 day, 20:36:06.921557 INFO: Finished candidate processing
1 day, 20:36:06.921670 INFO: Collecting candidate features
1 day, 20:36:07.350207 WARNING: intensity_correlation has 34 NaNs ( 0.01 % out of 302133)
1 day, 20:36:07.350771 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 302133)
1 day, 20:36:07.366441 INFO: Collecting fragment features
1 day, 20:36:07.548130 INFO: Finished candidate scoring
1 day, 20:36:07.697847 INFO: === FDR correction performed with classifier version 23 ===
1 day, 20:36:07.698700 INFO: performing precursor FDR with 47 features
1 day, 20:36:07.698747 INFO: Decoy channel: -1
1 day, 20:36:07.698771 INFO: Competetive: True
1 day, 20:36:07.794470 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 20:36:07.839330 WARNING: dropped 3 target PSMs due to missing features
1 day, 20:36:07.839471 WARNING: dropped 31 decoy PSMs due to missing features
1 day, 20:36:12.747649 INFO: Test AUC: 0.882
1 day, 20:36:12.747777 INFO: Train AUC: 0.886
1 day, 20:36:12.747808 INFO: AUC difference: 0.43%
1 day, 20:36:12.843484 INFO: Resetting torch num_threads to 100
1 day, 20:36:12.856906 INFO: Removing fragments below FDR threshold
1 day, 20:36:12.908359 PROGRESS: ============================= Precursor FDR =============================
1 day, 20:36:12.908631 PROGRESS: Total precursors accumulated: 81,954
1 day, 20:36:12.908706 PROGRESS: Target precursors: 81,296 (99.20%)
1 day, 20:36:12.908761 PROGRESS: Decoy precursors: 658 (0.80%)
1 day, 20:36:12.908812 PROGRESS: 
1 day, 20:36:12.908857 PROGRESS: Precursor Summary:
1 day, 20:36:12.943657 PROGRESS: Channel   0:	 0.05 FDR: 81,296; 0.01 FDR: 81,296; 0.001 FDR: 79,731
1 day, 20:36:12.943977 PROGRESS: 
1 day, 20:36:12.944045 PROGRESS: Protein Summary:
1 day, 20:36:12.992593 PROGRESS: Channel   0:	 0.05 FDR: 8,249; 0.01 FDR: 8,249; 0.001 FDR: 8,243
1 day, 20:36:12.992864 PROGRESS: =========================================================================
1 day, 20:36:13.659564 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 20:36:14.096495 PROGRESS: Processing search outputs
1 day, 20:36:14.096637 PROGRESS: Performing protein grouping and FDR
1 day, 20:36:14.096689 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 20:36:14.169183 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 20:36:14.237838 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 20:36:14.305371 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 20:36:14.379763 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 20:36:14.442785 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 20:36:14.510396 INFO: Building combined output
1 day, 20:36:14.653792 INFO: Performing protein inference
1 day, 20:36:15.171181 INFO: Inference strategy: library. Using library grouping for protein inference
1 day, 20:36:15.175302 INFO: Performing protein FDR
1 day, 20:36:19.899988 INFO: Normalizing q-values using 8,253 targets and 2,392 decoys
1 day, 20:36:19.909410 INFO: Test AUC: 1.000
1 day, 20:36:19.909468 INFO: Train AUC: 1.000
1 day, 20:36:19.909497 INFO: AUC difference: 0.03%
1 day, 20:36:20.456545 PROGRESS: ================ Protein FDR =================
1 day, 20:36:20.456690 PROGRESS: Unique protein groups in output
1 day, 20:36:20.456719 PROGRESS:   1% protein FDR: 8,247
1 day, 20:36:20.456740 PROGRESS: 
1 day, 20:36:20.456758 PROGRESS: Unique precursor in output
1 day, 20:36:20.456777 PROGRESS:   1% protein FDR: 82,019
1 day, 20:36:20.456796 PROGRESS: ================================================
1 day, 20:36:20.532171 PROGRESS: Building search statistics
1 day, 20:36:20.653512 INFO: Loaded OptimizationManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/optimization_manager.pkl
1 day, 20:36:20.653715 INFO: Initializing OptimizationManager
1 day, 20:36:20.653944 INFO: Loaded CalibrationManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/calibration_manager.pkl
1 day, 20:36:20.654024 INFO: Initializing CalibrationManager
1 day, 20:36:20.654223 INFO: Loaded RawFileManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/raw_file_manager.pkl
1 day, 20:36:20.654299 INFO: Initializing RawFileManager
1 day, 20:36:20.690016 INFO: Loaded OptimizationManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/optimization_manager.pkl
1 day, 20:36:20.690222 INFO: Initializing OptimizationManager
1 day, 20:36:20.690454 INFO: Loaded CalibrationManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/calibration_manager.pkl
1 day, 20:36:20.690549 INFO: Initializing CalibrationManager
1 day, 20:36:20.690752 INFO: Loaded RawFileManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/raw_file_manager.pkl
1 day, 20:36:20.690841 INFO: Initializing RawFileManager
1 day, 20:36:20.726555 INFO: Loaded OptimizationManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/optimization_manager.pkl
1 day, 20:36:20.726755 INFO: Initializing OptimizationManager
1 day, 20:36:20.726981 INFO: Loaded CalibrationManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/calibration_manager.pkl
1 day, 20:36:20.727063 INFO: Initializing CalibrationManager
1 day, 20:36:20.727265 INFO: Loaded RawFileManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/raw_file_manager.pkl
1 day, 20:36:20.727341 INFO: Initializing RawFileManager
1 day, 20:36:20.764880 INFO: Loaded OptimizationManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/optimization_manager.pkl
1 day, 20:36:20.765101 INFO: Initializing OptimizationManager
1 day, 20:36:20.765333 INFO: Loaded CalibrationManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/calibration_manager.pkl
1 day, 20:36:20.765413 INFO: Initializing CalibrationManager
1 day, 20:36:20.765608 INFO: Loaded RawFileManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/raw_file_manager.pkl
1 day, 20:36:20.765684 INFO: Initializing RawFileManager
1 day, 20:36:20.806334 INFO: Loaded OptimizationManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/optimization_manager.pkl
1 day, 20:36:20.806532 INFO: Initializing OptimizationManager
1 day, 20:36:20.806748 INFO: Loaded CalibrationManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/calibration_manager.pkl
1 day, 20:36:20.806829 INFO: Initializing CalibrationManager
1 day, 20:36:20.807023 INFO: Loaded RawFileManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/raw_file_manager.pkl
1 day, 20:36:20.807099 INFO: Initializing RawFileManager
1 day, 20:36:20.843202 INFO: Loaded OptimizationManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/optimization_manager.pkl
1 day, 20:36:20.843403 INFO: Initializing OptimizationManager
1 day, 20:36:20.843633 INFO: Loaded CalibrationManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/calibration_manager.pkl
1 day, 20:36:20.843714 INFO: Initializing CalibrationManager
1 day, 20:36:20.843907 INFO: Loaded RawFileManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/raw_file_manager.pkl
1 day, 20:36:20.843984 INFO: Initializing RawFileManager
1 day, 20:36:20.846730 INFO: Writing stat output to disk
1 day, 20:36:20.846789 INFO: Saving run_output/alphadia_1.10_defaultMBR/stat.tsv to disk
1 day, 20:36:20.856161 PROGRESS: Building internal statistics
1 day, 20:36:20.856467 INFO: Loaded TimingManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/timing_manager.pkl
1 day, 20:36:20.856514 INFO: Initializing TimingManager
1 day, 20:36:20.856942 INFO: Loaded TimingManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/timing_manager.pkl
1 day, 20:36:20.856985 INFO: Initializing TimingManager
1 day, 20:36:20.857174 INFO: Loaded TimingManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/timing_manager.pkl
1 day, 20:36:20.857214 INFO: Initializing TimingManager
1 day, 20:36:20.857374 INFO: Loaded TimingManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/timing_manager.pkl
1 day, 20:36:20.857423 INFO: Initializing TimingManager
1 day, 20:36:20.857582 INFO: Loaded TimingManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/timing_manager.pkl
1 day, 20:36:20.857617 INFO: Initializing TimingManager
1 day, 20:36:20.857769 INFO: Loaded TimingManager from run_output/alphadia_1.10_defaultMBR/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/timing_manager.pkl
1 day, 20:36:20.857804 INFO: Initializing TimingManager
1 day, 20:36:20.858217 INFO: Writing internal output to disk
1 day, 20:36:20.858262 INFO: Saving run_output/alphadia_1.10_defaultMBR/internal.tsv to disk
1 day, 20:36:20.858779 PROGRESS: Performing label free quantification
1 day, 20:36:20.945122 INFO: Accumulating fragment data
1 day, 20:36:20.945286 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 20:36:21.008922 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 20:36:22.130352 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 20:36:23.170397 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 20:36:24.212378 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 20:36:25.238708 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 20:36:26.445985 PROGRESS: Performing label free quantification on the precursor level
1 day, 20:36:26.446116 INFO: Filtering fragments by quality
1 day, 20:36:26.709476 INFO: Performing label-free quantification using directLFQ
1 day, 20:36:27.707112 INFO: 82019 lfq-groups total
1 day, 20:37:37.665622 INFO: using 100 processes
1 day, 20:37:37.868770 INFO: lfq-object 0
1 day, 20:37:37.986536 INFO: lfq-object 100
1 day, 20:37:38.051606 INFO: lfq-object 300
1 day, 20:37:38.106609 INFO: lfq-object 200
1 day, 20:37:38.126381 INFO: lfq-object 700
1 day, 20:37:38.131342 INFO: lfq-object 500
1 day, 20:37:38.190113 INFO: lfq-object 400
1 day, 20:37:38.210966 INFO: lfq-object 900
1 day, 20:37:38.240644 INFO: lfq-object 1100
1 day, 20:37:38.257289 INFO: lfq-object 1300
1 day, 20:37:38.272561 INFO: lfq-object 600
1 day, 20:37:38.281280 INFO: lfq-object 800
1 day, 20:37:38.316708 INFO: lfq-object 1500
1 day, 20:37:38.337315 INFO: lfq-object 1000
1 day, 20:37:38.359151 INFO: lfq-object 1200
1 day, 20:37:38.361068 INFO: lfq-object 1700
1 day, 20:37:38.378432 INFO: lfq-object 1400
1 day, 20:37:38.452329 INFO: lfq-object 1600
1 day, 20:37:38.467615 INFO: lfq-object 1900
1 day, 20:37:38.481573 INFO: lfq-object 1800
1 day, 20:37:38.515703 INFO: lfq-object 2100
1 day, 20:37:38.591924 INFO: lfq-object 2000
1 day, 20:37:38.593500 INFO: lfq-object 2300
1 day, 20:37:38.633810 INFO: lfq-object 2200
1 day, 20:37:38.685564 INFO: lfq-object 2500
1 day, 20:37:38.715111 INFO: lfq-object 2400
1 day, 20:37:38.782235 INFO: lfq-object 2700
1 day, 20:37:38.804365 INFO: lfq-object 2600
1 day, 20:37:38.855175 INFO: lfq-object 2900
1 day, 20:37:38.901472 INFO: lfq-object 2800
1 day, 20:37:38.913864 INFO: lfq-object 3100
1 day, 20:37:38.974448 INFO: lfq-object 3000
1 day, 20:37:39.032756 INFO: lfq-object 3200
1 day, 20:37:39.037812 INFO: lfq-object 3300
1 day, 20:37:39.164077 INFO: lfq-object 3400
1 day, 20:37:39.274960 INFO: lfq-object 3600
1 day, 20:37:39.283328 INFO: lfq-object 3500
1 day, 20:37:39.394556 INFO: lfq-object 3700
1 day, 20:37:39.429636 INFO: lfq-object 3800
1 day, 20:37:39.507329 INFO: lfq-object 4000
1 day, 20:37:39.549348 INFO: lfq-object 3900
1 day, 20:37:39.569550 INFO: lfq-object 4200
1 day, 20:37:39.625751 INFO: lfq-object 4100
1 day, 20:37:39.629472 INFO: lfq-object 4400
1 day, 20:37:39.687640 INFO: lfq-object 4300
1 day, 20:37:39.699042 INFO: lfq-object 4600
1 day, 20:37:39.745286 INFO: lfq-object 4500
1 day, 20:37:39.748196 INFO: lfq-object 4800
1 day, 20:37:39.817737 INFO: lfq-object 4700
1 day, 20:37:39.822118 INFO: lfq-object 5000
1 day, 20:37:39.864871 INFO: lfq-object 4900
1 day, 20:37:39.901626 INFO: lfq-object 5200
1 day, 20:37:39.940506 INFO: lfq-object 5100
1 day, 20:37:40.021183 INFO: lfq-object 5300
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1 day, 20:38:22.724890 INFO: lfq-object 77000
1 day, 20:38:22.799378 INFO: lfq-object 77300
1 day, 20:38:22.836470 INFO: lfq-object 77200
1 day, 20:38:22.918305 INFO: lfq-object 77400
1 day, 20:38:22.948925 INFO: lfq-object 77500
1 day, 20:38:23.037333 INFO: lfq-object 77700
1 day, 20:38:23.067708 INFO: lfq-object 77600
1 day, 20:38:23.113556 INFO: lfq-object 77900
1 day, 20:38:23.147850 INFO: lfq-object 77800
1 day, 20:38:23.180531 INFO: lfq-object 78100
1 day, 20:38:23.229293 INFO: lfq-object 78000
1 day, 20:38:23.266685 INFO: lfq-object 78300
1 day, 20:38:23.302029 INFO: lfq-object 78200
1 day, 20:38:23.334697 INFO: lfq-object 78500
1 day, 20:38:23.381359 INFO: lfq-object 78400
1 day, 20:38:23.395081 INFO: lfq-object 78700
1 day, 20:38:23.447564 INFO: lfq-object 78600
1 day, 20:38:23.455528 INFO: lfq-object 78900
1 day, 20:38:23.514247 INFO: lfq-object 78800
1 day, 20:38:23.573265 INFO: lfq-object 79000
1 day, 20:38:23.674446 INFO: lfq-object 79200
1 day, 20:38:23.693480 INFO: lfq-object 79100
1 day, 20:38:23.739523 INFO: lfq-object 79400
1 day, 20:38:23.792597 INFO: lfq-object 79300
1 day, 20:38:23.835175 INFO: lfq-object 79600
1 day, 20:38:23.856152 INFO: lfq-object 79500
1 day, 20:38:23.871823 INFO: lfq-object 79800
1 day, 20:38:23.941904 INFO: lfq-object 80000
1 day, 20:38:23.952787 INFO: lfq-object 79700
1 day, 20:38:23.989546 INFO: lfq-object 79900
1 day, 20:38:23.995879 INFO: lfq-object 80200
1 day, 20:38:24.060238 INFO: lfq-object 80100
1 day, 20:38:24.085465 INFO: lfq-object 80400
1 day, 20:38:24.112128 INFO: lfq-object 80300
1 day, 20:38:24.183229 INFO: lfq-object 80600
1 day, 20:38:24.201303 INFO: lfq-object 80500
1 day, 20:38:24.300031 INFO: lfq-object 80700
1 day, 20:38:24.362292 INFO: lfq-object 80800
1 day, 20:38:24.478556 INFO: lfq-object 80900
1 day, 20:38:24.516701 INFO: lfq-object 81000
1 day, 20:38:24.634422 INFO: lfq-object 81100
1 day, 20:38:24.671249 INFO: lfq-object 81200
1 day, 20:38:24.788815 INFO: lfq-object 81300
1 day, 20:38:29.215507 INFO: lfq-object 81400
1 day, 20:38:29.254927 INFO: lfq-object 81600
1 day, 20:38:29.305351 INFO: lfq-object 82000
1 day, 20:38:29.308494 INFO: lfq-object 81800
1 day, 20:38:29.331547 INFO: lfq-object 81500
1 day, 20:38:29.374889 INFO: lfq-object 81700
1 day, 20:38:29.425701 INFO: lfq-object 81900
1 day, 20:38:34.718784 INFO: Writing precursor output to disk
1 day, 20:38:34.718974 INFO: Saving run_output/alphadia_1.10_defaultMBR/precursor.matrix.tsv to disk
1 day, 20:38:35.169302 PROGRESS: Performing label free quantification on the pg level
1 day, 20:38:35.169410 INFO: Filtering fragments by quality
1 day, 20:38:35.419792 INFO: Performing label-free quantification using directLFQ
1 day, 20:38:35.881465 INFO: 8247 lfq-groups total
1 day, 20:39:34.430773 INFO: using 100 processes
1 day, 20:39:34.519204 INFO: lfq-object 0
1 day, 20:39:34.687771 INFO: lfq-object 300
1 day, 20:39:34.852339 INFO: lfq-object 400
1 day, 20:39:34.993015 INFO: lfq-object 100
1 day, 20:39:35.023940 INFO: lfq-object 200
1 day, 20:39:35.087982 INFO: lfq-object 700
1 day, 20:39:35.137345 INFO: lfq-object 800
1 day, 20:39:35.138164 INFO: lfq-object 600
1 day, 20:39:35.152001 INFO: lfq-object 500
1 day, 20:39:35.249520 INFO: lfq-object 1100
1 day, 20:39:35.289876 INFO: lfq-object 900
1 day, 20:39:35.354125 INFO: lfq-object 1600
1 day, 20:39:35.354949 INFO: lfq-object 1200
1 day, 20:39:35.407401 INFO: lfq-object 1700
1 day, 20:39:35.458599 INFO: lfq-object 1500
1 day, 20:39:35.475915 INFO: lfq-object 1000
1 day, 20:39:35.529522 INFO: lfq-object 1400
1 day, 20:39:35.618089 INFO: lfq-object 2100
1 day, 20:39:35.682074 INFO: lfq-object 1300
1 day, 20:39:35.750459 INFO: lfq-object 1800
1 day, 20:39:35.781311 INFO: lfq-object 2500
1 day, 20:39:35.841767 INFO: lfq-object 2400
1 day, 20:39:35.875718 INFO: lfq-object 2300
1 day, 20:39:35.885395 INFO: lfq-object 2000
1 day, 20:39:35.888169 INFO: lfq-object 1900
1 day, 20:39:35.957876 INFO: lfq-object 2800
1 day, 20:39:35.976885 INFO: lfq-object 2900
1 day, 20:39:36.024890 INFO: lfq-object 2200
1 day, 20:39:36.028826 INFO: lfq-object 2700
1 day, 20:39:36.116206 INFO: lfq-object 2600
1 day, 20:39:36.179673 INFO: lfq-object 3300
1 day, 20:39:36.229216 INFO: lfq-object 3100
1 day, 20:39:36.280878 INFO: lfq-object 3400
1 day, 20:39:36.287499 INFO: lfq-object 3200
1 day, 20:39:36.298787 INFO: lfq-object 3000
1 day, 20:39:36.333490 INFO: lfq-object 3500
1 day, 20:39:36.434322 INFO: lfq-object 3700
1 day, 20:39:36.480362 INFO: lfq-object 3600
1 day, 20:39:36.541707 INFO: lfq-object 4000
1 day, 20:39:36.599431 INFO: lfq-object 3800
1 day, 20:39:36.599928 INFO: lfq-object 4200
1 day, 20:39:36.601905 INFO: lfq-object 4100
1 day, 20:39:36.615119 INFO: lfq-object 3900
1 day, 20:39:36.797667 INFO: lfq-object 4500
1 day, 20:39:36.805854 INFO: lfq-object 4400
1 day, 20:39:36.820014 INFO: lfq-object 4600
1 day, 20:39:36.938053 INFO: lfq-object 4300
1 day, 20:39:36.987046 INFO: lfq-object 4900
1 day, 20:39:37.012633 INFO: lfq-object 4800
1 day, 20:39:37.031399 INFO: lfq-object 5000
1 day, 20:39:37.032637 INFO: lfq-object 4700
1 day, 20:39:37.188225 INFO: lfq-object 5100
1 day, 20:39:37.205151 INFO: lfq-object 5400
1 day, 20:39:37.224151 INFO: lfq-object 5300
1 day, 20:39:37.302872 INFO: lfq-object 5200
1 day, 20:39:37.303236 INFO: lfq-object 5500
1 day, 20:39:37.390937 INFO: lfq-object 5600
1 day, 20:39:37.409255 INFO: lfq-object 5700
1 day, 20:39:37.413619 INFO: lfq-object 5800
1 day, 20:39:37.497177 INFO: lfq-object 5900
1 day, 20:39:37.574402 INFO: lfq-object 6000
1 day, 20:39:37.583692 INFO: lfq-object 6200
1 day, 20:39:37.609307 INFO: lfq-object 6300
1 day, 20:39:37.619458 INFO: lfq-object 6100
1 day, 20:39:37.719368 INFO: lfq-object 6500
1 day, 20:39:37.732588 INFO: lfq-object 6400
1 day, 20:39:37.770419 INFO: lfq-object 6600
1 day, 20:39:37.827110 INFO: lfq-object 6700
1 day, 20:39:37.958870 INFO: lfq-object 6900
1 day, 20:39:37.963680 INFO: lfq-object 7100
1 day, 20:39:37.978794 INFO: lfq-object 7000
1 day, 20:39:37.990436 INFO: lfq-object 6800
1 day, 20:39:38.071666 INFO: lfq-object 7200
1 day, 20:39:38.117734 INFO: lfq-object 7300
1 day, 20:39:38.135960 INFO: lfq-object 7400
1 day, 20:39:38.150784 INFO: lfq-object 7500
1 day, 20:39:38.293964 INFO: lfq-object 7800
1 day, 20:39:38.299128 INFO: lfq-object 7600
1 day, 20:39:38.304153 INFO: lfq-object 7700
1 day, 20:39:38.327183 INFO: lfq-object 7900
1 day, 20:39:38.512142 INFO: lfq-object 8100
1 day, 20:39:38.577760 INFO: lfq-object 8000
1 day, 20:39:38.594546 INFO: lfq-object 8200
1 day, 20:39:41.508688 INFO: Writing pg output to disk
1 day, 20:39:41.508872 INFO: Saving run_output/alphadia_1.10_defaultMBR/pg.matrix.tsv to disk
1 day, 20:39:41.757547 INFO: Writing psm output to disk
1 day, 20:39:41.757703 INFO: Saving run_output/alphadia_1.10_defaultMBR/precursors.tsv to disk
1 day, 20:40:09.184576 PROGRESS: Building spectral library
1 day, 20:40:09.276563 INFO: Building MBR spectral library
1 day, 20:40:09.276708 INFO: Running MbrLibraryBuilder
1 day, 20:40:09.514988 INFO: MBR spectral library contains 82,019 precursors, 8,247 proteins
1 day, 20:40:09.515134 INFO: Writing MBR spectral library to disk
1 day, 20:40:10.129840 PROGRESS: =================== Search Finished ===================
1 day, 20:40:10.160387 WARNING: WARNING: Temp mmap arrays were written to /tmp/temp_mmap_93r89lay. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 696,495,505,408
