0:00:00.000053 INFO: Output directory: /home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds, cwd: /home/robbe/ProteoBench_diaPASEF.
0:00:00.000158 INFO: User provided config file: config_alphadia110_default_Astral.yaml.
0:00:00.000191 INFO: User provided config dict: {}.
0:00:00.013670 PROGRESS:           _      _         ___ ___   _   
0:00:00.013739 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.013768 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.013790 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.013815 PROGRESS:            |_|                           
0:00:00.013839 PROGRESS: 
0:00:00.013860 PROGRESS: version: 1.10.4-dev0
0:00:00.013888 INFO: hostname: thestral
0:00:00.013939 INFO: date: 2025-07-04 10:43:25
0:00:00.013960 INFO: ================ AlphaX Environment ===============
0:00:00.013982 INFO: alphatims       : 1.0.8
0:00:00.014002 INFO: alpharaw        : 0.4.5
0:00:00.014019 INFO: alphabase       : 1.5.0
0:00:00.014037 INFO: alphapeptdeep   : 1.3.0
0:00:00.014054 INFO: directlfq       : 0.2.19
0:00:00.014071 INFO: ===================================================
0:00:00.014089 INFO: ================= Pip Environment =================
0:00:00.073138 INFO: alphatims==1.0.8 click==8.1.8 partd==1.4.2 wget==3.2 torchmetrics==1.4.0.post0 uri-template==1.3.0 directlfq==0.2.19 nvidia-nvjitlink-cu12==12.4.127 lxml==5.3.1 fsspec==2025.3.0 fqdn==1.5.1 jsonref==1.1.0 simplejson==3.20.1 tornado==6.4.2 s3transfer==0.11.4 pythonnet==3.0.3 tqdm==4.67.1 psutil==7.0.0 urllib3==2.3.0 fonttools==4.56.0 arrow==1.3.0 dask==2024.11.2 numpy==1.26.4 tzdata==2025.1 gitdb==4.0.12 contextlib2==21.6.0 future==1.0.0 toolz==1.0.0 monotonic==1.6 argparse==1.4.0 nvidia-cuda-cupti-cu12==12.4.127 numba==0.59.1 importlib_resources==6.5.2 packaging==24.2 SQLAlchemy==2.0.39 typing_extensions==4.12.2 pyarrow==19.0.1 joblib==1.4.2 requests-oauthlib==2.0.0 rdkit==2024.3.3 webcolors==24.11.1 cffi==1.17.1 nvidia-cuda-nvrtc-cu12==12.4.127 protobuf==5.29.3 pyteomics==4.7.5 mpmath==1.3.0 pytz==2025.1 multiprocess==0.70.17 MarkupSafe==3.0.2 pyzstd==0.16.2 six==1.17.0 cycler==0.12.1 charset-normalizer==3.4.1 pyparsing==3.2.1 tenacity==9.0.0 llvmlite==0.42.0 attrs==25.2.0 pip==23.0.1 requests==2.32.3 triton==3.2.0 h5py==3.13.0 oauthlib==3.2.2 zstandard==0.22.0 pyahocorasick==2.1.0 swagger-spec-validator==3.0.4 blinker==1.9.0 pycparser==2.22 alpharaw==0.4.5 regex==2024.11.6 streamlit-aggrid==1.1.1 streamlit==1.43.2 tokenizers==0.19.1 websocket-client==1.8.0 certifi==2025.1.31 narwhals==1.30.0 isoduration==20.11.0 python-dateutil==2.9.0.post0 peptdeep==1.3.0 botocore==1.37.11 locket==1.0.0 referencing==0.36.2 torch==2.6.0 nvidia-cusparse-cu12==12.3.1.170 rocket-fft==0.2.5 lightning-utilities==0.14.0 neptune==1.10.4 importlib_metadata==8.6.1 cloudpickle==3.1.1 clr_loader==0.2.7.post0 setuptools==66.1.1 pandas==2.2.3 dill==0.3.9 jsonschema-specifications==2024.10.1 networkx==3.4.2 transformers==4.40.2 biopython==1.85 filelock==3.17.0 types-python-dateutil==2.9.0.20241206 seaborn==0.13.2 toml==0.10.2 zipp==3.21.0 rfc3339-validator==0.1.4 altair==5.5.0 greenlet==3.1.1 scipy==1.12.0 matplotlib==3.10.1 contourpy==1.3.1 pydeck==0.9.1 threadpoolctl==3.5.0 Jinja2==3.1.6 bravado-core==6.1.1 msgpack==1.1.0 nvidia-nvtx-cu12==12.4.127 nvidia-cusolver-cu12==11.6.1.9 xxhash==3.4.1 safetensors==0.5.3 idna==3.10 cachetools==5.5.2 huggingface-hub==0.29.3 jsonpointer==3.0.0 rpds-py==0.23.1 nvidia-cufft-cu12==11.2.1.3 jsonschema==4.23.0 watchdog==6.0.0 python-decouple==3.8 sympy==1.13.1 boto3==1.37.11 dask-expr==1.1.19 pillow==11.1.0 plotly==6.0.0 nvidia-cublas-cu12==12.4.5.8 nvidia-cudnn-cu12==9.1.0.70 smmap==5.0.2 nvidia-curand-cu12==10.3.5.147 GitPython==3.1.44 progressbar==2.5 PyJWT==2.10.1 kiwisolver==1.4.8 nvidia-cuda-runtime-cu12==12.4.127 scikit-learn==1.6.1 nvidia-nccl-cu12==2.21.5 jmespath==1.0.1 rfc3986-validator==0.1.1 bravado==11.1.0 nvidia-cusparselt-cu12==0.6.2 alphabase==1.5.0 alphadia==1.10.4.dev0 PyYAML==6.0.2
0:00:00.073240 INFO: ===================================================
0:00:00.073285 INFO: Running step 'library'
0:00:00.073563 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:00:00.084811 INFO: loading additional config provided via CLI
0:00:00.084882 INFO: loading additional config provided via CLI parameters
0:00:00.085112 INFO: Updating config with 'user defined'
0:00:00.085196 INFO: Updating config with 'user defined (cli)'
0:00:00.085221 INFO: Updating config with 'multistep search'
0:00:00.085256 INFO: ├──version: 1
0:00:00.085282 INFO: ├──workflow_name: None
0:00:00.085306 INFO: [32;20m├──output_directory: run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library [multistep search, default: None][0m
0:00:00.085329 INFO: ├──library_path: None
0:00:00.085349 INFO: ├──raw_paths:
0:00:00.085369 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
0:00:00.085390 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
0:00:00.085411 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
0:00:00.085433 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
0:00:00.085452 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
0:00:00.085470 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
0:00:00.085492 INFO: ├──fasta_paths:
0:00:00.085510 INFO: │   [32;20m- ./ProteoBenchFASTA_DDAQuantification.fasta [user defined (cli), default: None][0m
0:00:00.085532 INFO: ├──quant_directory: None
0:00:00.085551 INFO: ├──general
0:00:00.085572 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
0:00:00.085592 INFO: │   ├──transfer_step_enabled: False
0:00:00.085613 INFO: │   ├──mbr_step_enabled: True
0:00:00.085631 INFO: │   ├──reuse_calibration: False
0:00:00.085650 INFO: │   ├──reuse_quant: False
0:00:00.085669 INFO: │   ├──astral_ms1: False
0:00:00.085686 INFO: │   ├──log_level: INFO
0:00:00.085704 INFO: │   ├──mmap_detector_events: False
0:00:00.085725 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
0:00:00.085744 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.085764 INFO: │   ├──save_mbr_library: True
0:00:00.085782 INFO: │   └──save_figures: True
0:00:00.085802 INFO: ├──library_loading
0:00:00.085824 INFO: │   └──rt_heuristic: 180
0:00:00.085845 INFO: ├──library_prediction
0:00:00.085864 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.085883 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.085901 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.085919 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
0:00:00.085939 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.085958 INFO: │   ├──missed_cleavages: 1
0:00:00.085978 INFO: │   ├──precursor_len:
0:00:00.085996 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.086015 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.086034 INFO: │   ├──precursor_charge:
0:00:00.086052 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.086070 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:00:00.086088 INFO: │   ├──precursor_mz:
0:00:00.086107 INFO: │   │   [32;20m- 380 [user defined, default: 400][0m
0:00:00.086128 INFO: │   │   [32;20m- 980 [user defined, default: 1200][0m
0:00:00.086147 INFO: │   ├──fragment_mz:
0:00:00.086173 INFO: │   │   [32;20m- 150 [user defined, default: 200][0m
0:00:00.086191 INFO: │   │   [32;20m- 2000[0m
0:00:00.086210 INFO: │   ├──nce: 25
0:00:00.086229 INFO: │   ├──fragment_types:
0:00:00.086246 INFO: │   │   [32;20m- b[0m
0:00:00.086263 INFO: │   │   [32;20m- y[0m
0:00:00.086282 INFO: │   ├──max_fragment_charge: 2
0:00:00.086300 INFO: │   [32;20m├──instrument: Astral [user defined, default: Lumos][0m
0:00:00.086319 INFO: │   ├──peptdeep_model_path: None
0:00:00.086337 INFO: │   └──peptdeep_model_type: generic
0:00:00.086355 INFO: ├──custom_modifications:
0:00:00.086374 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.086391 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.086414 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.086435 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.086454 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.086472 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.086490 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.086507 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.086525 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.086544 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.086561 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.086581 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.086600 INFO: │   ├──name: Label:13C(12)@K
0:00:00.086619 INFO: │   └──composition: C(12)
0:00:00.086636 INFO: ├──search
0:00:00.086655 INFO: │   [32;20m├──target_ms1_tolerance: 0 [user defined, default: 5][0m
0:00:00.086675 INFO: │   [32;20m├──target_ms2_tolerance: 0 [user defined, default: 10][0m
0:00:00.086693 INFO: │   ├──target_rt_tolerance: 0
0:00:00.086711 INFO: │   ├──target_mobility_tolerance: 0
0:00:00.086730 INFO: │   ├──quant_window: 3
0:00:00.086748 INFO: │   [32;20m├──target_num_candidates: 2 [user defined, default: 3][0m
0:00:00.086767 INFO: │   ├──channel_filter: 
0:00:00.086785 INFO: │   ├──exclude_shared_ions: True
0:00:00.086803 INFO: │   ├──compete_for_fragments: True
0:00:00.086821 INFO: │   ├──quant_all: True
0:00:00.086839 INFO: │   ├──top_k_fragments: 12
0:00:00.086857 INFO: │   ├──experimental_xic: True
0:00:00.086875 INFO: │   └──optimized_peak_group_score: False
0:00:00.086893 INFO: ├──calibration
0:00:00.086912 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 8000][0m
0:00:00.086931 INFO: │   ├──optimization_lock_target: 200
0:00:00.086951 INFO: │   ├──max_steps: 20
0:00:00.086969 INFO: │   ├──min_steps: 2
0:00:00.086987 INFO: │   ├──max_skips: 1
0:00:00.087005 INFO: │   ├──norm_rt_mode: linear
0:00:00.087023 INFO: │   ├──max_fragments: 5000
0:00:00.087047 INFO: │   └──min_correlation: 0.7
0:00:00.087065 INFO: ├──search_initial
0:00:00.087083 INFO: │   ├──initial_num_candidates: 1
0:00:00.087101 INFO: │   ├──initial_ms1_tolerance: 30
0:00:00.087120 INFO: │   ├──initial_ms2_tolerance: 30
0:00:00.087140 INFO: │   ├──initial_mobility_tolerance: 0.1
0:00:00.087160 INFO: │   └──initial_rt_tolerance: 0.5
0:00:00.087179 INFO: ├──selection_config
0:00:00.087198 INFO: │   ├──peak_len_rt: 10.0
0:00:00.087217 INFO: │   ├──sigma_scale_rt: 0.5
0:00:00.087237 INFO: │   ├──peak_len_mobility: 0.01
0:00:00.087256 INFO: │   ├──sigma_scale_mobility: 1.0
0:00:00.087274 INFO: │   ├──top_k_precursors: 3
0:00:00.087292 INFO: │   ├──kernel_size: 30
0:00:00.087311 INFO: │   ├──f_mobility: 1.0
0:00:00.087330 INFO: │   ├──f_rt: 0.99
0:00:00.087349 INFO: │   ├──center_fraction: 0.5
0:00:00.087366 INFO: │   ├──min_size_mobility: 8
0:00:00.087384 INFO: │   ├──min_size_rt: 3
0:00:00.087405 INFO: │   ├──max_size_mobility: 20
0:00:00.087435 INFO: │   ├──max_size_rt: 15
0:00:00.087455 INFO: │   ├──group_channels: False
0:00:00.087474 INFO: │   ├──use_weighted_score: True
0:00:00.087493 INFO: │   ├──join_close_candidates: False
0:00:00.087512 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
0:00:00.087530 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
0:00:00.087547 INFO: ├──scoring_config
0:00:00.087565 INFO: │   ├──score_grouped: False
0:00:00.087583 INFO: │   ├──top_k_isotopes: 3
0:00:00.087601 INFO: │   ├──reference_channel: -1
0:00:00.087619 INFO: │   ├──precursor_mz_tolerance: 10
0:00:00.087638 INFO: │   └──fragment_mz_tolerance: 15
0:00:00.087656 INFO: ├──library_multiplexing
0:00:00.087675 INFO: │   ├──enabled: False
0:00:00.087693 INFO: │   ├──input_channel: 0
0:00:00.087711 INFO: │   └──multiplex_mapping:
0:00:00.087729 INFO: ├──multiplexing
0:00:00.087747 INFO: │   ├──enabled: False
0:00:00.087765 INFO: │   ├──target_channels: 4,8
0:00:00.087783 INFO: │   ├──decoy_channel: 12
0:00:00.087801 INFO: │   ├──reference_channel: 0
0:00:00.087818 INFO: │   └──competetive_scoring: True
0:00:00.087835 INFO: ├──fdr
0:00:00.087853 INFO: │   ├──fdr: 0.01
0:00:00.087872 INFO: │   ├──group_level: proteins
0:00:00.087891 INFO: │   ├──inference_strategy: heuristic
0:00:00.087909 INFO: │   ├──competetive_scoring: True
0:00:00.087927 INFO: │   ├──keep_decoys: False
0:00:00.087945 INFO: │   ├──channel_wise_fdr: False
0:00:00.087964 INFO: │   ├──enable_two_step_classifier: False
0:00:00.087982 INFO: │   ├──two_step_classifier_max_iterations: 5
0:00:00.088001 INFO: │   └──enable_nn_hyperparameter_tuning: False
0:00:00.088019 INFO: ├──search_output
0:00:00.088037 INFO: │   ├──file_format: tsv
0:00:00.088056 INFO: │   ├──peptide_level_lfq: False
0:00:00.088074 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
0:00:00.088093 INFO: │   ├──min_k_fragments: 12
0:00:00.088110 INFO: │   ├──min_correlation: 0.9
0:00:00.088128 INFO: │   ├──num_samples_quadratic: 50
0:00:00.088147 INFO: │   ├──min_nonnan: 3
0:00:00.088165 INFO: │   ├──normalize_lfq: True
0:00:00.088182 INFO: │   └──save_fragment_quant_matrix: False
0:00:00.088200 INFO: ├──optimization
0:00:00.088219 INFO: │   ├──order_of_optimization: None
0:00:00.088244 INFO: │   ├──ms2_error
0:00:00.088266 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.088284 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.088302 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.088321 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.088340 INFO: │   │   ├──try_narrower_values: True
0:00:00.088360 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.088378 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.088397 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.088415 INFO: │   ├──ms1_error
0:00:00.088434 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.088454 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.088473 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.088490 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.088510 INFO: │   │   ├──try_narrower_values: False
0:00:00.088530 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.088549 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.088568 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.088586 INFO: │   ├──mobility_error
0:00:00.088606 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.088624 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.088643 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.088669 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.088688 INFO: │   │   ├──try_narrower_values: False
0:00:00.088712 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.088732 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.088750 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.088768 INFO: │   └──rt_error
0:00:00.088787 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.088807 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.088827 INFO: │       ├──automatic_update_percentile_range: 0.99
0:00:00.088846 INFO: │       ├──automatic_update_factor: 1.1
0:00:00.088864 INFO: │       ├──try_narrower_values: True
0:00:00.088883 INFO: │       ├──maximal_decrease: 0.2
0:00:00.088902 INFO: │       ├──favour_narrower_optimum: True
0:00:00.088921 INFO: │       └──maximum_decrease_from_maximum: 0.1
0:00:00.088938 INFO: ├──optimization_manager
0:00:00.088956 INFO: │   ├──fwhm_rt: 5
0:00:00.088975 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.088994 INFO: │   └──score_cutoff: 0
0:00:00.089011 INFO: ├──transfer_library
0:00:00.089029 INFO: │   ├──enabled: False
0:00:00.089046 INFO: │   ├──fragment_types:
0:00:00.089063 INFO: │   │   [32;20m- b[0m
0:00:00.089082 INFO: │   │   [32;20m- y[0m
0:00:00.089099 INFO: │   ├──max_charge: 2
0:00:00.089117 INFO: │   ├──top_k_samples: 3
0:00:00.089134 INFO: │   ├──norm_delta_max: True
0:00:00.089152 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.089171 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.089189 INFO: └──transfer_learning
0:00:00.089207 INFO:     ├──enabled: False
0:00:00.089225 INFO:     ├──batch_size: 2000
0:00:00.089243 INFO:     ├──max_lr: 0.0001
0:00:00.089263 INFO:     ├──train_fraction: 0.7
0:00:00.089282 INFO:     ├──validation_fraction: 0.2
0:00:00.089301 INFO:     ├──test_fraction: 0.1
0:00:00.089319 INFO:     ├──test_interval: 1
0:00:00.089336 INFO:     ├──lr_patience: 3
0:00:00.089354 INFO:     [32;20m├──epochs: 20 [user defined, default: 51][0m
0:00:00.089374 INFO:     ├──warmup_epochs: 5
0:00:00.089391 INFO:     ├──nce: 25
0:00:00.089409 INFO:     [32;20m└──instrument: Astral [user defined, default: Lumos][0m
0:00:00.094144 INFO: Registering 7 custom modifications
0:00:00.121946 PROGRESS: No library provided. Building library from fasta files.
0:00:00.122039 INFO: Running FastaDigest
0:00:00.984682 INFO: Digesting fasta file
0:00:07.329682 INFO: Adding modifications
0:01:42.703668 INFO: Removing non-canonical amino acids
0:01:49.432216 INFO: Fasta library contains 6,380,650 precursors
0:01:49.432532 PROGRESS: Predicting library properties.
0:01:49.432614 INFO: Running PeptDeepPrediction
0:01:49.432714 INFO: Device set to cpu
0:01:50.360943 INFO: Loading PeptDeep models of type generic
0:01:51.127856 INFO: Predicting RT, MS2 and mobility
0:01:51.128042 INFO: Using multiprocessing with 100 processes ...
0:01:51.503778 INFO: Predicting rt,ms2,mobility ...
0:08:32.292106 INFO: Adding fragment mz information
0:08:32.662232 INFO: Adding fragment intensity information
0:08:33.037341 INFO: Adding precursor information
0:08:33.379055 INFO: Running PrecursorInitializer
0:08:33.411652 INFO: Running AnnotateFasta
0:08:33.560171 INFO: Dropping decoys from input library before annotation
0:09:00.545512 INFO: Running IsotopeGenerator
0:09:20.773033 INFO: Running RTNormalization
0:09:20.773654 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:09:20.773764 INFO: Saving library to run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/speclib.hdf
0:09:58.762796 INFO: Running DecoyGenerator
0:12:05.819170 INFO: Running FlattenLibrary
0:12:39.138468 INFO: Running InitFlatColumns
0:12:39.455906 INFO: Running LogFlatLibraryStats
0:12:39.456101 INFO: ============ Library Stats ============
0:12:39.456151 INFO: Number of precursors: 12,727,362
0:12:41.345805 INFO: 	thereof targets:6,380,650
0:12:41.345980 INFO: 	thereof decoys: 6,346,712
0:12:41.447189 INFO: Number of elution groups: 6,380,650
0:12:41.447338 INFO: 	average size: 1.99
0:12:41.831927 INFO: Number of proteins: 117,993
0:12:41.864673 INFO: Number of channels: 1 ([0])
0:12:41.864885 INFO: Isotopes Distribution for 4 isotopes
0:12:41.864920 INFO: =======================================
0:12:41.875921 INFO: Searching 6 files:
0:12:41.876062 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
0:12:41.876092 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
0:12:41.876116 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
0:12:41.876139 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
0:12:41.876162 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
0:12:41.876187 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
0:12:41.876209 INFO: Using 1 fasta files:
0:12:41.876234 INFO:   ./ProteoBenchFASTA_DDAQuantification.fasta
0:12:41.876273 INFO: Using library: None
0:12:41.876297 INFO: Saving output to: run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library
0:12:41.876342 PROGRESS: Starting Search Workflows
0:12:41.876438 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:12:41.876522 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant
0:12:41.876623 INFO: Creating folder run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/figures
0:12:41.877531 INFO: Initializing RawFileManager
0:12:52.304107 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:12:52.308467 INFO: Determining DIA cycle
0:12:53.225788 INFO: Found cycle with start 0.00 min and length 300.
0:12:53.392735 INFO: RT (min)            : 0.0 - 26.9
0:12:53.392836 INFO: RT duration (sec)   : 1611.2
0:12:53.392866 INFO: RT duration (min)   : 26.9
0:12:53.392892 INFO: Cycle len (scans)   : 300
0:12:53.392911 INFO: Cycle len (sec)     : 1.65
0:12:53.392930 INFO: Number of cycles    : 977
0:12:53.392950 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:12:54.805663 INFO: Initializing CalibrationManager
0:12:54.805979 INFO: Loading calibration config
0:12:54.806089 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6'}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6'}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed']}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed']}], 'name': 'precursor'}]
0:12:54.806157 INFO: Calibration group :fragment, found 1 estimator(s)
0:12:54.806271 INFO: Calibration group :precursor, found 3 estimator(s)
0:12:54.806346 INFO: Disabling ion mobility calibration
0:12:54.806377 INFO: removed mobility estimator from group precursor
0:12:54.806531 INFO: Initializing OptimizationManager
0:12:54.806653 INFO: initial parameter: ms1_error = 30
0:12:54.806708 INFO: initial parameter: ms2_error = 30
0:12:54.806771 INFO: initial parameter: rt_error = 805.5992431640625
0:12:54.806819 INFO: initial parameter: mobility_error = 0.1
0:12:54.806863 INFO: initial parameter: column_type = library
0:12:54.806913 INFO: initial parameter: num_candidates = 1
0:12:54.806954 INFO: initial parameter: classifier_version = -1
0:12:54.806996 INFO: initial parameter: fwhm_rt = 5
0:12:54.807035 INFO: initial parameter: fwhm_mobility = 0.01
0:12:54.807076 INFO: initial parameter: score_cutoff = 0
0:12:54.807147 INFO: Initializing TimingManager
0:12:54.807208 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:12:54.807337 INFO: FDRManager not loaded from disk.
0:12:54.807361 INFO: Initializing FDRManager
0:12:54.807402 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:12:56.347625 PROGRESS: 6,373,245 target precursors potentially observable (7,405 removed)
0:12:58.485118 PROGRESS: Starting initial search for precursors.
0:12:59.424987 INFO: Starting optimization step 0.
0:12:59.425238 PROGRESS: === Extracting elution groups 0 to 200 ===
0:12:59.425321 PROGRESS: Extracting batch of 396 precursors
0:13:00.901635 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:13:00.901809 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:13:00.901857 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:13:00.901881 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:13:04.401359 INFO: Starting candidate selection
0:14:24.634013 INFO: Starting candidate scoring
0:21:58.981144 INFO: Finished candidate processing
0:21:58.981557 INFO: Collecting candidate features
0:21:59.580592 INFO: Collecting fragment features
0:22:02.042538 INFO: Finished candidate scoring
0:22:02.043880 PROGRESS: === Extracted 394 precursors and 4059 fragments ===
0:22:02.044194 INFO: performing precursor FDR with 47 features
0:22:02.044234 INFO: Decoy channel: -1
0:22:02.044271 INFO: Competetive: True
0:22:02.045308 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:05.542036 INFO: Test AUC: 0.463
0:22:05.542230 INFO: Train AUC: 0.509
0:22:05.542305 INFO: AUC difference: 8.99%
0:22:05.542359 WARNING: AUC difference > 5%. This may indicate overfitting.
0:22:05.797549 INFO: Resetting torch num_threads to 100
0:22:05.798034 INFO: === FDR correction performed with classifier version -1 ===
0:22:05.798661 PROGRESS: ============================= Precursor FDR =============================
0:22:05.798754 PROGRESS: Total precursors accumulated: 199
0:22:05.798818 PROGRESS: Target precursors: 101 (50.75%)
0:22:05.798870 PROGRESS: Decoy precursors: 98 (49.25%)
0:22:05.798916 PROGRESS: 
0:22:05.798961 PROGRESS: Precursor Summary:
0:22:05.799834 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:05.799924 PROGRESS: 
0:22:05.799980 PROGRESS: Protein Summary:
0:22:05.800926 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:05.801015 PROGRESS: =========================================================================
0:22:05.877035 INFO: Starting optimization step 1.
0:22:05.877326 PROGRESS: === Extracting elution groups 200 to 600 ===
0:22:05.877405 PROGRESS: Extracting batch of 786 precursors
0:22:05.878622 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:22:05.878682 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:05.878722 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:22:05.878752 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:22:05.878997 INFO: Starting candidate selection
0:22:06.003765 INFO: Starting candidate scoring
0:22:06.042288 INFO: Finished candidate processing
0:22:06.042372 INFO: Collecting candidate features
0:22:06.051268 INFO: Collecting fragment features
0:22:06.053533 INFO: Finished candidate scoring
0:22:06.055420 PROGRESS: === Extracted 1180 precursors and 12108 fragments ===
0:22:06.056173 INFO: performing precursor FDR with 47 features
0:22:06.056222 INFO: Decoy channel: -1
0:22:06.056254 INFO: Competetive: True
0:22:06.058956 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:07.915702 INFO: Test AUC: 0.510
0:22:07.915879 INFO: Train AUC: 0.490
0:22:07.915996 INFO: AUC difference: 4.14%
0:22:08.118072 INFO: Resetting torch num_threads to 100
0:22:08.118721 INFO: === FDR correction performed with classifier version -1 ===
0:22:08.119399 PROGRESS: ============================= Precursor FDR =============================
0:22:08.119490 PROGRESS: Total precursors accumulated: 1
0:22:08.119551 PROGRESS: Target precursors: 1 (100.00%)
0:22:08.119605 PROGRESS: Decoy precursors: 0 (0.00%)
0:22:08.119655 PROGRESS: 
0:22:08.119701 PROGRESS: Precursor Summary:
0:22:08.120670 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:22:08.120762 PROGRESS: 
0:22:08.120817 PROGRESS: Protein Summary:
0:22:08.121846 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:22:08.121935 PROGRESS: =========================================================================
0:22:08.195369 INFO: Starting optimization step 2.
0:22:08.195611 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:22:08.195681 PROGRESS: Extracting batch of 1573 precursors
0:22:08.196617 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:22:08.196667 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:08.196700 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:22:08.196723 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:22:08.196913 INFO: Starting candidate selection
0:22:08.387399 INFO: Starting candidate scoring
0:22:08.429769 INFO: Finished candidate processing
0:22:08.429847 INFO: Collecting candidate features
0:22:08.442473 INFO: Collecting fragment features
0:22:08.446032 INFO: Finished candidate scoring
0:22:08.449547 PROGRESS: === Extracted 2747 precursors and 28150 fragments ===
0:22:08.450520 INFO: performing precursor FDR with 47 features
0:22:08.450564 INFO: Decoy channel: -1
0:22:08.450589 INFO: Competetive: True
0:22:08.453954 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:08.479867 INFO: Test AUC: 0.510
0:22:08.479948 INFO: Train AUC: 0.483
0:22:08.479979 INFO: AUC difference: 5.58%
0:22:08.480001 WARNING: AUC difference > 5%. This may indicate overfitting.
0:22:08.658284 INFO: Resetting torch num_threads to 100
0:22:08.659035 INFO: === FDR correction performed with classifier version -1 ===
0:22:08.659711 PROGRESS: ============================= Precursor FDR =============================
0:22:08.659801 PROGRESS: Total precursors accumulated: 1
0:22:08.659863 PROGRESS: Target precursors: 1 (100.00%)
0:22:08.659914 PROGRESS: Decoy precursors: 0 (0.00%)
0:22:08.659961 PROGRESS: 
0:22:08.660006 PROGRESS: Precursor Summary:
0:22:08.660955 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:22:08.661046 PROGRESS: 
0:22:08.661104 PROGRESS: Protein Summary:
0:22:08.662128 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:22:08.662216 PROGRESS: =========================================================================
0:22:08.741155 INFO: Starting optimization step 3.
0:22:08.741401 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:22:08.741470 PROGRESS: Extracting batch of 3149 precursors
0:22:08.742602 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:22:08.742651 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:08.742685 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:22:08.742708 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:22:08.742904 INFO: Starting candidate selection
0:22:08.993260 INFO: Starting candidate scoring
0:22:09.035724 INFO: Finished candidate processing
0:22:09.035813 INFO: Collecting candidate features
0:22:09.048977 INFO: Collecting fragment features
0:22:09.052513 INFO: Finished candidate scoring
0:22:09.057150 PROGRESS: === Extracted 5891 precursors and 60636 fragments ===
0:22:09.058335 INFO: performing precursor FDR with 47 features
0:22:09.058380 INFO: Decoy channel: -1
0:22:09.058404 INFO: Competetive: True
0:22:09.062499 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:09.118466 INFO: Test AUC: 0.478
0:22:09.118570 INFO: Train AUC: 0.483
0:22:09.118600 INFO: AUC difference: 1.03%
0:22:09.292503 INFO: Resetting torch num_threads to 100
0:22:09.293461 INFO: === FDR correction performed with classifier version -1 ===
0:22:09.294420 PROGRESS: ============================= Precursor FDR =============================
0:22:09.294517 PROGRESS: Total precursors accumulated: 2,994
0:22:09.294581 PROGRESS: Target precursors: 1,446 (48.30%)
0:22:09.294637 PROGRESS: Decoy precursors: 1,548 (51.70%)
0:22:09.294686 PROGRESS: 
0:22:09.294733 PROGRESS: Precursor Summary:
0:22:09.295624 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:09.295711 PROGRESS: 
0:22:09.295767 PROGRESS: Protein Summary:
0:22:09.296723 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:09.296810 PROGRESS: =========================================================================
0:22:09.383985 INFO: Starting optimization step 4.
0:22:09.384261 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:22:09.384337 PROGRESS: Extracting batch of 6319 precursors
0:22:09.385849 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:22:09.385897 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:09.385931 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:22:09.385953 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:22:09.386144 INFO: Starting candidate selection
0:22:09.818411 INFO: Starting candidate scoring
0:22:09.865006 INFO: Finished candidate processing
0:22:09.865114 INFO: Collecting candidate features
0:22:09.882585 INFO: Collecting fragment features
0:22:09.888081 INFO: Finished candidate scoring
0:22:09.896425 PROGRESS: === Extracted 12200 precursors and 125266 fragments ===
0:22:09.898499 INFO: performing precursor FDR with 47 features
0:22:09.898561 INFO: Decoy channel: -1
0:22:09.898587 INFO: Competetive: True
0:22:09.905876 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:09.991487 INFO: Test AUC: 0.501
0:22:09.991600 INFO: Train AUC: 0.486
0:22:09.991630 INFO: AUC difference: 2.92%
0:22:10.169305 INFO: Resetting torch num_threads to 100
0:22:10.170581 INFO: === FDR correction performed with classifier version -1 ===
0:22:10.171953 PROGRESS: ============================= Precursor FDR =============================
0:22:10.172045 PROGRESS: Total precursors accumulated: 6,188
0:22:10.172109 PROGRESS: Target precursors: 3,058 (49.42%)
0:22:10.172161 PROGRESS: Decoy precursors: 3,130 (50.58%)
0:22:10.172207 PROGRESS: 
0:22:10.172265 PROGRESS: Precursor Summary:
0:22:10.173237 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:10.173326 PROGRESS: 
0:22:10.173380 PROGRESS: Protein Summary:
0:22:10.174342 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:10.174430 PROGRESS: =========================================================================
0:22:10.275434 INFO: Starting optimization step 5.
0:22:10.275699 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:22:10.275783 PROGRESS: Extracting batch of 12617 precursors
0:22:10.278210 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:22:10.278261 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:10.278295 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:22:10.278317 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:22:10.278504 INFO: Starting candidate selection
0:22:11.067581 INFO: Starting candidate scoring
0:22:11.149232 INFO: Finished candidate processing
0:22:11.149340 INFO: Collecting candidate features
0:22:11.178201 INFO: Collecting fragment features
0:22:11.187595 INFO: Finished candidate scoring
0:22:11.202393 PROGRESS: === Extracted 24794 precursors and 254482 fragments ===
0:22:11.206127 INFO: performing precursor FDR with 47 features
0:22:11.206210 INFO: Decoy channel: -1
0:22:11.206235 INFO: Competetive: True
0:22:11.216361 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:11.589582 INFO: Test AUC: 0.511
0:22:11.589716 INFO: Train AUC: 0.501
0:22:11.589746 INFO: AUC difference: 1.90%
0:22:11.781928 INFO: Resetting torch num_threads to 100
0:22:11.798132 INFO: === FDR correction performed with classifier version -1 ===
0:22:11.800342 PROGRESS: ============================= Precursor FDR =============================
0:22:11.800452 PROGRESS: Total precursors accumulated: 12,578
0:22:11.800515 PROGRESS: Target precursors: 6,615 (52.59%)
0:22:11.800569 PROGRESS: Decoy precursors: 5,963 (47.41%)
0:22:11.800618 PROGRESS: 
0:22:11.800663 PROGRESS: Precursor Summary:
0:22:11.801625 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:11.801713 PROGRESS: 
0:22:11.801769 PROGRESS: Protein Summary:
0:22:11.802784 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:11.802872 PROGRESS: =========================================================================
0:22:11.947957 INFO: Starting optimization step 6.
0:22:11.948275 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:22:11.948369 PROGRESS: Extracting batch of 25256 precursors
0:22:11.955582 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:22:11.955658 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:11.955698 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:22:11.955727 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:22:11.956007 INFO: Starting candidate selection
0:22:13.516077 INFO: Starting candidate scoring
0:22:13.662009 INFO: Finished candidate processing
0:22:13.662124 INFO: Collecting candidate features
0:22:13.712390 INFO: Collecting fragment features
0:22:13.729516 INFO: Finished candidate scoring
0:22:13.758480 PROGRESS: === Extracted 50013 precursors and 512456 fragments ===
0:22:13.766346 INFO: performing precursor FDR with 47 features
0:22:13.766417 INFO: Decoy channel: -1
0:22:13.766443 INFO: Competetive: True
0:22:13.792011 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:14.513415 INFO: Test AUC: 0.549
0:22:14.513555 INFO: Train AUC: 0.550
0:22:14.513585 INFO: AUC difference: 0.32%
0:22:14.706157 INFO: Resetting torch num_threads to 100
0:22:14.708982 INFO: === FDR correction performed with classifier version -1 ===
0:22:14.712850 PROGRESS: ============================= Precursor FDR =============================
0:22:14.713017 PROGRESS: Total precursors accumulated: 25,346
0:22:14.713079 PROGRESS: Target precursors: 14,668 (57.87%)
0:22:14.713131 PROGRESS: Decoy precursors: 10,678 (42.13%)
0:22:14.713178 PROGRESS: 
0:22:14.713222 PROGRESS: Precursor Summary:
0:22:14.714239 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:14.714326 PROGRESS: 
0:22:14.714380 PROGRESS: Protein Summary:
0:22:14.715421 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:14.715507 PROGRESS: =========================================================================
0:22:14.885007 INFO: Starting optimization step 7.
0:22:14.885293 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:22:14.885370 PROGRESS: Extracting batch of 50439 precursors
0:22:14.896938 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:22:14.897059 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:14.897096 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:22:14.897118 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:22:14.897379 INFO: Starting candidate selection
0:22:17.883483 INFO: Starting candidate scoring
0:22:18.168216 INFO: Finished candidate processing
0:22:18.168381 INFO: Collecting candidate features
0:22:18.257152 INFO: Collecting fragment features
0:22:18.292881 INFO: Finished candidate scoring
0:22:18.343964 PROGRESS: === Extracted 100356 precursors and 1028470 fragments ===
0:22:18.355741 INFO: performing precursor FDR with 47 features
0:22:18.355836 INFO: Decoy channel: -1
0:22:18.355863 INFO: Competetive: True
0:22:18.396625 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:20.039421 INFO: Test AUC: 0.557
0:22:20.039562 INFO: Train AUC: 0.568
0:22:20.039593 INFO: AUC difference: 1.78%
0:22:20.250489 INFO: Resetting torch num_threads to 100
0:22:20.255541 INFO: === FDR correction performed with classifier version -1 ===
0:22:20.256221 PROGRESS: ============================= Precursor FDR =============================
0:22:20.256321 PROGRESS: Total precursors accumulated: 23
0:22:20.256381 PROGRESS: Target precursors: 21 (91.30%)
0:22:20.256433 PROGRESS: Decoy precursors: 2 (8.70%)
0:22:20.256490 PROGRESS: 
0:22:20.256536 PROGRESS: Precursor Summary:
0:22:20.257393 PROGRESS: Channel   0:	 0.05 FDR:     8; 0.01 FDR:     8; 0.001 FDR:     8
0:22:20.257480 PROGRESS: 
0:22:20.257536 PROGRESS: Protein Summary:
0:22:20.258481 PROGRESS: Channel   0:	 0.05 FDR:     8; 0.01 FDR:     8; 0.001 FDR:     8
0:22:20.258567 PROGRESS: =========================================================================
0:22:20.498272 INFO: Starting optimization step 8.
0:22:20.498576 PROGRESS: === Extracting elution groups 51000 to 102200 ===
0:22:20.498667 PROGRESS: Extracting batch of 100917 precursors
0:22:20.521246 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:22:20.521394 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:20.521430 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:22:20.521453 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:22:20.521693 INFO: Starting candidate selection
0:22:26.729540 INFO: Starting candidate scoring
0:22:27.307901 INFO: Finished candidate processing
0:22:27.308065 INFO: Collecting candidate features
0:22:27.500962 INFO: Collecting fragment features
0:22:27.580690 INFO: Finished candidate scoring
0:22:27.751146 PROGRESS: === Extracted 201068 precursors and 2060401 fragments ===
0:22:27.777458 INFO: performing precursor FDR with 47 features
0:22:27.777591 INFO: Decoy channel: -1
0:22:27.777619 INFO: Competetive: True
0:22:27.872994 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:31.310530 INFO: Test AUC: 0.561
0:22:31.310756 INFO: Train AUC: 0.574
0:22:31.310789 INFO: AUC difference: 2.32%
0:22:31.557612 INFO: Resetting torch num_threads to 100
0:22:31.572543 INFO: === FDR correction performed with classifier version -1 ===
0:22:31.573606 PROGRESS: ============================= Precursor FDR =============================
0:22:31.573733 PROGRESS: Total precursors accumulated: 1,023
0:22:31.573796 PROGRESS: Target precursors: 931 (91.01%)
0:22:31.573851 PROGRESS: Decoy precursors: 92 (8.99%)
0:22:31.573901 PROGRESS: 
0:22:31.573949 PROGRESS: Precursor Summary:
0:22:31.575095 PROGRESS: Channel   0:	 0.05 FDR:   754; 0.01 FDR:   519; 0.001 FDR:   154
0:22:31.575195 PROGRESS: 
0:22:31.575251 PROGRESS: Protein Summary:
0:22:31.576578 PROGRESS: Channel   0:	 0.05 FDR:   674; 0.01 FDR:   468; 0.001 FDR:   144
0:22:31.576674 PROGRESS: =========================================================================
0:22:31.743392 INFO: fragments_df: keeping 4539 of 2060401 [sum(precursor_idx_mask)=5982 sum(mass_error_mask)=2060401 stop_rank=4539
0:22:31.996812 INFO: calibration group: precursor, fitting rt estimator 
0:22:32.143181 INFO: calibration group: fragment, fitting mz estimator 
0:22:32.752383 INFO: Using score_cutoff 71.28570969085693 (fac=0.99, q=1)
0:22:32.752977 INFO: calibration group: precursor, predicting mz
0:22:32.753065 WARNING: mz prediction was skipped as it has not been fitted yet
0:22:32.753101 INFO: calibration group: precursor, predicting rt
0:22:32.821263 INFO: calibration group: fragment, predicting mz
0:22:32.968167 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:22:32.968476 INFO: Starting optimization step 9.
0:22:32.968558 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:22:32.968641 PROGRESS: Extracting batch of 100535 precursors
0:22:33.004197 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:22:33.004365 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:33.004413 INFO: FWHM in RT is 3.06 seconds, sigma is 0.39
0:22:33.004438 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:22:33.004766 INFO: Starting candidate selection
0:22:38.220232 INFO: Starting candidate scoring
0:22:39.467978 INFO: Finished candidate processing
0:22:39.468111 INFO: Collecting candidate features
0:22:39.795407 INFO: Collecting fragment features
0:22:39.916226 INFO: Finished candidate scoring
0:22:40.026647 PROGRESS: === Extracted 200712 precursors and 2031090 fragments ===
0:22:40.027042 INFO: performing precursor FDR with 47 features
0:22:40.027084 INFO: Decoy channel: -1
0:22:40.027111 INFO: Competetive: True
0:22:40.088703 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:43.538572 INFO: Test AUC: 0.564
0:22:43.539315 INFO: Train AUC: 0.578
0:22:43.539354 INFO: AUC difference: 2.32%
0:22:43.776116 INFO: Resetting torch num_threads to 100
0:22:43.781651 INFO: === FDR correction performed with classifier version 8 ===
0:22:43.782399 PROGRESS: ============================= Precursor FDR =============================
0:22:43.782496 PROGRESS: Total precursors accumulated: 533
0:22:43.782566 PROGRESS: Target precursors: 485 (90.99%)
0:22:43.782621 PROGRESS: Decoy precursors: 48 (9.01%)
0:22:43.782667 PROGRESS: 
0:22:43.782713 PROGRESS: Precursor Summary:
0:22:43.783695 PROGRESS: Channel   0:	 0.05 FDR:   408; 0.01 FDR:   322; 0.001 FDR:    90
0:22:43.783804 PROGRESS: 
0:22:43.783876 PROGRESS: Protein Summary:
0:22:43.785065 PROGRESS: Channel   0:	 0.05 FDR:   382; 0.01 FDR:   299; 0.001 FDR:    86
0:22:43.785170 PROGRESS: =========================================================================
0:22:43.921376 INFO: fragments_df: keeping 3519 of 2031090 [sum(precursor_idx_mask)=7254 sum(mass_error_mask)=2031090 stop_rank=3519
0:22:44.166695 INFO: calibration group: precursor, fitting rt estimator 
0:22:44.295083 INFO: calibration group: fragment, fitting mz estimator 
0:22:44.761857 INFO: Using score_cutoff 64.38518181381225 (fac=0.99, q=1)
0:22:44.762325 INFO: calibration group: precursor, predicting mz
0:22:44.762415 WARNING: mz prediction was skipped as it has not been fitted yet
0:22:44.762449 INFO: calibration group: precursor, predicting rt
0:22:44.825169 INFO: calibration group: fragment, predicting mz
0:22:44.974250 INFO: === checking if optimization conditions were reached ===
0:22:44.974597 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:22:44.977294 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 25.5013.
0:22:44.977362 INFO: ==============================================
0:22:44.977469 INFO: Starting optimization step 10.
0:22:44.977551 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:22:44.977638 PROGRESS: Extracting batch of 100535 precursors
0:22:45.014270 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:22:45.014438 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:45.014487 INFO: FWHM in RT is 3.04 seconds, sigma is 0.39
0:22:45.014519 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:22:45.014877 INFO: Starting candidate selection
0:22:49.600705 INFO: Starting candidate scoring
0:22:51.057104 INFO: Finished candidate processing
0:22:51.057218 INFO: Collecting candidate features
0:22:51.405675 INFO: Collecting fragment features
0:22:51.526681 INFO: Finished candidate scoring
0:22:51.663610 PROGRESS: === Extracted 200712 precursors and 1983701 fragments ===
0:22:51.664059 INFO: performing precursor FDR with 47 features
0:22:51.664100 INFO: Decoy channel: -1
0:22:51.664124 INFO: Competetive: True
0:22:51.723051 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:55.210302 INFO: Test AUC: 0.565
0:22:55.210491 INFO: Train AUC: 0.573
0:22:55.210522 INFO: AUC difference: 1.52%
0:22:55.452123 INFO: Resetting torch num_threads to 100
0:22:55.460737 INFO: === FDR correction performed with classifier version 8 ===
0:22:55.461699 PROGRESS: ============================= Precursor FDR =============================
0:22:55.461796 PROGRESS: Total precursors accumulated: 636
0:22:55.461860 PROGRESS: Target precursors: 580 (91.19%)
0:22:55.461912 PROGRESS: Decoy precursors: 56 (8.81%)
0:22:55.461960 PROGRESS: 
0:22:55.462003 PROGRESS: Precursor Summary:
0:22:55.463098 PROGRESS: Channel   0:	 0.05 FDR:   440; 0.01 FDR:   347; 0.001 FDR:    45
0:22:55.463188 PROGRESS: 
0:22:55.463243 PROGRESS: Protein Summary:
0:22:55.464420 PROGRESS: Channel   0:	 0.05 FDR:   408; 0.01 FDR:   325; 0.001 FDR:    44
0:22:55.464512 PROGRESS: =========================================================================
0:22:55.601873 INFO: fragments_df: keeping 3743 of 1983701 [sum(precursor_idx_mask)=7788 sum(mass_error_mask)=1983701 stop_rank=3743
0:22:55.845484 INFO: calibration group: precursor, fitting rt estimator 
0:22:55.977475 INFO: calibration group: fragment, fitting mz estimator 
0:22:56.464102 INFO: Using score_cutoff 62.96349288482666 (fac=0.99, q=1)
0:22:56.464609 INFO: calibration group: precursor, predicting mz
0:22:56.464701 WARNING: mz prediction was skipped as it has not been fitted yet
0:22:56.464735 INFO: calibration group: precursor, predicting rt
0:22:56.528036 INFO: calibration group: fragment, predicting mz
0:22:56.675380 INFO: === checking if optimization conditions were reached ===
0:22:56.675735 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:22:56.678710 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 21.5155.
0:22:56.678775 INFO: ==============================================
0:22:56.678883 INFO: Starting optimization step 11.
0:22:56.678961 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:22:56.679044 PROGRESS: Extracting batch of 100535 precursors
0:22:56.714472 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:22:56.714639 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:56.714689 INFO: FWHM in RT is 2.89 seconds, sigma is 0.37
0:22:56.714719 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:22:56.715076 INFO: Starting candidate selection
0:23:01.596493 INFO: Starting candidate scoring
0:23:02.875226 INFO: Finished candidate processing
0:23:02.875345 INFO: Collecting candidate features
0:23:03.249246 INFO: Collecting fragment features
0:23:03.396572 INFO: Finished candidate scoring
0:23:03.535765 PROGRESS: === Extracted 200710 precursors and 1928962 fragments ===
0:23:03.536186 INFO: performing precursor FDR with 47 features
0:23:03.536225 INFO: Decoy channel: -1
0:23:03.536279 INFO: Competetive: True
0:23:03.598040 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:07.042486 INFO: Test AUC: 0.563
0:23:07.042716 INFO: Train AUC: 0.573
0:23:07.042748 INFO: AUC difference: 1.81%
0:23:07.279895 INFO: Resetting torch num_threads to 100
0:23:07.285194 INFO: === FDR correction performed with classifier version 8 ===
0:23:07.285966 PROGRESS: ============================= Precursor FDR =============================
0:23:07.286063 PROGRESS: Total precursors accumulated: 673
0:23:07.286134 PROGRESS: Target precursors: 613 (91.08%)
0:23:07.286190 PROGRESS: Decoy precursors: 60 (8.92%)
0:23:07.286238 PROGRESS: 
0:23:07.286283 PROGRESS: Precursor Summary:
0:23:07.287294 PROGRESS: Channel   0:	 0.05 FDR:   495; 0.01 FDR:   275; 0.001 FDR:    71
0:23:07.287386 PROGRESS: 
0:23:07.287442 PROGRESS: Protein Summary:
0:23:07.288599 PROGRESS: Channel   0:	 0.05 FDR:   460; 0.01 FDR:   260; 0.001 FDR:    67
0:23:07.288697 PROGRESS: =========================================================================
0:23:07.412071 INFO: fragments_df: keeping 3099 of 1928962 [sum(precursor_idx_mask)=6146 sum(mass_error_mask)=1928962 stop_rank=3099
0:23:07.644844 INFO: calibration group: precursor, fitting rt estimator 
0:23:07.749274 INFO: calibration group: fragment, fitting mz estimator 
0:23:08.098149 INFO: Using score_cutoff 67.90373322143554 (fac=0.99, q=1)
0:23:08.098686 INFO: calibration group: precursor, predicting mz
0:23:08.098781 WARNING: mz prediction was skipped as it has not been fitted yet
0:23:08.098818 INFO: calibration group: precursor, predicting rt
0:23:08.166953 INFO: calibration group: fragment, predicting mz
0:23:08.327582 INFO: === checking if optimization conditions were reached ===
0:23:08.327891 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
0:23:08.330797 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 18.0358.
0:23:08.330854 INFO: ==============================================
0:23:08.330954 INFO: Starting optimization step 12.
0:23:08.331024 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:23:08.331124 PROGRESS: Extracting batch of 100535 precursors
0:23:08.456442 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:23:08.456590 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:23:08.456649 INFO: FWHM in RT is 2.78 seconds, sigma is 0.36
0:23:08.456675 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:23:08.457388 INFO: Starting candidate selection
0:23:13.187834 INFO: Starting candidate scoring
0:23:14.545544 INFO: Finished candidate processing
0:23:14.545658 INFO: Collecting candidate features
0:23:14.871634 INFO: Collecting fragment features
0:23:15.014608 INFO: Finished candidate scoring
0:23:15.125658 PROGRESS: === Extracted 200708 precursors and 1876327 fragments ===
0:23:15.126157 INFO: performing precursor FDR with 47 features
0:23:15.126196 INFO: Decoy channel: -1
0:23:15.126220 INFO: Competetive: True
0:23:15.189796 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:18.451185 INFO: Test AUC: 0.565
0:23:18.451334 INFO: Train AUC: 0.573
0:23:18.451363 INFO: AUC difference: 1.48%
0:23:18.687012 INFO: Resetting torch num_threads to 100
0:23:18.693895 INFO: === FDR correction performed with classifier version 8 ===
0:23:18.694659 PROGRESS: ============================= Precursor FDR =============================
0:23:18.694750 PROGRESS: Total precursors accumulated: 755
0:23:18.694811 PROGRESS: Target precursors: 688 (91.13%)
0:23:18.694864 PROGRESS: Decoy precursors: 67 (8.87%)
0:23:18.694909 PROGRESS: 
0:23:18.694953 PROGRESS: Precursor Summary:
0:23:18.695932 PROGRESS: Channel   0:	 0.05 FDR:   496; 0.01 FDR:   357; 0.001 FDR:   100
0:23:18.696018 PROGRESS: 
0:23:18.696071 PROGRESS: Protein Summary:
0:23:18.697227 PROGRESS: Channel   0:	 0.05 FDR:   459; 0.01 FDR:   334; 0.001 FDR:    95
0:23:18.697326 PROGRESS: =========================================================================
0:23:18.824508 INFO: fragments_df: keeping 3918 of 1876327 [sum(precursor_idx_mask)=7914 sum(mass_error_mask)=1876327 stop_rank=3918
0:23:19.078844 INFO: calibration group: precursor, fitting rt estimator 
0:23:19.190770 INFO: calibration group: fragment, fitting mz estimator 
0:23:19.653894 INFO: Using score_cutoff 57.444165692138675 (fac=0.99, q=1)
0:23:19.654450 INFO: calibration group: precursor, predicting mz
0:23:19.654546 WARNING: mz prediction was skipped as it has not been fitted yet
0:23:19.654589 INFO: calibration group: precursor, predicting rt
0:23:19.723734 INFO: calibration group: fragment, predicting mz
0:23:19.903842 INFO: === checking if optimization conditions were reached ===
0:23:19.904675 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
0:23:19.913717 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 16.0958.
0:23:19.913868 INFO: ==============================================
0:23:19.914029 INFO: Starting optimization step 13.
0:23:19.914139 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:23:19.914266 PROGRESS: Extracting batch of 100535 precursors
0:23:20.245292 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:23:20.245433 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:23:20.245480 INFO: FWHM in RT is 2.67 seconds, sigma is 0.34
0:23:20.245504 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:23:20.246150 INFO: Starting candidate selection
0:23:24.665970 INFO: Starting candidate scoring
0:23:25.985650 INFO: Finished candidate processing
0:23:25.985770 INFO: Collecting candidate features
0:23:26.341810 INFO: Collecting fragment features
0:23:26.490355 INFO: Finished candidate scoring
0:23:26.603953 PROGRESS: === Extracted 200708 precursors and 1831329 fragments ===
0:23:26.604440 INFO: performing precursor FDR with 47 features
0:23:26.604483 INFO: Decoy channel: -1
0:23:26.604508 INFO: Competetive: True
0:23:26.674658 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:30.398680 INFO: Test AUC: 0.559
0:23:30.398918 INFO: Train AUC: 0.573
0:23:30.398952 INFO: AUC difference: 2.45%
0:23:30.638787 INFO: Resetting torch num_threads to 100
0:23:30.645338 INFO: === FDR correction performed with classifier version 8 ===
0:23:30.646155 PROGRESS: ============================= Precursor FDR =============================
0:23:30.646254 PROGRESS: Total precursors accumulated: 785
0:23:30.646322 PROGRESS: Target precursors: 712 (90.70%)
0:23:30.646376 PROGRESS: Decoy precursors: 73 (9.30%)
0:23:30.646423 PROGRESS: 
0:23:30.646469 PROGRESS: Precursor Summary:
0:23:30.647498 PROGRESS: Channel   0:	 0.05 FDR:   576; 0.01 FDR:   362; 0.001 FDR:   112
0:23:30.647588 PROGRESS: 
0:23:30.647644 PROGRESS: Protein Summary:
0:23:30.648852 PROGRESS: Channel   0:	 0.05 FDR:   535; 0.01 FDR:   336; 0.001 FDR:   107
0:23:30.648945 PROGRESS: =========================================================================
0:23:30.776144 INFO: fragments_df: keeping 3890 of 1831329 [sum(precursor_idx_mask)=7970 sum(mass_error_mask)=1831329 stop_rank=3890
0:23:31.035388 INFO: calibration group: precursor, fitting rt estimator 
0:23:31.162500 INFO: calibration group: fragment, fitting mz estimator 
0:23:31.674578 INFO: Using score_cutoff 60.00684174385071 (fac=0.99, q=1)
0:23:31.675050 INFO: calibration group: precursor, predicting mz
0:23:31.675140 WARNING: mz prediction was skipped as it has not been fitted yet
0:23:31.675177 INFO: calibration group: precursor, predicting rt
0:23:31.737699 INFO: calibration group: fragment, predicting mz
0:23:31.887827 INFO: === checking if optimization conditions were reached ===
0:23:31.888198 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
0:23:31.891302 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 14.8560.
0:23:31.891375 INFO: ==============================================
0:23:31.891487 INFO: Starting optimization step 14.
0:23:31.891567 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:23:31.891665 PROGRESS: Extracting batch of 100535 precursors
0:23:31.933997 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:23:31.934156 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:23:31.934211 INFO: FWHM in RT is 2.69 seconds, sigma is 0.35
0:23:31.934241 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:23:31.934682 INFO: Starting candidate selection
0:23:36.671365 INFO: Starting candidate scoring
0:23:37.985033 INFO: Finished candidate processing
0:23:37.985153 INFO: Collecting candidate features
0:23:38.347556 INFO: Collecting fragment features
0:23:38.474427 INFO: Finished candidate scoring
0:23:38.588273 PROGRESS: === Extracted 200702 precursors and 1777525 fragments ===
0:23:38.588746 INFO: performing precursor FDR with 47 features
0:23:38.588788 INFO: Decoy channel: -1
0:23:38.588819 INFO: Competetive: True
0:23:38.656781 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:42.335921 INFO: Test AUC: 0.561
0:23:42.336921 INFO: Train AUC: 0.573
0:23:42.336973 INFO: AUC difference: 2.01%
0:23:42.577835 INFO: Resetting torch num_threads to 100
0:23:42.583610 INFO: === FDR correction performed with classifier version 8 ===
0:23:42.584482 PROGRESS: ============================= Precursor FDR =============================
0:23:42.584603 PROGRESS: Total precursors accumulated: 812
0:23:42.584681 PROGRESS: Target precursors: 741 (91.26%)
0:23:42.584751 PROGRESS: Decoy precursors: 71 (8.74%)
0:23:42.584824 PROGRESS: 
0:23:42.584888 PROGRESS: Precursor Summary:
0:23:42.585954 PROGRESS: Channel   0:	 0.05 FDR:   607; 0.01 FDR:   446; 0.001 FDR:    76
0:23:42.586057 PROGRESS: 
0:23:42.586130 PROGRESS: Protein Summary:
0:23:42.587375 PROGRESS: Channel   0:	 0.05 FDR:   563; 0.01 FDR:   413; 0.001 FDR:    73
0:23:42.587490 PROGRESS: =========================================================================
0:23:42.702568 INFO: fragments_df: keeping 4535 of 1777525 [sum(precursor_idx_mask)=9623 sum(mass_error_mask)=1777525 stop_rank=4535
0:23:42.915004 INFO: calibration group: precursor, fitting rt estimator 
0:23:43.046700 INFO: calibration group: fragment, fitting mz estimator 
0:23:43.651128 INFO: Using score_cutoff 53.960191812515255 (fac=0.99, q=1)
0:23:43.651639 INFO: calibration group: precursor, predicting mz
0:23:43.651742 WARNING: mz prediction was skipped as it has not been fitted yet
0:23:43.651787 INFO: calibration group: precursor, predicting rt
0:23:43.683373 INFO: calibration group: fragment, predicting mz
0:23:43.753441 INFO: === checking if optimization conditions were reached ===
0:23:43.753852 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
0:23:43.757087 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 13.0955.
0:23:43.757160 INFO: ==============================================
0:23:43.757278 INFO: Starting optimization step 15.
0:23:43.757363 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:23:43.757473 PROGRESS: Extracting batch of 50096 precursors
0:23:43.775442 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:23:43.775582 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:23:43.775654 INFO: FWHM in RT is 2.61 seconds, sigma is 0.34
0:23:43.775687 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:23:43.776153 INFO: Starting candidate selection
0:23:46.052802 INFO: Starting candidate scoring
0:23:46.655598 INFO: Finished candidate processing
0:23:46.655834 INFO: Collecting candidate features
0:23:46.838064 INFO: Collecting fragment features
0:23:46.900197 INFO: Finished candidate scoring
0:23:46.950368 PROGRESS: === Extracted 100023 precursors and 871520 fragments ===
0:23:46.950777 INFO: performing precursor FDR with 47 features
0:23:46.950817 INFO: Decoy channel: -1
0:23:46.950843 INFO: Competetive: True
0:23:46.988649 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:48.446795 INFO: Test AUC: 0.560
0:23:48.446926 INFO: Train AUC: 0.568
0:23:48.446956 INFO: AUC difference: 1.45%
0:23:48.662600 INFO: Resetting torch num_threads to 100
0:23:48.693515 INFO: === FDR correction performed with classifier version 8 ===
0:23:48.694263 PROGRESS: ============================= Precursor FDR =============================
0:23:48.694355 PROGRESS: Total precursors accumulated: 383
0:23:48.694426 PROGRESS: Target precursors: 349 (91.12%)
0:23:48.694481 PROGRESS: Decoy precursors: 34 (8.88%)
0:23:48.694533 PROGRESS: 
0:23:48.694580 PROGRESS: Precursor Summary:
0:23:48.695548 PROGRESS: Channel   0:	 0.05 FDR:   281; 0.01 FDR:   233; 0.001 FDR:   113
0:23:48.695637 PROGRESS: 
0:23:48.695697 PROGRESS: Protein Summary:
0:23:48.696814 PROGRESS: Channel   0:	 0.05 FDR:   266; 0.01 FDR:   221; 0.001 FDR:   110
0:23:48.696909 PROGRESS: =========================================================================
0:23:48.757829 INFO: fragments_df: keeping 2307 of 871520 [sum(precursor_idx_mask)=5018 sum(mass_error_mask)=871520 stop_rank=2307
0:23:48.942585 INFO: calibration group: precursor, fitting rt estimator 
0:23:49.046583 INFO: calibration group: fragment, fitting mz estimator 
0:23:49.309481 INFO: Using score_cutoff 54.8009768737793 (fac=0.99, q=1)
0:23:49.310084 INFO: calibration group: precursor, predicting mz
0:23:49.310173 WARNING: mz prediction was skipped as it has not been fitted yet
0:23:49.310218 INFO: calibration group: precursor, predicting rt
0:23:49.344868 INFO: calibration group: fragment, predicting mz
0:23:49.445279 INFO: === checking if optimization conditions were reached ===
0:23:49.445703 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
0:23:49.448850 PROGRESS: ❌ ms2_error      : optimization incomplete after 7 search(es). Will search with parameter 11.8633.
0:23:49.448940 INFO: ==============================================
0:23:49.449054 INFO: Starting optimization step 16.
0:23:49.449137 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:23:49.449221 PROGRESS: Extracting batch of 50096 precursors
0:23:49.469238 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:23:49.469373 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:23:49.469421 INFO: FWHM in RT is 2.57 seconds, sigma is 0.33
0:23:49.469451 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:23:49.469806 INFO: Starting candidate selection
0:23:51.596458 INFO: Starting candidate scoring
0:23:52.882450 INFO: Finished candidate processing
0:23:52.882557 INFO: Collecting candidate features
0:23:53.046070 INFO: Collecting fragment features
0:23:53.108604 INFO: Finished candidate scoring
0:23:53.160089 PROGRESS: === Extracted 100015 precursors and 835585 fragments ===
0:23:53.160523 INFO: performing precursor FDR with 47 features
0:23:53.160564 INFO: Decoy channel: -1
0:23:53.160588 INFO: Competetive: True
0:23:53.193779 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:54.707910 INFO: Test AUC: 0.553
0:23:54.708053 INFO: Train AUC: 0.571
0:23:54.708084 INFO: AUC difference: 3.17%
0:23:54.915412 INFO: Resetting torch num_threads to 100
0:23:54.918754 INFO: === FDR correction performed with classifier version 8 ===
0:23:54.919461 PROGRESS: ============================= Precursor FDR =============================
0:23:54.919552 PROGRESS: Total precursors accumulated: 468
0:23:54.919615 PROGRESS: Target precursors: 426 (91.03%)
0:23:54.919666 PROGRESS: Decoy precursors: 42 (8.97%)
0:23:54.919713 PROGRESS: 
0:23:54.919757 PROGRESS: Precursor Summary:
0:23:54.920749 PROGRESS: Channel   0:	 0.05 FDR:   307; 0.01 FDR:   209; 0.001 FDR:    33
0:23:54.920842 PROGRESS: 
0:23:54.920899 PROGRESS: Protein Summary:
0:23:54.921992 PROGRESS: Channel   0:	 0.05 FDR:   292; 0.01 FDR:   200; 0.001 FDR:    33
0:23:54.922082 PROGRESS: =========================================================================
0:23:54.979362 INFO: fragments_df: keeping 2104 of 835585 [sum(precursor_idx_mask)=4435 sum(mass_error_mask)=835585 stop_rank=2104
0:23:55.121759 INFO: calibration group: precursor, fitting rt estimator 
0:23:55.237671 INFO: calibration group: fragment, fitting mz estimator 
0:23:55.511466 INFO: Using score_cutoff 55.06795480957031 (fac=0.99, q=1)
0:23:55.511871 INFO: calibration group: precursor, predicting mz
0:23:55.511958 WARNING: mz prediction was skipped as it has not been fitted yet
0:23:55.511990 INFO: calibration group: precursor, predicting rt
0:23:55.543666 INFO: calibration group: fragment, predicting mz
0:23:55.610715 INFO: === checking if optimization conditions were reached ===
0:23:55.611044 PROGRESS: === Optimization of ms2_error has been performed 8 time(s); minimum number is 2 ===
0:23:55.613598 PROGRESS: ❌ ms2_error      : optimization incomplete after 8 search(es). Will search with parameter 9.3191.
0:23:55.613667 INFO: ==============================================
0:23:55.613771 INFO: Starting optimization step 17.
0:23:55.613851 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:23:55.613920 PROGRESS: Extracting batch of 50096 precursors
0:23:55.630592 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:23:55.630751 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:23:55.630792 INFO: FWHM in RT is 2.42 seconds, sigma is 0.31
0:23:55.630821 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:23:55.631098 INFO: Starting candidate selection
0:23:57.827925 INFO: Starting candidate scoring
0:23:58.433119 INFO: Finished candidate processing
0:23:58.433226 INFO: Collecting candidate features
0:23:58.580079 INFO: Collecting fragment features
0:23:58.632174 INFO: Finished candidate scoring
0:23:58.684177 PROGRESS: === Extracted 100013 precursors and 794539 fragments ===
0:23:58.684597 INFO: performing precursor FDR with 47 features
0:23:58.684637 INFO: Decoy channel: -1
0:23:58.684664 INFO: Competetive: True
0:23:58.713925 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:00.365067 INFO: Test AUC: 0.554
0:24:00.365277 INFO: Train AUC: 0.571
0:24:00.365308 INFO: AUC difference: 2.93%
0:24:00.577118 INFO: Resetting torch num_threads to 100
0:24:00.580249 INFO: === FDR correction performed with classifier version 8 ===
0:24:00.580953 PROGRESS: ============================= Precursor FDR =============================
0:24:00.581048 PROGRESS: Total precursors accumulated: 454
0:24:00.581117 PROGRESS: Target precursors: 412 (90.75%)
0:24:00.581171 PROGRESS: Decoy precursors: 42 (9.25%)
0:24:00.581219 PROGRESS: 
0:24:00.581267 PROGRESS: Precursor Summary:
0:24:00.582224 PROGRESS: Channel   0:	 0.05 FDR:   306; 0.01 FDR:   221; 0.001 FDR:   211
0:24:00.582318 PROGRESS: 
0:24:00.582374 PROGRESS: Protein Summary:
0:24:00.583488 PROGRESS: Channel   0:	 0.05 FDR:   292; 0.01 FDR:   208; 0.001 FDR:   199
0:24:00.583580 PROGRESS: =========================================================================
0:24:00.638713 INFO: fragments_df: keeping 2220 of 794539 [sum(precursor_idx_mask)=4606 sum(mass_error_mask)=794539 stop_rank=2220
0:24:00.796572 INFO: calibration group: precursor, fitting rt estimator 
0:24:00.904742 INFO: calibration group: fragment, fitting mz estimator 
0:24:01.160251 INFO: Using score_cutoff 48.16263441467285 (fac=0.99, q=1)
0:24:01.160788 INFO: calibration group: precursor, predicting mz
0:24:01.160878 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:01.160921 INFO: calibration group: precursor, predicting rt
0:24:01.193474 INFO: calibration group: fragment, predicting mz
0:24:01.273273 INFO: === checking if optimization conditions were reached ===
0:24:01.273580 PROGRESS: === Optimization of ms2_error has been performed 9 time(s); minimum number is 2 ===
0:24:01.276158 PROGRESS: ❌ ms2_error      : optimization incomplete after 9 search(es). Will search with parameter 8.8022.
0:24:01.276214 INFO: ==============================================
0:24:01.276322 INFO: Starting optimization step 18.
0:24:01.276397 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:01.276475 PROGRESS: Extracting batch of 50096 precursors
0:24:01.295289 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:24:01.295408 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:01.295452 INFO: FWHM in RT is 2.39 seconds, sigma is 0.31
0:24:01.295475 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:24:01.295789 INFO: Starting candidate selection
0:24:03.563787 INFO: Starting candidate scoring
0:24:04.227039 INFO: Finished candidate processing
0:24:04.227215 INFO: Collecting candidate features
0:24:04.407375 INFO: Collecting fragment features
0:24:04.475460 INFO: Finished candidate scoring
0:24:04.545437 PROGRESS: === Extracted 99990 precursors and 767724 fragments ===
0:24:04.545870 INFO: performing precursor FDR with 47 features
0:24:04.545914 INFO: Decoy channel: -1
0:24:04.545942 INFO: Competetive: True
0:24:04.595534 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:06.540014 INFO: Test AUC: 0.564
0:24:06.540165 INFO: Train AUC: 0.568
0:24:06.540196 INFO: AUC difference: 0.64%
0:24:06.762103 INFO: Resetting torch num_threads to 100
0:24:06.860020 INFO: === FDR correction performed with classifier version 8 ===
0:24:06.860947 PROGRESS: ============================= Precursor FDR =============================
0:24:06.861056 PROGRESS: Total precursors accumulated: 441
0:24:06.861119 PROGRESS: Target precursors: 401 (90.93%)
0:24:06.861172 PROGRESS: Decoy precursors: 40 (9.07%)
0:24:06.861221 PROGRESS: 
0:24:06.861267 PROGRESS: Precursor Summary:
0:24:06.862259 PROGRESS: Channel   0:	 0.05 FDR:   303; 0.01 FDR:   208; 0.001 FDR:   138
0:24:06.862350 PROGRESS: 
0:24:06.862409 PROGRESS: Protein Summary:
0:24:06.863514 PROGRESS: Channel   0:	 0.05 FDR:   289; 0.01 FDR:   198; 0.001 FDR:   134
0:24:06.863606 PROGRESS: =========================================================================
0:24:06.917458 INFO: fragments_df: keeping 2116 of 767724 [sum(precursor_idx_mask)=4276 sum(mass_error_mask)=767724 stop_rank=2116
0:24:07.132346 INFO: calibration group: precursor, fitting rt estimator 
0:24:07.230230 INFO: calibration group: fragment, fitting mz estimator 
0:24:07.482370 INFO: Using score_cutoff 55.017638206100465 (fac=0.99, q=1)
0:24:07.482934 INFO: calibration group: precursor, predicting mz
0:24:07.483030 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:07.483074 INFO: calibration group: precursor, predicting rt
0:24:07.515528 INFO: calibration group: fragment, predicting mz
0:24:07.603237 INFO: === checking if optimization conditions were reached ===
0:24:07.603554 PROGRESS: === Optimization of ms2_error has been performed 10 time(s); minimum number is 2 ===
0:24:07.606377 PROGRESS: ❌ ms2_error      : optimization incomplete after 10 search(es). Will search with parameter 7.6957.
0:24:07.606437 INFO: ==============================================
0:24:07.606557 INFO: Starting optimization step 19.
0:24:07.606654 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:07.606761 PROGRESS: Extracting batch of 50096 precursors
0:24:07.715094 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:24:07.715232 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:07.715280 INFO: FWHM in RT is 2.36 seconds, sigma is 0.30
0:24:07.715304 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:24:07.715646 INFO: Starting candidate selection
0:24:09.893686 INFO: Starting candidate scoring
0:24:10.540614 INFO: Finished candidate processing
0:24:10.540727 INFO: Collecting candidate features
0:24:10.710035 INFO: Collecting fragment features
0:24:10.770844 INFO: Finished candidate scoring
0:24:10.829071 PROGRESS: === Extracted 99974 precursors and 740001 fragments ===
0:24:10.829556 INFO: performing precursor FDR with 47 features
0:24:10.829595 INFO: Decoy channel: -1
0:24:10.829623 INFO: Competetive: True
0:24:10.866332 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:12.339154 INFO: Test AUC: 0.557
0:24:12.339290 INFO: Train AUC: 0.571
0:24:12.339320 INFO: AUC difference: 2.38%
0:24:12.546634 INFO: Resetting torch num_threads to 100
0:24:12.550101 INFO: === FDR correction performed with classifier version 8 ===
0:24:12.550802 PROGRESS: ============================= Precursor FDR =============================
0:24:12.550893 PROGRESS: Total precursors accumulated: 418
0:24:12.550961 PROGRESS: Target precursors: 385 (92.11%)
0:24:12.551013 PROGRESS: Decoy precursors: 33 (7.89%)
0:24:12.551065 PROGRESS: 
0:24:12.551109 PROGRESS: Precursor Summary:
0:24:12.552089 PROGRESS: Channel   0:	 0.05 FDR:   306; 0.01 FDR:   246; 0.001 FDR:   172
0:24:12.552177 PROGRESS: 
0:24:12.552233 PROGRESS: Protein Summary:
0:24:12.553369 PROGRESS: Channel   0:	 0.05 FDR:   292; 0.01 FDR:   232; 0.001 FDR:   166
0:24:12.553458 PROGRESS: =========================================================================
0:24:12.603718 INFO: fragments_df: keeping 2401 of 740001 [sum(precursor_idx_mask)=4993 sum(mass_error_mask)=740001 stop_rank=2401
0:24:12.746806 INFO: calibration group: precursor, fitting rt estimator 
0:24:12.862836 INFO: calibration group: fragment, fitting mz estimator 
0:24:13.185628 INFO: Using score_cutoff 51.130959703445434 (fac=0.99, q=1)
0:24:13.186066 INFO: calibration group: precursor, predicting mz
0:24:13.186153 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:13.186186 INFO: calibration group: precursor, predicting rt
0:24:13.218058 INFO: calibration group: fragment, predicting mz
0:24:13.286149 INFO: === checking if optimization conditions were reached ===
0:24:13.286430 PROGRESS: === Optimization of ms2_error has been performed 11 time(s); minimum number is 2 ===
0:24:13.288601 PROGRESS: ❌ ms2_error      : optimization incomplete after 11 search(es). Will search with parameter 6.6242.
0:24:13.288660 INFO: ==============================================
0:24:13.288743 WARNING: Optimization did not converge within the maximum number of steps, which is 20.
0:24:13.288836 INFO: Starting optimization step 0.
0:24:13.288923 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:13.288986 PROGRESS: Extracting batch of 50096 precursors
0:24:13.302051 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:24:13.302170 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:13.302206 INFO: FWHM in RT is 2.35 seconds, sigma is 0.30
0:24:13.302231 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:24:13.302482 INFO: Starting candidate selection
0:24:15.586405 INFO: Starting candidate scoring
0:24:16.238954 INFO: Finished candidate processing
0:24:16.239117 INFO: Collecting candidate features
0:24:16.453187 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 99961)
0:24:16.460138 INFO: Collecting fragment features
0:24:16.519480 INFO: Finished candidate scoring
0:24:16.604340 PROGRESS: === Extracted 99961 precursors and 708291 fragments ===
0:24:16.604909 INFO: performing precursor FDR with 47 features
0:24:16.604950 INFO: Decoy channel: -1
0:24:16.604977 INFO: Competetive: True
0:24:16.657440 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:16.675490 WARNING: dropped 1 decoy PSMs due to missing features
0:24:18.232020 INFO: Test AUC: 0.564
0:24:18.232161 INFO: Train AUC: 0.568
0:24:18.232192 INFO: AUC difference: 0.76%
0:24:18.448262 INFO: Resetting torch num_threads to 100
0:24:18.451827 INFO: === FDR correction performed with classifier version 8 ===
0:24:18.452518 PROGRESS: ============================= Precursor FDR =============================
0:24:18.452611 PROGRESS: Total precursors accumulated: 438
0:24:18.452673 PROGRESS: Target precursors: 401 (91.55%)
0:24:18.452726 PROGRESS: Decoy precursors: 37 (8.45%)
0:24:18.452772 PROGRESS: 
0:24:18.452817 PROGRESS: Precursor Summary:
0:24:18.453790 PROGRESS: Channel   0:	 0.05 FDR:   329; 0.01 FDR:   229; 0.001 FDR:   150
0:24:18.453877 PROGRESS: 
0:24:18.453935 PROGRESS: Protein Summary:
0:24:18.455038 PROGRESS: Channel   0:	 0.05 FDR:   313; 0.01 FDR:   219; 0.001 FDR:   146
0:24:18.455127 PROGRESS: =========================================================================
0:24:18.503596 INFO: fragments_df: keeping 2229 of 708291 [sum(precursor_idx_mask)=4547 sum(mass_error_mask)=708291 stop_rank=2229
0:24:18.647505 INFO: calibration group: precursor, fitting rt estimator 
0:24:18.769100 INFO: calibration group: fragment, fitting mz estimator 
0:24:19.027246 INFO: Using score_cutoff 47.81356741790771 (fac=0.99, q=1)
0:24:19.027780 INFO: calibration group: precursor, predicting mz
0:24:19.027878 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:19.027915 INFO: calibration group: precursor, predicting rt
0:24:19.060471 INFO: calibration group: fragment, predicting mz
0:24:19.132798 INFO: === checking if optimization conditions were reached ===
0:24:19.133121 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:24:19.135230 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 295.4187.
0:24:19.135284 INFO: ==============================================
0:24:19.135379 INFO: Starting optimization step 1.
0:24:19.135448 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:19.135525 PROGRESS: Extracting batch of 50096 precursors
0:24:19.151018 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:24:19.151141 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:19.151190 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
0:24:19.151214 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:24:19.151595 INFO: Starting candidate selection
0:24:21.263647 INFO: Starting candidate scoring
0:24:21.904806 INFO: Finished candidate processing
0:24:21.904934 INFO: Collecting candidate features
0:24:22.061671 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 99770)
0:24:22.068478 INFO: Collecting fragment features
0:24:22.131512 INFO: Finished candidate scoring
0:24:22.199210 PROGRESS: === Extracted 99770 precursors and 677451 fragments ===
0:24:22.199603 INFO: performing precursor FDR with 47 features
0:24:22.199655 INFO: Decoy channel: -1
0:24:22.199680 INFO: Competetive: True
0:24:22.239875 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:22.260076 WARNING: dropped 4 decoy PSMs due to missing features
0:24:24.250585 INFO: Test AUC: 0.554
0:24:24.250828 INFO: Train AUC: 0.569
0:24:24.250862 INFO: AUC difference: 2.69%
0:24:24.467294 INFO: Resetting torch num_threads to 100
0:24:24.470765 INFO: === FDR correction performed with classifier version 8 ===
0:24:24.471513 PROGRESS: ============================= Precursor FDR =============================
0:24:24.471629 PROGRESS: Total precursors accumulated: 451
0:24:24.471693 PROGRESS: Target precursors: 411 (91.13%)
0:24:24.471750 PROGRESS: Decoy precursors: 40 (8.87%)
0:24:24.471798 PROGRESS: 
0:24:24.471842 PROGRESS: Precursor Summary:
0:24:24.472843 PROGRESS: Channel   0:	 0.05 FDR:   353; 0.01 FDR:   255; 0.001 FDR:   211
0:24:24.472937 PROGRESS: 
0:24:24.472993 PROGRESS: Protein Summary:
0:24:24.474145 PROGRESS: Channel   0:	 0.05 FDR:   337; 0.01 FDR:   241; 0.001 FDR:   200
0:24:24.474246 PROGRESS: =========================================================================
0:24:24.522358 INFO: fragments_df: keeping 2429 of 677451 [sum(precursor_idx_mask)=5079 sum(mass_error_mask)=677451 stop_rank=2429
0:24:24.701340 INFO: calibration group: precursor, fitting rt estimator 
0:24:24.817292 INFO: calibration group: fragment, fitting mz estimator 
0:24:25.143187 INFO: Using score_cutoff 48.988042307281496 (fac=0.99, q=1)
0:24:25.143655 INFO: calibration group: precursor, predicting mz
0:24:25.143742 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:25.143782 INFO: calibration group: precursor, predicting rt
0:24:25.175444 INFO: calibration group: fragment, predicting mz
0:24:25.251467 INFO: === checking if optimization conditions were reached ===
0:24:25.251841 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:24:25.254201 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 204.6006.
0:24:25.254271 INFO: ==============================================
0:24:25.254378 INFO: Starting optimization step 2.
0:24:25.254471 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:25.254558 PROGRESS: Extracting batch of 50096 precursors
0:24:25.274250 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:24:25.274388 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:25.274440 INFO: FWHM in RT is 2.24 seconds, sigma is 0.29
0:24:25.274469 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:24:25.274833 INFO: Starting candidate selection
0:24:27.378844 INFO: Starting candidate scoring
0:24:27.973983 INFO: Finished candidate processing
0:24:27.974095 INFO: Collecting candidate features
0:24:28.125715 WARNING: intensity_correlation has 6 NaNs ( 0.01 % out of 99487)
0:24:28.132332 INFO: Collecting fragment features
0:24:28.182605 INFO: Finished candidate scoring
0:24:28.236929 PROGRESS: === Extracted 99487 precursors and 645418 fragments ===
0:24:28.237352 INFO: performing precursor FDR with 47 features
0:24:28.237391 INFO: Decoy channel: -1
0:24:28.237416 INFO: Competetive: True
0:24:28.269047 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:28.288457 WARNING: dropped 2 target PSMs due to missing features
0:24:28.288600 WARNING: dropped 4 decoy PSMs due to missing features
0:24:29.881227 INFO: Test AUC: 0.556
0:24:29.881369 INFO: Train AUC: 0.564
0:24:29.881399 INFO: AUC difference: 1.30%
0:24:30.095528 INFO: Resetting torch num_threads to 100
0:24:30.098762 INFO: === FDR correction performed with classifier version 8 ===
0:24:30.099419 PROGRESS: ============================= Precursor FDR =============================
0:24:30.099508 PROGRESS: Total precursors accumulated: 418
0:24:30.099567 PROGRESS: Target precursors: 384 (91.87%)
0:24:30.099617 PROGRESS: Decoy precursors: 34 (8.13%)
0:24:30.099663 PROGRESS: 
0:24:30.099708 PROGRESS: Precursor Summary:
0:24:30.100690 PROGRESS: Channel   0:	 0.05 FDR:   323; 0.01 FDR:   242; 0.001 FDR:   217
0:24:30.100780 PROGRESS: 
0:24:30.100834 PROGRESS: Protein Summary:
0:24:30.101948 PROGRESS: Channel   0:	 0.05 FDR:   308; 0.01 FDR:   230; 0.001 FDR:   208
0:24:30.102049 PROGRESS: =========================================================================
0:24:30.145954 INFO: fragments_df: keeping 2325 of 645418 [sum(precursor_idx_mask)=4759 sum(mass_error_mask)=645418 stop_rank=2325
0:24:30.287227 INFO: calibration group: precursor, fitting rt estimator 
0:24:30.409310 INFO: calibration group: fragment, fitting mz estimator 
0:24:30.722837 INFO: Using score_cutoff 46.54102775344849 (fac=0.99, q=1)
0:24:30.723234 INFO: calibration group: precursor, predicting mz
0:24:30.723319 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:30.723350 INFO: calibration group: precursor, predicting rt
0:24:30.755284 INFO: calibration group: fragment, predicting mz
0:24:30.819654 INFO: === checking if optimization conditions were reached ===
0:24:30.819949 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:24:30.822314 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 125.7405.
0:24:30.822380 INFO: ==============================================
0:24:30.822481 INFO: Starting optimization step 3.
0:24:30.822554 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:30.822622 PROGRESS: Extracting batch of 50096 precursors
0:24:30.841305 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:24:30.841451 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:30.841491 INFO: FWHM in RT is 2.26 seconds, sigma is 0.29
0:24:30.841518 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:24:30.841786 INFO: Starting candidate selection
0:24:32.989007 INFO: Starting candidate scoring
0:24:33.591639 INFO: Finished candidate processing
0:24:33.591811 INFO: Collecting candidate features
0:24:33.766419 WARNING: intensity_correlation has 11 NaNs ( 0.01 % out of 98466)
0:24:33.773038 INFO: Collecting fragment features
0:24:33.826778 INFO: Finished candidate scoring
0:24:33.886722 PROGRESS: === Extracted 98466 precursors and 590870 fragments ===
0:24:33.887203 INFO: performing precursor FDR with 47 features
0:24:33.887242 INFO: Decoy channel: -1
0:24:33.887268 INFO: Competetive: True
0:24:33.924057 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:33.943819 WARNING: dropped 6 target PSMs due to missing features
0:24:33.943969 WARNING: dropped 5 decoy PSMs due to missing features
0:24:35.518445 INFO: Test AUC: 0.551
0:24:35.518602 INFO: Train AUC: 0.561
0:24:35.518633 INFO: AUC difference: 1.77%
0:24:35.732262 INFO: Resetting torch num_threads to 100
0:24:35.735300 INFO: === FDR correction performed with classifier version 8 ===
0:24:35.735983 PROGRESS: ============================= Precursor FDR =============================
0:24:35.736079 PROGRESS: Total precursors accumulated: 483
0:24:35.736141 PROGRESS: Target precursors: 441 (91.30%)
0:24:35.736194 PROGRESS: Decoy precursors: 42 (8.70%)
0:24:35.736248 PROGRESS: 
0:24:35.736294 PROGRESS: Precursor Summary:
0:24:35.737274 PROGRESS: Channel   0:	 0.05 FDR:   344; 0.01 FDR:   226; 0.001 FDR:   215
0:24:35.737363 PROGRESS: 
0:24:35.737418 PROGRESS: Protein Summary:
0:24:35.738539 PROGRESS: Channel   0:	 0.05 FDR:   328; 0.01 FDR:   218; 0.001 FDR:   208
0:24:35.738627 PROGRESS: =========================================================================
0:24:35.778703 INFO: fragments_df: keeping 2178 of 590870 [sum(precursor_idx_mask)=4491 sum(mass_error_mask)=590870 stop_rank=2178
0:24:35.916977 INFO: calibration group: precursor, fitting rt estimator 
0:24:36.034732 INFO: calibration group: fragment, fitting mz estimator 
0:24:36.327155 INFO: Using score_cutoff 50.71274188041687 (fac=0.99, q=1)
0:24:36.327637 INFO: calibration group: precursor, predicting mz
0:24:36.327732 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:36.327773 INFO: calibration group: precursor, predicting rt
0:24:36.359903 INFO: calibration group: fragment, predicting mz
0:24:36.439616 INFO: === checking if optimization conditions were reached ===
0:24:36.439987 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:24:36.442586 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 97.6395.
0:24:36.442655 INFO: ==============================================
0:24:36.442775 INFO: Starting optimization step 4.
0:24:36.442871 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:36.442973 PROGRESS: Extracting batch of 50096 precursors
0:24:36.461689 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:24:36.461834 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:36.461903 INFO: FWHM in RT is 2.35 seconds, sigma is 0.30
0:24:36.461932 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:24:36.462392 INFO: Starting candidate selection
0:24:38.391640 INFO: Starting candidate scoring
0:24:38.964536 INFO: Finished candidate processing
0:24:38.964654 INFO: Collecting candidate features
0:24:39.102972 WARNING: intensity_correlation has 20 NaNs ( 0.02 % out of 97834)
0:24:39.109415 INFO: Collecting fragment features
0:24:39.158641 INFO: Finished candidate scoring
0:24:39.214472 PROGRESS: === Extracted 97834 precursors and 566727 fragments ===
0:24:39.214891 INFO: performing precursor FDR with 47 features
0:24:39.214929 INFO: Decoy channel: -1
0:24:39.214954 INFO: Competetive: True
0:24:39.243714 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:39.261948 WARNING: dropped 11 target PSMs due to missing features
0:24:39.262097 WARNING: dropped 9 decoy PSMs due to missing features
0:24:40.851789 INFO: Test AUC: 0.548
0:24:40.851995 INFO: Train AUC: 0.561
0:24:40.852027 INFO: AUC difference: 2.34%
0:24:41.067212 INFO: Resetting torch num_threads to 100
0:24:41.070290 INFO: === FDR correction performed with classifier version 8 ===
0:24:41.071029 PROGRESS: ============================= Precursor FDR =============================
0:24:41.071124 PROGRESS: Total precursors accumulated: 548
0:24:41.071185 PROGRESS: Target precursors: 502 (91.61%)
0:24:41.071239 PROGRESS: Decoy precursors: 46 (8.39%)
0:24:41.071286 PROGRESS: 
0:24:41.071330 PROGRESS: Precursor Summary:
0:24:41.072332 PROGRESS: Channel   0:	 0.05 FDR:   377; 0.01 FDR:   262; 0.001 FDR:   221
0:24:41.072425 PROGRESS: 
0:24:41.072483 PROGRESS: Protein Summary:
0:24:41.073620 PROGRESS: Channel   0:	 0.05 FDR:   358; 0.01 FDR:   249; 0.001 FDR:   211
0:24:41.073712 PROGRESS: =========================================================================
0:24:41.114259 INFO: fragments_df: keeping 2374 of 566727 [sum(precursor_idx_mask)=5171 sum(mass_error_mask)=566727 stop_rank=2374
0:24:41.274739 INFO: calibration group: precursor, fitting rt estimator 
0:24:41.386629 INFO: calibration group: fragment, fitting mz estimator 
0:24:42.739915 INFO: Using score_cutoff 49.50845690460205 (fac=0.99, q=1)
0:24:42.740341 INFO: calibration group: precursor, predicting mz
0:24:42.740437 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:42.740472 INFO: calibration group: precursor, predicting rt
0:24:42.772825 INFO: calibration group: fragment, predicting mz
0:24:42.838616 INFO: === checking if optimization conditions were reached ===
0:24:42.838936 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:24:42.841374 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 79.7781.
0:24:42.841441 INFO: ==============================================
0:24:42.841547 INFO: Starting optimization step 5.
0:24:42.841623 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:42.841692 PROGRESS: Extracting batch of 50096 precursors
0:24:42.859110 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:24:42.859256 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:42.859298 INFO: FWHM in RT is 2.31 seconds, sigma is 0.30
0:24:42.860035 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:24:42.860371 INFO: Starting candidate selection
0:24:44.542164 INFO: Starting candidate scoring
0:24:45.122343 INFO: Finished candidate processing
0:24:45.122465 INFO: Collecting candidate features
0:24:45.271240 WARNING: intensity_correlation has 22 NaNs ( 0.02 % out of 97658)
0:24:45.277734 INFO: Collecting fragment features
0:24:45.329903 INFO: Finished candidate scoring
0:24:45.380835 PROGRESS: === Extracted 97658 precursors and 561549 fragments ===
0:24:45.381237 INFO: performing precursor FDR with 47 features
0:24:45.381276 INFO: Decoy channel: -1
0:24:45.381300 INFO: Competetive: True
0:24:45.410382 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:45.428284 WARNING: dropped 9 target PSMs due to missing features
0:24:45.428438 WARNING: dropped 13 decoy PSMs due to missing features
0:24:46.889549 INFO: Test AUC: 0.552
0:24:46.889698 INFO: Train AUC: 0.561
0:24:46.889727 INFO: AUC difference: 1.68%
0:24:47.098677 INFO: Resetting torch num_threads to 100
0:24:47.101611 INFO: === FDR correction performed with classifier version 8 ===
0:24:47.102273 PROGRESS: ============================= Precursor FDR =============================
0:24:47.102878 PROGRESS: Total precursors accumulated: 500
0:24:47.102956 PROGRESS: Target precursors: 458 (91.60%)
0:24:47.103010 PROGRESS: Decoy precursors: 42 (8.40%)
0:24:47.103058 PROGRESS: 
0:24:47.103103 PROGRESS: Precursor Summary:
0:24:47.104063 PROGRESS: Channel   0:	 0.05 FDR:   354; 0.01 FDR:   239; 0.001 FDR:   166
0:24:47.104152 PROGRESS: 
0:24:47.104206 PROGRESS: Protein Summary:
0:24:47.105303 PROGRESS: Channel   0:	 0.05 FDR:   336; 0.01 FDR:   227; 0.001 FDR:   161
0:24:47.105393 PROGRESS: =========================================================================
0:24:47.143277 INFO: fragments_df: keeping 2207 of 561549 [sum(precursor_idx_mask)=4733 sum(mass_error_mask)=561549 stop_rank=2207
0:24:47.281070 INFO: calibration group: precursor, fitting rt estimator 
0:24:47.403490 INFO: calibration group: fragment, fitting mz estimator 
0:24:47.698329 INFO: Using score_cutoff 52.373931735992436 (fac=0.99, q=1)
0:24:47.698738 INFO: calibration group: precursor, predicting mz
0:24:47.698823 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:47.698855 INFO: calibration group: precursor, predicting rt
0:24:47.730988 INFO: calibration group: fragment, predicting mz
0:24:47.796965 INFO: === checking if optimization conditions were reached ===
0:24:47.797294 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:24:47.799629 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 77.7107.
0:24:47.799692 INFO: ==============================================
0:24:47.799794 INFO: Starting optimization step 6.
0:24:47.799892 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:47.799966 PROGRESS: Extracting batch of 50096 precursors
0:24:47.816861 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:24:47.817013 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:47.817054 INFO: FWHM in RT is 2.32 seconds, sigma is 0.30
0:24:47.817083 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:24:47.817346 INFO: Starting candidate selection
0:24:49.311055 INFO: Starting candidate scoring
0:24:49.877832 INFO: Finished candidate processing
0:24:49.878134 INFO: Collecting candidate features
0:24:50.035306 WARNING: intensity_correlation has 27 NaNs ( 0.03 % out of 97268)
0:24:50.041785 INFO: Collecting fragment features
0:24:50.086217 INFO: Finished candidate scoring
0:24:50.137421 PROGRESS: === Extracted 97268 precursors and 552224 fragments ===
0:24:50.137833 INFO: performing precursor FDR with 47 features
0:24:50.137873 INFO: Decoy channel: -1
0:24:50.137897 INFO: Competetive: True
0:24:50.166244 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:50.184508 WARNING: dropped 11 target PSMs due to missing features
0:24:50.184681 WARNING: dropped 16 decoy PSMs due to missing features
0:24:51.728901 INFO: Test AUC: 0.549
0:24:51.729073 INFO: Train AUC: 0.561
0:24:51.729104 INFO: AUC difference: 2.14%
0:24:51.951582 INFO: Resetting torch num_threads to 100
0:24:51.956753 INFO: === FDR correction performed with classifier version 8 ===
0:24:51.957640 PROGRESS: ============================= Precursor FDR =============================
0:24:51.957735 PROGRESS: Total precursors accumulated: 498
0:24:51.957799 PROGRESS: Target precursors: 458 (91.97%)
0:24:51.957851 PROGRESS: Decoy precursors: 40 (8.03%)
0:24:51.957897 PROGRESS: 
0:24:51.957941 PROGRESS: Precursor Summary:
0:24:51.958966 PROGRESS: Channel   0:	 0.05 FDR:   370; 0.01 FDR:   260; 0.001 FDR:   173
0:24:51.959053 PROGRESS: 
0:24:51.959107 PROGRESS: Protein Summary:
0:24:51.960255 PROGRESS: Channel   0:	 0.05 FDR:   353; 0.01 FDR:   248; 0.001 FDR:   167
0:24:51.960351 PROGRESS: =========================================================================
0:24:51.999155 INFO: fragments_df: keeping 2342 of 552224 [sum(precursor_idx_mask)=5073 sum(mass_error_mask)=552224 stop_rank=2342
0:24:52.158851 INFO: calibration group: precursor, fitting rt estimator 
0:24:52.277765 INFO: calibration group: fragment, fitting mz estimator 
0:24:52.592325 INFO: Using score_cutoff 49.71626902427673 (fac=0.99, q=1)
0:24:52.592798 INFO: calibration group: precursor, predicting mz
0:24:52.592888 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:52.592922 INFO: calibration group: precursor, predicting rt
0:24:52.625258 INFO: calibration group: fragment, predicting mz
0:24:52.694778 INFO: === checking if optimization conditions were reached ===
0:24:52.695113 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:24:52.696796 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 77.7107 found after 7 searches.
0:24:52.696854 INFO: ==============================================
0:24:52.696965 PROGRESS: Optimization finished for rt_error.
0:24:52.844124 INFO: calibration group: precursor, predicting mz
0:24:52.844427 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:52.844463 INFO: calibration group: precursor, predicting rt
0:24:52.876889 INFO: calibration group: fragment, predicting mz
0:24:52.977180 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:24:52.977409 PROGRESS: ==============================================
0:24:52.977503 PROGRESS: ms2_error      : 6.6242
0:24:52.977573 PROGRESS: rt_error       : 77.7107
0:24:52.977636 PROGRESS: ==============================================
0:24:52.978797 INFO: calibration group: precursor, predicting mz
0:24:52.978923 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:52.978961 INFO: calibration group: precursor, predicting rt
0:25:01.289541 INFO: calibration group: fragment, predicting mz
0:25:19.009444 PROGRESS: Extracting batch of 12567710 precursors
0:25:21.660547 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:25:21.660704 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:25:21.660747 INFO: FWHM in RT is 2.28 seconds, sigma is 0.29
0:25:21.660773 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:25:21.661183 INFO: Starting candidate selection
0:31:14.060085 INFO: Applying score cutoff of 49.71626902427673
0:31:14.173105 INFO: Removed 23233926 precursors with score below cutoff
0:31:16.862293 INFO: Starting candidate scoring
0:31:29.918819 INFO: Finished candidate processing
0:31:29.919053 INFO: Collecting candidate features
0:31:35.227057 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 1840426)
0:31:35.286119 INFO: Collecting fragment features
0:31:36.988408 INFO: Finished candidate scoring
0:31:38.876114 INFO: === FDR correction performed with classifier version 26 ===
0:31:38.877070 INFO: performing precursor FDR with 47 features
0:31:38.877109 INFO: Decoy channel: -1
0:31:38.877135 INFO: Competetive: True
0:31:39.418663 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:39.711973 WARNING: dropped 1 decoy PSMs due to missing features
0:32:10.442069 INFO: Test AUC: 0.632
0:32:10.442322 INFO: Train AUC: 0.635
0:32:10.442357 INFO: AUC difference: 0.52%
0:32:11.110663 INFO: Resetting torch num_threads to 100
0:32:11.175613 INFO: Removing fragments below FDR threshold
0:32:11.378577 PROGRESS: ============================= Precursor FDR =============================
0:32:11.378910 PROGRESS: Total precursors accumulated: 76,300
0:32:11.378976 PROGRESS: Target precursors: 75,545 (99.01%)
0:32:11.379030 PROGRESS: Decoy precursors: 755 (0.99%)
0:32:11.379076 PROGRESS: 
0:32:11.379125 PROGRESS: Precursor Summary:
0:32:11.410127 PROGRESS: Channel   0:	 0.05 FDR: 75,545; 0.01 FDR: 75,545; 0.001 FDR: 52,934
0:32:11.410417 PROGRESS: 
0:32:11.410482 PROGRESS: Protein Summary:
0:32:11.452772 PROGRESS: Channel   0:	 0.05 FDR: 11,730; 0.01 FDR: 11,730; 0.001 FDR: 9,034
0:32:11.453073 PROGRESS: =========================================================================
0:32:12.053744 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:32:12.515152 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:32:12.515347 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant
0:32:12.515434 INFO: Creating folder run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/figures
0:32:12.516222 INFO: Initializing RawFileManager
0:32:22.427463 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:32:22.431568 INFO: Determining DIA cycle
0:32:22.447111 INFO: Found cycle with start 0.00 min and length 300.
0:32:22.610149 INFO: RT (min)            : 0.0 - 26.9
0:32:22.610244 INFO: RT duration (sec)   : 1611.2
0:32:22.610274 INFO: RT duration (min)   : 26.9
0:32:22.610306 INFO: Cycle len (scans)   : 300
0:32:22.610327 INFO: Cycle len (sec)     : 1.65
0:32:22.610348 INFO: Number of cycles    : 978
0:32:22.610367 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:32:24.108404 INFO: Initializing CalibrationManager
0:32:24.108730 INFO: Loading calibration config
0:32:24.109925 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'}]
0:32:24.110030 INFO: Calibration group :fragment, found 1 estimator(s)
0:32:24.110126 INFO: Calibration group :precursor, found 3 estimator(s)
0:32:24.110210 INFO: Disabling ion mobility calibration
0:32:24.110240 INFO: removed mobility estimator from group precursor
0:32:24.110390 INFO: Initializing OptimizationManager
0:32:24.110503 INFO: initial parameter: ms1_error = 30
0:32:24.110570 INFO: initial parameter: ms2_error = 30
0:32:24.110622 INFO: initial parameter: rt_error = 805.6019897460938
0:32:24.110671 INFO: initial parameter: mobility_error = 0.1
0:32:24.110720 INFO: initial parameter: column_type = library
0:32:24.110776 INFO: initial parameter: num_candidates = 1
0:32:24.110820 INFO: initial parameter: classifier_version = -1
0:32:24.110862 INFO: initial parameter: fwhm_rt = 5
0:32:24.110908 INFO: initial parameter: fwhm_mobility = 0.01
0:32:24.110950 INFO: initial parameter: score_cutoff = 0
0:32:24.111017 INFO: Initializing TimingManager
0:32:24.111077 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:32:24.111202 INFO: FDRManager not loaded from disk.
0:32:24.111227 INFO: Initializing FDRManager
0:32:24.111266 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:32:25.628110 PROGRESS: 6,373,245 target precursors potentially observable (7,405 removed)
0:32:27.757286 PROGRESS: Starting initial search for precursors.
0:32:28.011464 INFO: Starting optimization step 0.
0:32:28.011715 PROGRESS: === Extracting elution groups 0 to 200 ===
0:32:28.011792 PROGRESS: Extracting batch of 396 precursors
0:32:28.012762 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:32:28.012812 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:32:28.012851 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:32:28.012873 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:32:28.013163 INFO: Starting candidate selection
0:32:28.177790 INFO: Starting candidate scoring
0:32:28.215744 INFO: Finished candidate processing
0:32:28.215818 INFO: Collecting candidate features
0:32:28.224313 INFO: Collecting fragment features
0:32:28.226355 INFO: Finished candidate scoring
0:32:28.227155 PROGRESS: === Extracted 394 precursors and 4021 fragments ===
0:32:28.227426 INFO: performing precursor FDR with 47 features
0:32:28.227462 INFO: Decoy channel: -1
0:32:28.227485 INFO: Competetive: True
0:32:28.228482 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:28.249660 INFO: Test AUC: 0.448
0:32:28.249732 INFO: Train AUC: 0.522
0:32:28.249761 INFO: AUC difference: 14.13%
0:32:28.249782 WARNING: AUC difference > 5%. This may indicate overfitting.
0:32:28.424646 INFO: Resetting torch num_threads to 100
0:32:28.425208 INFO: === FDR correction performed with classifier version -1 ===
0:32:28.425835 PROGRESS: ============================= Precursor FDR =============================
0:32:28.425925 PROGRESS: Total precursors accumulated: 199
0:32:28.425984 PROGRESS: Target precursors: 101 (50.75%)
0:32:28.426036 PROGRESS: Decoy precursors: 98 (49.25%)
0:32:28.426081 PROGRESS: 
0:32:28.426124 PROGRESS: Precursor Summary:
0:32:28.426970 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:32:28.427059 PROGRESS: 
0:32:28.427114 PROGRESS: Protein Summary:
0:32:28.428032 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:32:28.428120 PROGRESS: =========================================================================
0:32:28.495259 INFO: Starting optimization step 1.
0:32:28.495484 PROGRESS: === Extracting elution groups 200 to 600 ===
0:32:28.495553 PROGRESS: Extracting batch of 786 precursors
0:32:28.496371 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:32:28.496419 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:32:28.496457 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:32:28.496479 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:32:28.496656 INFO: Starting candidate selection
0:32:28.634061 INFO: Starting candidate scoring
0:32:28.676749 INFO: Finished candidate processing
0:32:28.676830 INFO: Collecting candidate features
0:32:28.685687 INFO: Collecting fragment features
0:32:28.687944 INFO: Finished candidate scoring
0:32:28.689979 PROGRESS: === Extracted 1180 precursors and 12006 fragments ===
0:32:28.690723 INFO: performing precursor FDR with 47 features
0:32:28.690766 INFO: Decoy channel: -1
0:32:28.690790 INFO: Competetive: True
0:32:28.693595 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:28.726162 INFO: Test AUC: 0.536
0:32:28.726237 INFO: Train AUC: 0.505
0:32:28.726267 INFO: AUC difference: 6.28%
0:32:28.726305 WARNING: AUC difference > 5%. This may indicate overfitting.
0:32:28.893682 INFO: Resetting torch num_threads to 100
0:32:28.894323 INFO: === FDR correction performed with classifier version -1 ===
0:32:28.894983 PROGRESS: ============================= Precursor FDR =============================
0:32:28.895076 PROGRESS: Total precursors accumulated: 599
0:32:28.895137 PROGRESS: Target precursors: 319 (53.26%)
0:32:28.895195 PROGRESS: Decoy precursors: 280 (46.74%)
0:32:28.895242 PROGRESS: 
0:32:28.895288 PROGRESS: Precursor Summary:
0:32:28.896141 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:32:28.896254 PROGRESS: 
0:32:28.896314 PROGRESS: Protein Summary:
0:32:28.897235 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:32:28.897323 PROGRESS: =========================================================================
0:32:28.966931 INFO: Starting optimization step 2.
0:32:28.967176 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:32:28.967245 PROGRESS: Extracting batch of 1573 precursors
0:32:28.968161 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:32:28.968207 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:32:28.968252 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:32:28.968275 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:32:28.968451 INFO: Starting candidate selection
0:32:29.140040 INFO: Starting candidate scoring
0:32:29.178419 INFO: Finished candidate processing
0:32:29.178499 INFO: Collecting candidate features
0:32:29.188639 INFO: Collecting fragment features
0:32:29.191955 INFO: Finished candidate scoring
0:32:29.194750 PROGRESS: === Extracted 2747 precursors and 27960 fragments ===
0:32:29.195701 INFO: performing precursor FDR with 47 features
0:32:29.195744 INFO: Decoy channel: -1
0:32:29.195767 INFO: Competetive: True
0:32:29.198992 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:29.239327 INFO: Test AUC: 0.517
0:32:29.239414 INFO: Train AUC: 0.519
0:32:29.239445 INFO: AUC difference: 0.38%
0:32:29.414566 INFO: Resetting torch num_threads to 100
0:32:29.415339 INFO: === FDR correction performed with classifier version -1 ===
0:32:29.416087 PROGRESS: ============================= Precursor FDR =============================
0:32:29.416180 PROGRESS: Total precursors accumulated: 1,396
0:32:29.416253 PROGRESS: Target precursors: 751 (53.80%)
0:32:29.416308 PROGRESS: Decoy precursors: 645 (46.20%)
0:32:29.416355 PROGRESS: 
0:32:29.416400 PROGRESS: Precursor Summary:
0:32:29.417269 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:32:29.417360 PROGRESS: 
0:32:29.417419 PROGRESS: Protein Summary:
0:32:29.418371 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:32:29.418461 PROGRESS: =========================================================================
0:32:29.490378 INFO: Starting optimization step 3.
0:32:29.490622 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:32:29.490692 PROGRESS: Extracting batch of 3149 precursors
0:32:29.491807 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:32:29.491862 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:32:29.491895 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:32:29.491918 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:32:29.492093 INFO: Starting candidate selection
0:32:29.709136 INFO: Starting candidate scoring
0:32:29.749868 INFO: Finished candidate processing
0:32:29.749965 INFO: Collecting candidate features
0:32:29.763005 INFO: Collecting fragment features
0:32:29.767032 INFO: Finished candidate scoring
0:32:29.771686 PROGRESS: === Extracted 5891 precursors and 60269 fragments ===
0:32:29.772951 INFO: performing precursor FDR with 47 features
0:32:29.772998 INFO: Decoy channel: -1
0:32:29.773023 INFO: Competetive: True
0:32:29.777006 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:29.831023 INFO: Test AUC: 0.520
0:32:29.831131 INFO: Train AUC: 0.514
0:32:29.831181 INFO: AUC difference: 1.06%
0:32:30.013276 INFO: Resetting torch num_threads to 100
0:32:30.014237 INFO: === FDR correction performed with classifier version -1 ===
0:32:30.015173 PROGRESS: ============================= Precursor FDR =============================
0:32:30.015272 PROGRESS: Total precursors accumulated: 2,994
0:32:30.015334 PROGRESS: Target precursors: 1,610 (53.77%)
0:32:30.015388 PROGRESS: Decoy precursors: 1,384 (46.23%)
0:32:30.015435 PROGRESS: 
0:32:30.015480 PROGRESS: Precursor Summary:
0:32:30.016386 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:32:30.016478 PROGRESS: 
0:32:30.016534 PROGRESS: Protein Summary:
0:32:30.017479 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:32:30.017566 PROGRESS: =========================================================================
0:32:30.093435 INFO: Starting optimization step 4.
0:32:30.093706 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:32:30.093780 PROGRESS: Extracting batch of 6319 precursors
0:32:30.095292 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:32:30.095341 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:32:30.095373 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:32:30.095393 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:32:30.095575 INFO: Starting candidate selection
0:32:30.534882 INFO: Starting candidate scoring
0:32:30.584000 INFO: Finished candidate processing
0:32:30.584101 INFO: Collecting candidate features
0:32:30.603216 INFO: Collecting fragment features
0:32:30.608982 INFO: Finished candidate scoring
0:32:30.617776 PROGRESS: === Extracted 12200 precursors and 124775 fragments ===
0:32:30.619637 INFO: performing precursor FDR with 47 features
0:32:30.619694 INFO: Decoy channel: -1
0:32:30.619719 INFO: Competetive: True
0:32:30.625575 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:30.709524 INFO: Test AUC: 0.525
0:32:30.709649 INFO: Train AUC: 0.515
0:32:30.709679 INFO: AUC difference: 1.86%
0:32:30.884611 INFO: Resetting torch num_threads to 100
0:32:30.885867 INFO: === FDR correction performed with classifier version -1 ===
0:32:30.887194 PROGRESS: ============================= Precursor FDR =============================
0:32:30.887292 PROGRESS: Total precursors accumulated: 6,188
0:32:30.887358 PROGRESS: Target precursors: 3,315 (53.57%)
0:32:30.887412 PROGRESS: Decoy precursors: 2,873 (46.43%)
0:32:30.887461 PROGRESS: 
0:32:30.887505 PROGRESS: Precursor Summary:
0:32:30.888436 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:32:30.888534 PROGRESS: 
0:32:30.888589 PROGRESS: Protein Summary:
0:32:30.889552 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:32:30.889642 PROGRESS: =========================================================================
0:32:30.973271 INFO: Starting optimization step 5.
0:32:30.973546 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:32:30.973616 PROGRESS: Extracting batch of 12617 precursors
0:32:30.976033 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:32:30.976084 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:32:30.976119 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:32:30.976141 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:32:30.976413 INFO: Starting candidate selection
0:32:31.793481 INFO: Starting candidate scoring
0:32:31.880153 INFO: Finished candidate processing
0:32:31.880278 INFO: Collecting candidate features
0:32:31.908421 INFO: Collecting fragment features
0:32:31.918606 INFO: Finished candidate scoring
0:32:31.930960 PROGRESS: === Extracted 24794 precursors and 253718 fragments ===
0:32:31.934275 INFO: performing precursor FDR with 47 features
0:32:31.934330 INFO: Decoy channel: -1
0:32:31.934358 INFO: Competetive: True
0:32:31.944156 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:32.268293 INFO: Test AUC: 0.499
0:32:32.268428 INFO: Train AUC: 0.501
0:32:32.268460 INFO: AUC difference: 0.36%
0:32:32.441949 INFO: Resetting torch num_threads to 100
0:32:32.443707 INFO: === FDR correction performed with classifier version -1 ===
0:32:32.445759 PROGRESS: ============================= Precursor FDR =============================
0:32:32.445868 PROGRESS: Total precursors accumulated: 12,577
0:32:32.445928 PROGRESS: Target precursors: 6,492 (51.62%)
0:32:32.445979 PROGRESS: Decoy precursors: 6,085 (48.38%)
0:32:32.446027 PROGRESS: 
0:32:32.446072 PROGRESS: Precursor Summary:
0:32:32.447007 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:32:32.447096 PROGRESS: 
0:32:32.447151 PROGRESS: Protein Summary:
0:32:32.448125 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:32:32.448219 PROGRESS: =========================================================================
0:32:32.547236 INFO: Starting optimization step 6.
0:32:32.547534 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:32:32.547604 PROGRESS: Extracting batch of 25256 precursors
0:32:32.553053 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:32:32.553126 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:32:32.553159 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:32:32.553181 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:32:32.553376 INFO: Starting candidate selection
0:32:34.125595 INFO: Starting candidate scoring
0:32:34.285493 INFO: Finished candidate processing
0:32:34.285608 INFO: Collecting candidate features
0:32:34.332977 INFO: Collecting fragment features
0:32:34.349460 INFO: Finished candidate scoring
0:32:34.371072 PROGRESS: === Extracted 50013 precursors and 510883 fragments ===
0:32:34.377187 INFO: performing precursor FDR with 47 features
0:32:34.377274 INFO: Decoy channel: -1
0:32:34.377300 INFO: Competetive: True
0:32:34.397481 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:35.058591 INFO: Test AUC: 0.531
0:32:35.058737 INFO: Train AUC: 0.535
0:32:35.058769 INFO: AUC difference: 0.76%
0:32:35.239445 INFO: Resetting torch num_threads to 100
0:32:35.242120 INFO: === FDR correction performed with classifier version -1 ===
0:32:35.242769 PROGRESS: ============================= Precursor FDR =============================
0:32:35.242862 PROGRESS: Total precursors accumulated: 108
0:32:35.242923 PROGRESS: Target precursors: 99 (91.67%)
0:32:35.242974 PROGRESS: Decoy precursors: 9 (8.33%)
0:32:35.243022 PROGRESS: 
0:32:35.243067 PROGRESS: Precursor Summary:
0:32:35.243906 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:32:35.243994 PROGRESS: 
0:32:35.244049 PROGRESS: Protein Summary:
0:32:35.244972 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:32:35.245062 PROGRESS: =========================================================================
0:32:35.377523 INFO: Starting optimization step 7.
0:32:35.377829 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:32:35.377919 PROGRESS: Extracting batch of 50439 precursors
0:32:35.389099 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:32:35.389228 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:32:35.389265 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:32:35.389289 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:32:35.389508 INFO: Starting candidate selection
0:32:38.427688 INFO: Starting candidate scoring
0:32:38.792025 INFO: Finished candidate processing
0:32:38.792137 INFO: Collecting candidate features
0:32:38.877777 INFO: Collecting fragment features
0:32:38.909627 INFO: Finished candidate scoring
0:32:38.957340 PROGRESS: === Extracted 100356 precursors and 1025476 fragments ===
0:32:38.970871 INFO: performing precursor FDR with 47 features
0:32:38.970994 INFO: Decoy channel: -1
0:32:38.971020 INFO: Competetive: True
0:32:39.011798 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:40.881630 INFO: Test AUC: 0.546
0:32:40.881834 INFO: Train AUC: 0.556
0:32:40.881867 INFO: AUC difference: 1.66%
0:32:41.072494 INFO: Resetting torch num_threads to 100
0:32:41.077708 INFO: === FDR correction performed with classifier version -1 ===
0:32:41.078513 PROGRESS: ============================= Precursor FDR =============================
0:32:41.078612 PROGRESS: Total precursors accumulated: 1
0:32:41.078674 PROGRESS: Target precursors: 1 (100.00%)
0:32:41.078726 PROGRESS: Decoy precursors: 0 (0.00%)
0:32:41.078772 PROGRESS: 
0:32:41.078817 PROGRESS: Precursor Summary:
0:32:41.079765 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:32:41.079854 PROGRESS: 
0:32:41.079911 PROGRESS: Protein Summary:
0:32:41.080943 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:32:41.081035 PROGRESS: =========================================================================
0:32:41.337563 INFO: Starting optimization step 8.
0:32:41.337960 PROGRESS: === Extracting elution groups 51000 to 102200 ===
0:32:41.338054 PROGRESS: Extracting batch of 100917 precursors
0:32:41.362913 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:32:41.363059 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:32:41.363105 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:32:41.363130 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:32:41.363458 INFO: Starting candidate selection
0:32:47.348917 INFO: Starting candidate scoring
0:32:48.090081 INFO: Finished candidate processing
0:32:48.090240 INFO: Collecting candidate features
0:32:48.334191 INFO: Collecting fragment features
0:32:48.422558 INFO: Finished candidate scoring
0:32:48.614408 PROGRESS: === Extracted 201068 precursors and 2055384 fragments ===
0:32:48.649420 INFO: performing precursor FDR with 47 features
0:32:48.649567 INFO: Decoy channel: -1
0:32:48.649593 INFO: Competetive: True
0:32:48.776352 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:53.726962 INFO: Test AUC: 0.559
0:32:53.727170 INFO: Train AUC: 0.576
0:32:53.727204 INFO: AUC difference: 3.00%
0:32:53.972359 INFO: Resetting torch num_threads to 100
0:32:53.987416 INFO: === FDR correction performed with classifier version -1 ===
0:32:53.988380 PROGRESS: ============================= Precursor FDR =============================
0:32:53.988483 PROGRESS: Total precursors accumulated: 5
0:32:53.988544 PROGRESS: Target precursors: 5 (100.00%)
0:32:53.988596 PROGRESS: Decoy precursors: 0 (0.00%)
0:32:53.988645 PROGRESS: 
0:32:53.988694 PROGRESS: Precursor Summary:
0:32:53.989655 PROGRESS: Channel   0:	 0.05 FDR:     5; 0.01 FDR:     5; 0.001 FDR:     5
0:32:53.989749 PROGRESS: 
0:32:53.989805 PROGRESS: Protein Summary:
0:32:53.990836 PROGRESS: Channel   0:	 0.05 FDR:     5; 0.01 FDR:     5; 0.001 FDR:     5
0:32:53.990932 PROGRESS: =========================================================================
0:32:54.417048 INFO: Starting optimization step 9.
0:32:54.417435 PROGRESS: === Extracting elution groups 102200 to 204600 ===
0:32:54.417533 PROGRESS: Extracting batch of 201824 precursors
0:32:54.468635 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:32:54.468784 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:32:54.468830 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:32:54.468858 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:32:54.469194 INFO: Starting candidate selection
0:33:06.616113 INFO: Starting candidate scoring
0:33:07.969093 INFO: Finished candidate processing
0:33:07.969329 INFO: Collecting candidate features
0:33:08.494330 INFO: Collecting fragment features
0:33:08.649428 INFO: Finished candidate scoring
0:33:08.958863 PROGRESS: === Extracted 402505 precursors and 4113938 fragments ===
0:33:09.011208 INFO: performing precursor FDR with 47 features
0:33:09.011356 INFO: Decoy channel: -1
0:33:09.011384 INFO: Competetive: True
0:33:09.233968 INFO: Setting torch num_threads to 2 for FDR classification task
0:33:16.192903 INFO: Test AUC: 0.566
0:33:16.193054 INFO: Train AUC: 0.581
0:33:16.193086 INFO: AUC difference: 2.67%
0:33:16.487878 INFO: Resetting torch num_threads to 100
0:33:16.513638 INFO: === FDR correction performed with classifier version -1 ===
0:33:16.514617 PROGRESS: ============================= Precursor FDR =============================
0:33:16.514736 PROGRESS: Total precursors accumulated: 1
0:33:16.514802 PROGRESS: Target precursors: 1 (100.00%)
0:33:16.514859 PROGRESS: Decoy precursors: 0 (0.00%)
0:33:16.514907 PROGRESS: 
0:33:16.514956 PROGRESS: Precursor Summary:
0:33:16.515948 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:33:16.516038 PROGRESS: 
0:33:16.516093 PROGRESS: Protein Summary:
0:33:16.517131 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:33:16.517229 PROGRESS: =========================================================================
0:33:17.132599 INFO: Starting optimization step 10.
0:33:17.132923 PROGRESS: === Extracting elution groups 204600 to 409400 ===
0:33:17.133006 PROGRESS: Extracting batch of 403666 precursors
0:33:17.231135 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:33:17.231288 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:33:17.231333 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:33:17.231358 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:33:17.231691 INFO: Starting candidate selection
0:33:41.531826 INFO: Starting candidate scoring
0:33:44.213799 INFO: Finished candidate processing
0:33:44.213926 INFO: Collecting candidate features
0:33:45.106311 INFO: Collecting fragment features
0:33:45.386225 INFO: Finished candidate scoring
0:33:46.031337 PROGRESS: === Extracted 805386 precursors and 8230106 fragments ===
0:33:46.144444 INFO: performing precursor FDR with 47 features
0:33:46.144596 INFO: Decoy channel: -1
0:33:46.144622 INFO: Competetive: True
0:33:46.584889 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:00.387633 INFO: Test AUC: 0.570
0:34:00.387880 INFO: Train AUC: 0.580
0:34:00.387914 INFO: AUC difference: 1.75%
0:34:02.042592 INFO: Resetting torch num_threads to 100
0:34:02.089200 INFO: === FDR correction performed with classifier version -1 ===
0:34:02.090896 PROGRESS: ============================= Precursor FDR =============================
0:34:02.091054 PROGRESS: Total precursors accumulated: 3,428
0:34:02.091118 PROGRESS: Target precursors: 3,135 (91.45%)
0:34:02.091175 PROGRESS: Decoy precursors: 293 (8.55%)
0:34:02.091225 PROGRESS: 
0:34:02.091272 PROGRESS: Precursor Summary:
0:34:02.093041 PROGRESS: Channel   0:	 0.05 FDR: 2,613; 0.01 FDR: 1,816; 0.001 FDR: 1,018
0:34:02.093163 PROGRESS: 
0:34:02.093222 PROGRESS: Protein Summary:
0:34:02.095287 PROGRESS: Channel   0:	 0.05 FDR: 1,925; 0.01 FDR: 1,373; 0.001 FDR:   819
0:34:02.095391 PROGRESS: =========================================================================
0:34:02.719912 INFO: fragments_df: keeping 5000 of 8230106 [sum(precursor_idx_mask)=20800 sum(mass_error_mask)=8230106 stop_rank=5000
0:34:02.984150 INFO: calibration group: precursor, fitting rt estimator 
0:34:03.237866 INFO: calibration group: fragment, fitting mz estimator 
0:34:03.922589 INFO: Using score_cutoff 68.14593947982789 (fac=0.99, q=1)
0:34:03.923029 INFO: calibration group: precursor, predicting mz
0:34:03.923119 WARNING: mz prediction was skipped as it has not been fitted yet
0:34:03.923151 INFO: calibration group: precursor, predicting rt
0:34:03.984389 INFO: calibration group: fragment, predicting mz
0:34:04.134870 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:34:04.135229 INFO: Starting optimization step 11.
0:34:04.135314 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:34:04.135386 PROGRESS: Extracting batch of 100535 precursors
0:34:04.170998 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:34:04.171161 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:34:04.171204 INFO: FWHM in RT is 2.99 seconds, sigma is 0.38
0:34:04.171234 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:34:04.171556 INFO: Starting candidate selection
0:34:09.041279 INFO: Starting candidate scoring
0:34:10.345886 INFO: Finished candidate processing
0:34:10.346001 INFO: Collecting candidate features
0:34:10.709777 INFO: Collecting fragment features
0:34:10.835500 INFO: Finished candidate scoring
0:34:10.936912 PROGRESS: === Extracted 200712 precursors and 2024182 fragments ===
0:34:10.937363 INFO: performing precursor FDR with 47 features
0:34:10.937403 INFO: Decoy channel: -1
0:34:10.937427 INFO: Competetive: True
0:34:11.003975 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:14.279332 INFO: Test AUC: 0.566
0:34:14.279554 INFO: Train AUC: 0.593
0:34:14.279586 INFO: AUC difference: 4.58%
0:34:14.518157 INFO: Resetting torch num_threads to 100
0:34:14.523545 INFO: === FDR correction performed with classifier version 10 ===
0:34:14.524355 PROGRESS: ============================= Precursor FDR =============================
0:34:14.524452 PROGRESS: Total precursors accumulated: 532
0:34:14.524514 PROGRESS: Target precursors: 484 (90.98%)
0:34:14.524566 PROGRESS: Decoy precursors: 48 (9.02%)
0:34:14.524612 PROGRESS: 
0:34:14.524656 PROGRESS: Precursor Summary:
0:34:14.525638 PROGRESS: Channel   0:	 0.05 FDR:   389; 0.01 FDR:   238; 0.001 FDR:   175
0:34:14.525727 PROGRESS: 
0:34:14.525785 PROGRESS: Protein Summary:
0:34:14.526925 PROGRESS: Channel   0:	 0.05 FDR:   363; 0.01 FDR:   226; 0.001 FDR:   168
0:34:14.527014 PROGRESS: =========================================================================
0:34:14.658765 INFO: fragments_df: keeping 2786 of 2024182 [sum(precursor_idx_mask)=5396 sum(mass_error_mask)=2024182 stop_rank=2786
0:34:14.881679 INFO: calibration group: precursor, fitting rt estimator 
0:34:15.005977 INFO: calibration group: fragment, fitting mz estimator 
0:34:15.357782 INFO: Using score_cutoff 69.10468935699463 (fac=0.99, q=1)
0:34:15.358231 INFO: calibration group: precursor, predicting mz
0:34:15.358316 WARNING: mz prediction was skipped as it has not been fitted yet
0:34:15.358347 INFO: calibration group: precursor, predicting rt
0:34:15.421122 INFO: calibration group: fragment, predicting mz
0:34:15.570273 INFO: === checking if optimization conditions were reached ===
0:34:15.570646 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:34:15.573131 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 22.7298.
0:34:15.573200 INFO: ==============================================
0:34:15.573313 INFO: Starting optimization step 12.
0:34:15.573389 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:34:15.573471 PROGRESS: Extracting batch of 100535 precursors
0:34:15.609132 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:34:15.609356 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:34:15.609434 INFO: FWHM in RT is 2.88 seconds, sigma is 0.37
0:34:15.609488 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:34:15.609858 INFO: Starting candidate selection
0:34:20.516216 INFO: Starting candidate scoring
0:34:21.820554 INFO: Finished candidate processing
0:34:21.820669 INFO: Collecting candidate features
0:34:22.138160 INFO: Collecting fragment features
0:34:22.257210 INFO: Finished candidate scoring
0:34:22.359294 PROGRESS: === Extracted 200711 precursors and 1935571 fragments ===
0:34:22.359724 INFO: performing precursor FDR with 47 features
0:34:22.359762 INFO: Decoy channel: -1
0:34:22.359786 INFO: Competetive: True
0:34:22.418732 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:25.827900 INFO: Test AUC: 0.562
0:34:25.828135 INFO: Train AUC: 0.586
0:34:25.828173 INFO: AUC difference: 4.02%
0:34:26.068172 INFO: Resetting torch num_threads to 100
0:34:26.075799 INFO: === FDR correction performed with classifier version 10 ===
0:34:26.076544 PROGRESS: ============================= Precursor FDR =============================
0:34:26.076645 PROGRESS: Total precursors accumulated: 554
0:34:26.076707 PROGRESS: Target precursors: 505 (91.16%)
0:34:26.076761 PROGRESS: Decoy precursors: 49 (8.84%)
0:34:26.076809 PROGRESS: 
0:34:26.076854 PROGRESS: Precursor Summary:
0:34:26.077894 PROGRESS: Channel   0:	 0.05 FDR:   385; 0.01 FDR:   238; 0.001 FDR:     0
0:34:26.077996 PROGRESS: 
0:34:26.078057 PROGRESS: Protein Summary:
0:34:26.079182 PROGRESS: Channel   0:	 0.05 FDR:   364; 0.01 FDR:   225; 0.001 FDR:     0
0:34:26.079282 PROGRESS: =========================================================================
0:34:26.211829 INFO: fragments_df: keeping 2749 of 1935571 [sum(precursor_idx_mask)=5382 sum(mass_error_mask)=1935571 stop_rank=2749
0:34:26.446673 INFO: calibration group: precursor, fitting rt estimator 
0:34:26.565881 INFO: calibration group: fragment, fitting mz estimator 
0:34:26.924492 INFO: Using score_cutoff 70.51923199539185 (fac=0.99, q=1)
0:34:26.924954 INFO: calibration group: precursor, predicting mz
0:34:26.925044 WARNING: mz prediction was skipped as it has not been fitted yet
0:34:26.925077 INFO: calibration group: precursor, predicting rt
0:34:26.988246 INFO: calibration group: fragment, predicting mz
0:34:27.143960 INFO: === checking if optimization conditions were reached ===
0:34:27.144301 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:34:27.147044 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 19.2743.
0:34:27.147105 INFO: ==============================================
0:34:27.147216 INFO: Starting optimization step 13.
0:34:27.147294 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:34:27.147374 PROGRESS: Extracting batch of 100535 precursors
0:34:27.182809 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:34:27.182971 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:34:27.183018 INFO: FWHM in RT is 2.79 seconds, sigma is 0.36
0:34:27.183046 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:34:27.183397 INFO: Starting candidate selection
0:34:32.139439 INFO: Starting candidate scoring
0:34:33.439147 INFO: Finished candidate processing
0:34:33.439318 INFO: Collecting candidate features
0:34:33.780791 INFO: Collecting fragment features
0:34:33.895592 INFO: Finished candidate scoring
0:34:33.991339 PROGRESS: === Extracted 200710 precursors and 1887115 fragments ===
0:34:33.991781 INFO: performing precursor FDR with 47 features
0:34:33.991819 INFO: Decoy channel: -1
0:34:33.991844 INFO: Competetive: True
0:34:34.054291 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:37.608338 INFO: Test AUC: 0.563
0:34:37.608557 INFO: Train AUC: 0.586
0:34:37.608588 INFO: AUC difference: 3.92%
0:34:37.840833 INFO: Resetting torch num_threads to 100
0:34:37.846169 INFO: === FDR correction performed with classifier version 10 ===
0:34:37.846944 PROGRESS: ============================= Precursor FDR =============================
0:34:37.847039 PROGRESS: Total precursors accumulated: 634
0:34:37.847099 PROGRESS: Target precursors: 577 (91.01%)
0:34:37.847151 PROGRESS: Decoy precursors: 57 (8.99%)
0:34:37.847201 PROGRESS: 
0:34:37.847249 PROGRESS: Precursor Summary:
0:34:37.848287 PROGRESS: Channel   0:	 0.05 FDR:   443; 0.01 FDR:   283; 0.001 FDR:   238
0:34:37.848379 PROGRESS: 
0:34:37.848433 PROGRESS: Protein Summary:
0:34:37.849604 PROGRESS: Channel   0:	 0.05 FDR:   417; 0.01 FDR:   270; 0.001 FDR:   226
0:34:37.849696 PROGRESS: =========================================================================
0:34:37.973948 INFO: fragments_df: keeping 3225 of 1887115 [sum(precursor_idx_mask)=6318 sum(mass_error_mask)=1887115 stop_rank=3225
0:34:38.214157 INFO: calibration group: precursor, fitting rt estimator 
0:34:38.312043 INFO: calibration group: fragment, fitting mz estimator 
0:34:38.673973 INFO: Using score_cutoff 66.29384995422363 (fac=0.99, q=1)
0:34:38.674429 INFO: calibration group: precursor, predicting mz
0:34:38.674519 WARNING: mz prediction was skipped as it has not been fitted yet
0:34:38.674550 INFO: calibration group: precursor, predicting rt
0:34:38.736898 INFO: calibration group: fragment, predicting mz
0:34:38.893247 INFO: === checking if optimization conditions were reached ===
0:34:38.893610 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
0:34:38.896487 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 16.4011.
0:34:38.896550 INFO: ==============================================
0:34:38.896662 INFO: Starting optimization step 14.
0:34:38.896737 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:34:38.896821 PROGRESS: Extracting batch of 100535 precursors
0:34:38.932194 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:34:38.932369 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:34:38.932420 INFO: FWHM in RT is 2.72 seconds, sigma is 0.35
0:34:38.932448 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:34:38.932791 INFO: Starting candidate selection
0:34:43.954544 INFO: Starting candidate scoring
0:34:45.283676 INFO: Finished candidate processing
0:34:45.283787 INFO: Collecting candidate features
0:34:45.595789 INFO: Collecting fragment features
0:34:45.717320 INFO: Finished candidate scoring
0:34:45.810502 PROGRESS: === Extracted 200708 precursors and 1823771 fragments ===
0:34:45.810990 INFO: performing precursor FDR with 47 features
0:34:45.811029 INFO: Decoy channel: -1
0:34:45.811054 INFO: Competetive: True
0:34:45.882941 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:49.143907 INFO: Test AUC: 0.561
0:34:49.144046 INFO: Train AUC: 0.584
0:34:49.144078 INFO: AUC difference: 3.88%
0:34:49.377537 INFO: Resetting torch num_threads to 100
0:34:49.382701 INFO: === FDR correction performed with classifier version 10 ===
0:34:49.383476 PROGRESS: ============================= Precursor FDR =============================
0:34:49.383568 PROGRESS: Total precursors accumulated: 690
0:34:49.383629 PROGRESS: Target precursors: 630 (91.30%)
0:34:49.383679 PROGRESS: Decoy precursors: 60 (8.70%)
0:34:49.383725 PROGRESS: 
0:34:49.383769 PROGRESS: Precursor Summary:
0:34:49.384804 PROGRESS: Channel   0:	 0.05 FDR:   537; 0.01 FDR:   311; 0.001 FDR:   224
0:34:49.384909 PROGRESS: 
0:34:49.384965 PROGRESS: Protein Summary:
0:34:49.386158 PROGRESS: Channel   0:	 0.05 FDR:   501; 0.01 FDR:   291; 0.001 FDR:   215
0:34:49.386251 PROGRESS: =========================================================================
0:34:49.508732 INFO: fragments_df: keeping 3505 of 1823771 [sum(precursor_idx_mask)=6882 sum(mass_error_mask)=1823771 stop_rank=3505
0:34:49.720436 INFO: calibration group: precursor, fitting rt estimator 
0:34:49.817827 INFO: calibration group: fragment, fitting mz estimator 
0:34:50.278194 INFO: Using score_cutoff 65.43645309448242 (fac=0.99, q=1)
0:34:50.278639 INFO: calibration group: precursor, predicting mz
0:34:50.278733 WARNING: mz prediction was skipped as it has not been fitted yet
0:34:50.278769 INFO: calibration group: precursor, predicting rt
0:34:50.345875 INFO: calibration group: fragment, predicting mz
0:34:50.496286 INFO: === checking if optimization conditions were reached ===
0:34:50.496616 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
0:34:50.499365 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 13.4521.
0:34:50.499429 INFO: ==============================================
0:34:50.499538 INFO: Starting optimization step 15.
0:34:50.499612 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:34:50.499694 PROGRESS: Extracting batch of 100535 precursors
0:34:50.533176 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:34:50.533339 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:34:50.533384 INFO: FWHM in RT is 2.70 seconds, sigma is 0.35
0:34:50.533414 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:34:50.533729 INFO: Starting candidate selection
0:34:55.590112 INFO: Starting candidate scoring
0:34:56.913295 INFO: Finished candidate processing
0:34:56.913476 INFO: Collecting candidate features
0:34:57.335059 INFO: Collecting fragment features
0:34:57.490700 INFO: Finished candidate scoring
0:34:57.686135 PROGRESS: === Extracted 200704 precursors and 1742556 fragments ===
0:34:57.686713 INFO: performing precursor FDR with 47 features
0:34:57.686757 INFO: Decoy channel: -1
0:34:57.686781 INFO: Competetive: True
0:34:57.796899 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:02.086640 INFO: Test AUC: 0.562
0:35:02.086806 INFO: Train AUC: 0.586
0:35:02.086839 INFO: AUC difference: 4.21%
0:35:02.330836 INFO: Resetting torch num_threads to 100
0:35:02.339168 INFO: === FDR correction performed with classifier version 10 ===
0:35:02.339997 PROGRESS: ============================= Precursor FDR =============================
0:35:02.340094 PROGRESS: Total precursors accumulated: 631
0:35:02.340156 PROGRESS: Target precursors: 573 (90.81%)
0:35:02.340210 PROGRESS: Decoy precursors: 58 (9.19%)
0:35:02.340271 PROGRESS: 
0:35:02.340325 PROGRESS: Precursor Summary:
0:35:02.341420 PROGRESS: Channel   0:	 0.05 FDR:   494; 0.01 FDR:   415; 0.001 FDR:   245
0:35:02.341516 PROGRESS: 
0:35:02.341573 PROGRESS: Protein Summary:
0:35:02.342833 PROGRESS: Channel   0:	 0.05 FDR:   462; 0.01 FDR:   389; 0.001 FDR:   232
0:35:02.342929 PROGRESS: =========================================================================
0:35:02.455878 INFO: fragments_df: keeping 4479 of 1742556 [sum(precursor_idx_mask)=8951 sum(mass_error_mask)=1742556 stop_rank=4479
0:35:02.644319 INFO: calibration group: precursor, fitting rt estimator 
0:35:02.761697 INFO: calibration group: fragment, fitting mz estimator 
0:35:03.296522 INFO: Using score_cutoff 53.62811290969849 (fac=0.99, q=1)
0:35:03.297030 INFO: calibration group: precursor, predicting mz
0:35:03.297122 WARNING: mz prediction was skipped as it has not been fitted yet
0:35:03.297158 INFO: calibration group: precursor, predicting rt
0:35:03.329070 INFO: calibration group: fragment, predicting mz
0:35:03.402402 INFO: === checking if optimization conditions were reached ===
0:35:03.402744 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
0:35:03.406059 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 11.8508.
0:35:03.406126 INFO: ==============================================
0:35:03.406254 INFO: Starting optimization step 16.
0:35:03.406345 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:35:03.406433 PROGRESS: Extracting batch of 50096 precursors
0:35:03.480431 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:35:03.480562 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:03.480613 INFO: FWHM in RT is 2.54 seconds, sigma is 0.33
0:35:03.480637 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:35:03.480932 INFO: Starting candidate selection
0:35:05.998901 INFO: Starting candidate scoring
0:35:06.631271 INFO: Finished candidate processing
0:35:06.631385 INFO: Collecting candidate features
0:35:06.796595 INFO: Collecting fragment features
0:35:06.865709 INFO: Finished candidate scoring
0:35:06.910316 PROGRESS: === Extracted 100011 precursors and 831626 fragments ===
0:35:06.910828 INFO: performing precursor FDR with 47 features
0:35:06.910867 INFO: Decoy channel: -1
0:35:06.910892 INFO: Competetive: True
0:35:06.947999 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:08.470079 INFO: Test AUC: 0.562
0:35:08.470225 INFO: Train AUC: 0.581
0:35:08.470256 INFO: AUC difference: 3.28%
0:35:08.678106 INFO: Resetting torch num_threads to 100
0:35:08.681230 INFO: === FDR correction performed with classifier version 10 ===
0:35:08.681906 PROGRESS: ============================= Precursor FDR =============================
0:35:08.681997 PROGRESS: Total precursors accumulated: 335
0:35:08.682059 PROGRESS: Target precursors: 305 (91.04%)
0:35:08.682112 PROGRESS: Decoy precursors: 30 (8.96%)
0:35:08.682158 PROGRESS: 
0:35:08.682204 PROGRESS: Precursor Summary:
0:35:08.683164 PROGRESS: Channel   0:	 0.05 FDR:   268; 0.01 FDR:   164; 0.001 FDR:   145
0:35:08.683255 PROGRESS: 
0:35:08.683316 PROGRESS: Protein Summary:
0:35:08.684428 PROGRESS: Channel   0:	 0.05 FDR:   256; 0.01 FDR:   156; 0.001 FDR:   138
0:35:08.684529 PROGRESS: =========================================================================
0:35:08.857156 INFO: calibration group: precursor, predicting mz
0:35:08.857478 WARNING: mz prediction was skipped as it has not been fitted yet
0:35:08.857514 INFO: calibration group: precursor, predicting rt
0:35:08.889578 INFO: calibration group: fragment, predicting mz
0:35:08.954468 INFO: === skipping optimization until target number of precursors are found ===
0:35:08.954783 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:35:08.954851 INFO: Starting optimization step 17.
0:35:08.954927 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:35:08.955002 PROGRESS: Extracting batch of 50439 precursors
0:35:08.970433 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:35:08.970578 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:08.970625 INFO: FWHM in RT is 2.54 seconds, sigma is 0.33
0:35:08.970655 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:35:08.970968 INFO: Starting candidate selection
0:35:11.442443 INFO: Starting candidate scoring
0:35:12.085949 INFO: Finished candidate processing
0:35:12.086072 INFO: Collecting candidate features
0:35:12.235079 INFO: Collecting fragment features
0:35:12.293827 INFO: Finished candidate scoring
0:35:12.397063 PROGRESS: === Extracted 200682 precursors and 1669603 fragments ===
0:35:12.418832 INFO: performing precursor FDR with 47 features
0:35:12.418988 INFO: Decoy channel: -1
0:35:12.419016 INFO: Competetive: True
0:35:12.496751 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:15.872082 INFO: Test AUC: 0.564
0:35:15.872228 INFO: Train AUC: 0.585
0:35:15.876050 INFO: AUC difference: 3.65%
0:35:16.116616 INFO: Resetting torch num_threads to 100
0:35:16.183120 INFO: === FDR correction performed with classifier version 10 ===
0:35:16.184048 PROGRESS: ============================= Precursor FDR =============================
0:35:16.184162 PROGRESS: Total precursors accumulated: 738
0:35:16.184227 PROGRESS: Target precursors: 671 (90.92%)
0:35:16.184305 PROGRESS: Decoy precursors: 67 (9.08%)
0:35:16.184356 PROGRESS: 
0:35:16.184403 PROGRESS: Precursor Summary:
0:35:16.185466 PROGRESS: Channel   0:	 0.05 FDR:   564; 0.01 FDR:   400; 0.001 FDR:   211
0:35:16.185558 PROGRESS: 
0:35:16.185616 PROGRESS: Protein Summary:
0:35:16.186829 PROGRESS: Channel   0:	 0.05 FDR:   526; 0.01 FDR:   372; 0.001 FDR:   201
0:35:16.186922 PROGRESS: =========================================================================
0:35:16.325893 INFO: fragments_df: keeping 4264 of 1669603 [sum(precursor_idx_mask)=8493 sum(mass_error_mask)=1669603 stop_rank=4264
0:35:16.568219 INFO: calibration group: precursor, fitting rt estimator 
0:35:16.683575 INFO: calibration group: fragment, fitting mz estimator 
0:35:17.184706 INFO: Using score_cutoff 52.419403214263916 (fac=0.99, q=1)
0:35:17.185929 INFO: calibration group: precursor, predicting mz
0:35:17.186034 WARNING: mz prediction was skipped as it has not been fitted yet
0:35:17.186074 INFO: calibration group: precursor, predicting rt
0:35:17.254408 INFO: calibration group: fragment, predicting mz
0:35:17.442170 INFO: === checking if optimization conditions were reached ===
0:35:17.442477 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
0:35:17.445965 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 10.0707.
0:35:17.446023 INFO: ==============================================
0:35:17.446140 INFO: Starting optimization step 18.
0:35:17.446223 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:35:17.446338 PROGRESS: Extracting batch of 100535 precursors
0:35:17.481241 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:35:17.481378 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:17.481434 INFO: FWHM in RT is 2.55 seconds, sigma is 0.33
0:35:17.481464 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:35:17.481942 INFO: Starting candidate selection
0:35:22.422843 INFO: Starting candidate scoring
0:35:24.020827 INFO: Finished candidate processing
0:35:24.020948 INFO: Collecting candidate features
0:35:24.358993 INFO: Collecting fragment features
0:35:24.479442 INFO: Finished candidate scoring
0:35:24.622045 PROGRESS: === Extracted 200696 precursors and 1636278 fragments ===
0:35:24.622510 INFO: performing precursor FDR with 47 features
0:35:24.622549 INFO: Decoy channel: -1
0:35:24.622573 INFO: Competetive: True
0:35:24.696408 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:28.313888 INFO: Test AUC: 0.560
0:35:28.314066 INFO: Train AUC: 0.584
0:35:28.314103 INFO: AUC difference: 4.24%
0:35:28.557302 INFO: Resetting torch num_threads to 100
0:35:28.584486 INFO: === FDR correction performed with classifier version 10 ===
0:35:28.585356 PROGRESS: ============================= Precursor FDR =============================
0:35:28.585470 PROGRESS: Total precursors accumulated: 719
0:35:28.585534 PROGRESS: Target precursors: 654 (90.96%)
0:35:28.585587 PROGRESS: Decoy precursors: 65 (9.04%)
0:35:28.585636 PROGRESS: 
0:35:28.585680 PROGRESS: Precursor Summary:
0:35:28.586727 PROGRESS: Channel   0:	 0.05 FDR:   504; 0.01 FDR:   412; 0.001 FDR:   222
0:35:28.586819 PROGRESS: 
0:35:28.586875 PROGRESS: Protein Summary:
0:35:28.588105 PROGRESS: Channel   0:	 0.05 FDR:   469; 0.01 FDR:   384; 0.001 FDR:   210
0:35:28.588199 PROGRESS: =========================================================================
0:35:28.694033 INFO: fragments_df: keeping 4378 of 1636278 [sum(precursor_idx_mask)=8747 sum(mass_error_mask)=1636278 stop_rank=4378
0:35:28.875049 INFO: calibration group: precursor, fitting rt estimator 
0:35:29.007130 INFO: calibration group: fragment, fitting mz estimator 
0:35:29.602711 INFO: Using score_cutoff 57.84323663177491 (fac=0.99, q=1)
0:35:29.603318 INFO: calibration group: precursor, predicting mz
0:35:29.603412 WARNING: mz prediction was skipped as it has not been fitted yet
0:35:29.603444 INFO: calibration group: precursor, predicting rt
0:35:29.635686 INFO: calibration group: fragment, predicting mz
0:35:29.703248 INFO: === checking if optimization conditions were reached ===
0:35:29.703637 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
0:35:29.706938 PROGRESS: ❌ ms2_error      : optimization incomplete after 7 search(es). Will search with parameter 9.2415.
0:35:29.707002 INFO: ==============================================
0:35:29.707128 INFO: Starting optimization step 19.
0:35:29.707215 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:35:29.707305 PROGRESS: Extracting batch of 50096 precursors
0:35:29.725392 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:35:29.725521 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:29.725570 INFO: FWHM in RT is 2.49 seconds, sigma is 0.32
0:35:29.725600 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:35:29.725948 INFO: Starting candidate selection
0:35:32.279476 INFO: Starting candidate scoring
0:35:32.928162 INFO: Finished candidate processing
0:35:32.928289 INFO: Collecting candidate features
0:35:33.096640 INFO: Collecting fragment features
0:35:33.156923 INFO: Finished candidate scoring
0:35:33.198789 PROGRESS: === Extracted 100011 precursors and 791708 fragments ===
0:35:33.199221 INFO: performing precursor FDR with 47 features
0:35:33.199258 INFO: Decoy channel: -1
0:35:33.199284 INFO: Competetive: True
0:35:33.233037 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:34.773734 INFO: Test AUC: 0.564
0:35:34.773872 INFO: Train AUC: 0.578
0:35:34.773902 INFO: AUC difference: 2.51%
0:35:35.060876 INFO: Resetting torch num_threads to 100
0:35:35.067262 INFO: === FDR correction performed with classifier version 10 ===
0:35:35.068213 PROGRESS: ============================= Precursor FDR =============================
0:35:35.068334 PROGRESS: Total precursors accumulated: 339
0:35:35.068403 PROGRESS: Target precursors: 310 (91.45%)
0:35:35.068482 PROGRESS: Decoy precursors: 29 (8.55%)
0:35:35.068546 PROGRESS: 
0:35:35.068602 PROGRESS: Precursor Summary:
0:35:35.069790 PROGRESS: Channel   0:	 0.05 FDR:   218; 0.01 FDR:   155; 0.001 FDR:   153
0:35:35.069901 PROGRESS: 
0:35:35.069964 PROGRESS: Protein Summary:
0:35:35.071288 PROGRESS: Channel   0:	 0.05 FDR:   210; 0.01 FDR:   149; 0.001 FDR:   147
0:35:35.071390 PROGRESS: =========================================================================
0:35:35.214834 INFO: calibration group: precursor, predicting mz
0:35:35.215144 WARNING: mz prediction was skipped as it has not been fitted yet
0:35:35.215177 INFO: calibration group: precursor, predicting rt
0:35:35.246979 INFO: calibration group: fragment, predicting mz
0:35:35.312725 INFO: === skipping optimization until target number of precursors are found ===
0:35:35.313087 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:35:35.313143 WARNING: Optimization did not converge within the maximum number of steps, which is 20.
0:35:35.313255 INFO: Starting optimization step 0.
0:35:35.313333 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:35:35.313412 PROGRESS: Extracting batch of 50439 precursors
0:35:35.330758 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:35:35.330908 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:35.330953 INFO: FWHM in RT is 2.49 seconds, sigma is 0.32
0:35:35.330984 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:35:35.331251 INFO: Starting candidate selection
0:35:37.910767 INFO: Starting candidate scoring
0:35:38.567091 INFO: Finished candidate processing
0:35:38.567208 INFO: Collecting candidate features
0:35:38.735126 INFO: Collecting fragment features
0:35:38.791605 INFO: Finished candidate scoring
0:35:38.893745 PROGRESS: === Extracted 200680 precursors and 1590122 fragments ===
0:35:38.914559 INFO: performing precursor FDR with 47 features
0:35:38.914717 INFO: Decoy channel: -1
0:35:38.914744 INFO: Competetive: True
0:35:38.993538 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:42.447181 INFO: Test AUC: 0.571
0:35:42.447464 INFO: Train AUC: 0.581
0:35:42.447498 INFO: AUC difference: 1.60%
0:35:42.685774 INFO: Resetting torch num_threads to 100
0:35:42.697372 INFO: === FDR correction performed with classifier version 10 ===
0:35:42.698421 PROGRESS: ============================= Precursor FDR =============================
0:35:42.698538 PROGRESS: Total precursors accumulated: 748
0:35:42.698605 PROGRESS: Target precursors: 680 (90.91%)
0:35:42.698664 PROGRESS: Decoy precursors: 68 (9.09%)
0:35:42.698717 PROGRESS: 
0:35:42.698769 PROGRESS: Precursor Summary:
0:35:42.699886 PROGRESS: Channel   0:	 0.05 FDR:   535; 0.01 FDR:   407; 0.001 FDR:   271
0:35:42.699983 PROGRESS: 
0:35:42.700048 PROGRESS: Protein Summary:
0:35:42.701313 PROGRESS: Channel   0:	 0.05 FDR:   500; 0.01 FDR:   379; 0.001 FDR:   257
0:35:42.701412 PROGRESS: =========================================================================
0:35:42.820655 INFO: fragments_df: keeping 4326 of 1590122 [sum(precursor_idx_mask)=8536 sum(mass_error_mask)=1590122 stop_rank=4326
0:35:42.996005 INFO: calibration group: precursor, fitting rt estimator 
0:35:43.130388 INFO: calibration group: fragment, fitting mz estimator 
0:35:43.704371 INFO: Using score_cutoff 55.89052281188965 (fac=0.99, q=1)
0:35:43.704916 INFO: calibration group: precursor, predicting mz
0:35:43.705011 WARNING: mz prediction was skipped as it has not been fitted yet
0:35:43.705049 INFO: calibration group: precursor, predicting rt
0:35:43.736937 INFO: calibration group: fragment, predicting mz
0:35:43.807027 INFO: === checking if optimization conditions were reached ===
0:35:43.807410 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:35:43.809856 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 140.5521.
0:35:43.809920 INFO: ==============================================
0:35:43.810038 INFO: Starting optimization step 1.
0:35:43.810133 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:35:43.810241 PROGRESS: Extracting batch of 50096 precursors
0:35:43.824898 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:35:43.825025 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:43.825087 INFO: FWHM in RT is 2.46 seconds, sigma is 0.32
0:35:43.825112 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:35:43.825523 INFO: Starting candidate selection
0:35:45.854778 INFO: Starting candidate scoring
0:35:46.495310 INFO: Finished candidate processing
0:35:46.495425 INFO: Collecting candidate features
0:35:46.658407 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 99211)
0:35:46.667701 INFO: Collecting fragment features
0:35:46.717842 INFO: Finished candidate scoring
0:35:46.775286 PROGRESS: === Extracted 99211 precursors and 682255 fragments ===
0:35:46.775697 INFO: performing precursor FDR with 47 features
0:35:46.775736 INFO: Decoy channel: -1
0:35:46.775761 INFO: Competetive: True
0:35:46.808196 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:46.825663 WARNING: dropped 2 target PSMs due to missing features
0:35:46.825812 WARNING: dropped 1 decoy PSMs due to missing features
0:35:48.271918 INFO: Test AUC: 0.557
0:35:48.272062 INFO: Train AUC: 0.570
0:35:48.272093 INFO: AUC difference: 2.25%
0:35:48.478206 INFO: Resetting torch num_threads to 100
0:35:48.481169 INFO: === FDR correction performed with classifier version 10 ===
0:35:48.481821 PROGRESS: ============================= Precursor FDR =============================
0:35:48.481917 PROGRESS: Total precursors accumulated: 350
0:35:48.481981 PROGRESS: Target precursors: 318 (90.86%)
0:35:48.482034 PROGRESS: Decoy precursors: 32 (9.14%)
0:35:48.482083 PROGRESS: 
0:35:48.482129 PROGRESS: Precursor Summary:
0:35:48.483095 PROGRESS: Channel   0:	 0.05 FDR:   275; 0.01 FDR:   220; 0.001 FDR:   123
0:35:48.483194 PROGRESS: 
0:35:48.483252 PROGRESS: Protein Summary:
0:35:48.484368 PROGRESS: Channel   0:	 0.05 FDR:   263; 0.01 FDR:   209; 0.001 FDR:   119
0:35:48.484466 PROGRESS: =========================================================================
0:35:48.529967 INFO: fragments_df: keeping 2202 of 682255 [sum(precursor_idx_mask)=4532 sum(mass_error_mask)=682255 stop_rank=2202
0:35:48.665091 INFO: calibration group: precursor, fitting rt estimator 
0:35:48.778597 INFO: calibration group: fragment, fitting mz estimator 
0:35:49.068783 INFO: Using score_cutoff 55.24329399719238 (fac=0.99, q=1)
0:35:49.069197 INFO: calibration group: precursor, predicting mz
0:35:49.069283 WARNING: mz prediction was skipped as it has not been fitted yet
0:35:49.069315 INFO: calibration group: precursor, predicting rt
0:35:49.101189 INFO: calibration group: fragment, predicting mz
0:35:49.166498 INFO: === checking if optimization conditions were reached ===
0:35:49.166834 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:35:49.169072 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 98.9815.
0:35:49.169135 INFO: ==============================================
0:35:49.169239 INFO: Starting optimization step 2.
0:35:49.169314 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:35:49.169383 PROGRESS: Extracting batch of 50096 precursors
0:35:49.186371 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:35:49.186501 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:49.186540 INFO: FWHM in RT is 2.39 seconds, sigma is 0.31
0:35:49.186570 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:35:49.186819 INFO: Starting candidate selection
0:35:50.791803 INFO: Starting candidate scoring
0:35:51.477556 INFO: Finished candidate processing
0:35:51.477765 INFO: Collecting candidate features
0:35:51.628862 WARNING: intensity_correlation has 8 NaNs ( 0.01 % out of 98790)
0:35:51.635347 INFO: Collecting fragment features
0:35:51.685275 INFO: Finished candidate scoring
0:35:51.733084 PROGRESS: === Extracted 98790 precursors and 646474 fragments ===
0:35:51.733621 INFO: performing precursor FDR with 47 features
0:35:51.733660 INFO: Decoy channel: -1
0:35:51.733688 INFO: Competetive: True
0:35:51.770107 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:51.787868 WARNING: dropped 6 target PSMs due to missing features
0:35:51.788009 WARNING: dropped 2 decoy PSMs due to missing features
0:35:53.266641 INFO: Test AUC: 0.552
0:35:53.266778 INFO: Train AUC: 0.569
0:35:53.266815 INFO: AUC difference: 3.05%
0:35:53.479758 INFO: Resetting torch num_threads to 100
0:35:53.482881 INFO: === FDR correction performed with classifier version 10 ===
0:35:53.483557 PROGRESS: ============================= Precursor FDR =============================
0:35:53.483650 PROGRESS: Total precursors accumulated: 324
0:35:53.483711 PROGRESS: Target precursors: 294 (90.74%)
0:35:53.483764 PROGRESS: Decoy precursors: 30 (9.26%)
0:35:53.483812 PROGRESS: 
0:35:53.483858 PROGRESS: Precursor Summary:
0:35:53.484874 PROGRESS: Channel   0:	 0.05 FDR:   252; 0.01 FDR:   208; 0.001 FDR:   131
0:35:53.484974 PROGRESS: 
0:35:53.485032 PROGRESS: Protein Summary:
0:35:53.486121 PROGRESS: Channel   0:	 0.05 FDR:   243; 0.01 FDR:   201; 0.001 FDR:   126
0:35:53.486214 PROGRESS: =========================================================================
0:35:53.529296 INFO: fragments_df: keeping 2073 of 646474 [sum(precursor_idx_mask)=4290 sum(mass_error_mask)=646474 stop_rank=2073
0:35:53.667788 INFO: calibration group: precursor, fitting rt estimator 
0:35:53.784368 INFO: calibration group: fragment, fitting mz estimator 
0:35:54.062398 INFO: Using score_cutoff 54.811484331893915 (fac=0.99, q=1)
0:35:54.062867 INFO: calibration group: precursor, predicting mz
0:35:54.062958 WARNING: mz prediction was skipped as it has not been fitted yet
0:35:54.062989 INFO: calibration group: precursor, predicting rt
0:35:54.095409 INFO: calibration group: fragment, predicting mz
0:35:54.162623 INFO: === checking if optimization conditions were reached ===
0:35:54.162964 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:35:54.165414 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 66.6015.
0:35:54.165478 INFO: ==============================================
0:35:54.165588 INFO: Starting optimization step 3.
0:35:54.165665 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:35:54.165745 PROGRESS: Extracting batch of 50096 precursors
0:35:54.182329 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:35:54.182472 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:54.182522 INFO: FWHM in RT is 2.34 seconds, sigma is 0.30
0:35:54.182551 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:35:54.182862 INFO: Starting candidate selection
0:35:56.135198 INFO: Starting candidate scoring
0:35:56.794331 INFO: Finished candidate processing
0:35:56.794497 INFO: Collecting candidate features
0:35:56.955902 WARNING: intensity_correlation has 7 NaNs ( 0.01 % out of 98339)
0:35:56.962566 INFO: Collecting fragment features
0:35:57.010713 INFO: Finished candidate scoring
0:35:57.085539 PROGRESS: === Extracted 98339 precursors and 626823 fragments ===
0:35:57.085950 INFO: performing precursor FDR with 47 features
0:35:57.085987 INFO: Decoy channel: -1
0:35:57.086011 INFO: Competetive: True
0:35:57.114056 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:57.134631 WARNING: dropped 5 target PSMs due to missing features
0:35:57.134778 WARNING: dropped 2 decoy PSMs due to missing features
0:35:58.589761 INFO: Test AUC: 0.552
0:35:58.589897 INFO: Train AUC: 0.569
0:35:58.589928 INFO: AUC difference: 3.06%
0:35:58.805390 INFO: Resetting torch num_threads to 100
0:35:58.808382 INFO: === FDR correction performed with classifier version 10 ===
0:35:58.809044 PROGRESS: ============================= Precursor FDR =============================
0:35:58.809142 PROGRESS: Total precursors accumulated: 373
0:35:58.809206 PROGRESS: Target precursors: 341 (91.42%)
0:35:58.809271 PROGRESS: Decoy precursors: 32 (8.58%)
0:35:58.809319 PROGRESS: 
0:35:58.809364 PROGRESS: Precursor Summary:
0:35:58.810323 PROGRESS: Channel   0:	 0.05 FDR:   283; 0.01 FDR:   209; 0.001 FDR:   112
0:35:58.810420 PROGRESS: 
0:35:58.810475 PROGRESS: Protein Summary:
0:35:58.811556 PROGRESS: Channel   0:	 0.05 FDR:   270; 0.01 FDR:   201; 0.001 FDR:   108
0:35:58.811646 PROGRESS: =========================================================================
0:35:58.853891 INFO: fragments_df: keeping 2061 of 626823 [sum(precursor_idx_mask)=4271 sum(mass_error_mask)=626823 stop_rank=2061
0:35:58.999307 INFO: calibration group: precursor, fitting rt estimator 
0:35:59.115113 INFO: calibration group: fragment, fitting mz estimator 
0:35:59.388355 INFO: Using score_cutoff 54.825100117492674 (fac=0.99, q=1)
0:35:59.388765 INFO: calibration group: precursor, predicting mz
0:35:59.388851 WARNING: mz prediction was skipped as it has not been fitted yet
0:35:59.388882 INFO: calibration group: precursor, predicting rt
0:35:59.420830 INFO: calibration group: fragment, predicting mz
0:35:59.486553 INFO: === checking if optimization conditions were reached ===
0:35:59.486845 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:35:59.488863 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 64.9583.
0:35:59.488921 INFO: ==============================================
0:35:59.489021 INFO: Starting optimization step 4.
0:35:59.489090 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:35:59.489150 PROGRESS: Extracting batch of 50096 precursors
0:35:59.501242 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:35:59.501363 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:59.501397 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
0:35:59.501421 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:35:59.501640 INFO: Starting candidate selection
0:36:02.715605 INFO: Starting candidate scoring
0:36:03.397575 INFO: Finished candidate processing
0:36:03.397691 INFO: Collecting candidate features
0:36:03.548135 WARNING: intensity_correlation has 9 NaNs ( 0.01 % out of 97938)
0:36:03.554622 INFO: Collecting fragment features
0:36:03.609230 INFO: Finished candidate scoring
0:36:03.651012 PROGRESS: === Extracted 97938 precursors and 615237 fragments ===
0:36:03.651486 INFO: performing precursor FDR with 47 features
0:36:03.651526 INFO: Decoy channel: -1
0:36:03.651554 INFO: Competetive: True
0:36:03.685861 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:03.703887 WARNING: dropped 4 target PSMs due to missing features
0:36:03.704039 WARNING: dropped 5 decoy PSMs due to missing features
0:36:05.170592 INFO: Test AUC: 0.551
0:36:05.170739 INFO: Train AUC: 0.571
0:36:05.170769 INFO: AUC difference: 3.51%
0:36:05.380229 INFO: Resetting torch num_threads to 100
0:36:05.383162 INFO: === FDR correction performed with classifier version 10 ===
0:36:05.383824 PROGRESS: ============================= Precursor FDR =============================
0:36:05.383919 PROGRESS: Total precursors accumulated: 368
0:36:05.383980 PROGRESS: Target precursors: 334 (90.76%)
0:36:05.384032 PROGRESS: Decoy precursors: 34 (9.24%)
0:36:05.384081 PROGRESS: 
0:36:05.384126 PROGRESS: Precursor Summary:
0:36:05.386803 PROGRESS: Channel   0:	 0.05 FDR:   292; 0.01 FDR:   240; 0.001 FDR:   121
0:36:05.387210 PROGRESS: 
0:36:05.387369 PROGRESS: Protein Summary:
0:36:05.389367 PROGRESS: Channel   0:	 0.05 FDR:   279; 0.01 FDR:   229; 0.001 FDR:   117
0:36:05.389465 PROGRESS: =========================================================================
0:36:05.433169 INFO: fragments_df: keeping 2306 of 615237 [sum(precursor_idx_mask)=4829 sum(mass_error_mask)=615237 stop_rank=2306
0:36:05.574796 INFO: calibration group: precursor, fitting rt estimator 
0:36:05.690360 INFO: calibration group: fragment, fitting mz estimator 
0:36:05.996224 INFO: Using score_cutoff 43.402835347366334 (fac=0.99, q=1)
0:36:05.996944 INFO: calibration group: precursor, predicting mz
0:36:05.997052 WARNING: mz prediction was skipped as it has not been fitted yet
0:36:05.997085 INFO: calibration group: precursor, predicting rt
0:36:06.030281 INFO: calibration group: fragment, predicting mz
0:36:06.104975 INFO: === checking if optimization conditions were reached ===
0:36:06.105341 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:36:06.107042 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 64.9583 found after 5 searches.
0:36:06.107104 INFO: ==============================================
0:36:06.107218 PROGRESS: Optimization finished for rt_error.
0:36:06.277479 INFO: calibration group: precursor, predicting mz
0:36:06.277756 WARNING: mz prediction was skipped as it has not been fitted yet
0:36:06.277792 INFO: calibration group: precursor, predicting rt
0:36:06.311219 INFO: calibration group: fragment, predicting mz
0:36:06.414377 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:36:06.414636 PROGRESS: ==============================================
0:36:06.414722 PROGRESS: ms2_error      : 9.2415
0:36:06.414789 PROGRESS: rt_error       : 64.9583
0:36:06.414846 PROGRESS: ==============================================
0:36:06.415809 INFO: calibration group: precursor, predicting mz
0:36:06.415973 WARNING: mz prediction was skipped as it has not been fitted yet
0:36:06.416010 INFO: calibration group: precursor, predicting rt
0:36:14.843440 INFO: calibration group: fragment, predicting mz
0:36:32.203471 PROGRESS: Extracting batch of 12567710 precursors
0:36:34.908081 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:36:34.908260 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:36:34.908304 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
0:36:34.908328 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:36:34.908745 INFO: Starting candidate selection
0:42:31.781061 INFO: Applying score cutoff of 43.402835347366334
0:42:31.986192 INFO: Removed 20594084 precursors with score below cutoff
0:42:34.631264 INFO: Starting candidate scoring
0:43:05.705570 INFO: Finished candidate processing
0:43:05.705998 INFO: Collecting candidate features
0:43:15.709650 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 4475818)
0:43:15.857286 INFO: Collecting fragment features
0:43:19.405868 INFO: Finished candidate scoring
0:43:23.308193 INFO: === FDR correction performed with classifier version 24 ===
0:43:23.310512 INFO: performing precursor FDR with 47 features
0:43:23.310582 INFO: Decoy channel: -1
0:43:23.310612 INFO: Competetive: True
0:43:24.585217 INFO: Setting torch num_threads to 2 for FDR classification task
0:43:25.393204 WARNING: dropped 1 target PSMs due to missing features
0:43:25.393371 WARNING: dropped 2 decoy PSMs due to missing features
0:44:44.022051 INFO: Test AUC: 0.600
0:44:44.022312 INFO: Train AUC: 0.604
0:44:44.022362 INFO: AUC difference: 0.59%
0:44:45.411802 INFO: Resetting torch num_threads to 100
0:44:45.688517 INFO: Removing fragments below FDR threshold
0:44:46.060411 PROGRESS: ============================= Precursor FDR =============================
0:44:46.060754 PROGRESS: Total precursors accumulated: 74,584
0:44:46.060824 PROGRESS: Target precursors: 73,846 (99.01%)
0:44:46.060878 PROGRESS: Decoy precursors: 738 (0.99%)
0:44:46.060927 PROGRESS: 
0:44:46.060974 PROGRESS: Precursor Summary:
0:44:46.092429 PROGRESS: Channel   0:	 0.05 FDR: 73,846; 0.01 FDR: 73,846; 0.001 FDR: 52,357
0:44:46.092712 PROGRESS: 
0:44:46.092777 PROGRESS: Protein Summary:
0:44:46.138124 PROGRESS: Channel   0:	 0.05 FDR: 11,669; 0.01 FDR: 11,669; 0.001 FDR: 9,037
0:44:46.138420 PROGRESS: =========================================================================
0:44:46.733522 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:44:47.191576 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:44:47.191853 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant
0:44:47.191971 INFO: Creating folder run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/figures
0:44:47.193280 INFO: Initializing RawFileManager
0:44:58.098055 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:44:58.104765 INFO: Determining DIA cycle
0:44:58.121307 INFO: Found cycle with start 0.00 min and length 300.
0:44:58.282184 INFO: RT (min)            : 0.0 - 26.9
0:44:58.282281 INFO: RT duration (sec)   : 1611.2
0:44:58.282312 INFO: RT duration (min)   : 26.9
0:44:58.282339 INFO: Cycle len (scans)   : 300
0:44:58.282359 INFO: Cycle len (sec)     : 1.65
0:44:58.282380 INFO: Number of cycles    : 977
0:44:58.282399 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:44:59.790452 INFO: Initializing CalibrationManager
0:44:59.790776 INFO: Loading calibration config
0:44:59.791434 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'}]
0:44:59.791528 INFO: Calibration group :fragment, found 1 estimator(s)
0:44:59.791615 INFO: Calibration group :precursor, found 3 estimator(s)
0:44:59.791695 INFO: Disabling ion mobility calibration
0:44:59.791724 INFO: removed mobility estimator from group precursor
0:44:59.791871 INFO: Initializing OptimizationManager
0:44:59.791983 INFO: initial parameter: ms1_error = 30
0:44:59.792053 INFO: initial parameter: ms2_error = 30
0:44:59.792105 INFO: initial parameter: rt_error = 805.6004638671875
0:44:59.792150 INFO: initial parameter: mobility_error = 0.1
0:44:59.792193 INFO: initial parameter: column_type = library
0:44:59.792245 INFO: initial parameter: num_candidates = 1
0:44:59.792292 INFO: initial parameter: classifier_version = -1
0:44:59.792339 INFO: initial parameter: fwhm_rt = 5
0:44:59.792382 INFO: initial parameter: fwhm_mobility = 0.01
0:44:59.792423 INFO: initial parameter: score_cutoff = 0
0:44:59.792495 INFO: Initializing TimingManager
0:44:59.792553 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:44:59.792686 INFO: FDRManager not loaded from disk.
0:44:59.792709 INFO: Initializing FDRManager
0:44:59.792749 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:45:01.315368 PROGRESS: 6,373,245 target precursors potentially observable (7,405 removed)
0:45:03.476540 PROGRESS: Starting initial search for precursors.
0:45:03.737662 INFO: Starting optimization step 0.
0:45:03.737909 PROGRESS: === Extracting elution groups 0 to 200 ===
0:45:03.737987 PROGRESS: Extracting batch of 396 precursors
0:45:03.738983 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:03.739030 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:03.739068 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:45:03.739092 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:45:03.739391 INFO: Starting candidate selection
0:45:03.941269 INFO: Starting candidate scoring
0:45:03.978561 INFO: Finished candidate processing
0:45:03.978647 INFO: Collecting candidate features
0:45:03.987285 INFO: Collecting fragment features
0:45:03.989361 INFO: Finished candidate scoring
0:45:03.990149 PROGRESS: === Extracted 394 precursors and 4035 fragments ===
0:45:03.990436 INFO: performing precursor FDR with 47 features
0:45:03.990476 INFO: Decoy channel: -1
0:45:03.990505 INFO: Competetive: True
0:45:03.991497 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:04.010358 INFO: Test AUC: 0.675
0:45:04.010421 INFO: Train AUC: 0.484
0:45:04.010461 INFO: AUC difference: 39.67%
0:45:04.010489 WARNING: AUC difference > 5%. This may indicate overfitting.
0:45:04.188066 INFO: Resetting torch num_threads to 100
0:45:04.188886 INFO: === FDR correction performed with classifier version -1 ===
0:45:04.189578 PROGRESS: ============================= Precursor FDR =============================
0:45:04.189673 PROGRESS: Total precursors accumulated: 1
0:45:04.189735 PROGRESS: Target precursors: 1 (100.00%)
0:45:04.189790 PROGRESS: Decoy precursors: 0 (0.00%)
0:45:04.189838 PROGRESS: 
0:45:04.189885 PROGRESS: Precursor Summary:
0:45:04.190838 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:45:04.190929 PROGRESS: 
0:45:04.190990 PROGRESS: Protein Summary:
0:45:04.192030 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:45:04.192125 PROGRESS: =========================================================================
0:45:04.259424 INFO: Starting optimization step 1.
0:45:04.259647 PROGRESS: === Extracting elution groups 200 to 600 ===
0:45:04.259713 PROGRESS: Extracting batch of 786 precursors
0:45:04.260543 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:04.260592 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:04.260623 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:45:04.260646 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:45:04.260820 INFO: Starting candidate selection
0:45:04.450868 INFO: Starting candidate scoring
0:45:04.487383 INFO: Finished candidate processing
0:45:04.487458 INFO: Collecting candidate features
0:45:04.496242 INFO: Collecting fragment features
0:45:04.498570 INFO: Finished candidate scoring
0:45:04.500645 PROGRESS: === Extracted 1180 precursors and 12054 fragments ===
0:45:04.501390 INFO: performing precursor FDR with 47 features
0:45:04.501431 INFO: Decoy channel: -1
0:45:04.501455 INFO: Competetive: True
0:45:04.504273 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:04.523826 INFO: Test AUC: 0.506
0:45:04.523892 INFO: Train AUC: 0.515
0:45:04.523920 INFO: AUC difference: 1.89%
0:45:04.696026 INFO: Resetting torch num_threads to 100
0:45:04.696675 INFO: === FDR correction performed with classifier version -1 ===
0:45:04.697356 PROGRESS: ============================= Precursor FDR =============================
0:45:04.697451 PROGRESS: Total precursors accumulated: 1
0:45:04.697511 PROGRESS: Target precursors: 1 (100.00%)
0:45:04.697563 PROGRESS: Decoy precursors: 0 (0.00%)
0:45:04.697610 PROGRESS: 
0:45:04.697655 PROGRESS: Precursor Summary:
0:45:04.698590 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:45:04.698675 PROGRESS: 
0:45:04.698730 PROGRESS: Protein Summary:
0:45:04.699761 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:45:04.699849 PROGRESS: =========================================================================
0:45:04.769537 INFO: Starting optimization step 2.
0:45:04.769748 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:45:04.769816 PROGRESS: Extracting batch of 1573 precursors
0:45:04.770745 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:04.770792 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:04.770823 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:45:04.770846 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:45:04.771021 INFO: Starting candidate selection
0:45:04.966549 INFO: Starting candidate scoring
0:45:05.008030 INFO: Finished candidate processing
0:45:05.008109 INFO: Collecting candidate features
0:45:05.018323 INFO: Collecting fragment features
0:45:05.021890 INFO: Finished candidate scoring
0:45:05.024952 PROGRESS: === Extracted 2747 precursors and 28023 fragments ===
0:45:05.025944 INFO: performing precursor FDR with 47 features
0:45:05.025989 INFO: Decoy channel: -1
0:45:05.026014 INFO: Competetive: True
0:45:05.029315 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:05.058984 INFO: Test AUC: 0.499
0:45:05.059068 INFO: Train AUC: 0.499
0:45:05.059100 INFO: AUC difference: 0.01%
0:45:05.233455 INFO: Resetting torch num_threads to 100
0:45:05.234270 INFO: === FDR correction performed with classifier version -1 ===
0:45:05.235050 PROGRESS: ============================= Precursor FDR =============================
0:45:05.235145 PROGRESS: Total precursors accumulated: 1,396
0:45:05.235207 PROGRESS: Target precursors: 739 (52.94%)
0:45:05.235264 PROGRESS: Decoy precursors: 657 (47.06%)
0:45:05.235312 PROGRESS: 
0:45:05.235356 PROGRESS: Precursor Summary:
0:45:05.236254 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:45:05.236347 PROGRESS: 
0:45:05.236404 PROGRESS: Protein Summary:
0:45:05.237356 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:45:05.237445 PROGRESS: =========================================================================
0:45:05.309461 INFO: Starting optimization step 3.
0:45:05.309712 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:45:05.309780 PROGRESS: Extracting batch of 3149 precursors
0:45:05.310912 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:05.310962 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:05.310994 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:45:05.311016 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:45:05.311195 INFO: Starting candidate selection
0:45:05.550911 INFO: Starting candidate scoring
0:45:05.592757 INFO: Finished candidate processing
0:45:05.592850 INFO: Collecting candidate features
0:45:05.605781 INFO: Collecting fragment features
0:45:05.609802 INFO: Finished candidate scoring
0:45:05.614174 PROGRESS: === Extracted 5891 precursors and 60387 fragments ===
0:45:05.615446 INFO: performing precursor FDR with 47 features
0:45:05.615490 INFO: Decoy channel: -1
0:45:05.615515 INFO: Competetive: True
0:45:05.619608 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:05.675230 INFO: Test AUC: 0.495
0:45:05.675336 INFO: Train AUC: 0.491
0:45:05.675367 INFO: AUC difference: 0.91%
0:45:05.851863 INFO: Resetting torch num_threads to 100
0:45:05.852858 INFO: === FDR correction performed with classifier version -1 ===
0:45:05.853829 PROGRESS: ============================= Precursor FDR =============================
0:45:05.853925 PROGRESS: Total precursors accumulated: 2,994
0:45:05.853990 PROGRESS: Target precursors: 1,552 (51.84%)
0:45:05.854042 PROGRESS: Decoy precursors: 1,442 (48.16%)
0:45:05.854090 PROGRESS: 
0:45:05.854137 PROGRESS: Precursor Summary:
0:45:05.855017 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:45:05.855113 PROGRESS: 
0:45:05.855169 PROGRESS: Protein Summary:
0:45:05.856111 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:45:05.856199 PROGRESS: =========================================================================
0:45:05.932558 INFO: Starting optimization step 4.
0:45:05.932811 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:45:05.932881 PROGRESS: Extracting batch of 6319 precursors
0:45:05.934414 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:05.934464 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:05.934496 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:45:05.934519 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:45:05.934698 INFO: Starting candidate selection
0:45:06.269498 INFO: Starting candidate scoring
0:45:06.318749 INFO: Finished candidate processing
0:45:06.318854 INFO: Collecting candidate features
0:45:06.337094 INFO: Collecting fragment features
0:45:06.343484 INFO: Finished candidate scoring
0:45:06.350728 PROGRESS: === Extracted 12200 precursors and 124977 fragments ===
0:45:06.353276 INFO: performing precursor FDR with 47 features
0:45:06.353348 INFO: Decoy channel: -1
0:45:06.353376 INFO: Competetive: True
0:45:06.359496 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:06.442703 INFO: Test AUC: 0.494
0:45:06.442830 INFO: Train AUC: 0.489
0:45:06.442860 INFO: AUC difference: 0.93%
0:45:06.620092 INFO: Resetting torch num_threads to 100
0:45:06.621398 INFO: === FDR correction performed with classifier version -1 ===
0:45:06.622710 PROGRESS: ============================= Precursor FDR =============================
0:45:06.622811 PROGRESS: Total precursors accumulated: 6,189
0:45:06.622880 PROGRESS: Target precursors: 3,149 (50.88%)
0:45:06.622932 PROGRESS: Decoy precursors: 3,040 (49.12%)
0:45:06.622982 PROGRESS: 
0:45:06.623030 PROGRESS: Precursor Summary:
0:45:06.623935 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:45:06.624036 PROGRESS: 
0:45:06.624097 PROGRESS: Protein Summary:
0:45:06.625066 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:45:06.625158 PROGRESS: =========================================================================
0:45:06.708920 INFO: Starting optimization step 5.
0:45:06.709200 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:45:06.709271 PROGRESS: Extracting batch of 12617 precursors
0:45:06.711726 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:06.711778 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:06.711811 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:45:06.711833 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:45:06.712018 INFO: Starting candidate selection
0:45:07.491266 INFO: Starting candidate scoring
0:45:07.575952 INFO: Finished candidate processing
0:45:07.576062 INFO: Collecting candidate features
0:45:07.604657 INFO: Collecting fragment features
0:45:07.617067 INFO: Finished candidate scoring
0:45:07.631949 PROGRESS: === Extracted 24794 precursors and 254065 fragments ===
0:45:07.635565 INFO: performing precursor FDR with 47 features
0:45:07.635633 INFO: Decoy channel: -1
0:45:07.635659 INFO: Competetive: True
0:45:07.645627 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:07.925670 INFO: Test AUC: 0.500
0:45:07.925807 INFO: Train AUC: 0.500
0:45:07.925839 INFO: AUC difference: 0.00%
0:45:08.101989 INFO: Resetting torch num_threads to 100
0:45:08.103796 INFO: === FDR correction performed with classifier version -1 ===
0:45:08.105844 PROGRESS: ============================= Precursor FDR =============================
0:45:08.105950 PROGRESS: Total precursors accumulated: 12,557
0:45:08.106012 PROGRESS: Target precursors: 12,013 (95.67%)
0:45:08.106066 PROGRESS: Decoy precursors: 544 (4.33%)
0:45:08.106113 PROGRESS: 
0:45:08.106161 PROGRESS: Precursor Summary:
0:45:08.108450 PROGRESS: Channel   0:	 0.05 FDR: 12,013; 0.01 FDR:    92; 0.001 FDR:    92
0:45:08.108551 PROGRESS: 
0:45:08.108610 PROGRESS: Protein Summary:
0:45:08.112384 PROGRESS: Channel   0:	 0.05 FDR: 9,061; 0.01 FDR:    92; 0.001 FDR:    92
0:45:08.112495 PROGRESS: =========================================================================
0:45:08.212426 INFO: Starting optimization step 6.
0:45:08.212710 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:45:08.212780 PROGRESS: Extracting batch of 25256 precursors
0:45:08.218527 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:08.218607 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:08.218640 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:45:08.218664 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:45:08.218866 INFO: Starting candidate selection
0:45:09.745953 INFO: Starting candidate scoring
0:45:09.897542 INFO: Finished candidate processing
0:45:09.897670 INFO: Collecting candidate features
0:45:09.943868 INFO: Collecting fragment features
0:45:09.963461 INFO: Finished candidate scoring
0:45:09.987048 PROGRESS: === Extracted 50013 precursors and 511892 fragments ===
0:45:09.994629 INFO: performing precursor FDR with 47 features
0:45:09.994712 INFO: Decoy channel: -1
0:45:09.994738 INFO: Competetive: True
0:45:10.015105 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:10.742519 INFO: Test AUC: 0.500
0:45:10.742667 INFO: Train AUC: 0.500
0:45:10.742699 INFO: AUC difference: 0.00%
0:45:10.917329 INFO: Resetting torch num_threads to 100
0:45:10.920185 INFO: === FDR correction performed with classifier version -1 ===
0:45:10.923935 PROGRESS: ============================= Precursor FDR =============================
0:45:10.924071 PROGRESS: Total precursors accumulated: 25,292
0:45:10.924133 PROGRESS: Target precursors: 24,199 (95.68%)
0:45:10.924187 PROGRESS: Decoy precursors: 1,093 (4.32%)
0:45:10.924249 PROGRESS: 
0:45:10.924298 PROGRESS: Precursor Summary:
0:45:10.928067 PROGRESS: Channel   0:	 0.05 FDR: 24,199; 0.01 FDR:   172; 0.001 FDR:   172
0:45:10.928194 PROGRESS: 
0:45:10.928270 PROGRESS: Protein Summary:
0:45:10.934850 PROGRESS: Channel   0:	 0.05 FDR: 14,824; 0.01 FDR:   172; 0.001 FDR:   172
0:45:10.935003 PROGRESS: =========================================================================
0:45:11.067624 INFO: Starting optimization step 7.
0:45:11.067935 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:45:11.068037 PROGRESS: Extracting batch of 50439 precursors
0:45:11.079532 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:11.079667 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:11.079709 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:45:11.079736 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:45:11.079964 INFO: Starting candidate selection
0:45:14.190074 INFO: Starting candidate scoring
0:45:14.524882 INFO: Finished candidate processing
0:45:14.525036 INFO: Collecting candidate features
0:45:14.651534 INFO: Collecting fragment features
0:45:14.687876 INFO: Finished candidate scoring
0:45:14.782400 PROGRESS: === Extracted 100356 precursors and 1027225 fragments ===
0:45:14.796965 INFO: performing precursor FDR with 47 features
0:45:14.797129 INFO: Decoy channel: -1
0:45:14.797168 INFO: Competetive: True
0:45:14.846281 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:16.489535 INFO: Test AUC: 0.500
0:45:16.489707 INFO: Train AUC: 0.500
0:45:16.489743 INFO: AUC difference: 0.00%
0:45:16.668969 INFO: Resetting torch num_threads to 100
0:45:16.674035 INFO: === FDR correction performed with classifier version -1 ===
0:45:16.682887 PROGRESS: ============================= Precursor FDR =============================
0:45:16.683136 PROGRESS: Total precursors accumulated: 50,680
0:45:16.683207 PROGRESS: Target precursors: 48,559 (95.81%)
0:45:16.683271 PROGRESS: Decoy precursors: 2,121 (4.19%)
0:45:16.683331 PROGRESS: 
0:45:16.683386 PROGRESS: Precursor Summary:
0:45:16.691210 PROGRESS: Channel   0:	 0.05 FDR: 48,559; 0.01 FDR:   313; 0.001 FDR:   313
0:45:16.691385 PROGRESS: 
0:45:16.691453 PROGRESS: Protein Summary:
0:45:16.705529 PROGRESS: Channel   0:	 0.05 FDR: 21,768; 0.01 FDR:   312; 0.001 FDR:   312
0:45:16.705722 PROGRESS: =========================================================================
0:45:16.782999 INFO: fragments_df: keeping 725 of 1027225 [sum(precursor_idx_mask)=3012 sum(mass_error_mask)=1027225 stop_rank=725
0:45:16.998638 INFO: calibration group: precursor, fitting rt estimator 
0:45:17.124145 INFO: calibration group: fragment, fitting mz estimator 
0:45:17.276846 INFO: Using score_cutoff 43.85069965667724 (fac=0.99, q=1)
0:45:17.277310 INFO: calibration group: precursor, predicting mz
0:45:17.277410 WARNING: mz prediction was skipped as it has not been fitted yet
0:45:17.277447 INFO: calibration group: precursor, predicting rt
0:45:17.338449 INFO: calibration group: fragment, predicting mz
0:45:17.546721 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:45:17.547119 INFO: Starting optimization step 8.
0:45:17.547203 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:45:17.547292 PROGRESS: Extracting batch of 100535 precursors
0:45:17.582196 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:17.582365 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:17.582414 INFO: FWHM in RT is 3.14 seconds, sigma is 0.41
0:45:17.582446 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:45:17.582792 INFO: Starting candidate selection
0:45:21.793690 INFO: Starting candidate scoring
0:45:23.097715 INFO: Finished candidate processing
0:45:23.097830 INFO: Collecting candidate features
0:45:23.410737 INFO: Collecting fragment features
0:45:23.532068 INFO: Finished candidate scoring
0:45:23.630087 PROGRESS: === Extracted 200712 precursors and 2029481 fragments ===
0:45:23.630504 INFO: performing precursor FDR with 47 features
0:45:23.630541 INFO: Decoy channel: -1
0:45:23.630566 INFO: Competetive: True
0:45:23.687335 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:27.025602 INFO: Test AUC: 0.556
0:45:27.025794 INFO: Train AUC: 0.559
0:45:27.025826 INFO: AUC difference: 0.46%
0:45:27.272600 INFO: Resetting torch num_threads to 100
0:45:27.280190 INFO: === FDR correction performed with classifier version 7 ===
0:45:27.281180 PROGRESS: ============================= Precursor FDR =============================
0:45:27.281281 PROGRESS: Total precursors accumulated: 3
0:45:27.281350 PROGRESS: Target precursors: 3 (100.00%)
0:45:27.281406 PROGRESS: Decoy precursors: 0 (0.00%)
0:45:27.281456 PROGRESS: 
0:45:27.281501 PROGRESS: Precursor Summary:
0:45:27.282467 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
0:45:27.282557 PROGRESS: 
0:45:27.282617 PROGRESS: Protein Summary:
0:45:27.283653 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
0:45:27.283741 PROGRESS: =========================================================================
0:45:27.561688 INFO: calibration group: precursor, predicting mz
0:45:27.562031 WARNING: mz prediction was skipped as it has not been fitted yet
0:45:27.562066 INFO: calibration group: precursor, predicting rt
0:45:27.622988 INFO: calibration group: fragment, predicting mz
0:45:27.822856 INFO: === skipping optimization until target number of precursors are found ===
0:45:27.823227 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:45:27.823296 INFO: Starting optimization step 9.
0:45:27.823364 PROGRESS: === Extracting elution groups 51000 to 102200 ===
0:45:27.823440 PROGRESS: Extracting batch of 100917 precursors
0:45:27.848397 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:27.848533 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:27.848572 INFO: FWHM in RT is 3.14 seconds, sigma is 0.41
0:45:27.848595 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:45:27.848908 INFO: Starting candidate selection
0:45:32.081385 INFO: Starting candidate scoring
0:45:33.420547 INFO: Finished candidate processing
0:45:33.420662 INFO: Collecting candidate features
0:45:33.765798 INFO: Collecting fragment features
0:45:33.888810 INFO: Finished candidate scoring
0:45:34.086347 PROGRESS: === Extracted 402136 precursors and 4066798 fragments ===
0:45:34.130095 INFO: performing precursor FDR with 47 features
0:45:34.130250 INFO: Decoy channel: -1
0:45:34.130276 INFO: Competetive: True
0:45:34.300324 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:41.560549 INFO: Test AUC: 0.500
0:45:41.560774 INFO: Train AUC: 0.500
0:45:41.560811 INFO: AUC difference: 0.00%
0:45:41.757417 INFO: Resetting torch num_threads to 100
0:45:41.778527 INFO: === FDR correction performed with classifier version 7 ===
0:45:41.798464 PROGRESS: ============================= Precursor FDR =============================
0:45:41.798772 PROGRESS: Total precursors accumulated: 101,811
0:45:41.798842 PROGRESS: Target precursors: 97,402 (95.67%)
0:45:41.798912 PROGRESS: Decoy precursors: 4,409 (4.33%)
0:45:41.798961 PROGRESS: 
0:45:41.799010 PROGRESS: Precursor Summary:
0:45:41.815040 PROGRESS: Channel   0:	 0.05 FDR: 97,402; 0.01 FDR:   582; 0.001 FDR:   582
0:45:41.815237 PROGRESS: 
0:45:41.815298 PROGRESS: Protein Summary:
0:45:41.843957 PROGRESS: Channel   0:	 0.05 FDR: 28,369; 0.01 FDR:   574; 0.001 FDR:   574
0:45:41.844221 PROGRESS: =========================================================================
0:45:42.139198 INFO: fragments_df: keeping 2493 of 4066798 [sum(precursor_idx_mask)=11071 sum(mass_error_mask)=4066798 stop_rank=2493
0:45:42.398749 INFO: calibration group: precursor, fitting rt estimator 
0:45:42.536191 INFO: calibration group: fragment, fitting mz estimator 
0:45:42.870008 INFO: Using score_cutoff 40.93596418304443 (fac=0.99, q=1)
0:45:42.870471 INFO: calibration group: precursor, predicting mz
0:45:42.870571 WARNING: mz prediction was skipped as it has not been fitted yet
0:45:42.870602 INFO: calibration group: precursor, predicting rt
0:45:42.930194 INFO: calibration group: fragment, predicting mz
0:45:43.142862 INFO: === checking if optimization conditions were reached ===
0:45:43.143223 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:45:43.145691 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 30.8734.
0:45:43.145764 INFO: ==============================================
0:45:43.145875 INFO: Starting optimization step 10.
0:45:43.145952 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:45:43.146032 PROGRESS: Extracting batch of 100535 precursors
0:45:43.180255 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:43.180418 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:43.180471 INFO: FWHM in RT is 3.24 seconds, sigma is 0.42
0:45:43.180502 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:45:43.180856 INFO: Starting candidate selection
0:45:47.082219 INFO: Starting candidate scoring
0:45:48.508806 INFO: Finished candidate processing
0:45:48.508919 INFO: Collecting candidate features
0:45:48.817235 INFO: Collecting fragment features
0:45:48.931840 INFO: Finished candidate scoring
0:45:49.028904 PROGRESS: === Extracted 200712 precursors and 2032151 fragments ===
0:45:49.029341 INFO: performing precursor FDR with 47 features
0:45:49.029380 INFO: Decoy channel: -1
0:45:49.029403 INFO: Competetive: True
0:45:49.091323 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:52.364249 INFO: Test AUC: 0.550
0:45:52.364390 INFO: Train AUC: 0.558
0:45:52.364421 INFO: AUC difference: 1.37%
0:45:52.599921 INFO: Resetting torch num_threads to 100
0:45:52.657209 INFO: === FDR correction performed with classifier version 7 ===
0:45:52.658097 PROGRESS: ============================= Precursor FDR =============================
0:45:52.658193 PROGRESS: Total precursors accumulated: 1
0:45:52.658254 PROGRESS: Target precursors: 1 (100.00%)
0:45:52.658306 PROGRESS: Decoy precursors: 0 (0.00%)
0:45:52.658354 PROGRESS: 
0:45:52.658398 PROGRESS: Precursor Summary:
0:45:52.659342 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:45:52.659443 PROGRESS: 
0:45:52.659499 PROGRESS: Protein Summary:
0:45:52.660534 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:45:52.660628 PROGRESS: =========================================================================
0:45:52.933384 INFO: calibration group: precursor, predicting mz
0:45:52.933762 WARNING: mz prediction was skipped as it has not been fitted yet
0:45:52.933804 INFO: calibration group: precursor, predicting rt
0:45:52.995192 INFO: calibration group: fragment, predicting mz
0:45:53.212233 INFO: === skipping optimization until target number of precursors are found ===
0:45:53.212787 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:45:53.212898 INFO: Starting optimization step 11.
0:45:53.212987 PROGRESS: === Extracting elution groups 51000 to 102200 ===
0:45:53.213100 PROGRESS: Extracting batch of 100917 precursors
0:45:53.258416 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:53.258593 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:53.258645 INFO: FWHM in RT is 3.24 seconds, sigma is 0.42
0:45:53.258677 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:45:53.259100 INFO: Starting candidate selection
0:45:57.113724 INFO: Starting candidate scoring
0:45:58.717534 INFO: Finished candidate processing
0:45:58.717655 INFO: Collecting candidate features
0:45:59.041213 INFO: Collecting fragment features
0:45:59.162516 INFO: Finished candidate scoring
0:45:59.389515 PROGRESS: === Extracted 402136 precursors and 4072351 fragments ===
0:45:59.433490 INFO: performing precursor FDR with 47 features
0:45:59.433651 INFO: Decoy channel: -1
0:45:59.433679 INFO: Competetive: True
0:45:59.607707 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:07.397017 INFO: Test AUC: 0.500
0:46:07.397248 INFO: Train AUC: 0.500
0:46:07.397282 INFO: AUC difference: 0.00%
0:46:07.595297 INFO: Resetting torch num_threads to 100
0:46:07.616969 INFO: === FDR correction performed with classifier version 7 ===
0:46:07.636249 PROGRESS: ============================= Precursor FDR =============================
0:46:07.636496 PROGRESS: Total precursors accumulated: 101,789
0:46:07.636580 PROGRESS: Target precursors: 97,380 (95.67%)
0:46:07.636637 PROGRESS: Decoy precursors: 4,409 (4.33%)
0:46:07.636686 PROGRESS: 
0:46:07.636735 PROGRESS: Precursor Summary:
0:46:07.652806 PROGRESS: Channel   0:	 0.05 FDR: 97,380; 0.01 FDR:   581; 0.001 FDR:   581
0:46:07.653001 PROGRESS: 
0:46:07.653061 PROGRESS: Protein Summary:
0:46:07.680685 PROGRESS: Channel   0:	 0.05 FDR: 28,364; 0.01 FDR:   573; 0.001 FDR:   573
0:46:07.680947 PROGRESS: =========================================================================
0:46:07.967330 INFO: fragments_df: keeping 2508 of 4072351 [sum(precursor_idx_mask)=11032 sum(mass_error_mask)=4072351 stop_rank=2508
0:46:08.226048 INFO: calibration group: precursor, fitting rt estimator 
0:46:08.363828 INFO: calibration group: fragment, fitting mz estimator 
0:46:08.703171 INFO: Using score_cutoff 41.88092685699463 (fac=0.99, q=1)
0:46:08.703634 INFO: calibration group: precursor, predicting mz
0:46:08.703723 WARNING: mz prediction was skipped as it has not been fitted yet
0:46:08.703758 INFO: calibration group: precursor, predicting rt
0:46:08.765414 INFO: calibration group: fragment, predicting mz
0:46:08.977503 INFO: === checking if optimization conditions were reached ===
0:46:08.977890 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:46:08.980619 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 31.1346.
0:46:08.980682 INFO: ==============================================
0:46:08.980792 INFO: Starting optimization step 12.
0:46:08.980870 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:46:08.980967 PROGRESS: Extracting batch of 100535 precursors
0:46:09.015798 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:46:09.015971 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:46:09.016022 INFO: FWHM in RT is 3.27 seconds, sigma is 0.42
0:46:09.016051 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:46:09.016428 INFO: Starting candidate selection
0:46:12.941406 INFO: Starting candidate scoring
0:46:14.307451 INFO: Finished candidate processing
0:46:14.307603 INFO: Collecting candidate features
0:46:14.720586 INFO: Collecting fragment features
0:46:14.849730 INFO: Finished candidate scoring
0:46:14.972611 PROGRESS: === Extracted 200712 precursors and 2043492 fragments ===
0:46:14.973144 INFO: performing precursor FDR with 47 features
0:46:14.973185 INFO: Decoy channel: -1
0:46:14.973214 INFO: Competetive: True
0:46:15.043360 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:18.509098 INFO: Test AUC: 0.558
0:46:18.509299 INFO: Train AUC: 0.555
0:46:18.509354 INFO: AUC difference: 0.37%
0:46:18.758478 INFO: Resetting torch num_threads to 100
0:46:18.764141 INFO: === FDR correction performed with classifier version 7 ===
0:46:18.764967 PROGRESS: ============================= Precursor FDR =============================
0:46:18.765075 PROGRESS: Total precursors accumulated: 3
0:46:18.765153 PROGRESS: Target precursors: 3 (100.00%)
0:46:18.765220 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:18.765279 PROGRESS: 
0:46:18.765343 PROGRESS: Precursor Summary:
0:46:18.766323 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
0:46:18.766427 PROGRESS: 
0:46:18.766496 PROGRESS: Protein Summary:
0:46:18.767547 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
0:46:18.767652 PROGRESS: =========================================================================
0:46:19.022821 INFO: calibration group: precursor, predicting mz
0:46:19.023176 WARNING: mz prediction was skipped as it has not been fitted yet
0:46:19.023215 INFO: calibration group: precursor, predicting rt
0:46:19.083279 INFO: calibration group: fragment, predicting mz
0:46:19.278846 INFO: === skipping optimization until target number of precursors are found ===
0:46:19.279252 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:46:19.279345 INFO: Starting optimization step 13.
0:46:19.279441 PROGRESS: === Extracting elution groups 51000 to 102200 ===
0:46:19.279535 PROGRESS: Extracting batch of 100917 precursors
0:46:19.303826 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:46:19.303982 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:46:19.304037 INFO: FWHM in RT is 3.27 seconds, sigma is 0.42
0:46:19.304070 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:46:19.304447 INFO: Starting candidate selection
0:46:23.216385 INFO: Starting candidate scoring
0:46:24.556038 INFO: Finished candidate processing
0:46:24.556154 INFO: Collecting candidate features
0:46:24.874125 INFO: Collecting fragment features
0:46:24.993371 INFO: Finished candidate scoring
0:46:25.173312 PROGRESS: === Extracted 402136 precursors and 4094924 fragments ===
0:46:25.216880 INFO: performing precursor FDR with 47 features
0:46:25.217038 INFO: Decoy channel: -1
0:46:25.217067 INFO: Competetive: True
0:46:25.385338 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:32.379256 INFO: Test AUC: 0.558
0:46:32.379490 INFO: Train AUC: 0.559
0:46:32.379523 INFO: AUC difference: 0.21%
0:46:32.677551 INFO: Resetting torch num_threads to 100
0:46:32.698650 INFO: === FDR correction performed with classifier version 7 ===
0:46:32.699633 PROGRESS: ============================= Precursor FDR =============================
0:46:32.699736 PROGRESS: Total precursors accumulated: 3
0:46:32.699797 PROGRESS: Target precursors: 3 (100.00%)
0:46:32.699851 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:32.699897 PROGRESS: 
0:46:32.699943 PROGRESS: Precursor Summary:
0:46:32.700993 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
0:46:32.701102 PROGRESS: 
0:46:32.701160 PROGRESS: Protein Summary:
0:46:32.702190 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
0:46:32.702281 PROGRESS: =========================================================================
0:46:33.101255 INFO: calibration group: precursor, predicting mz
0:46:33.101577 WARNING: mz prediction was skipped as it has not been fitted yet
0:46:33.101625 INFO: calibration group: precursor, predicting rt
0:46:33.220406 INFO: calibration group: fragment, predicting mz
0:46:33.621695 INFO: === skipping optimization until target number of precursors are found ===
0:46:33.622033 PROGRESS: === Optimization of ms2_error has been skipped 2 time(s); maximum number is 1 ===
0:46:33.622481 PROGRESS: ✅ ms2_error      : optimization complete. Optimal parameter 30.0000 found after 2 searches.
0:46:33.622551 PROGRESS: Optimization finished for ms2_error.
0:46:33.838367 INFO: calibration group: precursor, predicting mz
0:46:33.838692 WARNING: mz prediction was skipped as it has not been fitted yet
0:46:33.838744 INFO: calibration group: precursor, predicting rt
0:46:33.898061 INFO: calibration group: fragment, predicting mz
0:46:34.120088 INFO: Starting optimization step 0.
0:46:34.120340 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:46:34.120424 PROGRESS: Extracting batch of 100535 precursors
0:46:34.144119 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:46:34.144271 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:46:34.144322 INFO: FWHM in RT is 3.24 seconds, sigma is 0.42
0:46:34.144351 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:46:34.144668 INFO: Starting candidate selection
0:46:38.047677 INFO: Starting candidate scoring
0:46:39.473945 INFO: Finished candidate processing
0:46:39.474112 INFO: Collecting candidate features
0:46:39.855595 INFO: Collecting fragment features
0:46:40.001894 INFO: Finished candidate scoring
0:46:40.134927 PROGRESS: === Extracted 200712 precursors and 2035605 fragments ===
0:46:40.135375 INFO: performing precursor FDR with 47 features
0:46:40.135419 INFO: Decoy channel: -1
0:46:40.135444 INFO: Competetive: True
0:46:40.221950 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:44.696577 INFO: Test AUC: 0.500
0:46:44.696722 INFO: Train AUC: 0.500
0:46:44.696753 INFO: AUC difference: 0.00%
0:46:44.881632 INFO: Resetting torch num_threads to 100
0:46:44.889786 INFO: === FDR correction performed with classifier version 9 ===
0:46:44.902893 PROGRESS: ============================= Precursor FDR =============================
0:46:44.903109 PROGRESS: Total precursors accumulated: 50,870
0:46:44.903177 PROGRESS: Target precursors: 48,637 (95.61%)
0:46:44.903233 PROGRESS: Decoy precursors: 2,233 (4.39%)
0:46:44.903282 PROGRESS: 
0:46:44.903330 PROGRESS: Precursor Summary:
0:46:44.915552 PROGRESS: Channel   0:	 0.05 FDR: 48,637; 0.01 FDR:   315; 0.001 FDR:   315
0:46:44.915749 PROGRESS: 
0:46:44.915811 PROGRESS: Protein Summary:
0:46:44.935839 PROGRESS: Channel   0:	 0.05 FDR: 21,587; 0.01 FDR:   314; 0.001 FDR:   314
0:46:44.936032 PROGRESS: =========================================================================
0:46:45.078421 INFO: fragments_df: keeping 1378 of 2035605 [sum(precursor_idx_mask)=5982 sum(mass_error_mask)=2035605 stop_rank=1378
0:46:45.381456 INFO: calibration group: precursor, fitting rt estimator 
0:46:45.483459 INFO: calibration group: fragment, fitting mz estimator 
0:46:45.660917 INFO: Using score_cutoff 40.42877091064453 (fac=0.99, q=1)
0:46:45.661437 INFO: calibration group: precursor, predicting mz
0:46:45.661526 WARNING: mz prediction was skipped as it has not been fitted yet
0:46:45.661559 INFO: calibration group: precursor, predicting rt
0:46:45.723685 INFO: calibration group: fragment, predicting mz
0:46:45.946813 INFO: === checking if optimization conditions were reached ===
0:46:45.947143 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:46:45.949423 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 416.8610.
0:46:45.949480 INFO: ==============================================
0:46:45.949574 INFO: Starting optimization step 1.
0:46:45.949645 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:46:45.949706 PROGRESS: Extracting batch of 100535 precursors
0:46:46.207143 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:46:46.207286 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:46:46.207327 INFO: FWHM in RT is 3.21 seconds, sigma is 0.41
0:46:46.207351 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:46:46.207625 INFO: Starting candidate selection
0:46:50.482502 INFO: Starting candidate scoring
0:46:51.795789 INFO: Finished candidate processing
0:46:51.795895 INFO: Collecting candidate features
0:46:52.133147 INFO: Collecting fragment features
0:46:52.258631 INFO: Finished candidate scoring
0:46:52.355914 PROGRESS: === Extracted 200709 precursors and 2020531 fragments ===
0:46:52.356424 INFO: performing precursor FDR with 47 features
0:46:52.356486 INFO: Decoy channel: -1
0:46:52.356509 INFO: Competetive: True
0:46:52.431462 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:56.080159 INFO: Test AUC: 0.500
0:46:56.080308 INFO: Train AUC: 0.500
0:46:56.080685 INFO: AUC difference: 0.00%
0:46:56.276785 INFO: Resetting torch num_threads to 100
0:46:56.329933 INFO: === FDR correction performed with classifier version 9 ===
0:46:56.340461 PROGRESS: ============================= Precursor FDR =============================
0:46:56.340673 PROGRESS: Total precursors accumulated: 50,863
0:46:56.340739 PROGRESS: Target precursors: 48,630 (95.61%)
0:46:56.340798 PROGRESS: Decoy precursors: 2,233 (4.39%)
0:46:56.340851 PROGRESS: 
0:46:56.340900 PROGRESS: Precursor Summary:
0:46:56.350594 PROGRESS: Channel   0:	 0.05 FDR: 48,630; 0.01 FDR:   315; 0.001 FDR:   315
0:46:56.350804 PROGRESS: 
0:46:56.350881 PROGRESS: Protein Summary:
0:46:56.366752 PROGRESS: Channel   0:	 0.05 FDR: 21,583; 0.01 FDR:   314; 0.001 FDR:   314
0:46:56.366926 PROGRESS: =========================================================================
0:46:56.508773 INFO: fragments_df: keeping 1344 of 2020531 [sum(precursor_idx_mask)=5975 sum(mass_error_mask)=2020531 stop_rank=1344
0:46:56.810459 INFO: calibration group: precursor, fitting rt estimator 
0:46:56.929433 INFO: calibration group: fragment, fitting mz estimator 
0:46:57.133901 INFO: Using score_cutoff 41.75282664871216 (fac=0.99, q=1)
0:46:57.134347 INFO: calibration group: precursor, predicting mz
0:46:57.134438 WARNING: mz prediction was skipped as it has not been fitted yet
0:46:57.134473 INFO: calibration group: precursor, predicting rt
0:46:57.199990 INFO: calibration group: fragment, predicting mz
0:46:57.452221 INFO: === checking if optimization conditions were reached ===
0:46:57.452658 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:46:57.455270 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 411.0126.
0:46:57.455336 INFO: ==============================================
0:46:57.455440 INFO: Starting optimization step 2.
0:46:57.455521 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:46:57.455597 PROGRESS: Extracting batch of 100535 precursors
0:46:57.488467 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:46:57.488608 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:46:57.488652 INFO: FWHM in RT is 3.19 seconds, sigma is 0.41
0:46:57.488678 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:46:57.489030 INFO: Starting candidate selection
0:47:01.657202 INFO: Starting candidate scoring
0:47:02.964784 INFO: Finished candidate processing
0:47:02.964896 INFO: Collecting candidate features
0:47:03.306279 INFO: Collecting fragment features
0:47:03.430308 INFO: Finished candidate scoring
0:47:03.603757 PROGRESS: === Extracted 200709 precursors and 2025067 fragments ===
0:47:03.604253 INFO: performing precursor FDR with 47 features
0:47:03.604296 INFO: Decoy channel: -1
0:47:03.604319 INFO: Competetive: True
0:47:03.675153 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:07.140206 INFO: Test AUC: 0.500
0:47:07.140362 INFO: Train AUC: 0.500
0:47:07.140392 INFO: AUC difference: 0.00%
0:47:07.331297 INFO: Resetting torch num_threads to 100
0:47:07.472774 INFO: === FDR correction performed with classifier version 9 ===
0:47:07.484828 PROGRESS: ============================= Precursor FDR =============================
0:47:07.485033 PROGRESS: Total precursors accumulated: 50,864
0:47:07.485104 PROGRESS: Target precursors: 48,631 (95.61%)
0:47:07.485157 PROGRESS: Decoy precursors: 2,233 (4.39%)
0:47:07.485204 PROGRESS: 
0:47:07.485248 PROGRESS: Precursor Summary:
0:47:07.494180 PROGRESS: Channel   0:	 0.05 FDR: 48,631; 0.01 FDR:   315; 0.001 FDR:   315
0:47:07.494392 PROGRESS: 
0:47:07.494449 PROGRESS: Protein Summary:
0:47:07.547774 PROGRESS: Channel   0:	 0.05 FDR: 21,584; 0.01 FDR:   314; 0.001 FDR:   314
0:47:07.548046 PROGRESS: =========================================================================
0:47:07.691095 INFO: fragments_df: keeping 1351 of 2025067 [sum(precursor_idx_mask)=5979 sum(mass_error_mask)=2025067 stop_rank=1351
0:47:07.980407 INFO: calibration group: precursor, fitting rt estimator 
0:47:08.108763 INFO: calibration group: fragment, fitting mz estimator 
0:47:08.312005 INFO: Using score_cutoff 41.70222019500732 (fac=0.99, q=1)
0:47:08.312584 INFO: calibration group: precursor, predicting mz
0:47:08.312676 WARNING: mz prediction was skipped as it has not been fitted yet
0:47:08.312709 INFO: calibration group: precursor, predicting rt
0:47:08.375475 INFO: calibration group: fragment, predicting mz
0:47:08.590383 INFO: === checking if optimization conditions were reached ===
0:47:08.591798 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:47:08.593920 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 411.0126 found after 3 searches.
0:47:08.594067 INFO: ==============================================
0:47:08.594366 PROGRESS: Optimization finished for rt_error.
0:47:08.808812 INFO: calibration group: precursor, predicting mz
0:47:08.809144 WARNING: mz prediction was skipped as it has not been fitted yet
0:47:08.809176 INFO: calibration group: precursor, predicting rt
0:47:08.870500 INFO: calibration group: fragment, predicting mz
0:47:09.112974 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:47:09.113259 PROGRESS: ==============================================
0:47:09.113344 PROGRESS: ms2_error      : 30.0000
0:47:09.113410 PROGRESS: rt_error       : 411.0126
0:47:09.113468 PROGRESS: ==============================================
0:47:09.117530 INFO: calibration group: precursor, predicting mz
0:47:09.117695 WARNING: mz prediction was skipped as it has not been fitted yet
0:47:09.117731 INFO: calibration group: precursor, predicting rt
0:47:16.938842 INFO: calibration group: fragment, predicting mz
0:47:41.846571 PROGRESS: Extracting batch of 12567710 precursors
0:47:44.510023 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:47:44.510181 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:47:44.510225 INFO: FWHM in RT is 3.19 seconds, sigma is 0.41
0:47:44.510249 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:47:44.510685 INFO: Starting candidate selection
0:56:15.647865 INFO: Applying score cutoff of 41.70222019500732
0:56:16.397480 INFO: Removed 2369094 precursors with score below cutoff
0:56:18.842521 INFO: Starting candidate scoring
0:58:55.273114 INFO: Finished candidate processing
0:58:55.273447 INFO: Collecting candidate features
0:59:32.708230 INFO: Collecting fragment features
0:59:48.030532 INFO: Finished candidate scoring
1:00:20.052155 INFO: === FDR correction performed with classifier version 16 ===
1:00:20.103964 INFO: performing precursor FDR with 47 features
1:00:20.104076 INFO: Decoy channel: -1
1:00:20.104109 INFO: Competetive: True
1:00:25.734362 INFO: Setting torch num_threads to 2 for FDR classification task
1:16:17.537156 INFO: Test AUC: 0.500
1:16:17.537449 INFO: Train AUC: 0.500
1:16:17.537486 INFO: AUC difference: 0.00%
1:16:18.403650 INFO: Resetting torch num_threads to 100
1:16:18.876400 INFO: Removing fragments below FDR threshold
1:16:20.947295 PROGRESS: ============================= Precursor FDR =============================
1:16:20.947825 PROGRESS: Total precursors accumulated: 25,155
1:16:20.947898 PROGRESS: Target precursors: 24,906 (99.01%)
1:16:20.947953 PROGRESS: Decoy precursors: 249 (0.99%)
1:16:20.948003 PROGRESS: 
1:16:20.948062 PROGRESS: Precursor Summary:
1:16:20.956958 PROGRESS: Channel   0:	 0.05 FDR: 24,906; 0.01 FDR: 24,906; 0.001 FDR: 24,906
1:16:20.957157 PROGRESS: 
1:16:20.957217 PROGRESS: Protein Summary:
1:16:20.973378 PROGRESS: Channel   0:	 0.05 FDR: 15,275; 0.01 FDR: 15,275; 0.001 FDR: 15,275
1:16:20.973620 PROGRESS: =========================================================================
1:16:21.624913 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:16:22.077694 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:16:22.077895 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant
1:16:22.077988 INFO: Creating folder run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/figures
1:16:22.078933 INFO: Initializing RawFileManager
1:16:33.334492 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
1:16:33.342311 INFO: Determining DIA cycle
1:16:33.358073 INFO: Found cycle with start 0.00 min and length 300.
1:16:33.536845 INFO: RT (min)            : 0.0 - 26.9
1:16:33.537027 INFO: RT duration (sec)   : 1611.2
1:16:33.537059 INFO: RT duration (min)   : 26.9
1:16:33.537084 INFO: Cycle len (scans)   : 300
1:16:33.537105 INFO: Cycle len (sec)     : 1.65
1:16:33.537126 INFO: Number of cycles    : 977
1:16:33.537144 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:16:35.357631 INFO: Initializing CalibrationManager
1:16:35.358146 INFO: Loading calibration config
1:16:35.358841 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'}]
1:16:35.358940 INFO: Calibration group :fragment, found 1 estimator(s)
1:16:35.359033 INFO: Calibration group :precursor, found 3 estimator(s)
1:16:35.359132 INFO: Disabling ion mobility calibration
1:16:35.359166 INFO: removed mobility estimator from group precursor
1:16:35.359340 INFO: Initializing OptimizationManager
1:16:35.359471 INFO: initial parameter: ms1_error = 30
1:16:35.359540 INFO: initial parameter: ms2_error = 30
1:16:35.359594 INFO: initial parameter: rt_error = 805.5982666015625
1:16:35.359646 INFO: initial parameter: mobility_error = 0.1
1:16:35.359693 INFO: initial parameter: column_type = library
1:16:35.359735 INFO: initial parameter: num_candidates = 1
1:16:35.359776 INFO: initial parameter: classifier_version = -1
1:16:35.359818 INFO: initial parameter: fwhm_rt = 5
1:16:35.359859 INFO: initial parameter: fwhm_mobility = 0.01
1:16:35.359900 INFO: initial parameter: score_cutoff = 0
1:16:35.359972 INFO: Initializing TimingManager
1:16:35.360039 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:16:35.360185 INFO: FDRManager not loaded from disk.
1:16:35.360209 INFO: Initializing FDRManager
1:16:35.360262 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:16:36.985528 PROGRESS: 6,373,245 target precursors potentially observable (7,405 removed)
1:16:39.316654 PROGRESS: Starting initial search for precursors.
1:16:39.576753 INFO: Starting optimization step 0.
1:16:39.577016 PROGRESS: === Extracting elution groups 0 to 200 ===
1:16:39.577095 PROGRESS: Extracting batch of 396 precursors
1:16:39.578126 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:16:39.578182 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:16:39.578222 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:16:39.578245 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:16:39.578569 INFO: Starting candidate selection
1:16:39.954528 INFO: Starting candidate scoring
1:16:39.992914 INFO: Finished candidate processing
1:16:39.992996 INFO: Collecting candidate features
1:16:40.001678 INFO: Collecting fragment features
1:16:40.003728 INFO: Finished candidate scoring
1:16:40.004497 PROGRESS: === Extracted 394 precursors and 4076 fragments ===
1:16:40.004780 INFO: performing precursor FDR with 47 features
1:16:40.004818 INFO: Decoy channel: -1
1:16:40.004841 INFO: Competetive: True
1:16:40.005854 INFO: Setting torch num_threads to 2 for FDR classification task
1:16:40.025514 INFO: Test AUC: 0.500
1:16:40.025582 INFO: Train AUC: 0.500
1:16:40.025611 INFO: AUC difference: 0.00%
1:16:40.204839 INFO: Resetting torch num_threads to 100
1:16:40.205414 INFO: === FDR correction performed with classifier version -1 ===
1:16:40.206068 PROGRESS: ============================= Precursor FDR =============================
1:16:40.206159 PROGRESS: Total precursors accumulated: 199
1:16:40.206220 PROGRESS: Target precursors: 91 (45.73%)
1:16:40.206273 PROGRESS: Decoy precursors: 108 (54.27%)
1:16:40.206320 PROGRESS: 
1:16:40.206367 PROGRESS: Precursor Summary:
1:16:40.207253 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
1:16:40.207341 PROGRESS: 
1:16:40.207397 PROGRESS: Protein Summary:
1:16:40.208375 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
1:16:40.208466 PROGRESS: =========================================================================
1:16:40.275893 INFO: Starting optimization step 1.
1:16:40.276124 PROGRESS: === Extracting elution groups 200 to 600 ===
1:16:40.276194 PROGRESS: Extracting batch of 786 precursors
1:16:40.277247 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:16:40.277296 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:16:40.277328 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:16:40.277350 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:16:40.277527 INFO: Starting candidate selection
1:16:40.553571 INFO: Starting candidate scoring
1:16:40.592289 INFO: Finished candidate processing
1:16:40.592371 INFO: Collecting candidate features
1:16:40.601545 INFO: Collecting fragment features
1:16:40.603941 INFO: Finished candidate scoring
1:16:40.606007 PROGRESS: === Extracted 1180 precursors and 12140 fragments ===
1:16:40.606778 INFO: performing precursor FDR with 47 features
1:16:40.606819 INFO: Decoy channel: -1
1:16:40.606844 INFO: Competetive: True
1:16:40.609693 INFO: Setting torch num_threads to 2 for FDR classification task
1:16:40.631140 INFO: Test AUC: 0.496
1:16:40.631209 INFO: Train AUC: 0.501
1:16:40.631240 INFO: AUC difference: 1.05%
1:16:40.801657 INFO: Resetting torch num_threads to 100
1:16:40.802337 INFO: === FDR correction performed with classifier version -1 ===
1:16:40.803033 PROGRESS: ============================= Precursor FDR =============================
1:16:40.803127 PROGRESS: Total precursors accumulated: 575
1:16:40.803187 PROGRESS: Target precursors: 542 (94.26%)
1:16:40.803240 PROGRESS: Decoy precursors: 33 (5.74%)
1:16:40.803291 PROGRESS: 
1:16:40.803335 PROGRESS: Precursor Summary:
1:16:40.804271 PROGRESS: Channel   0:	 0.05 FDR:   210; 0.01 FDR:     2; 0.001 FDR:     2
1:16:40.804364 PROGRESS: 
1:16:40.804424 PROGRESS: Protein Summary:
1:16:40.805443 PROGRESS: Channel   0:	 0.05 FDR:   209; 0.01 FDR:     2; 0.001 FDR:     2
1:16:40.805534 PROGRESS: =========================================================================
1:16:40.877272 INFO: Starting optimization step 2.
1:16:40.877517 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:16:40.877585 PROGRESS: Extracting batch of 1573 precursors
1:16:40.878523 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:16:40.878570 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:16:40.878612 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:16:40.878634 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:16:40.878813 INFO: Starting candidate selection
1:16:41.185559 INFO: Starting candidate scoring
1:16:41.226254 INFO: Finished candidate processing
1:16:41.226335 INFO: Collecting candidate features
1:16:41.236760 INFO: Collecting fragment features
1:16:41.240166 INFO: Finished candidate scoring
1:16:41.243321 PROGRESS: === Extracted 2747 precursors and 28235 fragments ===
1:16:41.244345 INFO: performing precursor FDR with 47 features
1:16:41.244388 INFO: Decoy channel: -1
1:16:41.244411 INFO: Competetive: True
1:16:41.247743 INFO: Setting torch num_threads to 2 for FDR classification task
1:16:41.283957 INFO: Test AUC: 0.498
1:16:41.284037 INFO: Train AUC: 0.499
1:16:41.284066 INFO: AUC difference: 0.16%
1:16:41.456560 INFO: Resetting torch num_threads to 100
1:16:41.457425 INFO: === FDR correction performed with classifier version -1 ===
1:16:41.458207 PROGRESS: ============================= Precursor FDR =============================
1:16:41.458298 PROGRESS: Total precursors accumulated: 1,394
1:16:41.458358 PROGRESS: Target precursors: 1,307 (93.76%)
1:16:41.458410 PROGRESS: Decoy precursors: 87 (6.24%)
1:16:41.458457 PROGRESS: 
1:16:41.458500 PROGRESS: Precursor Summary:
1:16:41.459376 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:16:41.459465 PROGRESS: 
1:16:41.459521 PROGRESS: Protein Summary:
1:16:41.460472 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:16:41.460564 PROGRESS: =========================================================================
1:16:41.535248 INFO: Starting optimization step 3.
1:16:41.535507 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:16:41.535580 PROGRESS: Extracting batch of 3149 precursors
1:16:41.536754 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:16:41.536803 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:16:41.536834 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:16:41.536857 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:16:41.537032 INFO: Starting candidate selection
1:16:41.868423 INFO: Starting candidate scoring
1:16:41.910321 INFO: Finished candidate processing
1:16:41.910414 INFO: Collecting candidate features
1:16:41.923680 INFO: Collecting fragment features
1:16:41.927825 INFO: Finished candidate scoring
1:16:41.932176 PROGRESS: === Extracted 5891 precursors and 60843 fragments ===
1:16:41.933438 INFO: performing precursor FDR with 47 features
1:16:41.933484 INFO: Decoy channel: -1
1:16:41.933509 INFO: Competetive: True
1:16:41.937958 INFO: Setting torch num_threads to 2 for FDR classification task
1:16:41.976052 INFO: Test AUC: 0.500
1:16:41.976148 INFO: Train AUC: 0.499
1:16:41.976177 INFO: AUC difference: 0.25%
1:16:42.147352 INFO: Resetting torch num_threads to 100
1:16:42.148380 INFO: === FDR correction performed with classifier version -1 ===
1:16:42.149376 PROGRESS: ============================= Precursor FDR =============================
1:16:42.149471 PROGRESS: Total precursors accumulated: 2,991
1:16:42.149533 PROGRESS: Target precursors: 2,803 (93.71%)
1:16:42.149587 PROGRESS: Decoy precursors: 188 (6.29%)
1:16:42.149635 PROGRESS: 
1:16:42.149680 PROGRESS: Precursor Summary:
1:16:42.150563 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:16:42.150652 PROGRESS: 
1:16:42.150708 PROGRESS: Protein Summary:
1:16:42.151647 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:16:42.151735 PROGRESS: =========================================================================
1:16:42.230262 INFO: Starting optimization step 4.
1:16:42.230527 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:16:42.230598 PROGRESS: Extracting batch of 6319 precursors
1:16:42.232274 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:16:42.232325 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:16:42.232358 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:16:42.232390 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:16:42.232571 INFO: Starting candidate selection
1:16:42.689785 INFO: Starting candidate scoring
1:16:42.740518 INFO: Finished candidate processing
1:16:42.740622 INFO: Collecting candidate features
1:16:42.759590 INFO: Collecting fragment features
1:16:42.765973 INFO: Finished candidate scoring
1:16:42.775815 PROGRESS: === Extracted 12200 precursors and 125895 fragments ===
1:16:42.778468 INFO: performing precursor FDR with 47 features
1:16:42.778530 INFO: Decoy channel: -1
1:16:42.778556 INFO: Competetive: True
1:16:42.784743 INFO: Setting torch num_threads to 2 for FDR classification task
1:16:42.853386 INFO: Test AUC: 0.499
1:16:42.853513 INFO: Train AUC: 0.499
1:16:42.853543 INFO: AUC difference: 0.03%
1:16:43.024351 INFO: Resetting torch num_threads to 100
1:16:43.025652 INFO: === FDR correction performed with classifier version -1 ===
1:16:43.026943 PROGRESS: ============================= Precursor FDR =============================
1:16:43.027039 PROGRESS: Total precursors accumulated: 6,185
1:16:43.027100 PROGRESS: Target precursors: 5,857 (94.70%)
1:16:43.027152 PROGRESS: Decoy precursors: 328 (5.30%)
1:16:43.027198 PROGRESS: 
1:16:43.027241 PROGRESS: Precursor Summary:
1:16:43.028159 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:16:43.028257 PROGRESS: 
1:16:43.028315 PROGRESS: Protein Summary:
1:16:43.029315 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:16:43.029408 PROGRESS: =========================================================================
1:16:43.114563 INFO: Starting optimization step 5.
1:16:43.114841 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:16:43.114924 PROGRESS: Extracting batch of 12617 precursors
1:16:43.117533 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:16:43.117587 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:16:43.117619 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:16:43.117641 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:16:43.117824 INFO: Starting candidate selection
1:16:43.849838 INFO: Starting candidate scoring
1:16:43.946085 INFO: Finished candidate processing
1:16:43.946192 INFO: Collecting candidate features
1:16:43.975775 INFO: Collecting fragment features
1:16:43.987280 INFO: Finished candidate scoring
1:16:44.002463 PROGRESS: === Extracted 24794 precursors and 255707 fragments ===
1:16:44.006021 INFO: performing precursor FDR with 47 features
1:16:44.006090 INFO: Decoy channel: -1
1:16:44.006115 INFO: Competetive: True
1:16:44.016329 INFO: Setting torch num_threads to 2 for FDR classification task
1:16:44.332537 INFO: Test AUC: 0.500
1:16:44.332672 INFO: Train AUC: 0.500
1:16:44.332703 INFO: AUC difference: 0.01%
1:16:44.509683 INFO: Resetting torch num_threads to 100
1:16:44.511611 INFO: === FDR correction performed with classifier version -1 ===
1:16:44.513793 PROGRESS: ============================= Precursor FDR =============================
1:16:44.513897 PROGRESS: Total precursors accumulated: 12,557
1:16:44.513960 PROGRESS: Target precursors: 11,997 (95.54%)
1:16:44.514013 PROGRESS: Decoy precursors: 560 (4.46%)
1:16:44.514060 PROGRESS: 
1:16:44.514103 PROGRESS: Precursor Summary:
1:16:44.516352 PROGRESS: Channel   0:	 0.05 FDR: 11,997; 0.01 FDR:     0; 0.001 FDR:     0
1:16:44.516456 PROGRESS: 
1:16:44.516512 PROGRESS: Protein Summary:
1:16:44.520310 PROGRESS: Channel   0:	 0.05 FDR: 9,044; 0.01 FDR:     0; 0.001 FDR:     0
1:16:44.520419 PROGRESS: =========================================================================
1:16:44.621140 INFO: Starting optimization step 6.
1:16:44.621446 PROGRESS: === Extracting elution groups 12600 to 25400 ===
1:16:44.621537 PROGRESS: Extracting batch of 25256 precursors
1:16:44.627529 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:16:44.627604 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:16:44.627637 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:16:44.627670 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:16:44.627892 INFO: Starting candidate selection
1:16:45.850947 INFO: Starting candidate scoring
1:16:46.027290 INFO: Finished candidate processing
1:16:46.027403 INFO: Collecting candidate features
1:16:46.077209 INFO: Collecting fragment features
1:16:46.095104 INFO: Finished candidate scoring
1:16:46.119826 PROGRESS: === Extracted 50013 precursors and 515130 fragments ===
1:16:46.126741 INFO: performing precursor FDR with 47 features
1:16:46.126835 INFO: Decoy channel: -1
1:16:46.126867 INFO: Competetive: True
1:16:46.146921 INFO: Setting torch num_threads to 2 for FDR classification task
1:16:46.816113 INFO: Test AUC: 0.541
1:16:46.816281 INFO: Train AUC: 0.548
1:16:46.816319 INFO: AUC difference: 1.28%
1:16:47.008065 INFO: Resetting torch num_threads to 100
1:16:47.011056 INFO: === FDR correction performed with classifier version -1 ===
1:16:47.011749 PROGRESS: ============================= Precursor FDR =============================
1:16:47.011847 PROGRESS: Total precursors accumulated: 19
1:16:47.011916 PROGRESS: Target precursors: 18 (94.74%)
1:16:47.011976 PROGRESS: Decoy precursors: 1 (5.26%)
1:16:47.012029 PROGRESS: 
1:16:47.012079 PROGRESS: Precursor Summary:
1:16:47.012990 PROGRESS: Channel   0:	 0.05 FDR:     8; 0.01 FDR:     8; 0.001 FDR:     8
1:16:47.013086 PROGRESS: 
1:16:47.013150 PROGRESS: Protein Summary:
1:16:47.014127 PROGRESS: Channel   0:	 0.05 FDR:     8; 0.01 FDR:     8; 0.001 FDR:     8
1:16:47.014224 PROGRESS: =========================================================================
1:16:47.149261 INFO: Starting optimization step 7.
1:16:47.149566 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1:16:47.149661 PROGRESS: Extracting batch of 50439 precursors
1:16:47.162122 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:16:47.162261 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:16:47.162300 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:16:47.162328 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:16:47.162568 INFO: Starting candidate selection
1:16:50.226662 INFO: Starting candidate scoring
1:16:50.551367 INFO: Finished candidate processing
1:16:50.551540 INFO: Collecting candidate features
1:16:50.666132 INFO: Collecting fragment features
1:16:50.703229 INFO: Finished candidate scoring
1:16:50.755672 PROGRESS: === Extracted 100356 precursors and 1033940 fragments ===
1:16:50.768646 INFO: performing precursor FDR with 47 features
1:16:50.768737 INFO: Decoy channel: -1
1:16:50.768764 INFO: Competetive: True
1:16:50.818420 INFO: Setting torch num_threads to 2 for FDR classification task
1:16:52.418911 INFO: Test AUC: 0.560
1:16:52.419058 INFO: Train AUC: 0.573
1:16:52.419089 INFO: AUC difference: 2.15%
1:16:52.619311 INFO: Resetting torch num_threads to 100
1:16:52.624691 INFO: === FDR correction performed with classifier version -1 ===
1:16:52.625427 PROGRESS: ============================= Precursor FDR =============================
1:16:52.625519 PROGRESS: Total precursors accumulated: 30
1:16:52.625580 PROGRESS: Target precursors: 28 (93.33%)
1:16:52.625633 PROGRESS: Decoy precursors: 2 (6.67%)
1:16:52.625679 PROGRESS: 
1:16:52.625724 PROGRESS: Precursor Summary:
1:16:52.626606 PROGRESS: Channel   0:	 0.05 FDR:    10; 0.01 FDR:    10; 0.001 FDR:    10
1:16:52.626693 PROGRESS: 
1:16:52.626750 PROGRESS: Protein Summary:
1:16:52.627711 PROGRESS: Channel   0:	 0.05 FDR:    10; 0.01 FDR:    10; 0.001 FDR:    10
1:16:52.627798 PROGRESS: =========================================================================
1:16:52.835124 INFO: Starting optimization step 8.
1:16:52.835471 PROGRESS: === Extracting elution groups 51000 to 102200 ===
1:16:52.835546 PROGRESS: Extracting batch of 100917 precursors
1:16:52.861305 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:16:52.861465 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:16:52.861504 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:16:52.861530 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:16:52.861801 INFO: Starting candidate selection
1:16:58.826687 INFO: Starting candidate scoring
1:16:59.543088 INFO: Finished candidate processing
1:16:59.543198 INFO: Collecting candidate features
1:16:59.782828 INFO: Collecting fragment features
1:16:59.858392 INFO: Finished candidate scoring
1:17:00.028342 PROGRESS: === Extracted 201068 precursors and 2071364 fragments ===
1:17:00.054247 INFO: performing precursor FDR with 47 features
1:17:00.054404 INFO: Decoy channel: -1
1:17:00.054430 INFO: Competetive: True
1:17:00.174953 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:03.673712 INFO: Test AUC: 0.568
1:17:03.673940 INFO: Train AUC: 0.578
1:17:03.673973 INFO: AUC difference: 1.83%
1:17:03.904354 INFO: Resetting torch num_threads to 100
1:17:03.917705 INFO: === FDR correction performed with classifier version -1 ===
1:17:03.918726 PROGRESS: ============================= Precursor FDR =============================
1:17:03.918854 PROGRESS: Total precursors accumulated: 1
1:17:03.918916 PROGRESS: Target precursors: 1 (100.00%)
1:17:03.918973 PROGRESS: Decoy precursors: 0 (0.00%)
1:17:03.919017 PROGRESS: 
1:17:03.919060 PROGRESS: Precursor Summary:
1:17:03.920020 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:17:03.920110 PROGRESS: 
1:17:03.920164 PROGRESS: Protein Summary:
1:17:03.921205 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:17:03.921298 PROGRESS: =========================================================================
1:17:04.312073 INFO: Starting optimization step 9.
1:17:04.312423 PROGRESS: === Extracting elution groups 102200 to 204600 ===
1:17:04.312519 PROGRESS: Extracting batch of 201824 precursors
1:17:04.363107 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:17:04.363264 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:17:04.363309 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:17:04.363337 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:17:04.363669 INFO: Starting candidate selection
1:17:16.240639 INFO: Starting candidate scoring
1:17:17.538437 INFO: Finished candidate processing
1:17:17.538556 INFO: Collecting candidate features
1:17:18.008911 INFO: Collecting fragment features
1:17:18.147558 INFO: Finished candidate scoring
1:17:18.389984 PROGRESS: === Extracted 402506 precursors and 4146880 fragments ===
1:17:18.440473 INFO: performing precursor FDR with 47 features
1:17:18.440636 INFO: Decoy channel: -1
1:17:18.440664 INFO: Competetive: True
1:17:18.649240 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:25.797710 INFO: Test AUC: 0.569
1:17:25.797988 INFO: Train AUC: 0.580
1:17:25.798021 INFO: AUC difference: 1.98%
1:17:26.096087 INFO: Resetting torch num_threads to 100
1:17:26.118328 INFO: === FDR correction performed with classifier version -1 ===
1:17:26.119479 PROGRESS: ============================= Precursor FDR =============================
1:17:26.119596 PROGRESS: Total precursors accumulated: 1,749
1:17:26.119659 PROGRESS: Target precursors: 1,599 (91.42%)
1:17:26.119711 PROGRESS: Decoy precursors: 150 (8.58%)
1:17:26.119760 PROGRESS: 
1:17:26.119804 PROGRESS: Precursor Summary:
1:17:26.121039 PROGRESS: Channel   0:	 0.05 FDR: 1,332; 0.01 FDR:   685; 0.001 FDR:    15
1:17:26.121138 PROGRESS: 
1:17:26.121196 PROGRESS: Protein Summary:
1:17:26.122612 PROGRESS: Channel   0:	 0.05 FDR: 1,114; 0.01 FDR:   588; 0.001 FDR:    15
1:17:26.122725 PROGRESS: =========================================================================
1:17:26.437315 INFO: fragments_df: keeping 5000 of 4146880 [sum(precursor_idx_mask)=7808 sum(mass_error_mask)=4146880 stop_rank=5000
1:17:26.830848 INFO: calibration group: precursor, fitting rt estimator 
1:17:26.986550 INFO: calibration group: fragment, fitting mz estimator 
1:17:27.664267 INFO: Using score_cutoff 67.5198057952881 (fac=0.99, q=1)
1:17:27.664745 INFO: calibration group: precursor, predicting mz
1:17:27.664835 WARNING: mz prediction was skipped as it has not been fitted yet
1:17:27.664869 INFO: calibration group: precursor, predicting rt
1:17:27.785646 INFO: calibration group: fragment, predicting mz
1:17:28.073438 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:17:28.073831 INFO: Starting optimization step 10.
1:17:28.073915 PROGRESS: === Extracting elution groups 0 to 102200 ===
1:17:28.074001 PROGRESS: Extracting batch of 201452 precursors
1:17:28.134504 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:17:28.134642 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:17:28.134687 INFO: FWHM in RT is 3.12 seconds, sigma is 0.40
1:17:28.134710 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:17:28.135011 INFO: Starting candidate selection
1:17:37.361138 INFO: Starting candidate scoring
1:17:40.021288 INFO: Finished candidate processing
1:17:40.021730 INFO: Collecting candidate features
1:17:40.834149 INFO: Collecting fragment features
1:17:41.079482 INFO: Finished candidate scoring
1:17:41.287471 PROGRESS: === Extracted 402136 precursors and 4092671 fragments ===
1:17:41.288224 INFO: performing precursor FDR with 47 features
1:17:41.288275 INFO: Decoy channel: -1
1:17:41.288299 INFO: Competetive: True
1:17:41.424715 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:48.098402 INFO: Test AUC: 0.572
1:17:48.098553 INFO: Train AUC: 0.583
1:17:48.098584 INFO: AUC difference: 1.91%
1:17:48.382918 INFO: Resetting torch num_threads to 100
1:17:48.393867 INFO: === FDR correction performed with classifier version 9 ===
1:17:48.394783 PROGRESS: ============================= Precursor FDR =============================
1:17:48.394879 PROGRESS: Total precursors accumulated: 1,078
1:17:48.394943 PROGRESS: Target precursors: 982 (91.09%)
1:17:48.394998 PROGRESS: Decoy precursors: 96 (8.91%)
1:17:48.395045 PROGRESS: 
1:17:48.395091 PROGRESS: Precursor Summary:
1:17:48.396299 PROGRESS: Channel   0:	 0.05 FDR:   817; 0.01 FDR:   588; 0.001 FDR:   425
1:17:48.396398 PROGRESS: 
1:17:48.396459 PROGRESS: Protein Summary:
1:17:48.397815 PROGRESS: Channel   0:	 0.05 FDR:   732; 0.01 FDR:   528; 0.001 FDR:   383
1:17:48.397909 PROGRESS: =========================================================================
1:17:48.665033 INFO: fragments_df: keeping 5000 of 4092671 [sum(precursor_idx_mask)=13288 sum(mass_error_mask)=4092671 stop_rank=5000
1:17:48.889859 INFO: calibration group: precursor, fitting rt estimator 
1:17:49.030923 INFO: calibration group: fragment, fitting mz estimator 
1:17:49.709848 INFO: Using score_cutoff 64.15695120849608 (fac=0.99, q=1)
1:17:49.710290 INFO: calibration group: precursor, predicting mz
1:17:49.710379 WARNING: mz prediction was skipped as it has not been fitted yet
1:17:49.710412 INFO: calibration group: precursor, predicting rt
1:17:49.771667 INFO: calibration group: fragment, predicting mz
1:17:49.921189 INFO: === checking if optimization conditions were reached ===
1:17:49.921537 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
1:17:49.924295 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 22.6650.
1:17:49.924359 INFO: ==============================================
1:17:49.924466 INFO: Starting optimization step 11.
1:17:49.924558 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:17:49.924636 PROGRESS: Extracting batch of 100535 precursors
1:17:49.958487 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:17:49.958650 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:17:49.958700 INFO: FWHM in RT is 2.97 seconds, sigma is 0.38
1:17:49.958730 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:17:49.959062 INFO: Starting candidate selection
1:17:54.775793 INFO: Starting candidate scoring
1:17:56.080019 INFO: Finished candidate processing
1:17:56.080138 INFO: Collecting candidate features
1:17:56.619429 INFO: Collecting fragment features
1:17:56.767355 INFO: Finished candidate scoring
1:17:56.916561 PROGRESS: === Extracted 200712 precursors and 1955505 fragments ===
1:17:56.917056 INFO: performing precursor FDR with 47 features
1:17:56.917110 INFO: Decoy channel: -1
1:17:56.917137 INFO: Competetive: True
1:17:57.008436 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:00.806388 INFO: Test AUC: 0.564
1:18:00.806607 INFO: Train AUC: 0.583
1:18:00.806639 INFO: AUC difference: 3.22%
1:18:01.042347 INFO: Resetting torch num_threads to 100
1:18:01.049161 INFO: === FDR correction performed with classifier version 9 ===
1:18:01.049961 PROGRESS: ============================= Precursor FDR =============================
1:18:01.050063 PROGRESS: Total precursors accumulated: 601
1:18:01.050125 PROGRESS: Target precursors: 548 (91.18%)
1:18:01.050183 PROGRESS: Decoy precursors: 53 (8.82%)
1:18:01.050231 PROGRESS: 
1:18:01.050277 PROGRESS: Precursor Summary:
1:18:01.051258 PROGRESS: Channel   0:	 0.05 FDR:   453; 0.01 FDR:   285; 0.001 FDR:    11
1:18:01.051350 PROGRESS: 
1:18:01.051406 PROGRESS: Protein Summary:
1:18:01.052561 PROGRESS: Channel   0:	 0.05 FDR:   424; 0.01 FDR:   269; 0.001 FDR:    11
1:18:01.052659 PROGRESS: =========================================================================
1:18:01.184793 INFO: fragments_df: keeping 3246 of 1955505 [sum(precursor_idx_mask)=6319 sum(mass_error_mask)=1955505 stop_rank=3246
1:18:01.414388 INFO: calibration group: precursor, fitting rt estimator 
1:18:01.541282 INFO: calibration group: fragment, fitting mz estimator 
1:18:01.963504 INFO: Using score_cutoff 63.31589412231445 (fac=0.99, q=1)
1:18:01.963959 INFO: calibration group: precursor, predicting mz
1:18:01.964049 WARNING: mz prediction was skipped as it has not been fitted yet
1:18:01.964084 INFO: calibration group: precursor, predicting rt
1:18:02.025409 INFO: calibration group: fragment, predicting mz
1:18:02.171306 INFO: === checking if optimization conditions were reached ===
1:18:02.171625 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
1:18:02.174397 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 18.0702.
1:18:02.174462 INFO: ==============================================
1:18:02.174573 INFO: Starting optimization step 12.
1:18:02.174649 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:18:02.174727 PROGRESS: Extracting batch of 100535 precursors
1:18:02.213336 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:18:02.213491 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:18:02.213539 INFO: FWHM in RT is 2.85 seconds, sigma is 0.37
1:18:02.213568 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:18:02.213918 INFO: Starting candidate selection
1:18:06.940732 INFO: Starting candidate scoring
1:18:08.251778 INFO: Finished candidate processing
1:18:08.251890 INFO: Collecting candidate features
1:18:08.587131 INFO: Collecting fragment features
1:18:08.703514 INFO: Finished candidate scoring
1:18:08.795867 PROGRESS: === Extracted 200712 precursors and 1889435 fragments ===
1:18:08.796303 INFO: performing precursor FDR with 47 features
1:18:08.796343 INFO: Decoy channel: -1
1:18:08.796366 INFO: Competetive: True
1:18:08.860788 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:12.323621 INFO: Test AUC: 0.563
1:18:12.323767 INFO: Train AUC: 0.580
1:18:12.323797 INFO: AUC difference: 2.96%
1:18:12.558927 INFO: Resetting torch num_threads to 100
1:18:12.564971 INFO: === FDR correction performed with classifier version 9 ===
1:18:12.565758 PROGRESS: ============================= Precursor FDR =============================
1:18:12.565854 PROGRESS: Total precursors accumulated: 676
1:18:12.565915 PROGRESS: Target precursors: 616 (91.12%)
1:18:12.565967 PROGRESS: Decoy precursors: 60 (8.88%)
1:18:12.566013 PROGRESS: 
1:18:12.566058 PROGRESS: Precursor Summary:
1:18:12.567105 PROGRESS: Channel   0:	 0.05 FDR:   526; 0.01 FDR:   366; 0.001 FDR:   186
1:18:12.567197 PROGRESS: 
1:18:12.567255 PROGRESS: Protein Summary:
1:18:12.568461 PROGRESS: Channel   0:	 0.05 FDR:   492; 0.01 FDR:   345; 0.001 FDR:   178
1:18:12.568555 PROGRESS: =========================================================================
1:18:12.690681 INFO: fragments_df: keeping 3963 of 1889435 [sum(precursor_idx_mask)=8031 sum(mass_error_mask)=1889435 stop_rank=3963
1:18:12.912868 INFO: calibration group: precursor, fitting rt estimator 
1:18:13.040928 INFO: calibration group: fragment, fitting mz estimator 
1:18:13.567177 INFO: Using score_cutoff 57.68565803146362 (fac=0.99, q=1)
1:18:13.567607 INFO: calibration group: precursor, predicting mz
1:18:13.567695 WARNING: mz prediction was skipped as it has not been fitted yet
1:18:13.567726 INFO: calibration group: precursor, predicting rt
1:18:13.630646 INFO: calibration group: fragment, predicting mz
1:18:13.784080 INFO: === checking if optimization conditions were reached ===
1:18:13.784441 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
1:18:13.787323 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 14.3595.
1:18:13.787403 INFO: ==============================================
1:18:13.787537 INFO: Starting optimization step 13.
1:18:13.787620 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:18:13.787692 PROGRESS: Extracting batch of 100535 precursors
1:18:13.881097 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:18:13.881245 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:18:13.881281 INFO: FWHM in RT is 2.71 seconds, sigma is 0.35
1:18:13.881305 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:18:13.881561 INFO: Starting candidate selection
1:18:18.760810 INFO: Starting candidate scoring
1:18:20.076056 INFO: Finished candidate processing
1:18:20.076174 INFO: Collecting candidate features
1:18:20.445920 INFO: Collecting fragment features
1:18:20.568089 INFO: Finished candidate scoring
1:18:20.677451 PROGRESS: === Extracted 200705 precursors and 1792078 fragments ===
1:18:20.678226 INFO: performing precursor FDR with 47 features
1:18:20.678267 INFO: Decoy channel: -1
1:18:20.678294 INFO: Competetive: True
1:18:20.741495 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:24.229238 INFO: Test AUC: 0.564
1:18:24.229378 INFO: Train AUC: 0.580
1:18:24.229409 INFO: AUC difference: 2.90%
1:18:24.471908 INFO: Resetting torch num_threads to 100
1:18:24.652335 INFO: === FDR correction performed with classifier version 9 ===
1:18:24.653264 PROGRESS: ============================= Precursor FDR =============================
1:18:24.653364 PROGRESS: Total precursors accumulated: 698
1:18:24.653424 PROGRESS: Target precursors: 636 (91.12%)
1:18:24.653478 PROGRESS: Decoy precursors: 62 (8.88%)
1:18:24.653525 PROGRESS: 
1:18:24.653571 PROGRESS: Precursor Summary:
1:18:24.654594 PROGRESS: Channel   0:	 0.05 FDR:   535; 0.01 FDR:   337; 0.001 FDR:   279
1:18:24.654685 PROGRESS: 
1:18:24.654742 PROGRESS: Protein Summary:
1:18:24.655983 PROGRESS: Channel   0:	 0.05 FDR:   500; 0.01 FDR:   321; 0.001 FDR:   267
1:18:24.656077 PROGRESS: =========================================================================
1:18:24.778611 INFO: fragments_df: keeping 3794 of 1792078 [sum(precursor_idx_mask)=7406 sum(mass_error_mask)=1792078 stop_rank=3794
1:18:25.056851 INFO: calibration group: precursor, fitting rt estimator 
1:18:25.163473 INFO: calibration group: fragment, fitting mz estimator 
1:18:25.596774 INFO: Using score_cutoff 60.95592754211425 (fac=0.99, q=1)
1:18:25.597326 INFO: calibration group: precursor, predicting mz
1:18:25.597415 WARNING: mz prediction was skipped as it has not been fitted yet
1:18:25.597447 INFO: calibration group: precursor, predicting rt
1:18:25.661433 INFO: calibration group: fragment, predicting mz
1:18:25.808999 INFO: === checking if optimization conditions were reached ===
1:18:25.809326 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
1:18:25.812381 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 12.8510.
1:18:25.812445 INFO: ==============================================
1:18:25.812575 INFO: Starting optimization step 14.
1:18:25.812653 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:18:25.812731 PROGRESS: Extracting batch of 100535 precursors
1:18:25.852255 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:18:25.852411 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:18:25.852458 INFO: FWHM in RT is 2.63 seconds, sigma is 0.34
1:18:25.852489 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:18:25.852846 INFO: Starting candidate selection
1:18:30.649372 INFO: Starting candidate scoring
1:18:32.131564 INFO: Finished candidate processing
1:18:32.131668 INFO: Collecting candidate features
1:18:32.458127 INFO: Collecting fragment features
1:18:32.575075 INFO: Finished candidate scoring
1:18:32.695521 PROGRESS: === Extracted 200702 precursors and 1725926 fragments ===
1:18:32.695979 INFO: performing precursor FDR with 47 features
1:18:32.696016 INFO: Decoy channel: -1
1:18:32.696041 INFO: Competetive: True
1:18:32.757395 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:36.326734 INFO: Test AUC: 0.562
1:18:36.326880 INFO: Train AUC: 0.584
1:18:36.326911 INFO: AUC difference: 3.85%
1:18:36.568660 INFO: Resetting torch num_threads to 100
1:18:36.628476 INFO: === FDR correction performed with classifier version 9 ===
1:18:36.629401 PROGRESS: ============================= Precursor FDR =============================
1:18:36.629508 PROGRESS: Total precursors accumulated: 708
1:18:36.629586 PROGRESS: Target precursors: 646 (91.24%)
1:18:36.629653 PROGRESS: Decoy precursors: 62 (8.76%)
1:18:36.629715 PROGRESS: 
1:18:36.629772 PROGRESS: Precursor Summary:
1:18:36.630975 PROGRESS: Channel   0:	 0.05 FDR:   541; 0.01 FDR:   341; 0.001 FDR:   170
1:18:36.631083 PROGRESS: 
1:18:36.631157 PROGRESS: Protein Summary:
1:18:36.632470 PROGRESS: Channel   0:	 0.05 FDR:   503; 0.01 FDR:   322; 0.001 FDR:   163
1:18:36.632578 PROGRESS: =========================================================================
1:18:36.751231 INFO: fragments_df: keeping 3791 of 1725926 [sum(precursor_idx_mask)=7425 sum(mass_error_mask)=1725926 stop_rank=3791
1:18:37.005940 INFO: calibration group: precursor, fitting rt estimator 
1:18:37.132827 INFO: calibration group: fragment, fitting mz estimator 
1:18:37.630180 INFO: Using score_cutoff 57.37844812774658 (fac=0.99, q=1)
1:18:37.630817 INFO: calibration group: precursor, predicting mz
1:18:37.630921 WARNING: mz prediction was skipped as it has not been fitted yet
1:18:37.630964 INFO: calibration group: precursor, predicting rt
1:18:37.695329 INFO: calibration group: fragment, predicting mz
1:18:37.846352 INFO: === checking if optimization conditions were reached ===
1:18:37.846770 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
1:18:37.850199 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 11.0883.
1:18:37.850265 INFO: ==============================================
1:18:37.850394 INFO: Starting optimization step 15.
1:18:37.850481 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:18:37.850567 PROGRESS: Extracting batch of 100535 precursors
1:18:37.894314 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:18:37.894454 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:18:37.894494 INFO: FWHM in RT is 2.56 seconds, sigma is 0.33
1:18:37.894518 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:18:37.894839 INFO: Starting candidate selection
1:18:42.746845 INFO: Starting candidate scoring
1:18:44.082352 INFO: Finished candidate processing
1:18:44.082478 INFO: Collecting candidate features
1:18:44.487546 INFO: Collecting fragment features
1:18:44.639832 INFO: Finished candidate scoring
1:18:44.765964 PROGRESS: === Extracted 200701 precursors and 1693241 fragments ===
1:18:44.766451 INFO: performing precursor FDR with 47 features
1:18:44.766492 INFO: Decoy channel: -1
1:18:44.766517 INFO: Competetive: True
1:18:44.881026 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:49.285622 INFO: Test AUC: 0.560
1:18:49.285782 INFO: Train AUC: 0.580
1:18:49.285814 INFO: AUC difference: 3.55%
1:18:49.528408 INFO: Resetting torch num_threads to 100
1:18:49.537826 INFO: === FDR correction performed with classifier version 9 ===
1:18:49.538925 PROGRESS: ============================= Precursor FDR =============================
1:18:49.539023 PROGRESS: Total precursors accumulated: 704
1:18:49.539087 PROGRESS: Target precursors: 644 (91.48%)
1:18:49.539137 PROGRESS: Decoy precursors: 60 (8.52%)
1:18:49.539184 PROGRESS: 
1:18:49.539230 PROGRESS: Precursor Summary:
1:18:49.540406 PROGRESS: Channel   0:	 0.05 FDR:   542; 0.01 FDR:   356; 0.001 FDR:     0
1:18:49.540512 PROGRESS: 
1:18:49.540571 PROGRESS: Protein Summary:
1:18:49.541786 PROGRESS: Channel   0:	 0.05 FDR:   504; 0.01 FDR:   333; 0.001 FDR:     0
1:18:49.541888 PROGRESS: =========================================================================
1:18:49.658098 INFO: fragments_df: keeping 3964 of 1693241 [sum(precursor_idx_mask)=7726 sum(mass_error_mask)=1693241 stop_rank=3964
1:18:50.352829 INFO: calibration group: precursor, fitting rt estimator 
1:18:50.480181 INFO: calibration group: fragment, fitting mz estimator 
1:18:50.937747 INFO: Using score_cutoff 57.83793930244446 (fac=0.99, q=1)
1:18:50.938215 INFO: calibration group: precursor, predicting mz
1:18:50.938307 WARNING: mz prediction was skipped as it has not been fitted yet
1:18:50.938341 INFO: calibration group: precursor, predicting rt
1:18:51.001772 INFO: calibration group: fragment, predicting mz
1:18:51.168337 INFO: === checking if optimization conditions were reached ===
1:18:51.168668 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
1:18:51.171597 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 10.0728.
1:18:51.171654 INFO: ==============================================
1:18:51.171761 INFO: Starting optimization step 16.
1:18:51.171856 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:18:51.171922 PROGRESS: Extracting batch of 100535 precursors
1:18:51.511464 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:18:51.511613 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:18:51.511659 INFO: FWHM in RT is 2.54 seconds, sigma is 0.33
1:18:51.511683 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:18:51.511970 INFO: Starting candidate selection
1:18:56.452221 INFO: Starting candidate scoring
1:18:57.766362 INFO: Finished candidate processing
1:18:57.766469 INFO: Collecting candidate features
1:18:58.122734 INFO: Collecting fragment features
1:18:58.246106 INFO: Finished candidate scoring
1:18:58.356810 PROGRESS: === Extracted 200701 precursors and 1654105 fragments ===
1:18:58.357308 INFO: performing precursor FDR with 47 features
1:18:58.357348 INFO: Decoy channel: -1
1:18:58.357373 INFO: Competetive: True
1:18:58.432256 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:01.951150 INFO: Test AUC: 0.567
1:19:01.951292 INFO: Train AUC: 0.579
1:19:01.951325 INFO: AUC difference: 2.20%
1:19:02.189462 INFO: Resetting torch num_threads to 100
1:19:02.196073 INFO: === FDR correction performed with classifier version 9 ===
1:19:02.196880 PROGRESS: ============================= Precursor FDR =============================
1:19:02.196974 PROGRESS: Total precursors accumulated: 751
1:19:02.197043 PROGRESS: Target precursors: 685 (91.21%)
1:19:02.197096 PROGRESS: Decoy precursors: 66 (8.79%)
1:19:02.197148 PROGRESS: 
1:19:02.197199 PROGRESS: Precursor Summary:
1:19:02.198301 PROGRESS: Channel   0:	 0.05 FDR:   589; 0.01 FDR:   414; 0.001 FDR:   308
1:19:02.198396 PROGRESS: 
1:19:02.198453 PROGRESS: Protein Summary:
1:19:02.199694 PROGRESS: Channel   0:	 0.05 FDR:   546; 0.01 FDR:   386; 0.001 FDR:   291
1:19:02.199785 PROGRESS: =========================================================================
1:19:02.309830 INFO: fragments_df: keeping 4434 of 1654105 [sum(precursor_idx_mask)=8856 sum(mass_error_mask)=1654105 stop_rank=4434
1:19:02.492027 INFO: calibration group: precursor, fitting rt estimator 
1:19:02.622426 INFO: calibration group: fragment, fitting mz estimator 
1:19:03.217111 INFO: Using score_cutoff 54.396329102325446 (fac=0.99, q=1)
1:19:03.217532 INFO: calibration group: precursor, predicting mz
1:19:03.217621 WARNING: mz prediction was skipped as it has not been fitted yet
1:19:03.217654 INFO: calibration group: precursor, predicting rt
1:19:03.248398 INFO: calibration group: fragment, predicting mz
1:19:03.313677 INFO: === checking if optimization conditions were reached ===
1:19:03.313960 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
1:19:03.316440 PROGRESS: ❌ ms2_error      : optimization incomplete after 7 search(es). Will search with parameter 9.1106.
1:19:03.316496 INFO: ==============================================
1:19:03.316612 INFO: Starting optimization step 17.
1:19:03.316680 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:19:03.316745 PROGRESS: Extracting batch of 50096 precursors
1:19:03.330256 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:19:03.330377 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:19:03.330415 INFO: FWHM in RT is 2.51 seconds, sigma is 0.32
1:19:03.330439 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:19:03.330692 INFO: Starting candidate selection
1:19:05.809798 INFO: Starting candidate scoring
1:19:06.452166 INFO: Finished candidate processing
1:19:06.452301 INFO: Collecting candidate features
1:19:06.656752 INFO: Collecting fragment features
1:19:06.734511 INFO: Finished candidate scoring
1:19:06.797269 PROGRESS: === Extracted 100020 precursors and 801505 fragments ===
1:19:06.797698 INFO: performing precursor FDR with 47 features
1:19:06.797739 INFO: Decoy channel: -1
1:19:06.797766 INFO: Competetive: True
1:19:06.849058 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:08.686399 INFO: Test AUC: 0.556
1:19:08.686749 INFO: Train AUC: 0.580
1:19:08.686781 INFO: AUC difference: 4.02%
1:19:08.905344 INFO: Resetting torch num_threads to 100
1:19:08.909695 INFO: === FDR correction performed with classifier version 9 ===
1:19:08.910668 PROGRESS: ============================= Precursor FDR =============================
1:19:08.910778 PROGRESS: Total precursors accumulated: 306
1:19:08.910838 PROGRESS: Target precursors: 280 (91.50%)
1:19:08.910891 PROGRESS: Decoy precursors: 26 (8.50%)
1:19:08.910939 PROGRESS: 
1:19:08.910984 PROGRESS: Precursor Summary:
1:19:08.912007 PROGRESS: Channel   0:	 0.05 FDR:   248; 0.01 FDR:   201; 0.001 FDR:   183
1:19:08.912096 PROGRESS: 
1:19:08.912152 PROGRESS: Protein Summary:
1:19:08.913283 PROGRESS: Channel   0:	 0.05 FDR:   237; 0.01 FDR:   193; 0.001 FDR:   177
1:19:08.913388 PROGRESS: =========================================================================
1:19:08.975590 INFO: fragments_df: keeping 2066 of 801505 [sum(precursor_idx_mask)=4227 sum(mass_error_mask)=801505 stop_rank=2066
1:19:09.146613 INFO: calibration group: precursor, fitting rt estimator 
1:19:09.242999 INFO: calibration group: fragment, fitting mz estimator 
1:19:09.477495 INFO: Using score_cutoff 44.691269416809085 (fac=0.99, q=1)
1:19:09.478007 INFO: calibration group: precursor, predicting mz
1:19:09.478105 WARNING: mz prediction was skipped as it has not been fitted yet
1:19:09.478138 INFO: calibration group: precursor, predicting rt
1:19:09.509080 INFO: calibration group: fragment, predicting mz
1:19:09.574858 INFO: === checking if optimization conditions were reached ===
1:19:09.575171 PROGRESS: === Optimization of ms2_error has been performed 8 time(s); minimum number is 2 ===
1:19:09.577600 PROGRESS: ❌ ms2_error      : optimization incomplete after 8 search(es). Will search with parameter 8.2521.
1:19:09.577657 INFO: ==============================================
1:19:09.577764 INFO: Starting optimization step 18.
1:19:09.577834 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:19:09.577917 PROGRESS: Extracting batch of 50096 precursors
1:19:09.594259 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:19:09.594396 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:19:09.594445 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
1:19:09.594470 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:19:09.594820 INFO: Starting candidate selection
1:19:12.038313 INFO: Starting candidate scoring
1:19:12.683535 INFO: Finished candidate processing
1:19:12.683707 INFO: Collecting candidate features
1:19:12.847600 INFO: Collecting fragment features
1:19:12.901132 INFO: Finished candidate scoring
1:19:12.940417 PROGRESS: === Extracted 100009 precursors and 773987 fragments ===
1:19:12.940893 INFO: performing precursor FDR with 47 features
1:19:12.940935 INFO: Decoy channel: -1
1:19:12.940960 INFO: Competetive: True
1:19:12.975110 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:14.581587 INFO: Test AUC: 0.561
1:19:14.581742 INFO: Train AUC: 0.580
1:19:14.581773 INFO: AUC difference: 3.32%
1:19:14.790801 INFO: Resetting torch num_threads to 100
1:19:14.794317 INFO: === FDR correction performed with classifier version 9 ===
1:19:14.795008 PROGRESS: ============================= Precursor FDR =============================
1:19:14.795102 PROGRESS: Total precursors accumulated: 366
1:19:14.795163 PROGRESS: Target precursors: 335 (91.53%)
1:19:14.795221 PROGRESS: Decoy precursors: 31 (8.47%)
1:19:14.795271 PROGRESS: 
1:19:14.795316 PROGRESS: Precursor Summary:
1:19:14.796308 PROGRESS: Channel   0:	 0.05 FDR:   292; 0.01 FDR:   227; 0.001 FDR:   211
1:19:14.796417 PROGRESS: 
1:19:14.796483 PROGRESS: Protein Summary:
1:19:14.797596 PROGRESS: Channel   0:	 0.05 FDR:   280; 0.01 FDR:   218; 0.001 FDR:   203
1:19:14.797687 PROGRESS: =========================================================================
1:19:14.861169 INFO: fragments_df: keeping 2294 of 773987 [sum(precursor_idx_mask)=4693 sum(mass_error_mask)=773987 stop_rank=2294
1:19:15.459530 INFO: calibration group: precursor, fitting rt estimator 
1:19:15.573457 INFO: calibration group: fragment, fitting mz estimator 
1:19:15.889495 INFO: Using score_cutoff 48.72335129928589 (fac=0.99, q=1)
1:19:15.889945 INFO: calibration group: precursor, predicting mz
1:19:15.890032 WARNING: mz prediction was skipped as it has not been fitted yet
1:19:15.890065 INFO: calibration group: precursor, predicting rt
1:19:15.921518 INFO: calibration group: fragment, predicting mz
1:19:15.988871 INFO: === checking if optimization conditions were reached ===
1:19:15.989238 PROGRESS: === Optimization of ms2_error has been performed 9 time(s); minimum number is 2 ===
1:19:15.991968 PROGRESS: ❌ ms2_error      : optimization incomplete after 9 search(es). Will search with parameter 7.5426.
1:19:15.992033 INFO: ==============================================
1:19:15.992138 INFO: Starting optimization step 19.
1:19:15.992215 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:19:15.992299 PROGRESS: Extracting batch of 50096 precursors
1:19:16.012675 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:19:16.012833 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:19:16.012873 INFO: FWHM in RT is 2.30 seconds, sigma is 0.30
1:19:16.012903 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:19:16.013474 INFO: Starting candidate selection
1:19:18.378070 INFO: Starting candidate scoring
1:19:19.104899 INFO: Finished candidate processing
1:19:19.105010 INFO: Collecting candidate features
1:19:19.271548 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 99996)
1:19:19.282731 INFO: Collecting fragment features
1:19:19.342555 INFO: Finished candidate scoring
1:19:19.404034 PROGRESS: === Extracted 99996 precursors and 744670 fragments ===
1:19:19.404443 INFO: performing precursor FDR with 47 features
1:19:19.404483 INFO: Decoy channel: -1
1:19:19.404506 INFO: Competetive: True
1:19:19.443507 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:19.463267 WARNING: dropped 1 target PSMs due to missing features
1:19:21.367244 INFO: Test AUC: 0.555
1:19:21.367387 INFO: Train AUC: 0.578
1:19:21.367431 INFO: AUC difference: 3.94%
1:19:21.577307 INFO: Resetting torch num_threads to 100
1:19:21.581572 INFO: === FDR correction performed with classifier version 9 ===
1:19:21.582292 PROGRESS: ============================= Precursor FDR =============================
1:19:21.582390 PROGRESS: Total precursors accumulated: 351
1:19:21.582449 PROGRESS: Target precursors: 319 (90.88%)
1:19:21.582502 PROGRESS: Decoy precursors: 32 (9.12%)
1:19:21.582548 PROGRESS: 
1:19:21.582593 PROGRESS: Precursor Summary:
1:19:21.583769 PROGRESS: Channel   0:	 0.05 FDR:   290; 0.01 FDR:   216; 0.001 FDR:   199
1:19:21.583879 PROGRESS: 
1:19:21.583946 PROGRESS: Protein Summary:
1:19:21.585322 PROGRESS: Channel   0:	 0.05 FDR:   277; 0.01 FDR:   208; 0.001 FDR:   191
1:19:21.585436 PROGRESS: =========================================================================
1:19:21.646737 INFO: fragments_df: keeping 2186 of 744670 [sum(precursor_idx_mask)=4440 sum(mass_error_mask)=744670 stop_rank=2186
1:19:21.813205 INFO: calibration group: precursor, fitting rt estimator 
1:19:21.904039 INFO: calibration group: fragment, fitting mz estimator 
1:19:22.151800 INFO: Using score_cutoff 50.18222418022155 (fac=0.99, q=1)
1:19:22.152225 INFO: calibration group: precursor, predicting mz
1:19:22.152329 WARNING: mz prediction was skipped as it has not been fitted yet
1:19:22.152361 INFO: calibration group: precursor, predicting rt
1:19:22.183689 INFO: calibration group: fragment, predicting mz
1:19:22.250614 INFO: === checking if optimization conditions were reached ===
1:19:22.250903 PROGRESS: === Optimization of ms2_error has been performed 10 time(s); minimum number is 2 ===
1:19:22.253288 PROGRESS: ❌ ms2_error      : optimization incomplete after 10 search(es). Will search with parameter 6.8580.
1:19:22.895478 INFO: ==============================================
1:19:22.895715 WARNING: Optimization did not converge within the maximum number of steps, which is 20.
1:19:22.895882 INFO: Starting optimization step 0.
1:19:22.895956 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:19:22.896027 PROGRESS: Extracting batch of 50096 precursors
1:19:22.938894 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:19:22.939034 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:19:22.939071 INFO: FWHM in RT is 2.25 seconds, sigma is 0.29
1:19:22.939094 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:19:22.939339 INFO: Starting candidate selection
1:19:25.580528 INFO: Starting candidate scoring
1:19:26.225721 INFO: Finished candidate processing
1:19:26.225846 INFO: Collecting candidate features
1:19:26.382809 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 99965)
1:19:26.392992 INFO: Collecting fragment features
1:19:26.447975 INFO: Finished candidate scoring
1:19:26.492109 PROGRESS: === Extracted 99965 precursors and 709397 fragments ===
1:19:26.492670 INFO: performing precursor FDR with 47 features
1:19:26.492711 INFO: Decoy channel: -1
1:19:26.492736 INFO: Competetive: True
1:19:26.531755 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:26.549647 WARNING: dropped 2 target PSMs due to missing features
1:19:28.180284 INFO: Test AUC: 0.553
1:19:28.180437 INFO: Train AUC: 0.579
1:19:28.180469 INFO: AUC difference: 4.54%
1:19:28.390523 INFO: Resetting torch num_threads to 100
1:19:28.393833 INFO: === FDR correction performed with classifier version 9 ===
1:19:28.394541 PROGRESS: ============================= Precursor FDR =============================
1:19:28.394639 PROGRESS: Total precursors accumulated: 335
1:19:28.394703 PROGRESS: Target precursors: 306 (91.34%)
1:19:28.394758 PROGRESS: Decoy precursors: 29 (8.66%)
1:19:28.394808 PROGRESS: 
1:19:28.394854 PROGRESS: Precursor Summary:
1:19:28.395835 PROGRESS: Channel   0:	 0.05 FDR:   270; 0.01 FDR:   206; 0.001 FDR:   125
1:19:28.395933 PROGRESS: 
1:19:28.395990 PROGRESS: Protein Summary:
1:19:28.397117 PROGRESS: Channel   0:	 0.05 FDR:   258; 0.01 FDR:   196; 0.001 FDR:   121
1:19:28.397212 PROGRESS: =========================================================================
1:19:28.447501 INFO: fragments_df: keeping 2117 of 709397 [sum(precursor_idx_mask)=4159 sum(mass_error_mask)=709397 stop_rank=2117
1:19:28.586378 INFO: calibration group: precursor, fitting rt estimator 
1:19:28.697363 INFO: calibration group: fragment, fitting mz estimator 
1:19:28.984467 INFO: Using score_cutoff 50.82195971488952 (fac=0.99, q=1)
1:19:28.984942 INFO: calibration group: precursor, predicting mz
1:19:28.985032 WARNING: mz prediction was skipped as it has not been fitted yet
1:19:28.985063 INFO: calibration group: precursor, predicting rt
1:19:29.015827 INFO: calibration group: fragment, predicting mz
1:19:29.080788 INFO: === checking if optimization conditions were reached ===
1:19:29.081165 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:19:29.083449 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 137.2091.
1:19:29.083512 INFO: ==============================================
1:19:29.083621 INFO: Starting optimization step 1.
1:19:29.083697 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:19:29.083775 PROGRESS: Extracting batch of 50096 precursors
1:19:29.101884 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:19:29.102036 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:19:29.102083 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
1:19:29.102112 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:19:29.102426 INFO: Starting candidate selection
1:19:33.552925 INFO: Starting candidate scoring
1:19:34.176511 INFO: Finished candidate processing
1:19:34.176628 INFO: Collecting candidate features
1:19:34.328942 WARNING: intensity_correlation has 19 NaNs ( 0.02 % out of 98593)
1:19:34.337820 INFO: Collecting fragment features
1:19:34.390925 INFO: Finished candidate scoring
1:19:34.462490 PROGRESS: === Extracted 98593 precursors and 605644 fragments ===
1:19:34.462942 INFO: performing precursor FDR with 47 features
1:19:34.462979 INFO: Decoy channel: -1
1:19:34.463003 INFO: Competetive: True
1:19:34.499001 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:34.518186 WARNING: dropped 12 target PSMs due to missing features
1:19:34.518345 WARNING: dropped 7 decoy PSMs due to missing features
1:19:36.169876 INFO: Test AUC: 0.553
1:19:36.170024 INFO: Train AUC: 0.572
1:19:36.170054 INFO: AUC difference: 3.45%
1:19:36.383736 INFO: Resetting torch num_threads to 100
1:19:36.387140 INFO: === FDR correction performed with classifier version 9 ===
1:19:36.387915 PROGRESS: ============================= Precursor FDR =============================
1:19:36.388016 PROGRESS: Total precursors accumulated: 417
1:19:36.388092 PROGRESS: Target precursors: 383 (91.85%)
1:19:36.388157 PROGRESS: Decoy precursors: 34 (8.15%)
1:19:36.388216 PROGRESS: 
1:19:36.388289 PROGRESS: Precursor Summary:
1:19:36.389377 PROGRESS: Channel   0:	 0.05 FDR:   293; 0.01 FDR:   171; 0.001 FDR:   110
1:19:36.389479 PROGRESS: 
1:19:36.389556 PROGRESS: Protein Summary:
1:19:36.390680 PROGRESS: Channel   0:	 0.05 FDR:   280; 0.01 FDR:   165; 0.001 FDR:   106
1:19:36.390781 PROGRESS: =========================================================================
1:19:36.552275 INFO: calibration group: precursor, predicting mz
1:19:36.552629 WARNING: mz prediction was skipped as it has not been fitted yet
1:19:36.552671 INFO: calibration group: precursor, predicting rt
1:19:36.584138 INFO: calibration group: fragment, predicting mz
1:19:36.651295 INFO: === skipping optimization until target number of precursors are found ===
1:19:36.651654 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1:19:36.651729 INFO: Starting optimization step 2.
1:19:36.651812 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1:19:36.651882 PROGRESS: Extracting batch of 50439 precursors
1:19:36.670605 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:19:36.670747 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:19:36.670810 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
1:19:36.670841 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:19:36.671108 INFO: Starting candidate selection
1:19:38.831616 INFO: Starting candidate scoring
1:19:39.480507 INFO: Finished candidate processing
1:19:39.480821 INFO: Collecting candidate features
1:19:39.654623 WARNING: intensity_correlation has 15 NaNs ( 0.02 % out of 99285)
1:19:39.664964 INFO: Collecting fragment features
1:19:39.720857 INFO: Finished candidate scoring
1:19:39.867807 PROGRESS: === Extracted 197878 precursors and 1216764 fragments ===
1:19:39.887408 INFO: performing precursor FDR with 47 features
1:19:39.887553 INFO: Decoy channel: -1
1:19:39.887580 INFO: Competetive: True
1:19:39.978096 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:40.014276 WARNING: dropped 18 target PSMs due to missing features
1:19:40.014427 WARNING: dropped 16 decoy PSMs due to missing features
1:19:43.381642 INFO: Test AUC: 0.556
1:19:43.381788 INFO: Train AUC: 0.571
1:19:43.381819 INFO: AUC difference: 2.54%
1:19:43.629407 INFO: Resetting torch num_threads to 100
1:19:43.638701 INFO: === FDR correction performed with classifier version 9 ===
1:19:43.639533 PROGRESS: ============================= Precursor FDR =============================
1:19:43.639644 PROGRESS: Total precursors accumulated: 878
1:19:43.639718 PROGRESS: Target precursors: 802 (91.34%)
1:19:43.639775 PROGRESS: Decoy precursors: 76 (8.66%)
1:19:43.639823 PROGRESS: 
1:19:43.639870 PROGRESS: Precursor Summary:
1:19:43.640976 PROGRESS: Channel   0:	 0.05 FDR:   652; 0.01 FDR:   427; 0.001 FDR:   220
1:19:43.641071 PROGRESS: 
1:19:43.641127 PROGRESS: Protein Summary:
1:19:43.642385 PROGRESS: Channel   0:	 0.05 FDR:   606; 0.01 FDR:   398; 0.001 FDR:   210
1:19:43.642481 PROGRESS: =========================================================================
1:19:43.747005 INFO: fragments_df: keeping 4388 of 1216764 [sum(precursor_idx_mask)=8566 sum(mass_error_mask)=1216764 stop_rank=4388
1:19:43.907673 INFO: calibration group: precursor, fitting rt estimator 
1:19:44.036667 INFO: calibration group: fragment, fitting mz estimator 
1:19:44.622395 INFO: Using score_cutoff 54.782018817901616 (fac=0.99, q=1)
1:19:44.622876 INFO: calibration group: precursor, predicting mz
1:19:44.622973 WARNING: mz prediction was skipped as it has not been fitted yet
1:19:44.623005 INFO: calibration group: precursor, predicting rt
1:19:44.654171 INFO: calibration group: fragment, predicting mz
1:19:44.730923 INFO: === checking if optimization conditions were reached ===
1:19:44.731284 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:19:44.733788 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 95.2074.
1:19:44.733850 INFO: ==============================================
1:19:44.733964 INFO: Starting optimization step 3.
1:19:44.734040 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:19:44.734117 PROGRESS: Extracting batch of 50096 precursors
1:19:44.751634 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:19:44.751759 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:19:44.751813 INFO: FWHM in RT is 2.30 seconds, sigma is 0.30
1:19:44.751843 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:19:44.752163 INFO: Starting candidate selection
1:19:46.767066 INFO: Starting candidate scoring
1:19:47.384892 INFO: Finished candidate processing
1:19:47.385000 INFO: Collecting candidate features
1:19:47.527460 WARNING: intensity_correlation has 28 NaNs ( 0.03 % out of 97408)
1:19:47.537507 INFO: Collecting fragment features
1:19:47.583368 INFO: Finished candidate scoring
1:19:47.621375 PROGRESS: === Extracted 97408 precursors and 565075 fragments ===
1:19:47.621789 INFO: performing precursor FDR with 47 features
1:19:47.621826 INFO: Decoy channel: -1
1:19:47.621854 INFO: Competetive: True
1:19:47.652628 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:47.670445 WARNING: dropped 20 target PSMs due to missing features
1:19:47.670623 WARNING: dropped 8 decoy PSMs due to missing features
1:19:49.188812 INFO: Test AUC: 0.553
1:19:49.188956 INFO: Train AUC: 0.568
1:19:49.188987 INFO: AUC difference: 2.56%
1:19:49.395402 INFO: Resetting torch num_threads to 100
1:19:49.398380 INFO: === FDR correction performed with classifier version 9 ===
1:19:49.399063 PROGRESS: ============================= Precursor FDR =============================
1:19:49.399158 PROGRESS: Total precursors accumulated: 369
1:19:49.399218 PROGRESS: Target precursors: 336 (91.06%)
1:19:49.399269 PROGRESS: Decoy precursors: 33 (8.94%)
1:19:49.399315 PROGRESS: 
1:19:49.399359 PROGRESS: Precursor Summary:
1:19:49.400941 PROGRESS: Channel   0:	 0.05 FDR:   293; 0.01 FDR:   184; 0.001 FDR:    99
1:19:49.401037 PROGRESS: 
1:19:49.401093 PROGRESS: Protein Summary:
1:19:49.402196 PROGRESS: Channel   0:	 0.05 FDR:   280; 0.01 FDR:   177; 0.001 FDR:    95
1:19:49.402291 PROGRESS: =========================================================================
1:19:49.548800 INFO: calibration group: precursor, predicting mz
1:19:49.549111 WARNING: mz prediction was skipped as it has not been fitted yet
1:19:49.549150 INFO: calibration group: precursor, predicting rt
1:19:49.580739 INFO: calibration group: fragment, predicting mz
1:19:49.647928 INFO: === skipping optimization until target number of precursors are found ===
1:19:49.648253 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1:19:49.648328 INFO: Starting optimization step 4.
1:19:49.648412 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1:19:49.648487 PROGRESS: Extracting batch of 50439 precursors
1:19:49.661041 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:19:49.661173 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:19:49.661215 INFO: FWHM in RT is 2.30 seconds, sigma is 0.30
1:19:49.661244 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:19:49.661484 INFO: Starting candidate selection
1:19:51.724735 INFO: Starting candidate scoring
1:19:52.386137 INFO: Finished candidate processing
1:19:52.387617 INFO: Collecting candidate features
1:19:52.535091 WARNING: intensity_correlation has 36 NaNs ( 0.04 % out of 98146)
1:19:52.541637 INFO: Collecting fragment features
1:19:52.587142 INFO: Finished candidate scoring
1:19:52.667446 PROGRESS: === Extracted 195554 precursors and 1134854 fragments ===
1:19:52.683393 INFO: performing precursor FDR with 47 features
1:19:52.683544 INFO: Decoy channel: -1
1:19:52.683571 INFO: Competetive: True
1:19:52.766275 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:52.800657 WARNING: dropped 34 target PSMs due to missing features
1:19:52.800803 WARNING: dropped 30 decoy PSMs due to missing features
1:19:56.003211 INFO: Test AUC: 0.550
1:19:56.003467 INFO: Train AUC: 0.570
1:19:56.003501 INFO: AUC difference: 3.40%
1:19:56.243412 INFO: Resetting torch num_threads to 100
1:19:56.252979 INFO: === FDR correction performed with classifier version 9 ===
1:19:56.253942 PROGRESS: ============================= Precursor FDR =============================
1:19:56.254056 PROGRESS: Total precursors accumulated: 878
1:19:56.254124 PROGRESS: Target precursors: 802 (91.34%)
1:19:56.254181 PROGRESS: Decoy precursors: 76 (8.66%)
1:19:56.254229 PROGRESS: 
1:19:56.254278 PROGRESS: Precursor Summary:
1:19:56.255408 PROGRESS: Channel   0:	 0.05 FDR:   690; 0.01 FDR:   424; 0.001 FDR:   223
1:19:56.255505 PROGRESS: 
1:19:56.255573 PROGRESS: Protein Summary:
1:19:56.256893 PROGRESS: Channel   0:	 0.05 FDR:   642; 0.01 FDR:   392; 0.001 FDR:   212
1:19:56.256998 PROGRESS: =========================================================================
1:19:56.355589 INFO: fragments_df: keeping 4326 of 1134854 [sum(precursor_idx_mask)=8520 sum(mass_error_mask)=1134854 stop_rank=4326
1:19:56.545178 INFO: calibration group: precursor, fitting rt estimator 
1:19:56.677815 INFO: calibration group: fragment, fitting mz estimator 
1:19:57.257486 INFO: Using score_cutoff 54.74436899070739 (fac=0.99, q=1)
1:19:57.257953 INFO: calibration group: precursor, predicting mz
1:19:57.258042 WARNING: mz prediction was skipped as it has not been fitted yet
1:19:57.258074 INFO: calibration group: precursor, predicting rt
1:19:57.289435 INFO: calibration group: fragment, predicting mz
1:19:57.352130 INFO: === checking if optimization conditions were reached ===
1:19:57.352473 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:19:57.354674 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 89.3169.
1:19:57.354735 INFO: ==============================================
1:19:57.354845 INFO: Starting optimization step 5.
1:19:57.354924 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:19:57.355001 PROGRESS: Extracting batch of 50096 precursors
1:19:57.368373 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:19:57.368492 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:19:57.368545 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
1:19:57.368575 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:19:57.368880 INFO: Starting candidate selection
1:19:59.342883 INFO: Starting candidate scoring
1:20:00.048052 INFO: Finished candidate processing
1:20:00.048177 INFO: Collecting candidate features
1:20:00.224451 WARNING: intensity_correlation has 39 NaNs ( 0.04 % out of 96926)
1:20:00.231167 INFO: Collecting fragment features
1:20:00.286941 INFO: Finished candidate scoring
1:20:00.339764 PROGRESS: === Extracted 96926 precursors and 553959 fragments ===
1:20:00.340523 INFO: performing precursor FDR with 47 features
1:20:00.340568 INFO: Decoy channel: -1
1:20:00.340593 INFO: Competetive: True
1:20:00.384434 INFO: Setting torch num_threads to 2 for FDR classification task
1:20:00.409484 WARNING: dropped 22 target PSMs due to missing features
1:20:00.409630 WARNING: dropped 17 decoy PSMs due to missing features
1:20:02.308028 INFO: Test AUC: 0.550
1:20:02.308174 INFO: Train AUC: 0.569
1:20:02.308205 INFO: AUC difference: 3.30%
1:20:02.519652 INFO: Resetting torch num_threads to 100
1:20:02.524174 INFO: === FDR correction performed with classifier version 9 ===
1:20:02.524901 PROGRESS: ============================= Precursor FDR =============================
1:20:02.525007 PROGRESS: Total precursors accumulated: 373
1:20:02.525067 PROGRESS: Target precursors: 341 (91.42%)
1:20:02.525121 PROGRESS: Decoy precursors: 32 (8.58%)
1:20:02.525171 PROGRESS: 
1:20:02.525216 PROGRESS: Precursor Summary:
1:20:02.526207 PROGRESS: Channel   0:	 0.05 FDR:   308; 0.01 FDR:   181; 0.001 FDR:   114
1:20:02.526299 PROGRESS: 
1:20:02.526355 PROGRESS: Protein Summary:
1:20:02.527513 PROGRESS: Channel   0:	 0.05 FDR:   294; 0.01 FDR:   175; 0.001 FDR:   111
1:20:02.527609 PROGRESS: =========================================================================
1:20:02.708202 INFO: calibration group: precursor, predicting mz
1:20:02.708505 WARNING: mz prediction was skipped as it has not been fitted yet
1:20:02.708542 INFO: calibration group: precursor, predicting rt
1:20:02.740967 INFO: calibration group: fragment, predicting mz
1:20:02.808682 INFO: === skipping optimization until target number of precursors are found ===
1:20:02.808993 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1:20:02.809078 INFO: Starting optimization step 6.
1:20:02.809154 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1:20:02.809223 PROGRESS: Extracting batch of 50439 precursors
1:20:02.826709 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:20:02.826833 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:20:02.826869 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
1:20:02.826894 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:20:02.827142 INFO: Starting candidate selection
1:20:04.894000 INFO: Starting candidate scoring
1:20:05.584991 INFO: Finished candidate processing
1:20:05.585103 INFO: Collecting candidate features
1:20:05.727878 WARNING: intensity_correlation has 35 NaNs ( 0.04 % out of 97621)
1:20:05.741428 INFO: Collecting fragment features
1:20:05.788174 INFO: Finished candidate scoring
1:20:05.876233 PROGRESS: === Extracted 194547 precursors and 1112342 fragments ===
1:20:05.892385 INFO: performing precursor FDR with 47 features
1:20:05.892495 INFO: Decoy channel: -1
1:20:05.892521 INFO: Competetive: True
1:20:05.965626 INFO: Setting torch num_threads to 2 for FDR classification task
1:20:06.001634 WARNING: dropped 41 target PSMs due to missing features
1:20:06.001800 WARNING: dropped 33 decoy PSMs due to missing features
1:20:09.278947 INFO: Test AUC: 0.553
1:20:09.279169 INFO: Train AUC: 0.569
1:20:09.279203 INFO: AUC difference: 2.82%
1:20:09.521589 INFO: Resetting torch num_threads to 100
1:20:09.531271 INFO: === FDR correction performed with classifier version 9 ===
1:20:09.532155 PROGRESS: ============================= Precursor FDR =============================
1:20:09.532283 PROGRESS: Total precursors accumulated: 892
1:20:09.532349 PROGRESS: Target precursors: 814 (91.26%)
1:20:09.532402 PROGRESS: Decoy precursors: 78 (8.74%)
1:20:09.532449 PROGRESS: 
1:20:09.532496 PROGRESS: Precursor Summary:
1:20:09.533571 PROGRESS: Channel   0:	 0.05 FDR:   686; 0.01 FDR:   363; 0.001 FDR:    85
1:20:09.533672 PROGRESS: 
1:20:09.533730 PROGRESS: Protein Summary:
1:20:09.534993 PROGRESS: Channel   0:	 0.05 FDR:   639; 0.01 FDR:   339; 0.001 FDR:    83
1:20:09.535090 PROGRESS: =========================================================================
1:20:09.636346 INFO: fragments_df: keeping 3833 of 1112342 [sum(precursor_idx_mask)=7355 sum(mass_error_mask)=1112342 stop_rank=3833
1:20:09.868493 INFO: calibration group: precursor, fitting rt estimator 
1:20:10.003033 INFO: calibration group: fragment, fitting mz estimator 
1:20:10.510430 INFO: Using score_cutoff 60.27657100982666 (fac=0.99, q=1)
1:20:10.510882 INFO: calibration group: precursor, predicting mz
1:20:10.510975 WARNING: mz prediction was skipped as it has not been fitted yet
1:20:10.511007 INFO: calibration group: precursor, predicting rt
1:20:10.572907 INFO: calibration group: fragment, predicting mz
1:20:10.724108 INFO: === checking if optimization conditions were reached ===
1:20:10.724487 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:20:10.727070 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 72.3494.
1:20:10.727137 INFO: ==============================================
1:20:10.727252 INFO: Starting optimization step 7.
1:20:10.727328 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:20:10.727406 PROGRESS: Extracting batch of 100535 precursors
1:20:10.761892 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:20:10.762055 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:20:10.762105 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
1:20:10.762133 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:20:10.762509 INFO: Starting candidate selection
1:20:14.532601 INFO: Starting candidate scoring
1:20:15.952871 INFO: Finished candidate processing
1:20:15.953120 INFO: Collecting candidate features
1:20:16.288485 WARNING: intensity_correlation has 80 NaNs ( 0.04 % out of 194036)
1:20:16.297904 INFO: Collecting fragment features
1:20:16.393701 INFO: Finished candidate scoring
1:20:16.483168 PROGRESS: === Extracted 194036 precursors and 1095718 fragments ===
1:20:16.483604 INFO: performing precursor FDR with 47 features
1:20:16.483644 INFO: Decoy channel: -1
1:20:16.483669 INFO: Competetive: True
1:20:16.542015 INFO: Setting torch num_threads to 2 for FDR classification task
1:20:16.575918 WARNING: dropped 42 target PSMs due to missing features
1:20:16.576072 WARNING: dropped 38 decoy PSMs due to missing features
1:20:19.599045 INFO: Test AUC: 0.551
1:20:19.599188 INFO: Train AUC: 0.567
1:20:19.599219 INFO: AUC difference: 2.90%
1:20:19.831410 INFO: Resetting torch num_threads to 100
1:20:19.836427 INFO: === FDR correction performed with classifier version 9 ===
1:20:19.837188 PROGRESS: ============================= Precursor FDR =============================
1:20:19.837281 PROGRESS: Total precursors accumulated: 888
1:20:19.837348 PROGRESS: Target precursors: 814 (91.67%)
1:20:19.837403 PROGRESS: Decoy precursors: 74 (8.33%)
1:20:19.837450 PROGRESS: 
1:20:19.837498 PROGRESS: Precursor Summary:
1:20:19.838546 PROGRESS: Channel   0:	 0.05 FDR:   688; 0.01 FDR:   372; 0.001 FDR:   221
1:20:19.838642 PROGRESS: 
1:20:19.838698 PROGRESS: Protein Summary:
1:20:19.839917 PROGRESS: Channel   0:	 0.05 FDR:   639; 0.01 FDR:   345; 0.001 FDR:   211
1:20:19.840014 PROGRESS: =========================================================================
1:20:19.920089 INFO: fragments_df: keeping 3854 of 1095718 [sum(precursor_idx_mask)=7486 sum(mass_error_mask)=1095718 stop_rank=3854
1:20:20.136407 INFO: calibration group: precursor, fitting rt estimator 
1:20:20.251481 INFO: calibration group: fragment, fitting mz estimator 
1:20:20.696854 INFO: Using score_cutoff 55.680737104797366 (fac=0.99, q=1)
1:20:20.697271 INFO: calibration group: precursor, predicting mz
1:20:20.697356 WARNING: mz prediction was skipped as it has not been fitted yet
1:20:20.697388 INFO: calibration group: precursor, predicting rt
1:20:20.759697 INFO: calibration group: fragment, predicting mz
1:20:20.910844 INFO: === checking if optimization conditions were reached ===
1:20:20.911185 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1:20:20.913785 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 73.8361.
1:20:20.913846 INFO: ==============================================
1:20:20.913954 INFO: Starting optimization step 8.
1:20:20.914041 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:20:20.914125 PROGRESS: Extracting batch of 100535 precursors
1:20:20.950420 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:20:20.950577 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:20:20.950616 INFO: FWHM in RT is 2.30 seconds, sigma is 0.30
1:20:20.950646 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:20:20.950933 INFO: Starting candidate selection
1:20:24.848492 INFO: Starting candidate scoring
1:20:26.266234 INFO: Finished candidate processing
1:20:26.266353 INFO: Collecting candidate features
1:20:26.567382 WARNING: intensity_correlation has 80 NaNs ( 0.04 % out of 194099)
1:20:26.577001 INFO: Collecting fragment features
1:20:26.672228 INFO: Finished candidate scoring
1:20:26.760000 PROGRESS: === Extracted 194099 precursors and 1096454 fragments ===
1:20:26.760529 INFO: performing precursor FDR with 47 features
1:20:26.760568 INFO: Decoy channel: -1
1:20:26.760591 INFO: Competetive: True
1:20:26.824281 INFO: Setting torch num_threads to 2 for FDR classification task
1:20:26.857854 WARNING: dropped 41 target PSMs due to missing features
1:20:26.858003 WARNING: dropped 39 decoy PSMs due to missing features
1:20:30.014982 INFO: Test AUC: 0.556
1:20:30.015125 INFO: Train AUC: 0.568
1:20:30.015158 INFO: AUC difference: 2.26%
1:20:30.252279 INFO: Resetting torch num_threads to 100
1:20:30.257399 INFO: === FDR correction performed with classifier version 9 ===
1:20:30.258185 PROGRESS: ============================= Precursor FDR =============================
1:20:30.258293 PROGRESS: Total precursors accumulated: 902
1:20:30.258352 PROGRESS: Target precursors: 825 (91.46%)
1:20:30.258404 PROGRESS: Decoy precursors: 77 (8.54%)
1:20:30.258450 PROGRESS: 
1:20:30.258499 PROGRESS: Precursor Summary:
1:20:30.259565 PROGRESS: Channel   0:	 0.05 FDR:   701; 0.01 FDR:   414; 0.001 FDR:   200
1:20:30.259659 PROGRESS: 
1:20:30.259714 PROGRESS: Protein Summary:
1:20:30.260979 PROGRESS: Channel   0:	 0.05 FDR:   653; 0.01 FDR:   385; 0.001 FDR:   190
1:20:30.261073 PROGRESS: =========================================================================
1:20:30.350276 INFO: fragments_df: keeping 4243 of 1096454 [sum(precursor_idx_mask)=8282 sum(mass_error_mask)=1096454 stop_rank=4243
1:20:30.501884 INFO: calibration group: precursor, fitting rt estimator 
1:20:30.640484 INFO: calibration group: fragment, fitting mz estimator 
1:20:31.209270 INFO: Using score_cutoff 55.51634794921875 (fac=0.99, q=1)
1:20:31.209707 INFO: calibration group: precursor, predicting mz
1:20:31.209795 WARNING: mz prediction was skipped as it has not been fitted yet
1:20:31.209827 INFO: calibration group: precursor, predicting rt
1:20:31.241130 INFO: calibration group: fragment, predicting mz
1:20:31.308128 INFO: === checking if optimization conditions were reached ===
1:20:31.308482 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1:20:31.309916 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 73.8361 found after 6 searches.
1:20:31.309978 INFO: ==============================================
1:20:31.310083 PROGRESS: Optimization finished for rt_error.
1:20:31.457142 INFO: calibration group: precursor, predicting mz
1:20:31.457444 WARNING: mz prediction was skipped as it has not been fitted yet
1:20:31.457477 INFO: calibration group: precursor, predicting rt
1:20:31.488961 INFO: calibration group: fragment, predicting mz
1:20:31.583383 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:20:31.583663 PROGRESS: ==============================================
1:20:31.583754 PROGRESS: ms2_error      : 6.8580
1:20:31.583821 PROGRESS: rt_error       : 73.8361
1:20:31.583877 PROGRESS: ==============================================
1:20:31.585152 INFO: calibration group: precursor, predicting mz
1:20:31.585253 WARNING: mz prediction was skipped as it has not been fitted yet
1:20:31.585287 INFO: calibration group: precursor, predicting rt
1:20:39.602598 INFO: calibration group: fragment, predicting mz
1:20:56.206992 PROGRESS: Extracting batch of 12567710 precursors
1:20:58.875014 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:20:58.875181 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:20:58.875225 INFO: FWHM in RT is 2.32 seconds, sigma is 0.30
1:20:58.875249 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:20:58.875666 INFO: Starting candidate selection
1:28:50.779178 INFO: Applying score cutoff of 55.51634794921875
1:28:50.840154 INFO: Removed 24225149 precursors with score below cutoff
1:28:53.481011 INFO: Starting candidate scoring
1:29:00.674453 INFO: Finished candidate processing
1:29:00.674880 INFO: Collecting candidate features
1:29:04.198187 INFO: Collecting fragment features
1:29:05.217332 INFO: Finished candidate scoring
1:29:06.240438 INFO: === FDR correction performed with classifier version 28 ===
1:29:06.241446 INFO: performing precursor FDR with 47 features
1:29:06.241502 INFO: Decoy channel: -1
1:29:06.241528 INFO: Competetive: True
1:29:06.509194 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:06.626025 WARNING: FDR calculation for 454877 target and 388242 decoy PSMs
1:29:06.626187 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1:29:21.283948 INFO: Test AUC: 0.672
1:29:21.284203 INFO: Train AUC: 0.679
1:29:21.284263 INFO: AUC difference: 0.97%
1:29:21.697067 INFO: Resetting torch num_threads to 100
1:29:21.733706 INFO: Removing fragments below FDR threshold
1:29:21.861874 PROGRESS: ============================= Precursor FDR =============================
1:29:21.862200 PROGRESS: Total precursors accumulated: 76,789
1:29:21.862284 PROGRESS: Target precursors: 76,029 (99.01%)
1:29:21.862364 PROGRESS: Decoy precursors: 760 (0.99%)
1:29:21.862418 PROGRESS: 
1:29:21.862464 PROGRESS: Precursor Summary:
1:29:21.893800 PROGRESS: Channel   0:	 0.05 FDR: 76,029; 0.01 FDR: 76,029; 0.001 FDR: 54,108
1:29:21.894098 PROGRESS: 
1:29:21.894165 PROGRESS: Protein Summary:
1:29:21.939234 PROGRESS: Channel   0:	 0.05 FDR: 11,255; 0.01 FDR: 11,255; 0.001 FDR: 8,749
1:29:21.939516 PROGRESS: =========================================================================
1:29:22.528904 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:29:23.022213 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:29:23.022404 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant
1:29:23.022485 INFO: Creating folder run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/figures
1:29:23.023318 INFO: Initializing RawFileManager
1:29:33.254566 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
1:29:33.261884 INFO: Determining DIA cycle
1:29:33.278319 INFO: Found cycle with start 0.00 min and length 300.
1:29:33.458120 INFO: RT (min)            : 0.0 - 26.9
1:29:33.458218 INFO: RT duration (sec)   : 1611.2
1:29:33.458252 INFO: RT duration (min)   : 26.9
1:29:33.458276 INFO: Cycle len (scans)   : 300
1:29:33.458296 INFO: Cycle len (sec)     : 1.65
1:29:33.458314 INFO: Number of cycles    : 977
1:29:33.458332 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:29:34.903132 INFO: Initializing CalibrationManager
1:29:34.903596 INFO: Loading calibration config
1:29:34.905172 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'}]
1:29:34.905346 INFO: Calibration group :fragment, found 1 estimator(s)
1:29:34.905447 INFO: Calibration group :precursor, found 3 estimator(s)
1:29:34.905568 INFO: Disabling ion mobility calibration
1:29:34.905600 INFO: removed mobility estimator from group precursor
1:29:34.905786 INFO: Initializing OptimizationManager
1:29:34.905921 INFO: initial parameter: ms1_error = 30
1:29:34.905990 INFO: initial parameter: ms2_error = 30
1:29:34.906045 INFO: initial parameter: rt_error = 805.6002197265625
1:29:34.906110 INFO: initial parameter: mobility_error = 0.1
1:29:34.906159 INFO: initial parameter: column_type = library
1:29:34.906202 INFO: initial parameter: num_candidates = 1
1:29:34.906244 INFO: initial parameter: classifier_version = -1
1:29:34.906286 INFO: initial parameter: fwhm_rt = 5
1:29:34.906329 INFO: initial parameter: fwhm_mobility = 0.01
1:29:34.906374 INFO: initial parameter: score_cutoff = 0
1:29:34.906456 INFO: Initializing TimingManager
1:29:34.906526 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:29:34.906685 INFO: FDRManager not loaded from disk.
1:29:34.906710 INFO: Initializing FDRManager
1:29:34.906759 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:29:36.526931 PROGRESS: 6,373,245 target precursors potentially observable (7,405 removed)
1:29:38.689904 PROGRESS: Starting initial search for precursors.
1:29:38.950888 INFO: Starting optimization step 0.
1:29:38.951141 PROGRESS: === Extracting elution groups 0 to 200 ===
1:29:38.951216 PROGRESS: Extracting batch of 396 precursors
1:29:38.952280 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:29:38.952336 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:38.952375 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:29:38.952399 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:29:38.952698 INFO: Starting candidate selection
1:29:39.100127 INFO: Starting candidate scoring
1:29:39.138077 INFO: Finished candidate processing
1:29:39.138156 INFO: Collecting candidate features
1:29:39.147521 INFO: Collecting fragment features
1:29:39.149643 INFO: Finished candidate scoring
1:29:39.150498 PROGRESS: === Extracted 394 precursors and 4082 fragments ===
1:29:39.150784 INFO: performing precursor FDR with 47 features
1:29:39.150824 INFO: Decoy channel: -1
1:29:39.150852 INFO: Competetive: True
1:29:39.151849 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:39.172224 INFO: Test AUC: 0.441
1:29:39.172311 INFO: Train AUC: 0.478
1:29:39.172345 INFO: AUC difference: 7.90%
1:29:39.172374 WARNING: AUC difference > 5%. This may indicate overfitting.
1:29:39.345895 INFO: Resetting torch num_threads to 100
1:29:39.346486 INFO: === FDR correction performed with classifier version -1 ===
1:29:39.347126 PROGRESS: ============================= Precursor FDR =============================
1:29:39.347223 PROGRESS: Total precursors accumulated: 199
1:29:39.347293 PROGRESS: Target precursors: 96 (48.24%)
1:29:39.347352 PROGRESS: Decoy precursors: 103 (51.76%)
1:29:39.347404 PROGRESS: 
1:29:39.347455 PROGRESS: Precursor Summary:
1:29:39.348334 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:29:39.348434 PROGRESS: 
1:29:39.348497 PROGRESS: Protein Summary:
1:29:39.349416 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:29:39.349517 PROGRESS: =========================================================================
1:29:39.417470 INFO: Starting optimization step 1.
1:29:39.417709 PROGRESS: === Extracting elution groups 200 to 600 ===
1:29:39.417798 PROGRESS: Extracting batch of 786 precursors
1:29:39.418667 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:29:39.418720 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:39.418756 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:29:39.418781 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:29:39.418967 INFO: Starting candidate selection
1:29:39.562454 INFO: Starting candidate scoring
1:29:39.601407 INFO: Finished candidate processing
1:29:39.601482 INFO: Collecting candidate features
1:29:39.610409 INFO: Collecting fragment features
1:29:39.613013 INFO: Finished candidate scoring
1:29:39.615034 PROGRESS: === Extracted 1180 precursors and 12118 fragments ===
1:29:39.615775 INFO: performing precursor FDR with 47 features
1:29:39.615820 INFO: Decoy channel: -1
1:29:39.615843 INFO: Competetive: True
1:29:39.618650 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:39.643393 INFO: Test AUC: 0.570
1:29:39.643464 INFO: Train AUC: 0.500
1:29:39.643494 INFO: AUC difference: 14.02%
1:29:39.643515 WARNING: AUC difference > 5%. This may indicate overfitting.
1:29:39.840141 INFO: Resetting torch num_threads to 100
1:29:39.840847 INFO: === FDR correction performed with classifier version -1 ===
1:29:39.842006 PROGRESS: ============================= Precursor FDR =============================
1:29:39.842121 PROGRESS: Total precursors accumulated: 599
1:29:39.842180 PROGRESS: Target precursors: 326 (54.42%)
1:29:39.842232 PROGRESS: Decoy precursors: 273 (45.58%)
1:29:39.842284 PROGRESS: 
1:29:39.842331 PROGRESS: Precursor Summary:
1:29:39.843228 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:29:39.843319 PROGRESS: 
1:29:39.843373 PROGRESS: Protein Summary:
1:29:39.844311 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:29:39.844401 PROGRESS: =========================================================================
1:29:39.915845 INFO: Starting optimization step 2.
1:29:39.916083 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:29:39.916160 PROGRESS: Extracting batch of 1573 precursors
1:29:39.917140 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:29:39.917195 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:39.917227 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:29:39.917249 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:29:39.917429 INFO: Starting candidate selection
1:29:40.083698 INFO: Starting candidate scoring
1:29:40.125057 INFO: Finished candidate processing
1:29:40.125140 INFO: Collecting candidate features
1:29:40.136023 INFO: Collecting fragment features
1:29:40.141391 INFO: Finished candidate scoring
1:29:40.144521 PROGRESS: === Extracted 2747 precursors and 28191 fragments ===
1:29:40.145521 INFO: performing precursor FDR with 47 features
1:29:40.145564 INFO: Decoy channel: -1
1:29:40.145588 INFO: Competetive: True
1:29:40.149580 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:40.190750 INFO: Test AUC: 0.513
1:29:40.190837 INFO: Train AUC: 0.518
1:29:40.190866 INFO: AUC difference: 0.94%
1:29:40.367259 INFO: Resetting torch num_threads to 100
1:29:40.368084 INFO: === FDR correction performed with classifier version -1 ===
1:29:40.368908 PROGRESS: ============================= Precursor FDR =============================
1:29:40.369006 PROGRESS: Total precursors accumulated: 1,396
1:29:40.369066 PROGRESS: Target precursors: 751 (53.80%)
1:29:40.369122 PROGRESS: Decoy precursors: 645 (46.20%)
1:29:40.369168 PROGRESS: 
1:29:40.369214 PROGRESS: Precursor Summary:
1:29:40.370110 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:29:40.370207 PROGRESS: 
1:29:40.370263 PROGRESS: Protein Summary:
1:29:40.371202 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:29:40.371293 PROGRESS: =========================================================================
1:29:40.445977 INFO: Starting optimization step 3.
1:29:40.446221 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:29:40.446304 PROGRESS: Extracting batch of 3149 precursors
1:29:40.447563 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:29:40.447618 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:40.447649 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:29:40.447670 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:29:40.447869 INFO: Starting candidate selection
1:29:40.688989 INFO: Starting candidate scoring
1:29:40.733505 INFO: Finished candidate processing
1:29:40.733597 INFO: Collecting candidate features
1:29:40.748628 INFO: Collecting fragment features
1:29:40.754241 INFO: Finished candidate scoring
1:29:40.758629 PROGRESS: === Extracted 5891 precursors and 60690 fragments ===
1:29:40.759855 INFO: performing precursor FDR with 47 features
1:29:40.759898 INFO: Decoy channel: -1
1:29:40.759922 INFO: Competetive: True
1:29:40.764473 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:40.796493 INFO: Test AUC: 0.527
1:29:40.796583 INFO: Train AUC: 0.518
1:29:40.796614 INFO: AUC difference: 1.73%
1:29:40.972194 INFO: Resetting torch num_threads to 100
1:29:40.973122 INFO: === FDR correction performed with classifier version -1 ===
1:29:40.973824 PROGRESS: ============================= Precursor FDR =============================
1:29:40.973914 PROGRESS: Total precursors accumulated: 1
1:29:40.973974 PROGRESS: Target precursors: 1 (100.00%)
1:29:40.974027 PROGRESS: Decoy precursors: 0 (0.00%)
1:29:40.974075 PROGRESS: 
1:29:40.974120 PROGRESS: Precursor Summary:
1:29:40.975045 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:29:40.975132 PROGRESS: 
1:29:40.975188 PROGRESS: Protein Summary:
1:29:40.976210 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:29:40.976304 PROGRESS: =========================================================================
1:29:41.054841 INFO: Starting optimization step 4.
1:29:41.055091 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:29:41.055157 PROGRESS: Extracting batch of 6319 precursors
1:29:41.056686 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:29:41.056743 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:41.056776 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:29:41.056798 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:29:41.056974 INFO: Starting candidate selection
1:29:41.481148 INFO: Starting candidate scoring
1:29:41.534648 INFO: Finished candidate processing
1:29:41.534747 INFO: Collecting candidate features
1:29:41.555498 INFO: Collecting fragment features
1:29:41.563025 INFO: Finished candidate scoring
1:29:41.571826 PROGRESS: === Extracted 12200 precursors and 125577 fragments ===
1:29:41.573809 INFO: performing precursor FDR with 47 features
1:29:41.573867 INFO: Decoy channel: -1
1:29:41.573890 INFO: Competetive: True
1:29:41.580222 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:41.667463 INFO: Test AUC: 0.505
1:29:41.667587 INFO: Train AUC: 0.515
1:29:41.667617 INFO: AUC difference: 1.89%
1:29:41.847348 INFO: Resetting torch num_threads to 100
1:29:41.848656 INFO: === FDR correction performed with classifier version -1 ===
1:29:41.850022 PROGRESS: ============================= Precursor FDR =============================
1:29:41.850118 PROGRESS: Total precursors accumulated: 6,190
1:29:41.850187 PROGRESS: Target precursors: 3,274 (52.89%)
1:29:41.850240 PROGRESS: Decoy precursors: 2,916 (47.11%)
1:29:41.850286 PROGRESS: 
1:29:41.850331 PROGRESS: Precursor Summary:
1:29:41.851240 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:29:41.851327 PROGRESS: 
1:29:41.851385 PROGRESS: Protein Summary:
1:29:41.852349 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:29:41.852440 PROGRESS: =========================================================================
1:29:41.938566 INFO: Starting optimization step 5.
1:29:41.938835 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:29:41.938906 PROGRESS: Extracting batch of 12617 precursors
1:29:41.941805 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:29:41.941858 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:41.941890 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:29:41.941914 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:29:41.942103 INFO: Starting candidate selection
1:29:42.750360 INFO: Starting candidate scoring
1:29:42.847048 INFO: Finished candidate processing
1:29:42.847161 INFO: Collecting candidate features
1:29:42.881322 INFO: Collecting fragment features
1:29:42.894495 INFO: Finished candidate scoring
1:29:42.907323 PROGRESS: === Extracted 24794 precursors and 255319 fragments ===
1:29:42.910815 INFO: performing precursor FDR with 47 features
1:29:42.910882 INFO: Decoy channel: -1
1:29:42.910908 INFO: Competetive: True
1:29:42.920855 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:43.116952 INFO: Test AUC: 0.516
1:29:43.117092 INFO: Train AUC: 0.518
1:29:43.117123 INFO: AUC difference: 0.40%
1:29:43.296366 INFO: Resetting torch num_threads to 100
1:29:43.298091 INFO: === FDR correction performed with classifier version -1 ===
1:29:43.298797 PROGRESS: ============================= Precursor FDR =============================
1:29:43.298891 PROGRESS: Total precursors accumulated: 1
1:29:43.298952 PROGRESS: Target precursors: 1 (100.00%)
1:29:43.299006 PROGRESS: Decoy precursors: 0 (0.00%)
1:29:43.299054 PROGRESS: 
1:29:43.299101 PROGRESS: Precursor Summary:
1:29:43.300028 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:29:43.300118 PROGRESS: 
1:29:43.300175 PROGRESS: Protein Summary:
1:29:43.301195 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:29:43.301285 PROGRESS: =========================================================================
1:29:43.402322 INFO: Starting optimization step 6.
1:29:43.402613 PROGRESS: === Extracting elution groups 12600 to 25400 ===
1:29:43.402683 PROGRESS: Extracting batch of 25256 precursors
1:29:43.408413 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:29:43.408483 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:43.408529 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:29:43.408553 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:29:43.408748 INFO: Starting candidate selection
1:29:44.963985 INFO: Starting candidate scoring
1:29:45.150421 INFO: Finished candidate processing
1:29:45.150623 INFO: Collecting candidate features
1:29:45.212990 INFO: Collecting fragment features
1:29:45.233548 INFO: Finished candidate scoring
1:29:45.268710 PROGRESS: === Extracted 50013 precursors and 514103 fragments ===
1:29:45.279800 INFO: performing precursor FDR with 47 features
1:29:45.279914 INFO: Decoy channel: -1
1:29:45.279940 INFO: Competetive: True
1:29:45.309227 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:46.190603 INFO: Test AUC: 0.556
1:29:46.190755 INFO: Train AUC: 0.555
1:29:46.190787 INFO: AUC difference: 0.12%
1:29:46.385713 INFO: Resetting torch num_threads to 100
1:29:46.390002 INFO: === FDR correction performed with classifier version -1 ===
1:29:46.390799 PROGRESS: ============================= Precursor FDR =============================
1:29:46.390900 PROGRESS: Total precursors accumulated: 2
1:29:46.390960 PROGRESS: Target precursors: 2 (100.00%)
1:29:46.391011 PROGRESS: Decoy precursors: 0 (0.00%)
1:29:46.391059 PROGRESS: 
1:29:46.391103 PROGRESS: Precursor Summary:
1:29:46.392034 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:29:46.392123 PROGRESS: 
1:29:46.392181 PROGRESS: Protein Summary:
1:29:46.393214 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:29:46.393308 PROGRESS: =========================================================================
1:29:46.609292 INFO: Starting optimization step 7.
1:29:46.609588 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1:29:46.609675 PROGRESS: Extracting batch of 50439 precursors
1:29:46.625460 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:29:46.625578 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:46.625613 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:29:46.625637 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:29:46.625902 INFO: Starting candidate selection
1:29:49.684484 INFO: Starting candidate scoring
1:29:50.056865 INFO: Finished candidate processing
1:29:50.056978 INFO: Collecting candidate features
1:29:50.158682 INFO: Collecting fragment features
1:29:50.193802 INFO: Finished candidate scoring
1:29:50.240866 PROGRESS: === Extracted 100355 precursors and 1031872 fragments ===
1:29:50.252844 INFO: performing precursor FDR with 47 features
1:29:50.252945 INFO: Decoy channel: -1
1:29:50.252971 INFO: Competetive: True
1:29:50.293465 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:51.959216 INFO: Test AUC: 0.569
1:29:51.959362 INFO: Train AUC: 0.570
1:29:51.959393 INFO: AUC difference: 0.12%
1:29:52.169813 INFO: Resetting torch num_threads to 100
1:29:52.174970 INFO: === FDR correction performed with classifier version -1 ===
1:29:52.175694 PROGRESS: ============================= Precursor FDR =============================
1:29:52.175813 PROGRESS: Total precursors accumulated: 333
1:29:52.175874 PROGRESS: Target precursors: 303 (90.99%)
1:29:52.175928 PROGRESS: Decoy precursors: 30 (9.01%)
1:29:52.175975 PROGRESS: 
1:29:52.176019 PROGRESS: Precursor Summary:
1:29:52.176944 PROGRESS: Channel   0:	 0.05 FDR:   144; 0.01 FDR:     8; 0.001 FDR:     8
1:29:52.177047 PROGRESS: 
1:29:52.177104 PROGRESS: Protein Summary:
1:29:52.178129 PROGRESS: Channel   0:	 0.05 FDR:   136; 0.01 FDR:     8; 0.001 FDR:     8
1:29:52.178232 PROGRESS: =========================================================================
1:29:52.378819 INFO: Starting optimization step 8.
1:29:52.379154 PROGRESS: === Extracting elution groups 51000 to 102200 ===
1:29:52.379226 PROGRESS: Extracting batch of 100917 precursors
1:29:52.401860 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:29:52.402013 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:52.402049 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:29:52.402099 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:29:52.402343 INFO: Starting candidate selection
1:29:58.484272 INFO: Starting candidate scoring
1:29:59.215550 INFO: Finished candidate processing
1:29:59.215662 INFO: Collecting candidate features
1:29:59.405674 INFO: Collecting fragment features
1:29:59.469310 INFO: Finished candidate scoring
1:29:59.637402 PROGRESS: === Extracted 201067 precursors and 2067884 fragments ===
1:29:59.664366 INFO: performing precursor FDR with 47 features
1:29:59.664516 INFO: Decoy channel: -1
1:29:59.664542 INFO: Competetive: True
1:29:59.760610 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:03.235463 INFO: Test AUC: 0.566
1:30:03.235609 INFO: Train AUC: 0.576
1:30:03.235640 INFO: AUC difference: 1.59%
1:30:03.469213 INFO: Resetting torch num_threads to 100
1:30:03.480639 INFO: === FDR correction performed with classifier version -1 ===
1:30:03.481581 PROGRESS: ============================= Precursor FDR =============================
1:30:03.481696 PROGRESS: Total precursors accumulated: 1,095
1:30:03.481759 PROGRESS: Target precursors: 998 (91.14%)
1:30:03.481811 PROGRESS: Decoy precursors: 97 (8.86%)
1:30:03.481858 PROGRESS: 
1:30:03.481904 PROGRESS: Precursor Summary:
1:30:03.483041 PROGRESS: Channel   0:	 0.05 FDR:   802; 0.01 FDR:   472; 0.001 FDR:   213
1:30:03.483137 PROGRESS: 
1:30:03.483194 PROGRESS: Protein Summary:
1:30:03.484554 PROGRESS: Channel   0:	 0.05 FDR:   710; 0.01 FDR:   430; 0.001 FDR:   198
1:30:03.484654 PROGRESS: =========================================================================
1:30:03.644777 INFO: fragments_df: keeping 4218 of 2067884 [sum(precursor_idx_mask)=5459 sum(mass_error_mask)=2067884 stop_rank=4218
1:30:03.872293 INFO: calibration group: precursor, fitting rt estimator 
1:30:04.003969 INFO: calibration group: fragment, fitting mz estimator 
1:30:04.557858 INFO: Using score_cutoff 71.67971688079834 (fac=0.99, q=1)
1:30:04.558298 INFO: calibration group: precursor, predicting mz
1:30:04.558386 WARNING: mz prediction was skipped as it has not been fitted yet
1:30:04.558418 INFO: calibration group: precursor, predicting rt
1:30:04.619182 INFO: calibration group: fragment, predicting mz
1:30:04.769917 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:30:04.770294 INFO: Starting optimization step 9.
1:30:04.770378 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:30:04.770456 PROGRESS: Extracting batch of 100535 precursors
1:30:04.805224 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:30:04.805388 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:04.805437 INFO: FWHM in RT is 3.02 seconds, sigma is 0.39
1:30:04.805468 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:30:04.805799 INFO: Starting candidate selection
1:30:09.671207 INFO: Starting candidate scoring
1:30:11.139365 INFO: Finished candidate processing
1:30:11.139481 INFO: Collecting candidate features
1:30:11.455355 INFO: Collecting fragment features
1:30:11.578862 INFO: Finished candidate scoring
1:30:11.666961 PROGRESS: === Extracted 200712 precursors and 2038101 fragments ===
1:30:11.667397 INFO: performing precursor FDR with 47 features
1:30:11.667439 INFO: Decoy channel: -1
1:30:11.667470 INFO: Competetive: True
1:30:11.748272 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:15.217070 INFO: Test AUC: 0.565
1:30:15.217298 INFO: Train AUC: 0.579
1:30:15.217330 INFO: AUC difference: 2.44%
1:30:15.454693 INFO: Resetting torch num_threads to 100
1:30:15.460184 INFO: === FDR correction performed with classifier version 8 ===
1:30:15.460992 PROGRESS: ============================= Precursor FDR =============================
1:30:15.461111 PROGRESS: Total precursors accumulated: 654
1:30:15.461176 PROGRESS: Target precursors: 597 (91.28%)
1:30:15.461230 PROGRESS: Decoy precursors: 57 (8.72%)
1:30:15.461278 PROGRESS: 
1:30:15.461323 PROGRESS: Precursor Summary:
1:30:15.462389 PROGRESS: Channel   0:	 0.05 FDR:   480; 0.01 FDR:   242; 0.001 FDR:   135
1:30:15.462495 PROGRESS: 
1:30:15.462551 PROGRESS: Protein Summary:
1:30:15.463711 PROGRESS: Channel   0:	 0.05 FDR:   449; 0.01 FDR:   230; 0.001 FDR:   129
1:30:15.463804 PROGRESS: =========================================================================
1:30:15.608058 INFO: fragments_df: keeping 2756 of 2038101 [sum(precursor_idx_mask)=5489 sum(mass_error_mask)=2038101 stop_rank=2756
1:30:15.842827 INFO: calibration group: precursor, fitting rt estimator 
1:30:15.939232 INFO: calibration group: fragment, fitting mz estimator 
1:30:16.241219 INFO: Using score_cutoff 69.31307524795531 (fac=0.99, q=1)
1:30:16.241664 INFO: calibration group: precursor, predicting mz
1:30:16.241754 WARNING: mz prediction was skipped as it has not been fitted yet
1:30:16.241786 INFO: calibration group: precursor, predicting rt
1:30:16.303443 INFO: calibration group: fragment, predicting mz
1:30:16.441281 INFO: === checking if optimization conditions were reached ===
1:30:16.441592 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
1:30:16.443703 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 22.1548.
1:30:16.443760 INFO: ==============================================
1:30:16.443862 INFO: Starting optimization step 10.
1:30:16.443931 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:30:16.444012 PROGRESS: Extracting batch of 100535 precursors
1:30:16.467878 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:30:16.468024 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:16.468067 INFO: FWHM in RT is 2.98 seconds, sigma is 0.38
1:30:16.468091 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:30:16.468389 INFO: Starting candidate selection
1:30:20.938428 INFO: Starting candidate scoring
1:30:22.405565 INFO: Finished candidate processing
1:30:22.405677 INFO: Collecting candidate features
1:30:22.722272 INFO: Collecting fragment features
1:30:22.847824 INFO: Finished candidate scoring
1:30:22.934767 PROGRESS: === Extracted 200711 precursors and 1954426 fragments ===
1:30:22.935192 INFO: performing precursor FDR with 47 features
1:30:22.935229 INFO: Decoy channel: -1
1:30:22.935253 INFO: Competetive: True
1:30:23.005250 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:26.383857 INFO: Test AUC: 0.559
1:30:26.383995 INFO: Train AUC: 0.575
1:30:26.384030 INFO: AUC difference: 2.69%
1:30:26.617281 INFO: Resetting torch num_threads to 100
1:30:26.622777 INFO: === FDR correction performed with classifier version 8 ===
1:30:26.623600 PROGRESS: ============================= Precursor FDR =============================
1:30:26.623716 PROGRESS: Total precursors accumulated: 797
1:30:26.623787 PROGRESS: Target precursors: 724 (90.84%)
1:30:26.623849 PROGRESS: Decoy precursors: 73 (9.16%)
1:30:26.623907 PROGRESS: 
1:30:26.623963 PROGRESS: Precursor Summary:
1:30:26.625056 PROGRESS: Channel   0:	 0.05 FDR:   509; 0.01 FDR:   264; 0.001 FDR:   185
1:30:26.625159 PROGRESS: 
1:30:26.625224 PROGRESS: Protein Summary:
1:30:26.626447 PROGRESS: Channel   0:	 0.05 FDR:   476; 0.01 FDR:   250; 0.001 FDR:   177
1:30:26.626554 PROGRESS: =========================================================================
1:30:26.770801 INFO: fragments_df: keeping 2999 of 1954426 [sum(precursor_idx_mask)=5941 sum(mass_error_mask)=1954426 stop_rank=2999
1:30:27.032368 INFO: calibration group: precursor, fitting rt estimator 
1:30:27.154685 INFO: calibration group: fragment, fitting mz estimator 
1:30:27.532299 INFO: Using score_cutoff 71.32049134140016 (fac=0.99, q=1)
1:30:27.532720 INFO: calibration group: precursor, predicting mz
1:30:27.532814 WARNING: mz prediction was skipped as it has not been fitted yet
1:30:27.532850 INFO: calibration group: precursor, predicting rt
1:30:27.594539 INFO: calibration group: fragment, predicting mz
1:30:27.742903 INFO: === checking if optimization conditions were reached ===
1:30:27.743239 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
1:30:27.745927 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 18.2271.
1:30:27.745992 INFO: ==============================================
1:30:27.746099 INFO: Starting optimization step 11.
1:30:27.746182 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:30:27.746250 PROGRESS: Extracting batch of 100535 precursors
1:30:27.780211 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:30:27.780375 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:27.780416 INFO: FWHM in RT is 2.85 seconds, sigma is 0.37
1:30:27.780444 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:30:27.780765 INFO: Starting candidate selection
1:30:32.539231 INFO: Starting candidate scoring
1:30:34.009394 INFO: Finished candidate processing
1:30:34.009848 INFO: Collecting candidate features
1:30:34.649477 INFO: Collecting fragment features
1:30:34.795870 INFO: Finished candidate scoring
1:30:34.971999 PROGRESS: === Extracted 200711 precursors and 1885302 fragments ===
1:30:34.972729 INFO: performing precursor FDR with 47 features
1:30:34.972772 INFO: Decoy channel: -1
1:30:34.972798 INFO: Competetive: True
1:30:35.078453 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:39.279938 INFO: Test AUC: 0.566
1:30:39.280076 INFO: Train AUC: 0.574
1:30:39.280107 INFO: AUC difference: 1.38%
1:30:39.525362 INFO: Resetting torch num_threads to 100
1:30:39.532919 INFO: === FDR correction performed with classifier version 8 ===
1:30:39.533820 PROGRESS: ============================= Precursor FDR =============================
1:30:39.533947 PROGRESS: Total precursors accumulated: 827
1:30:39.534013 PROGRESS: Target precursors: 755 (91.29%)
1:30:39.534068 PROGRESS: Decoy precursors: 72 (8.71%)
1:30:39.534115 PROGRESS: 
1:30:39.534158 PROGRESS: Precursor Summary:
1:30:39.535294 PROGRESS: Channel   0:	 0.05 FDR:   588; 0.01 FDR:   329; 0.001 FDR:   148
1:30:39.535390 PROGRESS: 
1:30:39.535449 PROGRESS: Protein Summary:
1:30:39.536734 PROGRESS: Channel   0:	 0.05 FDR:   547; 0.01 FDR:   309; 0.001 FDR:   142
1:30:39.536833 PROGRESS: =========================================================================
1:30:39.674620 INFO: fragments_df: keeping 3557 of 1885302 [sum(precursor_idx_mask)=7294 sum(mass_error_mask)=1885302 stop_rank=3557
1:30:39.957739 INFO: calibration group: precursor, fitting rt estimator 
1:30:40.065608 INFO: calibration group: fragment, fitting mz estimator 
1:30:40.473485 INFO: Using score_cutoff 66.70144366149903 (fac=0.99, q=1)
1:30:40.474018 INFO: calibration group: precursor, predicting mz
1:30:40.474109 WARNING: mz prediction was skipped as it has not been fitted yet
1:30:40.474148 INFO: calibration group: precursor, predicting rt
1:30:40.537186 INFO: calibration group: fragment, predicting mz
1:30:40.686900 INFO: === checking if optimization conditions were reached ===
1:30:40.687207 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
1:30:40.689780 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 16.6415.
1:30:40.689837 INFO: ==============================================
1:30:40.689942 INFO: Starting optimization step 12.
1:30:40.690028 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:30:40.690121 PROGRESS: Extracting batch of 100535 precursors
1:30:40.721380 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:30:40.721515 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:40.721570 INFO: FWHM in RT is 2.78 seconds, sigma is 0.36
1:30:40.721594 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:30:40.721968 INFO: Starting candidate selection
1:30:45.463282 INFO: Starting candidate scoring
1:30:46.866136 INFO: Finished candidate processing
1:30:46.866254 INFO: Collecting candidate features
1:30:47.209133 INFO: Collecting fragment features
1:30:47.325511 INFO: Finished candidate scoring
1:30:47.435383 PROGRESS: === Extracted 200707 precursors and 1839520 fragments ===
1:30:47.435870 INFO: performing precursor FDR with 47 features
1:30:47.435908 INFO: Decoy channel: -1
1:30:47.435931 INFO: Competetive: True
1:30:47.502113 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:51.183583 INFO: Test AUC: 0.563
1:30:51.183740 INFO: Train AUC: 0.574
1:30:51.183772 INFO: AUC difference: 1.89%
1:30:51.421567 INFO: Resetting torch num_threads to 100
1:30:51.427969 INFO: === FDR correction performed with classifier version 8 ===
1:30:51.428873 PROGRESS: ============================= Precursor FDR =============================
1:30:51.428990 PROGRESS: Total precursors accumulated: 823
1:30:51.429055 PROGRESS: Target precursors: 752 (91.37%)
1:30:51.429110 PROGRESS: Decoy precursors: 71 (8.63%)
1:30:51.429157 PROGRESS: 
1:30:51.429200 PROGRESS: Precursor Summary:
1:30:51.430287 PROGRESS: Channel   0:	 0.05 FDR:   575; 0.01 FDR:   309; 0.001 FDR:   207
1:30:51.430382 PROGRESS: 
1:30:51.430440 PROGRESS: Protein Summary:
1:30:51.431674 PROGRESS: Channel   0:	 0.05 FDR:   536; 0.01 FDR:   291; 0.001 FDR:   198
1:30:51.431768 PROGRESS: =========================================================================
1:30:51.564131 INFO: fragments_df: keeping 3408 of 1839520 [sum(precursor_idx_mask)=6864 sum(mass_error_mask)=1839520 stop_rank=3408
1:30:51.783327 INFO: calibration group: precursor, fitting rt estimator 
1:30:51.907798 INFO: calibration group: fragment, fitting mz estimator 
1:30:52.363003 INFO: Using score_cutoff 68.98303050842284 (fac=0.99, q=1)
1:30:52.363467 INFO: calibration group: precursor, predicting mz
1:30:52.363556 WARNING: mz prediction was skipped as it has not been fitted yet
1:30:52.363586 INFO: calibration group: precursor, predicting rt
1:30:52.428612 INFO: calibration group: fragment, predicting mz
1:30:52.560320 INFO: === checking if optimization conditions were reached ===
1:30:52.560652 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
1:30:52.563259 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 13.9977.
1:30:52.563319 INFO: ==============================================
1:30:52.563438 INFO: Starting optimization step 13.
1:30:52.563518 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:30:52.563592 PROGRESS: Extracting batch of 100535 precursors
1:30:52.646420 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:30:52.646585 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:52.646637 INFO: FWHM in RT is 2.75 seconds, sigma is 0.35
1:30:52.646674 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:30:52.646967 INFO: Starting candidate selection
1:30:57.517838 INFO: Starting candidate scoring
1:30:58.969937 INFO: Finished candidate processing
1:30:58.970064 INFO: Collecting candidate features
1:30:59.321250 INFO: Collecting fragment features
1:30:59.442973 INFO: Finished candidate scoring
1:30:59.535739 PROGRESS: === Extracted 200702 precursors and 1756274 fragments ===
1:30:59.536277 INFO: performing precursor FDR with 47 features
1:30:59.536318 INFO: Decoy channel: -1
1:30:59.536342 INFO: Competetive: True
1:30:59.616125 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:03.191235 INFO: Test AUC: 0.566
1:31:03.191401 INFO: Train AUC: 0.572
1:31:03.191433 INFO: AUC difference: 1.19%
1:31:03.430052 INFO: Resetting torch num_threads to 100
1:31:03.436221 INFO: === FDR correction performed with classifier version 8 ===
1:31:03.437084 PROGRESS: ============================= Precursor FDR =============================
1:31:03.437203 PROGRESS: Total precursors accumulated: 820
1:31:03.437267 PROGRESS: Target precursors: 748 (91.22%)
1:31:03.437321 PROGRESS: Decoy precursors: 72 (8.78%)
1:31:03.437370 PROGRESS: 
1:31:03.437415 PROGRESS: Precursor Summary:
1:31:03.438586 PROGRESS: Channel   0:	 0.05 FDR:   633; 0.01 FDR:   406; 0.001 FDR:   186
1:31:03.438680 PROGRESS: 
1:31:03.438738 PROGRESS: Protein Summary:
1:31:03.440010 PROGRESS: Channel   0:	 0.05 FDR:   586; 0.01 FDR:   378; 0.001 FDR:   178
1:31:03.440116 PROGRESS: =========================================================================
1:31:03.562531 INFO: fragments_df: keeping 4306 of 1756274 [sum(precursor_idx_mask)=8815 sum(mass_error_mask)=1756274 stop_rank=4306
1:31:03.718303 INFO: calibration group: precursor, fitting rt estimator 
1:31:03.852145 INFO: calibration group: fragment, fitting mz estimator 
1:31:04.424710 INFO: Using score_cutoff 59.63007764053344 (fac=0.99, q=1)
1:31:04.425204 INFO: calibration group: precursor, predicting mz
1:31:04.425299 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:04.425332 INFO: calibration group: precursor, predicting rt
1:31:04.456291 INFO: calibration group: fragment, predicting mz
1:31:04.517249 INFO: === checking if optimization conditions were reached ===
1:31:04.517561 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
1:31:04.520233 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 11.9693.
1:31:04.520304 INFO: ==============================================
1:31:04.520401 INFO: Starting optimization step 14.
1:31:04.520504 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:31:04.520575 PROGRESS: Extracting batch of 50096 precursors
1:31:04.534250 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:04.534384 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:04.534424 INFO: FWHM in RT is 2.65 seconds, sigma is 0.34
1:31:04.534450 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:04.534738 INFO: Starting candidate selection
1:31:07.122503 INFO: Starting candidate scoring
1:31:07.862619 INFO: Finished candidate processing
1:31:07.862734 INFO: Collecting candidate features
1:31:08.048977 INFO: Collecting fragment features
1:31:08.107583 INFO: Finished candidate scoring
1:31:08.147659 PROGRESS: === Extracted 100020 precursors and 839101 fragments ===
1:31:08.148284 INFO: performing precursor FDR with 47 features
1:31:08.148324 INFO: Decoy channel: -1
1:31:08.148348 INFO: Competetive: True
1:31:08.180458 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:09.698205 INFO: Test AUC: 0.556
1:31:09.698341 INFO: Train AUC: 0.569
1:31:09.698371 INFO: AUC difference: 2.38%
1:31:09.911304 INFO: Resetting torch num_threads to 100
1:31:09.914487 INFO: === FDR correction performed with classifier version 8 ===
1:31:09.915218 PROGRESS: ============================= Precursor FDR =============================
1:31:09.915311 PROGRESS: Total precursors accumulated: 493
1:31:09.915370 PROGRESS: Target precursors: 451 (91.48%)
1:31:09.915421 PROGRESS: Decoy precursors: 42 (8.52%)
1:31:09.915468 PROGRESS: 
1:31:09.915522 PROGRESS: Precursor Summary:
1:31:09.916528 PROGRESS: Channel   0:	 0.05 FDR:   363; 0.01 FDR:   236; 0.001 FDR:   129
1:31:09.916621 PROGRESS: 
1:31:09.916683 PROGRESS: Protein Summary:
1:31:09.917823 PROGRESS: Channel   0:	 0.05 FDR:   345; 0.01 FDR:   227; 0.001 FDR:   125
1:31:09.917918 PROGRESS: =========================================================================
1:31:09.981946 INFO: fragments_df: keeping 2358 of 839101 [sum(precursor_idx_mask)=5041 sum(mass_error_mask)=839101 stop_rank=2358
1:31:10.119114 INFO: calibration group: precursor, fitting rt estimator 
1:31:10.241165 INFO: calibration group: fragment, fitting mz estimator 
1:31:10.549049 INFO: Using score_cutoff 47.6340008354187 (fac=0.99, q=1)
1:31:10.549555 INFO: calibration group: precursor, predicting mz
1:31:10.549644 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:10.549681 INFO: calibration group: precursor, predicting rt
1:31:10.580910 INFO: calibration group: fragment, predicting mz
1:31:10.647690 INFO: === checking if optimization conditions were reached ===
1:31:10.648037 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
1:31:10.650941 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 10.8786.
1:31:10.651007 INFO: ==============================================
1:31:10.651143 INFO: Starting optimization step 15.
1:31:10.651221 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:31:10.651317 PROGRESS: Extracting batch of 50096 precursors
1:31:10.668772 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:10.668913 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:10.668967 INFO: FWHM in RT is 2.47 seconds, sigma is 0.32
1:31:10.668997 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:10.669408 INFO: Starting candidate selection
1:31:12.981622 INFO: Starting candidate scoring
1:31:13.719164 INFO: Finished candidate processing
1:31:13.719286 INFO: Collecting candidate features
1:31:13.894870 INFO: Collecting fragment features
1:31:13.956908 INFO: Finished candidate scoring
1:31:14.018439 PROGRESS: === Extracted 100016 precursors and 816841 fragments ===
1:31:14.018866 INFO: performing precursor FDR with 47 features
1:31:14.018904 INFO: Decoy channel: -1
1:31:14.018929 INFO: Competetive: True
1:31:14.061986 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:15.970251 INFO: Test AUC: 0.561
1:31:15.970398 INFO: Train AUC: 0.569
1:31:15.970428 INFO: AUC difference: 1.50%
1:31:16.186018 INFO: Resetting torch num_threads to 100
1:31:16.190433 INFO: === FDR correction performed with classifier version 8 ===
1:31:16.191713 PROGRESS: ============================= Precursor FDR =============================
1:31:16.191813 PROGRESS: Total precursors accumulated: 495
1:31:16.191876 PROGRESS: Target precursors: 453 (91.52%)
1:31:16.191931 PROGRESS: Decoy precursors: 42 (8.48%)
1:31:16.191977 PROGRESS: 
1:31:16.192021 PROGRESS: Precursor Summary:
1:31:16.193094 PROGRESS: Channel   0:	 0.05 FDR:   367; 0.01 FDR:   245; 0.001 FDR:   195
1:31:16.193187 PROGRESS: 
1:31:16.193242 PROGRESS: Protein Summary:
1:31:16.194419 PROGRESS: Channel   0:	 0.05 FDR:   350; 0.01 FDR:   234; 0.001 FDR:   187
1:31:16.194530 PROGRESS: =========================================================================
1:31:16.253311 INFO: fragments_df: keeping 2444 of 816841 [sum(precursor_idx_mask)=5170 sum(mass_error_mask)=816841 stop_rank=2444
1:31:16.750667 INFO: calibration group: precursor, fitting rt estimator 
1:31:16.854987 INFO: calibration group: fragment, fitting mz estimator 
1:31:17.131198 INFO: Using score_cutoff 58.81227813720703 (fac=0.99, q=1)
1:31:17.131659 INFO: calibration group: precursor, predicting mz
1:31:17.131750 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:17.131783 INFO: calibration group: precursor, predicting rt
1:31:17.164227 INFO: calibration group: fragment, predicting mz
1:31:17.233787 INFO: === checking if optimization conditions were reached ===
1:31:17.234069 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
1:31:17.236528 PROGRESS: ❌ ms2_error      : optimization incomplete after 7 search(es). Will search with parameter 9.1804.
1:31:17.236586 INFO: ==============================================
1:31:17.236680 INFO: Starting optimization step 16.
1:31:17.236762 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:31:17.236827 PROGRESS: Extracting batch of 50096 precursors
1:31:17.253150 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:17.253278 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:17.253313 INFO: FWHM in RT is 2.48 seconds, sigma is 0.32
1:31:17.253337 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:17.253593 INFO: Starting candidate selection
1:31:19.641078 INFO: Starting candidate scoring
1:31:20.353297 INFO: Finished candidate processing
1:31:20.353449 INFO: Collecting candidate features
1:31:20.539785 INFO: Collecting fragment features
1:31:20.602308 INFO: Finished candidate scoring
1:31:20.652781 PROGRESS: === Extracted 100015 precursors and 797832 fragments ===
1:31:20.653226 INFO: performing precursor FDR with 47 features
1:31:20.653264 INFO: Decoy channel: -1
1:31:20.653288 INFO: Competetive: True
1:31:20.691444 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:22.657388 INFO: Test AUC: 0.556
1:31:22.657531 INFO: Train AUC: 0.571
1:31:22.657562 INFO: AUC difference: 2.62%
1:31:22.874886 INFO: Resetting torch num_threads to 100
1:31:22.880268 INFO: === FDR correction performed with classifier version 8 ===
1:31:22.881037 PROGRESS: ============================= Precursor FDR =============================
1:31:22.881134 PROGRESS: Total precursors accumulated: 485
1:31:22.881194 PROGRESS: Target precursors: 443 (91.34%)
1:31:22.881252 PROGRESS: Decoy precursors: 42 (8.66%)
1:31:22.881299 PROGRESS: 
1:31:22.881342 PROGRESS: Precursor Summary:
1:31:22.882595 PROGRESS: Channel   0:	 0.05 FDR:   364; 0.01 FDR:   225; 0.001 FDR:   165
1:31:22.882691 PROGRESS: 
1:31:22.882748 PROGRESS: Protein Summary:
1:31:22.883900 PROGRESS: Channel   0:	 0.05 FDR:   345; 0.01 FDR:   217; 0.001 FDR:   159
1:31:22.883993 PROGRESS: =========================================================================
1:31:22.940718 INFO: fragments_df: keeping 2308 of 797832 [sum(precursor_idx_mask)=4762 sum(mass_error_mask)=797832 stop_rank=2308
1:31:23.118857 INFO: calibration group: precursor, fitting rt estimator 
1:31:23.221122 INFO: calibration group: fragment, fitting mz estimator 
1:31:23.483037 INFO: Using score_cutoff 59.54014883880615 (fac=0.99, q=1)
1:31:23.483506 INFO: calibration group: precursor, predicting mz
1:31:23.483595 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:23.483626 INFO: calibration group: precursor, predicting rt
1:31:23.515216 INFO: calibration group: fragment, predicting mz
1:31:23.576894 INFO: === checking if optimization conditions were reached ===
1:31:23.577211 PROGRESS: === Optimization of ms2_error has been performed 8 time(s); minimum number is 2 ===
1:31:23.579784 PROGRESS: ❌ ms2_error      : optimization incomplete after 8 search(es). Will search with parameter 8.3808.
1:31:23.579844 INFO: ==============================================
1:31:23.579952 INFO: Starting optimization step 17.
1:31:23.580034 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:31:23.580102 PROGRESS: Extracting batch of 50096 precursors
1:31:23.691557 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:23.691699 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:24.010738 INFO: FWHM in RT is 2.40 seconds, sigma is 0.31
1:31:24.010855 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:24.011245 INFO: Starting candidate selection
1:31:26.405262 INFO: Starting candidate scoring
1:31:27.156202 INFO: Finished candidate processing
1:31:27.156426 INFO: Collecting candidate features
1:31:27.319917 INFO: Collecting fragment features
1:31:27.375951 INFO: Finished candidate scoring
1:31:27.416572 PROGRESS: === Extracted 100006 precursors and 771210 fragments ===
1:31:27.417052 INFO: performing precursor FDR with 47 features
1:31:27.417090 INFO: Decoy channel: -1
1:31:27.417114 INFO: Competetive: True
1:31:27.449664 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:29.166371 INFO: Test AUC: 0.560
1:31:29.166514 INFO: Train AUC: 0.570
1:31:29.166546 INFO: AUC difference: 1.84%
1:31:29.375927 INFO: Resetting torch num_threads to 100
1:31:29.379088 INFO: === FDR correction performed with classifier version 8 ===
1:31:29.379774 PROGRESS: ============================= Precursor FDR =============================
1:31:29.379867 PROGRESS: Total precursors accumulated: 483
1:31:29.379930 PROGRESS: Target precursors: 444 (91.93%)
1:31:29.379982 PROGRESS: Decoy precursors: 39 (8.07%)
1:31:29.380028 PROGRESS: 
1:31:29.380075 PROGRESS: Precursor Summary:
1:31:29.381074 PROGRESS: Channel   0:	 0.05 FDR:   358; 0.01 FDR:   275; 0.001 FDR:   189
1:31:29.381165 PROGRESS: 
1:31:29.381219 PROGRESS: Protein Summary:
1:31:29.382361 PROGRESS: Channel   0:	 0.05 FDR:   339; 0.01 FDR:   261; 0.001 FDR:   182
1:31:29.382454 PROGRESS: =========================================================================
1:31:29.438328 INFO: fragments_df: keeping 2632 of 771210 [sum(precursor_idx_mask)=5675 sum(mass_error_mask)=771210 stop_rank=2632
1:31:29.596727 INFO: calibration group: precursor, fitting rt estimator 
1:31:29.720120 INFO: calibration group: fragment, fitting mz estimator 
1:31:30.079378 INFO: Using score_cutoff 53.149107431030274 (fac=0.99, q=1)
1:31:30.079823 INFO: calibration group: precursor, predicting mz
1:31:30.079912 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:30.079945 INFO: calibration group: precursor, predicting rt
1:31:30.110714 INFO: calibration group: fragment, predicting mz
1:31:30.179879 INFO: === checking if optimization conditions were reached ===
1:31:30.180218 PROGRESS: === Optimization of ms2_error has been performed 9 time(s); minimum number is 2 ===
1:31:30.182932 PROGRESS: ❌ ms2_error      : optimization incomplete after 9 search(es). Will search with parameter 7.8967.
1:31:30.182995 INFO: ==============================================
1:31:30.183123 INFO: Starting optimization step 18.
1:31:30.183202 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:31:30.183279 PROGRESS: Extracting batch of 50096 precursors
1:31:30.201895 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:30.202049 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:30.202094 INFO: FWHM in RT is 2.38 seconds, sigma is 0.31
1:31:30.202126 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:30.202441 INFO: Starting candidate selection
1:31:35.463658 INFO: Starting candidate scoring
1:31:36.161890 INFO: Finished candidate processing
1:31:36.162012 INFO: Collecting candidate features
1:31:36.320059 INFO: Collecting fragment features
1:31:36.375000 INFO: Finished candidate scoring
1:31:36.412590 PROGRESS: === Extracted 99991 precursors and 740678 fragments ===
1:31:36.413006 INFO: performing precursor FDR with 47 features
1:31:36.413043 INFO: Decoy channel: -1
1:31:36.413066 INFO: Competetive: True
1:31:36.444544 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:38.007877 INFO: Test AUC: 0.560
1:31:38.008022 INFO: Train AUC: 0.570
1:31:38.008054 INFO: AUC difference: 1.68%
1:31:38.217496 INFO: Resetting torch num_threads to 100
1:31:38.220613 INFO: === FDR correction performed with classifier version 8 ===
1:31:38.221278 PROGRESS: ============================= Precursor FDR =============================
1:31:38.221370 PROGRESS: Total precursors accumulated: 494
1:31:38.221431 PROGRESS: Target precursors: 454 (91.90%)
1:31:38.221483 PROGRESS: Decoy precursors: 40 (8.10%)
1:31:38.221529 PROGRESS: 
1:31:38.221574 PROGRESS: Precursor Summary:
1:31:38.222553 PROGRESS: Channel   0:	 0.05 FDR:   353; 0.01 FDR:   228; 0.001 FDR:   217
1:31:38.222642 PROGRESS: 
1:31:38.222698 PROGRESS: Protein Summary:
1:31:38.223840 PROGRESS: Channel   0:	 0.05 FDR:   338; 0.01 FDR:   220; 0.001 FDR:   209
1:31:38.223931 PROGRESS: =========================================================================
1:31:38.276709 INFO: fragments_df: keeping 2294 of 740678 [sum(precursor_idx_mask)=4693 sum(mass_error_mask)=740678 stop_rank=2294
1:31:38.444230 INFO: calibration group: precursor, fitting rt estimator 
1:31:38.542198 INFO: calibration group: fragment, fitting mz estimator 
1:31:38.805832 INFO: Using score_cutoff 48.9030789516449 (fac=0.99, q=1)
1:31:38.806244 INFO: calibration group: precursor, predicting mz
1:31:38.806331 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:38.806362 INFO: calibration group: precursor, predicting rt
1:31:38.837584 INFO: calibration group: fragment, predicting mz
1:31:38.904412 INFO: === checking if optimization conditions were reached ===
1:31:38.904683 PROGRESS: === Optimization of ms2_error has been performed 10 time(s); minimum number is 2 ===
1:31:38.906820 PROGRESS: ❌ ms2_error      : optimization incomplete after 10 search(es). Will search with parameter 6.5333.
1:31:38.906876 INFO: ==============================================
1:31:38.906970 INFO: Starting optimization step 19.
1:31:38.907038 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:31:38.907098 PROGRESS: Extracting batch of 50096 precursors
1:31:38.921685 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:38.921863 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:38.921902 INFO: FWHM in RT is 2.30 seconds, sigma is 0.30
1:31:38.921931 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:38.922198 INFO: Starting candidate selection
1:31:41.281835 INFO: Starting candidate scoring
1:31:42.013414 INFO: Finished candidate processing
1:31:42.013564 INFO: Collecting candidate features
1:31:42.238370 INFO: Collecting fragment features
1:31:42.294927 INFO: Finished candidate scoring
1:31:42.342331 PROGRESS: === Extracted 99972 precursors and 709427 fragments ===
1:31:42.342875 INFO: performing precursor FDR with 47 features
1:31:42.342929 INFO: Decoy channel: -1
1:31:42.342956 INFO: Competetive: True
1:31:42.378612 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:43.899074 INFO: Test AUC: 0.547
1:31:43.899218 INFO: Train AUC: 0.571
1:31:43.899251 INFO: AUC difference: 4.22%
1:31:44.110483 INFO: Resetting torch num_threads to 100
1:31:44.113679 INFO: === FDR correction performed with classifier version 8 ===
1:31:44.114427 PROGRESS: ============================= Precursor FDR =============================
1:31:44.114519 PROGRESS: Total precursors accumulated: 445
1:31:44.114582 PROGRESS: Target precursors: 408 (91.69%)
1:31:44.114633 PROGRESS: Decoy precursors: 37 (8.31%)
1:31:44.114680 PROGRESS: 
1:31:44.114724 PROGRESS: Precursor Summary:
1:31:44.115719 PROGRESS: Channel   0:	 0.05 FDR:   331; 0.01 FDR:   251; 0.001 FDR:   170
1:31:44.115806 PROGRESS: 
1:31:44.115863 PROGRESS: Protein Summary:
1:31:44.117018 PROGRESS: Channel   0:	 0.05 FDR:   315; 0.01 FDR:   240; 0.001 FDR:   163
1:31:44.117110 PROGRESS: =========================================================================
1:31:44.168593 INFO: fragments_df: keeping 2425 of 709427 [sum(precursor_idx_mask)=5040 sum(mass_error_mask)=709427 stop_rank=2425
1:31:44.326499 INFO: calibration group: precursor, fitting rt estimator 
1:31:44.448522 INFO: calibration group: fragment, fitting mz estimator 
1:31:44.774906 INFO: Using score_cutoff 45.25658878326416 (fac=0.99, q=1)
1:31:44.775355 INFO: calibration group: precursor, predicting mz
1:31:44.775444 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:44.775477 INFO: calibration group: precursor, predicting rt
1:31:44.806861 INFO: calibration group: fragment, predicting mz
1:31:44.873019 INFO: === checking if optimization conditions were reached ===
1:31:44.873355 PROGRESS: === Optimization of ms2_error has been performed 11 time(s); minimum number is 2 ===
1:31:44.876005 PROGRESS: ❌ ms2_error      : optimization incomplete after 11 search(es). Will search with parameter 5.9436.
1:31:44.876071 INFO: ==============================================
1:31:44.876183 WARNING: Optimization did not converge within the maximum number of steps, which is 20.
1:31:44.876301 INFO: Starting optimization step 0.
1:31:44.876376 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:31:44.876451 PROGRESS: Extracting batch of 50096 precursors
1:31:44.894990 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:44.895143 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:44.895191 INFO: FWHM in RT is 2.28 seconds, sigma is 0.29
1:31:44.895220 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:44.895540 INFO: Starting candidate selection
1:31:47.198556 INFO: Starting candidate scoring
1:31:47.890967 INFO: Finished candidate processing
1:31:47.891086 INFO: Collecting candidate features
1:31:48.044786 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 99871)
1:31:48.058427 INFO: Collecting fragment features
1:31:48.109725 INFO: Finished candidate scoring
1:31:48.150913 PROGRESS: === Extracted 99871 precursors and 668364 fragments ===
1:31:48.151295 INFO: performing precursor FDR with 47 features
1:31:48.151331 INFO: Decoy channel: -1
1:31:48.151354 INFO: Competetive: True
1:31:48.184210 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:48.201923 WARNING: dropped 1 target PSMs due to missing features
1:31:49.714374 INFO: Test AUC: 0.558
1:31:49.714505 INFO: Train AUC: 0.568
1:31:49.714540 INFO: AUC difference: 1.80%
1:31:49.927270 INFO: Resetting torch num_threads to 100
1:31:49.930361 INFO: === FDR correction performed with classifier version 8 ===
1:31:49.931028 PROGRESS: ============================= Precursor FDR =============================
1:31:49.931122 PROGRESS: Total precursors accumulated: 402
1:31:49.931185 PROGRESS: Target precursors: 366 (91.04%)
1:31:49.931237 PROGRESS: Decoy precursors: 36 (8.96%)
1:31:49.931285 PROGRESS: 
1:31:49.931329 PROGRESS: Precursor Summary:
1:31:49.932317 PROGRESS: Channel   0:	 0.05 FDR:   312; 0.01 FDR:   259; 0.001 FDR:   196
1:31:49.932409 PROGRESS: 
1:31:49.932464 PROGRESS: Protein Summary:
1:31:49.933590 PROGRESS: Channel   0:	 0.05 FDR:   295; 0.01 FDR:   247; 0.001 FDR:   188
1:31:49.933680 PROGRESS: =========================================================================
1:31:49.982289 INFO: fragments_df: keeping 2461 of 668364 [sum(precursor_idx_mask)=5094 sum(mass_error_mask)=668364 stop_rank=2461
1:31:50.283083 INFO: calibration group: precursor, fitting rt estimator 
1:31:50.384260 INFO: calibration group: fragment, fitting mz estimator 
1:31:50.655377 INFO: Using score_cutoff 51.69958932952881 (fac=0.99, q=1)
1:31:50.655802 INFO: calibration group: precursor, predicting mz
1:31:50.655888 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:50.655919 INFO: calibration group: precursor, predicting rt
1:31:50.686694 INFO: calibration group: fragment, predicting mz
1:31:50.753875 INFO: === checking if optimization conditions were reached ===
1:31:50.754161 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:31:50.755975 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 167.7926.
1:31:50.756029 INFO: ==============================================
1:31:50.756121 INFO: Starting optimization step 1.
1:31:50.756188 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:31:50.756256 PROGRESS: Extracting batch of 50096 precursors
1:31:50.770044 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:50.770173 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:50.770207 INFO: FWHM in RT is 2.24 seconds, sigma is 0.29
1:31:50.770229 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:50.770454 INFO: Starting candidate selection
1:31:52.840362 INFO: Starting candidate scoring
1:31:53.537580 INFO: Finished candidate processing
1:31:53.537699 INFO: Collecting candidate features
1:31:53.702041 WARNING: intensity_correlation has 27 NaNs ( 0.03 % out of 98574)
1:31:53.720509 INFO: Collecting fragment features
1:31:53.773535 INFO: Finished candidate scoring
1:31:53.812367 PROGRESS: === Extracted 98574 precursors and 582652 fragments ===
1:31:53.812799 INFO: performing precursor FDR with 47 features
1:31:53.812835 INFO: Decoy channel: -1
1:31:53.812857 INFO: Competetive: True
1:31:53.851424 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:53.870016 WARNING: dropped 18 target PSMs due to missing features
1:31:53.870170 WARNING: dropped 9 decoy PSMs due to missing features
1:31:55.321104 INFO: Test AUC: 0.559
1:31:55.321244 INFO: Train AUC: 0.565
1:31:55.321275 INFO: AUC difference: 1.18%
1:31:55.529490 INFO: Resetting torch num_threads to 100
1:31:55.532602 INFO: === FDR correction performed with classifier version 8 ===
1:31:55.533302 PROGRESS: ============================= Precursor FDR =============================
1:31:55.533391 PROGRESS: Total precursors accumulated: 501
1:31:55.533450 PROGRESS: Target precursors: 458 (91.42%)
1:31:55.533502 PROGRESS: Decoy precursors: 43 (8.58%)
1:31:55.533548 PROGRESS: 
1:31:55.533592 PROGRESS: Precursor Summary:
1:31:55.534586 PROGRESS: Channel   0:	 0.05 FDR:   355; 0.01 FDR:   270; 0.001 FDR:   195
1:31:55.534678 PROGRESS: 
1:31:55.534733 PROGRESS: Protein Summary:
1:31:55.535882 PROGRESS: Channel   0:	 0.05 FDR:   339; 0.01 FDR:   257; 0.001 FDR:   187
1:31:55.536178 PROGRESS: =========================================================================
1:31:55.579063 INFO: fragments_df: keeping 2489 of 582652 [sum(precursor_idx_mask)=5290 sum(mass_error_mask)=582652 stop_rank=2489
1:31:55.897887 INFO: calibration group: precursor, fitting rt estimator 
1:31:56.015954 INFO: calibration group: fragment, fitting mz estimator 
1:31:56.344607 INFO: Using score_cutoff 48.02545247154236 (fac=0.99, q=1)
1:31:56.345017 INFO: calibration group: precursor, predicting mz
1:31:56.345104 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:56.345134 INFO: calibration group: precursor, predicting rt
1:31:56.376723 INFO: calibration group: fragment, predicting mz
1:31:56.438807 INFO: === checking if optimization conditions were reached ===
1:31:56.439159 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:31:56.441491 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 97.1264.
1:31:56.441556 INFO: ==============================================
1:31:56.441659 INFO: Starting optimization step 2.
1:31:56.441734 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:31:56.441801 PROGRESS: Extracting batch of 50096 precursors
1:31:56.459579 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:56.459727 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:56.459765 INFO: FWHM in RT is 2.23 seconds, sigma is 0.29
1:31:56.459793 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:56.460055 INFO: Starting candidate selection
1:31:58.447034 INFO: Starting candidate scoring
1:31:59.127403 INFO: Finished candidate processing
1:31:59.127512 INFO: Collecting candidate features
1:31:59.278589 WARNING: intensity_correlation has 44 NaNs ( 0.05 % out of 96849)
1:31:59.291663 INFO: Collecting fragment features
1:31:59.335425 INFO: Finished candidate scoring
1:31:59.376455 PROGRESS: === Extracted 96849 precursors and 531752 fragments ===
1:31:59.376924 INFO: performing precursor FDR with 47 features
1:31:59.376967 INFO: Decoy channel: -1
1:31:59.376996 INFO: Competetive: True
1:31:59.406478 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:59.425481 WARNING: dropped 25 target PSMs due to missing features
1:31:59.425630 WARNING: dropped 19 decoy PSMs due to missing features
1:32:01.075649 INFO: Test AUC: 0.552
1:32:01.075882 INFO: Train AUC: 0.561
1:32:01.075913 INFO: AUC difference: 1.61%
1:32:01.292468 INFO: Resetting torch num_threads to 100
1:32:01.295567 INFO: === FDR correction performed with classifier version 8 ===
1:32:01.296275 PROGRESS: ============================= Precursor FDR =============================
1:32:01.296375 PROGRESS: Total precursors accumulated: 481
1:32:01.296435 PROGRESS: Target precursors: 440 (91.48%)
1:32:01.296487 PROGRESS: Decoy precursors: 41 (8.52%)
1:32:01.296536 PROGRESS: 
1:32:01.296581 PROGRESS: Precursor Summary:
1:32:01.297590 PROGRESS: Channel   0:	 0.05 FDR:   357; 0.01 FDR:   304; 0.001 FDR:   211
1:32:01.297679 PROGRESS: 
1:32:01.297736 PROGRESS: Protein Summary:
1:32:01.298884 PROGRESS: Channel   0:	 0.05 FDR:   339; 0.01 FDR:   289; 0.001 FDR:   202
1:32:01.298976 PROGRESS: =========================================================================
1:32:01.339552 INFO: fragments_df: keeping 2697 of 531752 [sum(precursor_idx_mask)=5882 sum(mass_error_mask)=531752 stop_rank=2697
1:32:01.519753 INFO: calibration group: precursor, fitting rt estimator 
1:32:01.648910 INFO: calibration group: fragment, fitting mz estimator 
1:32:02.007019 INFO: Using score_cutoff 41.104540890884394 (fac=0.99, q=1)
1:32:02.007482 INFO: calibration group: precursor, predicting mz
1:32:02.007569 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:02.007600 INFO: calibration group: precursor, predicting rt
1:32:02.038676 INFO: calibration group: fragment, predicting mz
1:32:02.103736 INFO: === checking if optimization conditions were reached ===
1:32:02.104088 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:32:02.106642 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 82.3790.
1:32:02.106710 INFO: ==============================================
1:32:02.106834 INFO: Starting optimization step 3.
1:32:02.106914 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:32:02.106990 PROGRESS: Extracting batch of 50096 precursors
1:32:02.125794 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:02.125933 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:02.125986 INFO: FWHM in RT is 2.15 seconds, sigma is 0.28
1:32:02.126014 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:02.126378 INFO: Starting candidate selection
1:32:03.741350 INFO: Starting candidate scoring
1:32:04.437832 INFO: Finished candidate processing
1:32:04.437948 INFO: Collecting candidate features
1:32:04.581447 WARNING: intensity_correlation has 52 NaNs ( 0.05 % out of 96511)
1:32:04.592880 INFO: Collecting fragment features
1:32:04.635607 INFO: Finished candidate scoring
1:32:04.678187 PROGRESS: === Extracted 96511 precursors and 522114 fragments ===
1:32:04.678617 INFO: performing precursor FDR with 47 features
1:32:04.678655 INFO: Decoy channel: -1
1:32:04.678681 INFO: Competetive: True
1:32:04.708586 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:04.726793 WARNING: dropped 29 target PSMs due to missing features
1:32:04.726944 WARNING: dropped 23 decoy PSMs due to missing features
1:32:06.207510 INFO: Test AUC: 0.554
1:32:06.207650 INFO: Train AUC: 0.561
1:32:06.207680 INFO: AUC difference: 1.29%
1:32:06.417391 INFO: Resetting torch num_threads to 100
1:32:06.420279 INFO: === FDR correction performed with classifier version 8 ===
1:32:06.420988 PROGRESS: ============================= Precursor FDR =============================
1:32:06.421078 PROGRESS: Total precursors accumulated: 514
1:32:06.421139 PROGRESS: Target precursors: 470 (91.44%)
1:32:06.421191 PROGRESS: Decoy precursors: 44 (8.56%)
1:32:06.421237 PROGRESS: 
1:32:06.421285 PROGRESS: Precursor Summary:
1:32:06.422283 PROGRESS: Channel   0:	 0.05 FDR:   389; 0.01 FDR:   262; 0.001 FDR:   226
1:32:06.422373 PROGRESS: 
1:32:06.422429 PROGRESS: Protein Summary:
1:32:06.423576 PROGRESS: Channel   0:	 0.05 FDR:   371; 0.01 FDR:   249; 0.001 FDR:   215
1:32:06.423666 PROGRESS: =========================================================================
1:32:06.470046 INFO: fragments_df: keeping 2416 of 522114 [sum(precursor_idx_mask)=5116 sum(mass_error_mask)=522114 stop_rank=2416
1:32:06.605295 INFO: calibration group: precursor, fitting rt estimator 
1:32:06.710948 INFO: calibration group: fragment, fitting mz estimator 
1:32:06.975882 INFO: Using score_cutoff 50.120726684188845 (fac=0.99, q=1)
1:32:06.976321 INFO: calibration group: precursor, predicting mz
1:32:06.976410 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:06.976442 INFO: calibration group: precursor, predicting rt
1:32:07.007523 INFO: calibration group: fragment, predicting mz
1:32:07.067812 INFO: === checking if optimization conditions were reached ===
1:32:07.068142 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:32:07.070508 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 78.9546.
1:32:07.070573 INFO: ==============================================
1:32:07.070679 INFO: Starting optimization step 4.
1:32:07.070754 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:32:07.070822 PROGRESS: Extracting batch of 50096 precursors
1:32:07.087857 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:07.088012 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:07.088053 INFO: FWHM in RT is 2.21 seconds, sigma is 0.28
1:32:07.088083 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:07.088359 INFO: Starting candidate selection
1:32:08.638844 INFO: Starting candidate scoring
1:32:09.302521 INFO: Finished candidate processing
1:32:09.302635 INFO: Collecting candidate features
1:32:09.444192 WARNING: intensity_correlation has 62 NaNs ( 0.06 % out of 96048)
1:32:09.450567 INFO: Collecting fragment features
1:32:09.492828 INFO: Finished candidate scoring
1:32:09.537141 PROGRESS: === Extracted 96048 precursors and 515011 fragments ===
1:32:09.537544 INFO: performing precursor FDR with 47 features
1:32:09.537583 INFO: Decoy channel: -1
1:32:09.537607 INFO: Competetive: True
1:32:09.566248 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:09.584211 WARNING: dropped 37 target PSMs due to missing features
1:32:09.584369 WARNING: dropped 25 decoy PSMs due to missing features
1:32:11.038164 INFO: Test AUC: 0.549
1:32:11.038304 INFO: Train AUC: 0.562
1:32:11.038335 INFO: AUC difference: 2.34%
1:32:11.249565 INFO: Resetting torch num_threads to 100
1:32:11.252436 INFO: === FDR correction performed with classifier version 8 ===
1:32:11.253095 PROGRESS: ============================= Precursor FDR =============================
1:32:11.253186 PROGRESS: Total precursors accumulated: 481
1:32:11.253246 PROGRESS: Target precursors: 441 (91.68%)
1:32:11.253298 PROGRESS: Decoy precursors: 40 (8.32%)
1:32:11.253345 PROGRESS: 
1:32:11.253391 PROGRESS: Precursor Summary:
1:32:11.254357 PROGRESS: Channel   0:	 0.05 FDR:   374; 0.01 FDR:   283; 0.001 FDR:   237
1:32:11.254447 PROGRESS: 
1:32:11.254509 PROGRESS: Protein Summary:
1:32:11.255650 PROGRESS: Channel   0:	 0.05 FDR:   355; 0.01 FDR:   269; 0.001 FDR:   226
1:32:11.255743 PROGRESS: =========================================================================
1:32:11.293544 INFO: fragments_df: keeping 2528 of 515011 [sum(precursor_idx_mask)=5483 sum(mass_error_mask)=515011 stop_rank=2528
1:32:11.436198 INFO: calibration group: precursor, fitting rt estimator 
1:32:11.562752 INFO: calibration group: fragment, fitting mz estimator 
1:32:11.898295 INFO: Using score_cutoff 48.621006484222406 (fac=0.99, q=1)
1:32:11.898706 INFO: calibration group: precursor, predicting mz
1:32:11.898793 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:11.898823 INFO: calibration group: precursor, predicting rt
1:32:11.930635 INFO: calibration group: fragment, predicting mz
1:32:11.994630 INFO: === checking if optimization conditions were reached ===
1:32:11.994947 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1:32:11.996373 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 78.9546 found after 5 searches.
1:32:11.996433 INFO: ==============================================
1:32:11.996536 PROGRESS: Optimization finished for rt_error.
1:32:12.142602 INFO: calibration group: precursor, predicting mz
1:32:12.142909 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:12.142943 INFO: calibration group: precursor, predicting rt
1:32:12.174936 INFO: calibration group: fragment, predicting mz
1:32:12.270499 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:32:12.270770 PROGRESS: ==============================================
1:32:12.270862 PROGRESS: ms2_error      : 5.9436
1:32:12.270934 PROGRESS: rt_error       : 78.9546
1:32:12.271005 PROGRESS: ==============================================
1:32:12.272047 INFO: calibration group: precursor, predicting mz
1:32:12.272201 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:12.272247 INFO: calibration group: precursor, predicting rt
1:32:20.417149 INFO: calibration group: fragment, predicting mz
1:32:37.521045 PROGRESS: Extracting batch of 12567710 precursors
1:32:40.227964 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:40.228133 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:40.228181 INFO: FWHM in RT is 2.19 seconds, sigma is 0.28
1:32:40.228205 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:40.228652 INFO: Starting candidate selection
1:39:05.348742 INFO: Applying score cutoff of 48.621006484222406
1:39:05.448796 INFO: Removed 23463496 precursors with score below cutoff
1:39:08.100336 INFO: Starting candidate scoring
1:39:20.855616 INFO: Finished candidate processing
1:39:20.855852 INFO: Collecting candidate features
1:39:25.584068 INFO: Collecting fragment features
1:39:27.121238 INFO: Finished candidate scoring
1:39:28.249417 INFO: === FDR correction performed with classifier version 24 ===
1:39:28.250817 INFO: performing precursor FDR with 47 features
1:39:28.250879 INFO: Decoy channel: -1
1:39:28.250905 INFO: Competetive: True
1:39:28.730792 INFO: Setting torch num_threads to 2 for FDR classification task
1:39:56.132765 INFO: Test AUC: 0.636
1:39:56.133017 INFO: Train AUC: 0.641
1:39:56.133053 INFO: AUC difference: 0.80%
1:39:56.748877 INFO: Resetting torch num_threads to 100
1:39:56.800420 INFO: Removing fragments below FDR threshold
1:39:56.983420 PROGRESS: ============================= Precursor FDR =============================
1:39:56.983754 PROGRESS: Total precursors accumulated: 79,429
1:39:56.983824 PROGRESS: Target precursors: 78,643 (99.01%)
1:39:56.983880 PROGRESS: Decoy precursors: 786 (0.99%)
1:39:56.983932 PROGRESS: 
1:39:56.983980 PROGRESS: Precursor Summary:
1:39:57.016058 PROGRESS: Channel   0:	 0.05 FDR: 78,643; 0.01 FDR: 78,643; 0.001 FDR: 56,284
1:39:57.016385 PROGRESS: 
1:39:57.016454 PROGRESS: Protein Summary:
1:39:57.061841 PROGRESS: Channel   0:	 0.05 FDR: 11,746; 0.01 FDR: 11,746; 0.001 FDR: 9,046
1:39:57.062118 PROGRESS: =========================================================================
1:39:57.677079 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:39:58.144832 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:39:58.145021 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant
1:39:58.145103 INFO: Creating folder run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/figures
1:39:58.146137 INFO: Initializing RawFileManager
1:40:08.223808 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
1:40:08.228397 INFO: Determining DIA cycle
1:40:08.244833 INFO: Found cycle with start 0.00 min and length 300.
1:40:08.410823 INFO: RT (min)            : 0.0 - 26.9
1:40:08.410923 INFO: RT duration (sec)   : 1611.2
1:40:08.410958 INFO: RT duration (min)   : 26.9
1:40:08.410983 INFO: Cycle len (scans)   : 300
1:40:08.411005 INFO: Cycle len (sec)     : 1.65
1:40:08.411026 INFO: Number of cycles    : 978
1:40:08.411045 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:40:09.901125 INFO: Initializing CalibrationManager
1:40:09.901447 INFO: Loading calibration config
1:40:09.902084 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'}]
1:40:09.902174 INFO: Calibration group :fragment, found 1 estimator(s)
1:40:09.902265 INFO: Calibration group :precursor, found 3 estimator(s)
1:40:09.902365 INFO: Disabling ion mobility calibration
1:40:09.902395 INFO: removed mobility estimator from group precursor
1:40:09.902544 INFO: Initializing OptimizationManager
1:40:09.902659 INFO: initial parameter: ms1_error = 30
1:40:09.902720 INFO: initial parameter: ms2_error = 30
1:40:09.902769 INFO: initial parameter: rt_error = 805.611083984375
1:40:09.902814 INFO: initial parameter: mobility_error = 0.1
1:40:09.902857 INFO: initial parameter: column_type = library
1:40:09.902905 INFO: initial parameter: num_candidates = 1
1:40:09.902949 INFO: initial parameter: classifier_version = -1
1:40:09.902991 INFO: initial parameter: fwhm_rt = 5
1:40:09.903033 INFO: initial parameter: fwhm_mobility = 0.01
1:40:09.903075 INFO: initial parameter: score_cutoff = 0
1:40:09.903147 INFO: Initializing TimingManager
1:40:09.903214 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:40:09.903349 INFO: FDRManager not loaded from disk.
1:40:09.903372 INFO: Initializing FDRManager
1:40:09.903412 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:40:11.413198 PROGRESS: 6,373,245 target precursors potentially observable (7,405 removed)
1:40:13.540715 PROGRESS: Starting initial search for precursors.
1:40:13.797945 INFO: Starting optimization step 0.
1:40:13.798209 PROGRESS: === Extracting elution groups 0 to 200 ===
1:40:13.798285 PROGRESS: Extracting batch of 396 precursors
1:40:13.799296 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:40:13.799348 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:40:13.799387 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:40:13.799411 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:40:13.799698 INFO: Starting candidate selection
1:40:13.955715 INFO: Starting candidate scoring
1:40:13.993172 INFO: Finished candidate processing
1:40:13.993253 INFO: Collecting candidate features
1:40:14.001813 INFO: Collecting fragment features
1:40:14.003888 INFO: Finished candidate scoring
1:40:14.004721 PROGRESS: === Extracted 394 precursors and 4067 fragments ===
1:40:14.004997 INFO: performing precursor FDR with 47 features
1:40:14.005034 INFO: Decoy channel: -1
1:40:14.005061 INFO: Competetive: True
1:40:14.006039 INFO: Setting torch num_threads to 2 for FDR classification task
1:40:14.025859 INFO: Test AUC: 0.519
1:40:14.025925 INFO: Train AUC: 0.484
1:40:14.025955 INFO: AUC difference: 7.18%
1:40:14.025977 WARNING: AUC difference > 5%. This may indicate overfitting.
1:40:14.202502 INFO: Resetting torch num_threads to 100
1:40:14.203071 INFO: === FDR correction performed with classifier version -1 ===
1:40:14.203707 PROGRESS: ============================= Precursor FDR =============================
1:40:14.203799 PROGRESS: Total precursors accumulated: 199
1:40:14.203860 PROGRESS: Target precursors: 93 (46.73%)
1:40:14.203917 PROGRESS: Decoy precursors: 106 (53.27%)
1:40:14.203965 PROGRESS: 
1:40:14.204010 PROGRESS: Precursor Summary:
1:40:14.204875 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:40:14.204964 PROGRESS: 
1:40:14.205019 PROGRESS: Protein Summary:
1:40:14.205928 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:40:14.206014 PROGRESS: =========================================================================
1:40:14.273381 INFO: Starting optimization step 1.
1:40:14.273619 PROGRESS: === Extracting elution groups 200 to 600 ===
1:40:14.273686 PROGRESS: Extracting batch of 786 precursors
1:40:14.274513 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:40:14.274561 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:40:14.274593 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:40:14.274616 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:40:14.274789 INFO: Starting candidate selection
1:40:14.420399 INFO: Starting candidate scoring
1:40:14.458536 INFO: Finished candidate processing
1:40:14.458615 INFO: Collecting candidate features
1:40:14.467803 INFO: Collecting fragment features
1:40:14.470590 INFO: Finished candidate scoring
1:40:14.472578 PROGRESS: === Extracted 1180 precursors and 12144 fragments ===
1:40:14.473349 INFO: performing precursor FDR with 47 features
1:40:14.473397 INFO: Decoy channel: -1
1:40:14.473429 INFO: Competetive: True
1:40:14.476249 INFO: Setting torch num_threads to 2 for FDR classification task
1:40:14.500252 INFO: Test AUC: 0.457
1:40:14.500328 INFO: Train AUC: 0.521
1:40:14.500370 INFO: AUC difference: 12.44%
1:40:14.500400 WARNING: AUC difference > 5%. This may indicate overfitting.
1:40:14.694208 INFO: Resetting torch num_threads to 100
1:40:14.694896 INFO: === FDR correction performed with classifier version -1 ===
1:40:14.695582 PROGRESS: ============================= Precursor FDR =============================
1:40:14.695684 PROGRESS: Total precursors accumulated: 599
1:40:14.695758 PROGRESS: Target precursors: 304 (50.75%)
1:40:14.695822 PROGRESS: Decoy precursors: 295 (49.25%)
1:40:14.695881 PROGRESS: 
1:40:14.695939 PROGRESS: Precursor Summary:
1:40:14.696848 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:40:14.696948 PROGRESS: 
1:40:14.697016 PROGRESS: Protein Summary:
1:40:14.697978 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:40:14.698076 PROGRESS: =========================================================================
1:40:14.767826 INFO: Starting optimization step 2.
1:40:14.768081 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:40:14.768163 PROGRESS: Extracting batch of 1573 precursors
1:40:14.769394 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:40:14.769448 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:40:14.769490 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:40:14.769518 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:40:14.769708 INFO: Starting candidate selection
1:40:14.942157 INFO: Starting candidate scoring
1:40:14.982428 INFO: Finished candidate processing
1:40:14.982512 INFO: Collecting candidate features
1:40:14.993353 INFO: Collecting fragment features
1:40:14.997617 INFO: Finished candidate scoring
1:40:15.000487 PROGRESS: === Extracted 2747 precursors and 28222 fragments ===
1:40:15.001458 INFO: performing precursor FDR with 47 features
1:40:15.001504 INFO: Decoy channel: -1
1:40:15.001536 INFO: Competetive: True
1:40:15.005611 INFO: Setting torch num_threads to 2 for FDR classification task
1:40:15.044511 INFO: Test AUC: 0.443
1:40:15.044601 INFO: Train AUC: 0.496
1:40:15.044641 INFO: AUC difference: 10.62%
1:40:15.044668 WARNING: AUC difference > 5%. This may indicate overfitting.
1:40:15.215113 INFO: Resetting torch num_threads to 100
1:40:15.215925 INFO: === FDR correction performed with classifier version -1 ===
1:40:15.216734 PROGRESS: ============================= Precursor FDR =============================
1:40:15.216837 PROGRESS: Total precursors accumulated: 1,396
1:40:15.216910 PROGRESS: Target precursors: 676 (48.42%)
1:40:15.216975 PROGRESS: Decoy precursors: 720 (51.58%)
1:40:15.217035 PROGRESS: 
1:40:15.217092 PROGRESS: Precursor Summary:
1:40:15.217992 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:40:15.218088 PROGRESS: 
1:40:15.218153 PROGRESS: Protein Summary:
1:40:15.219116 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:40:15.219214 PROGRESS: =========================================================================
1:40:15.291288 INFO: Starting optimization step 3.
1:40:15.291555 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:40:15.291634 PROGRESS: Extracting batch of 3149 precursors
1:40:15.292840 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:40:15.292891 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:40:15.292933 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:40:15.292961 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:40:15.293147 INFO: Starting candidate selection
1:40:15.514881 INFO: Starting candidate scoring
1:40:15.558331 INFO: Finished candidate processing
1:40:15.558436 INFO: Collecting candidate features
1:40:15.572303 INFO: Collecting fragment features
1:40:15.576899 INFO: Finished candidate scoring
1:40:15.581243 PROGRESS: === Extracted 5891 precursors and 60728 fragments ===
1:40:15.582468 INFO: performing precursor FDR with 47 features
1:40:15.582511 INFO: Decoy channel: -1
1:40:15.582536 INFO: Competetive: True
1:40:15.586564 INFO: Setting torch num_threads to 2 for FDR classification task
1:40:15.638524 INFO: Test AUC: 0.488
1:40:15.638628 INFO: Train AUC: 0.488
1:40:15.638660 INFO: AUC difference: 0.14%
1:40:15.813033 INFO: Resetting torch num_threads to 100
1:40:15.814020 INFO: === FDR correction performed with classifier version -1 ===
1:40:15.814992 PROGRESS: ============================= Precursor FDR =============================
1:40:15.815086 PROGRESS: Total precursors accumulated: 2,994
1:40:15.815147 PROGRESS: Target precursors: 1,478 (49.37%)
1:40:15.815200 PROGRESS: Decoy precursors: 1,516 (50.63%)
1:40:15.815247 PROGRESS: 
1:40:15.815291 PROGRESS: Precursor Summary:
1:40:15.816178 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:40:15.816276 PROGRESS: 
1:40:15.816332 PROGRESS: Protein Summary:
1:40:15.817278 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:40:15.817367 PROGRESS: =========================================================================
1:40:15.893830 INFO: Starting optimization step 4.
1:40:15.894105 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:40:15.894173 PROGRESS: Extracting batch of 6319 precursors
1:40:15.895674 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:40:15.895722 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:40:15.895753 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:40:15.895775 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:40:15.895952 INFO: Starting candidate selection
1:40:16.334251 INFO: Starting candidate scoring
1:40:16.386165 INFO: Finished candidate processing
1:40:16.386264 INFO: Collecting candidate features
1:40:16.406336 INFO: Collecting fragment features
1:40:16.412716 INFO: Finished candidate scoring
1:40:16.420921 PROGRESS: === Extracted 12200 precursors and 125530 fragments ===
1:40:16.422799 INFO: performing precursor FDR with 47 features
1:40:16.422856 INFO: Decoy channel: -1
1:40:16.422881 INFO: Competetive: True
1:40:16.428893 INFO: Setting torch num_threads to 2 for FDR classification task
1:40:16.514523 INFO: Test AUC: 0.463
1:40:16.514642 INFO: Train AUC: 0.496
1:40:16.514672 INFO: AUC difference: 6.62%
1:40:16.514693 WARNING: AUC difference > 5%. This may indicate overfitting.
1:40:16.694090 INFO: Resetting torch num_threads to 100
1:40:16.695357 INFO: === FDR correction performed with classifier version -1 ===
1:40:16.696688 PROGRESS: ============================= Precursor FDR =============================
1:40:16.696792 PROGRESS: Total precursors accumulated: 6,189
1:40:16.696860 PROGRESS: Target precursors: 3,060 (49.44%)
1:40:16.696912 PROGRESS: Decoy precursors: 3,129 (50.56%)
1:40:16.696957 PROGRESS: 
1:40:16.697001 PROGRESS: Precursor Summary:
1:40:16.697913 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:40:16.698003 PROGRESS: 
1:40:16.698056 PROGRESS: Protein Summary:
1:40:16.699018 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:40:16.699110 PROGRESS: =========================================================================
1:40:16.783331 INFO: Starting optimization step 5.
1:40:16.783617 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:40:16.783693 PROGRESS: Extracting batch of 12617 precursors
1:40:16.786424 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:40:16.786482 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:40:16.786513 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:40:16.786534 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:40:16.786721 INFO: Starting candidate selection
1:40:17.590383 INFO: Starting candidate scoring
1:40:17.672299 INFO: Finished candidate processing
1:40:17.672416 INFO: Collecting candidate features
1:40:17.706126 INFO: Collecting fragment features
1:40:17.717838 INFO: Finished candidate scoring
1:40:17.731200 PROGRESS: === Extracted 24794 precursors and 255139 fragments ===
1:40:17.734879 INFO: performing precursor FDR with 47 features
1:40:17.734959 INFO: Decoy channel: -1
1:40:17.734985 INFO: Competetive: True
1:40:17.747234 INFO: Setting torch num_threads to 2 for FDR classification task
1:40:17.997061 INFO: Test AUC: 0.537
1:40:17.997190 INFO: Train AUC: 0.551
1:40:17.997223 INFO: AUC difference: 2.50%
1:40:18.181653 INFO: Resetting torch num_threads to 100
1:40:18.183372 INFO: === FDR correction performed with classifier version -1 ===
1:40:18.184059 PROGRESS: ============================= Precursor FDR =============================
1:40:18.184159 PROGRESS: Total precursors accumulated: 2
1:40:18.184223 PROGRESS: Target precursors: 2 (100.00%)
1:40:18.184304 PROGRESS: Decoy precursors: 0 (0.00%)
1:40:18.184365 PROGRESS: 
1:40:18.184412 PROGRESS: Precursor Summary:
1:40:18.185339 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:40:18.185426 PROGRESS: 
1:40:18.185481 PROGRESS: Protein Summary:
1:40:18.186489 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:40:18.186578 PROGRESS: =========================================================================
1:40:18.288206 INFO: Starting optimization step 6.
1:40:18.288510 PROGRESS: === Extracting elution groups 12600 to 25400 ===
1:40:18.288580 PROGRESS: Extracting batch of 25256 precursors
1:40:18.294204 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:40:18.294283 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:40:18.294315 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:40:18.294338 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:40:18.294537 INFO: Starting candidate selection
1:40:19.842160 INFO: Starting candidate scoring
1:40:19.993721 INFO: Finished candidate processing
1:40:19.993836 INFO: Collecting candidate features
1:40:20.042325 INFO: Collecting fragment features
1:40:20.058835 INFO: Finished candidate scoring
1:40:20.081522 PROGRESS: === Extracted 50013 precursors and 513889 fragments ===
1:40:20.087666 INFO: performing precursor FDR with 47 features
1:40:20.087751 INFO: Decoy channel: -1
1:40:20.087779 INFO: Competetive: True
1:40:20.106232 INFO: Setting torch num_threads to 2 for FDR classification task
1:40:20.749952 INFO: Test AUC: 0.551
1:40:20.750106 INFO: Train AUC: 0.572
1:40:20.750135 INFO: AUC difference: 3.76%
1:40:20.943912 INFO: Resetting torch num_threads to 100
1:40:20.946590 INFO: === FDR correction performed with classifier version -1 ===
1:40:20.947258 PROGRESS: ============================= Precursor FDR =============================
1:40:20.947353 PROGRESS: Total precursors accumulated: 115
1:40:20.947414 PROGRESS: Target precursors: 105 (91.30%)
1:40:20.947467 PROGRESS: Decoy precursors: 10 (8.70%)
1:40:20.947513 PROGRESS: 
1:40:20.947556 PROGRESS: Precursor Summary:
1:40:20.948457 PROGRESS: Channel   0:	 0.05 FDR:    46; 0.01 FDR:    21; 0.001 FDR:    21
1:40:20.948550 PROGRESS: 
1:40:20.948606 PROGRESS: Protein Summary:
1:40:20.949577 PROGRESS: Channel   0:	 0.05 FDR:    45; 0.01 FDR:    21; 0.001 FDR:    21
1:40:20.949667 PROGRESS: =========================================================================
1:40:21.083018 INFO: Starting optimization step 7.
1:40:21.083324 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1:40:21.083411 PROGRESS: Extracting batch of 50439 precursors
1:40:21.094540 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:40:21.094673 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:40:21.094708 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:40:21.094730 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:40:21.094954 INFO: Starting candidate selection
1:40:24.161627 INFO: Starting candidate scoring
1:40:24.487862 INFO: Finished candidate processing
1:40:24.487989 INFO: Collecting candidate features
1:40:24.573181 INFO: Collecting fragment features
1:40:24.605166 INFO: Finished candidate scoring
1:40:24.649289 PROGRESS: === Extracted 100356 precursors and 1031580 fragments ===
1:40:24.661145 INFO: performing precursor FDR with 47 features
1:40:24.661247 INFO: Decoy channel: -1
1:40:24.661273 INFO: Competetive: True
1:40:24.702474 INFO: Setting torch num_threads to 2 for FDR classification task
1:40:26.279911 INFO: Test AUC: 0.564
1:40:26.280056 INFO: Train AUC: 0.582
1:40:26.280090 INFO: AUC difference: 3.23%
1:40:26.486306 INFO: Resetting torch num_threads to 100
1:40:26.491166 INFO: === FDR correction performed with classifier version -1 ===
1:40:26.491905 PROGRESS: ============================= Precursor FDR =============================
1:40:26.492002 PROGRESS: Total precursors accumulated: 495
1:40:26.492062 PROGRESS: Target precursors: 451 (91.11%)
1:40:26.492116 PROGRESS: Decoy precursors: 44 (8.89%)
1:40:26.492162 PROGRESS: 
1:40:26.492209 PROGRESS: Precursor Summary:
1:40:26.493243 PROGRESS: Channel   0:	 0.05 FDR:   354; 0.01 FDR:   281; 0.001 FDR:   259
1:40:26.493336 PROGRESS: 
1:40:26.493392 PROGRESS: Protein Summary:
1:40:26.494566 PROGRESS: Channel   0:	 0.05 FDR:   335; 0.01 FDR:   268; 0.001 FDR:   247
1:40:26.494659 PROGRESS: =========================================================================
1:40:26.583656 INFO: fragments_df: keeping 2486 of 1031580 [sum(precursor_idx_mask)=3213 sum(mass_error_mask)=1031580 stop_rank=2486
1:40:26.788341 INFO: calibration group: precursor, fitting rt estimator 
1:40:26.888426 INFO: calibration group: fragment, fitting mz estimator 
1:40:27.162204 INFO: Using score_cutoff 61.417782119750974 (fac=0.99, q=1)
1:40:27.162653 INFO: calibration group: precursor, predicting mz
1:40:27.162740 WARNING: mz prediction was skipped as it has not been fitted yet
1:40:27.162770 INFO: calibration group: precursor, predicting rt
1:40:27.225333 INFO: calibration group: fragment, predicting mz
1:40:27.374631 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:40:27.374987 INFO: Starting optimization step 8.
1:40:27.375072 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:40:27.375146 PROGRESS: Extracting batch of 100535 precursors
1:40:27.409161 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:40:27.409319 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:40:27.409358 INFO: FWHM in RT is 2.99 seconds, sigma is 0.39
1:40:27.409388 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:40:27.409686 INFO: Starting candidate selection
1:40:32.049369 INFO: Starting candidate scoring
1:40:33.444521 INFO: Finished candidate processing
1:40:33.444643 INFO: Collecting candidate features
1:40:33.829921 INFO: Collecting fragment features
1:40:33.970310 INFO: Finished candidate scoring
1:40:34.097589 PROGRESS: === Extracted 200712 precursors and 2037831 fragments ===
1:40:34.098043 INFO: performing precursor FDR with 47 features
1:40:34.098082 INFO: Decoy channel: -1
1:40:34.098107 INFO: Competetive: True
1:40:34.186258 INFO: Setting torch num_threads to 2 for FDR classification task
1:40:38.732551 INFO: Test AUC: 0.565
1:40:38.732785 INFO: Train AUC: 0.585
1:40:38.732817 INFO: AUC difference: 3.51%
1:40:38.965693 INFO: Resetting torch num_threads to 100
1:40:38.972379 INFO: === FDR correction performed with classifier version 7 ===
1:40:38.973205 PROGRESS: ============================= Precursor FDR =============================
1:40:38.973305 PROGRESS: Total precursors accumulated: 547
1:40:38.973375 PROGRESS: Target precursors: 498 (91.04%)
1:40:38.973430 PROGRESS: Decoy precursors: 49 (8.96%)
1:40:38.973479 PROGRESS: 
1:40:38.973527 PROGRESS: Precursor Summary:
1:40:38.974544 PROGRESS: Channel   0:	 0.05 FDR:   400; 0.01 FDR:   230; 0.001 FDR:   190
1:40:38.974641 PROGRESS: 
1:40:38.974697 PROGRESS: Protein Summary:
1:40:38.975852 PROGRESS: Channel   0:	 0.05 FDR:   377; 0.01 FDR:   220; 0.001 FDR:   182
1:40:38.975944 PROGRESS: =========================================================================
1:40:39.112584 INFO: fragments_df: keeping 2756 of 2037831 [sum(precursor_idx_mask)=5237 sum(mass_error_mask)=2037831 stop_rank=2756
1:40:39.350912 INFO: calibration group: precursor, fitting rt estimator 
1:40:39.471695 INFO: calibration group: fragment, fitting mz estimator 
1:40:39.835904 INFO: Using score_cutoff 74.18544168548584 (fac=0.99, q=1)
1:40:39.836356 INFO: calibration group: precursor, predicting mz
1:40:39.836450 WARNING: mz prediction was skipped as it has not been fitted yet
1:40:39.836484 INFO: calibration group: precursor, predicting rt
1:40:39.900065 INFO: calibration group: fragment, predicting mz
1:40:40.037165 INFO: === checking if optimization conditions were reached ===
1:40:40.037463 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
1:40:40.039574 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 22.6668.
1:40:40.039632 INFO: ==============================================
1:40:40.039732 INFO: Starting optimization step 9.
1:40:40.039800 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:40:40.039884 PROGRESS: Extracting batch of 100535 precursors
1:40:40.066199 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:40:40.066346 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:40:40.066388 INFO: FWHM in RT is 2.90 seconds, sigma is 0.37
1:40:40.066412 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:40:40.066714 INFO: Starting candidate selection
1:40:44.783108 INFO: Starting candidate scoring
1:40:46.197079 INFO: Finished candidate processing
1:40:46.197194 INFO: Collecting candidate features
1:40:46.540936 INFO: Collecting fragment features
1:40:46.657632 INFO: Finished candidate scoring
1:40:46.746235 PROGRESS: === Extracted 200709 precursors and 1952102 fragments ===
1:40:46.746664 INFO: performing precursor FDR with 47 features
1:40:46.746703 INFO: Decoy channel: -1
1:40:46.746728 INFO: Competetive: True
1:40:46.821191 INFO: Setting torch num_threads to 2 for FDR classification task
1:40:50.198508 INFO: Test AUC: 0.556
1:40:50.198644 INFO: Train AUC: 0.582
1:40:50.198673 INFO: AUC difference: 4.48%
1:40:50.428538 INFO: Resetting torch num_threads to 100
1:40:50.434791 INFO: === FDR correction performed with classifier version 7 ===
1:40:50.435530 PROGRESS: ============================= Precursor FDR =============================
1:40:50.435623 PROGRESS: Total precursors accumulated: 559
1:40:50.435687 PROGRESS: Target precursors: 510 (91.23%)
1:40:50.435739 PROGRESS: Decoy precursors: 49 (8.77%)
1:40:50.435786 PROGRESS: 
1:40:50.435831 PROGRESS: Precursor Summary:
1:40:50.436852 PROGRESS: Channel   0:	 0.05 FDR:   394; 0.01 FDR:   291; 0.001 FDR:   233
1:40:50.436944 PROGRESS: 
1:40:50.436999 PROGRESS: Protein Summary:
1:40:50.438170 PROGRESS: Channel   0:	 0.05 FDR:   367; 0.01 FDR:   270; 0.001 FDR:   221
1:40:50.438273 PROGRESS: =========================================================================
1:40:50.571237 INFO: fragments_df: keeping 3338 of 1952102 [sum(precursor_idx_mask)=6509 sum(mass_error_mask)=1952102 stop_rank=3338
1:40:50.789354 INFO: calibration group: precursor, fitting rt estimator 
1:40:50.910855 INFO: calibration group: fragment, fitting mz estimator 
1:40:51.342820 INFO: Using score_cutoff 64.22492631912232 (fac=0.99, q=1)
1:40:51.343243 INFO: calibration group: precursor, predicting mz
1:40:51.343330 WARNING: mz prediction was skipped as it has not been fitted yet
1:40:51.343362 INFO: calibration group: precursor, predicting rt
1:40:51.404898 INFO: calibration group: fragment, predicting mz
1:40:51.553772 INFO: === checking if optimization conditions were reached ===
1:40:51.554106 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
1:40:51.556850 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 17.6845.
1:40:51.556912 INFO: ==============================================
1:40:51.557018 INFO: Starting optimization step 10.
1:40:51.557119 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:40:51.557190 PROGRESS: Extracting batch of 100535 precursors
1:40:51.594947 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:40:51.595105 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:40:51.595143 INFO: FWHM in RT is 2.77 seconds, sigma is 0.36
1:40:51.595173 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:40:51.595463 INFO: Starting candidate selection
1:40:56.390764 INFO: Starting candidate scoring
1:40:57.814638 INFO: Finished candidate processing
1:40:57.814921 INFO: Collecting candidate features
1:40:58.301042 INFO: Collecting fragment features
1:40:58.422859 INFO: Finished candidate scoring
1:40:58.535249 PROGRESS: === Extracted 200709 precursors and 1861584 fragments ===
1:40:58.535759 INFO: performing precursor FDR with 47 features
1:40:58.535800 INFO: Decoy channel: -1
1:40:58.535833 INFO: Competetive: True
1:40:58.614912 INFO: Setting torch num_threads to 2 for FDR classification task
1:41:02.038670 INFO: Test AUC: 0.560
1:41:02.038857 INFO: Train AUC: 0.580
1:41:02.038889 INFO: AUC difference: 3.50%
1:41:02.272197 INFO: Resetting torch num_threads to 100
1:41:02.278590 INFO: === FDR correction performed with classifier version 7 ===
1:41:02.279379 PROGRESS: ============================= Precursor FDR =============================
1:41:02.279488 PROGRESS: Total precursors accumulated: 578
1:41:02.280365 PROGRESS: Target precursors: 526 (91.00%)
1:41:02.280438 PROGRESS: Decoy precursors: 52 (9.00%)
1:41:02.280486 PROGRESS: 
1:41:02.280531 PROGRESS: Precursor Summary:
1:41:02.281601 PROGRESS: Channel   0:	 0.05 FDR:   431; 0.01 FDR:   286; 0.001 FDR:   195
1:41:02.281699 PROGRESS: 
1:41:02.281756 PROGRESS: Protein Summary:
1:41:02.282935 PROGRESS: Channel   0:	 0.05 FDR:   403; 0.01 FDR:   269; 0.001 FDR:   188
1:41:02.283031 PROGRESS: =========================================================================
1:41:02.406578 INFO: fragments_df: keeping 3289 of 1861584 [sum(precursor_idx_mask)=6344 sum(mass_error_mask)=1861584 stop_rank=3289
1:41:02.619283 INFO: calibration group: precursor, fitting rt estimator 
1:41:02.740227 INFO: calibration group: fragment, fitting mz estimator 
1:41:03.173582 INFO: Using score_cutoff 67.34813190078737 (fac=0.99, q=1)
1:41:03.174034 INFO: calibration group: precursor, predicting mz
1:41:03.174122 WARNING: mz prediction was skipped as it has not been fitted yet
1:41:03.174156 INFO: calibration group: precursor, predicting rt
1:41:03.235539 INFO: calibration group: fragment, predicting mz
1:41:03.369647 INFO: === checking if optimization conditions were reached ===
1:41:03.369955 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
1:41:03.372367 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 14.9355.
1:41:03.372425 INFO: ==============================================
1:41:03.372523 INFO: Starting optimization step 11.
1:41:03.372589 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:41:03.372677 PROGRESS: Extracting batch of 100535 precursors
1:41:03.399425 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:41:03.399560 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:41:03.399606 INFO: FWHM in RT is 2.68 seconds, sigma is 0.35
1:41:03.399630 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:41:03.399922 INFO: Starting candidate selection
1:41:08.243652 INFO: Starting candidate scoring
1:41:09.648592 INFO: Finished candidate processing
1:41:09.648769 INFO: Collecting candidate features
1:41:10.021792 INFO: Collecting fragment features
1:41:10.138828 INFO: Finished candidate scoring
1:41:10.252305 PROGRESS: === Extracted 200693 precursors and 1784091 fragments ===
1:41:10.252724 INFO: performing precursor FDR with 47 features
1:41:10.252761 INFO: Decoy channel: -1
1:41:10.252784 INFO: Competetive: True
1:41:10.318701 INFO: Setting torch num_threads to 2 for FDR classification task
1:41:13.714697 INFO: Test AUC: 0.559
1:41:13.714849 INFO: Train AUC: 0.578
1:41:13.714880 INFO: AUC difference: 3.42%
1:41:13.949281 INFO: Resetting torch num_threads to 100
1:41:13.955819 INFO: === FDR correction performed with classifier version 7 ===
1:41:13.956602 PROGRESS: ============================= Precursor FDR =============================
1:41:13.956704 PROGRESS: Total precursors accumulated: 693
1:41:13.956767 PROGRESS: Target precursors: 630 (90.91%)
1:41:13.956821 PROGRESS: Decoy precursors: 63 (9.09%)
1:41:13.956868 PROGRESS: 
1:41:13.956913 PROGRESS: Precursor Summary:
1:41:13.957930 PROGRESS: Channel   0:	 0.05 FDR:   489; 0.01 FDR:   304; 0.001 FDR:   198
1:41:13.958024 PROGRESS: 
1:41:13.958082 PROGRESS: Protein Summary:
1:41:13.959265 PROGRESS: Channel   0:	 0.05 FDR:   455; 0.01 FDR:   284; 0.001 FDR:   190
1:41:13.959359 PROGRESS: =========================================================================
1:41:14.077024 INFO: fragments_df: keeping 3451 of 1784091 [sum(precursor_idx_mask)=6712 sum(mass_error_mask)=1784091 stop_rank=3451
1:41:14.295994 INFO: calibration group: precursor, fitting rt estimator 
1:41:14.418148 INFO: calibration group: fragment, fitting mz estimator 
1:41:14.871651 INFO: Using score_cutoff 67.62878117523194 (fac=0.99, q=1)
1:41:14.872063 INFO: calibration group: precursor, predicting mz
1:41:14.872152 WARNING: mz prediction was skipped as it has not been fitted yet
1:41:14.872183 INFO: calibration group: precursor, predicting rt
1:41:14.934170 INFO: calibration group: fragment, predicting mz
1:41:15.086650 INFO: === checking if optimization conditions were reached ===
1:41:15.087004 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
1:41:15.089888 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 11.9698.
1:41:15.089977 INFO: ==============================================
1:41:15.090094 INFO: Starting optimization step 12.
1:41:15.090174 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:41:15.090247 PROGRESS: Extracting batch of 100535 precursors
1:41:15.152279 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:41:15.152435 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:41:15.152470 INFO: FWHM in RT is 2.65 seconds, sigma is 0.34
1:41:15.152494 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:41:15.152756 INFO: Starting candidate selection
1:41:20.138454 INFO: Starting candidate scoring
1:41:21.550169 INFO: Finished candidate processing
1:41:21.550283 INFO: Collecting candidate features
1:41:21.855421 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 200682)
1:41:21.865073 INFO: Collecting fragment features
1:41:21.979627 INFO: Finished candidate scoring
1:41:22.070700 PROGRESS: === Extracted 200682 precursors and 1685684 fragments ===
1:41:22.071192 INFO: performing precursor FDR with 47 features
1:41:22.071229 INFO: Decoy channel: -1
1:41:22.071252 INFO: Competetive: True
1:41:22.134272 INFO: Setting torch num_threads to 2 for FDR classification task
1:41:22.163335 WARNING: dropped 1 decoy PSMs due to missing features
1:41:25.519636 INFO: Test AUC: 0.557
1:41:25.519781 INFO: Train AUC: 0.580
1:41:25.519811 INFO: AUC difference: 4.01%
1:41:25.752762 INFO: Resetting torch num_threads to 100
1:41:25.757915 INFO: === FDR correction performed with classifier version 7 ===
1:41:25.758662 PROGRESS: ============================= Precursor FDR =============================
1:41:25.758753 PROGRESS: Total precursors accumulated: 660
1:41:25.758824 PROGRESS: Target precursors: 600 (90.91%)
1:41:25.758879 PROGRESS: Decoy precursors: 60 (9.09%)
1:41:25.758926 PROGRESS: 
1:41:25.758970 PROGRESS: Precursor Summary:
1:41:25.759990 PROGRESS: Channel   0:	 0.05 FDR:   476; 0.01 FDR:   319; 0.001 FDR:   163
1:41:25.760081 PROGRESS: 
1:41:25.760137 PROGRESS: Protein Summary:
1:41:25.761306 PROGRESS: Channel   0:	 0.05 FDR:   442; 0.01 FDR:   297; 0.001 FDR:   158
1:41:25.761400 PROGRESS: =========================================================================
1:41:25.874736 INFO: fragments_df: keeping 3630 of 1685684 [sum(precursor_idx_mask)=6915 sum(mass_error_mask)=1685684 stop_rank=3630
1:41:26.084894 INFO: calibration group: precursor, fitting rt estimator 
1:41:26.208019 INFO: calibration group: fragment, fitting mz estimator 
1:41:26.678250 INFO: Using score_cutoff 62.433577619934084 (fac=0.99, q=1)
1:41:26.678690 INFO: calibration group: precursor, predicting mz
1:41:26.678777 WARNING: mz prediction was skipped as it has not been fitted yet
1:41:26.678809 INFO: calibration group: precursor, predicting rt
1:41:26.741442 INFO: calibration group: fragment, predicting mz
1:41:26.891549 INFO: === checking if optimization conditions were reached ===
1:41:26.891885 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
1:41:26.894724 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 10.2300.
1:41:26.894791 INFO: ==============================================
1:41:26.894900 INFO: Starting optimization step 13.
1:41:26.894976 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:41:26.895072 PROGRESS: Extracting batch of 100535 precursors
1:41:26.928971 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:41:26.929126 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:41:26.929173 INFO: FWHM in RT is 2.54 seconds, sigma is 0.33
1:41:26.929202 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:41:26.929532 INFO: Starting candidate selection
1:41:31.785959 INFO: Starting candidate scoring
1:41:33.244101 INFO: Finished candidate processing
1:41:33.244553 INFO: Collecting candidate features
1:41:33.735899 INFO: Collecting fragment features
1:41:33.872600 INFO: Finished candidate scoring
1:41:34.047646 PROGRESS: === Extracted 200695 precursors and 1647742 fragments ===
1:41:34.048618 INFO: performing precursor FDR with 47 features
1:41:34.048663 INFO: Decoy channel: -1
1:41:34.048686 INFO: Competetive: True
1:41:34.157678 INFO: Setting torch num_threads to 2 for FDR classification task
1:41:38.370126 INFO: Test AUC: 0.560
1:41:38.370261 INFO: Train AUC: 0.579
1:41:38.370291 INFO: AUC difference: 3.24%
1:41:38.616424 INFO: Resetting torch num_threads to 100
1:41:38.624613 INFO: === FDR correction performed with classifier version 7 ===
1:41:38.625803 PROGRESS: ============================= Precursor FDR =============================
1:41:38.625903 PROGRESS: Total precursors accumulated: 691
1:41:38.625964 PROGRESS: Target precursors: 630 (91.17%)
1:41:38.626017 PROGRESS: Decoy precursors: 61 (8.83%)
1:41:38.626064 PROGRESS: 
1:41:38.626109 PROGRESS: Precursor Summary:
1:41:38.627230 PROGRESS: Channel   0:	 0.05 FDR:   518; 0.01 FDR:   329; 0.001 FDR:   147
1:41:38.627322 PROGRESS: 
1:41:38.627383 PROGRESS: Protein Summary:
1:41:38.628856 PROGRESS: Channel   0:	 0.05 FDR:   479; 0.01 FDR:   306; 0.001 FDR:   141
1:41:38.628955 PROGRESS: =========================================================================
1:41:38.739593 INFO: fragments_df: keeping 3697 of 1647742 [sum(precursor_idx_mask)=7071 sum(mass_error_mask)=1647742 stop_rank=3697
1:41:39.018965 INFO: calibration group: precursor, fitting rt estimator 
1:41:39.129370 INFO: calibration group: fragment, fitting mz estimator 
1:41:39.554486 INFO: Using score_cutoff 60.69412196960449 (fac=0.99, q=1)
1:41:39.554978 INFO: calibration group: precursor, predicting mz
1:41:39.555075 WARNING: mz prediction was skipped as it has not been fitted yet
1:41:39.555110 INFO: calibration group: precursor, predicting rt
1:41:39.618801 INFO: calibration group: fragment, predicting mz
1:41:39.769460 INFO: === checking if optimization conditions were reached ===
1:41:39.769755 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
1:41:39.772388 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 9.3251.
1:41:39.772446 INFO: ==============================================
1:41:39.772552 INFO: Starting optimization step 14.
1:41:39.772622 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:41:39.772713 PROGRESS: Extracting batch of 100535 precursors
1:41:39.804468 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:41:39.804597 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:41:39.804650 INFO: FWHM in RT is 2.44 seconds, sigma is 0.32
1:41:39.804676 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:41:39.805297 INFO: Starting candidate selection
1:41:44.275807 INFO: Starting candidate scoring
1:41:45.748986 INFO: Finished candidate processing
1:41:45.749100 INFO: Collecting candidate features
1:41:46.075368 INFO: Collecting fragment features
1:41:46.189131 INFO: Finished candidate scoring
1:41:46.280632 PROGRESS: === Extracted 200682 precursors and 1601003 fragments ===
1:41:46.281066 INFO: performing precursor FDR with 47 features
1:41:46.281104 INFO: Decoy channel: -1
1:41:46.281128 INFO: Competetive: True
1:41:46.341280 INFO: Setting torch num_threads to 2 for FDR classification task
1:41:49.889456 INFO: Test AUC: 0.561
1:41:49.889607 INFO: Train AUC: 0.578
1:41:49.889637 INFO: AUC difference: 2.93%
1:41:50.122736 INFO: Resetting torch num_threads to 100
1:41:50.128590 INFO: === FDR correction performed with classifier version 7 ===
1:41:50.129421 PROGRESS: ============================= Precursor FDR =============================
1:41:50.129524 PROGRESS: Total precursors accumulated: 653
1:41:50.129586 PROGRESS: Target precursors: 595 (91.12%)
1:41:50.129638 PROGRESS: Decoy precursors: 58 (8.88%)
1:41:50.129685 PROGRESS: 
1:41:50.129728 PROGRESS: Precursor Summary:
1:41:50.130764 PROGRESS: Channel   0:	 0.05 FDR:   494; 0.01 FDR:   315; 0.001 FDR:   173
1:41:50.130855 PROGRESS: 
1:41:50.130910 PROGRESS: Protein Summary:
1:41:50.132099 PROGRESS: Channel   0:	 0.05 FDR:   458; 0.01 FDR:   295; 0.001 FDR:   167
1:41:50.132201 PROGRESS: =========================================================================
1:41:50.244838 INFO: fragments_df: keeping 3520 of 1601003 [sum(precursor_idx_mask)=6711 sum(mass_error_mask)=1601003 stop_rank=3520
1:41:50.461571 INFO: calibration group: precursor, fitting rt estimator 
1:41:50.572392 INFO: calibration group: fragment, fitting mz estimator 
1:41:50.970517 INFO: Using score_cutoff 58.74528553390503 (fac=0.99, q=1)
1:41:50.970978 INFO: calibration group: precursor, predicting mz
1:41:50.971066 WARNING: mz prediction was skipped as it has not been fitted yet
1:41:50.971097 INFO: calibration group: precursor, predicting rt
1:41:51.033621 INFO: calibration group: fragment, predicting mz
1:41:51.181414 INFO: === checking if optimization conditions were reached ===
1:41:51.181767 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
1:41:51.184704 PROGRESS: ❌ ms2_error      : optimization incomplete after 7 search(es). Will search with parameter 8.5826.
1:41:51.184769 INFO: ==============================================
1:41:51.184877 INFO: Starting optimization step 15.
1:41:51.184954 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:41:51.185043 PROGRESS: Extracting batch of 100535 precursors
1:41:51.222003 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:41:51.222187 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:41:51.222229 INFO: FWHM in RT is 2.40 seconds, sigma is 0.31
1:41:51.222258 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:41:51.222576 INFO: Starting candidate selection
1:41:55.983831 INFO: Starting candidate scoring
1:41:57.455007 INFO: Finished candidate processing
1:41:57.455256 INFO: Collecting candidate features
1:41:58.060377 INFO: Collecting fragment features
1:41:58.198737 INFO: Finished candidate scoring
1:41:58.394062 PROGRESS: === Extracted 200656 precursors and 1548632 fragments ===
1:41:58.394655 INFO: performing precursor FDR with 47 features
1:41:58.394701 INFO: Decoy channel: -1
1:41:58.394726 INFO: Competetive: True
1:41:58.507231 INFO: Setting torch num_threads to 2 for FDR classification task
1:42:02.312268 INFO: Test AUC: 0.558
1:42:02.312447 INFO: Train AUC: 0.579
1:42:02.312498 INFO: AUC difference: 3.61%
1:42:02.549752 INFO: Resetting torch num_threads to 100
1:42:02.557135 INFO: === FDR correction performed with classifier version 7 ===
1:42:02.557984 PROGRESS: ============================= Precursor FDR =============================
1:42:02.558080 PROGRESS: Total precursors accumulated: 695
1:42:02.558141 PROGRESS: Target precursors: 631 (90.79%)
1:42:02.558196 PROGRESS: Decoy precursors: 64 (9.21%)
1:42:02.558242 PROGRESS: 
1:42:02.558285 PROGRESS: Precursor Summary:
1:42:02.559318 PROGRESS: Channel   0:	 0.05 FDR:   540; 0.01 FDR:   359; 0.001 FDR:   128
1:42:02.559408 PROGRESS: 
1:42:02.559469 PROGRESS: Protein Summary:
1:42:02.560702 PROGRESS: Channel   0:	 0.05 FDR:   501; 0.01 FDR:   335; 0.001 FDR:   125
1:42:02.560798 PROGRESS: =========================================================================
1:42:02.662974 INFO: fragments_df: keeping 3941 of 1548632 [sum(precursor_idx_mask)=7543 sum(mass_error_mask)=1548632 stop_rank=3941
1:42:02.884891 INFO: calibration group: precursor, fitting rt estimator 
1:42:03.013335 INFO: calibration group: fragment, fitting mz estimator 
1:42:03.542613 INFO: Using score_cutoff 59.768158062744135 (fac=0.99, q=1)
1:42:03.543102 INFO: calibration group: precursor, predicting mz
1:42:03.543194 WARNING: mz prediction was skipped as it has not been fitted yet
1:42:03.543226 INFO: calibration group: precursor, predicting rt
1:42:03.605676 INFO: calibration group: fragment, predicting mz
1:42:03.754889 INFO: === checking if optimization conditions were reached ===
1:42:03.755263 PROGRESS: === Optimization of ms2_error has been performed 8 time(s); minimum number is 2 ===
1:42:03.758406 PROGRESS: ❌ ms2_error      : optimization incomplete after 8 search(es). Will search with parameter 7.0623.
1:42:03.758474 INFO: ==============================================
1:42:03.758594 INFO: Starting optimization step 16.
1:42:03.758676 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:42:03.758758 PROGRESS: Extracting batch of 100535 precursors
1:42:03.802762 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:42:03.802947 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:42:03.802995 INFO: FWHM in RT is 2.36 seconds, sigma is 0.30
1:42:03.803025 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:42:03.803388 INFO: Starting candidate selection
1:42:08.622185 INFO: Starting candidate scoring
1:42:10.083032 INFO: Finished candidate processing
1:42:10.083213 INFO: Collecting candidate features
1:42:10.438719 INFO: Collecting fragment features
1:42:10.547513 INFO: Finished candidate scoring
1:42:10.643557 PROGRESS: === Extracted 200676 precursors and 1497514 fragments ===
1:42:10.643983 INFO: performing precursor FDR with 47 features
1:42:10.644022 INFO: Decoy channel: -1
1:42:10.644046 INFO: Competetive: True
1:42:10.713247 INFO: Setting torch num_threads to 2 for FDR classification task
1:42:14.370154 INFO: Test AUC: 0.553
1:42:14.370309 INFO: Train AUC: 0.581
1:42:14.370340 INFO: AUC difference: 4.77%
1:42:14.605057 INFO: Resetting torch num_threads to 100
1:42:14.612122 INFO: === FDR correction performed with classifier version 7 ===
1:42:14.612947 PROGRESS: ============================= Precursor FDR =============================
1:42:14.613050 PROGRESS: Total precursors accumulated: 754
1:42:14.613115 PROGRESS: Target precursors: 685 (90.85%)
1:42:14.613169 PROGRESS: Decoy precursors: 69 (9.15%)
1:42:14.613221 PROGRESS: 
1:42:14.613266 PROGRESS: Precursor Summary:
1:42:14.614321 PROGRESS: Channel   0:	 0.05 FDR:   580; 0.01 FDR:   337; 0.001 FDR:   129
1:42:14.614410 PROGRESS: 
1:42:14.614465 PROGRESS: Protein Summary:
1:42:14.615663 PROGRESS: Channel   0:	 0.05 FDR:   538; 0.01 FDR:   314; 0.001 FDR:   124
1:42:14.615755 PROGRESS: =========================================================================
1:42:14.715072 INFO: fragments_df: keeping 3737 of 1497514 [sum(precursor_idx_mask)=7033 sum(mass_error_mask)=1497514 stop_rank=3737
1:42:14.944282 INFO: calibration group: precursor, fitting rt estimator 
1:42:15.072623 INFO: calibration group: fragment, fitting mz estimator 
1:42:15.566819 INFO: Using score_cutoff 58.74674124298095 (fac=0.99, q=1)
1:42:15.567269 INFO: calibration group: precursor, predicting mz
1:42:15.567358 WARNING: mz prediction was skipped as it has not been fitted yet
1:42:15.567390 INFO: calibration group: precursor, predicting rt
1:42:15.630047 INFO: calibration group: fragment, predicting mz
1:42:15.768190 INFO: === checking if optimization conditions were reached ===
1:42:15.768514 PROGRESS: === Optimization of ms2_error has been performed 9 time(s); minimum number is 2 ===
1:42:15.771066 PROGRESS: ❌ ms2_error      : optimization incomplete after 9 search(es). Will search with parameter 6.2641.
1:42:15.771127 INFO: ==============================================
1:42:15.771225 INFO: Starting optimization step 17.
1:42:15.771309 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:42:15.771372 PROGRESS: Extracting batch of 100535 precursors
1:42:15.801059 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:42:15.801217 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:42:15.801255 INFO: FWHM in RT is 2.35 seconds, sigma is 0.30
1:42:15.801280 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:42:15.801550 INFO: Starting candidate selection
1:42:20.494750 INFO: Starting candidate scoring
1:42:21.888148 INFO: Finished candidate processing
1:42:21.888277 INFO: Collecting candidate features
1:42:22.237793 INFO: Collecting fragment features
1:42:22.348017 INFO: Finished candidate scoring
1:42:22.444590 PROGRESS: === Extracted 200639 precursors and 1431630 fragments ===
1:42:22.445043 INFO: performing precursor FDR with 47 features
1:42:22.445081 INFO: Decoy channel: -1
1:42:22.445111 INFO: Competetive: True
1:42:22.516866 INFO: Setting torch num_threads to 2 for FDR classification task
1:42:26.131398 INFO: Test AUC: 0.564
1:42:26.131552 INFO: Train AUC: 0.582
1:42:26.131584 INFO: AUC difference: 3.07%
1:42:26.373921 INFO: Resetting torch num_threads to 100
1:42:26.401419 INFO: === FDR correction performed with classifier version 7 ===
1:42:26.402661 PROGRESS: ============================= Precursor FDR =============================
1:42:26.402792 PROGRESS: Total precursors accumulated: 797
1:42:26.402858 PROGRESS: Target precursors: 724 (90.84%)
1:42:26.402912 PROGRESS: Decoy precursors: 73 (9.16%)
1:42:26.402963 PROGRESS: 
1:42:26.403006 PROGRESS: Precursor Summary:
1:42:26.404201 PROGRESS: Channel   0:	 0.05 FDR:   608; 0.01 FDR:   412; 0.001 FDR:   116
1:42:26.404317 PROGRESS: 
1:42:26.404376 PROGRESS: Protein Summary:
1:42:26.405665 PROGRESS: Channel   0:	 0.05 FDR:   563; 0.01 FDR:   382; 0.001 FDR:   113
1:42:26.405767 PROGRESS: =========================================================================
1:42:26.502190 INFO: fragments_df: keeping 4287 of 1431630 [sum(precursor_idx_mask)=8457 sum(mass_error_mask)=1431630 stop_rank=4287
1:42:26.683815 INFO: calibration group: precursor, fitting rt estimator 
1:42:26.802099 INFO: calibration group: fragment, fitting mz estimator 
1:42:27.313320 INFO: Using score_cutoff 55.95280088310241 (fac=0.99, q=1)
1:42:27.313941 INFO: calibration group: precursor, predicting mz
1:42:27.314051 WARNING: mz prediction was skipped as it has not been fitted yet
1:42:27.314091 INFO: calibration group: precursor, predicting rt
1:42:27.345743 INFO: calibration group: fragment, predicting mz
1:42:27.409375 INFO: === checking if optimization conditions were reached ===
1:42:27.409693 PROGRESS: === Optimization of ms2_error has been performed 10 time(s); minimum number is 2 ===
1:42:27.412556 PROGRESS: ❌ ms2_error      : optimization incomplete after 10 search(es). Will search with parameter 5.7856.
1:42:27.412622 INFO: ==============================================
1:42:27.412754 INFO: Starting optimization step 18.
1:42:27.412835 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:42:27.412923 PROGRESS: Extracting batch of 50096 precursors
1:42:27.428102 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:42:27.428231 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:42:27.428316 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
1:42:27.428347 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:42:27.428976 INFO: Starting candidate selection
1:42:29.899989 INFO: Starting candidate scoring
1:42:30.574103 INFO: Finished candidate processing
1:42:30.574219 INFO: Collecting candidate features
1:42:30.735429 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 99890)
1:42:30.744528 INFO: Collecting fragment features
1:42:30.794905 INFO: Finished candidate scoring
1:42:30.837770 PROGRESS: === Extracted 99890 precursors and 670262 fragments ===
1:42:30.838268 INFO: performing precursor FDR with 47 features
1:42:30.838307 INFO: Decoy channel: -1
1:42:30.838331 INFO: Competetive: True
1:42:30.873827 INFO: Setting torch num_threads to 2 for FDR classification task
1:42:30.896413 WARNING: dropped 2 target PSMs due to missing features
1:42:30.896561 WARNING: dropped 1 decoy PSMs due to missing features
1:42:32.447964 INFO: Test AUC: 0.556
1:42:32.448115 INFO: Train AUC: 0.582
1:42:32.448147 INFO: AUC difference: 4.46%
1:42:32.655365 INFO: Resetting torch num_threads to 100
1:42:32.659075 INFO: === FDR correction performed with classifier version 7 ===
1:42:32.659776 PROGRESS: ============================= Precursor FDR =============================
1:42:32.659880 PROGRESS: Total precursors accumulated: 355
1:42:32.659944 PROGRESS: Target precursors: 323 (90.99%)
1:42:32.659998 PROGRESS: Decoy precursors: 32 (9.01%)
1:42:32.660045 PROGRESS: 
1:42:32.660091 PROGRESS: Precursor Summary:
1:42:32.661194 PROGRESS: Channel   0:	 0.05 FDR:   272; 0.01 FDR:   215; 0.001 FDR:    45
1:42:32.661292 PROGRESS: 
1:42:32.661349 PROGRESS: Protein Summary:
1:42:32.662433 PROGRESS: Channel   0:	 0.05 FDR:   259; 0.01 FDR:   205; 0.001 FDR:    45
1:42:32.662534 PROGRESS: =========================================================================
1:42:32.706218 INFO: fragments_df: keeping 2136 of 670262 [sum(precursor_idx_mask)=4265 sum(mass_error_mask)=670262 stop_rank=2136
1:42:32.846193 INFO: calibration group: precursor, fitting rt estimator 
1:42:32.938416 INFO: calibration group: fragment, fitting mz estimator 
1:42:33.175634 INFO: Using score_cutoff 41.02581420593262 (fac=0.99, q=1)
1:42:33.176059 INFO: calibration group: precursor, predicting mz
1:42:33.176147 WARNING: mz prediction was skipped as it has not been fitted yet
1:42:33.176180 INFO: calibration group: precursor, predicting rt
1:42:33.207717 INFO: calibration group: fragment, predicting mz
1:42:33.271556 INFO: === checking if optimization conditions were reached ===
1:42:33.271854 PROGRESS: === Optimization of ms2_error has been performed 11 time(s); minimum number is 2 ===
1:42:33.274136 PROGRESS: ❌ ms2_error      : optimization incomplete after 11 search(es). Will search with parameter 4.9330.
1:42:33.274194 INFO: ==============================================
1:42:33.274286 INFO: Starting optimization step 19.
1:42:33.274369 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:42:33.274430 PROGRESS: Extracting batch of 50096 precursors
1:42:33.291647 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:42:33.291777 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:42:33.291810 INFO: FWHM in RT is 2.06 seconds, sigma is 0.27
1:42:33.291833 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:42:33.292066 INFO: Starting candidate selection
1:42:35.537467 INFO: Starting candidate scoring
1:42:36.217932 INFO: Finished candidate processing
1:42:36.218095 INFO: Collecting candidate features
1:42:36.399710 WARNING: intensity_correlation has 9 NaNs ( 0.01 % out of 99715)
1:42:36.410845 INFO: Collecting fragment features
1:42:36.465614 INFO: Finished candidate scoring
1:42:36.517442 PROGRESS: === Extracted 99715 precursors and 620386 fragments ===
1:42:36.517859 INFO: performing precursor FDR with 47 features
1:42:36.517900 INFO: Decoy channel: -1
1:42:36.517926 INFO: Competetive: True
1:42:36.554400 INFO: Setting torch num_threads to 2 for FDR classification task
1:42:36.578678 WARNING: dropped 5 target PSMs due to missing features
1:42:36.578823 WARNING: dropped 4 decoy PSMs due to missing features
1:42:38.445661 INFO: Test AUC: 0.556
1:42:38.445798 INFO: Train AUC: 0.578
1:42:38.445829 INFO: AUC difference: 3.72%
1:42:38.659862 INFO: Resetting torch num_threads to 100
1:42:38.664891 INFO: === FDR correction performed with classifier version 7 ===
1:42:38.665723 PROGRESS: ============================= Precursor FDR =============================
1:42:38.665822 PROGRESS: Total precursors accumulated: 342
1:42:38.665885 PROGRESS: Target precursors: 311 (90.94%)
1:42:38.665946 PROGRESS: Decoy precursors: 31 (9.06%)
1:42:38.665996 PROGRESS: 
1:42:38.666043 PROGRESS: Precursor Summary:
1:42:38.667094 PROGRESS: Channel   0:	 0.05 FDR:   244; 0.01 FDR:   117; 0.001 FDR:    99
1:42:38.667185 PROGRESS: 
1:42:38.667243 PROGRESS: Protein Summary:
1:42:38.668313 PROGRESS: Channel   0:	 0.05 FDR:   231; 0.01 FDR:   113; 0.001 FDR:    95
1:42:38.668408 PROGRESS: =========================================================================
1:42:38.843872 INFO: calibration group: precursor, predicting mz
1:42:38.844152 WARNING: mz prediction was skipped as it has not been fitted yet
1:42:38.844187 INFO: calibration group: precursor, predicting rt
1:42:38.876633 INFO: calibration group: fragment, predicting mz
1:42:38.944810 INFO: === skipping optimization until target number of precursors are found ===
1:42:38.945127 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
1:42:38.945185 WARNING: Optimization did not converge within the maximum number of steps, which is 20.
1:42:38.945292 INFO: Starting optimization step 0.
1:42:38.945362 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1:42:38.945424 PROGRESS: Extracting batch of 50439 precursors
1:42:38.960144 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:42:38.960273 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:42:38.960307 INFO: FWHM in RT is 2.06 seconds, sigma is 0.27
1:42:38.960329 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:42:38.960560 INFO: Starting candidate selection
1:42:41.241628 INFO: Starting candidate scoring
1:42:41.908075 INFO: Finished candidate processing
1:42:41.908193 INFO: Collecting candidate features
1:42:42.061750 WARNING: intensity_correlation has 16 NaNs ( 0.02 % out of 100431)
1:42:42.072009 INFO: Collecting fragment features
1:42:42.123825 INFO: Finished candidate scoring
1:42:42.224418 PROGRESS: === Extracted 200146 precursors and 1245930 fragments ===
1:42:42.245969 INFO: performing precursor FDR with 47 features
1:42:42.246129 INFO: Decoy channel: -1
1:42:42.246157 INFO: Competetive: True
1:42:42.338285 INFO: Setting torch num_threads to 2 for FDR classification task
1:42:42.380610 WARNING: dropped 13 target PSMs due to missing features
1:42:42.380765 WARNING: dropped 12 decoy PSMs due to missing features
1:42:46.194233 INFO: Test AUC: 0.554
1:42:46.194402 INFO: Train AUC: 0.578
1:42:46.194435 INFO: AUC difference: 4.25%
1:42:46.430063 INFO: Resetting torch num_threads to 100
1:42:46.440452 INFO: === FDR correction performed with classifier version 7 ===
1:42:46.441360 PROGRESS: ============================= Precursor FDR =============================
1:42:46.441453 PROGRESS: Total precursors accumulated: 763
1:42:46.441516 PROGRESS: Target precursors: 694 (90.96%)
1:42:46.441574 PROGRESS: Decoy precursors: 69 (9.04%)
1:42:46.441632 PROGRESS: 
1:42:46.441679 PROGRESS: Precursor Summary:
1:42:46.442717 PROGRESS: Channel   0:	 0.05 FDR:   536; 0.01 FDR:   341; 0.001 FDR:   209
1:42:46.442811 PROGRESS: 
1:42:46.442868 PROGRESS: Protein Summary:
1:42:46.444096 PROGRESS: Channel   0:	 0.05 FDR:   493; 0.01 FDR:   318; 0.001 FDR:   199
1:42:46.444186 PROGRESS: =========================================================================
1:42:46.534352 INFO: fragments_df: keeping 3527 of 1245930 [sum(precursor_idx_mask)=6744 sum(mass_error_mask)=1245930 stop_rank=3527
1:42:46.753577 INFO: calibration group: precursor, fitting rt estimator 
1:42:46.879540 INFO: calibration group: fragment, fitting mz estimator 
1:42:47.309681 INFO: Using score_cutoff 54.549900329589846 (fac=0.99, q=1)
1:42:47.310124 INFO: calibration group: precursor, predicting mz
1:42:47.310209 WARNING: mz prediction was skipped as it has not been fitted yet
1:42:47.310240 INFO: calibration group: precursor, predicting rt
1:42:47.373506 INFO: calibration group: fragment, predicting mz
1:42:47.521084 INFO: === checking if optimization conditions were reached ===
1:42:47.521430 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:42:47.523802 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 83.1647.
1:42:47.523874 INFO: ==============================================
1:42:47.523988 INFO: Starting optimization step 1.
1:42:47.524068 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:42:47.524138 PROGRESS: Extracting batch of 100535 precursors
1:42:47.576005 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:42:47.576147 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:42:47.576184 INFO: FWHM in RT is 2.22 seconds, sigma is 0.29
1:42:47.576209 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:42:47.576505 INFO: Starting candidate selection
1:42:51.935788 INFO: Starting candidate scoring
1:42:53.234141 INFO: Finished candidate processing
1:42:53.234257 INFO: Collecting candidate features
1:42:53.629405 WARNING: intensity_correlation has 158 NaNs ( 0.08 % out of 190508)
1:42:53.639445 INFO: Collecting fragment features
1:42:53.736403 INFO: Finished candidate scoring
1:42:53.909796 PROGRESS: === Extracted 190508 precursors and 961380 fragments ===
1:42:53.910356 INFO: performing precursor FDR with 47 features
1:42:53.910395 INFO: Decoy channel: -1
1:42:53.910417 INFO: Competetive: True
1:42:54.019758 INFO: Setting torch num_threads to 2 for FDR classification task
1:42:54.065810 WARNING: dropped 75 target PSMs due to missing features
1:42:54.065957 WARNING: dropped 83 decoy PSMs due to missing features
1:42:57.989360 INFO: Test AUC: 0.551
1:42:57.989507 INFO: Train AUC: 0.570
1:42:57.989538 INFO: AUC difference: 3.25%
1:42:58.233165 INFO: Resetting torch num_threads to 100
1:42:58.241296 INFO: === FDR correction performed with classifier version 7 ===
1:42:58.242210 PROGRESS: ============================= Precursor FDR =============================
1:42:58.242308 PROGRESS: Total precursors accumulated: 858
1:42:58.242374 PROGRESS: Target precursors: 780 (90.91%)
1:42:58.242426 PROGRESS: Decoy precursors: 78 (9.09%)
1:42:58.242487 PROGRESS: 
1:42:58.242533 PROGRESS: Precursor Summary:
1:42:58.243918 PROGRESS: Channel   0:	 0.05 FDR:   646; 0.01 FDR:   458; 0.001 FDR:   244
1:42:58.244015 PROGRESS: 
1:42:58.244070 PROGRESS: Protein Summary:
1:42:58.245371 PROGRESS: Channel   0:	 0.05 FDR:   596; 0.01 FDR:   423; 0.001 FDR:   230
1:42:58.245470 PROGRESS: =========================================================================
1:42:58.311283 INFO: fragments_df: keeping 4395 of 961380 [sum(precursor_idx_mask)=8796 sum(mass_error_mask)=961380 stop_rank=4395
1:42:58.893701 INFO: calibration group: precursor, fitting rt estimator 
1:42:59.014521 INFO: calibration group: fragment, fitting mz estimator 
1:42:59.546518 INFO: Using score_cutoff 52.81515063858032 (fac=0.99, q=1)
1:42:59.547034 INFO: calibration group: precursor, predicting mz
1:42:59.547129 WARNING: mz prediction was skipped as it has not been fitted yet
1:42:59.547161 INFO: calibration group: precursor, predicting rt
1:42:59.582934 INFO: calibration group: fragment, predicting mz
1:42:59.655369 INFO: === checking if optimization conditions were reached ===
1:42:59.655720 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:42:59.658314 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 75.8260.
1:42:59.658378 INFO: ==============================================
1:42:59.658485 INFO: Starting optimization step 2.
1:42:59.658581 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:42:59.658657 PROGRESS: Extracting batch of 50096 precursors
1:42:59.676390 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:42:59.676525 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:42:59.676570 INFO: FWHM in RT is 2.14 seconds, sigma is 0.28
1:42:59.676599 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:42:59.676902 INFO: Starting candidate selection
1:43:01.137423 INFO: Starting candidate scoring
1:43:01.774030 INFO: Finished candidate processing
1:43:01.774157 INFO: Collecting candidate features
1:43:01.913257 WARNING: intensity_correlation has 97 NaNs ( 0.10 % out of 94063)
1:43:01.924481 INFO: Collecting fragment features
1:43:01.968150 INFO: Finished candidate scoring
1:43:02.007965 PROGRESS: === Extracted 94063 precursors and 467161 fragments ===
1:43:02.008382 INFO: performing precursor FDR with 47 features
1:43:02.008421 INFO: Decoy channel: -1
1:43:02.008445 INFO: Competetive: True
1:43:02.037313 INFO: Setting torch num_threads to 2 for FDR classification task
1:43:02.055982 WARNING: dropped 58 target PSMs due to missing features
1:43:02.056130 WARNING: dropped 39 decoy PSMs due to missing features
1:43:03.641901 INFO: Test AUC: 0.545
1:43:03.642052 INFO: Train AUC: 0.575
1:43:03.642083 INFO: AUC difference: 5.22%
1:43:03.642107 WARNING: AUC difference > 5%. This may indicate overfitting.
1:43:03.849100 INFO: Resetting torch num_threads to 100
1:43:03.852844 INFO: === FDR correction performed with classifier version 7 ===
1:43:03.853531 PROGRESS: ============================= Precursor FDR =============================
1:43:03.853624 PROGRESS: Total precursors accumulated: 423
1:43:03.853687 PROGRESS: Target precursors: 385 (91.02%)
1:43:03.853740 PROGRESS: Decoy precursors: 38 (8.98%)
1:43:03.853796 PROGRESS: 
1:43:03.853844 PROGRESS: Precursor Summary:
1:43:03.854816 PROGRESS: Channel   0:	 0.05 FDR:   313; 0.01 FDR:   250; 0.001 FDR:   189
1:43:03.854908 PROGRESS: 
1:43:03.854965 PROGRESS: Protein Summary:
1:43:03.856083 PROGRESS: Channel   0:	 0.05 FDR:   296; 0.01 FDR:   238; 0.001 FDR:   180
1:43:03.856175 PROGRESS: =========================================================================
1:43:03.889090 INFO: fragments_df: keeping 2217 of 467161 [sum(precursor_idx_mask)=4675 sum(mass_error_mask)=467161 stop_rank=2217
1:43:04.054140 INFO: calibration group: precursor, fitting rt estimator 
1:43:04.170767 INFO: calibration group: fragment, fitting mz estimator 
1:43:04.481049 INFO: Using score_cutoff 45.754473614501954 (fac=0.99, q=1)
1:43:04.481482 INFO: calibration group: precursor, predicting mz
1:43:04.481569 WARNING: mz prediction was skipped as it has not been fitted yet
1:43:04.481600 INFO: calibration group: precursor, predicting rt
1:43:04.513295 INFO: calibration group: fragment, predicting mz
1:43:04.581096 INFO: === checking if optimization conditions were reached ===
1:43:04.581459 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:43:04.583938 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 67.7794.
1:43:04.583999 INFO: ==============================================
1:43:04.584106 INFO: Starting optimization step 3.
1:43:04.584185 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:43:04.584268 PROGRESS: Extracting batch of 50096 precursors
1:43:04.639019 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:43:04.639155 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:43:04.639193 INFO: FWHM in RT is 1.97 seconds, sigma is 0.25
1:43:04.639216 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:43:04.639437 INFO: Starting candidate selection
1:43:09.547776 INFO: Starting candidate scoring
1:43:10.210315 INFO: Finished candidate processing
1:43:10.210427 INFO: Collecting candidate features
1:43:10.371442 WARNING: intensity_correlation has 91 NaNs ( 0.10 % out of 94448)
1:43:10.383317 INFO: Collecting fragment features
1:43:10.426777 INFO: Finished candidate scoring
1:43:10.463823 PROGRESS: === Extracted 94448 precursors and 469446 fragments ===
1:43:10.464280 INFO: performing precursor FDR with 47 features
1:43:10.464321 INFO: Decoy channel: -1
1:43:10.464345 INFO: Competetive: True
1:43:10.495824 INFO: Setting torch num_threads to 2 for FDR classification task
1:43:10.513618 WARNING: dropped 53 target PSMs due to missing features
1:43:10.513772 WARNING: dropped 38 decoy PSMs due to missing features
1:43:12.095101 INFO: Test AUC: 0.538
1:43:12.095246 INFO: Train AUC: 0.574
1:43:12.095277 INFO: AUC difference: 6.31%
1:43:12.095300 WARNING: AUC difference > 5%. This may indicate overfitting.
1:43:12.313665 INFO: Resetting torch num_threads to 100
1:43:12.316477 INFO: === FDR correction performed with classifier version 7 ===
1:43:12.317151 PROGRESS: ============================= Precursor FDR =============================
1:43:12.317245 PROGRESS: Total precursors accumulated: 386
1:43:12.317308 PROGRESS: Target precursors: 350 (90.67%)
1:43:12.317361 PROGRESS: Decoy precursors: 36 (9.33%)
1:43:12.317409 PROGRESS: 
1:43:12.317455 PROGRESS: Precursor Summary:
1:43:12.318449 PROGRESS: Channel   0:	 0.05 FDR:   301; 0.01 FDR:   187; 0.001 FDR:   187
1:43:12.318541 PROGRESS: 
1:43:12.318598 PROGRESS: Protein Summary:
1:43:12.319716 PROGRESS: Channel   0:	 0.05 FDR:   287; 0.01 FDR:   178; 0.001 FDR:   178
1:43:12.319809 PROGRESS: =========================================================================
1:43:12.508292 INFO: calibration group: precursor, predicting mz
1:43:12.508586 WARNING: mz prediction was skipped as it has not been fitted yet
1:43:12.508621 INFO: calibration group: precursor, predicting rt
1:43:12.540639 INFO: calibration group: fragment, predicting mz
1:43:12.606106 INFO: === skipping optimization until target number of precursors are found ===
1:43:12.606369 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1:43:12.606430 INFO: Starting optimization step 4.
1:43:12.606497 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1:43:12.606557 PROGRESS: Extracting batch of 50439 precursors
1:43:12.619181 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:43:12.619304 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:43:12.619341 INFO: FWHM in RT is 1.97 seconds, sigma is 0.25
1:43:12.619367 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:43:12.619624 INFO: Starting candidate selection
1:43:14.087769 INFO: Starting candidate scoring
1:43:14.779520 INFO: Finished candidate processing
1:43:14.779637 INFO: Collecting candidate features
1:43:14.920432 WARNING: intensity_correlation has 101 NaNs ( 0.11 % out of 95131)
1:43:14.926888 INFO: Collecting fragment features
1:43:14.970489 INFO: Finished candidate scoring
1:43:15.061190 PROGRESS: === Extracted 189579 precursors and 941755 fragments ===
1:43:15.079009 INFO: performing precursor FDR with 47 features
1:43:15.079159 INFO: Decoy channel: -1
1:43:15.079187 INFO: Competetive: True
1:43:15.153523 INFO: Setting torch num_threads to 2 for FDR classification task
1:43:15.190620 WARNING: dropped 95 target PSMs due to missing features
1:43:15.190775 WARNING: dropped 97 decoy PSMs due to missing features
1:43:18.638145 INFO: Test AUC: 0.548
1:43:18.638287 INFO: Train AUC: 0.571
1:43:18.638319 INFO: AUC difference: 4.10%
1:43:18.868369 INFO: Resetting torch num_threads to 100
1:43:18.876451 INFO: === FDR correction performed with classifier version 7 ===
1:43:18.877273 PROGRESS: ============================= Precursor FDR =============================
1:43:18.877366 PROGRESS: Total precursors accumulated: 764
1:43:18.877427 PROGRESS: Target precursors: 693 (90.71%)
1:43:18.877479 PROGRESS: Decoy precursors: 71 (9.29%)
1:43:18.877526 PROGRESS: 
1:43:18.877571 PROGRESS: Precursor Summary:
1:43:18.878659 PROGRESS: Channel   0:	 0.05 FDR:   623; 0.01 FDR:   431; 0.001 FDR:   244
1:43:18.878749 PROGRESS: 
1:43:18.878804 PROGRESS: Protein Summary:
1:43:18.880048 PROGRESS: Channel   0:	 0.05 FDR:   575; 0.01 FDR:   396; 0.001 FDR:   230
1:43:18.880162 PROGRESS: =========================================================================
1:43:18.950768 INFO: fragments_df: keeping 4155 of 941755 [sum(precursor_idx_mask)=8316 sum(mass_error_mask)=941755 stop_rank=4155
1:43:19.118774 INFO: calibration group: precursor, fitting rt estimator 
1:43:19.254256 INFO: calibration group: fragment, fitting mz estimator 
1:43:19.804951 INFO: Using score_cutoff 50.43939535903931 (fac=0.99, q=1)
1:43:19.805372 INFO: calibration group: precursor, predicting mz
1:43:19.805461 WARNING: mz prediction was skipped as it has not been fitted yet
1:43:19.805490 INFO: calibration group: precursor, predicting rt
1:43:19.837197 INFO: calibration group: fragment, predicting mz
1:43:19.902524 INFO: === checking if optimization conditions were reached ===
1:43:19.902860 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:43:19.905452 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 68.2151.
1:43:19.905539 INFO: ==============================================
1:43:19.905674 INFO: Starting optimization step 5.
1:43:19.905751 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:43:19.905822 PROGRESS: Extracting batch of 50096 precursors
1:43:19.923336 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:43:19.923486 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:43:19.923527 INFO: FWHM in RT is 2.14 seconds, sigma is 0.28
1:43:19.923557 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:43:19.923834 INFO: Starting candidate selection
1:43:21.385657 INFO: Starting candidate scoring
1:43:22.074635 INFO: Finished candidate processing
1:43:22.074747 INFO: Collecting candidate features
1:43:22.223019 WARNING: intensity_correlation has 104 NaNs ( 0.11 % out of 94190)
1:43:22.229419 INFO: Collecting fragment features
1:43:22.274251 INFO: Finished candidate scoring
1:43:22.311821 PROGRESS: === Extracted 94190 precursors and 467713 fragments ===
1:43:22.312268 INFO: performing precursor FDR with 47 features
1:43:22.312308 INFO: Decoy channel: -1
1:43:22.312334 INFO: Competetive: True
1:43:22.342484 INFO: Setting torch num_threads to 2 for FDR classification task
1:43:22.360425 WARNING: dropped 59 target PSMs due to missing features
1:43:22.360566 WARNING: dropped 45 decoy PSMs due to missing features
1:43:24.053712 INFO: Test AUC: 0.551
1:43:24.929284 INFO: Train AUC: 0.572
1:43:24.929379 INFO: AUC difference: 3.61%
1:43:25.142388 INFO: Resetting torch num_threads to 100
1:43:25.157051 INFO: === FDR correction performed with classifier version 7 ===
1:43:25.157740 PROGRESS: ============================= Precursor FDR =============================
1:43:25.157833 PROGRESS: Total precursors accumulated: 399
1:43:25.157894 PROGRESS: Target precursors: 364 (91.23%)
1:43:25.157946 PROGRESS: Decoy precursors: 35 (8.77%)
1:43:25.157994 PROGRESS: 
1:43:25.158038 PROGRESS: Precursor Summary:
1:43:25.159178 PROGRESS: Channel   0:	 0.05 FDR:   297; 0.01 FDR:   207; 0.001 FDR:   189
1:43:25.159291 PROGRESS: 
1:43:25.159354 PROGRESS: Protein Summary:
1:43:25.160626 PROGRESS: Channel   0:	 0.05 FDR:   281; 0.01 FDR:   198; 0.001 FDR:   180
1:43:25.160727 PROGRESS: =========================================================================
1:43:25.193042 INFO: fragments_df: keeping 1977 of 467713 [sum(precursor_idx_mask)=3961 sum(mass_error_mask)=467713 stop_rank=1977
1:43:25.375273 INFO: calibration group: precursor, fitting rt estimator 
1:43:25.498720 INFO: calibration group: fragment, fitting mz estimator 
1:43:25.769906 INFO: Using score_cutoff 54.04497344055176 (fac=0.99, q=1)
1:43:25.770370 INFO: calibration group: precursor, predicting mz
1:43:25.770468 WARNING: mz prediction was skipped as it has not been fitted yet
1:43:25.770509 INFO: calibration group: precursor, predicting rt
1:43:25.803470 INFO: calibration group: fragment, predicting mz
1:43:25.869829 INFO: === checking if optimization conditions were reached ===
1:43:25.870203 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1:43:25.871811 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 75.8260 found after 5 searches.
1:43:25.871873 INFO: ==============================================
1:43:25.871986 PROGRESS: Optimization finished for rt_error.
1:43:26.090662 INFO: calibration group: precursor, predicting mz
1:43:26.090965 WARNING: mz prediction was skipped as it has not been fitted yet
1:43:26.090999 INFO: calibration group: precursor, predicting rt
1:43:26.123372 INFO: calibration group: fragment, predicting mz
1:43:26.225844 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:43:26.226155 PROGRESS: ==============================================
1:43:26.226239 PROGRESS: ms2_error      : 4.9330
1:43:26.226319 PROGRESS: rt_error       : 75.8260
1:43:26.226378 PROGRESS: ==============================================
1:43:26.227407 INFO: calibration group: precursor, predicting mz
1:43:26.227569 WARNING: mz prediction was skipped as it has not been fitted yet
1:43:26.227606 INFO: calibration group: precursor, predicting rt
1:43:34.458320 INFO: calibration group: fragment, predicting mz
1:43:52.294008 PROGRESS: Extracting batch of 12567710 precursors
1:43:55.158471 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:43:55.158632 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:43:55.158678 INFO: FWHM in RT is 1.97 seconds, sigma is 0.25
1:43:55.158704 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:43:55.159685 INFO: Starting candidate selection
1:49:46.589694 INFO: Applying score cutoff of 45.754473614501954
1:49:46.693188 INFO: Removed 23380214 precursors with score below cutoff
1:49:49.321348 INFO: Starting candidate scoring
1:50:02.447753 INFO: Finished candidate processing
1:50:02.447988 INFO: Collecting candidate features
1:50:07.572998 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 1682453)
1:50:07.627436 INFO: Collecting fragment features
1:50:09.199817 INFO: Finished candidate scoring
1:50:10.588617 INFO: === FDR correction performed with classifier version 22 ===
1:50:10.590386 INFO: performing precursor FDR with 47 features
1:50:10.590461 INFO: Decoy channel: -1
1:50:10.590492 INFO: Competetive: True
1:50:11.119592 INFO: Setting torch num_threads to 2 for FDR classification task
1:50:11.385533 WARNING: dropped 1 decoy PSMs due to missing features
1:50:41.075057 INFO: Test AUC: 0.637
1:50:41.075308 INFO: Train AUC: 0.642
1:50:41.075344 INFO: AUC difference: 0.74%
1:50:41.717019 INFO: Resetting torch num_threads to 100
1:50:41.768668 INFO: Removing fragments below FDR threshold
1:50:41.952930 PROGRESS: ============================= Precursor FDR =============================
1:50:41.953269 PROGRESS: Total precursors accumulated: 76,039
1:50:41.953342 PROGRESS: Target precursors: 75,287 (99.01%)
1:50:41.953397 PROGRESS: Decoy precursors: 752 (0.99%)
1:50:41.953446 PROGRESS: 
1:50:41.953495 PROGRESS: Precursor Summary:
1:50:41.984454 PROGRESS: Channel   0:	 0.05 FDR: 75,287; 0.01 FDR: 75,287; 0.001 FDR: 54,639
1:50:41.984742 PROGRESS: 
1:50:41.984807 PROGRESS: Protein Summary:
1:50:42.028660 PROGRESS: Channel   0:	 0.05 FDR: 11,390; 0.01 FDR: 11,390; 0.001 FDR: 8,943
1:50:42.028932 PROGRESS: =========================================================================
1:50:42.624166 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:51:10.904407 PROGRESS: Processing search outputs
1:51:10.904792 PROGRESS: Performing protein grouping and FDR
1:51:10.904834 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:51:10.964192 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:51:10.997004 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:51:11.012896 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:51:11.061654 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:51:11.115093 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:51:11.165593 INFO: Building combined output
1:51:11.545651 INFO: Performing protein inference
1:51:11.970434 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
1:52:07.501544 INFO: Performing protein FDR
1:52:15.460952 INFO: Normalizing q-values using 23,574 targets and 3,252 decoys
1:52:15.478396 INFO: Test AUC: 0.932
1:52:15.478500 INFO: Train AUC: 0.939
1:52:15.478537 INFO: AUC difference: 0.78%
1:52:16.063837 PROGRESS: ================ Protein FDR =================
1:52:16.064008 PROGRESS: Unique protein groups in output
1:52:16.064039 PROGRESS:   1% protein FDR: 11,998
1:52:16.064062 PROGRESS: 
1:52:16.064080 PROGRESS: Unique precursor in output
1:52:16.064099 PROGRESS:   1% protein FDR: 123,909
1:52:16.064121 PROGRESS: ================================================
1:52:16.130380 PROGRESS: Building search statistics
1:52:16.251667 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
1:52:16.251907 INFO: Initializing OptimizationManager
1:52:16.252206 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
1:52:16.252313 INFO: Initializing CalibrationManager
1:52:16.252540 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
1:52:16.252616 INFO: Initializing RawFileManager
1:52:16.283075 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
1:52:16.283291 INFO: Initializing OptimizationManager
1:52:16.283530 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
1:52:16.283612 INFO: Initializing CalibrationManager
1:52:16.283807 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
1:52:16.283889 INFO: Initializing RawFileManager
1:52:16.305131 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
1:52:16.305289 INFO: Initializing OptimizationManager
1:52:16.305486 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
1:52:16.305572 INFO: Initializing CalibrationManager
1:52:16.305760 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
1:52:16.305832 INFO: Initializing RawFileManager
1:52:16.336477 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
1:52:16.336689 INFO: Initializing OptimizationManager
1:52:16.336886 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
1:52:16.336988 INFO: Initializing CalibrationManager
1:52:16.337182 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
1:52:16.337255 INFO: Initializing RawFileManager
1:52:16.369930 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
1:52:16.370161 INFO: Initializing OptimizationManager
1:52:16.370365 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
1:52:16.370440 INFO: Initializing CalibrationManager
1:52:16.370624 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
1:52:16.370698 INFO: Initializing RawFileManager
1:52:16.403049 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
1:52:16.403256 INFO: Initializing OptimizationManager
1:52:16.403464 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
1:52:16.403947 INFO: Initializing CalibrationManager
1:52:16.404156 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
1:52:16.404230 INFO: Initializing RawFileManager
1:52:16.407103 INFO: Writing stat output to disk
1:52:16.407182 INFO: Saving run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/stat.tsv to disk
1:52:16.415684 PROGRESS: Building internal statistics
1:52:16.416107 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
1:52:16.416155 INFO: Initializing TimingManager
1:52:16.416513 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
1:52:16.416557 INFO: Initializing TimingManager
1:52:16.416737 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
1:52:16.416774 INFO: Initializing TimingManager
1:52:16.416938 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
1:52:16.416975 INFO: Initializing TimingManager
1:52:16.417135 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
1:52:16.417172 INFO: Initializing TimingManager
1:52:16.417326 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
1:52:16.417361 INFO: Initializing TimingManager
1:52:16.417764 INFO: Writing internal output to disk
1:52:16.417809 INFO: Saving run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/internal.tsv to disk
1:52:16.418324 PROGRESS: Performing label free quantification
1:52:16.497204 INFO: Accumulating fragment data
1:52:16.497386 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:52:16.736359 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:52:17.954224 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:52:19.033213 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:52:20.460688 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:52:21.955998 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:52:23.783924 PROGRESS: Performing label free quantification on the precursor level
1:52:23.784089 INFO: Filtering fragments by quality
1:52:24.168017 INFO: Performing label-free quantification using directLFQ
1:52:24.736869 INFO: to few values for normalization without missing values. Including missing values
1:52:26.360850 INFO: 123909 lfq-groups total
1:53:44.734404 INFO: using 100 processes
1:53:44.999011 INFO: lfq-object 0
1:53:45.081955 INFO: lfq-object 100
1:53:45.158319 INFO: lfq-object 400
1:53:45.171280 INFO: lfq-object 200
1:53:45.232089 INFO: lfq-object 700
1:53:45.250789 INFO: lfq-object 500
1:53:45.265764 INFO: lfq-object 300
1:53:45.294859 INFO: lfq-object 1000
1:53:45.321548 INFO: lfq-object 800
1:53:45.346742 INFO: lfq-object 600
1:53:45.360276 INFO: lfq-object 1300
1:53:45.384068 INFO: lfq-object 1100
1:53:45.412428 INFO: lfq-object 900
1:53:45.431975 INFO: lfq-object 1600
1:53:45.456850 INFO: lfq-object 1400
1:53:45.474641 INFO: lfq-object 1200
1:53:45.515915 INFO: lfq-object 1700
1:53:45.531788 INFO: lfq-object 1900
1:53:45.552061 INFO: lfq-object 1500
1:53:45.606875 INFO: lfq-object 1800
1:53:45.623679 INFO: lfq-object 2000
1:53:45.630214 INFO: lfq-object 2200
1:53:45.714063 INFO: lfq-object 2100
1:53:45.731580 INFO: lfq-object 2300
1:53:45.760696 INFO: lfq-object 2500
1:53:45.830614 INFO: lfq-object 2400
1:53:45.850632 INFO: lfq-object 2600
1:53:45.851586 INFO: lfq-object 2800
1:53:45.934550 INFO: lfq-object 3100
1:53:45.939391 INFO: lfq-object 2900
1:53:45.939978 INFO: lfq-object 2700
1:53:46.026645 INFO: lfq-object 3000
1:53:46.029687 INFO: lfq-object 3200
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1:53:46.134485 INFO: lfq-object 3500
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1:53:46.709777 INFO: lfq-object 5000
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1:53:53.251711 INFO: lfq-object 6000
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1:54:55.332973 INFO: lfq-object 113800
1:54:55.394645 INFO: lfq-object 113700
1:54:55.425342 INFO: lfq-object 113900
1:54:55.425870 INFO: lfq-object 114100
1:54:55.510575 INFO: lfq-object 114000
1:54:55.531198 INFO: lfq-object 114200
1:54:55.594039 INFO: lfq-object 114400
1:54:55.623624 INFO: lfq-object 114300
1:54:55.670059 INFO: lfq-object 114700
1:54:55.695617 INFO: lfq-object 114500
1:54:55.774931 INFO: lfq-object 114800
1:54:55.783722 INFO: lfq-object 114600
1:54:55.864675 INFO: lfq-object 114900
1:54:55.883526 INFO: lfq-object 115100
1:54:55.954914 INFO: lfq-object 115000
1:54:55.981611 INFO: lfq-object 115200
1:54:55.986176 INFO: lfq-object 115400
1:54:56.018931 INFO: lfq-object 115700
1:54:56.070324 INFO: lfq-object 115300
1:54:56.073046 INFO: lfq-object 115500
1:54:56.099524 INFO: lfq-object 116000
1:54:56.110129 INFO: lfq-object 115800
1:54:56.166245 INFO: lfq-object 115600
1:54:56.171784 INFO: lfq-object 116300
1:54:56.190465 INFO: lfq-object 116100
1:54:56.202681 INFO: lfq-object 115900
1:54:56.255966 INFO: lfq-object 116600
1:54:56.262948 INFO: lfq-object 116400
1:54:56.277978 INFO: lfq-object 116200
1:54:56.346451 INFO: lfq-object 116700
1:54:56.348574 INFO: lfq-object 116500
1:54:56.368422 INFO: lfq-object 116900
1:54:56.436898 INFO: lfq-object 116800
1:54:56.458173 INFO: lfq-object 117000
1:54:56.516732 INFO: lfq-object 117200
1:54:56.541830 INFO: lfq-object 117100
1:54:56.611742 INFO: lfq-object 117300
1:54:56.705474 INFO: lfq-object 117400
1:54:56.731903 INFO: lfq-object 117500
1:54:56.830504 INFO: lfq-object 117600
1:54:56.909649 INFO: lfq-object 117800
1:54:56.919906 INFO: lfq-object 117700
1:54:56.999787 INFO: lfq-object 117900
1:54:57.086239 INFO: lfq-object 118000
1:54:57.131902 INFO: lfq-object 118200
1:54:57.179572 INFO: lfq-object 118100
1:54:57.199240 INFO: lfq-object 118500
1:54:57.216947 INFO: lfq-object 118300
1:54:57.292290 INFO: lfq-object 118600
1:54:57.297366 INFO: lfq-object 118800
1:54:57.311810 INFO: lfq-object 118400
1:54:57.366016 INFO: lfq-object 119100
1:54:57.379543 INFO: lfq-object 118700
1:54:57.388421 INFO: lfq-object 118900
1:54:57.456826 INFO: lfq-object 119200
1:54:57.481843 INFO: lfq-object 119000
1:54:57.482295 INFO: lfq-object 119400
1:54:57.549572 INFO: lfq-object 119300
1:54:57.575053 INFO: lfq-object 119500
1:54:57.614219 INFO: lfq-object 119700
1:54:57.669523 INFO: lfq-object 119600
1:54:57.703363 INFO: lfq-object 119800
1:54:57.718567 INFO: lfq-object 120000
1:54:57.768785 INFO: lfq-object 120300
1:54:57.791713 INFO: lfq-object 119900
1:54:57.811626 INFO: lfq-object 120100
1:54:57.856807 INFO: lfq-object 120400
1:54:57.900019 INFO: lfq-object 120600
1:54:57.905138 INFO: lfq-object 120200
1:54:57.948328 INFO: lfq-object 120500
1:54:57.983827 INFO: lfq-object 120700
1:54:58.016432 INFO: lfq-object 120900
1:54:58.075212 INFO: lfq-object 120800
1:54:58.105954 INFO: lfq-object 121000
1:54:58.200270 INFO: lfq-object 121100
1:54:58.223696 INFO: lfq-object 121300
1:54:58.294077 INFO: lfq-object 121200
1:54:58.308614 INFO: lfq-object 121400
1:54:58.398500 INFO: lfq-object 121600
1:54:58.409756 INFO: lfq-object 121500
1:54:58.487186 INFO: lfq-object 121700
1:54:58.574897 INFO: lfq-object 121800
1:54:58.630362 INFO: lfq-object 121900
1:54:58.723425 INFO: lfq-object 122000
1:54:58.815301 INFO: lfq-object 122100
1:55:06.376393 INFO: lfq-object 122200
1:55:06.463183 INFO: lfq-object 122300
1:55:06.501220 INFO: lfq-object 122500
1:55:06.553832 INFO: lfq-object 122400
1:55:06.571319 INFO: lfq-object 122800
1:55:06.585492 INFO: lfq-object 122600
1:55:06.646356 INFO: lfq-object 123100
1:55:06.666658 INFO: lfq-object 122900
1:55:06.680671 INFO: lfq-object 122700
1:55:06.712174 INFO: lfq-object 123400
1:55:06.738454 INFO: lfq-object 123200
1:55:06.755592 INFO: lfq-object 123000
1:55:06.796720 INFO: lfq-object 123700
1:55:06.803213 INFO: lfq-object 123500
1:55:06.826140 INFO: lfq-object 123300
1:55:06.885183 INFO: lfq-object 123800
1:55:06.893968 INFO: lfq-object 123600
1:55:06.984825 INFO: lfq-object 123900
1:55:14.026638 INFO: Writing precursor output to disk
1:55:14.027072 INFO: Saving run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/precursor.matrix.tsv to disk
1:55:14.492131 PROGRESS: Performing label free quantification on the pg level
1:55:14.492249 INFO: Filtering fragments by quality
1:55:14.893389 INFO: Performing label-free quantification using directLFQ
1:55:15.013782 INFO: to few values for normalization without missing values. Including missing values
1:55:15.119159 INFO: 11998 lfq-groups total
1:56:14.059060 INFO: using 100 processes
1:56:14.188165 INFO: lfq-object 0
1:56:14.229454 INFO: lfq-object 100
1:56:14.286097 INFO: lfq-object 200
1:56:14.309598 INFO: lfq-object 300
1:56:14.359529 INFO: lfq-object 400
1:56:14.420439 INFO: lfq-object 500
1:56:14.447727 INFO: lfq-object 600
1:56:14.511520 INFO: lfq-object 700
1:56:14.566578 INFO: lfq-object 900
1:56:14.567514 INFO: lfq-object 800
1:56:14.632370 INFO: lfq-object 1000
1:56:14.700817 INFO: lfq-object 1100
1:56:14.709169 INFO: lfq-object 1200
1:56:14.765110 INFO: lfq-object 1300
1:56:14.841761 INFO: lfq-object 1400
1:56:14.843657 INFO: lfq-object 1500
1:56:14.889613 INFO: lfq-object 1600
1:56:14.929242 INFO: lfq-object 1700
1:56:14.951142 INFO: lfq-object 1800
1:56:15.019176 INFO: lfq-object 1900
1:56:15.052929 INFO: lfq-object 2000
1:56:15.085608 INFO: lfq-object 2100
1:56:15.137356 INFO: lfq-object 2200
1:56:15.188267 INFO: lfq-object 2300
1:56:15.192820 INFO: lfq-object 2400
1:56:15.241647 INFO: lfq-object 2500
1:56:15.273965 INFO: lfq-object 2600
1:56:15.317026 INFO: lfq-object 2700
1:56:15.372437 INFO: lfq-object 2800
1:56:15.409668 INFO: lfq-object 2900
1:56:15.418501 INFO: lfq-object 3000
1:56:15.464538 INFO: lfq-object 3100
1:56:15.525551 INFO: lfq-object 3200
1:56:15.548383 INFO: lfq-object 3300
1:56:15.591867 INFO: lfq-object 3400
1:56:15.638492 INFO: lfq-object 3500
1:56:15.649165 INFO: lfq-object 3600
1:56:15.696600 INFO: lfq-object 3700
1:56:15.741012 INFO: lfq-object 3800
1:56:15.792772 INFO: lfq-object 3900
1:56:15.838256 INFO: lfq-object 4000
1:56:15.883446 INFO: lfq-object 4100
1:56:15.915236 INFO: lfq-object 4200
1:56:15.957132 INFO: lfq-object 4300
1:56:15.994633 INFO: lfq-object 4400
1:56:16.015412 INFO: lfq-object 4500
1:56:16.058119 INFO: lfq-object 4600
1:56:16.106642 INFO: lfq-object 4700
1:56:16.131145 INFO: lfq-object 4800
1:56:16.175006 INFO: lfq-object 4900
1:56:16.216511 INFO: lfq-object 5000
1:56:16.244684 INFO: lfq-object 5100
1:56:16.323235 INFO: lfq-object 5200
1:56:16.371796 INFO: lfq-object 5300
1:56:16.378266 INFO: lfq-object 5400
1:56:16.418128 INFO: lfq-object 5500
1:56:16.495201 INFO: lfq-object 5600
1:56:16.518765 INFO: lfq-object 5700
1:56:16.551838 INFO: lfq-object 5800
1:56:16.593000 INFO: lfq-object 5900
1:56:16.608188 INFO: lfq-object 6000
1:56:16.643121 INFO: lfq-object 6100
1:56:16.700079 INFO: lfq-object 6200
1:56:16.709173 INFO: lfq-object 6300
1:56:16.766369 INFO: lfq-object 6400
1:56:16.819482 INFO: lfq-object 6500
1:56:16.823689 INFO: lfq-object 6600
1:56:16.871679 INFO: lfq-object 6700
1:56:16.920405 INFO: lfq-object 6900
1:56:16.922860 INFO: lfq-object 6800
1:56:16.968571 INFO: lfq-object 7000
1:56:17.016774 INFO: lfq-object 7100
1:56:17.026621 INFO: lfq-object 7200
1:56:17.069234 INFO: lfq-object 7300
1:56:17.104133 INFO: lfq-object 7400
1:56:17.117290 INFO: lfq-object 7500
1:56:17.169819 INFO: lfq-object 7600
1:56:17.219323 INFO: lfq-object 7800
1:56:17.225483 INFO: lfq-object 7700
1:56:17.262355 INFO: lfq-object 7900
1:56:17.309897 INFO: lfq-object 8000
1:56:17.348978 INFO: lfq-object 8100
1:56:17.388950 INFO: lfq-object 8200
1:56:17.447164 INFO: lfq-object 8300
1:56:17.486283 INFO: lfq-object 8400
1:56:17.523146 INFO: lfq-object 8500
1:56:17.579204 INFO: lfq-object 8600
1:56:17.585897 INFO: lfq-object 8700
1:56:17.637097 INFO: lfq-object 8800
1:56:17.676489 INFO: lfq-object 8900
1:56:17.690954 INFO: lfq-object 9000
1:56:17.729998 INFO: lfq-object 9100
1:56:17.770471 INFO: lfq-object 9200
1:56:17.833362 INFO: lfq-object 9300
1:56:17.887614 INFO: lfq-object 9400
1:56:17.939342 INFO: lfq-object 9500
1:56:17.958637 INFO: lfq-object 9600
1:56:18.016107 INFO: lfq-object 9700
1:56:18.083675 INFO: lfq-object 9800
1:56:18.117713 INFO: lfq-object 9900
1:56:18.200281 INFO: lfq-object 10000
1:56:18.240009 INFO: lfq-object 10100
1:56:18.283863 INFO: lfq-object 10200
1:56:18.363041 INFO: lfq-object 10300
1:56:18.427965 INFO: lfq-object 10500
1:56:18.434337 INFO: lfq-object 10400
1:56:18.478999 INFO: lfq-object 10600
1:56:18.518511 INFO: lfq-object 10700
1:56:18.544590 INFO: lfq-object 10800
1:56:18.586323 INFO: lfq-object 10900
1:56:18.642449 INFO: lfq-object 11000
1:56:18.654578 INFO: lfq-object 11100
1:56:18.720511 INFO: lfq-object 11200
1:56:18.752930 INFO: lfq-object 11300
1:56:18.768632 INFO: lfq-object 11400
1:56:18.843040 INFO: lfq-object 11500
1:56:18.882259 INFO: lfq-object 11700
1:56:18.888629 INFO: lfq-object 11600
1:56:18.931542 INFO: lfq-object 11800
1:56:18.985450 INFO: lfq-object 11900
1:56:22.735444 INFO: Writing pg output to disk
1:56:22.735647 INFO: Saving run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/pg.matrix.tsv to disk
1:56:22.959152 INFO: Writing psm output to disk
1:56:22.959325 INFO: Saving run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/precursors.tsv to disk
1:56:43.025716 PROGRESS: Building spectral library
1:56:43.120060 INFO: Building MBR spectral library
1:56:43.120223 INFO: Running MbrLibraryBuilder
1:56:45.331666 INFO: MBR spectral library contains 123,909 precursors, 11,998 proteins
1:56:45.331844 INFO: Writing MBR spectral library to disk
1:56:46.722749 PROGRESS: =================== Search Finished ===================
1:56:47.968401 INFO: Running step 'mbr'
1:56:47.971563 INFO: Extracted extra_config from previous step: defaultdict(<class 'dict'>, {'search': {'target_ms1_tolerance': 30.0, 'target_ms2_tolerance': 6.741074}})
1:56:47.971737 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
1:56:47.983297 INFO: loading additional config provided via CLI
1:56:47.983384 INFO: loading additional config provided via CLI parameters
1:56:47.983646 INFO: Updating config with 'user defined'
1:56:47.983740 INFO: Updating config with 'user defined (cli)'
1:56:47.983764 INFO: Updating config with 'multistep search'
1:56:47.983808 INFO: ├──version: 1
1:56:47.983836 INFO: ├──workflow_name: None
1:56:47.983859 INFO: [32;20m├──output_directory: run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds [multistep search, default: None][0m
1:56:47.983881 INFO: [32;20m├──library_path: run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/speclib.mbr.hdf [multistep search, default: None][0m
1:56:47.983901 INFO: ├──raw_paths:
1:56:47.983922 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
1:56:47.983942 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
1:56:47.983962 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
1:56:47.983983 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
1:56:47.984001 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
1:56:47.984021 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
1:56:47.984039 INFO: ├──fasta_paths:
1:56:47.984058 INFO: ├──quant_directory: None
1:56:47.984078 INFO: ├──general
1:56:47.984098 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
1:56:47.984119 INFO: │   ├──transfer_step_enabled: False
1:56:47.984138 INFO: │   ├──mbr_step_enabled: True
1:56:47.984156 INFO: │   ├──reuse_calibration: False
1:56:47.984174 INFO: │   ├──reuse_quant: False
1:56:47.984194 INFO: │   ├──astral_ms1: False
1:56:47.984212 INFO: │   ├──log_level: INFO
1:56:47.984230 INFO: │   ├──mmap_detector_events: False
1:56:47.984259 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
1:56:47.984278 INFO: │   ├──save_library: True
1:56:47.984298 INFO: │   ├──save_mbr_library: True
1:56:47.984317 INFO: │   └──save_figures: True
1:56:47.984337 INFO: ├──library_loading
1:56:47.984356 INFO: │   └──rt_heuristic: 180
1:56:47.984372 INFO: ├──library_prediction
1:56:47.984390 INFO: │   ├──enabled: False
1:56:47.984409 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
1:56:47.984427 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
1:56:47.984445 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
1:56:47.984465 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
1:56:47.984483 INFO: │   ├──missed_cleavages: 1
1:56:47.984502 INFO: │   ├──precursor_len:
1:56:47.984520 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
1:56:47.984539 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
1:56:47.984556 INFO: │   ├──precursor_charge:
1:56:47.984576 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
1:56:47.984595 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
1:56:47.984613 INFO: │   ├──precursor_mz:
1:56:47.984633 INFO: │   │   [32;20m- 380 [user defined, default: 400][0m
1:56:47.984652 INFO: │   │   [32;20m- 980 [user defined, default: 1200][0m
1:56:47.984670 INFO: │   ├──fragment_mz:
1:56:47.984690 INFO: │   │   [32;20m- 150 [user defined, default: 200][0m
1:56:47.984720 INFO: │   │   [32;20m- 2000[0m
1:56:47.984740 INFO: │   ├──nce: 25
1:56:47.984758 INFO: │   ├──fragment_types:
1:56:47.984777 INFO: │   │   [32;20m- b[0m
1:56:47.984795 INFO: │   │   [32;20m- y[0m
1:56:47.984813 INFO: │   ├──max_fragment_charge: 2
1:56:47.984832 INFO: │   [32;20m├──instrument: Astral [user defined, default: Lumos][0m
1:56:47.984850 INFO: │   ├──peptdeep_model_path: None
1:56:47.984870 INFO: │   └──peptdeep_model_type: generic
1:56:47.984890 INFO: ├──custom_modifications:
1:56:47.984909 INFO: │   ├──name: Dimethyl:d12@K
1:56:47.984927 INFO: │   └──composition: H(-2)2H(8)13C(2)
1:56:47.984947 INFO: │   ├──name: Dimethyl:d12@Any_N-term
1:56:47.984967 INFO: │   └──composition: H(-2)2H(8)13C(2)
1:56:47.984986 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
1:56:47.985005 INFO: │   └──composition: H(-2)2H(8)13C(2)
1:56:47.985024 INFO: │   ├──name: mTRAQ:d12@K
1:56:47.985042 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
1:56:47.985061 INFO: │   ├──name: mTRAQ:d12@Any_N-term
1:56:47.985079 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
1:56:47.985097 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
1:56:47.985115 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
1:56:47.985134 INFO: │   ├──name: Label:13C(12)@K
1:56:47.985154 INFO: │   └──composition: C(12)
1:56:47.985172 INFO: ├──search
1:56:47.985194 INFO: │   [32;20m├──target_ms1_tolerance: 30.0 [multistep search, default: 5][0m
1:56:47.985214 INFO: │   [32;20m├──target_ms2_tolerance: 6.741074 [multistep search, default: 10][0m
1:56:47.985233 INFO: │   ├──target_rt_tolerance: 0
1:56:47.985251 INFO: │   ├──target_mobility_tolerance: 0
1:56:47.985270 INFO: │   ├──quant_window: 3
1:56:47.985289 INFO: │   [32;20m├──target_num_candidates: 2 [user defined, default: 3][0m
1:56:47.985308 INFO: │   ├──channel_filter: 
1:56:47.985327 INFO: │   ├──exclude_shared_ions: True
1:56:47.985345 INFO: │   ├──compete_for_fragments: True
1:56:47.985363 INFO: │   ├──quant_all: True
1:56:47.985382 INFO: │   ├──top_k_fragments: 12
1:56:47.985402 INFO: │   ├──experimental_xic: True
1:56:47.985421 INFO: │   └──optimized_peak_group_score: False
1:56:47.985439 INFO: ├──calibration
1:56:47.985458 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 8000][0m
1:56:47.985476 INFO: │   ├──optimization_lock_target: 200
1:56:47.985494 INFO: │   ├──max_steps: 20
1:56:47.985513 INFO: │   ├──min_steps: 2
1:56:47.985530 INFO: │   ├──max_skips: 1
1:56:47.985548 INFO: │   ├──norm_rt_mode: linear
1:56:47.985566 INFO: │   ├──max_fragments: 5000
1:56:47.985590 INFO: │   └──min_correlation: 0.7
1:56:47.985610 INFO: ├──search_initial
1:56:47.985628 INFO: │   ├──initial_num_candidates: 1
1:56:47.985646 INFO: │   ├──initial_ms1_tolerance: 30
1:56:47.985664 INFO: │   ├──initial_ms2_tolerance: 30
1:56:47.985682 INFO: │   ├──initial_mobility_tolerance: 0.1
1:56:47.985702 INFO: │   └──initial_rt_tolerance: 0.5
1:56:47.985721 INFO: ├──selection_config
1:56:47.985740 INFO: │   ├──peak_len_rt: 10.0
1:56:47.985760 INFO: │   ├──sigma_scale_rt: 0.5
1:56:47.985778 INFO: │   ├──peak_len_mobility: 0.01
1:56:47.985797 INFO: │   ├──sigma_scale_mobility: 1.0
1:56:47.985816 INFO: │   ├──top_k_precursors: 3
1:56:47.985834 INFO: │   ├──kernel_size: 30
1:56:47.985852 INFO: │   ├──f_mobility: 1.0
1:56:47.985870 INFO: │   ├──f_rt: 0.99
1:56:47.985889 INFO: │   ├──center_fraction: 0.5
1:56:47.985908 INFO: │   ├──min_size_mobility: 8
1:56:47.985925 INFO: │   ├──min_size_rt: 3
1:56:47.985944 INFO: │   ├──max_size_mobility: 20
1:56:47.985969 INFO: │   ├──max_size_rt: 15
1:56:47.985987 INFO: │   ├──group_channels: False
1:56:47.986006 INFO: │   ├──use_weighted_score: True
1:56:47.986024 INFO: │   ├──join_close_candidates: False
1:56:47.986043 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
1:56:47.986063 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
1:56:47.986081 INFO: ├──scoring_config
1:56:47.986099 INFO: │   ├──score_grouped: False
1:56:47.986117 INFO: │   ├──top_k_isotopes: 3
1:56:47.986135 INFO: │   ├──reference_channel: -1
1:56:47.986153 INFO: │   ├──precursor_mz_tolerance: 10
1:56:47.986171 INFO: │   └──fragment_mz_tolerance: 15
1:56:47.986190 INFO: ├──library_multiplexing
1:56:47.986208 INFO: │   ├──enabled: False
1:56:47.986227 INFO: │   ├──input_channel: 0
1:56:47.986245 INFO: │   └──multiplex_mapping:
1:56:47.986265 INFO: ├──multiplexing
1:56:47.986284 INFO: │   ├──enabled: False
1:56:47.986302 INFO: │   ├──target_channels: 4,8
1:56:47.986321 INFO: │   ├──decoy_channel: 12
1:56:47.986340 INFO: │   ├──reference_channel: 0
1:56:47.986358 INFO: │   └──competetive_scoring: True
1:56:47.986376 INFO: ├──fdr
1:56:47.986395 INFO: │   ├──fdr: 0.01
1:56:47.986413 INFO: │   ├──group_level: proteins
1:56:47.986432 INFO: │   [32;20m├──inference_strategy: library [multistep search, default: heuristic][0m
1:56:47.986451 INFO: │   ├──competetive_scoring: True
1:56:47.986469 INFO: │   ├──keep_decoys: False
1:56:47.986487 INFO: │   ├──channel_wise_fdr: False
1:56:47.986506 INFO: │   ├──enable_two_step_classifier: False
1:56:47.986525 INFO: │   ├──two_step_classifier_max_iterations: 5
1:56:47.986545 INFO: │   └──enable_nn_hyperparameter_tuning: False
1:56:47.986563 INFO: ├──search_output
1:56:47.986582 INFO: │   ├──file_format: tsv
1:56:47.986601 INFO: │   ├──peptide_level_lfq: False
1:56:47.986620 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
1:56:47.986639 INFO: │   ├──min_k_fragments: 12
1:56:47.986659 INFO: │   ├──min_correlation: 0.9
1:56:47.986676 INFO: │   ├──num_samples_quadratic: 50
1:56:47.986694 INFO: │   ├──min_nonnan: 3
1:56:47.986713 INFO: │   ├──normalize_lfq: True
1:56:47.986732 INFO: │   └──save_fragment_quant_matrix: False
1:56:47.986750 INFO: ├──optimization
1:56:47.986770 INFO: │   ├──order_of_optimization: None
1:56:47.986787 INFO: │   ├──ms2_error
1:56:47.986807 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1:56:47.986825 INFO: │   │   ├──targeted_update_factor: 1.0
1:56:47.986845 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1:56:47.986864 INFO: │   │   ├──automatic_update_factor: 1.1
1:56:47.986882 INFO: │   │   ├──try_narrower_values: True
1:56:47.986902 INFO: │   │   ├──maximal_decrease: 0.5
1:56:47.986921 INFO: │   │   ├──favour_narrower_optimum: False
1:56:47.986941 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1:56:47.986959 INFO: │   ├──ms1_error
1:56:47.986977 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1:56:47.986997 INFO: │   │   ├──targeted_update_factor: 1.0
1:56:47.987015 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1:56:47.987033 INFO: │   │   ├──automatic_update_factor: 1.1
1:56:47.987051 INFO: │   │   ├──try_narrower_values: False
1:56:47.987070 INFO: │   │   ├──maximal_decrease: 0.2
1:56:47.987088 INFO: │   │   ├──favour_narrower_optimum: False
1:56:47.987107 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1:56:47.987124 INFO: │   ├──mobility_error
1:56:47.987142 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1:56:47.987160 INFO: │   │   ├──targeted_update_factor: 1.0
1:56:47.987187 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1:56:47.987206 INFO: │   │   ├──automatic_update_factor: 1.1
1:56:47.987224 INFO: │   │   ├──try_narrower_values: False
1:56:47.987243 INFO: │   │   ├──maximal_decrease: 0.2
1:56:47.987262 INFO: │   │   ├──favour_narrower_optimum: False
1:56:47.987280 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1:56:47.987298 INFO: │   └──rt_error
1:56:47.987316 INFO: │       ├──targeted_update_percentile_range: 0.95
1:56:47.987334 INFO: │       ├──targeted_update_factor: 1.0
1:56:47.987355 INFO: │       ├──automatic_update_percentile_range: 0.99
1:56:47.987374 INFO: │       ├──automatic_update_factor: 1.1
1:56:47.987392 INFO: │       ├──try_narrower_values: True
1:56:47.987410 INFO: │       ├──maximal_decrease: 0.2
1:56:47.987428 INFO: │       ├──favour_narrower_optimum: True
1:56:47.987447 INFO: │       └──maximum_decrease_from_maximum: 0.1
1:56:47.987465 INFO: ├──optimization_manager
1:56:47.987484 INFO: │   ├──fwhm_rt: 5
1:56:47.987502 INFO: │   ├──fwhm_mobility: 0.01
1:56:47.987520 INFO: │   └──score_cutoff: 0
1:56:47.987540 INFO: ├──transfer_library
1:56:47.987558 INFO: │   ├──enabled: False
1:56:47.987576 INFO: │   ├──fragment_types:
1:56:47.987595 INFO: │   │   [32;20m- b[0m
1:56:47.987613 INFO: │   │   [32;20m- y[0m
1:56:47.987633 INFO: │   ├──max_charge: 2
1:56:47.987653 INFO: │   ├──top_k_samples: 3
1:56:47.987671 INFO: │   ├──norm_delta_max: True
1:56:47.987690 INFO: │   ├──precursor_correlation_cutoff: 0.5
1:56:47.987709 INFO: │   └──fragment_correlation_ratio: 0.75
1:56:47.987727 INFO: └──transfer_learning
1:56:47.987747 INFO:     ├──enabled: False
1:56:47.987766 INFO:     ├──batch_size: 2000
1:56:47.987784 INFO:     ├──max_lr: 0.0001
1:56:47.987803 INFO:     ├──train_fraction: 0.7
1:56:47.987822 INFO:     ├──validation_fraction: 0.2
1:56:47.987840 INFO:     ├──test_fraction: 0.1
1:56:47.987859 INFO:     ├──test_interval: 1
1:56:47.987878 INFO:     ├──lr_patience: 3
1:56:47.987898 INFO:     [32;20m├──epochs: 20 [user defined, default: 51][0m
1:56:47.987917 INFO:     ├──warmup_epochs: 5
1:56:47.987934 INFO:     ├──nce: 25
1:56:47.987953 INFO:     [32;20m└──instrument: Astral [user defined, default: Lumos][0m
1:56:47.993839 INFO: Registering 7 custom modifications
1:56:48.009890 INFO: Running DynamicLoader
1:56:48.009995 INFO: Loading .hdf library from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/speclib.mbr.hdf
1:56:48.558943 INFO: Running PrecursorInitializer
1:56:48.559114 INFO: Running AnnotateFasta
1:56:48.559403 INFO: Dropping decoys from input library before annotation
1:56:48.583466 INFO: Running IsotopeGenerator
1:56:48.583798 WARNING: Input library already contains isotope information. Skipping isotope generation. 
 Please note that isotope generation outside of alphabase is not supported.
1:56:48.583849 INFO: Running RTNormalization
1:56:48.587583 INFO: Saving library to run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/speclib.hdf
1:56:49.471595 INFO: Running DecoyGenerator
1:56:57.213948 INFO: Running FlattenLibrary
1:56:58.224304 INFO: Running InitFlatColumns
1:56:58.230987 INFO: Running LogFlatLibraryStats
1:56:58.231130 INFO: ============ Library Stats ============
1:56:58.231163 INFO: Number of precursors: 247,784
1:56:58.298628 INFO: 	thereof targets:123,909
1:56:58.298785 INFO: 	thereof decoys: 123,875
1:56:58.301348 INFO: Number of elution groups: 123,909
1:56:58.301428 INFO: 	average size: 2.00
1:56:58.320081 INFO: Number of proteins: 11,998
1:56:58.321128 INFO: Number of channels: 1 ([0])
1:56:58.321229 INFO: Isotopes Distribution for 4 isotopes
1:56:58.321256 INFO: =======================================
1:56:58.321951 INFO: Searching 6 files:
1:56:58.322001 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
1:56:58.322021 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
1:56:58.322041 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
1:56:58.322058 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
1:56:58.322076 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
1:56:58.322093 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
1:56:58.322111 INFO: Using 0 fasta files:
1:56:58.322129 INFO: Using library: run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/library/speclib.mbr.hdf
1:56:58.322154 INFO: Saving output to: run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds
1:56:58.322193 PROGRESS: Starting Search Workflows
1:56:58.322250 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:56:58.322342 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant
1:56:58.322403 INFO: Creating folder run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/figures
1:56:58.323124 INFO: Initializing RawFileManager
1:57:08.471240 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
1:57:08.475920 INFO: Determining DIA cycle
1:57:08.492657 INFO: Found cycle with start 0.00 min and length 300.
1:57:08.651055 INFO: RT (min)            : 0.0 - 26.9
1:57:08.651165 INFO: RT duration (sec)   : 1611.2
1:57:08.651196 INFO: RT duration (min)   : 26.9
1:57:08.651221 INFO: Cycle len (scans)   : 300
1:57:08.651244 INFO: Cycle len (sec)     : 1.65
1:57:08.651268 INFO: Number of cycles    : 977
1:57:08.651289 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:57:08.694642 INFO: Initializing CalibrationManager
1:57:08.695009 INFO: Loading calibration config
1:57:08.695788 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'}]
1:57:08.695882 INFO: Calibration group :fragment, found 1 estimator(s)
1:57:08.695983 INFO: Calibration group :precursor, found 3 estimator(s)
1:57:08.696079 INFO: Disabling ion mobility calibration
1:57:08.696110 INFO: removed mobility estimator from group precursor
1:57:08.696268 INFO: Initializing OptimizationManager
1:57:08.696392 INFO: initial parameter: ms1_error = 30
1:57:08.696464 INFO: initial parameter: ms2_error = 30
1:57:08.696519 INFO: initial parameter: rt_error = 805.5992431640625
1:57:08.696564 INFO: initial parameter: mobility_error = 0.1
1:57:08.696606 INFO: initial parameter: column_type = library
1:57:08.696651 INFO: initial parameter: num_candidates = 1
1:57:08.696694 INFO: initial parameter: classifier_version = -1
1:57:08.696737 INFO: initial parameter: fwhm_rt = 5
1:57:08.696777 INFO: initial parameter: fwhm_mobility = 0.01
1:57:08.696817 INFO: initial parameter: score_cutoff = 0
1:57:08.696893 INFO: Initializing TimingManager
1:57:08.696955 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:57:08.697117 INFO: FDRManager not loaded from disk.
1:57:08.697144 INFO: Initializing FDRManager
1:57:08.697190 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:57:08.735386 PROGRESS: 123,909 target precursors potentially observable (0 removed)
1:57:08.789857 PROGRESS: Starting initial search for precursors.
1:57:08.798249 INFO: Starting optimization step 0.
1:57:08.798430 PROGRESS: === Extracting elution groups 0 to 200 ===
1:57:08.798506 PROGRESS: Extracting batch of 392 precursors
1:57:08.799607 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:08.799661 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:08.799704 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:57:08.799727 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:57:08.800054 INFO: Starting candidate selection
1:57:08.939562 INFO: Starting candidate scoring
1:57:08.978451 INFO: Finished candidate processing
1:57:08.978532 INFO: Collecting candidate features
1:57:08.987114 INFO: Collecting fragment features
1:57:08.989281 INFO: Finished candidate scoring
1:57:08.990045 PROGRESS: === Extracted 392 precursors and 4291 fragments ===
1:57:08.990321 INFO: performing precursor FDR with 47 features
1:57:08.990357 INFO: Decoy channel: -1
1:57:08.990381 INFO: Competetive: True
1:57:08.991416 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:09.011395 INFO: Test AUC: 0.481
1:57:09.011460 INFO: Train AUC: 0.503
1:57:09.011489 INFO: AUC difference: 4.42%
1:57:09.215883 INFO: Resetting torch num_threads to 100
1:57:09.216656 INFO: === FDR correction performed with classifier version -1 ===
1:57:09.217465 PROGRESS: ============================= Precursor FDR =============================
1:57:09.217559 PROGRESS: Total precursors accumulated: 1
1:57:09.217623 PROGRESS: Target precursors: 1 (100.00%)
1:57:09.217677 PROGRESS: Decoy precursors: 0 (0.00%)
1:57:09.217739 PROGRESS: 
1:57:09.217788 PROGRESS: Precursor Summary:
1:57:09.218741 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:57:09.218827 PROGRESS: 
1:57:09.218885 PROGRESS: Protein Summary:
1:57:09.219921 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:57:09.220008 PROGRESS: =========================================================================
1:57:09.224718 INFO: Starting optimization step 1.
1:57:09.224826 PROGRESS: === Extracting elution groups 200 to 600 ===
1:57:09.224893 PROGRESS: Extracting batch of 771 precursors
1:57:09.225802 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:09.225852 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:09.225885 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:57:09.225910 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:57:09.226104 INFO: Starting candidate selection
1:57:09.371324 INFO: Starting candidate scoring
1:57:09.412097 INFO: Finished candidate processing
1:57:09.412179 INFO: Collecting candidate features
1:57:09.421658 INFO: Collecting fragment features
1:57:09.424222 INFO: Finished candidate scoring
1:57:09.426998 PROGRESS: === Extracted 1163 precursors and 12637 fragments ===
1:57:09.427779 INFO: performing precursor FDR with 47 features
1:57:09.427824 INFO: Decoy channel: -1
1:57:09.427848 INFO: Competetive: True
1:57:09.431928 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:09.453322 INFO: Test AUC: 0.534
1:57:09.453395 INFO: Train AUC: 0.479
1:57:09.453427 INFO: AUC difference: 11.52%
1:57:09.453449 WARNING: AUC difference > 5%. This may indicate overfitting.
1:57:09.633617 INFO: Resetting torch num_threads to 100
1:57:09.634415 INFO: === FDR correction performed with classifier version -1 ===
1:57:09.635210 PROGRESS: ============================= Precursor FDR =============================
1:57:09.635307 PROGRESS: Total precursors accumulated: 1
1:57:09.635370 PROGRESS: Target precursors: 1 (100.00%)
1:57:09.635422 PROGRESS: Decoy precursors: 0 (0.00%)
1:57:09.635479 PROGRESS: 
1:57:09.635523 PROGRESS: Precursor Summary:
1:57:09.636497 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:57:09.636586 PROGRESS: 
1:57:09.636641 PROGRESS: Protein Summary:
1:57:09.637679 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:57:09.637767 PROGRESS: =========================================================================
1:57:09.643746 INFO: Starting optimization step 2.
1:57:09.643863 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:57:09.643928 PROGRESS: Extracting batch of 1538 precursors
1:57:09.644886 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:09.644938 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:09.644970 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:57:09.644993 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:57:09.645169 INFO: Starting candidate selection
1:57:09.822325 INFO: Starting candidate scoring
1:57:09.865226 INFO: Finished candidate processing
1:57:09.865311 INFO: Collecting candidate features
1:57:09.875475 INFO: Collecting fragment features
1:57:09.878259 INFO: Finished candidate scoring
1:57:09.881285 PROGRESS: === Extracted 2701 precursors and 29333 fragments ===
1:57:09.882233 INFO: performing precursor FDR with 47 features
1:57:09.882279 INFO: Decoy channel: -1
1:57:09.882304 INFO: Competetive: True
1:57:09.885678 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:09.926639 INFO: Test AUC: 0.452
1:57:09.926732 INFO: Train AUC: 0.497
1:57:09.926763 INFO: AUC difference: 9.06%
1:57:09.926784 WARNING: AUC difference > 5%. This may indicate overfitting.
1:57:10.104069 INFO: Resetting torch num_threads to 100
1:57:10.104861 INFO: === FDR correction performed with classifier version -1 ===
1:57:10.105634 PROGRESS: ============================= Precursor FDR =============================
1:57:10.105726 PROGRESS: Total precursors accumulated: 1,398
1:57:10.105785 PROGRESS: Target precursors: 699 (50.00%)
1:57:10.105836 PROGRESS: Decoy precursors: 699 (50.00%)
1:57:10.105883 PROGRESS: 
1:57:10.105926 PROGRESS: Precursor Summary:
1:57:10.106798 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:57:10.106885 PROGRESS: 
1:57:10.106941 PROGRESS: Protein Summary:
1:57:10.107876 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:57:10.107965 PROGRESS: =========================================================================
1:57:10.114553 INFO: Starting optimization step 3.
1:57:10.114670 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:57:10.114733 PROGRESS: Extracting batch of 3065 precursors
1:57:10.115799 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:10.115849 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:10.115882 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:57:10.115909 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:57:10.116077 INFO: Starting candidate selection
1:57:10.367992 INFO: Starting candidate scoring
1:57:10.411775 INFO: Finished candidate processing
1:57:10.411872 INFO: Collecting candidate features
1:57:10.423907 INFO: Collecting fragment features
1:57:10.427700 INFO: Finished candidate scoring
1:57:10.432747 PROGRESS: === Extracted 5766 precursors and 62466 fragments ===
1:57:10.433985 INFO: performing precursor FDR with 47 features
1:57:10.434031 INFO: Decoy channel: -1
1:57:10.434057 INFO: Competetive: True
1:57:10.437985 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:10.470141 INFO: Test AUC: 0.497
1:57:10.470242 INFO: Train AUC: 0.503
1:57:10.470272 INFO: AUC difference: 1.16%
1:57:10.649645 INFO: Resetting torch num_threads to 100
1:57:10.650450 INFO: === FDR correction performed with classifier version -1 ===
1:57:10.651158 PROGRESS: ============================= Precursor FDR =============================
1:57:10.651247 PROGRESS: Total precursors accumulated: 1
1:57:10.651306 PROGRESS: Target precursors: 1 (100.00%)
1:57:10.651359 PROGRESS: Decoy precursors: 0 (0.00%)
1:57:10.651414 PROGRESS: 
1:57:10.651459 PROGRESS: Precursor Summary:
1:57:10.652404 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:57:10.652493 PROGRESS: 
1:57:10.652549 PROGRESS: Protein Summary:
1:57:10.653558 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:57:10.653647 PROGRESS: =========================================================================
1:57:10.663128 INFO: Starting optimization step 4.
1:57:10.663263 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:57:10.663328 PROGRESS: Extracting batch of 6167 precursors
1:57:10.664694 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:10.664745 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:10.664776 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:57:10.664797 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:57:10.664971 INFO: Starting candidate selection
1:57:11.073073 INFO: Starting candidate scoring
1:57:11.122425 INFO: Finished candidate processing
1:57:11.122529 INFO: Collecting candidate features
1:57:11.138850 INFO: Collecting fragment features
1:57:11.144765 INFO: Finished candidate scoring
1:57:11.153437 PROGRESS: === Extracted 11933 precursors and 129166 fragments ===
1:57:11.155393 INFO: performing precursor FDR with 47 features
1:57:11.155452 INFO: Decoy channel: -1
1:57:11.155477 INFO: Competetive: True
1:57:11.161165 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:11.212510 INFO: Test AUC: 0.503
1:57:11.212622 INFO: Train AUC: 0.502
1:57:11.212652 INFO: AUC difference: 0.08%
1:57:11.396353 INFO: Resetting torch num_threads to 100
1:57:11.397348 INFO: === FDR correction performed with classifier version -1 ===
1:57:11.398046 PROGRESS: ============================= Precursor FDR =============================
1:57:11.398138 PROGRESS: Total precursors accumulated: 1
1:57:11.398197 PROGRESS: Target precursors: 1 (100.00%)
1:57:11.398248 PROGRESS: Decoy precursors: 0 (0.00%)
1:57:11.398294 PROGRESS: 
1:57:11.398338 PROGRESS: Precursor Summary:
1:57:11.399263 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:57:11.399349 PROGRESS: 
1:57:11.399402 PROGRESS: Protein Summary:
1:57:11.400436 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:57:11.400526 PROGRESS: =========================================================================
1:57:11.415795 INFO: Starting optimization step 5.
1:57:11.416038 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:57:11.416105 PROGRESS: Extracting batch of 12312 precursors
1:57:11.418354 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:11.418407 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:11.418441 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:57:11.418467 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:57:11.418653 INFO: Starting candidate selection
1:57:12.155808 INFO: Starting candidate scoring
1:57:12.238433 INFO: Finished candidate processing
1:57:12.238546 INFO: Collecting candidate features
1:57:12.267466 INFO: Collecting fragment features
1:57:12.278481 INFO: Finished candidate scoring
1:57:12.291603 PROGRESS: === Extracted 24245 precursors and 262867 fragments ===
1:57:12.295139 INFO: performing precursor FDR with 47 features
1:57:12.295212 INFO: Decoy channel: -1
1:57:12.295238 INFO: Competetive: True
1:57:12.304495 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:12.575480 INFO: Test AUC: 0.758
1:57:12.575613 INFO: Train AUC: 0.770
1:57:12.575643 INFO: AUC difference: 1.62%
1:57:12.764741 INFO: Resetting torch num_threads to 100
1:57:12.766184 INFO: === FDR correction performed with classifier version -1 ===
1:57:12.767010 PROGRESS: ============================= Precursor FDR =============================
1:57:12.767101 PROGRESS: Total precursors accumulated: 1,702
1:57:12.767162 PROGRESS: Target precursors: 1,586 (93.18%)
1:57:12.767214 PROGRESS: Decoy precursors: 116 (6.82%)
1:57:12.767262 PROGRESS: 
1:57:12.767304 PROGRESS: Precursor Summary:
1:57:12.768200 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:57:12.768306 PROGRESS: 
1:57:12.768362 PROGRESS: Protein Summary:
1:57:12.769309 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:57:12.769408 PROGRESS: =========================================================================
1:57:12.791687 INFO: Starting optimization step 6.
1:57:12.791980 PROGRESS: === Extracting elution groups 12600 to 25400 ===
1:57:12.792048 PROGRESS: Extracting batch of 24645 precursors
1:57:12.797374 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:12.797442 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:12.797476 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:57:12.797499 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:57:12.797696 INFO: Starting candidate selection
1:57:14.230821 INFO: Starting candidate scoring
1:57:14.420321 INFO: Finished candidate processing
1:57:14.420437 INFO: Collecting candidate features
1:57:14.478140 INFO: Collecting fragment features
1:57:14.495776 INFO: Finished candidate scoring
1:57:14.533687 PROGRESS: === Extracted 48890 precursors and 530567 fragments ===
1:57:14.541955 INFO: performing precursor FDR with 47 features
1:57:14.542061 INFO: Decoy channel: -1
1:57:14.542089 INFO: Competetive: True
1:57:14.566447 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:15.537930 INFO: Test AUC: 0.821
1:57:15.538081 INFO: Train AUC: 0.822
1:57:15.538112 INFO: AUC difference: 0.16%
1:57:15.741903 INFO: Resetting torch num_threads to 100
1:57:15.745245 INFO: === FDR correction performed with classifier version -1 ===
1:57:15.747745 PROGRESS: ============================= Precursor FDR =============================
1:57:15.747874 PROGRESS: Total precursors accumulated: 14,156
1:57:15.747940 PROGRESS: Target precursors: 13,405 (94.69%)
1:57:15.747993 PROGRESS: Decoy precursors: 751 (5.31%)
1:57:15.748039 PROGRESS: 
1:57:15.748083 PROGRESS: Precursor Summary:
1:57:15.752028 PROGRESS: Channel   0:	 0.05 FDR: 12,950; 0.01 FDR: 9,946; 0.001 FDR: 6,005
1:57:15.752145 PROGRESS: 
1:57:15.752203 PROGRESS: Protein Summary:
1:57:15.758291 PROGRESS: Channel   0:	 0.05 FDR: 5,429; 0.01 FDR: 4,334; 0.001 FDR: 3,060
1:57:15.758415 PROGRESS: =========================================================================
1:57:15.816018 INFO: fragments_df: keeping 5000 of 530567 [sum(precursor_idx_mask)=112520 sum(mass_error_mask)=530567 stop_rank=5000
1:57:15.854201 INFO: calibration group: precursor, fitting rt estimator 
1:57:17.720261 INFO: calibration group: fragment, fitting mz estimator 
1:57:18.412258 INFO: Using score_cutoff 58.93826196670532 (fac=0.99, q=1)
1:57:18.412921 INFO: calibration group: precursor, predicting mz
1:57:18.413011 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:18.413045 INFO: calibration group: precursor, predicting rt
1:57:18.414742 INFO: calibration group: fragment, predicting mz
1:57:18.416938 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:57:18.417053 INFO: Starting optimization step 7.
1:57:18.417120 PROGRESS: === Extracting elution groups 0 to 600 ===
1:57:18.417178 PROGRESS: Extracting batch of 1163 precursors
1:57:18.418360 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:18.418409 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:18.418442 INFO: FWHM in RT is 3.01 seconds, sigma is 0.39
1:57:18.418464 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:57:18.418649 INFO: Starting candidate selection
1:57:18.583055 INFO: Starting candidate scoring
1:57:18.627027 INFO: Finished candidate processing
1:57:18.627124 INFO: Collecting candidate features
1:57:18.638814 INFO: Collecting fragment features
1:57:18.642280 INFO: Finished candidate scoring
1:57:18.644587 PROGRESS: === Extracted 2326 precursors and 24947 fragments ===
1:57:18.644889 INFO: performing precursor FDR with 47 features
1:57:18.644929 INFO: Decoy channel: -1
1:57:18.644952 INFO: Competetive: True
1:57:18.648103 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:18.673826 INFO: Test AUC: 0.743
1:57:18.673905 INFO: Train AUC: 0.701
1:57:18.673934 INFO: AUC difference: 5.97%
1:57:18.673955 WARNING: AUC difference > 5%. This may indicate overfitting.
1:57:18.862094 INFO: Resetting torch num_threads to 100
1:57:18.862881 INFO: === FDR correction performed with classifier version 6 ===
1:57:18.863549 PROGRESS: ============================= Precursor FDR =============================
1:57:18.863642 PROGRESS: Total precursors accumulated: 334
1:57:18.863701 PROGRESS: Target precursors: 320 (95.81%)
1:57:18.863770 PROGRESS: Decoy precursors: 14 (4.19%)
1:57:18.863817 PROGRESS: 
1:57:18.863863 PROGRESS: Precursor Summary:
1:57:18.864928 PROGRESS: Channel   0:	 0.05 FDR:   320; 0.01 FDR:   250; 0.001 FDR:   221
1:57:18.865020 PROGRESS: 
1:57:18.865076 PROGRESS: Protein Summary:
1:57:18.866460 PROGRESS: Channel   0:	 0.05 FDR:   310; 0.01 FDR:   243; 0.001 FDR:   218
1:57:18.866554 PROGRESS: =========================================================================
1:57:18.871015 INFO: fragments_df: keeping 2495 of 24947 [sum(precursor_idx_mask)=5507 sum(mass_error_mask)=24947 stop_rank=2495
1:57:18.877801 INFO: calibration group: precursor, fitting rt estimator 
1:57:18.992769 INFO: calibration group: fragment, fitting mz estimator 
1:57:19.273349 INFO: Using score_cutoff 55.430853384017944 (fac=0.99, q=1)
1:57:19.273784 INFO: calibration group: precursor, predicting mz
1:57:19.273867 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:19.273898 INFO: calibration group: precursor, predicting rt
1:57:19.275490 INFO: calibration group: fragment, predicting mz
1:57:19.277656 INFO: === checking if optimization conditions were reached ===
1:57:19.278969 PROGRESS: ❌ ms2_error      : 14.1997 > 6.7411 or insufficient steps taken.
1:57:19.279021 INFO: ==============================================
1:57:19.279102 INFO: Starting optimization step 8.
1:57:19.279165 PROGRESS: === Extracting elution groups 0 to 600 ===
1:57:19.279221 PROGRESS: Extracting batch of 1163 precursors
1:57:19.280137 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:19.280183 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:19.280213 INFO: FWHM in RT is 2.94 seconds, sigma is 0.38
1:57:19.280234 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:57:19.280401 INFO: Starting candidate selection
1:57:19.432878 INFO: Starting candidate scoring
1:57:19.476201 INFO: Finished candidate processing
1:57:19.476296 INFO: Collecting candidate features
1:57:19.487023 INFO: Collecting fragment features
1:57:19.490496 INFO: Finished candidate scoring
1:57:19.492357 PROGRESS: === Extracted 2326 precursors and 23197 fragments ===
1:57:19.492640 INFO: performing precursor FDR with 47 features
1:57:19.492679 INFO: Decoy channel: -1
1:57:19.492704 INFO: Competetive: True
1:57:19.495357 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:19.518257 INFO: Test AUC: 0.741
1:57:19.518337 INFO: Train AUC: 0.722
1:57:19.518368 INFO: AUC difference: 2.57%
1:57:19.696105 INFO: Resetting torch num_threads to 100
1:57:19.696757 INFO: === FDR correction performed with classifier version 7 ===
1:57:19.697398 PROGRESS: ============================= Precursor FDR =============================
1:57:19.697488 PROGRESS: Total precursors accumulated: 415
1:57:19.697548 PROGRESS: Target precursors: 401 (96.63%)
1:57:19.697604 PROGRESS: Decoy precursors: 14 (3.37%)
1:57:19.697652 PROGRESS: 
1:57:19.697697 PROGRESS: Precursor Summary:
1:57:19.698684 PROGRESS: Channel   0:	 0.05 FDR:   401; 0.01 FDR:   308; 0.001 FDR:   278
1:57:19.698774 PROGRESS: 
1:57:19.698830 PROGRESS: Protein Summary:
1:57:19.699988 PROGRESS: Channel   0:	 0.05 FDR:   383; 0.01 FDR:   298; 0.001 FDR:   271
1:57:19.700078 PROGRESS: =========================================================================
1:57:19.703174 INFO: fragments_df: keeping 2894 of 23197 [sum(precursor_idx_mask)=6503 sum(mass_error_mask)=23197 stop_rank=2894
1:57:19.708744 INFO: calibration group: precursor, fitting rt estimator 
1:57:19.804173 INFO: calibration group: fragment, fitting mz estimator 
1:57:20.127176 INFO: Using score_cutoff 51.03480861968994 (fac=0.99, q=1)
1:57:20.127597 INFO: calibration group: precursor, predicting mz
1:57:20.127682 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:20.127715 INFO: calibration group: precursor, predicting rt
1:57:20.129301 INFO: calibration group: fragment, predicting mz
1:57:20.131454 INFO: === checking if optimization conditions were reached ===
1:57:20.132776 PROGRESS: ❌ ms2_error      : 7.7344 > 6.7411 or insufficient steps taken.
1:57:20.132831 INFO: ==============================================
1:57:20.132914 INFO: Starting optimization step 9.
1:57:20.132978 PROGRESS: === Extracting elution groups 0 to 600 ===
1:57:20.133036 PROGRESS: Extracting batch of 1163 precursors
1:57:20.133951 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:20.133999 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:20.134030 INFO: FWHM in RT is 2.57 seconds, sigma is 0.33
1:57:20.134051 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:57:20.134213 INFO: Starting candidate selection
1:57:20.276848 INFO: Starting candidate scoring
1:57:20.320551 INFO: Finished candidate processing
1:57:20.320637 INFO: Collecting candidate features
1:57:20.331370 INFO: Collecting fragment features
1:57:20.334840 INFO: Finished candidate scoring
1:57:20.336802 PROGRESS: === Extracted 2325 precursors and 20711 fragments ===
1:57:20.337091 INFO: performing precursor FDR with 47 features
1:57:20.337129 INFO: Decoy channel: -1
1:57:20.337153 INFO: Competetive: True
1:57:20.339759 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:20.364201 INFO: Test AUC: 0.715
1:57:20.364283 INFO: Train AUC: 0.728
1:57:20.364314 INFO: AUC difference: 1.82%
1:57:20.543993 INFO: Resetting torch num_threads to 100
1:57:20.544678 INFO: === FDR correction performed with classifier version 8 ===
1:57:20.545339 PROGRESS: ============================= Precursor FDR =============================
1:57:20.545429 PROGRESS: Total precursors accumulated: 416
1:57:20.545489 PROGRESS: Target precursors: 397 (95.43%)
1:57:20.545547 PROGRESS: Decoy precursors: 19 (4.57%)
1:57:20.545594 PROGRESS: 
1:57:20.545638 PROGRESS: Precursor Summary:
1:57:20.546636 PROGRESS: Channel   0:	 0.05 FDR:   397; 0.01 FDR:   327; 0.001 FDR:   291
1:57:20.546725 PROGRESS: 
1:57:20.546780 PROGRESS: Protein Summary:
1:57:20.547923 PROGRESS: Channel   0:	 0.05 FDR:   380; 0.01 FDR:   316; 0.001 FDR:   284
1:57:20.548013 PROGRESS: =========================================================================
1:57:20.551112 INFO: fragments_df: keeping 3040 of 20711 [sum(precursor_idx_mask)=6438 sum(mass_error_mask)=20711 stop_rank=3040
1:57:20.556770 INFO: calibration group: precursor, fitting rt estimator 
1:57:20.659889 INFO: calibration group: fragment, fitting mz estimator 
1:57:21.005387 INFO: Using score_cutoff 44.871142957305906 (fac=0.99, q=1)
1:57:21.005815 INFO: calibration group: precursor, predicting mz
1:57:21.005908 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:21.005952 INFO: calibration group: precursor, predicting rt
1:57:21.007549 INFO: calibration group: fragment, predicting mz
1:57:21.009724 INFO: === checking if optimization conditions were reached ===
1:57:21.011049 PROGRESS: ✅ ms2_error      : 6.7411 <= 6.7411
1:57:21.011103 INFO: ==============================================
1:57:21.011187 PROGRESS: Optimization finished for ms2_error.
1:57:21.016875 INFO: calibration group: precursor, predicting mz
1:57:21.017002 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:21.017034 INFO: calibration group: precursor, predicting rt
1:57:21.018273 INFO: calibration group: fragment, predicting mz
1:57:21.020437 INFO: Starting optimization step 0.
1:57:21.020538 PROGRESS: === Extracting elution groups 0 to 600 ===
1:57:21.020599 PROGRESS: Extracting batch of 1163 precursors
1:57:21.021470 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:21.021519 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:21.021553 INFO: FWHM in RT is 2.39 seconds, sigma is 0.31
1:57:21.021575 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:57:21.021741 INFO: Starting candidate selection
1:57:21.187134 INFO: Starting candidate scoring
1:57:21.231448 INFO: Finished candidate processing
1:57:21.231536 INFO: Collecting candidate features
1:57:21.243231 INFO: Collecting fragment features
1:57:21.248042 INFO: Finished candidate scoring
1:57:21.249884 PROGRESS: === Extracted 2325 precursors and 20114 fragments ===
1:57:21.250177 INFO: performing precursor FDR with 47 features
1:57:21.250214 INFO: Decoy channel: -1
1:57:21.250239 INFO: Competetive: True
1:57:21.253239 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:21.280232 INFO: Test AUC: 0.718
1:57:21.280326 INFO: Train AUC: 0.724
1:57:21.280356 INFO: AUC difference: 0.90%
1:57:21.466365 INFO: Resetting torch num_threads to 100
1:57:21.467307 INFO: === FDR correction performed with classifier version 9 ===
1:57:21.468011 PROGRESS: ============================= Precursor FDR =============================
1:57:21.468108 PROGRESS: Total precursors accumulated: 416
1:57:21.468167 PROGRESS: Target precursors: 398 (95.67%)
1:57:21.468219 PROGRESS: Decoy precursors: 18 (4.33%)
1:57:21.468277 PROGRESS: 
1:57:21.468324 PROGRESS: Precursor Summary:
1:57:21.469334 PROGRESS: Channel   0:	 0.05 FDR:   398; 0.01 FDR:   292; 0.001 FDR:   231
1:57:21.469423 PROGRESS: 
1:57:21.469478 PROGRESS: Protein Summary:
1:57:21.470661 PROGRESS: Channel   0:	 0.05 FDR:   381; 0.01 FDR:   283; 0.001 FDR:   226
1:57:21.470757 PROGRESS: =========================================================================
1:57:21.473796 INFO: fragments_df: keeping 2793 of 20114 [sum(precursor_idx_mask)=5718 sum(mass_error_mask)=20114 stop_rank=2793
1:57:21.480194 INFO: calibration group: precursor, fitting rt estimator 
1:57:21.578637 INFO: calibration group: fragment, fitting mz estimator 
1:57:21.900577 INFO: Using score_cutoff 46.68670504646301 (fac=0.99, q=1)
1:57:21.901199 INFO: calibration group: precursor, predicting mz
1:57:21.901288 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:21.901320 INFO: calibration group: precursor, predicting rt
1:57:21.903318 INFO: calibration group: fragment, predicting mz
1:57:21.905522 INFO: === checking if optimization conditions were reached ===
1:57:21.905638 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:57:21.907248 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 110.6275.
1:57:21.907300 INFO: ==============================================
1:57:21.907390 INFO: Starting optimization step 1.
1:57:21.907455 PROGRESS: === Extracting elution groups 0 to 600 ===
1:57:21.907516 PROGRESS: Extracting batch of 1163 precursors
1:57:21.908692 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:21.908741 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:21.908777 INFO: FWHM in RT is 2.38 seconds, sigma is 0.31
1:57:21.908800 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:57:21.909005 INFO: Starting candidate selection
1:57:22.031020 INFO: Starting candidate scoring
1:57:22.076514 INFO: Finished candidate processing
1:57:22.076596 INFO: Collecting candidate features
1:57:22.089755 INFO: Collecting fragment features
1:57:22.094368 INFO: Finished candidate scoring
1:57:22.096295 PROGRESS: === Extracted 2324 precursors and 19160 fragments ===
1:57:22.096632 INFO: performing precursor FDR with 47 features
1:57:22.096673 INFO: Decoy channel: -1
1:57:22.096701 INFO: Competetive: True
1:57:22.099912 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:22.125676 INFO: Test AUC: 0.704
1:57:22.125755 INFO: Train AUC: 0.727
1:57:22.125785 INFO: AUC difference: 3.12%
1:57:22.310064 INFO: Resetting torch num_threads to 100
1:57:22.310695 INFO: === FDR correction performed with classifier version 9 ===
1:57:22.311364 PROGRESS: ============================= Precursor FDR =============================
1:57:22.311452 PROGRESS: Total precursors accumulated: 409
1:57:22.311511 PROGRESS: Target precursors: 391 (95.60%)
1:57:22.311561 PROGRESS: Decoy precursors: 18 (4.40%)
1:57:22.311605 PROGRESS: 
1:57:22.311649 PROGRESS: Precursor Summary:
1:57:22.312649 PROGRESS: Channel   0:	 0.05 FDR:   391; 0.01 FDR:   312; 0.001 FDR:   198
1:57:22.312740 PROGRESS: 
1:57:22.312794 PROGRESS: Protein Summary:
1:57:22.313946 PROGRESS: Channel   0:	 0.05 FDR:   375; 0.01 FDR:   303; 0.001 FDR:   195
1:57:22.314034 PROGRESS: =========================================================================
1:57:22.316907 INFO: fragments_df: keeping 2870 of 19160 [sum(precursor_idx_mask)=5957 sum(mass_error_mask)=19160 stop_rank=2870
1:57:22.322606 INFO: calibration group: precursor, fitting rt estimator 
1:57:22.427636 INFO: calibration group: fragment, fitting mz estimator 
1:57:22.748598 INFO: Using score_cutoff 32.89496018829346 (fac=0.99, q=1)
1:57:22.749032 INFO: calibration group: precursor, predicting mz
1:57:22.749127 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:22.749158 INFO: calibration group: precursor, predicting rt
1:57:22.750705 INFO: calibration group: fragment, predicting mz
1:57:22.752925 INFO: === checking if optimization conditions were reached ===
1:57:22.753046 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:57:22.754563 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 44.7996.
1:57:22.754615 INFO: ==============================================
1:57:22.754702 INFO: Starting optimization step 2.
1:57:22.754767 PROGRESS: === Extracting elution groups 0 to 600 ===
1:57:22.754823 PROGRESS: Extracting batch of 1163 precursors
1:57:22.755764 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:22.755846 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:22.755887 INFO: FWHM in RT is 2.37 seconds, sigma is 0.30
1:57:22.755916 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:57:22.756086 INFO: Starting candidate selection
1:57:22.873608 INFO: Starting candidate scoring
1:57:22.918509 INFO: Finished candidate processing
1:57:22.918593 INFO: Collecting candidate features
1:57:22.929986 INFO: Collecting fragment features
1:57:22.934921 INFO: Finished candidate scoring
1:57:22.936704 PROGRESS: === Extracted 2318 precursors and 18393 fragments ===
1:57:22.936989 INFO: performing precursor FDR with 47 features
1:57:22.937027 INFO: Decoy channel: -1
1:57:22.937051 INFO: Competetive: True
1:57:22.939703 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:22.962290 INFO: Test AUC: 0.747
1:57:22.962366 INFO: Train AUC: 0.732
1:57:22.962395 INFO: AUC difference: 2.13%
1:57:23.139540 INFO: Resetting torch num_threads to 100
1:57:23.140173 INFO: === FDR correction performed with classifier version 9 ===
1:57:23.140826 PROGRESS: ============================= Precursor FDR =============================
1:57:23.140919 PROGRESS: Total precursors accumulated: 431
1:57:23.140978 PROGRESS: Target precursors: 412 (95.59%)
1:57:23.141030 PROGRESS: Decoy precursors: 19 (4.41%)
1:57:23.141075 PROGRESS: 
1:57:23.141121 PROGRESS: Precursor Summary:
1:57:23.142132 PROGRESS: Channel   0:	 0.05 FDR:   412; 0.01 FDR:   261; 0.001 FDR:   230
1:57:23.142221 PROGRESS: 
1:57:23.142275 PROGRESS: Protein Summary:
1:57:23.143439 PROGRESS: Channel   0:	 0.05 FDR:   394; 0.01 FDR:   256; 0.001 FDR:   226
1:57:23.143528 PROGRESS: =========================================================================
1:57:23.146236 INFO: fragments_df: keeping 2480 of 18393 [sum(precursor_idx_mask)=4998 sum(mass_error_mask)=18393 stop_rank=2480
1:57:23.151706 INFO: calibration group: precursor, fitting rt estimator 
1:57:23.253784 INFO: calibration group: fragment, fitting mz estimator 
1:57:23.531942 INFO: Using score_cutoff 47.013478500366205 (fac=0.99, q=1)
1:57:23.532380 INFO: calibration group: precursor, predicting mz
1:57:23.532468 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:23.532498 INFO: calibration group: precursor, predicting rt
1:57:23.534038 INFO: calibration group: fragment, predicting mz
1:57:23.536165 INFO: === checking if optimization conditions were reached ===
1:57:23.536278 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:57:23.537854 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 34.6174.
1:57:23.537907 INFO: ==============================================
1:57:23.537990 INFO: Starting optimization step 3.
1:57:23.538059 PROGRESS: === Extracting elution groups 0 to 600 ===
1:57:23.538114 PROGRESS: Extracting batch of 1163 precursors
1:57:23.538982 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:23.539029 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:23.539060 INFO: FWHM in RT is 2.36 seconds, sigma is 0.30
1:57:23.539081 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:57:23.539237 INFO: Starting candidate selection
1:57:23.657862 INFO: Starting candidate scoring
1:57:23.702250 INFO: Finished candidate processing
1:57:23.702336 INFO: Collecting candidate features
1:57:23.710976 WARNING: intensity_correlation has 2 NaNs ( 0.09 % out of 2307)
1:57:23.714009 INFO: Collecting fragment features
1:57:23.718048 INFO: Finished candidate scoring
1:57:23.719802 PROGRESS: === Extracted 2307 precursors and 18005 fragments ===
1:57:23.720099 INFO: performing precursor FDR with 47 features
1:57:23.720136 INFO: Decoy channel: -1
1:57:23.720160 INFO: Competetive: True
1:57:23.722919 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:23.724164 WARNING: dropped 2 decoy PSMs due to missing features
1:57:23.746049 INFO: Test AUC: 0.750
1:57:23.746126 INFO: Train AUC: 0.715
1:57:23.746156 INFO: AUC difference: 4.95%
1:57:23.922481 INFO: Resetting torch num_threads to 100
1:57:23.923096 INFO: === FDR correction performed with classifier version 9 ===
1:57:23.923751 PROGRESS: ============================= Precursor FDR =============================
1:57:23.923841 PROGRESS: Total precursors accumulated: 416
1:57:23.923901 PROGRESS: Target precursors: 396 (95.19%)
1:57:23.923952 PROGRESS: Decoy precursors: 20 (4.81%)
1:57:23.923997 PROGRESS: 
1:57:23.924041 PROGRESS: Precursor Summary:
1:57:23.925078 PROGRESS: Channel   0:	 0.05 FDR:   389; 0.01 FDR:   229; 0.001 FDR:   210
1:57:23.925169 PROGRESS: 
1:57:23.925224 PROGRESS: Protein Summary:
1:57:23.926358 PROGRESS: Channel   0:	 0.05 FDR:   372; 0.01 FDR:   225; 0.001 FDR:   207
1:57:23.926446 PROGRESS: =========================================================================
1:57:23.929031 INFO: fragments_df: keeping 2218 of 18005 [sum(precursor_idx_mask)=4413 sum(mass_error_mask)=18005 stop_rank=2218
1:57:23.934437 INFO: calibration group: precursor, fitting rt estimator 
1:57:24.031395 INFO: calibration group: fragment, fitting mz estimator 
1:57:24.281953 INFO: Using score_cutoff 47.6402992904663 (fac=0.99, q=1)
1:57:24.282385 INFO: calibration group: precursor, predicting mz
1:57:24.282470 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:24.282501 INFO: calibration group: precursor, predicting rt
1:57:24.284076 INFO: calibration group: fragment, predicting mz
1:57:24.286254 INFO: === checking if optimization conditions were reached ===
1:57:24.286362 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:57:24.287936 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 26.0154.
1:57:24.287993 INFO: ==============================================
1:57:24.288078 INFO: Starting optimization step 4.
1:57:24.288147 PROGRESS: === Extracting elution groups 0 to 600 ===
1:57:24.288203 PROGRESS: Extracting batch of 1163 precursors
1:57:24.289102 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:24.289152 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:24.289192 INFO: FWHM in RT is 2.38 seconds, sigma is 0.31
1:57:24.289214 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:57:24.289374 INFO: Starting candidate selection
1:57:24.407307 INFO: Starting candidate scoring
1:57:24.452537 INFO: Finished candidate processing
1:57:24.452620 INFO: Collecting candidate features
1:57:24.463807 INFO: Collecting fragment features
1:57:24.467661 INFO: Finished candidate scoring
1:57:24.469260 PROGRESS: === Extracted 2238 precursors and 16778 fragments ===
1:57:24.469530 INFO: performing precursor FDR with 47 features
1:57:24.469567 INFO: Decoy channel: -1
1:57:24.469589 INFO: Competetive: True
1:57:24.472107 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:24.493600 INFO: Test AUC: 0.741
1:57:24.493679 INFO: Train AUC: 0.710
1:57:24.493712 INFO: AUC difference: 4.35%
1:57:24.675748 INFO: Resetting torch num_threads to 100
1:57:24.676375 INFO: === FDR correction performed with classifier version 9 ===
1:57:24.677030 PROGRESS: ============================= Precursor FDR =============================
1:57:24.677124 PROGRESS: Total precursors accumulated: 416
1:57:24.677191 PROGRESS: Target precursors: 394 (94.71%)
1:57:24.677253 PROGRESS: Decoy precursors: 22 (5.29%)
1:57:24.677308 PROGRESS: 
1:57:24.677359 PROGRESS: Precursor Summary:
1:57:24.678403 PROGRESS: Channel   0:	 0.05 FDR:   373; 0.01 FDR:   248; 0.001 FDR:   184
1:57:24.678504 PROGRESS: 
1:57:24.678574 PROGRESS: Protein Summary:
1:57:24.679765 PROGRESS: Channel   0:	 0.05 FDR:   358; 0.01 FDR:   243; 0.001 FDR:   182
1:57:24.679860 PROGRESS: =========================================================================
1:57:24.682447 INFO: fragments_df: keeping 2294 of 16778 [sum(precursor_idx_mask)=4530 sum(mass_error_mask)=16778 stop_rank=2294
1:57:24.687812 INFO: calibration group: precursor, fitting rt estimator 
1:57:24.784805 INFO: calibration group: fragment, fitting mz estimator 
1:57:25.043056 INFO: Using score_cutoff 45.933624663162234 (fac=0.99, q=1)
1:57:25.043496 INFO: calibration group: precursor, predicting mz
1:57:25.043580 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:25.043612 INFO: calibration group: precursor, predicting rt
1:57:25.045187 INFO: calibration group: fragment, predicting mz
1:57:25.047323 INFO: === checking if optimization conditions were reached ===
1:57:25.047426 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1:57:25.049017 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 21.9289.
1:57:25.049071 INFO: ==============================================
1:57:25.049154 INFO: Starting optimization step 5.
1:57:25.049219 PROGRESS: === Extracting elution groups 0 to 600 ===
1:57:25.049274 PROGRESS: Extracting batch of 1163 precursors
1:57:25.050173 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:25.050222 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:25.050254 INFO: FWHM in RT is 2.36 seconds, sigma is 0.30
1:57:25.050277 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:57:25.050433 INFO: Starting candidate selection
1:57:25.167519 INFO: Starting candidate scoring
1:57:25.210596 INFO: Finished candidate processing
1:57:25.210685 INFO: Collecting candidate features
1:57:25.219129 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2246)
1:57:25.222232 INFO: Collecting fragment features
1:57:25.226070 INFO: Finished candidate scoring
1:57:25.227697 PROGRESS: === Extracted 2246 precursors and 16812 fragments ===
1:57:25.227977 INFO: performing precursor FDR with 47 features
1:57:25.228014 INFO: Decoy channel: -1
1:57:25.228038 INFO: Competetive: True
1:57:25.230649 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:25.231889 WARNING: dropped 1 decoy PSMs due to missing features
1:57:25.254172 INFO: Test AUC: 0.739
1:57:25.254248 INFO: Train AUC: 0.718
1:57:25.254277 INFO: AUC difference: 2.92%
1:57:25.436020 INFO: Resetting torch num_threads to 100
1:57:25.436620 INFO: === FDR correction performed with classifier version 9 ===
1:57:25.437250 PROGRESS: ============================= Precursor FDR =============================
1:57:25.437341 PROGRESS: Total precursors accumulated: 400
1:57:25.437401 PROGRESS: Target precursors: 380 (95.00%)
1:57:25.437458 PROGRESS: Decoy precursors: 20 (5.00%)
1:57:25.437506 PROGRESS: 
1:57:25.437551 PROGRESS: Precursor Summary:
1:57:25.438562 PROGRESS: Channel   0:	 0.05 FDR:   349; 0.01 FDR:   234; 0.001 FDR:   180
1:57:25.438658 PROGRESS: 
1:57:25.438715 PROGRESS: Protein Summary:
1:57:25.439849 PROGRESS: Channel   0:	 0.05 FDR:   335; 0.01 FDR:   229; 0.001 FDR:   178
1:57:25.439946 PROGRESS: =========================================================================
1:57:25.442443 INFO: fragments_df: keeping 2210 of 16812 [sum(precursor_idx_mask)=4314 sum(mass_error_mask)=16812 stop_rank=2210
1:57:25.447846 INFO: calibration group: precursor, fitting rt estimator 
1:57:25.556924 INFO: calibration group: fragment, fitting mz estimator 
1:57:25.806889 INFO: Using score_cutoff 46.9381455368042 (fac=0.99, q=1)
1:57:25.807307 INFO: calibration group: precursor, predicting mz
1:57:25.807393 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:25.807425 INFO: calibration group: precursor, predicting rt
1:57:25.809006 INFO: calibration group: fragment, predicting mz
1:57:25.811132 INFO: === checking if optimization conditions were reached ===
1:57:25.811250 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1:57:25.812835 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 11.6056.
1:57:25.812892 INFO: ==============================================
1:57:25.812985 INFO: Starting optimization step 6.
1:57:25.813057 PROGRESS: === Extracting elution groups 0 to 600 ===
1:57:25.813122 PROGRESS: Extracting batch of 1163 precursors
1:57:25.814036 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:25.814088 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:25.814124 INFO: FWHM in RT is 2.36 seconds, sigma is 0.30
1:57:25.814150 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:57:25.814313 INFO: Starting candidate selection
1:57:25.931933 INFO: Starting candidate scoring
1:57:25.977096 INFO: Finished candidate processing
1:57:25.977190 INFO: Collecting candidate features
1:57:25.985614 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2257)
1:57:25.988689 INFO: Collecting fragment features
1:57:25.992776 INFO: Finished candidate scoring
1:57:25.994495 PROGRESS: === Extracted 2257 precursors and 16986 fragments ===
1:57:25.994784 INFO: performing precursor FDR with 47 features
1:57:25.994821 INFO: Decoy channel: -1
1:57:25.994843 INFO: Competetive: True
1:57:25.997476 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:25.998705 WARNING: dropped 1 decoy PSMs due to missing features
1:57:26.020609 INFO: Test AUC: 0.748
1:57:26.020676 INFO: Train AUC: 0.715
1:57:26.020705 INFO: AUC difference: 4.60%
1:57:26.202397 INFO: Resetting torch num_threads to 100
1:57:26.203004 INFO: === FDR correction performed with classifier version 9 ===
1:57:26.203648 PROGRESS: ============================= Precursor FDR =============================
1:57:26.203737 PROGRESS: Total precursors accumulated: 422
1:57:26.203796 PROGRESS: Target precursors: 396 (93.84%)
1:57:26.203849 PROGRESS: Decoy precursors: 26 (6.16%)
1:57:26.203896 PROGRESS: 
1:57:26.203939 PROGRESS: Precursor Summary:
1:57:26.204925 PROGRESS: Channel   0:	 0.05 FDR:   366; 0.01 FDR:   230; 0.001 FDR:   180
1:57:26.205015 PROGRESS: 
1:57:26.205071 PROGRESS: Protein Summary:
1:57:26.206194 PROGRESS: Channel   0:	 0.05 FDR:   352; 0.01 FDR:   226; 0.001 FDR:   178
1:57:26.206284 PROGRESS: =========================================================================
1:57:26.208857 INFO: fragments_df: keeping 2171 of 16986 [sum(precursor_idx_mask)=4336 sum(mass_error_mask)=16986 stop_rank=2171
1:57:26.214287 INFO: calibration group: precursor, fitting rt estimator 
1:57:26.306707 INFO: calibration group: fragment, fitting mz estimator 
1:57:26.554581 INFO: Using score_cutoff 46.92649091377258 (fac=0.99, q=1)
1:57:26.555014 INFO: calibration group: precursor, predicting mz
1:57:26.555098 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:26.555129 INFO: calibration group: precursor, predicting rt
1:57:26.556707 INFO: calibration group: fragment, predicting mz
1:57:26.558855 INFO: === checking if optimization conditions were reached ===
1:57:26.558954 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1:57:26.560513 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 6.5418.
1:57:26.560570 INFO: ==============================================
1:57:26.560659 INFO: Starting optimization step 7.
1:57:26.560724 PROGRESS: === Extracting elution groups 0 to 600 ===
1:57:26.560779 PROGRESS: Extracting batch of 1163 precursors
1:57:26.561668 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:26.561714 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:26.561745 INFO: FWHM in RT is 2.36 seconds, sigma is 0.30
1:57:26.561767 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:57:26.561928 INFO: Starting candidate selection
1:57:26.679744 INFO: Starting candidate scoring
1:57:26.723642 INFO: Finished candidate processing
1:57:26.723729 INFO: Collecting candidate features
1:57:26.732041 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2263)
1:57:26.735129 INFO: Collecting fragment features
1:57:26.739116 INFO: Finished candidate scoring
1:57:26.740869 PROGRESS: === Extracted 2263 precursors and 17059 fragments ===
1:57:26.741145 INFO: performing precursor FDR with 47 features
1:57:26.741179 INFO: Decoy channel: -1
1:57:26.741202 INFO: Competetive: True
1:57:26.743800 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:26.745052 WARNING: dropped 1 decoy PSMs due to missing features
1:57:26.767358 INFO: Test AUC: 0.723
1:57:26.767431 INFO: Train AUC: 0.725
1:57:26.767460 INFO: AUC difference: 0.26%
1:57:26.943828 INFO: Resetting torch num_threads to 100
1:57:26.944458 INFO: === FDR correction performed with classifier version 9 ===
1:57:26.945139 PROGRESS: ============================= Precursor FDR =============================
1:57:26.945228 PROGRESS: Total precursors accumulated: 425
1:57:26.945286 PROGRESS: Target precursors: 402 (94.59%)
1:57:26.945337 PROGRESS: Decoy precursors: 23 (5.41%)
1:57:26.945381 PROGRESS: 
1:57:26.945423 PROGRESS: Precursor Summary:
1:57:26.946363 PROGRESS: Channel   0:	 0.05 FDR:   365; 0.01 FDR:   208; 0.001 FDR:   160
1:57:26.946451 PROGRESS: 
1:57:26.946505 PROGRESS: Protein Summary:
1:57:26.947615 PROGRESS: Channel   0:	 0.05 FDR:   350; 0.01 FDR:   205; 0.001 FDR:   159
1:57:26.947702 PROGRESS: =========================================================================
1:57:26.950166 INFO: fragments_df: keeping 2060 of 17059 [sum(precursor_idx_mask)=4019 sum(mass_error_mask)=17059 stop_rank=2060
1:57:26.955528 INFO: calibration group: precursor, fitting rt estimator 
1:57:27.050229 INFO: calibration group: fragment, fitting mz estimator 
1:57:27.285925 INFO: Using score_cutoff 49.871843824768064 (fac=0.99, q=1)
1:57:27.286362 INFO: calibration group: precursor, predicting mz
1:57:27.286446 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:27.286476 INFO: calibration group: precursor, predicting rt
1:57:27.288069 INFO: calibration group: fragment, predicting mz
1:57:27.290176 INFO: === checking if optimization conditions were reached ===
1:57:27.290281 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
1:57:27.291852 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 6.1174.
1:57:27.291903 INFO: ==============================================
1:57:27.291989 INFO: Starting optimization step 8.
1:57:27.292053 PROGRESS: === Extracting elution groups 0 to 600 ===
1:57:27.292360 PROGRESS: Extracting batch of 1163 precursors
1:57:27.293270 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:27.293318 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:27.293349 INFO: FWHM in RT is 2.38 seconds, sigma is 0.31
1:57:27.293370 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:57:27.293525 INFO: Starting candidate selection
1:57:27.411234 INFO: Starting candidate scoring
1:57:27.454637 INFO: Finished candidate processing
1:57:27.454722 INFO: Collecting candidate features
1:57:27.463308 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2262)
1:57:27.466302 INFO: Collecting fragment features
1:57:27.470005 INFO: Finished candidate scoring
1:57:27.471739 PROGRESS: === Extracted 2262 precursors and 17105 fragments ===
1:57:27.472014 INFO: performing precursor FDR with 47 features
1:57:27.472052 INFO: Decoy channel: -1
1:57:27.472075 INFO: Competetive: True
1:57:27.474667 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:27.475897 WARNING: dropped 1 decoy PSMs due to missing features
1:57:27.498356 INFO: Test AUC: 0.705
1:57:27.498432 INFO: Train AUC: 0.729
1:57:27.498462 INFO: AUC difference: 3.20%
1:57:27.680479 INFO: Resetting torch num_threads to 100
1:57:27.681097 INFO: === FDR correction performed with classifier version 9 ===
1:57:27.681740 PROGRESS: ============================= Precursor FDR =============================
1:57:27.681828 PROGRESS: Total precursors accumulated: 417
1:57:27.681888 PROGRESS: Target precursors: 388 (93.05%)
1:57:27.681940 PROGRESS: Decoy precursors: 29 (6.95%)
1:57:27.681988 PROGRESS: 
1:57:27.682031 PROGRESS: Precursor Summary:
1:57:27.682985 PROGRESS: Channel   0:	 0.05 FDR:   363; 0.01 FDR:   208; 0.001 FDR:   160
1:57:27.683072 PROGRESS: 
1:57:27.683126 PROGRESS: Protein Summary:
1:57:27.684232 PROGRESS: Channel   0:	 0.05 FDR:   348; 0.01 FDR:   205; 0.001 FDR:   159
1:57:27.684340 PROGRESS: =========================================================================
1:57:27.686805 INFO: fragments_df: keeping 2065 of 17105 [sum(precursor_idx_mask)=4035 sum(mass_error_mask)=17105 stop_rank=2065
1:57:27.692281 INFO: calibration group: precursor, fitting rt estimator 
1:57:27.783388 INFO: calibration group: fragment, fitting mz estimator 
1:57:28.020900 INFO: Using score_cutoff 49.914605703735354 (fac=0.99, q=1)
1:57:28.021345 INFO: calibration group: precursor, predicting mz
1:57:28.021429 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:28.021460 INFO: calibration group: precursor, predicting rt
1:57:28.023068 INFO: calibration group: fragment, predicting mz
1:57:28.025207 INFO: === checking if optimization conditions were reached ===
1:57:28.025306 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
1:57:28.026867 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 5.2862.
1:57:28.026917 INFO: ==============================================
1:57:28.027004 INFO: Starting optimization step 9.
1:57:28.027068 PROGRESS: === Extracting elution groups 0 to 600 ===
1:57:28.027123 PROGRESS: Extracting batch of 1163 precursors
1:57:28.028246 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:28.028292 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:28.028323 INFO: FWHM in RT is 2.39 seconds, sigma is 0.31
1:57:28.028346 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:57:28.028505 INFO: Starting candidate selection
1:57:28.146497 INFO: Starting candidate scoring
1:57:28.191864 INFO: Finished candidate processing
1:57:28.191951 INFO: Collecting candidate features
1:57:28.200430 WARNING: intensity_correlation has 2 NaNs ( 0.09 % out of 2270)
1:57:28.203440 INFO: Collecting fragment features
1:57:28.207369 INFO: Finished candidate scoring
1:57:28.209105 PROGRESS: === Extracted 2270 precursors and 17174 fragments ===
1:57:28.209379 INFO: performing precursor FDR with 47 features
1:57:28.209416 INFO: Decoy channel: -1
1:57:28.209455 INFO: Competetive: True
1:57:28.212052 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:28.213290 WARNING: dropped 2 decoy PSMs due to missing features
1:57:28.236829 INFO: Test AUC: 0.667
1:57:28.236908 INFO: Train AUC: 0.740
1:57:28.236936 INFO: AUC difference: 9.79%
1:57:28.236956 WARNING: AUC difference > 5%. This may indicate overfitting.
1:57:28.414633 INFO: Resetting torch num_threads to 100
1:57:28.415261 INFO: === FDR correction performed with classifier version 9 ===
1:57:28.415903 PROGRESS: ============================= Precursor FDR =============================
1:57:28.415994 PROGRESS: Total precursors accumulated: 411
1:57:28.416055 PROGRESS: Target precursors: 385 (93.67%)
1:57:28.416107 PROGRESS: Decoy precursors: 26 (6.33%)
1:57:28.416152 PROGRESS: 
1:57:28.416197 PROGRESS: Precursor Summary:
1:57:28.417198 PROGRESS: Channel   0:	 0.05 FDR:   367; 0.01 FDR:   208; 0.001 FDR:   162
1:57:28.417287 PROGRESS: 
1:57:28.417342 PROGRESS: Protein Summary:
1:57:28.418458 PROGRESS: Channel   0:	 0.05 FDR:   352; 0.01 FDR:   205; 0.001 FDR:   161
1:57:28.418547 PROGRESS: =========================================================================
1:57:28.421092 INFO: fragments_df: keeping 2043 of 17174 [sum(precursor_idx_mask)=4031 sum(mass_error_mask)=17174 stop_rank=2043
1:57:28.426633 INFO: calibration group: precursor, fitting rt estimator 
1:57:28.517927 INFO: calibration group: fragment, fitting mz estimator 
1:57:28.751983 INFO: Using score_cutoff 49.922693488311765 (fac=0.99, q=1)
1:57:28.752420 INFO: calibration group: precursor, predicting mz
1:57:28.752505 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:28.752536 INFO: calibration group: precursor, predicting rt
1:57:28.754124 INFO: calibration group: fragment, predicting mz
1:57:28.756481 INFO: === checking if optimization conditions were reached ===
1:57:28.756588 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
1:57:28.758148 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 6.4239.
1:57:28.758201 INFO: ==============================================
1:57:28.758286 INFO: Starting optimization step 10.
1:57:28.758350 PROGRESS: === Extracting elution groups 0 to 600 ===
1:57:28.758405 PROGRESS: Extracting batch of 1163 precursors
1:57:28.759286 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:28.759334 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:28.759364 INFO: FWHM in RT is 2.38 seconds, sigma is 0.31
1:57:28.759387 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:57:28.759543 INFO: Starting candidate selection
1:57:28.877203 INFO: Starting candidate scoring
1:57:28.921672 INFO: Finished candidate processing
1:57:28.921766 INFO: Collecting candidate features
1:57:28.930185 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2261)
1:57:28.933286 INFO: Collecting fragment features
1:57:28.937266 INFO: Finished candidate scoring
1:57:28.939057 PROGRESS: === Extracted 2261 precursors and 17166 fragments ===
1:57:28.939350 INFO: performing precursor FDR with 47 features
1:57:28.939391 INFO: Decoy channel: -1
1:57:28.939421 INFO: Competetive: True
1:57:28.942108 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:28.943351 WARNING: dropped 1 decoy PSMs due to missing features
1:57:28.965601 INFO: Test AUC: 0.736
1:57:28.965677 INFO: Train AUC: 0.722
1:57:28.965714 INFO: AUC difference: 1.94%
1:57:29.143914 INFO: Resetting torch num_threads to 100
1:57:29.144593 INFO: === FDR correction performed with classifier version 9 ===
1:57:29.145248 PROGRESS: ============================= Precursor FDR =============================
1:57:29.145350 PROGRESS: Total precursors accumulated: 418
1:57:29.145428 PROGRESS: Target precursors: 391 (93.54%)
1:57:29.145498 PROGRESS: Decoy precursors: 27 (6.46%)
1:57:29.145559 PROGRESS: 
1:57:29.145615 PROGRESS: Precursor Summary:
1:57:29.146609 PROGRESS: Channel   0:	 0.05 FDR:   366; 0.01 FDR:   206; 0.001 FDR:   160
1:57:29.146718 PROGRESS: 
1:57:29.146791 PROGRESS: Protein Summary:
1:57:29.147947 PROGRESS: Channel   0:	 0.05 FDR:   351; 0.01 FDR:   203; 0.001 FDR:   159
1:57:29.148047 PROGRESS: =========================================================================
1:57:29.150597 INFO: fragments_df: keeping 2038 of 17166 [sum(precursor_idx_mask)=4000 sum(mass_error_mask)=17166 stop_rank=2038
1:57:29.156056 INFO: calibration group: precursor, fitting rt estimator 
1:57:29.245632 INFO: calibration group: fragment, fitting mz estimator 
1:57:29.480203 INFO: Using score_cutoff 49.85457426452637 (fac=0.99, q=1)
1:57:29.480660 INFO: calibration group: precursor, predicting mz
1:57:29.480754 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:29.480793 INFO: calibration group: precursor, predicting rt
1:57:29.482411 INFO: calibration group: fragment, predicting mz
1:57:29.484591 INFO: === checking if optimization conditions were reached ===
1:57:29.484703 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 2 ===
1:57:29.486286 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 4.8877.
1:57:29.486338 INFO: ==============================================
1:57:29.486438 INFO: Starting optimization step 11.
1:57:29.486521 PROGRESS: === Extracting elution groups 0 to 600 ===
1:57:29.486603 PROGRESS: Extracting batch of 1163 precursors
1:57:29.487541 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:29.487590 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:29.487633 INFO: FWHM in RT is 2.38 seconds, sigma is 0.31
1:57:29.487663 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:57:29.487844 INFO: Starting candidate selection
1:57:29.606136 INFO: Starting candidate scoring
1:57:29.651484 INFO: Finished candidate processing
1:57:29.651567 INFO: Collecting candidate features
1:57:29.659977 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2271)
1:57:29.663142 INFO: Collecting fragment features
1:57:29.666832 INFO: Finished candidate scoring
1:57:29.668652 PROGRESS: === Extracted 2271 precursors and 17248 fragments ===
1:57:29.668941 INFO: performing precursor FDR with 47 features
1:57:29.668979 INFO: Decoy channel: -1
1:57:29.669009 INFO: Competetive: True
1:57:29.671589 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:29.672817 WARNING: dropped 1 decoy PSMs due to missing features
1:57:29.695123 INFO: Test AUC: 0.703
1:57:29.695197 INFO: Train AUC: 0.736
1:57:29.695233 INFO: AUC difference: 4.50%
1:57:29.880137 INFO: Resetting torch num_threads to 100
1:57:29.880803 INFO: === FDR correction performed with classifier version 9 ===
1:57:29.881440 PROGRESS: ============================= Precursor FDR =============================
1:57:29.881540 PROGRESS: Total precursors accumulated: 413
1:57:29.881618 PROGRESS: Target precursors: 391 (94.67%)
1:57:29.881688 PROGRESS: Decoy precursors: 22 (5.33%)
1:57:29.881748 PROGRESS: 
1:57:29.881804 PROGRESS: Precursor Summary:
1:57:29.882804 PROGRESS: Channel   0:	 0.05 FDR:   371; 0.01 FDR:   208; 0.001 FDR:   166
1:57:29.882903 PROGRESS: 
1:57:29.882974 PROGRESS: Protein Summary:
1:57:29.884129 PROGRESS: Channel   0:	 0.05 FDR:   356; 0.01 FDR:   205; 0.001 FDR:   165
1:57:29.884228 PROGRESS: =========================================================================
1:57:29.886805 INFO: fragments_df: keeping 2043 of 17248 [sum(precursor_idx_mask)=4035 sum(mass_error_mask)=17248 stop_rank=2043
1:57:29.892272 INFO: calibration group: precursor, fitting rt estimator 
1:57:29.984135 INFO: calibration group: fragment, fitting mz estimator 
1:57:30.220058 INFO: Using score_cutoff 49.906915287780755 (fac=0.99, q=1)
1:57:30.220533 INFO: calibration group: precursor, predicting mz
1:57:30.220649 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:30.220691 INFO: calibration group: precursor, predicting rt
1:57:30.222293 INFO: calibration group: fragment, predicting mz
1:57:30.224471 INFO: === checking if optimization conditions were reached ===
1:57:30.224594 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 2 ===
1:57:30.226185 PROGRESS: ❌ rt_error       : optimization incomplete after 12 search(es). Will search with parameter 6.4700.
1:57:30.226237 INFO: ==============================================
1:57:30.226338 INFO: Starting optimization step 12.
1:57:30.226420 PROGRESS: === Extracting elution groups 0 to 600 ===
1:57:30.226494 PROGRESS: Extracting batch of 1163 precursors
1:57:30.227437 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:30.227484 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:30.227524 INFO: FWHM in RT is 2.37 seconds, sigma is 0.31
1:57:30.227553 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:57:30.227739 INFO: Starting candidate selection
1:57:30.347380 INFO: Starting candidate scoring
1:57:30.392594 INFO: Finished candidate processing
1:57:30.392679 INFO: Collecting candidate features
1:57:30.401340 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2267)
1:57:30.404547 INFO: Collecting fragment features
1:57:30.408638 INFO: Finished candidate scoring
1:57:30.410416 PROGRESS: === Extracted 2267 precursors and 17226 fragments ===
1:57:30.410702 INFO: performing precursor FDR with 47 features
1:57:30.410740 INFO: Decoy channel: -1
1:57:30.410769 INFO: Competetive: True
1:57:30.413418 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:30.414662 WARNING: dropped 1 decoy PSMs due to missing features
1:57:30.437901 INFO: Test AUC: 0.711
1:57:30.437975 INFO: Train AUC: 0.728
1:57:30.438012 INFO: AUC difference: 2.43%
1:57:30.615746 INFO: Resetting torch num_threads to 100
1:57:30.616424 INFO: === FDR correction performed with classifier version 9 ===
1:57:30.617078 PROGRESS: ============================= Precursor FDR =============================
1:57:30.617176 PROGRESS: Total precursors accumulated: 409
1:57:30.617254 PROGRESS: Target precursors: 382 (93.40%)
1:57:30.617324 PROGRESS: Decoy precursors: 27 (6.60%)
1:57:30.617388 PROGRESS: 
1:57:30.617446 PROGRESS: Precursor Summary:
1:57:30.618488 PROGRESS: Channel   0:	 0.05 FDR:   354; 0.01 FDR:   205; 0.001 FDR:   159
1:57:30.618586 PROGRESS: 
1:57:30.618666 PROGRESS: Protein Summary:
1:57:30.619869 PROGRESS: Channel   0:	 0.05 FDR:   342; 0.01 FDR:   202; 0.001 FDR:   158
1:57:30.619967 PROGRESS: =========================================================================
1:57:30.622703 INFO: fragments_df: keeping 2027 of 17226 [sum(precursor_idx_mask)=3994 sum(mass_error_mask)=17226 stop_rank=2027
1:57:30.628185 INFO: calibration group: precursor, fitting rt estimator 
1:57:30.719834 INFO: calibration group: fragment, fitting mz estimator 
1:57:30.954181 INFO: Using score_cutoff 52.392188259887696 (fac=0.99, q=1)
1:57:30.954633 INFO: calibration group: precursor, predicting mz
1:57:30.954730 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:30.954769 INFO: calibration group: precursor, predicting rt
1:57:30.956383 INFO: calibration group: fragment, predicting mz
1:57:30.958541 INFO: === checking if optimization conditions were reached ===
1:57:30.958652 PROGRESS: === Optimization of rt_error has been performed 13 time(s); minimum number is 2 ===
1:57:30.960224 PROGRESS: ❌ rt_error       : optimization incomplete after 13 search(es). Will search with parameter 6.2034.
1:57:30.960287 INFO: ==============================================
1:57:30.960397 INFO: Starting optimization step 13.
1:57:30.960490 PROGRESS: === Extracting elution groups 0 to 600 ===
1:57:30.960575 PROGRESS: Extracting batch of 1163 precursors
1:57:30.961496 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:30.961544 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:30.961585 INFO: FWHM in RT is 2.39 seconds, sigma is 0.31
1:57:30.961612 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:57:30.961793 INFO: Starting candidate selection
1:57:31.081038 INFO: Starting candidate scoring
1:57:31.126222 INFO: Finished candidate processing
1:57:31.126321 INFO: Collecting candidate features
1:57:31.134956 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2265)
1:57:31.138181 INFO: Collecting fragment features
1:57:31.142268 INFO: Finished candidate scoring
1:57:31.144041 PROGRESS: === Extracted 2265 precursors and 17202 fragments ===
1:57:31.144342 INFO: performing precursor FDR with 47 features
1:57:31.144388 INFO: Decoy channel: -1
1:57:31.144418 INFO: Competetive: True
1:57:31.147060 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:31.148368 WARNING: dropped 1 decoy PSMs due to missing features
1:57:31.180673 INFO: Test AUC: 0.730
1:57:31.180751 INFO: Train AUC: 0.725
1:57:31.180788 INFO: AUC difference: 0.65%
1:57:31.360153 INFO: Resetting torch num_threads to 100
1:57:31.360846 INFO: === FDR correction performed with classifier version 9 ===
1:57:31.361520 PROGRESS: ============================= Precursor FDR =============================
1:57:31.361621 PROGRESS: Total precursors accumulated: 419
1:57:31.361696 PROGRESS: Target precursors: 393 (93.79%)
1:57:31.361764 PROGRESS: Decoy precursors: 26 (6.21%)
1:57:31.361830 PROGRESS: 
1:57:31.361889 PROGRESS: Precursor Summary:
1:57:31.362882 PROGRESS: Channel   0:	 0.05 FDR:   355; 0.01 FDR:   204; 0.001 FDR:   160
1:57:31.362988 PROGRESS: 
1:57:31.363058 PROGRESS: Protein Summary:
1:57:31.364218 PROGRESS: Channel   0:	 0.05 FDR:   345; 0.01 FDR:   201; 0.001 FDR:   159
1:57:31.364340 PROGRESS: =========================================================================
1:57:31.366909 INFO: fragments_df: keeping 2015 of 17202 [sum(precursor_idx_mask)=3969 sum(mass_error_mask)=17202 stop_rank=2015
1:57:31.372447 INFO: calibration group: precursor, fitting rt estimator 
1:57:31.467427 INFO: calibration group: fragment, fitting mz estimator 
1:57:31.700167 INFO: Using score_cutoff 52.37258048629761 (fac=0.99, q=1)
1:57:31.700642 INFO: calibration group: precursor, predicting mz
1:57:31.700738 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:31.700777 INFO: calibration group: precursor, predicting rt
1:57:31.702379 INFO: calibration group: fragment, predicting mz
1:57:31.704526 INFO: === checking if optimization conditions were reached ===
1:57:31.704638 PROGRESS: === Optimization of rt_error has been performed 14 time(s); minimum number is 2 ===
1:57:31.705685 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 110.6275 found after 14 searches.
1:57:31.705735 INFO: ==============================================
1:57:31.705835 PROGRESS: Optimization finished for rt_error.
1:57:31.710959 INFO: calibration group: precursor, predicting mz
1:57:31.711086 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:31.711125 INFO: calibration group: precursor, predicting rt
1:57:31.712488 INFO: calibration group: fragment, predicting mz
1:57:31.741110 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:57:31.741271 PROGRESS: ==============================================
1:57:31.741362 PROGRESS: ms2_error      : 6.7411
1:57:31.741439 PROGRESS: rt_error       : 110.6275
1:57:31.741505 PROGRESS: ==============================================
1:57:31.742120 INFO: calibration group: precursor, predicting mz
1:57:31.742223 WARNING: mz prediction was skipped as it has not been fitted yet
1:57:31.742259 INFO: calibration group: precursor, predicting rt
1:57:31.879565 INFO: calibration group: fragment, predicting mz
1:57:32.228940 PROGRESS: Extracting batch of 238438 precursors
1:57:32.299397 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:57:32.299561 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:57:32.299607 INFO: FWHM in RT is 2.37 seconds, sigma is 0.30
1:57:32.299637 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:57:32.299914 INFO: Starting candidate selection
1:57:41.316669 INFO: Applying score cutoff of 32.89496018829346
1:57:41.325129 INFO: Removed 91213 precursors with score below cutoff
1:57:41.393209 INFO: Starting candidate scoring
1:57:44.056846 INFO: Finished candidate processing
1:57:44.057303 INFO: Collecting candidate features
1:57:44.676596 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 385661)
1:57:44.692223 INFO: Collecting fragment features
1:57:44.916689 INFO: Finished candidate scoring
1:57:45.127602 INFO: === FDR correction performed with classifier version 11 ===
1:57:45.128414 INFO: performing precursor FDR with 47 features
1:57:45.128466 INFO: Decoy channel: -1
1:57:45.128493 INFO: Competetive: True
1:57:45.254766 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:45.320847 WARNING: dropped 1 target PSMs due to missing features
1:57:45.321000 WARNING: dropped 1 decoy PSMs due to missing features
1:57:45.321063 WARNING: FDR calculation for 219842 target and 165817 decoy PSMs
1:57:45.321087 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1:57:55.793280 INFO: Test AUC: 0.836
1:57:55.793438 INFO: Train AUC: 0.839
1:57:55.793472 INFO: AUC difference: 0.26%
1:57:56.099758 INFO: Resetting torch num_threads to 100
1:57:56.122682 INFO: Removing fragments below FDR threshold
1:57:56.196360 PROGRESS: ============================= Precursor FDR =============================
1:57:56.196666 PROGRESS: Total precursors accumulated: 98,112
1:57:56.196741 PROGRESS: Target precursors: 97,141 (99.01%)
1:57:56.196805 PROGRESS: Decoy precursors: 971 (0.99%)
1:57:56.196863 PROGRESS: 
1:57:56.196916 PROGRESS: Precursor Summary:
1:57:56.240657 PROGRESS: Channel   0:	 0.05 FDR: 97,141; 0.01 FDR: 97,141; 0.001 FDR: 85,081
1:57:56.240973 PROGRESS: 
1:57:56.241043 PROGRESS: Protein Summary:
1:57:56.302162 PROGRESS: Channel   0:	 0.05 FDR: 10,748; 0.01 FDR: 10,748; 0.001 FDR: 9,390
1:57:56.302460 PROGRESS: =========================================================================
1:57:57.014460 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:57:57.039888 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:57:57.040081 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant
1:57:57.040163 INFO: Creating folder run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/figures
1:57:57.041096 INFO: Initializing RawFileManager
1:58:07.592881 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
1:58:07.597573 INFO: Determining DIA cycle
1:58:07.614053 INFO: Found cycle with start 0.00 min and length 300.
1:58:07.780088 INFO: RT (min)            : 0.0 - 26.9
1:58:07.780186 INFO: RT duration (sec)   : 1611.2
1:58:07.780215 INFO: RT duration (min)   : 26.9
1:58:07.780254 INFO: Cycle len (scans)   : 300
1:58:07.780275 INFO: Cycle len (sec)     : 1.65
1:58:07.780293 INFO: Number of cycles    : 978
1:58:07.780313 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:58:07.833134 INFO: Initializing CalibrationManager
1:58:07.833487 INFO: Loading calibration config
1:58:07.834160 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'}]
1:58:07.834269 INFO: Calibration group :fragment, found 1 estimator(s)
1:58:07.834359 INFO: Calibration group :precursor, found 3 estimator(s)
1:58:07.834445 INFO: Disabling ion mobility calibration
1:58:07.834474 INFO: removed mobility estimator from group precursor
1:58:07.834619 INFO: Initializing OptimizationManager
1:58:07.834737 INFO: initial parameter: ms1_error = 30
1:58:07.834804 INFO: initial parameter: ms2_error = 30
1:58:07.834857 INFO: initial parameter: rt_error = 805.6019897460938
1:58:07.834906 INFO: initial parameter: mobility_error = 0.1
1:58:07.834949 INFO: initial parameter: column_type = library
1:58:07.834992 INFO: initial parameter: num_candidates = 1
1:58:07.835036 INFO: initial parameter: classifier_version = -1
1:58:07.835078 INFO: initial parameter: fwhm_rt = 5
1:58:07.835120 INFO: initial parameter: fwhm_mobility = 0.01
1:58:07.835160 INFO: initial parameter: score_cutoff = 0
1:58:07.835235 INFO: Initializing TimingManager
1:58:07.835293 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:58:07.835439 INFO: FDRManager not loaded from disk.
1:58:07.835465 INFO: Initializing FDRManager
1:58:07.835508 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:58:07.874384 PROGRESS: 123,909 target precursors potentially observable (0 removed)
1:58:07.930091 PROGRESS: Starting initial search for precursors.
1:58:07.938246 INFO: Starting optimization step 0.
1:58:07.938433 PROGRESS: === Extracting elution groups 0 to 200 ===
1:58:07.938510 PROGRESS: Extracting batch of 392 precursors
1:58:07.939596 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:07.939648 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:07.939689 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:58:07.939713 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:58:07.940019 INFO: Starting candidate selection
1:58:08.077772 INFO: Starting candidate scoring
1:58:08.116344 INFO: Finished candidate processing
1:58:08.116418 INFO: Collecting candidate features
1:58:08.126060 INFO: Collecting fragment features
1:58:08.128107 INFO: Finished candidate scoring
1:58:08.128892 PROGRESS: === Extracted 392 precursors and 4286 fragments ===
1:58:08.129169 INFO: performing precursor FDR with 47 features
1:58:08.129206 INFO: Decoy channel: -1
1:58:08.129229 INFO: Competetive: True
1:58:08.130218 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:08.150306 INFO: Test AUC: 0.519
1:58:08.150371 INFO: Train AUC: 0.588
1:58:08.150401 INFO: AUC difference: 11.85%
1:58:08.150422 WARNING: AUC difference > 5%. This may indicate overfitting.
1:58:08.327905 INFO: Resetting torch num_threads to 100
1:58:08.328467 INFO: === FDR correction performed with classifier version -1 ===
1:58:08.329118 PROGRESS: ============================= Precursor FDR =============================
1:58:08.329212 PROGRESS: Total precursors accumulated: 200
1:58:08.329277 PROGRESS: Target precursors: 124 (62.00%)
1:58:08.329331 PROGRESS: Decoy precursors: 76 (38.00%)
1:58:08.329381 PROGRESS: 
1:58:08.329425 PROGRESS: Precursor Summary:
1:58:08.330275 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:58:08.330364 PROGRESS: 
1:58:08.330421 PROGRESS: Protein Summary:
1:58:08.331322 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:58:08.331411 PROGRESS: =========================================================================
1:58:08.335185 INFO: Starting optimization step 1.
1:58:08.335296 PROGRESS: === Extracting elution groups 200 to 600 ===
1:58:08.335361 PROGRESS: Extracting batch of 771 precursors
1:58:08.336107 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:08.336158 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:08.336191 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:58:08.336225 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:58:08.336402 INFO: Starting candidate selection
1:58:08.474698 INFO: Starting candidate scoring
1:58:12.407415 INFO: Finished candidate processing
1:58:12.407515 INFO: Collecting candidate features
1:58:12.417142 INFO: Collecting fragment features
1:58:12.419594 INFO: Finished candidate scoring
1:58:12.421928 PROGRESS: === Extracted 1163 precursors and 12620 fragments ===
1:58:12.422702 INFO: performing precursor FDR with 47 features
1:58:12.422746 INFO: Decoy channel: -1
1:58:12.422772 INFO: Competetive: True
1:58:12.425547 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:12.445455 INFO: Test AUC: 0.583
1:58:12.445525 INFO: Train AUC: 0.603
1:58:12.445554 INFO: AUC difference: 3.29%
1:58:12.616513 INFO: Resetting torch num_threads to 100
1:58:12.617144 INFO: === FDR correction performed with classifier version -1 ===
1:58:12.617817 PROGRESS: ============================= Precursor FDR =============================
1:58:12.617914 PROGRESS: Total precursors accumulated: 1
1:58:12.617975 PROGRESS: Target precursors: 1 (100.00%)
1:58:12.618028 PROGRESS: Decoy precursors: 0 (0.00%)
1:58:12.618077 PROGRESS: 
1:58:12.618126 PROGRESS: Precursor Summary:
1:58:12.619071 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:58:12.619158 PROGRESS: 
1:58:12.619214 PROGRESS: Protein Summary:
1:58:12.620261 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:58:12.620353 PROGRESS: =========================================================================
1:58:12.625260 INFO: Starting optimization step 2.
1:58:12.625371 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:58:12.625434 PROGRESS: Extracting batch of 1538 precursors
1:58:12.626269 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:12.626318 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:12.626349 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:58:12.626371 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:58:12.626529 INFO: Starting candidate selection
1:58:12.785917 INFO: Starting candidate scoring
1:58:12.824386 INFO: Finished candidate processing
1:58:12.824468 INFO: Collecting candidate features
1:58:12.834989 INFO: Collecting fragment features
1:58:12.838910 INFO: Finished candidate scoring
1:58:12.841755 PROGRESS: === Extracted 2701 precursors and 29274 fragments ===
1:58:12.842714 INFO: performing precursor FDR with 47 features
1:58:12.842756 INFO: Decoy channel: -1
1:58:12.842780 INFO: Competetive: True
1:58:12.846217 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:12.876228 INFO: Test AUC: 0.612
1:58:12.876322 INFO: Train AUC: 0.579
1:58:12.876351 INFO: AUC difference: 5.66%
1:58:12.876373 WARNING: AUC difference > 5%. This may indicate overfitting.
1:58:13.047823 INFO: Resetting torch num_threads to 100
1:58:13.048566 INFO: === FDR correction performed with classifier version -1 ===
1:58:13.049414 PROGRESS: ============================= Precursor FDR =============================
1:58:13.049509 PROGRESS: Total precursors accumulated: 1,400
1:58:13.049571 PROGRESS: Target precursors: 886 (63.29%)
1:58:13.049623 PROGRESS: Decoy precursors: 514 (36.71%)
1:58:13.049671 PROGRESS: 
1:58:13.049717 PROGRESS: Precursor Summary:
1:58:13.050588 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:58:13.050675 PROGRESS: 
1:58:13.050732 PROGRESS: Protein Summary:
1:58:13.051667 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:58:13.051755 PROGRESS: =========================================================================
1:58:13.058212 INFO: Starting optimization step 3.
1:58:13.058331 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:58:13.058396 PROGRESS: Extracting batch of 3065 precursors
1:58:13.059454 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:13.059501 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:13.059533 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:58:13.059565 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:58:13.059727 INFO: Starting candidate selection
1:58:13.297772 INFO: Starting candidate scoring
1:58:13.339892 INFO: Finished candidate processing
1:58:13.339985 INFO: Collecting candidate features
1:58:13.352849 INFO: Collecting fragment features
1:58:13.357249 INFO: Finished candidate scoring
1:58:13.362382 PROGRESS: === Extracted 5766 precursors and 62436 fragments ===
1:58:13.363595 INFO: performing precursor FDR with 47 features
1:58:13.363638 INFO: Decoy channel: -1
1:58:13.363663 INFO: Competetive: True
1:58:13.367830 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:13.421659 INFO: Test AUC: 0.590
1:58:13.421760 INFO: Train AUC: 0.594
1:58:13.421790 INFO: AUC difference: 0.61%
1:58:13.597879 INFO: Resetting torch num_threads to 100
1:58:13.598746 INFO: === FDR correction performed with classifier version -1 ===
1:58:13.599666 PROGRESS: ============================= Precursor FDR =============================
1:58:13.599761 PROGRESS: Total precursors accumulated: 2,998
1:58:13.599821 PROGRESS: Target precursors: 1,943 (64.81%)
1:58:13.599872 PROGRESS: Decoy precursors: 1,055 (35.19%)
1:58:13.599920 PROGRESS: 
1:58:13.599965 PROGRESS: Precursor Summary:
1:58:13.600868 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:58:13.600957 PROGRESS: 
1:58:13.601013 PROGRESS: Protein Summary:
1:58:13.601963 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:58:13.602051 PROGRESS: =========================================================================
1:58:13.612250 INFO: Starting optimization step 4.
1:58:13.612385 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:58:13.612449 PROGRESS: Extracting batch of 6167 precursors
1:58:13.613966 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:13.614015 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:13.614046 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:58:13.614068 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:58:13.614236 INFO: Starting candidate selection
1:58:14.030619 INFO: Starting candidate scoring
1:58:14.081442 INFO: Finished candidate processing
1:58:14.081546 INFO: Collecting candidate features
1:58:14.099305 INFO: Collecting fragment features
1:58:14.105374 INFO: Finished candidate scoring
1:58:14.112250 PROGRESS: === Extracted 11933 precursors and 129085 fragments ===
1:58:14.114092 INFO: performing precursor FDR with 47 features
1:58:14.114147 INFO: Decoy channel: -1
1:58:14.114172 INFO: Competetive: True
1:58:14.120307 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:14.204986 INFO: Test AUC: 0.617
1:58:14.205104 INFO: Train AUC: 0.589
1:58:14.205136 INFO: AUC difference: 4.87%
1:58:14.382921 INFO: Resetting torch num_threads to 100
1:58:14.383982 INFO: === FDR correction performed with classifier version -1 ===
1:58:14.385265 PROGRESS: ============================= Precursor FDR =============================
1:58:14.385367 PROGRESS: Total precursors accumulated: 6,191
1:58:14.385428 PROGRESS: Target precursors: 3,999 (64.59%)
1:58:14.385481 PROGRESS: Decoy precursors: 2,192 (35.41%)
1:58:14.385529 PROGRESS: 
1:58:14.385575 PROGRESS: Precursor Summary:
1:58:14.386475 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:58:14.386567 PROGRESS: 
1:58:14.386622 PROGRESS: Protein Summary:
1:58:14.387582 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:58:14.387673 PROGRESS: =========================================================================
1:58:14.403574 INFO: Starting optimization step 5.
1:58:14.403797 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:58:14.403864 PROGRESS: Extracting batch of 12312 precursors
1:58:14.406579 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:14.406632 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:14.406664 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:58:14.406686 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:58:14.406877 INFO: Starting candidate selection
1:58:15.156255 INFO: Starting candidate scoring
1:58:15.245438 INFO: Finished candidate processing
1:58:15.245543 INFO: Collecting candidate features
1:58:15.272801 INFO: Collecting fragment features
1:58:15.283247 INFO: Finished candidate scoring
1:58:15.295920 PROGRESS: === Extracted 24245 precursors and 262582 fragments ===
1:58:15.299299 INFO: performing precursor FDR with 47 features
1:58:15.299384 INFO: Decoy channel: -1
1:58:15.299409 INFO: Competetive: True
1:58:15.308306 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:15.613361 INFO: Test AUC: 0.765
1:58:15.613492 INFO: Train AUC: 0.776
1:58:15.613523 INFO: AUC difference: 1.46%
1:58:15.796824 INFO: Resetting torch num_threads to 100
1:58:15.798227 INFO: === FDR correction performed with classifier version -1 ===
1:58:15.799163 PROGRESS: ============================= Precursor FDR =============================
1:58:15.799258 PROGRESS: Total precursors accumulated: 3,006
1:58:15.799322 PROGRESS: Target precursors: 2,799 (93.11%)
1:58:15.799375 PROGRESS: Decoy precursors: 207 (6.89%)
1:58:15.799422 PROGRESS: 
1:58:15.799466 PROGRESS: Precursor Summary:
1:58:15.800362 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:58:15.800451 PROGRESS: 
1:58:15.800507 PROGRESS: Protein Summary:
1:58:15.801462 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:58:15.801554 PROGRESS: =========================================================================
1:58:15.823828 INFO: Starting optimization step 6.
1:58:15.824122 PROGRESS: === Extracting elution groups 12600 to 25400 ===
1:58:15.824193 PROGRESS: Extracting batch of 24645 precursors
1:58:15.829241 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:15.829305 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:15.829339 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:58:15.829362 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:58:15.829551 INFO: Starting candidate selection
1:58:19.298414 INFO: Starting candidate scoring
1:58:19.467369 INFO: Finished candidate processing
1:58:19.467480 INFO: Collecting candidate features
1:58:19.513389 INFO: Collecting fragment features
1:58:19.529210 INFO: Finished candidate scoring
1:58:19.550891 PROGRESS: === Extracted 48890 precursors and 529898 fragments ===
1:58:19.557699 INFO: performing precursor FDR with 47 features
1:58:19.557773 INFO: Decoy channel: -1
1:58:19.557798 INFO: Competetive: True
1:58:19.575663 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:20.330516 INFO: Test AUC: 0.814
1:58:20.330666 INFO: Train AUC: 0.816
1:58:20.330696 INFO: AUC difference: 0.24%
1:58:20.531039 INFO: Resetting torch num_threads to 100
1:58:20.533274 INFO: === FDR correction performed with classifier version -1 ===
1:58:20.535392 PROGRESS: ============================= Precursor FDR =============================
1:58:20.535497 PROGRESS: Total precursors accumulated: 14,036
1:58:20.535564 PROGRESS: Target precursors: 13,326 (94.94%)
1:58:20.535618 PROGRESS: Decoy precursors: 710 (5.06%)
1:58:20.535666 PROGRESS: 
1:58:20.535712 PROGRESS: Precursor Summary:
1:58:20.539439 PROGRESS: Channel   0:	 0.05 FDR: 13,162; 0.01 FDR: 9,398; 0.001 FDR: 5,582
1:58:20.539557 PROGRESS: 
1:58:20.539616 PROGRESS: Protein Summary:
1:58:20.545132 PROGRESS: Channel   0:	 0.05 FDR: 5,444; 0.01 FDR: 4,158; 0.001 FDR: 2,854
1:58:20.545245 PROGRESS: =========================================================================
1:58:20.600267 INFO: fragments_df: keeping 5000 of 529898 [sum(precursor_idx_mask)=106360 sum(mass_error_mask)=529898 stop_rank=5000
1:58:20.609154 INFO: calibration group: precursor, fitting rt estimator 
1:58:22.258068 INFO: calibration group: fragment, fitting mz estimator 
1:58:22.881494 INFO: Using score_cutoff 58.7870056892395 (fac=0.99, q=1)
1:58:22.882052 INFO: calibration group: precursor, predicting mz
1:58:22.882140 WARNING: mz prediction was skipped as it has not been fitted yet
1:58:22.882178 INFO: calibration group: precursor, predicting rt
1:58:22.883687 INFO: calibration group: fragment, predicting mz
1:58:22.885752 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:58:22.885873 INFO: Starting optimization step 7.
1:58:22.885939 PROGRESS: === Extracting elution groups 0 to 600 ===
1:58:22.885996 PROGRESS: Extracting batch of 1163 precursors
1:58:22.887257 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:22.887304 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:22.887334 INFO: FWHM in RT is 3.00 seconds, sigma is 0.39
1:58:22.887356 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:58:22.887518 INFO: Starting candidate selection
1:58:23.039774 INFO: Starting candidate scoring
1:58:23.079759 INFO: Finished candidate processing
1:58:23.079842 INFO: Collecting candidate features
1:58:23.091595 INFO: Collecting fragment features
1:58:23.097501 INFO: Finished candidate scoring
1:58:23.099236 PROGRESS: === Extracted 2326 precursors and 24908 fragments ===
1:58:23.099524 INFO: performing precursor FDR with 47 features
1:58:23.099560 INFO: Decoy channel: -1
1:58:23.099584 INFO: Competetive: True
1:58:23.102206 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:23.125913 INFO: Test AUC: 0.693
1:58:23.125985 INFO: Train AUC: 0.692
1:58:23.126014 INFO: AUC difference: 0.12%
1:58:23.303041 INFO: Resetting torch num_threads to 100
1:58:23.303648 INFO: === FDR correction performed with classifier version 6 ===
1:58:23.304292 PROGRESS: ============================= Precursor FDR =============================
1:58:23.304392 PROGRESS: Total precursors accumulated: 314
1:58:23.304454 PROGRESS: Target precursors: 298 (94.90%)
1:58:23.304514 PROGRESS: Decoy precursors: 16 (5.10%)
1:58:23.304565 PROGRESS: 
1:58:23.304611 PROGRESS: Precursor Summary:
1:58:23.305576 PROGRESS: Channel   0:	 0.05 FDR:   282; 0.01 FDR:   207; 0.001 FDR:   153
1:58:23.305669 PROGRESS: 
1:58:23.305725 PROGRESS: Protein Summary:
1:58:23.306805 PROGRESS: Channel   0:	 0.05 FDR:   273; 0.01 FDR:   202; 0.001 FDR:   152
1:58:23.306894 PROGRESS: =========================================================================
1:58:23.310435 INFO: fragments_df: keeping 2194 of 24908 [sum(precursor_idx_mask)=4599 sum(mass_error_mask)=24908 stop_rank=2194
1:58:23.320963 INFO: calibration group: precursor, fitting rt estimator 
1:58:23.412354 INFO: calibration group: fragment, fitting mz estimator 
1:58:23.655592 INFO: Using score_cutoff 59.123776993560796 (fac=0.99, q=1)
1:58:23.655998 INFO: calibration group: precursor, predicting mz
1:58:23.656084 WARNING: mz prediction was skipped as it has not been fitted yet
1:58:23.656115 INFO: calibration group: precursor, predicting rt
1:58:23.657696 INFO: calibration group: fragment, predicting mz
1:58:23.659805 INFO: === checking if optimization conditions were reached ===
1:58:23.661059 PROGRESS: ❌ ms2_error      : 15.0252 > 6.7411 or insufficient steps taken.
1:58:23.661113 INFO: ==============================================
1:58:23.661198 INFO: Starting optimization step 8.
1:58:23.661266 PROGRESS: === Extracting elution groups 0 to 600 ===
1:58:23.661321 PROGRESS: Extracting batch of 1163 precursors
1:58:23.662250 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:23.662297 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:23.662328 INFO: FWHM in RT is 2.89 seconds, sigma is 0.37
1:58:23.662350 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:58:23.662512 INFO: Starting candidate selection
1:58:23.814291 INFO: Starting candidate scoring
1:58:23.854672 INFO: Finished candidate processing
1:58:23.854755 INFO: Collecting candidate features
1:58:23.865927 INFO: Collecting fragment features
1:58:23.870327 INFO: Finished candidate scoring
1:58:23.871948 PROGRESS: === Extracted 2326 precursors and 23316 fragments ===
1:58:23.872247 INFO: performing precursor FDR with 47 features
1:58:23.872288 INFO: Decoy channel: -1
1:58:23.872311 INFO: Competetive: True
1:58:23.874867 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:23.898678 INFO: Test AUC: 0.762
1:58:23.898752 INFO: Train AUC: 0.721
1:58:23.898783 INFO: AUC difference: 5.70%
1:58:23.898806 WARNING: AUC difference > 5%. This may indicate overfitting.
1:58:24.079247 INFO: Resetting torch num_threads to 100
1:58:24.079848 INFO: === FDR correction performed with classifier version 7 ===
1:58:24.080482 PROGRESS: ============================= Precursor FDR =============================
1:58:24.080577 PROGRESS: Total precursors accumulated: 392
1:58:24.080638 PROGRESS: Target precursors: 376 (95.92%)
1:58:24.080692 PROGRESS: Decoy precursors: 16 (4.08%)
1:58:24.080738 PROGRESS: 
1:58:24.080782 PROGRESS: Precursor Summary:
1:58:24.081761 PROGRESS: Channel   0:	 0.05 FDR:   376; 0.01 FDR:   308; 0.001 FDR:   240
1:58:24.081854 PROGRESS: 
1:58:24.081910 PROGRESS: Protein Summary:
1:58:24.083066 PROGRESS: Channel   0:	 0.05 FDR:   362; 0.01 FDR:   296; 0.001 FDR:   233
1:58:24.083158 PROGRESS: =========================================================================
1:58:24.086270 INFO: fragments_df: keeping 2926 of 23316 [sum(precursor_idx_mask)=6508 sum(mass_error_mask)=23316 stop_rank=2926
1:58:24.091255 INFO: calibration group: precursor, fitting rt estimator 
1:58:24.187390 INFO: calibration group: fragment, fitting mz estimator 
1:58:24.522747 INFO: Using score_cutoff 50.77906093597412 (fac=0.99, q=1)
1:58:24.523167 INFO: calibration group: precursor, predicting mz
1:58:24.523255 WARNING: mz prediction was skipped as it has not been fitted yet
1:58:24.523286 INFO: calibration group: precursor, predicting rt
1:58:24.524848 INFO: calibration group: fragment, predicting mz
1:58:24.526966 INFO: === checking if optimization conditions were reached ===
1:58:24.528269 PROGRESS: ❌ ms2_error      : 8.0475 > 6.7411 or insufficient steps taken.
1:58:24.528322 INFO: ==============================================
1:58:24.528408 INFO: Starting optimization step 9.
1:58:24.528474 PROGRESS: === Extracting elution groups 0 to 600 ===
1:58:24.528534 PROGRESS: Extracting batch of 1163 precursors
1:58:24.529463 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:24.529512 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:24.529543 INFO: FWHM in RT is 2.59 seconds, sigma is 0.33
1:58:24.529564 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:58:24.529723 INFO: Starting candidate selection
1:58:24.682142 INFO: Starting candidate scoring
1:58:24.722786 INFO: Finished candidate processing
1:58:24.722868 INFO: Collecting candidate features
1:58:24.734830 INFO: Collecting fragment features
1:58:24.739135 INFO: Finished candidate scoring
1:58:24.740767 PROGRESS: === Extracted 2326 precursors and 21284 fragments ===
1:58:24.741046 INFO: performing precursor FDR with 47 features
1:58:24.741082 INFO: Decoy channel: -1
1:58:24.741105 INFO: Competetive: True
1:58:24.743676 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:24.776502 INFO: Test AUC: 0.752
1:58:24.776584 INFO: Train AUC: 0.737
1:58:24.776613 INFO: AUC difference: 2.01%
1:58:24.952806 INFO: Resetting torch num_threads to 100
1:58:24.953435 INFO: === FDR correction performed with classifier version 8 ===
1:58:24.954097 PROGRESS: ============================= Precursor FDR =============================
1:58:24.954191 PROGRESS: Total precursors accumulated: 422
1:58:24.954253 PROGRESS: Target precursors: 401 (95.02%)
1:58:24.954313 PROGRESS: Decoy precursors: 21 (4.98%)
1:58:24.954362 PROGRESS: 
1:58:24.954409 PROGRESS: Precursor Summary:
1:58:24.955368 PROGRESS: Channel   0:	 0.05 FDR:   401; 0.01 FDR:   221; 0.001 FDR:    94
1:58:24.955457 PROGRESS: 
1:58:24.955514 PROGRESS: Protein Summary:
1:58:24.956670 PROGRESS: Channel   0:	 0.05 FDR:   384; 0.01 FDR:   215; 0.001 FDR:    93
1:58:24.956763 PROGRESS: =========================================================================
1:58:24.959856 INFO: fragments_df: keeping 2360 of 21284 [sum(precursor_idx_mask)=4540 sum(mass_error_mask)=21284 stop_rank=2360
1:58:24.965142 INFO: calibration group: precursor, fitting rt estimator 
1:58:25.060283 INFO: calibration group: fragment, fitting mz estimator 
1:58:25.330198 INFO: Using score_cutoff 53.19504931640625 (fac=0.99, q=1)
1:58:25.330600 INFO: calibration group: precursor, predicting mz
1:58:25.330687 WARNING: mz prediction was skipped as it has not been fitted yet
1:58:25.330718 INFO: calibration group: precursor, predicting rt
1:58:25.332286 INFO: calibration group: fragment, predicting mz
1:58:25.334390 INFO: === checking if optimization conditions were reached ===
1:58:25.335630 PROGRESS: ✅ ms2_error      : 6.7411 <= 6.7411
1:58:25.335683 INFO: ==============================================
1:58:25.335768 PROGRESS: Optimization finished for ms2_error.
1:58:25.340474 INFO: calibration group: precursor, predicting mz
1:58:25.340582 WARNING: mz prediction was skipped as it has not been fitted yet
1:58:25.340613 INFO: calibration group: precursor, predicting rt
1:58:25.341871 INFO: calibration group: fragment, predicting mz
1:58:25.343918 INFO: Starting optimization step 0.
1:58:25.344019 PROGRESS: === Extracting elution groups 0 to 600 ===
1:58:25.344082 PROGRESS: Extracting batch of 1163 precursors
1:58:25.344907 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:25.344956 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:25.344987 INFO: FWHM in RT is 2.37 seconds, sigma is 0.31
1:58:25.345010 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:58:25.345165 INFO: Starting candidate selection
1:58:25.484281 INFO: Starting candidate scoring
1:58:25.527905 INFO: Finished candidate processing
1:58:25.527992 INFO: Collecting candidate features
1:58:25.539085 INFO: Collecting fragment features
1:58:25.543438 INFO: Finished candidate scoring
1:58:25.545114 PROGRESS: === Extracted 2325 precursors and 20147 fragments ===
1:58:25.545392 INFO: performing precursor FDR with 47 features
1:58:25.545427 INFO: Decoy channel: -1
1:58:25.545449 INFO: Competetive: True
1:58:25.548085 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:25.570652 INFO: Test AUC: 0.733
1:58:25.570728 INFO: Train AUC: 0.722
1:58:25.570756 INFO: AUC difference: 1.56%
1:58:25.747067 INFO: Resetting torch num_threads to 100
1:58:25.747670 INFO: === FDR correction performed with classifier version 9 ===
1:58:25.748317 PROGRESS: ============================= Precursor FDR =============================
1:58:25.748408 PROGRESS: Total precursors accumulated: 414
1:58:25.748468 PROGRESS: Target precursors: 396 (95.65%)
1:58:25.748523 PROGRESS: Decoy precursors: 18 (4.35%)
1:58:25.748570 PROGRESS: 
1:58:25.748614 PROGRESS: Precursor Summary:
1:58:25.749620 PROGRESS: Channel   0:	 0.05 FDR:   396; 0.01 FDR:   303; 0.001 FDR:   228
1:58:25.749711 PROGRESS: 
1:58:25.749767 PROGRESS: Protein Summary:
1:58:25.750940 PROGRESS: Channel   0:	 0.05 FDR:   382; 0.01 FDR:   292; 0.001 FDR:   222
1:58:25.751031 PROGRESS: =========================================================================
1:58:25.753854 INFO: fragments_df: keeping 2908 of 20147 [sum(precursor_idx_mask)=5922 sum(mass_error_mask)=20147 stop_rank=2908
1:58:25.758797 INFO: calibration group: precursor, fitting rt estimator 
1:58:25.857321 INFO: calibration group: fragment, fitting mz estimator 
1:58:26.181372 INFO: Using score_cutoff 38.86553400650024 (fac=0.99, q=1)
1:58:26.181801 INFO: calibration group: precursor, predicting mz
1:58:26.181888 WARNING: mz prediction was skipped as it has not been fitted yet
1:58:26.181918 INFO: calibration group: precursor, predicting rt
1:58:26.183466 INFO: calibration group: fragment, predicting mz
1:58:26.185627 INFO: === checking if optimization conditions were reached ===
1:58:26.185733 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:58:26.187135 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 220.3196.
1:58:26.187189 INFO: ==============================================
1:58:26.187276 INFO: Starting optimization step 1.
1:58:26.187353 PROGRESS: === Extracting elution groups 0 to 600 ===
1:58:26.187410 PROGRESS: Extracting batch of 1163 precursors
1:58:26.188320 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:26.188366 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:26.188395 INFO: FWHM in RT is 2.31 seconds, sigma is 0.30
1:58:26.188415 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:58:26.188571 INFO: Starting candidate selection
1:58:26.308566 INFO: Starting candidate scoring
1:58:26.351109 INFO: Finished candidate processing
1:58:26.351190 INFO: Collecting candidate features
1:58:26.362811 INFO: Collecting fragment features
1:58:26.367664 INFO: Finished candidate scoring
1:58:26.369347 PROGRESS: === Extracted 2325 precursors and 19813 fragments ===
1:58:26.369649 INFO: performing precursor FDR with 47 features
1:58:26.369684 INFO: Decoy channel: -1
1:58:26.369707 INFO: Competetive: True
1:58:26.372279 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:26.395290 INFO: Test AUC: 0.704
1:58:26.395358 INFO: Train AUC: 0.745
1:58:26.395388 INFO: AUC difference: 5.43%
1:58:26.395409 WARNING: AUC difference > 5%. This may indicate overfitting.
1:58:26.571691 INFO: Resetting torch num_threads to 100
1:58:26.572311 INFO: === FDR correction performed with classifier version 9 ===
1:58:26.572967 PROGRESS: ============================= Precursor FDR =============================
1:58:26.573059 PROGRESS: Total precursors accumulated: 423
1:58:26.573119 PROGRESS: Target precursors: 408 (96.45%)
1:58:26.573172 PROGRESS: Decoy precursors: 15 (3.55%)
1:58:26.573217 PROGRESS: 
1:58:26.573261 PROGRESS: Precursor Summary:
1:58:26.574252 PROGRESS: Channel   0:	 0.05 FDR:   408; 0.01 FDR:   302; 0.001 FDR:   117
1:58:26.574344 PROGRESS: 
1:58:26.574401 PROGRESS: Protein Summary:
1:58:26.575533 PROGRESS: Channel   0:	 0.05 FDR:   392; 0.01 FDR:   292; 0.001 FDR:   115
1:58:26.575630 PROGRESS: =========================================================================
1:58:26.578501 INFO: fragments_df: keeping 2894 of 19813 [sum(precursor_idx_mask)=5908 sum(mass_error_mask)=19813 stop_rank=2894
1:58:26.584037 INFO: calibration group: precursor, fitting rt estimator 
1:58:26.684966 INFO: calibration group: fragment, fitting mz estimator 
1:58:27.006635 INFO: Using score_cutoff 48.01592725639343 (fac=0.99, q=1)
1:58:27.007074 INFO: calibration group: precursor, predicting mz
1:58:27.007159 WARNING: mz prediction was skipped as it has not been fitted yet
1:58:27.007190 INFO: calibration group: precursor, predicting rt
1:58:27.008767 INFO: calibration group: fragment, predicting mz
1:58:27.010898 INFO: === checking if optimization conditions were reached ===
1:58:27.011006 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:58:27.012551 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 8.8706.
1:58:27.012604 INFO: ==============================================
1:58:27.012691 INFO: Starting optimization step 2.
1:58:27.012758 PROGRESS: === Extracting elution groups 0 to 600 ===
1:58:27.012817 PROGRESS: Extracting batch of 1163 precursors
1:58:27.013743 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:27.013789 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:27.013818 INFO: FWHM in RT is 2.28 seconds, sigma is 0.29
1:58:27.013839 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:58:27.013998 INFO: Starting candidate selection
1:58:27.128665 INFO: Starting candidate scoring
1:58:27.172173 INFO: Finished candidate processing
1:58:27.172277 INFO: Collecting candidate features
1:58:27.184015 INFO: Collecting fragment features
1:58:27.187980 INFO: Finished candidate scoring
1:58:27.189690 PROGRESS: === Extracted 2268 precursors and 17451 fragments ===
1:58:27.189986 INFO: performing precursor FDR with 47 features
1:58:27.190025 INFO: Decoy channel: -1
1:58:27.190052 INFO: Competetive: True
1:58:27.192936 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:27.226068 INFO: Test AUC: 0.713
1:58:27.226148 INFO: Train AUC: 0.735
1:58:27.226178 INFO: AUC difference: 3.03%
1:58:27.396653 INFO: Resetting torch num_threads to 100
1:58:27.397262 INFO: === FDR correction performed with classifier version 9 ===
1:58:27.397898 PROGRESS: ============================= Precursor FDR =============================
1:58:27.397992 PROGRESS: Total precursors accumulated: 457
1:58:27.398054 PROGRESS: Target precursors: 440 (96.28%)
1:58:27.398105 PROGRESS: Decoy precursors: 17 (3.72%)
1:58:27.398150 PROGRESS: 
1:58:27.398193 PROGRESS: Precursor Summary:
1:58:27.399175 PROGRESS: Channel   0:	 0.05 FDR:   440; 0.01 FDR:   393; 0.001 FDR:   160
1:58:27.399263 PROGRESS: 
1:58:27.399319 PROGRESS: Protein Summary:
1:58:27.400502 PROGRESS: Channel   0:	 0.05 FDR:   422; 0.01 FDR:   378; 0.001 FDR:   156
1:58:27.400593 PROGRESS: =========================================================================
1:58:27.403425 INFO: fragments_df: keeping 3222 of 17451 [sum(precursor_idx_mask)=7246 sum(mass_error_mask)=17451 stop_rank=3222
1:58:27.408411 INFO: calibration group: precursor, fitting rt estimator 
1:58:27.514970 INFO: calibration group: fragment, fitting mz estimator 
1:58:27.875395 INFO: Using score_cutoff 28.095301407623293 (fac=0.99, q=1)
1:58:27.875813 INFO: calibration group: precursor, predicting mz
1:58:27.875897 WARNING: mz prediction was skipped as it has not been fitted yet
1:58:27.875926 INFO: calibration group: precursor, predicting rt
1:58:27.877499 INFO: calibration group: fragment, predicting mz
1:58:27.879696 INFO: === checking if optimization conditions were reached ===
1:58:27.879809 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:58:27.881470 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 12.8586.
1:58:27.881527 INFO: ==============================================
1:58:27.881642 INFO: Starting optimization step 3.
1:58:27.881712 PROGRESS: === Extracting elution groups 0 to 600 ===
1:58:27.881772 PROGRESS: Extracting batch of 1163 precursors
1:58:27.883871 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:27.883921 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:27.883950 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
1:58:27.883972 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:58:27.884144 INFO: Starting candidate selection
1:58:27.998152 INFO: Starting candidate scoring
1:58:28.040045 INFO: Finished candidate processing
1:58:28.040131 INFO: Collecting candidate features
1:58:28.051886 INFO: Collecting fragment features
1:58:28.055841 INFO: Finished candidate scoring
1:58:28.057508 PROGRESS: === Extracted 2265 precursors and 17379 fragments ===
1:58:28.057810 INFO: performing precursor FDR with 47 features
1:58:28.057847 INFO: Decoy channel: -1
1:58:28.057869 INFO: Competetive: True
1:58:28.060361 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:28.085954 INFO: Test AUC: 0.768
1:58:28.086034 INFO: Train AUC: 0.720
1:58:28.086064 INFO: AUC difference: 6.62%
1:58:28.086084 WARNING: AUC difference > 5%. This may indicate overfitting.
1:58:28.263271 INFO: Resetting torch num_threads to 100
1:58:28.263874 INFO: === FDR correction performed with classifier version 9 ===
1:58:28.264565 PROGRESS: ============================= Precursor FDR =============================
1:58:28.264659 PROGRESS: Total precursors accumulated: 452
1:58:28.264723 PROGRESS: Target precursors: 438 (96.90%)
1:58:28.264776 PROGRESS: Decoy precursors: 14 (3.10%)
1:58:28.264821 PROGRESS: 
1:58:28.264865 PROGRESS: Precursor Summary:
1:58:28.265853 PROGRESS: Channel   0:	 0.05 FDR:   438; 0.01 FDR:   316; 0.001 FDR:   145
1:58:28.265941 PROGRESS: 
1:58:28.265996 PROGRESS: Protein Summary:
1:58:28.267151 PROGRESS: Channel   0:	 0.05 FDR:   420; 0.01 FDR:   305; 0.001 FDR:   142
1:58:28.267242 PROGRESS: =========================================================================
1:58:28.269930 INFO: fragments_df: keeping 2833 of 17379 [sum(precursor_idx_mask)=5939 sum(mass_error_mask)=17379 stop_rank=2833
1:58:28.275379 INFO: calibration group: precursor, fitting rt estimator 
1:58:28.383047 INFO: calibration group: fragment, fitting mz estimator 
1:58:28.699883 INFO: Using score_cutoff 44.509242713928224 (fac=0.99, q=1)
1:58:28.700324 INFO: calibration group: precursor, predicting mz
1:58:28.700411 WARNING: mz prediction was skipped as it has not been fitted yet
1:58:28.700441 INFO: calibration group: precursor, predicting rt
1:58:28.701997 INFO: calibration group: fragment, predicting mz
1:58:28.704207 INFO: === checking if optimization conditions were reached ===
1:58:28.704352 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:58:28.705977 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 11.1926.
1:58:28.706030 INFO: ==============================================
1:58:28.706117 INFO: Starting optimization step 4.
1:58:28.706180 PROGRESS: === Extracting elution groups 0 to 600 ===
1:58:28.706237 PROGRESS: Extracting batch of 1163 precursors
1:58:28.707172 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:28.707219 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:28.707249 INFO: FWHM in RT is 2.28 seconds, sigma is 0.29
1:58:28.707270 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:58:28.707430 INFO: Starting candidate selection
1:58:28.822799 INFO: Starting candidate scoring
1:58:28.864334 INFO: Finished candidate processing
1:58:28.864416 INFO: Collecting candidate features
1:58:28.878133 INFO: Collecting fragment features
1:58:28.882648 INFO: Finished candidate scoring
1:58:28.884535 PROGRESS: === Extracted 2269 precursors and 17424 fragments ===
1:58:28.884831 INFO: performing precursor FDR with 47 features
1:58:28.884871 INFO: Decoy channel: -1
1:58:28.884900 INFO: Competetive: True
1:58:28.887442 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:28.910253 INFO: Test AUC: 0.745
1:58:28.910330 INFO: Train AUC: 0.728
1:58:28.910367 INFO: AUC difference: 2.29%
1:58:29.088051 INFO: Resetting torch num_threads to 100
1:58:29.088842 INFO: === FDR correction performed with classifier version 9 ===
1:58:29.089501 PROGRESS: ============================= Precursor FDR =============================
1:58:29.089599 PROGRESS: Total precursors accumulated: 449
1:58:29.089668 PROGRESS: Target precursors: 436 (97.10%)
1:58:29.089728 PROGRESS: Decoy precursors: 13 (2.90%)
1:58:29.089782 PROGRESS: 
1:58:29.089833 PROGRESS: Precursor Summary:
1:58:29.090829 PROGRESS: Channel   0:	 0.05 FDR:   436; 0.01 FDR:   390; 0.001 FDR:   145
1:58:29.090925 PROGRESS: 
1:58:29.090989 PROGRESS: Protein Summary:
1:58:29.092213 PROGRESS: Channel   0:	 0.05 FDR:   418; 0.01 FDR:   375; 0.001 FDR:   142
1:58:29.095209 PROGRESS: =========================================================================
1:58:29.098528 INFO: fragments_df: keeping 3232 of 17424 [sum(precursor_idx_mask)=7170 sum(mass_error_mask)=17424 stop_rank=3232
1:58:29.107213 INFO: calibration group: precursor, fitting rt estimator 
1:58:29.215399 INFO: calibration group: fragment, fitting mz estimator 
1:58:29.583470 INFO: Using score_cutoff 24.711373538017273 (fac=0.99, q=1)
1:58:29.583979 INFO: calibration group: precursor, predicting mz
1:58:29.584080 WARNING: mz prediction was skipped as it has not been fitted yet
1:58:29.584117 INFO: calibration group: precursor, predicting rt
1:58:29.585940 INFO: calibration group: fragment, predicting mz
1:58:29.588184 INFO: === checking if optimization conditions were reached ===
1:58:29.588322 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1:58:29.590127 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 12.8288.
1:58:29.590183 INFO: ==============================================
1:58:29.590283 INFO: Starting optimization step 5.
1:58:29.590368 PROGRESS: === Extracting elution groups 0 to 600 ===
1:58:29.590443 PROGRESS: Extracting batch of 1163 precursors
1:58:29.593044 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:29.593099 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:29.593137 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
1:58:29.593161 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:58:29.593351 INFO: Starting candidate selection
1:58:29.710312 INFO: Starting candidate scoring
1:58:29.752871 INFO: Finished candidate processing
1:58:29.752951 INFO: Collecting candidate features
1:58:29.764977 INFO: Collecting fragment features
1:58:29.769043 INFO: Finished candidate scoring
1:58:29.770665 PROGRESS: === Extracted 2268 precursors and 17378 fragments ===
1:58:29.770967 INFO: performing precursor FDR with 47 features
1:58:29.771003 INFO: Decoy channel: -1
1:58:29.771025 INFO: Competetive: True
1:58:29.774030 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:29.797632 INFO: Test AUC: 0.725
1:58:29.797712 INFO: Train AUC: 0.729
1:58:29.797741 INFO: AUC difference: 0.55%
1:58:29.978627 INFO: Resetting torch num_threads to 100
1:58:29.979689 INFO: === FDR correction performed with classifier version 9 ===
1:58:29.980497 PROGRESS: ============================= Precursor FDR =============================
1:58:29.980592 PROGRESS: Total precursors accumulated: 451
1:58:29.980653 PROGRESS: Target precursors: 436 (96.67%)
1:58:29.980705 PROGRESS: Decoy precursors: 15 (3.33%)
1:58:29.980752 PROGRESS: 
1:58:29.980796 PROGRESS: Precursor Summary:
1:58:29.981802 PROGRESS: Channel   0:	 0.05 FDR:   436; 0.01 FDR:   317; 0.001 FDR:   144
1:58:29.981900 PROGRESS: 
1:58:29.981957 PROGRESS: Protein Summary:
1:58:29.983132 PROGRESS: Channel   0:	 0.05 FDR:   418; 0.01 FDR:   306; 0.001 FDR:   142
1:58:29.983224 PROGRESS: =========================================================================
1:58:29.986197 INFO: fragments_df: keeping 2839 of 17378 [sum(precursor_idx_mask)=5954 sum(mass_error_mask)=17378 stop_rank=2839
1:58:29.991421 INFO: calibration group: precursor, fitting rt estimator 
1:58:30.095337 INFO: calibration group: fragment, fitting mz estimator 
1:58:30.419381 INFO: Using score_cutoff 41.61840162506103 (fac=0.99, q=1)
1:58:30.419968 INFO: calibration group: precursor, predicting mz
1:58:30.420060 WARNING: mz prediction was skipped as it has not been fitted yet
1:58:30.420089 INFO: calibration group: precursor, predicting rt
1:58:30.421860 INFO: calibration group: fragment, predicting mz
1:58:30.424095 INFO: === checking if optimization conditions were reached ===
1:58:30.424210 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1:58:30.425938 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 11.1808.
1:58:30.425991 INFO: ==============================================
1:58:30.426079 INFO: Starting optimization step 6.
1:58:30.426156 PROGRESS: === Extracting elution groups 0 to 600 ===
1:58:30.426220 PROGRESS: Extracting batch of 1163 precursors
1:58:30.427278 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:30.427324 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:30.427359 INFO: FWHM in RT is 2.28 seconds, sigma is 0.29
1:58:30.427384 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:58:30.427577 INFO: Starting candidate selection
1:58:30.545816 INFO: Starting candidate scoring
1:58:30.588845 INFO: Finished candidate processing
1:58:30.588932 INFO: Collecting candidate features
1:58:30.601347 INFO: Collecting fragment features
1:58:30.605945 INFO: Finished candidate scoring
1:58:30.607630 PROGRESS: === Extracted 2269 precursors and 17422 fragments ===
1:58:30.607913 INFO: performing precursor FDR with 47 features
1:58:30.607948 INFO: Decoy channel: -1
1:58:30.607970 INFO: Competetive: True
1:58:30.610889 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:30.634180 INFO: Test AUC: 0.673
1:58:30.634257 INFO: Train AUC: 0.744
1:58:30.634287 INFO: AUC difference: 9.56%
1:58:30.634309 WARNING: AUC difference > 5%. This may indicate overfitting.
1:58:30.813050 INFO: Resetting torch num_threads to 100
1:58:30.813667 INFO: === FDR correction performed with classifier version 9 ===
1:58:30.814327 PROGRESS: ============================= Precursor FDR =============================
1:58:30.814419 PROGRESS: Total precursors accumulated: 449
1:58:30.814479 PROGRESS: Target precursors: 436 (97.10%)
1:58:30.814532 PROGRESS: Decoy precursors: 13 (2.90%)
1:58:30.814580 PROGRESS: 
1:58:30.814627 PROGRESS: Precursor Summary:
1:58:30.815616 PROGRESS: Channel   0:	 0.05 FDR:   436; 0.01 FDR:   390; 0.001 FDR:   146
1:58:30.815713 PROGRESS: 
1:58:30.815769 PROGRESS: Protein Summary:
1:58:30.816974 PROGRESS: Channel   0:	 0.05 FDR:   418; 0.01 FDR:   375; 0.001 FDR:   143
1:58:30.817068 PROGRESS: =========================================================================
1:58:30.819959 INFO: fragments_df: keeping 3236 of 17422 [sum(precursor_idx_mask)=7175 sum(mass_error_mask)=17422 stop_rank=3236
1:58:30.824940 INFO: calibration group: precursor, fitting rt estimator 
1:58:30.940083 INFO: calibration group: fragment, fitting mz estimator 
1:58:31.305252 INFO: Using score_cutoff 24.71207414474487 (fac=0.99, q=1)
1:58:31.305681 INFO: calibration group: precursor, predicting mz
1:58:31.305766 WARNING: mz prediction was skipped as it has not been fitted yet
1:58:31.305795 INFO: calibration group: precursor, predicting rt
1:58:31.307326 INFO: calibration group: fragment, predicting mz
1:58:31.309493 INFO: === checking if optimization conditions were reached ===
1:58:31.309596 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1:58:31.311231 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 12.8288.
1:58:31.311283 INFO: ==============================================
1:58:31.311370 INFO: Starting optimization step 7.
1:58:31.311435 PROGRESS: === Extracting elution groups 0 to 600 ===
1:58:31.311492 PROGRESS: Extracting batch of 1163 precursors
1:58:31.312417 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:31.312466 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:31.312497 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
1:58:31.312518 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:58:31.312675 INFO: Starting candidate selection
1:58:31.430282 INFO: Starting candidate scoring
1:58:31.472252 INFO: Finished candidate processing
1:58:31.472335 INFO: Collecting candidate features
1:58:31.484252 INFO: Collecting fragment features
1:58:31.488270 INFO: Finished candidate scoring
1:58:31.489840 PROGRESS: === Extracted 2267 precursors and 17391 fragments ===
1:58:31.490117 INFO: performing precursor FDR with 47 features
1:58:31.490152 INFO: Decoy channel: -1
1:58:31.490174 INFO: Competetive: True
1:58:31.492697 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:31.515462 INFO: Test AUC: 0.736
1:58:31.515533 INFO: Train AUC: 0.726
1:58:31.515563 INFO: AUC difference: 1.38%
1:58:31.692068 INFO: Resetting torch num_threads to 100
1:58:31.692702 INFO: === FDR correction performed with classifier version 9 ===
1:58:31.693384 PROGRESS: ============================= Precursor FDR =============================
1:58:31.693478 PROGRESS: Total precursors accumulated: 451
1:58:31.693537 PROGRESS: Target precursors: 437 (96.90%)
1:58:31.693588 PROGRESS: Decoy precursors: 14 (3.10%)
1:58:31.693635 PROGRESS: 
1:58:31.693681 PROGRESS: Precursor Summary:
1:58:31.694681 PROGRESS: Channel   0:	 0.05 FDR:   437; 0.01 FDR:   369; 0.001 FDR:   144
1:58:31.694770 PROGRESS: 
1:58:31.694826 PROGRESS: Protein Summary:
1:58:31.695999 PROGRESS: Channel   0:	 0.05 FDR:   419; 0.01 FDR:   355; 0.001 FDR:   142
1:58:31.696093 PROGRESS: =========================================================================
1:58:31.698929 INFO: fragments_df: keeping 3109 of 17391 [sum(precursor_idx_mask)=6826 sum(mass_error_mask)=17391 stop_rank=3109
1:58:31.703861 INFO: calibration group: precursor, fitting rt estimator 
1:58:31.809016 INFO: calibration group: fragment, fitting mz estimator 
1:58:32.157249 INFO: Using score_cutoff 24.552373802947997 (fac=0.99, q=1)
1:58:32.157690 INFO: calibration group: precursor, predicting mz
1:58:32.157777 WARNING: mz prediction was skipped as it has not been fitted yet
1:58:32.157808 INFO: calibration group: precursor, predicting rt
1:58:32.159330 INFO: calibration group: fragment, predicting mz
1:58:32.161436 INFO: === checking if optimization conditions were reached ===
1:58:32.161547 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
1:58:32.163168 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 12.3363.
1:58:32.163224 INFO: ==============================================
1:58:32.163314 INFO: Starting optimization step 8.
1:58:32.163378 PROGRESS: === Extracting elution groups 0 to 600 ===
1:58:32.163432 PROGRESS: Extracting batch of 1163 precursors
1:58:32.164330 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:32.164376 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:32.164405 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
1:58:32.164426 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:58:32.164583 INFO: Starting candidate selection
1:58:32.282136 INFO: Starting candidate scoring
1:58:32.323871 INFO: Finished candidate processing
1:58:32.323952 INFO: Collecting candidate features
1:58:32.335872 INFO: Collecting fragment features
1:58:32.339845 INFO: Finished candidate scoring
1:58:32.341614 PROGRESS: === Extracted 2266 precursors and 17396 fragments ===
1:58:32.341895 INFO: performing precursor FDR with 47 features
1:58:32.341933 INFO: Decoy channel: -1
1:58:32.341956 INFO: Competetive: True
1:58:32.344521 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:32.367959 INFO: Test AUC: 0.702
1:58:32.368031 INFO: Train AUC: 0.734
1:58:32.368060 INFO: AUC difference: 4.41%
1:58:32.544089 INFO: Resetting torch num_threads to 100
1:58:32.544705 INFO: === FDR correction performed with classifier version 9 ===
1:58:32.545358 PROGRESS: ============================= Precursor FDR =============================
1:58:32.545451 PROGRESS: Total precursors accumulated: 450
1:58:32.545511 PROGRESS: Target precursors: 434 (96.44%)
1:58:32.545563 PROGRESS: Decoy precursors: 16 (3.56%)
1:58:32.545609 PROGRESS: 
1:58:32.545656 PROGRESS: Precursor Summary:
1:58:32.546681 PROGRESS: Channel   0:	 0.05 FDR:   434; 0.01 FDR:   318; 0.001 FDR:   145
1:58:32.546772 PROGRESS: 
1:58:32.546829 PROGRESS: Protein Summary:
1:58:32.547972 PROGRESS: Channel   0:	 0.05 FDR:   416; 0.01 FDR:   307; 0.001 FDR:   142
1:58:32.548066 PROGRESS: =========================================================================
1:58:32.550815 INFO: fragments_df: keeping 2842 of 17396 [sum(precursor_idx_mask)=5970 sum(mass_error_mask)=17396 stop_rank=2842
1:58:32.555727 INFO: calibration group: precursor, fitting rt estimator 
1:58:32.659071 INFO: calibration group: fragment, fitting mz estimator 
1:58:32.983262 INFO: Using score_cutoff 41.64965386276245 (fac=0.99, q=1)
1:58:32.983675 INFO: calibration group: precursor, predicting mz
1:58:32.983766 WARNING: mz prediction was skipped as it has not been fitted yet
1:58:32.983797 INFO: calibration group: precursor, predicting rt
1:58:32.985358 INFO: calibration group: fragment, predicting mz
1:58:32.987500 INFO: === checking if optimization conditions were reached ===
1:58:32.987599 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
1:58:32.988580 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 8.8706 found after 9 searches.
1:58:32.988631 INFO: ==============================================
1:58:32.988720 PROGRESS: Optimization finished for rt_error.
1:58:32.993324 INFO: calibration group: precursor, predicting mz
1:58:32.993433 WARNING: mz prediction was skipped as it has not been fitted yet
1:58:32.993463 INFO: calibration group: precursor, predicting rt
1:58:32.994710 INFO: calibration group: fragment, predicting mz
1:58:33.023061 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:58:33.023219 PROGRESS: ==============================================
1:58:33.023291 PROGRESS: ms2_error      : 6.7411
1:58:33.023348 PROGRESS: rt_error       : 8.8706
1:58:33.023396 PROGRESS: ==============================================
1:58:33.024018 INFO: calibration group: precursor, predicting mz
1:58:33.024103 WARNING: mz prediction was skipped as it has not been fitted yet
1:58:33.024131 INFO: calibration group: precursor, predicting rt
1:58:33.154609 INFO: calibration group: fragment, predicting mz
1:58:33.509337 PROGRESS: Extracting batch of 238438 precursors
1:58:33.602318 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:58:33.602476 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:33.602516 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
1:58:33.602541 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:58:33.602811 INFO: Starting candidate selection
1:58:40.444283 INFO: Applying score cutoff of 28.095301407623293
1:58:40.451615 INFO: Removed 123415 precursors with score below cutoff
1:58:40.511040 INFO: Starting candidate scoring
1:58:42.868469 INFO: Finished candidate processing
1:58:42.868596 INFO: Collecting candidate features
1:58:43.390130 WARNING: intensity_correlation has 8 NaNs ( 0.00 % out of 343679)
1:58:43.404347 INFO: Collecting fragment features
1:58:43.594179 INFO: Finished candidate scoring
1:58:43.873568 INFO: === FDR correction performed with classifier version 12 ===
1:58:43.874260 INFO: performing precursor FDR with 47 features
1:58:43.874306 INFO: Decoy channel: -1
1:58:43.874330 INFO: Competetive: True
1:58:43.979822 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:44.037182 WARNING: dropped 2 target PSMs due to missing features
1:58:44.037346 WARNING: dropped 6 decoy PSMs due to missing features
1:58:44.037395 WARNING: FDR calculation for 207970 target and 135701 decoy PSMs
1:58:44.037418 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1:58:51.928890 INFO: Test AUC: 0.879
1:58:51.929047 INFO: Train AUC: 0.881
1:58:51.929080 INFO: AUC difference: 0.24%
1:58:52.194088 INFO: Resetting torch num_threads to 100
1:58:52.216925 INFO: Removing fragments below FDR threshold
1:58:52.285815 PROGRESS: ============================= Precursor FDR =============================
1:58:52.286090 PROGRESS: Total precursors accumulated: 98,354
1:58:52.286161 PROGRESS: Target precursors: 97,381 (99.01%)
1:58:52.286218 PROGRESS: Decoy precursors: 973 (0.99%)
1:58:52.286268 PROGRESS: 
1:58:52.286314 PROGRESS: Precursor Summary:
1:58:52.327730 PROGRESS: Channel   0:	 0.05 FDR: 97,381; 0.01 FDR: 97,381; 0.001 FDR: 86,311
1:58:52.328035 PROGRESS: 
1:58:52.328115 PROGRESS: Protein Summary:
1:58:52.390474 PROGRESS: Channel   0:	 0.05 FDR: 10,536; 0.01 FDR: 10,536; 0.001 FDR: 9,388
1:58:52.390770 PROGRESS: =========================================================================
1:58:53.101018 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:58:53.125003 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:58:53.125143 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant
1:58:53.125214 INFO: Creating folder run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/figures
1:58:53.126012 INFO: Initializing RawFileManager
1:59:02.999407 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
1:59:03.003579 INFO: Determining DIA cycle
1:59:03.020017 INFO: Found cycle with start 0.00 min and length 300.
1:59:03.177589 INFO: RT (min)            : 0.0 - 26.9
1:59:03.177687 INFO: RT duration (sec)   : 1611.2
1:59:03.177731 INFO: RT duration (min)   : 26.9
1:59:03.177756 INFO: Cycle len (scans)   : 300
1:59:03.177777 INFO: Cycle len (sec)     : 1.65
1:59:03.177798 INFO: Number of cycles    : 977
1:59:03.177817 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:59:03.225147 INFO: Initializing CalibrationManager
1:59:03.225504 INFO: Loading calibration config
1:59:03.226160 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'}]
1:59:03.226253 INFO: Calibration group :fragment, found 1 estimator(s)
1:59:03.226347 INFO: Calibration group :precursor, found 3 estimator(s)
1:59:03.226441 INFO: Disabling ion mobility calibration
1:59:03.226472 INFO: removed mobility estimator from group precursor
1:59:03.226614 INFO: Initializing OptimizationManager
1:59:03.226733 INFO: initial parameter: ms1_error = 30
1:59:03.226803 INFO: initial parameter: ms2_error = 30
1:59:03.226854 INFO: initial parameter: rt_error = 805.6004638671875
1:59:03.226899 INFO: initial parameter: mobility_error = 0.1
1:59:03.226941 INFO: initial parameter: column_type = library
1:59:03.226983 INFO: initial parameter: num_candidates = 1
1:59:03.227024 INFO: initial parameter: classifier_version = -1
1:59:03.227065 INFO: initial parameter: fwhm_rt = 5
1:59:03.227107 INFO: initial parameter: fwhm_mobility = 0.01
1:59:03.227148 INFO: initial parameter: score_cutoff = 0
1:59:03.227219 INFO: Initializing TimingManager
1:59:03.227276 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:59:03.227393 INFO: FDRManager not loaded from disk.
1:59:03.227417 INFO: Initializing FDRManager
1:59:03.227459 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:59:03.264377 PROGRESS: 123,909 target precursors potentially observable (0 removed)
1:59:03.318282 PROGRESS: Starting initial search for precursors.
1:59:03.326213 INFO: Starting optimization step 0.
1:59:03.326389 PROGRESS: === Extracting elution groups 0 to 200 ===
1:59:03.326465 PROGRESS: Extracting batch of 392 precursors
1:59:03.327513 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:03.327563 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:03.327602 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:59:03.327624 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:59:03.327900 INFO: Starting candidate selection
1:59:03.462307 INFO: Starting candidate scoring
1:59:03.498893 INFO: Finished candidate processing
1:59:03.498971 INFO: Collecting candidate features
1:59:03.507367 INFO: Collecting fragment features
1:59:03.509386 INFO: Finished candidate scoring
1:59:03.510126 PROGRESS: === Extracted 392 precursors and 4284 fragments ===
1:59:03.510396 INFO: performing precursor FDR with 47 features
1:59:03.510432 INFO: Decoy channel: -1
1:59:03.510454 INFO: Competetive: True
1:59:03.511424 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:03.530901 INFO: Test AUC: 0.420
1:59:03.530969 INFO: Train AUC: 0.431
1:59:03.530999 INFO: AUC difference: 2.51%
1:59:03.710436 INFO: Resetting torch num_threads to 100
1:59:03.711186 INFO: === FDR correction performed with classifier version -1 ===
1:59:03.711817 PROGRESS: ============================= Precursor FDR =============================
1:59:03.711908 PROGRESS: Total precursors accumulated: 200
1:59:03.711969 PROGRESS: Target precursors: 90 (45.00%)
1:59:03.712023 PROGRESS: Decoy precursors: 110 (55.00%)
1:59:03.712070 PROGRESS: 
1:59:03.712116 PROGRESS: Precursor Summary:
1:59:03.712972 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:59:03.713061 PROGRESS: 
1:59:03.713117 PROGRESS: Protein Summary:
1:59:03.714046 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:59:03.714134 PROGRESS: =========================================================================
1:59:03.717844 INFO: Starting optimization step 1.
1:59:03.717963 PROGRESS: === Extracting elution groups 200 to 600 ===
1:59:03.718027 PROGRESS: Extracting batch of 771 precursors
1:59:03.718782 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:03.718832 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:03.718863 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:59:03.718886 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:59:03.719048 INFO: Starting candidate selection
1:59:03.854621 INFO: Starting candidate scoring
1:59:03.890790 INFO: Finished candidate processing
1:59:03.890862 INFO: Collecting candidate features
1:59:03.899753 INFO: Collecting fragment features
1:59:03.902304 INFO: Finished candidate scoring
1:59:03.904375 PROGRESS: === Extracted 1163 precursors and 12611 fragments ===
1:59:03.905140 INFO: performing precursor FDR with 47 features
1:59:03.905184 INFO: Decoy channel: -1
1:59:03.905207 INFO: Competetive: True
1:59:03.908016 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:03.940644 INFO: Test AUC: 0.406
1:59:03.940724 INFO: Train AUC: 0.431
1:59:03.940752 INFO: AUC difference: 5.87%
1:59:03.940774 WARNING: AUC difference > 5%. This may indicate overfitting.
1:59:04.112249 INFO: Resetting torch num_threads to 100
1:59:04.112907 INFO: === FDR correction performed with classifier version -1 ===
1:59:04.113597 PROGRESS: ============================= Precursor FDR =============================
1:59:04.113690 PROGRESS: Total precursors accumulated: 600
1:59:04.113753 PROGRESS: Target precursors: 277 (46.17%)
1:59:04.113806 PROGRESS: Decoy precursors: 323 (53.83%)
1:59:04.113856 PROGRESS: 
1:59:04.113904 PROGRESS: Precursor Summary:
1:59:04.114782 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:59:04.114874 PROGRESS: 
1:59:04.114931 PROGRESS: Protein Summary:
1:59:04.115864 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:59:04.115953 PROGRESS: =========================================================================
1:59:04.120595 INFO: Starting optimization step 2.
1:59:04.120708 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:59:04.120773 PROGRESS: Extracting batch of 1538 precursors
1:59:04.121621 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:04.121667 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:04.121698 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:59:04.121720 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:59:04.121883 INFO: Starting candidate selection
1:59:04.278833 INFO: Starting candidate scoring
1:59:04.318530 INFO: Finished candidate processing
1:59:04.318612 INFO: Collecting candidate features
1:59:04.328766 INFO: Collecting fragment features
1:59:04.332731 INFO: Finished candidate scoring
1:59:04.335819 PROGRESS: === Extracted 2701 precursors and 29321 fragments ===
1:59:04.336790 INFO: performing precursor FDR with 47 features
1:59:04.336836 INFO: Decoy channel: -1
1:59:04.336859 INFO: Competetive: True
1:59:04.340039 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:04.379712 INFO: Test AUC: 0.430
1:59:04.379803 INFO: Train AUC: 0.428
1:59:04.379834 INFO: AUC difference: 0.53%
1:59:04.550251 INFO: Resetting torch num_threads to 100
1:59:04.550984 INFO: === FDR correction performed with classifier version -1 ===
1:59:04.551746 PROGRESS: ============================= Precursor FDR =============================
1:59:04.551839 PROGRESS: Total precursors accumulated: 1,399
1:59:04.551909 PROGRESS: Target precursors: 638 (45.60%)
1:59:04.551960 PROGRESS: Decoy precursors: 761 (54.40%)
1:59:04.552009 PROGRESS: 
1:59:04.552053 PROGRESS: Precursor Summary:
1:59:04.552949 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:59:04.553040 PROGRESS: 
1:59:04.553096 PROGRESS: Protein Summary:
1:59:04.554045 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:59:04.554135 PROGRESS: =========================================================================
1:59:04.560472 INFO: Starting optimization step 3.
1:59:04.560596 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:59:04.560661 PROGRESS: Extracting batch of 3065 precursors
1:59:04.561720 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:04.561767 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:04.561797 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:59:04.561820 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:59:04.561980 INFO: Starting candidate selection
1:59:04.805392 INFO: Starting candidate scoring
1:59:04.849144 INFO: Finished candidate processing
1:59:04.849234 INFO: Collecting candidate features
1:59:04.861864 INFO: Collecting fragment features
1:59:04.865738 INFO: Finished candidate scoring
1:59:04.869974 PROGRESS: === Extracted 5766 precursors and 62453 fragments ===
1:59:04.871215 INFO: performing precursor FDR with 47 features
1:59:04.871260 INFO: Decoy channel: -1
1:59:04.871284 INFO: Competetive: True
1:59:04.875154 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:04.906433 INFO: Test AUC: 0.410
1:59:04.906527 INFO: Train AUC: 0.425
1:59:04.906557 INFO: AUC difference: 3.63%
1:59:05.078912 INFO: Resetting torch num_threads to 100
1:59:05.079700 INFO: === FDR correction performed with classifier version -1 ===
1:59:05.080406 PROGRESS: ============================= Precursor FDR =============================
1:59:05.080504 PROGRESS: Total precursors accumulated: 1
1:59:05.080564 PROGRESS: Target precursors: 1 (100.00%)
1:59:05.080617 PROGRESS: Decoy precursors: 0 (0.00%)
1:59:05.080666 PROGRESS: 
1:59:05.080710 PROGRESS: Precursor Summary:
1:59:05.081651 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:59:05.081747 PROGRESS: 
1:59:05.081803 PROGRESS: Protein Summary:
1:59:05.082821 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:59:05.082909 PROGRESS: =========================================================================
1:59:05.092651 INFO: Starting optimization step 4.
1:59:05.092782 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:59:05.092855 PROGRESS: Extracting batch of 6167 precursors
1:59:05.094325 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:05.094372 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:05.094402 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:59:05.094423 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:59:05.094591 INFO: Starting candidate selection
1:59:05.497245 INFO: Starting candidate scoring
1:59:05.547217 INFO: Finished candidate processing
1:59:05.547324 INFO: Collecting candidate features
1:59:05.565218 INFO: Collecting fragment features
1:59:05.572156 INFO: Finished candidate scoring
1:59:05.578952 PROGRESS: === Extracted 11933 precursors and 129092 fragments ===
1:59:05.580819 INFO: performing precursor FDR with 47 features
1:59:05.580879 INFO: Decoy channel: -1
1:59:05.580904 INFO: Competetive: True
1:59:05.586246 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:05.635735 INFO: Test AUC: 0.410
1:59:05.635854 INFO: Train AUC: 0.425
1:59:05.635883 INFO: AUC difference: 3.51%
1:59:05.815045 INFO: Resetting torch num_threads to 100
1:59:05.816049 INFO: === FDR correction performed with classifier version -1 ===
1:59:05.816797 PROGRESS: ============================= Precursor FDR =============================
1:59:05.816893 PROGRESS: Total precursors accumulated: 2
1:59:05.816954 PROGRESS: Target precursors: 2 (100.00%)
1:59:05.817007 PROGRESS: Decoy precursors: 0 (0.00%)
1:59:05.817053 PROGRESS: 
1:59:05.817101 PROGRESS: Precursor Summary:
1:59:05.818034 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:59:05.818123 PROGRESS: 
1:59:05.818178 PROGRESS: Protein Summary:
1:59:05.819201 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:59:05.819292 PROGRESS: =========================================================================
1:59:05.834592 INFO: Starting optimization step 5.
1:59:05.834797 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:59:05.834866 PROGRESS: Extracting batch of 12312 precursors
1:59:05.837072 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:05.837132 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:05.837164 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:59:05.837186 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:59:05.837366 INFO: Starting candidate selection
1:59:06.582011 INFO: Starting candidate scoring
1:59:06.668712 INFO: Finished candidate processing
1:59:06.668816 INFO: Collecting candidate features
1:59:06.695841 INFO: Collecting fragment features
1:59:06.705912 INFO: Finished candidate scoring
1:59:06.719435 PROGRESS: === Extracted 24245 precursors and 262746 fragments ===
1:59:06.722421 INFO: performing precursor FDR with 47 features
1:59:06.722487 INFO: Decoy channel: -1
1:59:06.722512 INFO: Competetive: True
1:59:06.731915 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:07.047454 INFO: Test AUC: 0.781
1:59:07.047593 INFO: Train AUC: 0.795
1:59:07.047623 INFO: AUC difference: 1.72%
1:59:07.233925 INFO: Resetting torch num_threads to 100
1:59:07.235297 INFO: === FDR correction performed with classifier version -1 ===
1:59:07.236586 PROGRESS: ============================= Precursor FDR =============================
1:59:07.236682 PROGRESS: Total precursors accumulated: 5,863
1:59:07.236742 PROGRESS: Target precursors: 5,531 (94.34%)
1:59:07.236792 PROGRESS: Decoy precursors: 332 (5.66%)
1:59:07.236838 PROGRESS: 
1:59:07.236881 PROGRESS: Precursor Summary:
1:59:07.238317 PROGRESS: Channel   0:	 0.05 FDR: 5,045; 0.01 FDR:     2; 0.001 FDR:     2
1:59:07.238413 PROGRESS: 
1:59:07.238468 PROGRESS: Protein Summary:
1:59:07.240298 PROGRESS: Channel   0:	 0.05 FDR: 2,979; 0.01 FDR:     2; 0.001 FDR:     2
1:59:07.240396 PROGRESS: =========================================================================
1:59:07.261985 INFO: Starting optimization step 6.
1:59:07.262295 PROGRESS: === Extracting elution groups 12600 to 25400 ===
1:59:07.262365 PROGRESS: Extracting batch of 24645 precursors
1:59:07.267233 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:07.267293 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:07.267324 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:59:07.267346 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:59:07.267545 INFO: Starting candidate selection
1:59:08.676130 INFO: Starting candidate scoring
1:59:08.835068 INFO: Finished candidate processing
1:59:08.835182 INFO: Collecting candidate features
1:59:08.877584 INFO: Collecting fragment features
1:59:08.900283 INFO: Finished candidate scoring
1:59:08.924272 PROGRESS: === Extracted 48890 precursors and 530152 fragments ===
1:59:08.930351 INFO: performing precursor FDR with 47 features
1:59:08.930463 INFO: Decoy channel: -1
1:59:08.930489 INFO: Competetive: True
1:59:08.947550 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:11.592497 INFO: Test AUC: 0.821
1:59:11.592639 INFO: Train AUC: 0.822
1:59:11.592668 INFO: AUC difference: 0.09%
1:59:11.789629 INFO: Resetting torch num_threads to 100
1:59:11.791759 INFO: === FDR correction performed with classifier version -1 ===
1:59:11.793991 PROGRESS: ============================= Precursor FDR =============================
1:59:11.794117 PROGRESS: Total precursors accumulated: 14,758
1:59:11.794179 PROGRESS: Target precursors: 13,997 (94.84%)
1:59:11.794234 PROGRESS: Decoy precursors: 761 (5.16%)
1:59:11.794287 PROGRESS: 
1:59:11.794331 PROGRESS: Precursor Summary:
1:59:11.798371 PROGRESS: Channel   0:	 0.05 FDR: 13,714; 0.01 FDR: 10,614; 0.001 FDR: 7,564
1:59:11.798510 PROGRESS: 
1:59:11.798569 PROGRESS: Protein Summary:
1:59:11.804599 PROGRESS: Channel   0:	 0.05 FDR: 5,702; 0.01 FDR: 4,485; 0.001 FDR: 3,548
1:59:11.804726 PROGRESS: =========================================================================
1:59:11.859018 INFO: fragments_df: keeping 5000 of 530152 [sum(precursor_idx_mask)=119563 sum(mass_error_mask)=530152 stop_rank=5000
1:59:11.867553 INFO: calibration group: precursor, fitting rt estimator 
1:59:13.850204 INFO: calibration group: fragment, fitting mz estimator 
1:59:14.474683 INFO: Using score_cutoff 58.15168581047058 (fac=0.99, q=1)
1:59:14.475312 INFO: calibration group: precursor, predicting mz
1:59:14.475409 WARNING: mz prediction was skipped as it has not been fitted yet
1:59:14.475440 INFO: calibration group: precursor, predicting rt
1:59:14.477030 INFO: calibration group: fragment, predicting mz
1:59:14.479123 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:59:14.479251 INFO: Starting optimization step 7.
1:59:14.479323 PROGRESS: === Extracting elution groups 0 to 600 ===
1:59:14.479382 PROGRESS: Extracting batch of 1163 precursors
1:59:14.482419 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:14.482468 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:14.482503 INFO: FWHM in RT is 3.02 seconds, sigma is 0.39
1:59:14.482528 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:59:14.482708 INFO: Starting candidate selection
1:59:14.631614 INFO: Starting candidate scoring
1:59:14.671469 INFO: Finished candidate processing
1:59:14.671555 INFO: Collecting candidate features
1:59:14.683296 INFO: Collecting fragment features
1:59:14.687519 INFO: Finished candidate scoring
1:59:14.689159 PROGRESS: === Extracted 2326 precursors and 24922 fragments ===
1:59:14.689466 INFO: performing precursor FDR with 47 features
1:59:14.689502 INFO: Decoy channel: -1
1:59:14.689527 INFO: Competetive: True
1:59:14.692205 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:14.716703 INFO: Test AUC: 0.694
1:59:14.716798 INFO: Train AUC: 0.726
1:59:14.716829 INFO: AUC difference: 4.42%
1:59:14.893451 INFO: Resetting torch num_threads to 100
1:59:14.894077 INFO: === FDR correction performed with classifier version 6 ===
1:59:14.894729 PROGRESS: ============================= Precursor FDR =============================
1:59:14.894825 PROGRESS: Total precursors accumulated: 372
1:59:14.894890 PROGRESS: Target precursors: 351 (94.35%)
1:59:14.894955 PROGRESS: Decoy precursors: 21 (5.65%)
1:59:14.895005 PROGRESS: 
1:59:14.895051 PROGRESS: Precursor Summary:
1:59:14.896041 PROGRESS: Channel   0:	 0.05 FDR:   337; 0.01 FDR:   266; 0.001 FDR:   235
1:59:14.896133 PROGRESS: 
1:59:14.896190 PROGRESS: Protein Summary:
1:59:14.897339 PROGRESS: Channel   0:	 0.05 FDR:   327; 0.01 FDR:   259; 0.001 FDR:   229
1:59:14.897432 PROGRESS: =========================================================================
1:59:14.908101 INFO: fragments_df: keeping 2582 of 24922 [sum(precursor_idx_mask)=5876 sum(mass_error_mask)=24922 stop_rank=2582
1:59:14.914583 INFO: calibration group: precursor, fitting rt estimator 
1:59:15.011009 INFO: calibration group: fragment, fitting mz estimator 
1:59:15.303129 INFO: Using score_cutoff 51.69599375152588 (fac=0.99, q=1)
1:59:15.303726 INFO: calibration group: precursor, predicting mz
1:59:15.303817 WARNING: mz prediction was skipped as it has not been fitted yet
1:59:15.303850 INFO: calibration group: precursor, predicting rt
1:59:15.305776 INFO: calibration group: fragment, predicting mz
1:59:15.307905 INFO: === checking if optimization conditions were reached ===
1:59:15.309226 PROGRESS: ❌ ms2_error      : 14.0853 > 6.7411 or insufficient steps taken.
1:59:15.309278 INFO: ==============================================
1:59:15.309369 INFO: Starting optimization step 8.
1:59:15.309437 PROGRESS: === Extracting elution groups 0 to 600 ===
1:59:15.309498 PROGRESS: Extracting batch of 1163 precursors
1:59:15.310666 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:15.310714 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:15.310750 INFO: FWHM in RT is 2.92 seconds, sigma is 0.38
1:59:15.310772 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:59:15.310976 INFO: Starting candidate selection
1:59:15.461784 INFO: Starting candidate scoring
1:59:15.502151 INFO: Finished candidate processing
1:59:15.502233 INFO: Collecting candidate features
1:59:15.513507 INFO: Collecting fragment features
1:59:15.518301 INFO: Finished candidate scoring
1:59:15.519934 PROGRESS: === Extracted 2326 precursors and 23093 fragments ===
1:59:15.520215 INFO: performing precursor FDR with 47 features
1:59:15.520258 INFO: Decoy channel: -1
1:59:15.520281 INFO: Competetive: True
1:59:15.522957 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:15.556111 INFO: Test AUC: 0.773
1:59:15.556189 INFO: Train AUC: 0.735
1:59:15.556218 INFO: AUC difference: 5.24%
1:59:15.556249 WARNING: AUC difference > 5%. This may indicate overfitting.
1:59:15.729164 INFO: Resetting torch num_threads to 100
1:59:15.729776 INFO: === FDR correction performed with classifier version 7 ===
1:59:15.730409 PROGRESS: ============================= Precursor FDR =============================
1:59:15.730501 PROGRESS: Total precursors accumulated: 437
1:59:15.730562 PROGRESS: Target precursors: 416 (95.19%)
1:59:15.730616 PROGRESS: Decoy precursors: 21 (4.81%)
1:59:15.730664 PROGRESS: 
1:59:15.730712 PROGRESS: Precursor Summary:
1:59:15.731729 PROGRESS: Channel   0:	 0.05 FDR:   416; 0.01 FDR:   262; 0.001 FDR:   209
1:59:15.731822 PROGRESS: 
1:59:15.731880 PROGRESS: Protein Summary:
1:59:15.733015 PROGRESS: Channel   0:	 0.05 FDR:   403; 0.01 FDR:   256; 0.001 FDR:   204
1:59:15.733111 PROGRESS: =========================================================================
1:59:15.736154 INFO: fragments_df: keeping 2657 of 23093 [sum(precursor_idx_mask)=5614 sum(mass_error_mask)=23093 stop_rank=2657
1:59:15.741139 INFO: calibration group: precursor, fitting rt estimator 
1:59:15.835036 INFO: calibration group: fragment, fitting mz estimator 
1:59:16.130272 INFO: Using score_cutoff 52.15815015106201 (fac=0.99, q=1)
1:59:16.130754 INFO: calibration group: precursor, predicting mz
1:59:16.130843 WARNING: mz prediction was skipped as it has not been fitted yet
1:59:16.130873 INFO: calibration group: precursor, predicting rt
1:59:16.132571 INFO: calibration group: fragment, predicting mz
1:59:16.134693 INFO: === checking if optimization conditions were reached ===
1:59:16.135987 PROGRESS: ❌ ms2_error      : 7.1260 > 6.7411 or insufficient steps taken.
1:59:16.136039 INFO: ==============================================
1:59:16.136124 INFO: Starting optimization step 9.
1:59:16.136191 PROGRESS: === Extracting elution groups 0 to 600 ===
1:59:16.136261 PROGRESS: Extracting batch of 1163 precursors
1:59:16.137255 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:16.137305 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:16.137337 INFO: FWHM in RT is 2.58 seconds, sigma is 0.33
1:59:16.137359 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:59:16.137525 INFO: Starting candidate selection
1:59:16.288023 INFO: Starting candidate scoring
1:59:16.329181 INFO: Finished candidate processing
1:59:16.329272 INFO: Collecting candidate features
1:59:16.340431 INFO: Collecting fragment features
1:59:16.345096 INFO: Finished candidate scoring
1:59:16.346755 PROGRESS: === Extracted 2325 precursors and 20831 fragments ===
1:59:16.347037 INFO: performing precursor FDR with 47 features
1:59:16.347072 INFO: Decoy channel: -1
1:59:16.347095 INFO: Competetive: True
1:59:16.349728 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:16.372718 INFO: Test AUC: 0.736
1:59:16.372787 INFO: Train AUC: 0.745
1:59:16.372819 INFO: AUC difference: 1.18%
1:59:16.545056 INFO: Resetting torch num_threads to 100
1:59:16.545666 INFO: === FDR correction performed with classifier version 8 ===
1:59:16.546313 PROGRESS: ============================= Precursor FDR =============================
1:59:16.546407 PROGRESS: Total precursors accumulated: 443
1:59:16.546468 PROGRESS: Target precursors: 430 (97.07%)
1:59:16.547223 PROGRESS: Decoy precursors: 13 (2.93%)
1:59:16.547282 PROGRESS: 
1:59:16.547328 PROGRESS: Precursor Summary:
1:59:16.548371 PROGRESS: Channel   0:	 0.05 FDR:   430; 0.01 FDR:   373; 0.001 FDR:   192
1:59:16.548465 PROGRESS: 
1:59:16.548521 PROGRESS: Protein Summary:
1:59:16.549693 PROGRESS: Channel   0:	 0.05 FDR:   415; 0.01 FDR:   360; 0.001 FDR:   187
1:59:16.549787 PROGRESS: =========================================================================
1:59:16.552874 INFO: fragments_df: keeping 3413 of 20831 [sum(precursor_idx_mask)=7352 sum(mass_error_mask)=20831 stop_rank=3413
1:59:16.557883 INFO: calibration group: precursor, fitting rt estimator 
1:59:16.661186 INFO: calibration group: fragment, fitting mz estimator 
1:59:17.045649 INFO: Using score_cutoff 38.196919116210935 (fac=0.99, q=1)
1:59:17.046069 INFO: calibration group: precursor, predicting mz
1:59:17.046153 WARNING: mz prediction was skipped as it has not been fitted yet
1:59:17.046184 INFO: calibration group: precursor, predicting rt
1:59:17.047722 INFO: calibration group: fragment, predicting mz
1:59:17.049809 INFO: === checking if optimization conditions were reached ===
1:59:17.051174 PROGRESS: ✅ ms2_error      : 6.7411 <= 6.7411
1:59:17.051227 INFO: ==============================================
1:59:17.051312 PROGRESS: Optimization finished for ms2_error.
1:59:17.056013 INFO: calibration group: precursor, predicting mz
1:59:17.056126 WARNING: mz prediction was skipped as it has not been fitted yet
1:59:17.056157 INFO: calibration group: precursor, predicting rt
1:59:17.057395 INFO: calibration group: fragment, predicting mz
1:59:17.059449 INFO: Starting optimization step 0.
1:59:17.059549 PROGRESS: === Extracting elution groups 0 to 600 ===
1:59:17.059614 PROGRESS: Extracting batch of 1163 precursors
1:59:17.060444 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:17.060497 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:17.060529 INFO: FWHM in RT is 2.34 seconds, sigma is 0.30
1:59:17.060551 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:59:17.060707 INFO: Starting candidate selection
1:59:17.208983 INFO: Starting candidate scoring
1:59:17.252102 INFO: Finished candidate processing
1:59:17.252188 INFO: Collecting candidate features
1:59:17.263238 INFO: Collecting fragment features
1:59:17.267884 INFO: Finished candidate scoring
1:59:17.269584 PROGRESS: === Extracted 2325 precursors and 20108 fragments ===
1:59:17.269866 INFO: performing precursor FDR with 47 features
1:59:17.269901 INFO: Decoy channel: -1
1:59:17.269924 INFO: Competetive: True
1:59:17.272469 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:17.296153 INFO: Test AUC: 0.723
1:59:17.296221 INFO: Train AUC: 0.740
1:59:17.296259 INFO: AUC difference: 2.26%
1:59:17.468856 INFO: Resetting torch num_threads to 100
1:59:17.469476 INFO: === FDR correction performed with classifier version 9 ===
1:59:17.470121 PROGRESS: ============================= Precursor FDR =============================
1:59:17.470215 PROGRESS: Total precursors accumulated: 429
1:59:17.470276 PROGRESS: Target precursors: 418 (97.44%)
1:59:17.470329 PROGRESS: Decoy precursors: 11 (2.56%)
1:59:17.470375 PROGRESS: 
1:59:17.470420 PROGRESS: Precursor Summary:
1:59:17.471433 PROGRESS: Channel   0:	 0.05 FDR:   418; 0.01 FDR:   374; 0.001 FDR:   313
1:59:17.471522 PROGRESS: 
1:59:17.471578 PROGRESS: Protein Summary:
1:59:17.472796 PROGRESS: Channel   0:	 0.05 FDR:   405; 0.01 FDR:   361; 0.001 FDR:   305
1:59:17.472900 PROGRESS: =========================================================================
1:59:17.475903 INFO: fragments_df: keeping 3347 of 20108 [sum(precursor_idx_mask)=7180 sum(mass_error_mask)=20108 stop_rank=3347
1:59:17.480889 INFO: calibration group: precursor, fitting rt estimator 
1:59:17.583318 INFO: calibration group: fragment, fitting mz estimator 
1:59:17.960726 INFO: Using score_cutoff 38.37868402862549 (fac=0.99, q=1)
1:59:17.961153 INFO: calibration group: precursor, predicting mz
1:59:17.961237 WARNING: mz prediction was skipped as it has not been fitted yet
1:59:17.961266 INFO: calibration group: precursor, predicting rt
1:59:17.962806 INFO: calibration group: fragment, predicting mz
1:59:17.964924 INFO: === checking if optimization conditions were reached ===
1:59:17.965039 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:59:17.966544 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 210.7607.
1:59:17.966594 INFO: ==============================================
1:59:17.966681 INFO: Starting optimization step 1.
1:59:17.966745 PROGRESS: === Extracting elution groups 0 to 600 ===
1:59:17.966802 PROGRESS: Extracting batch of 1163 precursors
1:59:17.967696 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:17.967741 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:17.967771 INFO: FWHM in RT is 2.26 seconds, sigma is 0.29
1:59:17.967792 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:59:17.967951 INFO: Starting candidate selection
1:59:18.086309 INFO: Starting candidate scoring
1:59:18.127842 INFO: Finished candidate processing
1:59:18.127924 INFO: Collecting candidate features
1:59:18.139255 INFO: Collecting fragment features
1:59:18.143495 INFO: Finished candidate scoring
1:59:18.145264 PROGRESS: === Extracted 2326 precursors and 19758 fragments ===
1:59:18.145554 INFO: performing precursor FDR with 47 features
1:59:18.145590 INFO: Decoy channel: -1
1:59:18.145612 INFO: Competetive: True
1:59:18.148155 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:18.172007 INFO: Test AUC: 0.747
1:59:18.172085 INFO: Train AUC: 0.740
1:59:18.172114 INFO: AUC difference: 0.99%
1:59:18.344998 INFO: Resetting torch num_threads to 100
1:59:18.345620 INFO: === FDR correction performed with classifier version 9 ===
1:59:18.346260 PROGRESS: ============================= Precursor FDR =============================
1:59:18.346354 PROGRESS: Total precursors accumulated: 430
1:59:18.346416 PROGRESS: Target precursors: 419 (97.44%)
1:59:18.346469 PROGRESS: Decoy precursors: 11 (2.56%)
1:59:18.346516 PROGRESS: 
1:59:18.346561 PROGRESS: Precursor Summary:
1:59:18.347561 PROGRESS: Channel   0:	 0.05 FDR:   419; 0.01 FDR:   331; 0.001 FDR:   270
1:59:18.347651 PROGRESS: 
1:59:18.347708 PROGRESS: Protein Summary:
1:59:18.348886 PROGRESS: Channel   0:	 0.05 FDR:   405; 0.01 FDR:   322; 0.001 FDR:   262
1:59:18.348982 PROGRESS: =========================================================================
1:59:18.351885 INFO: fragments_df: keeping 3053 of 19758 [sum(precursor_idx_mask)=6406 sum(mass_error_mask)=19758 stop_rank=3053
1:59:18.356869 INFO: calibration group: precursor, fitting rt estimator 
1:59:18.456522 INFO: calibration group: fragment, fitting mz estimator 
1:59:18.796659 INFO: Using score_cutoff 39.493998653411865 (fac=0.99, q=1)
1:59:18.797077 INFO: calibration group: precursor, predicting mz
1:59:18.797162 WARNING: mz prediction was skipped as it has not been fitted yet
1:59:18.797193 INFO: calibration group: precursor, predicting rt
1:59:18.798746 INFO: calibration group: fragment, predicting mz
1:59:18.800936 INFO: === checking if optimization conditions were reached ===
1:59:18.801044 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:59:18.802587 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 18.8472.
1:59:18.802640 INFO: ==============================================
1:59:18.802739 INFO: Starting optimization step 2.
1:59:18.802805 PROGRESS: === Extracting elution groups 0 to 600 ===
1:59:18.802860 PROGRESS: Extracting batch of 1163 precursors
1:59:18.803779 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:18.803823 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:18.803853 INFO: FWHM in RT is 2.30 seconds, sigma is 0.30
1:59:18.803874 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:59:18.804029 INFO: Starting candidate selection
1:59:18.918958 INFO: Starting candidate scoring
1:59:18.960689 INFO: Finished candidate processing
1:59:18.960775 INFO: Collecting candidate features
1:59:18.969194 WARNING: intensity_correlation has 2 NaNs ( 0.09 % out of 2250)
1:59:18.972157 INFO: Collecting fragment features
1:59:18.976264 INFO: Finished candidate scoring
1:59:18.977980 PROGRESS: === Extracted 2250 precursors and 17314 fragments ===
1:59:18.978258 INFO: performing precursor FDR with 47 features
1:59:18.978294 INFO: Decoy channel: -1
1:59:18.978317 INFO: Competetive: True
1:59:18.980820 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:18.981990 WARNING: dropped 2 decoy PSMs due to missing features
1:59:19.003852 INFO: Test AUC: 0.745
1:59:19.003923 INFO: Train AUC: 0.734
1:59:19.003953 INFO: AUC difference: 1.50%
1:59:19.175961 INFO: Resetting torch num_threads to 100
1:59:19.176584 INFO: === FDR correction performed with classifier version 9 ===
1:59:19.177225 PROGRESS: ============================= Precursor FDR =============================
1:59:19.177324 PROGRESS: Total precursors accumulated: 455
1:59:19.177385 PROGRESS: Target precursors: 442 (97.14%)
1:59:19.177438 PROGRESS: Decoy precursors: 13 (2.86%)
1:59:19.177487 PROGRESS: 
1:59:19.177533 PROGRESS: Precursor Summary:
1:59:19.178540 PROGRESS: Channel   0:	 0.05 FDR:   442; 0.01 FDR:   347; 0.001 FDR:   220
1:59:19.178635 PROGRESS: 
1:59:19.178696 PROGRESS: Protein Summary:
1:59:19.179873 PROGRESS: Channel   0:	 0.05 FDR:   427; 0.01 FDR:   338; 0.001 FDR:   215
1:59:19.179965 PROGRESS: =========================================================================
1:59:19.182699 INFO: fragments_df: keeping 2938 of 17314 [sum(precursor_idx_mask)=6321 sum(mass_error_mask)=17314 stop_rank=2938
1:59:19.187766 INFO: calibration group: precursor, fitting rt estimator 
1:59:19.296199 INFO: calibration group: fragment, fitting mz estimator 
1:59:19.624674 INFO: Using score_cutoff 38.82360243988037 (fac=0.99, q=1)
1:59:19.625092 INFO: calibration group: precursor, predicting mz
1:59:19.625178 WARNING: mz prediction was skipped as it has not been fitted yet
1:59:19.625208 INFO: calibration group: precursor, predicting rt
1:59:19.626752 INFO: calibration group: fragment, predicting mz
1:59:19.628857 INFO: === checking if optimization conditions were reached ===
1:59:19.628961 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:59:19.630583 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 9.3330.
1:59:19.630636 INFO: ==============================================
1:59:19.630725 INFO: Starting optimization step 3.
1:59:19.630790 PROGRESS: === Extracting elution groups 0 to 600 ===
1:59:19.630849 PROGRESS: Extracting batch of 1163 precursors
1:59:19.631753 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:19.631805 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:19.631837 INFO: FWHM in RT is 2.28 seconds, sigma is 0.29
1:59:19.631859 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:59:19.632020 INFO: Starting candidate selection
1:59:19.745813 INFO: Starting candidate scoring
1:59:19.787596 INFO: Finished candidate processing
1:59:19.787676 INFO: Collecting candidate features
1:59:19.798871 INFO: Collecting fragment features
1:59:19.802807 INFO: Finished candidate scoring
1:59:19.804439 PROGRESS: === Extracted 2268 precursors and 17459 fragments ===
1:59:19.804731 INFO: performing precursor FDR with 47 features
1:59:19.804767 INFO: Decoy channel: -1
1:59:19.804797 INFO: Competetive: True
1:59:19.807273 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:19.829751 INFO: Test AUC: 0.740
1:59:19.829828 INFO: Train AUC: 0.735
1:59:19.829856 INFO: AUC difference: 0.61%
1:59:20.001640 INFO: Resetting torch num_threads to 100
1:59:20.002243 INFO: === FDR correction performed with classifier version 9 ===
1:59:20.002873 PROGRESS: ============================= Precursor FDR =============================
1:59:20.002965 PROGRESS: Total precursors accumulated: 433
1:59:20.003025 PROGRESS: Target precursors: 420 (97.00%)
1:59:20.003076 PROGRESS: Decoy precursors: 13 (3.00%)
1:59:20.003121 PROGRESS: 
1:59:20.003164 PROGRESS: Precursor Summary:
1:59:20.004144 PROGRESS: Channel   0:	 0.05 FDR:   420; 0.01 FDR:   320; 0.001 FDR:   210
1:59:20.004232 PROGRESS: 
1:59:20.004306 PROGRESS: Protein Summary:
1:59:20.005477 PROGRESS: Channel   0:	 0.05 FDR:   408; 0.01 FDR:   312; 0.001 FDR:   205
1:59:20.005570 PROGRESS: =========================================================================
1:59:20.008212 INFO: fragments_df: keeping 2794 of 17459 [sum(precursor_idx_mask)=5960 sum(mass_error_mask)=17459 stop_rank=2794
1:59:20.013115 INFO: calibration group: precursor, fitting rt estimator 
1:59:20.111928 INFO: calibration group: fragment, fitting mz estimator 
1:59:20.421786 INFO: Using score_cutoff 39.43014949951172 (fac=0.99, q=1)
1:59:20.422207 INFO: calibration group: precursor, predicting mz
1:59:20.422291 WARNING: mz prediction was skipped as it has not been fitted yet
1:59:20.422321 INFO: calibration group: precursor, predicting rt
1:59:20.423875 INFO: calibration group: fragment, predicting mz
1:59:20.425986 INFO: === checking if optimization conditions were reached ===
1:59:20.426096 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:59:20.427694 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 7.2441.
1:59:20.427747 INFO: ==============================================
1:59:20.427834 INFO: Starting optimization step 4.
1:59:20.427905 PROGRESS: === Extracting elution groups 0 to 600 ===
1:59:20.427959 PROGRESS: Extracting batch of 1163 precursors
1:59:20.428858 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:20.428903 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:20.428932 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
1:59:20.428954 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:59:20.429108 INFO: Starting candidate selection
1:59:20.544507 INFO: Starting candidate scoring
1:59:20.585645 INFO: Finished candidate processing
1:59:20.585725 INFO: Collecting candidate features
1:59:20.594328 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2272)
1:59:20.597246 INFO: Collecting fragment features
1:59:20.601119 INFO: Finished candidate scoring
1:59:20.602762 PROGRESS: === Extracted 2272 precursors and 17481 fragments ===
1:59:20.603038 INFO: performing precursor FDR with 47 features
1:59:20.603074 INFO: Decoy channel: -1
1:59:20.603096 INFO: Competetive: True
1:59:20.605594 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:20.606752 WARNING: dropped 1 target PSMs due to missing features
1:59:20.628149 INFO: Test AUC: 0.743
1:59:20.628217 INFO: Train AUC: 0.738
1:59:20.628252 INFO: AUC difference: 0.68%
1:59:20.798913 INFO: Resetting torch num_threads to 100
1:59:20.799516 INFO: === FDR correction performed with classifier version 9 ===
1:59:20.800144 PROGRESS: ============================= Precursor FDR =============================
1:59:20.800377 PROGRESS: Total precursors accumulated: 433
1:59:20.800453 PROGRESS: Target precursors: 420 (97.00%)
1:59:20.800505 PROGRESS: Decoy precursors: 13 (3.00%)
1:59:20.800552 PROGRESS: 
1:59:20.800597 PROGRESS: Precursor Summary:
1:59:20.801593 PROGRESS: Channel   0:	 0.05 FDR:   420; 0.01 FDR:   318; 0.001 FDR:   216
1:59:20.801684 PROGRESS: 
1:59:20.801740 PROGRESS: Protein Summary:
1:59:20.802896 PROGRESS: Channel   0:	 0.05 FDR:   405; 0.01 FDR:   310; 0.001 FDR:   211
1:59:20.802998 PROGRESS: =========================================================================
1:59:20.805696 INFO: fragments_df: keeping 2787 of 17481 [sum(precursor_idx_mask)=5906 sum(mass_error_mask)=17481 stop_rank=2787
1:59:20.810606 INFO: calibration group: precursor, fitting rt estimator 
1:59:20.909495 INFO: calibration group: fragment, fitting mz estimator 
1:59:21.219803 INFO: Using score_cutoff 38.747350263977054 (fac=0.99, q=1)
1:59:21.220226 INFO: calibration group: precursor, predicting mz
1:59:21.220320 WARNING: mz prediction was skipped as it has not been fitted yet
1:59:21.220350 INFO: calibration group: precursor, predicting rt
1:59:21.221876 INFO: calibration group: fragment, predicting mz
1:59:21.224002 INFO: === checking if optimization conditions were reached ===
1:59:21.224105 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1:59:21.225702 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 9.2205.
1:59:21.225761 INFO: ==============================================
1:59:21.225851 INFO: Starting optimization step 5.
1:59:21.225925 PROGRESS: === Extracting elution groups 0 to 600 ===
1:59:21.225980 PROGRESS: Extracting batch of 1163 precursors
1:59:21.226885 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:21.226930 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:21.226960 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
1:59:21.226981 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:59:21.227137 INFO: Starting candidate selection
1:59:21.342718 INFO: Starting candidate scoring
1:59:21.385025 INFO: Finished candidate processing
1:59:21.385105 INFO: Collecting candidate features
1:59:21.396194 INFO: Collecting fragment features
1:59:21.400632 INFO: Finished candidate scoring
1:59:21.402302 PROGRESS: === Extracted 2263 precursors and 17406 fragments ===
1:59:21.402582 INFO: performing precursor FDR with 47 features
1:59:21.402618 INFO: Decoy channel: -1
1:59:21.402640 INFO: Competetive: True
1:59:21.405132 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:21.428138 INFO: Test AUC: 0.740
1:59:21.428212 INFO: Train AUC: 0.738
1:59:21.428251 INFO: AUC difference: 0.33%
1:59:21.601063 INFO: Resetting torch num_threads to 100
1:59:21.601669 INFO: === FDR correction performed with classifier version 9 ===
1:59:21.602327 PROGRESS: ============================= Precursor FDR =============================
1:59:21.602423 PROGRESS: Total precursors accumulated: 428
1:59:21.602489 PROGRESS: Target precursors: 414 (96.73%)
1:59:21.602547 PROGRESS: Decoy precursors: 14 (3.27%)
1:59:21.602601 PROGRESS: 
1:59:21.602651 PROGRESS: Precursor Summary:
1:59:21.603654 PROGRESS: Channel   0:	 0.05 FDR:   414; 0.01 FDR:   321; 0.001 FDR:   212
1:59:21.603752 PROGRESS: 
1:59:21.603815 PROGRESS: Protein Summary:
1:59:21.604990 PROGRESS: Channel   0:	 0.05 FDR:   401; 0.01 FDR:   313; 0.001 FDR:   207
1:59:21.605090 PROGRESS: =========================================================================
1:59:21.607775 INFO: fragments_df: keeping 2799 of 17406 [sum(precursor_idx_mask)=5966 sum(mass_error_mask)=17406 stop_rank=2799
1:59:21.612689 INFO: calibration group: precursor, fitting rt estimator 
1:59:21.711406 INFO: calibration group: fragment, fitting mz estimator 
1:59:22.021807 INFO: Using score_cutoff 38.75409201049805 (fac=0.99, q=1)
1:59:22.022236 INFO: calibration group: precursor, predicting mz
1:59:22.022326 WARNING: mz prediction was skipped as it has not been fitted yet
1:59:22.022359 INFO: calibration group: precursor, predicting rt
1:59:22.023925 INFO: calibration group: fragment, predicting mz
1:59:22.026057 INFO: === checking if optimization conditions were reached ===
1:59:22.026174 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1:59:22.027776 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 9.8475.
1:59:22.027828 INFO: ==============================================
1:59:22.027926 INFO: Starting optimization step 6.
1:59:22.028003 PROGRESS: === Extracting elution groups 0 to 600 ===
1:59:22.028057 PROGRESS: Extracting batch of 1163 precursors
1:59:22.028975 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:22.029024 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:22.029054 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
1:59:22.029075 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:59:22.029232 INFO: Starting candidate selection
1:59:22.145651 INFO: Starting candidate scoring
1:59:22.186837 INFO: Finished candidate processing
1:59:22.186922 INFO: Collecting candidate features
1:59:22.197873 INFO: Collecting fragment features
1:59:22.201738 INFO: Finished candidate scoring
1:59:22.203352 PROGRESS: === Extracted 2260 precursors and 17395 fragments ===
1:59:22.203634 INFO: performing precursor FDR with 47 features
1:59:22.203669 INFO: Decoy channel: -1
1:59:22.203691 INFO: Competetive: True
1:59:22.206178 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:22.229110 INFO: Test AUC: 0.746
1:59:22.229181 INFO: Train AUC: 0.735
1:59:22.229209 INFO: AUC difference: 1.48%
1:59:22.400548 INFO: Resetting torch num_threads to 100
1:59:22.401162 INFO: === FDR correction performed with classifier version 9 ===
1:59:22.401793 PROGRESS: ============================= Precursor FDR =============================
1:59:22.401885 PROGRESS: Total precursors accumulated: 428
1:59:22.401944 PROGRESS: Target precursors: 414 (96.73%)
1:59:22.401997 PROGRESS: Decoy precursors: 14 (3.27%)
1:59:22.402042 PROGRESS: 
1:59:22.402086 PROGRESS: Precursor Summary:
1:59:22.403059 PROGRESS: Channel   0:	 0.05 FDR:   414; 0.01 FDR:   321; 0.001 FDR:   207
1:59:22.403148 PROGRESS: 
1:59:22.403203 PROGRESS: Protein Summary:
1:59:22.404370 PROGRESS: Channel   0:	 0.05 FDR:   401; 0.01 FDR:   313; 0.001 FDR:   202
1:59:22.404463 PROGRESS: =========================================================================
1:59:22.407176 INFO: fragments_df: keeping 2791 of 17395 [sum(precursor_idx_mask)=5965 sum(mass_error_mask)=17395 stop_rank=2791
1:59:22.412080 INFO: calibration group: precursor, fitting rt estimator 
1:59:22.510073 INFO: calibration group: fragment, fitting mz estimator 
1:59:22.818892 INFO: Using score_cutoff 38.75463054656982 (fac=0.99, q=1)
1:59:22.819320 INFO: calibration group: precursor, predicting mz
1:59:22.819409 WARNING: mz prediction was skipped as it has not been fitted yet
1:59:22.819438 INFO: calibration group: precursor, predicting rt
1:59:22.821000 INFO: calibration group: fragment, predicting mz
1:59:22.823135 INFO: === checking if optimization conditions were reached ===
1:59:22.823236 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1:59:22.824869 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 9.8475.
1:59:22.824920 INFO: ==============================================
1:59:22.825010 INFO: Starting optimization step 7.
1:59:22.825073 PROGRESS: === Extracting elution groups 0 to 600 ===
1:59:22.825132 PROGRESS: Extracting batch of 1163 precursors
1:59:22.826053 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:22.826098 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:22.826128 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
1:59:22.826149 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:59:22.826307 INFO: Starting candidate selection
1:59:22.941842 INFO: Starting candidate scoring
1:59:22.984401 INFO: Finished candidate processing
1:59:22.984477 INFO: Collecting candidate features
1:59:22.995569 INFO: Collecting fragment features
1:59:22.999623 INFO: Finished candidate scoring
1:59:23.001267 PROGRESS: === Extracted 2261 precursors and 17396 fragments ===
1:59:23.001541 INFO: performing precursor FDR with 47 features
1:59:23.001576 INFO: Decoy channel: -1
1:59:23.001598 INFO: Competetive: True
1:59:23.004084 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:23.028535 INFO: Test AUC: 0.761
1:59:23.028642 INFO: Train AUC: 0.732
1:59:23.028672 INFO: AUC difference: 3.93%
1:59:23.199763 INFO: Resetting torch num_threads to 100
1:59:23.200379 INFO: === FDR correction performed with classifier version 9 ===
1:59:23.201015 PROGRESS: ============================= Precursor FDR =============================
1:59:23.201108 PROGRESS: Total precursors accumulated: 429
1:59:23.201169 PROGRESS: Target precursors: 416 (96.97%)
1:59:23.201221 PROGRESS: Decoy precursors: 13 (3.03%)
1:59:23.201269 PROGRESS: 
1:59:23.201314 PROGRESS: Precursor Summary:
1:59:23.202294 PROGRESS: Channel   0:	 0.05 FDR:   416; 0.01 FDR:   335; 0.001 FDR:   208
1:59:23.202384 PROGRESS: 
1:59:23.202442 PROGRESS: Protein Summary:
1:59:23.203609 PROGRESS: Channel   0:	 0.05 FDR:   403; 0.01 FDR:   327; 0.001 FDR:   203
1:59:23.203707 PROGRESS: =========================================================================
1:59:23.206443 INFO: fragments_df: keeping 2855 of 17396 [sum(precursor_idx_mask)=6192 sum(mass_error_mask)=17396 stop_rank=2855
1:59:23.211366 INFO: calibration group: precursor, fitting rt estimator 
1:59:23.311753 INFO: calibration group: fragment, fitting mz estimator 
1:59:23.629768 INFO: Using score_cutoff 37.72888021087646 (fac=0.99, q=1)
1:59:23.630178 INFO: calibration group: precursor, predicting mz
1:59:23.630265 WARNING: mz prediction was skipped as it has not been fitted yet
1:59:23.630296 INFO: calibration group: precursor, predicting rt
1:59:23.631835 INFO: calibration group: fragment, predicting mz
1:59:23.633979 INFO: === checking if optimization conditions were reached ===
1:59:23.634091 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
1:59:23.635065 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 18.8472 found after 8 searches.
1:59:23.635114 INFO: ==============================================
1:59:23.635200 PROGRESS: Optimization finished for rt_error.
1:59:23.639831 INFO: calibration group: precursor, predicting mz
1:59:23.639949 WARNING: mz prediction was skipped as it has not been fitted yet
1:59:23.639980 INFO: calibration group: precursor, predicting rt
1:59:23.641248 INFO: calibration group: fragment, predicting mz
1:59:23.669375 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:59:23.669519 PROGRESS: ==============================================
1:59:23.669588 PROGRESS: ms2_error      : 6.7411
1:59:23.669645 PROGRESS: rt_error       : 18.8472
1:59:23.669692 PROGRESS: ==============================================
1:59:23.670348 INFO: calibration group: precursor, predicting mz
1:59:23.670450 WARNING: mz prediction was skipped as it has not been fitted yet
1:59:23.670478 INFO: calibration group: precursor, predicting rt
1:59:23.804057 INFO: calibration group: fragment, predicting mz
1:59:24.170387 PROGRESS: Extracting batch of 238438 precursors
1:59:24.275672 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:24.275825 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:24.275863 INFO: FWHM in RT is 2.28 seconds, sigma is 0.29
1:59:24.275888 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:59:24.276176 INFO: Starting candidate selection
1:59:30.909109 INFO: Applying score cutoff of 38.82360243988037
1:59:30.914730 INFO: Removed 228473 precursors with score below cutoff
1:59:30.975326 INFO: Starting candidate scoring
1:59:32.532352 INFO: Finished candidate processing
1:59:32.532456 INFO: Collecting candidate features
1:59:32.950808 INFO: Collecting fragment features
1:59:33.094777 INFO: Finished candidate scoring
1:59:33.214056 INFO: === FDR correction performed with classifier version 12 ===
1:59:33.214648 INFO: performing precursor FDR with 47 features
1:59:33.214688 INFO: Decoy channel: -1
1:59:33.214711 INFO: Competetive: True
1:59:33.288833 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:33.315959 WARNING: FDR calculation for 163755 target and 72340 decoy PSMs
1:59:33.316124 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1:59:38.478136 INFO: Test AUC: 0.899
1:59:38.478366 INFO: Train AUC: 0.902
1:59:38.478403 INFO: AUC difference: 0.31%
1:59:38.719257 INFO: Resetting torch num_threads to 100
1:59:38.740260 INFO: Removing fragments below FDR threshold
1:59:38.805016 PROGRESS: ============================= Precursor FDR =============================
1:59:38.805369 PROGRESS: Total precursors accumulated: 95,425
1:59:38.805440 PROGRESS: Target precursors: 94,481 (99.01%)
1:59:38.805494 PROGRESS: Decoy precursors: 944 (0.99%)
1:59:38.805541 PROGRESS: 
1:59:38.805589 PROGRESS: Precursor Summary:
1:59:38.847457 PROGRESS: Channel   0:	 0.05 FDR: 94,481; 0.01 FDR: 94,481; 0.001 FDR: 81,130
1:59:38.847794 PROGRESS: 
1:59:38.847867 PROGRESS: Protein Summary:
1:59:38.914839 PROGRESS: Channel   0:	 0.05 FDR: 10,341; 0.01 FDR: 10,341; 0.001 FDR: 9,087
1:59:38.915134 PROGRESS: =========================================================================
1:59:39.581449 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:59:39.614668 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:59:39.614853 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant
1:59:39.614932 INFO: Creating folder run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/figures
1:59:39.615798 INFO: Initializing RawFileManager
1:59:49.249178 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
1:59:49.253312 INFO: Determining DIA cycle
1:59:49.269759 INFO: Found cycle with start 0.00 min and length 300.
1:59:49.437801 INFO: RT (min)            : 0.0 - 26.9
1:59:49.437899 INFO: RT duration (sec)   : 1611.2
1:59:49.437927 INFO: RT duration (min)   : 26.9
1:59:49.437951 INFO: Cycle len (scans)   : 300
1:59:49.437970 INFO: Cycle len (sec)     : 1.65
1:59:49.437988 INFO: Number of cycles    : 977
1:59:49.438006 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:59:49.474753 INFO: Initializing CalibrationManager
1:59:49.475094 INFO: Loading calibration config
1:59:49.475581 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'}]
1:59:49.475670 INFO: Calibration group :fragment, found 1 estimator(s)
1:59:49.475749 INFO: Calibration group :precursor, found 3 estimator(s)
1:59:49.475827 INFO: Disabling ion mobility calibration
1:59:49.475854 INFO: removed mobility estimator from group precursor
1:59:49.475986 INFO: Initializing OptimizationManager
1:59:49.476099 INFO: initial parameter: ms1_error = 30
1:59:49.476737 INFO: initial parameter: ms2_error = 30
1:59:49.476801 INFO: initial parameter: rt_error = 805.5982666015625
1:59:49.476847 INFO: initial parameter: mobility_error = 0.1
1:59:49.476890 INFO: initial parameter: column_type = library
1:59:49.476950 INFO: initial parameter: num_candidates = 1
1:59:49.476995 INFO: initial parameter: classifier_version = -1
1:59:49.477041 INFO: initial parameter: fwhm_rt = 5
1:59:49.477081 INFO: initial parameter: fwhm_mobility = 0.01
1:59:49.477121 INFO: initial parameter: score_cutoff = 0
1:59:49.477177 INFO: Initializing TimingManager
1:59:49.477227 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:59:49.477305 INFO: FDRManager not loaded from disk.
1:59:49.477327 INFO: Initializing FDRManager
1:59:49.477362 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:59:49.518610 PROGRESS: 123,909 target precursors potentially observable (0 removed)
1:59:49.586505 PROGRESS: Starting initial search for precursors.
1:59:49.594670 INFO: Starting optimization step 0.
1:59:49.594844 PROGRESS: === Extracting elution groups 0 to 200 ===
1:59:49.594920 PROGRESS: Extracting batch of 392 precursors
1:59:49.595909 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:49.595960 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:49.595998 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:59:49.596022 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:59:49.596289 INFO: Starting candidate selection
1:59:49.723159 INFO: Starting candidate scoring
1:59:49.760108 INFO: Finished candidate processing
1:59:49.760185 INFO: Collecting candidate features
1:59:49.768694 INFO: Collecting fragment features
1:59:49.770777 INFO: Finished candidate scoring
1:59:49.771527 PROGRESS: === Extracted 392 precursors and 4298 fragments ===
1:59:49.771804 INFO: performing precursor FDR with 47 features
1:59:49.771843 INFO: Decoy channel: -1
1:59:49.771869 INFO: Competetive: True
1:59:49.772851 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:49.791643 INFO: Test AUC: 0.376
1:59:49.791713 INFO: Train AUC: 0.346
1:59:49.791742 INFO: AUC difference: 8.78%
1:59:49.791765 WARNING: AUC difference > 5%. This may indicate overfitting.
1:59:49.968101 INFO: Resetting torch num_threads to 100
1:59:49.968689 INFO: === FDR correction performed with classifier version -1 ===
1:59:49.969368 PROGRESS: ============================= Precursor FDR =============================
1:59:49.969462 PROGRESS: Total precursors accumulated: 200
1:59:49.969522 PROGRESS: Target precursors: 75 (37.50%)
1:59:49.969575 PROGRESS: Decoy precursors: 125 (62.50%)
1:59:49.969619 PROGRESS: 
1:59:49.969670 PROGRESS: Precursor Summary:
1:59:49.970539 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:59:49.970629 PROGRESS: 
1:59:49.970684 PROGRESS: Protein Summary:
1:59:49.971590 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:59:49.971681 PROGRESS: =========================================================================
1:59:49.975430 INFO: Starting optimization step 1.
1:59:49.975535 PROGRESS: === Extracting elution groups 200 to 600 ===
1:59:49.975597 PROGRESS: Extracting batch of 771 precursors
1:59:49.976357 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:49.976403 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:49.976436 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:59:49.976460 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:59:49.976633 INFO: Starting candidate selection
1:59:50.110810 INFO: Starting candidate scoring
1:59:50.148778 INFO: Finished candidate processing
1:59:50.148855 INFO: Collecting candidate features
1:59:50.157744 INFO: Collecting fragment features
1:59:50.160264 INFO: Finished candidate scoring
1:59:50.162256 PROGRESS: === Extracted 1163 precursors and 12699 fragments ===
1:59:50.163015 INFO: performing precursor FDR with 47 features
1:59:50.163059 INFO: Decoy channel: -1
1:59:50.163083 INFO: Competetive: True
1:59:50.165848 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:50.188180 INFO: Test AUC: 0.347
1:59:50.188258 INFO: Train AUC: 0.370
1:59:50.188289 INFO: AUC difference: 6.20%
1:59:50.188325 WARNING: AUC difference > 5%. This may indicate overfitting.
1:59:50.375456 INFO: Resetting torch num_threads to 100
1:59:50.376105 INFO: === FDR correction performed with classifier version -1 ===
1:59:50.376792 PROGRESS: ============================= Precursor FDR =============================
1:59:50.376887 PROGRESS: Total precursors accumulated: 600
1:59:50.376948 PROGRESS: Target precursors: 231 (38.50%)
1:59:50.377000 PROGRESS: Decoy precursors: 369 (61.50%)
1:59:50.377046 PROGRESS: 
1:59:50.377090 PROGRESS: Precursor Summary:
1:59:50.377965 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:59:50.378055 PROGRESS: 
1:59:50.378110 PROGRESS: Protein Summary:
1:59:50.379028 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:59:50.379118 PROGRESS: =========================================================================
1:59:50.383805 INFO: Starting optimization step 2.
1:59:50.383917 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:59:50.383981 PROGRESS: Extracting batch of 1538 precursors
1:59:50.384824 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:50.384871 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:50.384902 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:59:50.384923 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:59:50.385084 INFO: Starting candidate selection
1:59:50.542659 INFO: Starting candidate scoring
1:59:50.583421 INFO: Finished candidate processing
1:59:50.583500 INFO: Collecting candidate features
1:59:50.593604 INFO: Collecting fragment features
1:59:50.597559 INFO: Finished candidate scoring
1:59:50.600435 PROGRESS: === Extracted 2701 precursors and 29421 fragments ===
1:59:50.601401 INFO: performing precursor FDR with 47 features
1:59:50.601443 INFO: Decoy channel: -1
1:59:50.601467 INFO: Competetive: True
1:59:50.604537 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:50.643172 INFO: Test AUC: 0.376
1:59:50.643260 INFO: Train AUC: 0.344
1:59:50.643289 INFO: AUC difference: 9.17%
1:59:50.643311 WARNING: AUC difference > 5%. This may indicate overfitting.
1:59:50.818986 INFO: Resetting torch num_threads to 100
1:59:50.819735 INFO: === FDR correction performed with classifier version -1 ===
1:59:50.820570 PROGRESS: ============================= Precursor FDR =============================
1:59:50.820688 PROGRESS: Total precursors accumulated: 1,400
1:59:50.820751 PROGRESS: Target precursors: 524 (37.43%)
1:59:50.820802 PROGRESS: Decoy precursors: 876 (62.57%)
1:59:50.820849 PROGRESS: 
1:59:50.820893 PROGRESS: Precursor Summary:
1:59:50.821779 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:59:50.821868 PROGRESS: 
1:59:50.821923 PROGRESS: Protein Summary:
1:59:50.822873 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:59:50.822962 PROGRESS: =========================================================================
1:59:50.829470 INFO: Starting optimization step 3.
1:59:50.829583 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:59:50.829650 PROGRESS: Extracting batch of 3065 precursors
1:59:50.830723 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:50.830769 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:50.830800 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:59:50.830820 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:59:50.830982 INFO: Starting candidate selection
1:59:51.082875 INFO: Starting candidate scoring
1:59:51.125749 INFO: Finished candidate processing
1:59:51.125843 INFO: Collecting candidate features
1:59:51.138777 INFO: Collecting fragment features
1:59:51.143040 INFO: Finished candidate scoring
1:59:51.147745 PROGRESS: === Extracted 5766 precursors and 62639 fragments ===
1:59:51.148992 INFO: performing precursor FDR with 47 features
1:59:51.149036 INFO: Decoy channel: -1
1:59:51.149060 INFO: Competetive: True
1:59:51.152788 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:51.203837 INFO: Test AUC: 0.326
1:59:51.203952 INFO: Train AUC: 0.348
1:59:51.203983 INFO: AUC difference: 6.12%
1:59:51.204005 WARNING: AUC difference > 5%. This may indicate overfitting.
1:59:51.382665 INFO: Resetting torch num_threads to 100
1:59:51.383554 INFO: === FDR correction performed with classifier version -1 ===
1:59:51.384512 PROGRESS: ============================= Precursor FDR =============================
1:59:51.384606 PROGRESS: Total precursors accumulated: 2,997
1:59:51.384671 PROGRESS: Target precursors: 1,133 (37.80%)
1:59:51.384724 PROGRESS: Decoy precursors: 1,864 (62.20%)
1:59:51.384770 PROGRESS: 
1:59:51.384813 PROGRESS: Precursor Summary:
1:59:51.385706 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:59:51.385794 PROGRESS: 
1:59:51.385849 PROGRESS: Protein Summary:
1:59:51.386818 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:59:51.386905 PROGRESS: =========================================================================
1:59:51.396702 INFO: Starting optimization step 4.
1:59:51.396847 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:59:51.396912 PROGRESS: Extracting batch of 6167 precursors
1:59:51.398424 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:51.398474 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:51.398504 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:59:51.398526 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:59:51.398690 INFO: Starting candidate selection
1:59:51.804128 INFO: Starting candidate scoring
1:59:51.853841 INFO: Finished candidate processing
1:59:51.853943 INFO: Collecting candidate features
1:59:51.871387 INFO: Collecting fragment features
1:59:51.878247 INFO: Finished candidate scoring
1:59:51.885762 PROGRESS: === Extracted 11933 precursors and 129470 fragments ===
1:59:51.887665 INFO: performing precursor FDR with 47 features
1:59:51.887725 INFO: Decoy channel: -1
1:59:51.887754 INFO: Competetive: True
1:59:51.893144 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:51.973232 INFO: Test AUC: 0.337
1:59:51.973361 INFO: Train AUC: 0.347
1:59:51.973391 INFO: AUC difference: 2.72%
1:59:52.149255 INFO: Resetting torch num_threads to 100
1:59:52.150348 INFO: === FDR correction performed with classifier version -1 ===
1:59:52.151774 PROGRESS: ============================= Precursor FDR =============================
1:59:52.151876 PROGRESS: Total precursors accumulated: 6,186
1:59:52.151938 PROGRESS: Target precursors: 2,272 (36.73%)
1:59:52.151989 PROGRESS: Decoy precursors: 3,914 (63.27%)
1:59:52.152035 PROGRESS: 
1:59:52.152079 PROGRESS: Precursor Summary:
1:59:52.153001 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:59:52.153092 PROGRESS: 
1:59:52.153147 PROGRESS: Protein Summary:
1:59:52.154119 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:59:52.154208 PROGRESS: =========================================================================
1:59:52.169979 INFO: Starting optimization step 5.
1:59:52.170199 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:59:52.170267 PROGRESS: Extracting batch of 12312 precursors
1:59:52.172794 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:52.172848 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:52.172880 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:59:52.172903 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:59:52.173081 INFO: Starting candidate selection
1:59:52.933467 INFO: Starting candidate scoring
1:59:53.019159 INFO: Finished candidate processing
1:59:53.019269 INFO: Collecting candidate features
1:59:53.046763 INFO: Collecting fragment features
1:59:53.056999 INFO: Finished candidate scoring
1:59:53.070586 PROGRESS: === Extracted 24245 precursors and 263600 fragments ===
1:59:53.073954 INFO: performing precursor FDR with 47 features
1:59:53.074023 INFO: Decoy channel: -1
1:59:53.074049 INFO: Competetive: True
1:59:53.082943 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:53.353054 INFO: Test AUC: 0.718
1:59:53.353195 INFO: Train AUC: 0.721
1:59:53.353229 INFO: AUC difference: 0.53%
1:59:53.541527 INFO: Resetting torch num_threads to 100
1:59:53.543945 INFO: === FDR correction performed with classifier version -1 ===
1:59:53.544667 PROGRESS: ============================= Precursor FDR =============================
1:59:53.544762 PROGRESS: Total precursors accumulated: 3
1:59:53.544829 PROGRESS: Target precursors: 3 (100.00%)
1:59:53.544883 PROGRESS: Decoy precursors: 0 (0.00%)
1:59:53.544930 PROGRESS: 
1:59:53.544975 PROGRESS: Precursor Summary:
1:59:53.545927 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1:59:53.546016 PROGRESS: 
1:59:53.546072 PROGRESS: Protein Summary:
1:59:53.547090 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1:59:53.547181 PROGRESS: =========================================================================
1:59:53.572006 INFO: Starting optimization step 6.
1:59:53.572321 PROGRESS: === Extracting elution groups 12600 to 25400 ===
1:59:53.572394 PROGRESS: Extracting batch of 24645 precursors
1:59:53.577469 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:53.577533 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:53.577568 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:59:53.577590 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:59:53.577786 INFO: Starting candidate selection
1:59:55.039726 INFO: Starting candidate scoring
1:59:55.198892 INFO: Finished candidate processing
1:59:55.199002 INFO: Collecting candidate features
1:59:55.243471 INFO: Collecting fragment features
1:59:55.259791 INFO: Finished candidate scoring
1:59:55.286126 PROGRESS: === Extracted 48890 precursors and 531729 fragments ===
1:59:55.292648 INFO: performing precursor FDR with 47 features
1:59:55.292724 INFO: Decoy channel: -1
1:59:55.292751 INFO: Competetive: True
1:59:55.310046 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:56.043249 INFO: Test AUC: 0.825
1:59:56.043418 INFO: Train AUC: 0.822
1:59:56.043449 INFO: AUC difference: 0.35%
1:59:56.244154 INFO: Resetting torch num_threads to 100
1:59:56.246462 INFO: === FDR correction performed with classifier version -1 ===
1:59:56.248608 PROGRESS: ============================= Precursor FDR =============================
1:59:56.248718 PROGRESS: Total precursors accumulated: 13,927
1:59:56.248779 PROGRESS: Target precursors: 13,203 (94.80%)
1:59:56.248833 PROGRESS: Decoy precursors: 724 (5.20%)
1:59:56.248879 PROGRESS: 
1:59:56.248924 PROGRESS: Precursor Summary:
1:59:56.252470 PROGRESS: Channel   0:	 0.05 FDR: 12,866; 0.01 FDR: 8,770; 0.001 FDR: 5,541
1:59:56.252585 PROGRESS: 
1:59:56.252644 PROGRESS: Protein Summary:
1:59:56.258338 PROGRESS: Channel   0:	 0.05 FDR: 5,244; 0.01 FDR: 3,800; 0.001 FDR: 2,728
1:59:56.258477 PROGRESS: =========================================================================
1:59:56.309522 INFO: fragments_df: keeping 5000 of 531729 [sum(precursor_idx_mask)=99303 sum(mass_error_mask)=531729 stop_rank=5000
1:59:56.319721 INFO: calibration group: precursor, fitting rt estimator 
1:59:57.789132 INFO: calibration group: fragment, fitting mz estimator 
1:59:58.407854 INFO: Using score_cutoff 57.85410422172546 (fac=0.99, q=1)
1:59:58.408446 INFO: calibration group: precursor, predicting mz
1:59:58.408540 WARNING: mz prediction was skipped as it has not been fitted yet
1:59:58.408574 INFO: calibration group: precursor, predicting rt
1:59:58.410085 INFO: calibration group: fragment, predicting mz
1:59:58.412167 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:59:58.412303 INFO: Starting optimization step 7.
1:59:58.412374 PROGRESS: === Extracting elution groups 0 to 600 ===
1:59:58.412437 PROGRESS: Extracting batch of 1163 precursors
1:59:58.413449 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:58.413496 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:58.413530 INFO: FWHM in RT is 3.04 seconds, sigma is 0.39
1:59:58.413565 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:59:58.413765 INFO: Starting candidate selection
1:59:58.556344 INFO: Starting candidate scoring
1:59:58.596074 INFO: Finished candidate processing
1:59:58.596168 INFO: Collecting candidate features
1:59:58.608512 INFO: Collecting fragment features
1:59:58.612648 INFO: Finished candidate scoring
1:59:58.614316 PROGRESS: === Extracted 2326 precursors and 25039 fragments ===
1:59:58.614596 INFO: performing precursor FDR with 47 features
1:59:58.614632 INFO: Decoy channel: -1
1:59:58.614655 INFO: Competetive: True
1:59:58.617199 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:58.639361 INFO: Test AUC: 0.709
1:59:58.639432 INFO: Train AUC: 0.700
1:59:58.639460 INFO: AUC difference: 1.22%
1:59:58.818951 INFO: Resetting torch num_threads to 100
1:59:58.819560 INFO: === FDR correction performed with classifier version 6 ===
1:59:58.820206 PROGRESS: ============================= Precursor FDR =============================
1:59:58.820310 PROGRESS: Total precursors accumulated: 340
1:59:58.820371 PROGRESS: Target precursors: 323 (95.00%)
1:59:58.820429 PROGRESS: Decoy precursors: 17 (5.00%)
1:59:58.820479 PROGRESS: 
1:59:58.820527 PROGRESS: Precursor Summary:
1:59:58.821530 PROGRESS: Channel   0:	 0.05 FDR:   316; 0.01 FDR:   221; 0.001 FDR:   191
1:59:58.821620 PROGRESS: 
1:59:58.821677 PROGRESS: Protein Summary:
1:59:58.822797 PROGRESS: Channel   0:	 0.05 FDR:   301; 0.01 FDR:   215; 0.001 FDR:   185
1:59:58.822888 PROGRESS: =========================================================================
1:59:58.826450 INFO: fragments_df: keeping 2308 of 25039 [sum(precursor_idx_mask)=4920 sum(mass_error_mask)=25039 stop_rank=2308
1:59:58.831523 INFO: calibration group: precursor, fitting rt estimator 
1:59:58.930721 INFO: calibration group: fragment, fitting mz estimator 
1:59:59.187325 INFO: Using score_cutoff 60.554468009948735 (fac=0.99, q=1)
1:59:59.187736 INFO: calibration group: precursor, predicting mz
1:59:59.187823 WARNING: mz prediction was skipped as it has not been fitted yet
1:59:59.187854 INFO: calibration group: precursor, predicting rt
1:59:59.189429 INFO: calibration group: fragment, predicting mz
1:59:59.191515 INFO: === checking if optimization conditions were reached ===
1:59:59.192793 PROGRESS: ❌ ms2_error      : 14.9649 > 6.7411 or insufficient steps taken.
1:59:59.192847 INFO: ==============================================
1:59:59.192933 INFO: Starting optimization step 8.
1:59:59.193000 PROGRESS: === Extracting elution groups 0 to 600 ===
1:59:59.193058 PROGRESS: Extracting batch of 1163 precursors
1:59:59.193987 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:59:59.194035 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:59.194066 INFO: FWHM in RT is 2.84 seconds, sigma is 0.37
1:59:59.194088 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:59:59.194246 INFO: Starting candidate selection
1:59:59.334951 INFO: Starting candidate scoring
1:59:59.377274 INFO: Finished candidate processing
1:59:59.377356 INFO: Collecting candidate features
1:59:59.388532 INFO: Collecting fragment features
1:59:59.392657 INFO: Finished candidate scoring
1:59:59.394331 PROGRESS: === Extracted 2326 precursors and 23227 fragments ===
1:59:59.394621 INFO: performing precursor FDR with 47 features
1:59:59.394657 INFO: Decoy channel: -1
1:59:59.394681 INFO: Competetive: True
1:59:59.397189 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:59.419658 INFO: Test AUC: 0.695
1:59:59.419729 INFO: Train AUC: 0.742
1:59:59.419758 INFO: AUC difference: 6.33%
1:59:59.419781 WARNING: AUC difference > 5%. This may indicate overfitting.
2:00:04.338610 INFO: Resetting torch num_threads to 100
2:00:04.339224 INFO: === FDR correction performed with classifier version 7 ===
2:00:04.339884 PROGRESS: ============================= Precursor FDR =============================
2:00:04.339986 PROGRESS: Total precursors accumulated: 409
2:00:04.340049 PROGRESS: Target precursors: 391 (95.60%)
2:00:04.340101 PROGRESS: Decoy precursors: 18 (4.40%)
2:00:04.340157 PROGRESS: 
2:00:04.340202 PROGRESS: Precursor Summary:
2:00:04.341213 PROGRESS: Channel   0:	 0.05 FDR:   391; 0.01 FDR:   298; 0.001 FDR:   276
2:00:04.341307 PROGRESS: 
2:00:04.341363 PROGRESS: Protein Summary:
2:00:04.342524 PROGRESS: Channel   0:	 0.05 FDR:   376; 0.01 FDR:   286; 0.001 FDR:   266
2:00:04.342617 PROGRESS: =========================================================================
2:00:04.345776 INFO: fragments_df: keeping 2829 of 23227 [sum(precursor_idx_mask)=6255 sum(mass_error_mask)=23227 stop_rank=2829
2:00:04.350771 INFO: calibration group: precursor, fitting rt estimator 
2:00:04.446799 INFO: calibration group: fragment, fitting mz estimator 
2:00:04.758257 INFO: Using score_cutoff 47.090382055664065 (fac=0.99, q=1)
2:00:04.758688 INFO: calibration group: precursor, predicting mz
2:00:04.758775 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:04.758804 INFO: calibration group: precursor, predicting rt
2:00:04.760372 INFO: calibration group: fragment, predicting mz
2:00:04.762519 INFO: === checking if optimization conditions were reached ===
2:00:04.763838 PROGRESS: ❌ ms2_error      : 7.4450 > 6.7411 or insufficient steps taken.
2:00:04.763890 INFO: ==============================================
2:00:04.763976 INFO: Starting optimization step 9.
2:00:04.764041 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:04.764097 PROGRESS: Extracting batch of 1163 precursors
2:00:04.765031 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:04.765077 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:04.765107 INFO: FWHM in RT is 2.56 seconds, sigma is 0.33
2:00:04.765129 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:04.765285 INFO: Starting candidate selection
2:00:04.907189 INFO: Starting candidate scoring
2:00:04.946829 INFO: Finished candidate processing
2:00:04.946913 INFO: Collecting candidate features
2:00:04.958307 INFO: Collecting fragment features
2:00:04.961666 INFO: Finished candidate scoring
2:00:04.963379 PROGRESS: === Extracted 2326 precursors and 20730 fragments ===
2:00:04.963649 INFO: performing precursor FDR with 47 features
2:00:04.963685 INFO: Decoy channel: -1
2:00:04.963708 INFO: Competetive: True
2:00:04.966234 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:04.989932 INFO: Test AUC: 0.766
2:00:04.990012 INFO: Train AUC: 0.712
2:00:04.990044 INFO: AUC difference: 7.57%
2:00:04.990067 WARNING: AUC difference > 5%. This may indicate overfitting.
2:00:05.165951 INFO: Resetting torch num_threads to 100
2:00:05.166559 INFO: === FDR correction performed with classifier version 8 ===
2:00:05.167200 PROGRESS: ============================= Precursor FDR =============================
2:00:05.167293 PROGRESS: Total precursors accumulated: 427
2:00:05.167354 PROGRESS: Target precursors: 410 (96.02%)
2:00:05.167414 PROGRESS: Decoy precursors: 17 (3.98%)
2:00:05.167463 PROGRESS: 
2:00:05.167509 PROGRESS: Precursor Summary:
2:00:05.168499 PROGRESS: Channel   0:	 0.05 FDR:   410; 0.01 FDR:   284; 0.001 FDR:   134
2:00:05.168595 PROGRESS: 
2:00:05.168652 PROGRESS: Protein Summary:
2:00:05.169783 PROGRESS: Channel   0:	 0.05 FDR:   396; 0.01 FDR:   275; 0.001 FDR:   133
2:00:05.169874 PROGRESS: =========================================================================
2:00:05.172754 INFO: fragments_df: keeping 2697 of 20730 [sum(precursor_idx_mask)=5608 sum(mass_error_mask)=20730 stop_rank=2697
2:00:05.177716 INFO: calibration group: precursor, fitting rt estimator 
2:00:05.273010 INFO: calibration group: fragment, fitting mz estimator 
2:00:05.571437 INFO: Using score_cutoff 38.05927885093689 (fac=0.99, q=1)
2:00:05.571847 INFO: calibration group: precursor, predicting mz
2:00:05.571938 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:05.571968 INFO: calibration group: precursor, predicting rt
2:00:05.573526 INFO: calibration group: fragment, predicting mz
2:00:05.575677 INFO: === checking if optimization conditions were reached ===
2:00:05.576965 PROGRESS: ✅ ms2_error      : 6.7411 <= 6.7411
2:00:05.577017 INFO: ==============================================
2:00:05.577105 PROGRESS: Optimization finished for ms2_error.
2:00:05.581796 INFO: calibration group: precursor, predicting mz
2:00:05.581904 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:05.581934 INFO: calibration group: precursor, predicting rt
2:00:05.583197 INFO: calibration group: fragment, predicting mz
2:00:05.585325 INFO: Starting optimization step 0.
2:00:05.585434 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:05.585498 PROGRESS: Extracting batch of 1163 precursors
2:00:05.586301 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:05.586349 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:05.586380 INFO: FWHM in RT is 2.41 seconds, sigma is 0.31
2:00:05.586402 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:05.586555 INFO: Starting candidate selection
2:00:05.736988 INFO: Starting candidate scoring
2:00:05.777743 INFO: Finished candidate processing
2:00:05.777834 INFO: Collecting candidate features
2:00:05.789033 INFO: Collecting fragment features
2:00:05.793164 INFO: Finished candidate scoring
2:00:05.794775 PROGRESS: === Extracted 2325 precursors and 20123 fragments ===
2:00:05.795049 INFO: performing precursor FDR with 47 features
2:00:05.795085 INFO: Decoy channel: -1
2:00:05.795109 INFO: Competetive: True
2:00:05.797674 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:05.830307 INFO: Test AUC: 0.703
2:00:05.830386 INFO: Train AUC: 0.722
2:00:05.830415 INFO: AUC difference: 2.69%
2:00:06.003816 INFO: Resetting torch num_threads to 100
2:00:06.004441 INFO: === FDR correction performed with classifier version 9 ===
2:00:06.005091 PROGRESS: ============================= Precursor FDR =============================
2:00:06.005185 PROGRESS: Total precursors accumulated: 430
2:00:06.005244 PROGRESS: Target precursors: 408 (94.88%)
2:00:06.005295 PROGRESS: Decoy precursors: 22 (5.12%)
2:00:06.005343 PROGRESS: 
2:00:06.005388 PROGRESS: Precursor Summary:
2:00:06.006371 PROGRESS: Channel   0:	 0.05 FDR:   408; 0.01 FDR:   244; 0.001 FDR:   124
2:00:06.006460 PROGRESS: 
2:00:06.006515 PROGRESS: Protein Summary:
2:00:06.007659 PROGRESS: Channel   0:	 0.05 FDR:   394; 0.01 FDR:   237; 0.001 FDR:   123
2:00:06.007758 PROGRESS: =========================================================================
2:00:06.010583 INFO: fragments_df: keeping 2395 of 20123 [sum(precursor_idx_mask)=4837 sum(mass_error_mask)=20123 stop_rank=2395
2:00:06.015526 INFO: calibration group: precursor, fitting rt estimator 
2:00:06.104385 INFO: calibration group: fragment, fitting mz estimator 
2:00:06.370646 INFO: Using score_cutoff 39.68648851547241 (fac=0.99, q=1)
2:00:06.371052 INFO: calibration group: precursor, predicting mz
2:00:06.371146 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:06.371177 INFO: calibration group: precursor, predicting rt
2:00:06.372715 INFO: calibration group: fragment, predicting mz
2:00:06.374820 INFO: === checking if optimization conditions were reached ===
2:00:06.374923 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2:00:06.376305 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 170.3459.
2:00:06.376368 INFO: ==============================================
2:00:06.376471 INFO: Starting optimization step 1.
2:00:06.376541 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:06.376598 PROGRESS: Extracting batch of 1163 precursors
2:00:06.377527 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:06.377575 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:06.377605 INFO: FWHM in RT is 2.46 seconds, sigma is 0.32
2:00:06.377626 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:06.377785 INFO: Starting candidate selection
2:00:06.495336 INFO: Starting candidate scoring
2:00:06.535500 INFO: Finished candidate processing
2:00:06.535600 INFO: Collecting candidate features
2:00:06.546758 INFO: Collecting fragment features
2:00:06.550769 INFO: Finished candidate scoring
2:00:06.552461 PROGRESS: === Extracted 2326 precursors and 19677 fragments ===
2:00:06.552753 INFO: performing precursor FDR with 47 features
2:00:06.552796 INFO: Decoy channel: -1
2:00:06.552827 INFO: Competetive: True
2:00:06.555382 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:06.588025 INFO: Test AUC: 0.753
2:00:06.588106 INFO: Train AUC: 0.726
2:00:06.588147 INFO: AUC difference: 3.82%
2:00:06.761195 INFO: Resetting torch num_threads to 100
2:00:06.761835 INFO: === FDR correction performed with classifier version 9 ===
2:00:06.762497 PROGRESS: ============================= Precursor FDR =============================
2:00:06.762599 PROGRESS: Total precursors accumulated: 424
2:00:06.762670 PROGRESS: Target precursors: 406 (95.75%)
2:00:06.762734 PROGRESS: Decoy precursors: 18 (4.25%)
2:00:06.762794 PROGRESS: 
2:00:06.762852 PROGRESS: Precursor Summary:
2:00:06.763866 PROGRESS: Channel   0:	 0.05 FDR:   406; 0.01 FDR:   253; 0.001 FDR:   120
2:00:06.763963 PROGRESS: 
2:00:06.764031 PROGRESS: Protein Summary:
2:00:06.765198 PROGRESS: Channel   0:	 0.05 FDR:   393; 0.01 FDR:   247; 0.001 FDR:   119
2:00:06.765302 PROGRESS: =========================================================================
2:00:06.768089 INFO: fragments_df: keeping 2464 of 19677 [sum(precursor_idx_mask)=4975 sum(mass_error_mask)=19677 stop_rank=2464
2:00:06.773114 INFO: calibration group: precursor, fitting rt estimator 
2:00:06.873607 INFO: calibration group: fragment, fitting mz estimator 
2:00:07.146940 INFO: Using score_cutoff 37.47111373443603 (fac=0.99, q=1)
2:00:07.147342 INFO: calibration group: precursor, predicting mz
2:00:07.147426 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:07.147455 INFO: calibration group: precursor, predicting rt
2:00:07.149025 INFO: calibration group: fragment, predicting mz
2:00:07.151172 INFO: === checking if optimization conditions were reached ===
2:00:07.151279 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2:00:07.152766 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 52.1621.
2:00:07.152820 INFO: ==============================================
2:00:07.152907 INFO: Starting optimization step 2.
2:00:07.152972 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:07.153029 PROGRESS: Extracting batch of 1163 precursors
2:00:07.153924 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:07.153970 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:07.154000 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
2:00:07.154022 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:07.154175 INFO: Starting candidate selection
2:00:07.280622 INFO: Starting candidate scoring
2:00:07.321778 INFO: Finished candidate processing
2:00:07.321867 INFO: Collecting candidate features
2:00:07.333354 INFO: Collecting fragment features
2:00:07.337391 INFO: Finished candidate scoring
2:00:07.339087 PROGRESS: === Extracted 2318 precursors and 18590 fragments ===
2:00:07.339374 INFO: performing precursor FDR with 47 features
2:00:07.339415 INFO: Decoy channel: -1
2:00:07.339443 INFO: Competetive: True
2:00:07.342002 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:07.364351 INFO: Test AUC: 0.709
2:00:07.364422 INFO: Train AUC: 0.739
2:00:07.364450 INFO: AUC difference: 4.14%
2:00:07.540256 INFO: Resetting torch num_threads to 100
2:00:07.540878 INFO: === FDR correction performed with classifier version 9 ===
2:00:07.541507 PROGRESS: ============================= Precursor FDR =============================
2:00:07.541598 PROGRESS: Total precursors accumulated: 438
2:00:07.541657 PROGRESS: Target precursors: 422 (96.35%)
2:00:07.541708 PROGRESS: Decoy precursors: 16 (3.65%)
2:00:07.541754 PROGRESS: 
2:00:07.541799 PROGRESS: Precursor Summary:
2:00:07.542789 PROGRESS: Channel   0:	 0.05 FDR:   422; 0.01 FDR:   270; 0.001 FDR:   126
2:00:07.542889 PROGRESS: 
2:00:07.542946 PROGRESS: Protein Summary:
2:00:07.544086 PROGRESS: Channel   0:	 0.05 FDR:   406; 0.01 FDR:   263; 0.001 FDR:   125
2:00:07.544178 PROGRESS: =========================================================================
2:00:07.546921 INFO: fragments_df: keeping 2471 of 18590 [sum(precursor_idx_mask)=5228 sum(mass_error_mask)=18590 stop_rank=2471
2:00:07.551877 INFO: calibration group: precursor, fitting rt estimator 
2:00:07.652531 INFO: calibration group: fragment, fitting mz estimator 
2:00:07.927021 INFO: Using score_cutoff 36.198321550941465 (fac=0.99, q=1)
2:00:07.927452 INFO: calibration group: precursor, predicting mz
2:00:07.927538 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:07.927569 INFO: calibration group: precursor, predicting rt
2:00:07.929138 INFO: calibration group: fragment, predicting mz
2:00:07.931200 INFO: === checking if optimization conditions were reached ===
2:00:07.931304 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2:00:07.932921 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 16.2909.
2:00:07.932979 INFO: ==============================================
2:00:07.933074 INFO: Starting optimization step 3.
2:00:07.933149 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:07.933212 PROGRESS: Extracting batch of 1163 precursors
2:00:07.934127 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:07.934180 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:07.934216 INFO: FWHM in RT is 2.42 seconds, sigma is 0.31
2:00:07.934238 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:07.934396 INFO: Starting candidate selection
2:00:08.049010 INFO: Starting candidate scoring
2:00:08.091537 INFO: Finished candidate processing
2:00:08.091637 INFO: Collecting candidate features
2:00:08.103080 INFO: Collecting fragment features
2:00:08.106891 INFO: Finished candidate scoring
2:00:08.108579 PROGRESS: === Extracted 2274 precursors and 17554 fragments ===
2:00:08.108862 INFO: performing precursor FDR with 47 features
2:00:08.108897 INFO: Decoy channel: -1
2:00:08.108919 INFO: Competetive: True
2:00:08.111421 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:08.134166 INFO: Test AUC: 0.743
2:00:08.134238 INFO: Train AUC: 0.742
2:00:08.134267 INFO: AUC difference: 0.18%
2:00:08.311098 INFO: Resetting torch num_threads to 100
2:00:08.311716 INFO: === FDR correction performed with classifier version 9 ===
2:00:08.312366 PROGRESS: ============================= Precursor FDR =============================
2:00:08.312459 PROGRESS: Total precursors accumulated: 456
2:00:08.312519 PROGRESS: Target precursors: 438 (96.05%)
2:00:08.312569 PROGRESS: Decoy precursors: 18 (3.95%)
2:00:08.312616 PROGRESS: 
2:00:08.312660 PROGRESS: Precursor Summary:
2:00:08.313639 PROGRESS: Channel   0:	 0.05 FDR:   438; 0.01 FDR:   283; 0.001 FDR:   224
2:00:08.313728 PROGRESS: 
2:00:08.313782 PROGRESS: Protein Summary:
2:00:08.314940 PROGRESS: Channel   0:	 0.05 FDR:   420; 0.01 FDR:   275; 0.001 FDR:   217
2:00:08.315033 PROGRESS: =========================================================================
2:00:08.317700 INFO: fragments_df: keeping 2500 of 17554 [sum(precursor_idx_mask)=5294 sum(mass_error_mask)=17554 stop_rank=2500
2:00:08.322702 INFO: calibration group: precursor, fitting rt estimator 
2:00:08.427315 INFO: calibration group: fragment, fitting mz estimator 
2:00:08.706137 INFO: Using score_cutoff 38.96644229736328 (fac=0.99, q=1)
2:00:08.706548 INFO: calibration group: precursor, predicting mz
2:00:08.706635 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:08.706665 INFO: calibration group: precursor, predicting rt
2:00:08.708265 INFO: calibration group: fragment, predicting mz
2:00:08.710393 INFO: === checking if optimization conditions were reached ===
2:00:08.710509 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2:00:08.712292 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 5.7780.
2:00:08.712343 INFO: ==============================================
2:00:08.712429 INFO: Starting optimization step 4.
2:00:08.712492 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:08.712546 PROGRESS: Extracting batch of 1163 precursors
2:00:08.713545 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:08.713591 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:08.713621 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
2:00:08.713645 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:08.713807 INFO: Starting candidate selection
2:00:08.830454 INFO: Starting candidate scoring
2:00:08.872329 INFO: Finished candidate processing
2:00:08.872409 INFO: Collecting candidate features
2:00:08.883544 INFO: Collecting fragment features
2:00:08.887464 INFO: Finished candidate scoring
2:00:08.889076 PROGRESS: === Extracted 2281 precursors and 17614 fragments ===
2:00:08.889356 INFO: performing precursor FDR with 47 features
2:00:08.889394 INFO: Decoy channel: -1
2:00:08.889418 INFO: Competetive: True
2:00:08.892010 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:08.914355 INFO: Test AUC: 0.788
2:00:08.914428 INFO: Train AUC: 0.736
2:00:08.914458 INFO: AUC difference: 7.00%
2:00:08.914479 WARNING: AUC difference > 5%. This may indicate overfitting.
2:00:09.084620 INFO: Resetting torch num_threads to 100
2:00:09.085222 INFO: === FDR correction performed with classifier version 9 ===
2:00:09.085877 PROGRESS: ============================= Precursor FDR =============================
2:00:09.085969 PROGRESS: Total precursors accumulated: 450
2:00:09.086030 PROGRESS: Target precursors: 431 (95.78%)
2:00:09.086082 PROGRESS: Decoy precursors: 19 (4.22%)
2:00:09.086128 PROGRESS: 
2:00:09.086173 PROGRESS: Precursor Summary:
2:00:09.087176 PROGRESS: Channel   0:	 0.05 FDR:   431; 0.01 FDR:   242; 0.001 FDR:   141
2:00:09.087266 PROGRESS: 
2:00:09.087321 PROGRESS: Protein Summary:
2:00:09.088508 PROGRESS: Channel   0:	 0.05 FDR:   413; 0.01 FDR:   236; 0.001 FDR:   141
2:00:09.088602 PROGRESS: =========================================================================
2:00:09.091245 INFO: fragments_df: keeping 2239 of 17614 [sum(precursor_idx_mask)=4655 sum(mass_error_mask)=17614 stop_rank=2239
2:00:09.097306 INFO: calibration group: precursor, fitting rt estimator 
2:00:09.194774 INFO: calibration group: fragment, fitting mz estimator 
2:00:09.446687 INFO: Using score_cutoff 48.24369440345764 (fac=0.99, q=1)
2:00:09.447105 INFO: calibration group: precursor, predicting mz
2:00:09.447191 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:09.447220 INFO: calibration group: precursor, predicting rt
2:00:09.448771 INFO: calibration group: fragment, predicting mz
2:00:09.450843 INFO: === checking if optimization conditions were reached ===
2:00:09.450944 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2:00:09.452506 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 3.3474.
2:00:09.452561 INFO: ==============================================
2:00:09.452650 INFO: Starting optimization step 5.
2:00:09.452717 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:09.452775 PROGRESS: Extracting batch of 1163 precursors
2:00:09.453674 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:09.453721 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:09.453750 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
2:00:09.453772 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:09.453929 INFO: Starting candidate selection
2:00:09.568670 INFO: Starting candidate scoring
2:00:09.611188 INFO: Finished candidate processing
2:00:09.611271 INFO: Collecting candidate features
2:00:09.622410 INFO: Collecting fragment features
2:00:09.626286 INFO: Finished candidate scoring
2:00:09.627912 PROGRESS: === Extracted 2277 precursors and 17438 fragments ===
2:00:09.628216 INFO: performing precursor FDR with 47 features
2:00:09.628279 INFO: Decoy channel: -1
2:00:09.628302 INFO: Competetive: True
2:00:09.630764 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:09.652653 INFO: Test AUC: 0.726
2:00:09.652724 INFO: Train AUC: 0.726
2:00:09.652753 INFO: AUC difference: 0.04%
2:00:09.828799 INFO: Resetting torch num_threads to 100
2:00:09.829387 INFO: === FDR correction performed with classifier version 9 ===
2:00:09.830019 PROGRESS: ============================= Precursor FDR =============================
2:00:09.830112 PROGRESS: Total precursors accumulated: 413
2:00:09.830173 PROGRESS: Target precursors: 393 (95.16%)
2:00:09.830226 PROGRESS: Decoy precursors: 20 (4.84%)
2:00:09.830273 PROGRESS: 
2:00:09.830318 PROGRESS: Precursor Summary:
2:00:09.831271 PROGRESS: Channel   0:	 0.05 FDR:   393; 0.01 FDR:   217; 0.001 FDR:   128
2:00:09.831360 PROGRESS: 
2:00:09.831416 PROGRESS: Protein Summary:
2:00:09.832545 PROGRESS: Channel   0:	 0.05 FDR:   380; 0.01 FDR:   212; 0.001 FDR:   126
2:00:09.832641 PROGRESS: =========================================================================
2:00:09.835089 INFO: fragments_df: keeping 2038 of 17438 [sum(precursor_idx_mask)=4181 sum(mass_error_mask)=17438 stop_rank=2038
2:00:09.839983 INFO: calibration group: precursor, fitting rt estimator 
2:00:09.935982 INFO: calibration group: fragment, fitting mz estimator 
2:00:10.167609 INFO: Using score_cutoff 40.43727388916015 (fac=0.99, q=1)
2:00:10.168017 INFO: calibration group: precursor, predicting mz
2:00:10.168106 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:10.168137 INFO: calibration group: precursor, predicting rt
2:00:10.169688 INFO: calibration group: fragment, predicting mz
2:00:10.171788 INFO: === checking if optimization conditions were reached ===
2:00:13.134147 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2:00:13.136394 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 15.7174.
2:00:13.136453 INFO: ==============================================
2:00:13.136548 INFO: Starting optimization step 6.
2:00:13.136614 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:13.136671 PROGRESS: Extracting batch of 1163 precursors
2:00:13.137607 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:13.137653 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:13.137684 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
2:00:13.137705 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:13.137872 INFO: Starting candidate selection
2:00:13.253770 INFO: Starting candidate scoring
2:00:13.295285 INFO: Finished candidate processing
2:00:13.295370 INFO: Collecting candidate features
2:00:13.303706 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2275)
2:00:13.306645 INFO: Collecting fragment features
2:00:13.310589 INFO: Finished candidate scoring
2:00:13.312197 PROGRESS: === Extracted 2275 precursors and 17546 fragments ===
2:00:13.312480 INFO: performing precursor FDR with 47 features
2:00:13.312517 INFO: Decoy channel: -1
2:00:13.312540 INFO: Competetive: True
2:00:13.315028 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:13.316195 WARNING: dropped 1 target PSMs due to missing features
2:00:13.337374 INFO: Test AUC: 0.776
2:00:13.337450 INFO: Train AUC: 0.731
2:00:13.337478 INFO: AUC difference: 6.21%
2:00:13.337500 WARNING: AUC difference > 5%. This may indicate overfitting.
2:00:13.512122 INFO: Resetting torch num_threads to 100
2:00:13.512739 INFO: === FDR correction performed with classifier version 9 ===
2:00:13.513393 PROGRESS: ============================= Precursor FDR =============================
2:00:13.513486 PROGRESS: Total precursors accumulated: 453
2:00:13.513547 PROGRESS: Target precursors: 436 (96.25%)
2:00:13.513600 PROGRESS: Decoy precursors: 17 (3.75%)
2:00:13.513648 PROGRESS: 
2:00:13.513692 PROGRESS: Precursor Summary:
2:00:13.514697 PROGRESS: Channel   0:	 0.05 FDR:   436; 0.01 FDR:   281; 0.001 FDR:   224
2:00:13.514789 PROGRESS: 
2:00:13.514852 PROGRESS: Protein Summary:
2:00:13.516013 PROGRESS: Channel   0:	 0.05 FDR:   418; 0.01 FDR:   273; 0.001 FDR:   217
2:00:13.516109 PROGRESS: =========================================================================
2:00:13.518721 INFO: fragments_df: keeping 2493 of 17546 [sum(precursor_idx_mask)=5277 sum(mass_error_mask)=17546 stop_rank=2493
2:00:13.523925 INFO: calibration group: precursor, fitting rt estimator 
2:00:13.622315 INFO: calibration group: fragment, fitting mz estimator 
2:00:13.899997 INFO: Using score_cutoff 38.94546038818359 (fac=0.99, q=1)
2:00:13.900425 INFO: calibration group: precursor, predicting mz
2:00:13.900512 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:13.900542 INFO: calibration group: precursor, predicting rt
2:00:13.902109 INFO: calibration group: fragment, predicting mz
2:00:13.904203 INFO: === checking if optimization conditions were reached ===
2:00:13.904323 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
2:00:13.905915 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 5.7786.
2:00:13.905972 INFO: ==============================================
2:00:13.906062 INFO: Starting optimization step 7.
2:00:13.906129 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:13.906184 PROGRESS: Extracting batch of 1163 precursors
2:00:13.907085 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:13.907130 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:13.907161 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
2:00:13.907184 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:13.907342 INFO: Starting candidate selection
2:00:14.021840 INFO: Starting candidate scoring
2:00:14.063183 INFO: Finished candidate processing
2:00:14.063272 INFO: Collecting candidate features
2:00:14.074357 INFO: Collecting fragment features
2:00:14.078316 INFO: Finished candidate scoring
2:00:14.079862 PROGRESS: === Extracted 2281 precursors and 17619 fragments ===
2:00:14.080136 INFO: performing precursor FDR with 47 features
2:00:14.080172 INFO: Decoy channel: -1
2:00:14.080195 INFO: Competetive: True
2:00:14.082729 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:14.105484 INFO: Test AUC: 0.751
2:00:14.105554 INFO: Train AUC: 0.745
2:00:14.105583 INFO: AUC difference: 0.80%
2:00:14.275386 INFO: Resetting torch num_threads to 100
2:00:14.275984 INFO: === FDR correction performed with classifier version 9 ===
2:00:14.276641 PROGRESS: ============================= Precursor FDR =============================
2:00:14.276738 PROGRESS: Total precursors accumulated: 449
2:00:14.276799 PROGRESS: Target precursors: 430 (95.77%)
2:00:14.276851 PROGRESS: Decoy precursors: 19 (4.23%)
2:00:14.276898 PROGRESS: 
2:00:14.276942 PROGRESS: Precursor Summary:
2:00:14.277895 PROGRESS: Channel   0:	 0.05 FDR:   430; 0.01 FDR:   242; 0.001 FDR:   141
2:00:14.277983 PROGRESS: 
2:00:14.278039 PROGRESS: Protein Summary:
2:00:14.279151 PROGRESS: Channel   0:	 0.05 FDR:   412; 0.01 FDR:   236; 0.001 FDR:   141
2:00:14.279244 PROGRESS: =========================================================================
2:00:14.281823 INFO: fragments_df: keeping 2239 of 17619 [sum(precursor_idx_mask)=4665 sum(mass_error_mask)=17619 stop_rank=2239
2:00:14.286775 INFO: calibration group: precursor, fitting rt estimator 
2:00:14.382550 INFO: calibration group: fragment, fitting mz estimator 
2:00:14.633260 INFO: Using score_cutoff 48.24369440345764 (fac=0.99, q=1)
2:00:14.633668 INFO: calibration group: precursor, predicting mz
2:00:14.633757 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:14.633786 INFO: calibration group: precursor, predicting rt
2:00:14.635319 INFO: calibration group: fragment, predicting mz
2:00:14.637457 INFO: === checking if optimization conditions were reached ===
2:00:14.637569 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
2:00:14.639138 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 3.3474.
2:00:14.639191 INFO: ==============================================
2:00:14.639279 INFO: Starting optimization step 8.
2:00:14.639344 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:14.639402 PROGRESS: Extracting batch of 1163 precursors
2:00:14.640312 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:14.640358 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:14.640388 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
2:00:14.640411 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:14.640573 INFO: Starting candidate selection
2:00:14.756916 INFO: Starting candidate scoring
2:00:14.798284 INFO: Finished candidate processing
2:00:14.798371 INFO: Collecting candidate features
2:00:14.809682 INFO: Collecting fragment features
2:00:14.814245 INFO: Finished candidate scoring
2:00:14.815813 PROGRESS: === Extracted 2277 precursors and 17437 fragments ===
2:00:14.816090 INFO: performing precursor FDR with 47 features
2:00:14.816126 INFO: Decoy channel: -1
2:00:14.816149 INFO: Competetive: True
2:00:14.818664 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:14.840551 INFO: Test AUC: 0.752
2:00:14.840623 INFO: Train AUC: 0.719
2:00:14.840651 INFO: AUC difference: 4.58%
2:00:15.016231 INFO: Resetting torch num_threads to 100
2:00:15.016875 INFO: === FDR correction performed with classifier version 9 ===
2:00:15.017512 PROGRESS: ============================= Precursor FDR =============================
2:00:15.017604 PROGRESS: Total precursors accumulated: 413
2:00:15.017665 PROGRESS: Target precursors: 393 (95.16%)
2:00:15.017719 PROGRESS: Decoy precursors: 20 (4.84%)
2:00:15.017766 PROGRESS: 
2:00:15.017811 PROGRESS: Precursor Summary:
2:00:15.018775 PROGRESS: Channel   0:	 0.05 FDR:   393; 0.01 FDR:   217; 0.001 FDR:   128
2:00:15.018865 PROGRESS: 
2:00:15.018920 PROGRESS: Protein Summary:
2:00:15.020038 PROGRESS: Channel   0:	 0.05 FDR:   380; 0.01 FDR:   212; 0.001 FDR:   126
2:00:15.020129 PROGRESS: =========================================================================
2:00:15.022696 INFO: fragments_df: keeping 2038 of 17437 [sum(precursor_idx_mask)=4181 sum(mass_error_mask)=17437 stop_rank=2038
2:00:15.027653 INFO: calibration group: precursor, fitting rt estimator 
2:00:15.123665 INFO: calibration group: fragment, fitting mz estimator 
2:00:15.356143 INFO: Using score_cutoff 40.43727388916015 (fac=0.99, q=1)
2:00:15.356571 INFO: calibration group: precursor, predicting mz
2:00:15.356658 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:15.356687 INFO: calibration group: precursor, predicting rt
2:00:15.358229 INFO: calibration group: fragment, predicting mz
2:00:15.360350 INFO: === checking if optimization conditions were reached ===
2:00:15.360454 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
2:00:15.361996 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 15.7174.
2:00:15.362049 INFO: ==============================================
2:00:15.362137 INFO: Starting optimization step 9.
2:00:15.362203 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:15.362260 PROGRESS: Extracting batch of 1163 precursors
2:00:15.363158 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:15.363203 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:15.363234 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
2:00:15.363255 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:15.363409 INFO: Starting candidate selection
2:00:15.479390 INFO: Starting candidate scoring
2:00:15.520778 INFO: Finished candidate processing
2:00:15.520859 INFO: Collecting candidate features
2:00:15.529248 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2275)
2:00:15.532187 INFO: Collecting fragment features
2:00:15.536272 INFO: Finished candidate scoring
2:00:15.537944 PROGRESS: === Extracted 2275 precursors and 17546 fragments ===
2:00:15.538221 INFO: performing precursor FDR with 47 features
2:00:15.538257 INFO: Decoy channel: -1
2:00:15.538281 INFO: Competetive: True
2:00:15.540788 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:15.541973 WARNING: dropped 1 target PSMs due to missing features
2:00:15.563259 INFO: Test AUC: 0.763
2:00:15.563332 INFO: Train AUC: 0.734
2:00:15.563361 INFO: AUC difference: 3.89%
2:00:15.740004 INFO: Resetting torch num_threads to 100
2:00:15.740619 INFO: === FDR correction performed with classifier version 9 ===
2:00:15.741254 PROGRESS: ============================= Precursor FDR =============================
2:00:15.741345 PROGRESS: Total precursors accumulated: 453
2:00:15.741404 PROGRESS: Target precursors: 436 (96.25%)
2:00:15.741457 PROGRESS: Decoy precursors: 17 (3.75%)
2:00:15.741506 PROGRESS: 
2:00:15.741553 PROGRESS: Precursor Summary:
2:00:15.742526 PROGRESS: Channel   0:	 0.05 FDR:   436; 0.01 FDR:   281; 0.001 FDR:   224
2:00:15.742616 PROGRESS: 
2:00:15.742671 PROGRESS: Protein Summary:
2:00:15.743799 PROGRESS: Channel   0:	 0.05 FDR:   418; 0.01 FDR:   273; 0.001 FDR:   217
2:00:15.743893 PROGRESS: =========================================================================
2:00:15.746537 INFO: fragments_df: keeping 2493 of 17546 [sum(precursor_idx_mask)=5277 sum(mass_error_mask)=17546 stop_rank=2493
2:00:15.751434 INFO: calibration group: precursor, fitting rt estimator 
2:00:15.848766 INFO: calibration group: fragment, fitting mz estimator 
2:00:16.128422 INFO: Using score_cutoff 38.94546038818359 (fac=0.99, q=1)
2:00:16.128836 INFO: calibration group: precursor, predicting mz
2:00:16.128925 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:16.128955 INFO: calibration group: precursor, predicting rt
2:00:16.130516 INFO: calibration group: fragment, predicting mz
2:00:16.132689 INFO: === checking if optimization conditions were reached ===
2:00:16.132801 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
2:00:16.134411 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 5.7786.
2:00:16.134465 INFO: ==============================================
2:00:16.134552 INFO: Starting optimization step 10.
2:00:16.134628 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:16.134684 PROGRESS: Extracting batch of 1163 precursors
2:00:16.135595 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:16.135642 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:16.135674 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
2:00:16.135697 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:16.135854 INFO: Starting candidate selection
2:00:16.251325 INFO: Starting candidate scoring
2:00:16.292831 INFO: Finished candidate processing
2:00:16.292916 INFO: Collecting candidate features
2:00:16.303906 INFO: Collecting fragment features
2:00:16.308435 INFO: Finished candidate scoring
2:00:16.310097 PROGRESS: === Extracted 2281 precursors and 17619 fragments ===
2:00:16.310370 INFO: performing precursor FDR with 47 features
2:00:16.310405 INFO: Decoy channel: -1
2:00:16.310428 INFO: Competetive: True
2:00:16.313138 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:16.335250 INFO: Test AUC: 0.731
2:00:16.335324 INFO: Train AUC: 0.751
2:00:16.335354 INFO: AUC difference: 2.67%
2:00:16.507628 INFO: Resetting torch num_threads to 100
2:00:16.508214 INFO: === FDR correction performed with classifier version 9 ===
2:00:16.508882 PROGRESS: ============================= Precursor FDR =============================
2:00:16.508976 PROGRESS: Total precursors accumulated: 449
2:00:16.509035 PROGRESS: Target precursors: 430 (95.77%)
2:00:16.509088 PROGRESS: Decoy precursors: 19 (4.23%)
2:00:16.509135 PROGRESS: 
2:00:16.509179 PROGRESS: Precursor Summary:
2:00:16.510150 PROGRESS: Channel   0:	 0.05 FDR:   430; 0.01 FDR:   242; 0.001 FDR:   141
2:00:16.510252 PROGRESS: 
2:00:16.510309 PROGRESS: Protein Summary:
2:00:16.511445 PROGRESS: Channel   0:	 0.05 FDR:   412; 0.01 FDR:   236; 0.001 FDR:   141
2:00:16.511536 PROGRESS: =========================================================================
2:00:16.514114 INFO: fragments_df: keeping 2239 of 17619 [sum(precursor_idx_mask)=4665 sum(mass_error_mask)=17619 stop_rank=2239
2:00:16.519014 INFO: calibration group: precursor, fitting rt estimator 
2:00:16.614841 INFO: calibration group: fragment, fitting mz estimator 
2:00:16.866744 INFO: Using score_cutoff 48.24369440345764 (fac=0.99, q=1)
2:00:16.867151 INFO: calibration group: precursor, predicting mz
2:00:16.867236 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:16.867265 INFO: calibration group: precursor, predicting rt
2:00:16.868803 INFO: calibration group: fragment, predicting mz
2:00:16.870891 INFO: === checking if optimization conditions were reached ===
2:00:16.870992 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 2 ===
2:00:16.872548 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 3.3474.
2:00:16.872603 INFO: ==============================================
2:00:16.872692 INFO: Starting optimization step 11.
2:00:16.872757 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:16.872814 PROGRESS: Extracting batch of 1163 precursors
2:00:16.873709 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:16.873756 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:16.873788 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
2:00:16.873809 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:16.873966 INFO: Starting candidate selection
2:00:16.990093 INFO: Starting candidate scoring
2:00:17.031636 INFO: Finished candidate processing
2:00:17.031717 INFO: Collecting candidate features
2:00:17.042719 INFO: Collecting fragment features
2:00:17.047021 INFO: Finished candidate scoring
2:00:17.048653 PROGRESS: === Extracted 2277 precursors and 17437 fragments ===
2:00:17.048928 INFO: performing precursor FDR with 47 features
2:00:17.048964 INFO: Decoy channel: -1
2:00:17.048988 INFO: Competetive: True
2:00:17.051439 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:17.074844 INFO: Test AUC: 0.693
2:00:17.074922 INFO: Train AUC: 0.734
2:00:17.074952 INFO: AUC difference: 5.68%
2:00:17.074974 WARNING: AUC difference > 5%. This may indicate overfitting.
2:00:17.250728 INFO: Resetting torch num_threads to 100
2:00:17.251322 INFO: === FDR correction performed with classifier version 9 ===
2:00:17.251953 PROGRESS: ============================= Precursor FDR =============================
2:00:17.252043 PROGRESS: Total precursors accumulated: 413
2:00:17.252103 PROGRESS: Target precursors: 393 (95.16%)
2:00:17.252154 PROGRESS: Decoy precursors: 20 (4.84%)
2:00:17.252200 PROGRESS: 
2:00:17.252259 PROGRESS: Precursor Summary:
2:00:17.253207 PROGRESS: Channel   0:	 0.05 FDR:   393; 0.01 FDR:   217; 0.001 FDR:   128
2:00:17.253297 PROGRESS: 
2:00:17.253354 PROGRESS: Protein Summary:
2:00:17.254454 PROGRESS: Channel   0:	 0.05 FDR:   380; 0.01 FDR:   212; 0.001 FDR:   126
2:00:17.254550 PROGRESS: =========================================================================
2:00:17.257082 INFO: fragments_df: keeping 2038 of 17437 [sum(precursor_idx_mask)=4181 sum(mass_error_mask)=17437 stop_rank=2038
2:00:17.261969 INFO: calibration group: precursor, fitting rt estimator 
2:00:17.358121 INFO: calibration group: fragment, fitting mz estimator 
2:00:17.589900 INFO: Using score_cutoff 40.43727388916015 (fac=0.99, q=1)
2:00:17.590309 INFO: calibration group: precursor, predicting mz
2:00:17.590396 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:17.590426 INFO: calibration group: precursor, predicting rt
2:00:17.591972 INFO: calibration group: fragment, predicting mz
2:00:17.594094 INFO: === checking if optimization conditions were reached ===
2:00:17.594211 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 2 ===
2:00:17.595752 PROGRESS: ❌ rt_error       : optimization incomplete after 12 search(es). Will search with parameter 15.7174.
2:00:17.595805 INFO: ==============================================
2:00:17.595891 INFO: Starting optimization step 12.
2:00:17.595956 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:17.596013 PROGRESS: Extracting batch of 1163 precursors
2:00:17.596923 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:17.596973 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:17.597004 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
2:00:17.597026 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:17.597189 INFO: Starting candidate selection
2:00:17.713216 INFO: Starting candidate scoring
2:00:17.754700 INFO: Finished candidate processing
2:00:17.754789 INFO: Collecting candidate features
2:00:17.763109 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2275)
2:00:17.766068 INFO: Collecting fragment features
2:00:17.770000 INFO: Finished candidate scoring
2:00:17.771666 PROGRESS: === Extracted 2275 precursors and 17546 fragments ===
2:00:17.771950 INFO: performing precursor FDR with 47 features
2:00:17.771985 INFO: Decoy channel: -1
2:00:17.772006 INFO: Competetive: True
2:00:17.774638 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:17.775804 WARNING: dropped 1 target PSMs due to missing features
2:00:17.797604 INFO: Test AUC: 0.765
2:00:17.797676 INFO: Train AUC: 0.734
2:00:17.797706 INFO: AUC difference: 4.20%
2:00:17.972913 INFO: Resetting torch num_threads to 100
2:00:17.973506 INFO: === FDR correction performed with classifier version 9 ===
2:00:17.974140 PROGRESS: ============================= Precursor FDR =============================
2:00:17.974232 PROGRESS: Total precursors accumulated: 453
2:00:17.974294 PROGRESS: Target precursors: 436 (96.25%)
2:00:17.974347 PROGRESS: Decoy precursors: 17 (3.75%)
2:00:17.974394 PROGRESS: 
2:00:17.974438 PROGRESS: Precursor Summary:
2:00:17.975409 PROGRESS: Channel   0:	 0.05 FDR:   436; 0.01 FDR:   281; 0.001 FDR:   224
2:00:17.975499 PROGRESS: 
2:00:17.975554 PROGRESS: Protein Summary:
2:00:17.976718 PROGRESS: Channel   0:	 0.05 FDR:   418; 0.01 FDR:   273; 0.001 FDR:   217
2:00:17.976813 PROGRESS: =========================================================================
2:00:17.979451 INFO: fragments_df: keeping 2493 of 17546 [sum(precursor_idx_mask)=5277 sum(mass_error_mask)=17546 stop_rank=2493
2:00:17.984340 INFO: calibration group: precursor, fitting rt estimator 
2:00:18.082493 INFO: calibration group: fragment, fitting mz estimator 
2:00:18.359033 INFO: Using score_cutoff 38.94546038818359 (fac=0.99, q=1)
2:00:18.359454 INFO: calibration group: precursor, predicting mz
2:00:18.359541 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:18.359572 INFO: calibration group: precursor, predicting rt
2:00:18.361114 INFO: calibration group: fragment, predicting mz
2:00:18.363241 INFO: === checking if optimization conditions were reached ===
2:00:18.363346 PROGRESS: === Optimization of rt_error has been performed 13 time(s); minimum number is 2 ===
2:00:18.364933 PROGRESS: ❌ rt_error       : optimization incomplete after 13 search(es). Will search with parameter 5.7786.
2:00:18.364990 INFO: ==============================================
2:00:18.365080 INFO: Starting optimization step 13.
2:00:18.365148 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:18.365206 PROGRESS: Extracting batch of 1163 precursors
2:00:18.366117 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:18.366167 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:18.366200 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
2:00:18.366223 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:18.366381 INFO: Starting candidate selection
2:00:18.482504 INFO: Starting candidate scoring
2:00:18.523508 INFO: Finished candidate processing
2:00:18.523593 INFO: Collecting candidate features
2:00:18.534696 INFO: Collecting fragment features
2:00:18.538870 INFO: Finished candidate scoring
2:00:18.540513 PROGRESS: === Extracted 2281 precursors and 17619 fragments ===
2:00:18.540792 INFO: performing precursor FDR with 47 features
2:00:18.540829 INFO: Decoy channel: -1
2:00:18.540853 INFO: Competetive: True
2:00:18.543356 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:18.565917 INFO: Test AUC: 0.717
2:00:18.565986 INFO: Train AUC: 0.754
2:00:18.566017 INFO: AUC difference: 4.92%
2:00:18.736631 INFO: Resetting torch num_threads to 100
2:00:18.737229 INFO: === FDR correction performed with classifier version 9 ===
2:00:18.737863 PROGRESS: ============================= Precursor FDR =============================
2:00:18.737956 PROGRESS: Total precursors accumulated: 449
2:00:18.738015 PROGRESS: Target precursors: 430 (95.77%)
2:00:18.738068 PROGRESS: Decoy precursors: 19 (4.23%)
2:00:18.738114 PROGRESS: 
2:00:18.738158 PROGRESS: Precursor Summary:
2:00:18.739124 PROGRESS: Channel   0:	 0.05 FDR:   430; 0.01 FDR:   242; 0.001 FDR:   141
2:00:18.739216 PROGRESS: 
2:00:18.739272 PROGRESS: Protein Summary:
2:00:18.740412 PROGRESS: Channel   0:	 0.05 FDR:   412; 0.01 FDR:   236; 0.001 FDR:   141
2:00:18.740509 PROGRESS: =========================================================================
2:00:18.743102 INFO: fragments_df: keeping 2239 of 17619 [sum(precursor_idx_mask)=4665 sum(mass_error_mask)=17619 stop_rank=2239
2:00:18.747986 INFO: calibration group: precursor, fitting rt estimator 
2:00:18.852598 INFO: calibration group: fragment, fitting mz estimator 
2:00:19.105310 INFO: Using score_cutoff 48.24369440345764 (fac=0.99, q=1)
2:00:19.105721 INFO: calibration group: precursor, predicting mz
2:00:19.105807 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:19.105837 INFO: calibration group: precursor, predicting rt
2:00:19.107377 INFO: calibration group: fragment, predicting mz
2:00:19.109514 INFO: === checking if optimization conditions were reached ===
2:00:19.109627 PROGRESS: === Optimization of rt_error has been performed 14 time(s); minimum number is 2 ===
2:00:19.111195 PROGRESS: ❌ rt_error       : optimization incomplete after 14 search(es). Will search with parameter 3.3474.
2:00:19.111248 INFO: ==============================================
2:00:19.111336 INFO: Starting optimization step 14.
2:00:19.111404 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:19.111462 PROGRESS: Extracting batch of 1163 precursors
2:00:19.112375 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:19.112424 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:19.112454 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
2:00:19.112476 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:19.112634 INFO: Starting candidate selection
2:00:19.228609 INFO: Starting candidate scoring
2:00:19.270215 INFO: Finished candidate processing
2:00:19.270300 INFO: Collecting candidate features
2:00:19.281332 INFO: Collecting fragment features
2:00:19.285277 INFO: Finished candidate scoring
2:00:19.286893 PROGRESS: === Extracted 2277 precursors and 17437 fragments ===
2:00:19.287171 INFO: performing precursor FDR with 47 features
2:00:19.287206 INFO: Decoy channel: -1
2:00:19.287230 INFO: Competetive: True
2:00:19.289755 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:19.311889 INFO: Test AUC: 0.698
2:00:19.311962 INFO: Train AUC: 0.732
2:00:19.311991 INFO: AUC difference: 4.55%
2:00:19.487782 INFO: Resetting torch num_threads to 100
2:00:19.488400 INFO: === FDR correction performed with classifier version 9 ===
2:00:19.489046 PROGRESS: ============================= Precursor FDR =============================
2:00:19.489136 PROGRESS: Total precursors accumulated: 413
2:00:19.489197 PROGRESS: Target precursors: 393 (95.16%)
2:00:19.489249 PROGRESS: Decoy precursors: 20 (4.84%)
2:00:19.489295 PROGRESS: 
2:00:19.489339 PROGRESS: Precursor Summary:
2:00:19.490301 PROGRESS: Channel   0:	 0.05 FDR:   393; 0.01 FDR:   217; 0.001 FDR:   128
2:00:19.490391 PROGRESS: 
2:00:19.490457 PROGRESS: Protein Summary:
2:00:19.491584 PROGRESS: Channel   0:	 0.05 FDR:   380; 0.01 FDR:   212; 0.001 FDR:   126
2:00:19.491676 PROGRESS: =========================================================================
2:00:19.494177 INFO: fragments_df: keeping 2038 of 17437 [sum(precursor_idx_mask)=4181 sum(mass_error_mask)=17437 stop_rank=2038
2:00:19.499098 INFO: calibration group: precursor, fitting rt estimator 
2:00:19.600869 INFO: calibration group: fragment, fitting mz estimator 
2:00:19.832129 INFO: Using score_cutoff 40.43727388916015 (fac=0.99, q=1)
2:00:19.832789 INFO: calibration group: precursor, predicting mz
2:00:19.832886 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:19.832920 INFO: calibration group: precursor, predicting rt
2:00:19.834476 INFO: calibration group: fragment, predicting mz
2:00:19.836549 INFO: === checking if optimization conditions were reached ===
2:00:19.836660 PROGRESS: === Optimization of rt_error has been performed 15 time(s); minimum number is 2 ===
2:00:19.838197 PROGRESS: ❌ rt_error       : optimization incomplete after 15 search(es). Will search with parameter 15.7174.
2:00:19.838248 INFO: ==============================================
2:00:19.838351 INFO: Starting optimization step 15.
2:00:19.838423 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:19.838496 PROGRESS: Extracting batch of 1163 precursors
2:00:19.839423 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:19.839473 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:19.839511 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
2:00:19.839537 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:19.839701 INFO: Starting candidate selection
2:00:19.955273 INFO: Starting candidate scoring
2:00:19.997013 INFO: Finished candidate processing
2:00:19.997089 INFO: Collecting candidate features
2:00:20.005446 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2275)
2:00:20.008422 INFO: Collecting fragment features
2:00:20.012376 INFO: Finished candidate scoring
2:00:20.014010 PROGRESS: === Extracted 2275 precursors and 17546 fragments ===
2:00:20.014286 INFO: performing precursor FDR with 47 features
2:00:20.014323 INFO: Decoy channel: -1
2:00:20.014346 INFO: Competetive: True
2:00:20.016877 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:20.018043 WARNING: dropped 1 target PSMs due to missing features
2:00:20.039167 INFO: Test AUC: 0.747
2:00:20.039234 INFO: Train AUC: 0.737
2:00:20.039265 INFO: AUC difference: 1.30%
2:00:20.213950 INFO: Resetting torch num_threads to 100
2:00:20.214568 INFO: === FDR correction performed with classifier version 9 ===
2:00:20.215204 PROGRESS: ============================= Precursor FDR =============================
2:00:20.215297 PROGRESS: Total precursors accumulated: 453
2:00:20.215357 PROGRESS: Target precursors: 436 (96.25%)
2:00:20.215408 PROGRESS: Decoy precursors: 17 (3.75%)
2:00:20.215453 PROGRESS: 
2:00:20.215496 PROGRESS: Precursor Summary:
2:00:20.216472 PROGRESS: Channel   0:	 0.05 FDR:   436; 0.01 FDR:   281; 0.001 FDR:   224
2:00:20.216563 PROGRESS: 
2:00:20.216619 PROGRESS: Protein Summary:
2:00:20.217749 PROGRESS: Channel   0:	 0.05 FDR:   418; 0.01 FDR:   273; 0.001 FDR:   217
2:00:20.217841 PROGRESS: =========================================================================
2:00:20.220522 INFO: fragments_df: keeping 2493 of 17546 [sum(precursor_idx_mask)=5277 sum(mass_error_mask)=17546 stop_rank=2493
2:00:20.225433 INFO: calibration group: precursor, fitting rt estimator 
2:00:20.322492 INFO: calibration group: fragment, fitting mz estimator 
2:00:20.599744 INFO: Using score_cutoff 38.94546038818359 (fac=0.99, q=1)
2:00:20.600202 INFO: calibration group: precursor, predicting mz
2:00:20.600299 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:20.600330 INFO: calibration group: precursor, predicting rt
2:00:20.601889 INFO: calibration group: fragment, predicting mz
2:00:20.604027 INFO: === checking if optimization conditions were reached ===
2:00:20.604141 PROGRESS: === Optimization of rt_error has been performed 16 time(s); minimum number is 2 ===
2:00:20.605732 PROGRESS: ❌ rt_error       : optimization incomplete after 16 search(es). Will search with parameter 5.7786.
2:00:20.605787 INFO: ==============================================
2:00:20.605878 INFO: Starting optimization step 16.
2:00:20.605953 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:20.606007 PROGRESS: Extracting batch of 1163 precursors
2:00:20.606904 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:20.606950 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:20.606980 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
2:00:20.607001 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:20.607158 INFO: Starting candidate selection
2:00:20.721642 INFO: Starting candidate scoring
2:00:20.762604 INFO: Finished candidate processing
2:00:20.762685 INFO: Collecting candidate features
2:00:20.773852 INFO: Collecting fragment features
2:00:20.777693 INFO: Finished candidate scoring
2:00:20.779318 PROGRESS: === Extracted 2281 precursors and 17619 fragments ===
2:00:20.779594 INFO: performing precursor FDR with 47 features
2:00:20.779631 INFO: Decoy channel: -1
2:00:20.779653 INFO: Competetive: True
2:00:20.782156 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:20.805079 INFO: Test AUC: 0.784
2:00:20.805150 INFO: Train AUC: 0.737
2:00:20.805179 INFO: AUC difference: 6.48%
2:00:20.805200 WARNING: AUC difference > 5%. This may indicate overfitting.
2:00:20.975926 INFO: Resetting torch num_threads to 100
2:00:20.976546 INFO: === FDR correction performed with classifier version 9 ===
2:00:20.977186 PROGRESS: ============================= Precursor FDR =============================
2:00:20.977277 PROGRESS: Total precursors accumulated: 449
2:00:20.977335 PROGRESS: Target precursors: 430 (95.77%)
2:00:20.977387 PROGRESS: Decoy precursors: 19 (4.23%)
2:00:20.977432 PROGRESS: 
2:00:20.977475 PROGRESS: Precursor Summary:
2:00:20.978436 PROGRESS: Channel   0:	 0.05 FDR:   430; 0.01 FDR:   242; 0.001 FDR:   141
2:00:20.978525 PROGRESS: 
2:00:20.978581 PROGRESS: Protein Summary:
2:00:20.979719 PROGRESS: Channel   0:	 0.05 FDR:   412; 0.01 FDR:   236; 0.001 FDR:   141
2:00:20.979809 PROGRESS: =========================================================================
2:00:20.982365 INFO: fragments_df: keeping 2239 of 17619 [sum(precursor_idx_mask)=4665 sum(mass_error_mask)=17619 stop_rank=2239
2:00:20.987273 INFO: calibration group: precursor, fitting rt estimator 
2:00:21.094083 INFO: calibration group: fragment, fitting mz estimator 
2:00:21.344820 INFO: Using score_cutoff 48.24369440345764 (fac=0.99, q=1)
2:00:21.345245 INFO: calibration group: precursor, predicting mz
2:00:21.345330 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:21.345359 INFO: calibration group: precursor, predicting rt
2:00:21.346902 INFO: calibration group: fragment, predicting mz
2:00:21.349042 INFO: === checking if optimization conditions were reached ===
2:00:21.349149 PROGRESS: === Optimization of rt_error has been performed 17 time(s); minimum number is 2 ===
2:00:21.350723 PROGRESS: ❌ rt_error       : optimization incomplete after 17 search(es). Will search with parameter 3.3474.
2:00:21.350775 INFO: ==============================================
2:00:21.350861 INFO: Starting optimization step 17.
2:00:21.350926 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:21.350983 PROGRESS: Extracting batch of 1163 precursors
2:00:21.351890 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:21.351938 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:21.351968 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
2:00:21.351989 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:21.352144 INFO: Starting candidate selection
2:00:21.467086 INFO: Starting candidate scoring
2:00:21.508670 INFO: Finished candidate processing
2:00:21.508749 INFO: Collecting candidate features
2:00:21.519763 INFO: Collecting fragment features
2:00:21.524262 INFO: Finished candidate scoring
2:00:21.525836 PROGRESS: === Extracted 2277 precursors and 17437 fragments ===
2:00:21.526112 INFO: performing precursor FDR with 47 features
2:00:21.526147 INFO: Decoy channel: -1
2:00:21.526169 INFO: Competetive: True
2:00:21.528719 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:21.550309 INFO: Test AUC: 0.714
2:00:21.550380 INFO: Train AUC: 0.729
2:00:21.550408 INFO: AUC difference: 2.05%
2:00:21.727139 INFO: Resetting torch num_threads to 100
2:00:21.727740 INFO: === FDR correction performed with classifier version 9 ===
2:00:21.728390 PROGRESS: ============================= Precursor FDR =============================
2:00:21.728485 PROGRESS: Total precursors accumulated: 413
2:00:21.728544 PROGRESS: Target precursors: 393 (95.16%)
2:00:21.728596 PROGRESS: Decoy precursors: 20 (4.84%)
2:00:21.728641 PROGRESS: 
2:00:21.728684 PROGRESS: Precursor Summary:
2:00:21.729630 PROGRESS: Channel   0:	 0.05 FDR:   393; 0.01 FDR:   217; 0.001 FDR:   128
2:00:21.729719 PROGRESS: 
2:00:21.729773 PROGRESS: Protein Summary:
2:00:21.730867 PROGRESS: Channel   0:	 0.05 FDR:   380; 0.01 FDR:   212; 0.001 FDR:   126
2:00:21.730959 PROGRESS: =========================================================================
2:00:21.733474 INFO: fragments_df: keeping 2038 of 17437 [sum(precursor_idx_mask)=4181 sum(mass_error_mask)=17437 stop_rank=2038
2:00:21.738397 INFO: calibration group: precursor, fitting rt estimator 
2:00:21.834773 INFO: calibration group: fragment, fitting mz estimator 
2:00:22.066646 INFO: Using score_cutoff 40.43727388916015 (fac=0.99, q=1)
2:00:22.067074 INFO: calibration group: precursor, predicting mz
2:00:22.067160 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:22.067189 INFO: calibration group: precursor, predicting rt
2:00:22.068760 INFO: calibration group: fragment, predicting mz
2:00:22.070881 INFO: === checking if optimization conditions were reached ===
2:00:22.070989 PROGRESS: === Optimization of rt_error has been performed 18 time(s); minimum number is 2 ===
2:00:22.072570 PROGRESS: ❌ rt_error       : optimization incomplete after 18 search(es). Will search with parameter 15.7174.
2:00:22.072623 INFO: ==============================================
2:00:22.072710 INFO: Starting optimization step 18.
2:00:22.072785 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:22.072841 PROGRESS: Extracting batch of 1163 precursors
2:00:22.073738 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:22.073783 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:22.073814 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
2:00:22.073835 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:22.073998 INFO: Starting candidate selection
2:00:22.190702 INFO: Starting candidate scoring
2:00:22.233065 INFO: Finished candidate processing
2:00:22.233141 INFO: Collecting candidate features
2:00:22.241418 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2275)
2:00:22.244360 INFO: Collecting fragment features
2:00:22.248834 INFO: Finished candidate scoring
2:00:22.250444 PROGRESS: === Extracted 2275 precursors and 17546 fragments ===
2:00:22.250711 INFO: performing precursor FDR with 47 features
2:00:22.250746 INFO: Decoy channel: -1
2:00:22.250767 INFO: Competetive: True
2:00:22.253335 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:22.254502 WARNING: dropped 1 target PSMs due to missing features
2:00:22.276852 INFO: Test AUC: 0.715
2:00:22.276928 INFO: Train AUC: 0.746
2:00:22.276958 INFO: AUC difference: 4.12%
2:00:22.453220 INFO: Resetting torch num_threads to 100
2:00:22.453844 INFO: === FDR correction performed with classifier version 9 ===
2:00:22.454482 PROGRESS: ============================= Precursor FDR =============================
2:00:22.454576 PROGRESS: Total precursors accumulated: 453
2:00:22.454635 PROGRESS: Target precursors: 436 (96.25%)
2:00:22.454686 PROGRESS: Decoy precursors: 17 (3.75%)
2:00:22.454731 PROGRESS: 
2:00:22.454774 PROGRESS: Precursor Summary:
2:00:22.455758 PROGRESS: Channel   0:	 0.05 FDR:   436; 0.01 FDR:   281; 0.001 FDR:   224
2:00:22.455850 PROGRESS: 
2:00:22.455906 PROGRESS: Protein Summary:
2:00:22.457090 PROGRESS: Channel   0:	 0.05 FDR:   418; 0.01 FDR:   273; 0.001 FDR:   217
2:00:22.457187 PROGRESS: =========================================================================
2:00:22.459876 INFO: fragments_df: keeping 2493 of 17546 [sum(precursor_idx_mask)=5277 sum(mass_error_mask)=17546 stop_rank=2493
2:00:22.464820 INFO: calibration group: precursor, fitting rt estimator 
2:00:22.563086 INFO: calibration group: fragment, fitting mz estimator 
2:00:22.840297 INFO: Using score_cutoff 38.94546038818359 (fac=0.99, q=1)
2:00:22.840728 INFO: calibration group: precursor, predicting mz
2:00:22.840815 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:22.840845 INFO: calibration group: precursor, predicting rt
2:00:22.842392 INFO: calibration group: fragment, predicting mz
2:00:22.844532 INFO: === checking if optimization conditions were reached ===
2:00:22.844635 PROGRESS: === Optimization of rt_error has been performed 19 time(s); minimum number is 2 ===
2:00:22.846313 PROGRESS: ❌ rt_error       : optimization incomplete after 19 search(es). Will search with parameter 5.7786.
2:00:22.846364 INFO: ==============================================
2:00:22.846456 INFO: Starting optimization step 19.
2:00:22.846531 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:22.846588 PROGRESS: Extracting batch of 1163 precursors
2:00:22.847499 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:22.847544 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:22.847574 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
2:00:22.847595 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:22.847751 INFO: Starting candidate selection
2:00:22.962973 INFO: Starting candidate scoring
2:00:23.005163 INFO: Finished candidate processing
2:00:23.005245 INFO: Collecting candidate features
2:00:23.016583 INFO: Collecting fragment features
2:00:23.020579 INFO: Finished candidate scoring
2:00:23.022257 PROGRESS: === Extracted 2281 precursors and 17619 fragments ===
2:00:23.022540 INFO: performing precursor FDR with 47 features
2:00:23.022577 INFO: Decoy channel: -1
2:00:23.022601 INFO: Competetive: True
2:00:23.025158 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:23.048024 INFO: Test AUC: 0.735
2:00:23.048103 INFO: Train AUC: 0.750
2:00:23.048132 INFO: AUC difference: 2.08%
2:00:23.218641 INFO: Resetting torch num_threads to 100
2:00:23.219255 INFO: === FDR correction performed with classifier version 9 ===
2:00:23.219898 PROGRESS: ============================= Precursor FDR =============================
2:00:23.219990 PROGRESS: Total precursors accumulated: 449
2:00:23.220050 PROGRESS: Target precursors: 430 (95.77%)
2:00:23.220101 PROGRESS: Decoy precursors: 19 (4.23%)
2:00:23.220148 PROGRESS: 
2:00:23.220194 PROGRESS: Precursor Summary:
2:00:23.221682 PROGRESS: Channel   0:	 0.05 FDR:   430; 0.01 FDR:   242; 0.001 FDR:   141
2:00:23.221781 PROGRESS: 
2:00:23.221837 PROGRESS: Protein Summary:
2:00:23.222970 PROGRESS: Channel   0:	 0.05 FDR:   412; 0.01 FDR:   236; 0.001 FDR:   141
2:00:23.223067 PROGRESS: =========================================================================
2:00:23.225698 INFO: fragments_df: keeping 2239 of 17619 [sum(precursor_idx_mask)=4665 sum(mass_error_mask)=17619 stop_rank=2239
2:00:23.230698 INFO: calibration group: precursor, fitting rt estimator 
2:00:23.326908 INFO: calibration group: fragment, fitting mz estimator 
2:00:23.578344 INFO: Using score_cutoff 48.24369440345764 (fac=0.99, q=1)
2:00:23.578779 INFO: calibration group: precursor, predicting mz
2:00:23.578866 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:23.578897 INFO: calibration group: precursor, predicting rt
2:00:23.580464 INFO: calibration group: fragment, predicting mz
2:00:23.582560 INFO: === checking if optimization conditions were reached ===
2:00:23.582669 PROGRESS: === Optimization of rt_error has been performed 20 time(s); minimum number is 2 ===
2:00:23.584248 PROGRESS: ❌ rt_error       : optimization incomplete after 20 search(es). Will search with parameter 3.3474.
2:00:23.584302 INFO: ==============================================
2:00:23.584377 WARNING: Optimization did not converge within the maximum number of steps, which is 20.
2:00:23.584440 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:00:23.584503 PROGRESS: ==============================================
2:00:23.584553 PROGRESS: ms2_error      : 6.7411
2:00:23.584599 PROGRESS: rt_error       : 3.3474
2:00:23.584641 PROGRESS: ==============================================
2:00:23.585138 INFO: calibration group: precursor, predicting mz
2:00:23.585222 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:23.585249 INFO: calibration group: precursor, predicting rt
2:00:23.718961 INFO: calibration group: fragment, predicting mz
2:00:24.068051 PROGRESS: Extracting batch of 238438 precursors
2:00:24.125381 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:24.125566 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:24.125610 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
2:00:24.125642 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:24.125897 INFO: Starting candidate selection
2:00:32.615723 INFO: Applying score cutoff of 48.24369440345764
2:00:32.620535 INFO: Removed 312064 precursors with score below cutoff
2:00:32.697192 INFO: Starting candidate scoring
2:00:33.790050 INFO: Finished candidate processing
2:00:33.790166 INFO: Collecting candidate features
2:00:34.046146 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 156364)
2:00:34.054500 INFO: Collecting fragment features
2:00:34.150982 INFO: Finished candidate scoring
2:00:34.278055 INFO: === FDR correction performed with classifier version 9 ===
2:00:34.278781 INFO: performing precursor FDR with 47 features
2:00:34.278827 INFO: Decoy channel: -1
2:00:34.278852 INFO: Competetive: True
2:00:34.323783 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:34.348790 WARNING: dropped 1 target PSMs due to missing features
2:00:34.348953 WARNING: FDR calculation for 125470 target and 30893 decoy PSMs
2:00:34.348979 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:00:37.376300 INFO: Test AUC: 0.919
2:00:37.376440 INFO: Train AUC: 0.921
2:00:37.376468 INFO: AUC difference: 0.22%
2:00:37.590091 INFO: Resetting torch num_threads to 100
2:00:37.607649 INFO: Removing fragments below FDR threshold
2:00:37.660650 PROGRESS: ============================= Precursor FDR =============================
2:00:37.660969 PROGRESS: Total precursors accumulated: 90,904
2:00:37.661053 PROGRESS: Target precursors: 90,004 (99.01%)
2:00:37.661106 PROGRESS: Decoy precursors: 900 (0.99%)
2:00:37.661156 PROGRESS: 
2:00:37.661204 PROGRESS: Precursor Summary:
2:00:37.699649 PROGRESS: Channel   0:	 0.05 FDR: 90,004; 0.01 FDR: 90,004; 0.001 FDR: 81,961
2:00:37.699964 PROGRESS: 
2:00:37.700048 PROGRESS: Protein Summary:
2:00:37.756654 PROGRESS: Channel   0:	 0.05 FDR: 9,907; 0.01 FDR: 9,907; 0.001 FDR: 9,276
2:00:37.756921 PROGRESS: =========================================================================
2:00:38.408704 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:00:38.436595 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:00:38.436782 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant
2:00:38.436858 INFO: Creating folder run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/figures
2:00:38.437780 INFO: Initializing RawFileManager
2:00:48.053460 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
2:00:48.057857 INFO: Determining DIA cycle
2:00:48.074318 INFO: Found cycle with start 0.00 min and length 300.
2:00:48.246423 INFO: RT (min)            : 0.0 - 26.9
2:00:48.246520 INFO: RT duration (sec)   : 1611.2
2:00:48.246547 INFO: RT duration (min)   : 26.9
2:00:48.246570 INFO: Cycle len (scans)   : 300
2:00:48.246591 INFO: Cycle len (sec)     : 1.65
2:00:48.246610 INFO: Number of cycles    : 977
2:00:48.246634 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:00:48.293813 INFO: Initializing CalibrationManager
2:00:48.294165 INFO: Loading calibration config
2:00:48.294800 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed'], 'function': LOESSRegression()}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed'], 'function': LOESSRegression(n_kernels=2)}], 'name': 'precursor'}]
2:00:48.294893 INFO: Calibration group :fragment, found 1 estimator(s)
2:00:48.294977 INFO: Calibration group :precursor, found 3 estimator(s)
2:00:48.295058 INFO: Disabling ion mobility calibration
2:00:48.295087 INFO: removed mobility estimator from group precursor
2:00:48.295238 INFO: Initializing OptimizationManager
2:00:48.295353 INFO: initial parameter: ms1_error = 30
2:00:48.295425 INFO: initial parameter: ms2_error = 30
2:00:48.295481 INFO: initial parameter: rt_error = 805.6002197265625
2:00:48.295530 INFO: initial parameter: mobility_error = 0.1
2:00:48.295575 INFO: initial parameter: column_type = library
2:00:48.295618 INFO: initial parameter: num_candidates = 1
2:00:48.295664 INFO: initial parameter: classifier_version = -1
2:00:48.295712 INFO: initial parameter: fwhm_rt = 5
2:00:48.295756 INFO: initial parameter: fwhm_mobility = 0.01
2:00:48.295802 INFO: initial parameter: score_cutoff = 0
2:00:48.295873 INFO: Initializing TimingManager
2:00:48.295931 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:00:48.296048 INFO: FDRManager not loaded from disk.
2:00:48.296071 INFO: Initializing FDRManager
2:00:48.296113 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
2:00:48.333794 PROGRESS: 123,909 target precursors potentially observable (0 removed)
2:00:48.387786 PROGRESS: Starting initial search for precursors.
2:00:48.395508 INFO: Starting optimization step 0.
2:00:48.395684 PROGRESS: === Extracting elution groups 0 to 200 ===
2:00:48.395760 PROGRESS: Extracting batch of 392 precursors
2:00:48.396821 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:48.396873 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:48.396912 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:00:48.396934 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:00:48.397221 INFO: Starting candidate selection
2:00:48.529030 INFO: Starting candidate scoring
2:00:48.567694 INFO: Finished candidate processing
2:00:48.567775 INFO: Collecting candidate features
2:00:48.576217 INFO: Collecting fragment features
2:00:48.578217 INFO: Finished candidate scoring
2:00:48.578955 PROGRESS: === Extracted 392 precursors and 4293 fragments ===
2:00:48.579236 INFO: performing precursor FDR with 47 features
2:00:48.579272 INFO: Decoy channel: -1
2:00:48.579310 INFO: Competetive: True
2:00:48.580287 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:48.600053 INFO: Test AUC: 0.478
2:00:48.600117 INFO: Train AUC: 0.557
2:00:48.600146 INFO: AUC difference: 14.13%
2:00:48.600167 WARNING: AUC difference > 5%. This may indicate overfitting.
2:00:48.775339 INFO: Resetting torch num_threads to 100
2:00:48.775912 INFO: === FDR correction performed with classifier version -1 ===
2:00:48.776555 PROGRESS: ============================= Precursor FDR =============================
2:00:48.776651 PROGRESS: Total precursors accumulated: 200
2:00:48.776714 PROGRESS: Target precursors: 115 (57.50%)
2:00:48.776768 PROGRESS: Decoy precursors: 85 (42.50%)
2:00:48.776818 PROGRESS: 
2:00:48.776863 PROGRESS: Precursor Summary:
2:00:48.777712 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:00:48.777800 PROGRESS: 
2:00:48.777855 PROGRESS: Protein Summary:
2:00:48.778760 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:00:48.778847 PROGRESS: =========================================================================
2:00:48.782547 INFO: Starting optimization step 1.
2:00:48.782654 PROGRESS: === Extracting elution groups 200 to 600 ===
2:00:48.782719 PROGRESS: Extracting batch of 771 precursors
2:00:48.783470 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:48.783516 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:48.783548 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:00:48.783569 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:00:48.783734 INFO: Starting candidate selection
2:00:48.918190 INFO: Starting candidate scoring
2:00:48.955459 INFO: Finished candidate processing
2:00:48.955534 INFO: Collecting candidate features
2:00:48.964499 INFO: Collecting fragment features
2:00:48.966967 INFO: Finished candidate scoring
2:00:48.968916 PROGRESS: === Extracted 1163 precursors and 12634 fragments ===
2:00:48.969699 INFO: performing precursor FDR with 47 features
2:00:48.969740 INFO: Decoy channel: -1
2:00:48.969764 INFO: Competetive: True
2:00:48.972542 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:49.005043 INFO: Test AUC: 0.560
2:00:49.005118 INFO: Train AUC: 0.540
2:00:49.005147 INFO: AUC difference: 3.78%
2:00:49.178232 INFO: Resetting torch num_threads to 100
2:00:49.178887 INFO: === FDR correction performed with classifier version -1 ===
2:00:49.179590 PROGRESS: ============================= Precursor FDR =============================
2:00:49.179680 PROGRESS: Total precursors accumulated: 600
2:00:49.179741 PROGRESS: Target precursors: 351 (58.50%)
2:00:49.179793 PROGRESS: Decoy precursors: 249 (41.50%)
2:00:49.179840 PROGRESS: 
2:00:49.179884 PROGRESS: Precursor Summary:
2:00:49.180752 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:00:49.180843 PROGRESS: 
2:00:49.180900 PROGRESS: Protein Summary:
2:00:49.181819 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:00:49.181906 PROGRESS: =========================================================================
2:00:49.186776 INFO: Starting optimization step 2.
2:00:49.186883 PROGRESS: === Extracting elution groups 600 to 1400 ===
2:00:49.186948 PROGRESS: Extracting batch of 1538 precursors
2:00:49.187797 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:49.187844 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:49.187874 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:00:49.187896 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:00:49.188060 INFO: Starting candidate selection
2:00:49.354553 INFO: Starting candidate scoring
2:00:49.397307 INFO: Finished candidate processing
2:00:49.397397 INFO: Collecting candidate features
2:00:49.408475 INFO: Collecting fragment features
2:00:49.412515 INFO: Finished candidate scoring
2:00:49.415623 PROGRESS: === Extracted 2701 precursors and 29352 fragments ===
2:00:49.416703 INFO: performing precursor FDR with 47 features
2:00:49.416747 INFO: Decoy channel: -1
2:00:49.416788 INFO: Competetive: True
2:00:49.420007 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:49.448738 INFO: Test AUC: 0.512
2:00:49.448825 INFO: Train AUC: 0.531
2:00:49.448855 INFO: AUC difference: 3.55%
2:00:49.619483 INFO: Resetting torch num_threads to 100
2:00:49.620221 INFO: === FDR correction performed with classifier version -1 ===
2:00:49.621028 PROGRESS: ============================= Precursor FDR =============================
2:00:49.621130 PROGRESS: Total precursors accumulated: 1,398
2:00:49.621192 PROGRESS: Target precursors: 795 (56.87%)
2:00:49.621246 PROGRESS: Decoy precursors: 603 (43.13%)
2:00:49.621293 PROGRESS: 
2:00:49.621337 PROGRESS: Precursor Summary:
2:00:49.622211 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:00:49.622303 PROGRESS: 
2:00:49.622359 PROGRESS: Protein Summary:
2:00:49.623291 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:00:49.623382 PROGRESS: =========================================================================
2:00:49.629695 INFO: Starting optimization step 3.
2:00:49.629820 PROGRESS: === Extracting elution groups 1400 to 3000 ===
2:00:49.629884 PROGRESS: Extracting batch of 3065 precursors
2:00:49.631139 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:49.631190 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:49.631222 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:00:49.631248 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:00:49.631411 INFO: Starting candidate selection
2:00:49.870284 INFO: Starting candidate scoring
2:00:49.913304 INFO: Finished candidate processing
2:00:49.913394 INFO: Collecting candidate features
2:00:49.926036 INFO: Collecting fragment features
2:00:49.929771 INFO: Finished candidate scoring
2:00:49.933896 PROGRESS: === Extracted 5766 precursors and 62508 fragments ===
2:00:49.935095 INFO: performing precursor FDR with 47 features
2:00:49.935137 INFO: Decoy channel: -1
2:00:49.935160 INFO: Competetive: True
2:00:49.938906 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:49.969427 INFO: Test AUC: 0.512
2:00:49.969520 INFO: Train AUC: 0.524
2:00:49.969548 INFO: AUC difference: 2.16%
2:00:50.145084 INFO: Resetting torch num_threads to 100
2:00:50.145957 INFO: === FDR correction performed with classifier version -1 ===
2:00:50.146671 PROGRESS: ============================= Precursor FDR =============================
2:00:50.146782 PROGRESS: Total precursors accumulated: 1
2:00:50.146842 PROGRESS: Target precursors: 1 (100.00%)
2:00:50.146894 PROGRESS: Decoy precursors: 0 (0.00%)
2:00:50.146940 PROGRESS: 
2:00:50.146984 PROGRESS: Precursor Summary:
2:00:50.147908 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:00:50.147995 PROGRESS: 
2:00:50.148050 PROGRESS: Protein Summary:
2:00:50.149094 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:00:50.149187 PROGRESS: =========================================================================
2:00:50.158764 INFO: Starting optimization step 4.
2:00:50.158894 PROGRESS: === Extracting elution groups 3000 to 6200 ===
2:00:50.158959 PROGRESS: Extracting batch of 6167 precursors
2:00:50.160773 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:50.160821 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:50.160853 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:00:50.160875 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:00:50.161042 INFO: Starting candidate selection
2:00:50.618041 INFO: Starting candidate scoring
2:00:50.668116 INFO: Finished candidate processing
2:00:50.668214 INFO: Collecting candidate features
2:00:50.685706 INFO: Collecting fragment features
2:00:50.691936 INFO: Finished candidate scoring
2:00:50.699479 PROGRESS: === Extracted 11933 precursors and 129351 fragments ===
2:00:50.701359 INFO: performing precursor FDR with 47 features
2:00:50.701420 INFO: Decoy channel: -1
2:00:50.701446 INFO: Competetive: True
2:00:50.706768 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:50.755733 INFO: Test AUC: 0.533
2:00:50.755838 INFO: Train AUC: 0.528
2:00:50.755868 INFO: AUC difference: 1.01%
2:00:50.935470 INFO: Resetting torch num_threads to 100
2:00:50.936464 INFO: === FDR correction performed with classifier version -1 ===
2:00:50.937155 PROGRESS: ============================= Precursor FDR =============================
2:00:50.937247 PROGRESS: Total precursors accumulated: 1
2:00:50.937310 PROGRESS: Target precursors: 1 (100.00%)
2:00:50.937362 PROGRESS: Decoy precursors: 0 (0.00%)
2:00:50.937409 PROGRESS: 
2:00:50.937454 PROGRESS: Precursor Summary:
2:00:50.938399 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:00:50.938489 PROGRESS: 
2:00:50.938546 PROGRESS: Protein Summary:
2:00:50.939574 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:00:50.939674 PROGRESS: =========================================================================
2:00:50.955434 INFO: Starting optimization step 5.
2:00:50.955676 PROGRESS: === Extracting elution groups 6200 to 12600 ===
2:00:50.955744 PROGRESS: Extracting batch of 12312 precursors
2:00:50.957963 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:50.958018 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:50.958051 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:00:50.958074 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:00:50.958254 INFO: Starting candidate selection
2:00:51.707555 INFO: Starting candidate scoring
2:00:51.789943 INFO: Finished candidate processing
2:00:51.790051 INFO: Collecting candidate features
2:00:51.817017 INFO: Collecting fragment features
2:00:51.826708 INFO: Finished candidate scoring
2:00:51.839699 PROGRESS: === Extracted 24245 precursors and 263338 fragments ===
2:00:51.842857 INFO: performing precursor FDR with 47 features
2:00:51.842918 INFO: Decoy channel: -1
2:00:51.842944 INFO: Competetive: True
2:00:51.852042 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:52.155858 INFO: Test AUC: 0.779
2:00:52.155990 INFO: Train AUC: 0.777
2:00:52.156021 INFO: AUC difference: 0.20%
2:00:52.345588 INFO: Resetting torch num_threads to 100
2:00:52.346987 INFO: === FDR correction performed with classifier version -1 ===
2:00:52.348252 PROGRESS: ============================= Precursor FDR =============================
2:00:52.348351 PROGRESS: Total precursors accumulated: 6,256
2:00:52.348415 PROGRESS: Target precursors: 5,928 (94.76%)
2:00:52.348467 PROGRESS: Decoy precursors: 328 (5.24%)
2:00:52.348514 PROGRESS: 
2:00:52.348563 PROGRESS: Precursor Summary:
2:00:52.350545 PROGRESS: Channel   0:	 0.05 FDR: 5,772; 0.01 FDR: 3,414; 0.001 FDR: 1,206
2:00:52.350644 PROGRESS: 
2:00:52.350702 PROGRESS: Protein Summary:
2:00:52.353432 PROGRESS: Channel   0:	 0.05 FDR: 3,234; 0.01 FDR: 2,084; 0.001 FDR:   884
2:00:52.353543 PROGRESS: =========================================================================
2:00:52.377763 INFO: fragments_df: keeping 5000 of 263338 [sum(precursor_idx_mask)=39020 sum(mass_error_mask)=263338 stop_rank=5000
2:00:52.387025 INFO: calibration group: precursor, fitting rt estimator 
2:00:52.777529 INFO: calibration group: fragment, fitting mz estimator 
2:00:53.395156 INFO: Using score_cutoff 64.55699219284057 (fac=0.99, q=1)
2:00:53.395627 INFO: calibration group: precursor, predicting mz
2:00:53.395713 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:53.395743 INFO: calibration group: precursor, predicting rt
2:00:53.398057 INFO: calibration group: fragment, predicting mz
2:00:53.402168 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:00:53.402300 INFO: Starting optimization step 6.
2:00:53.402367 PROGRESS: === Extracting elution groups 0 to 1400 ===
2:00:53.402422 PROGRESS: Extracting batch of 2701 precursors
2:00:53.403593 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:53.403640 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:53.403683 INFO: FWHM in RT is 3.02 seconds, sigma is 0.39
2:00:53.403705 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:53.403867 INFO: Starting candidate selection
2:00:53.630532 INFO: Starting candidate scoring
2:00:53.678729 INFO: Finished candidate processing
2:00:53.678820 INFO: Collecting candidate features
2:00:53.694620 INFO: Collecting fragment features
2:00:53.700383 INFO: Finished candidate scoring
2:00:53.703513 PROGRESS: === Extracted 5402 precursors and 58095 fragments ===
2:00:53.703803 INFO: performing precursor FDR with 47 features
2:00:53.703839 INFO: Decoy channel: -1
2:00:53.703863 INFO: Competetive: True
2:00:53.707104 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:53.740605 INFO: Test AUC: 0.678
2:00:53.740731 INFO: Train AUC: 0.675
2:00:53.740761 INFO: AUC difference: 0.42%
2:00:53.921242 INFO: Resetting torch num_threads to 100
2:00:53.921933 INFO: === FDR correction performed with classifier version 5 ===
2:00:53.922647 PROGRESS: ============================= Precursor FDR =============================
2:00:53.922739 PROGRESS: Total precursors accumulated: 728
2:00:53.922801 PROGRESS: Target precursors: 693 (95.19%)
2:00:53.922853 PROGRESS: Decoy precursors: 35 (4.81%)
2:00:53.922909 PROGRESS: 
2:00:53.922956 PROGRESS: Precursor Summary:
2:00:53.924004 PROGRESS: Channel   0:	 0.05 FDR:   689; 0.01 FDR:   438; 0.001 FDR:   130
2:00:53.924098 PROGRESS: 
2:00:53.924155 PROGRESS: Protein Summary:
2:00:53.925400 PROGRESS: Channel   0:	 0.05 FDR:   634; 0.01 FDR:   406; 0.001 FDR:   121
2:00:53.925500 PROGRESS: =========================================================================
2:00:53.931352 INFO: fragments_df: keeping 4860 of 58095 [sum(precursor_idx_mask)=9811 sum(mass_error_mask)=58095 stop_rank=4860
2:00:53.938686 INFO: calibration group: precursor, fitting rt estimator 
2:00:54.047611 INFO: calibration group: fragment, fitting mz estimator 
2:00:54.642957 INFO: Using score_cutoff 64.64486972351075 (fac=0.99, q=1)
2:00:54.643366 INFO: calibration group: precursor, predicting mz
2:00:54.643450 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:54.643480 INFO: calibration group: precursor, predicting rt
2:00:54.645795 INFO: calibration group: fragment, predicting mz
2:00:54.650194 INFO: === checking if optimization conditions were reached ===
2:00:54.651800 PROGRESS: ❌ ms2_error      : 13.9423 > 6.7411 or insufficient steps taken.
2:00:54.651854 INFO: ==============================================
2:00:54.651941 INFO: Starting optimization step 7.
2:00:54.652005 PROGRESS: === Extracting elution groups 0 to 1400 ===
2:00:54.652064 PROGRESS: Extracting batch of 2701 precursors
2:00:54.653249 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:54.653298 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:54.653331 INFO: FWHM in RT is 2.91 seconds, sigma is 0.37
2:00:54.653354 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:54.653515 INFO: Starting candidate selection
2:00:54.874422 INFO: Starting candidate scoring
2:00:54.923243 INFO: Finished candidate processing
2:00:54.923344 INFO: Collecting candidate features
2:00:54.939080 INFO: Collecting fragment features
2:00:54.944828 INFO: Finished candidate scoring
2:00:54.947829 PROGRESS: === Extracted 5402 precursors and 53381 fragments ===
2:00:54.948159 INFO: performing precursor FDR with 47 features
2:00:54.948202 INFO: Decoy channel: -1
2:00:54.948233 INFO: Competetive: True
2:00:54.951320 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:54.982770 INFO: Test AUC: 0.700
2:00:54.982860 INFO: Train AUC: 0.690
2:00:54.982903 INFO: AUC difference: 1.46%
2:00:55.157870 INFO: Resetting torch num_threads to 100
2:00:55.158636 INFO: === FDR correction performed with classifier version 6 ===
2:00:55.159357 PROGRESS: ============================= Precursor FDR =============================
2:00:55.159461 PROGRESS: Total precursors accumulated: 939
2:00:55.159535 PROGRESS: Target precursors: 904 (96.27%)
2:00:55.159601 PROGRESS: Decoy precursors: 35 (3.73%)
2:00:55.159673 PROGRESS: 
2:00:55.159734 PROGRESS: Precursor Summary:
2:00:55.160882 PROGRESS: Channel   0:	 0.05 FDR:   904; 0.01 FDR:   707; 0.001 FDR:   331
2:00:55.160989 PROGRESS: 
2:00:55.161059 PROGRESS: Protein Summary:
2:00:55.162471 PROGRESS: Channel   0:	 0.05 FDR:   825; 0.01 FDR:   650; 0.001 FDR:   314
2:00:55.162577 PROGRESS: =========================================================================
2:00:55.168547 INFO: fragments_df: keeping 5000 of 53381 [sum(precursor_idx_mask)=14897 sum(mass_error_mask)=53381 stop_rank=5000
2:00:55.173699 INFO: calibration group: precursor, fitting rt estimator 
2:00:55.316885 INFO: calibration group: fragment, fitting mz estimator 
2:00:55.963726 INFO: Using score_cutoff 51.25406410217285 (fac=0.99, q=1)
2:00:55.964146 INFO: calibration group: precursor, predicting mz
2:00:55.964243 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:55.964276 INFO: calibration group: precursor, predicting rt
2:00:55.965825 INFO: calibration group: fragment, predicting mz
2:00:55.967990 INFO: === checking if optimization conditions were reached ===
2:00:55.969563 PROGRESS: ✅ ms2_error      : 6.7411 <= 6.7411
2:00:55.969619 INFO: ==============================================
2:00:55.969708 PROGRESS: Optimization finished for ms2_error.
2:00:55.974437 INFO: calibration group: precursor, predicting mz
2:00:55.974551 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:55.974581 INFO: calibration group: precursor, predicting rt
2:00:55.975821 INFO: calibration group: fragment, predicting mz
2:00:55.977906 INFO: Starting optimization step 0.
2:00:55.978003 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:55.978065 PROGRESS: Extracting batch of 1163 precursors
2:00:55.978907 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:55.978953 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:55.978984 INFO: FWHM in RT is 2.58 seconds, sigma is 0.33
2:00:55.979008 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:55.979169 INFO: Starting candidate selection
2:00:56.129561 INFO: Starting candidate scoring
2:00:56.170777 INFO: Finished candidate processing
2:00:56.170864 INFO: Collecting candidate features
2:00:56.181929 INFO: Collecting fragment features
2:00:56.185837 INFO: Finished candidate scoring
2:00:56.187455 PROGRESS: === Extracted 2325 precursors and 20187 fragments ===
2:00:56.187751 INFO: performing precursor FDR with 47 features
2:00:56.187787 INFO: Decoy channel: -1
2:00:56.187809 INFO: Competetive: True
2:00:56.190409 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:56.212544 INFO: Test AUC: 0.672
2:00:56.212615 INFO: Train AUC: 0.693
2:00:56.212644 INFO: AUC difference: 2.94%
2:00:56.395948 INFO: Resetting torch num_threads to 100
2:00:56.396558 INFO: === FDR correction performed with classifier version 7 ===
2:00:56.397221 PROGRESS: ============================= Precursor FDR =============================
2:00:56.397313 PROGRESS: Total precursors accumulated: 395
2:00:56.397375 PROGRESS: Target precursors: 383 (96.96%)
2:00:56.397426 PROGRESS: Decoy precursors: 12 (3.04%)
2:00:56.397472 PROGRESS: 
2:00:56.397515 PROGRESS: Precursor Summary:
2:00:56.398515 PROGRESS: Channel   0:	 0.05 FDR:   383; 0.01 FDR:   303; 0.001 FDR:   183
2:00:56.398603 PROGRESS: 
2:00:56.398658 PROGRESS: Protein Summary:
2:00:56.399803 PROGRESS: Channel   0:	 0.05 FDR:   368; 0.01 FDR:   293; 0.001 FDR:   178
2:00:56.399897 PROGRESS: =========================================================================
2:00:56.402753 INFO: fragments_df: keeping 2875 of 20187 [sum(precursor_idx_mask)=5957 sum(mass_error_mask)=20187 stop_rank=2875
2:00:56.407852 INFO: calibration group: precursor, fitting rt estimator 
2:00:56.511970 INFO: calibration group: fragment, fitting mz estimator 
2:00:56.831539 INFO: Using score_cutoff 46.87825284805297 (fac=0.99, q=1)
2:00:56.831938 INFO: calibration group: precursor, predicting mz
2:00:56.832023 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:56.832061 INFO: calibration group: precursor, predicting rt
2:00:56.833627 INFO: calibration group: fragment, predicting mz
2:00:56.835762 INFO: === checking if optimization conditions were reached ===
2:00:56.835869 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2:00:56.837326 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 9.2664.
2:00:56.837379 INFO: ==============================================
2:00:56.837476 INFO: Starting optimization step 1.
2:00:56.837542 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:56.837598 PROGRESS: Extracting batch of 1163 precursors
2:00:56.838826 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:56.838873 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:56.838905 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
2:00:56.838927 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:56.839084 INFO: Starting candidate selection
2:00:56.954469 INFO: Starting candidate scoring
2:00:56.996624 INFO: Finished candidate processing
2:00:56.996703 INFO: Collecting candidate features
2:00:57.008130 INFO: Collecting fragment features
2:00:57.012253 INFO: Finished candidate scoring
2:00:57.013891 PROGRESS: === Extracted 2265 precursors and 17477 fragments ===
2:00:57.014189 INFO: performing precursor FDR with 47 features
2:00:57.014225 INFO: Decoy channel: -1
2:00:57.014248 INFO: Competetive: True
2:00:57.016819 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:57.050800 INFO: Test AUC: 0.706
2:00:57.050884 INFO: Train AUC: 0.743
2:00:57.050917 INFO: AUC difference: 5.00%
2:00:57.225925 INFO: Resetting torch num_threads to 100
2:00:57.226859 INFO: === FDR correction performed with classifier version 7 ===
2:00:57.227507 PROGRESS: ============================= Precursor FDR =============================
2:00:57.227599 PROGRESS: Total precursors accumulated: 464
2:00:57.227663 PROGRESS: Target precursors: 448 (96.55%)
2:00:57.227715 PROGRESS: Decoy precursors: 16 (3.45%)
2:00:57.227765 PROGRESS: 
2:00:57.227810 PROGRESS: Precursor Summary:
2:00:57.228819 PROGRESS: Channel   0:	 0.05 FDR:   448; 0.01 FDR:   380; 0.001 FDR:   274
2:00:57.228913 PROGRESS: 
2:00:57.228971 PROGRESS: Protein Summary:
2:00:57.230168 PROGRESS: Channel   0:	 0.05 FDR:   429; 0.01 FDR:   366; 0.001 FDR:   266
2:00:57.230263 PROGRESS: =========================================================================
2:00:57.233134 INFO: fragments_df: keeping 3111 of 17477 [sum(precursor_idx_mask)=7002 sum(mass_error_mask)=17477 stop_rank=3111
2:00:57.238456 INFO: calibration group: precursor, fitting rt estimator 
2:00:57.348984 INFO: calibration group: fragment, fitting mz estimator 
2:00:57.712055 INFO: Using score_cutoff 44.007173842620844 (fac=0.99, q=1)
2:00:57.712530 INFO: calibration group: precursor, predicting mz
2:00:57.712622 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:57.712656 INFO: calibration group: precursor, predicting rt
2:00:57.714437 INFO: calibration group: fragment, predicting mz
2:00:57.716669 INFO: === checking if optimization conditions were reached ===
2:00:57.716792 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2:00:57.718405 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 6.7755.
2:00:57.718457 INFO: ==============================================
2:00:57.718562 INFO: Starting optimization step 2.
2:00:57.718641 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:57.718710 PROGRESS: Extracting batch of 1163 precursors
2:00:57.721966 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:57.722014 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:57.722048 INFO: FWHM in RT is 2.30 seconds, sigma is 0.30
2:00:57.722070 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:57.722251 INFO: Starting candidate selection
2:00:57.837963 INFO: Starting candidate scoring
2:00:57.881228 INFO: Finished candidate processing
2:00:57.881310 INFO: Collecting candidate features
2:00:57.892555 INFO: Collecting fragment features
2:00:57.896329 INFO: Finished candidate scoring
2:00:57.897977 PROGRESS: === Extracted 2265 precursors and 17520 fragments ===
2:00:57.898270 INFO: performing precursor FDR with 47 features
2:00:57.898306 INFO: Decoy channel: -1
2:00:57.898329 INFO: Competetive: True
2:00:57.901461 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:57.924708 INFO: Test AUC: 0.735
2:00:57.924780 INFO: Train AUC: 0.742
2:00:57.924810 INFO: AUC difference: 0.93%
2:00:58.102119 INFO: Resetting torch num_threads to 100
2:00:58.102955 INFO: === FDR correction performed with classifier version 7 ===
2:00:58.103746 PROGRESS: ============================= Precursor FDR =============================
2:00:58.103847 PROGRESS: Total precursors accumulated: 462
2:00:58.103907 PROGRESS: Target precursors: 447 (96.75%)
2:00:58.103959 PROGRESS: Decoy precursors: 15 (3.25%)
2:00:58.104005 PROGRESS: 
2:00:58.104050 PROGRESS: Precursor Summary:
2:00:58.105116 PROGRESS: Channel   0:	 0.05 FDR:   447; 0.01 FDR:   378; 0.001 FDR:   305
2:00:58.105207 PROGRESS: 
2:00:58.105262 PROGRESS: Protein Summary:
2:00:58.106467 PROGRESS: Channel   0:	 0.05 FDR:   428; 0.01 FDR:   365; 0.001 FDR:   296
2:00:58.106558 PROGRESS: =========================================================================
2:00:58.109592 INFO: fragments_df: keeping 3107 of 17520 [sum(precursor_idx_mask)=6970 sum(mass_error_mask)=17520 stop_rank=3107
2:00:58.117912 INFO: calibration group: precursor, fitting rt estimator 
2:00:58.234874 INFO: calibration group: fragment, fitting mz estimator 
2:00:58.582002 INFO: Using score_cutoff 44.292497693252564 (fac=0.99, q=1)
2:00:58.582681 INFO: calibration group: precursor, predicting mz
2:00:58.582774 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:58.582804 INFO: calibration group: precursor, predicting rt
2:00:58.584519 INFO: calibration group: fragment, predicting mz
2:00:58.586727 INFO: === checking if optimization conditions were reached ===
2:00:58.586833 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2:00:58.588603 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 6.0593.
2:00:58.588659 INFO: ==============================================
2:00:58.588755 INFO: Starting optimization step 3.
2:00:58.588825 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:58.588886 PROGRESS: Extracting batch of 1163 precursors
2:00:58.589865 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:58.589911 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:58.589945 INFO: FWHM in RT is 2.30 seconds, sigma is 0.30
2:00:58.589968 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:58.590161 INFO: Starting candidate selection
2:00:58.705546 INFO: Starting candidate scoring
2:00:58.747937 INFO: Finished candidate processing
2:00:58.748022 INFO: Collecting candidate features
2:00:58.759355 INFO: Collecting fragment features
2:00:58.763457 INFO: Finished candidate scoring
2:00:58.765119 PROGRESS: === Extracted 2273 precursors and 17560 fragments ===
2:00:58.765396 INFO: performing precursor FDR with 47 features
2:00:58.765431 INFO: Decoy channel: -1
2:00:58.765455 INFO: Competetive: True
2:00:58.768072 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:58.802082 INFO: Test AUC: 0.739
2:00:58.802162 INFO: Train AUC: 0.737
2:00:58.802191 INFO: AUC difference: 0.25%
2:00:58.977973 INFO: Resetting torch num_threads to 100
2:00:58.978583 INFO: === FDR correction performed with classifier version 7 ===
2:00:58.979223 PROGRESS: ============================= Precursor FDR =============================
2:00:58.979316 PROGRESS: Total precursors accumulated: 462
2:00:58.979376 PROGRESS: Target precursors: 447 (96.75%)
2:00:58.979428 PROGRESS: Decoy precursors: 15 (3.25%)
2:00:58.979474 PROGRESS: 
2:00:58.979518 PROGRESS: Precursor Summary:
2:00:58.980531 PROGRESS: Channel   0:	 0.05 FDR:   447; 0.01 FDR:   378; 0.001 FDR:   327
2:00:58.980628 PROGRESS: 
2:00:58.980686 PROGRESS: Protein Summary:
2:00:58.981874 PROGRESS: Channel   0:	 0.05 FDR:   429; 0.01 FDR:   365; 0.001 FDR:   316
2:00:58.981971 PROGRESS: =========================================================================
2:00:58.984823 INFO: fragments_df: keeping 3104 of 17560 [sum(precursor_idx_mask)=6978 sum(mass_error_mask)=17560 stop_rank=3104
2:00:58.989775 INFO: calibration group: precursor, fitting rt estimator 
2:00:59.096369 INFO: calibration group: fragment, fitting mz estimator 
2:00:59.443056 INFO: Using score_cutoff 43.94731283912659 (fac=0.99, q=1)
2:00:59.443478 INFO: calibration group: precursor, predicting mz
2:00:59.443567 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:59.443598 INFO: calibration group: precursor, predicting rt
2:00:59.445151 INFO: calibration group: fragment, predicting mz
2:00:59.447337 INFO: === checking if optimization conditions were reached ===
2:00:59.447444 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2:00:59.449077 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 4.9492.
2:00:59.449131 INFO: ==============================================
2:00:59.449219 INFO: Starting optimization step 4.
2:00:59.449284 PROGRESS: === Extracting elution groups 0 to 600 ===
2:00:59.449342 PROGRESS: Extracting batch of 1163 precursors
2:00:59.450254 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:00:59.450303 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:59.450334 INFO: FWHM in RT is 2.30 seconds, sigma is 0.30
2:00:59.450356 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:59.450513 INFO: Starting candidate selection
2:00:59.563737 INFO: Starting candidate scoring
2:00:59.607106 INFO: Finished candidate processing
2:00:59.607191 INFO: Collecting candidate features
2:00:59.615670 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2268)
2:00:59.618666 INFO: Collecting fragment features
2:00:59.622590 INFO: Finished candidate scoring
2:00:59.624213 PROGRESS: === Extracted 2268 precursors and 17517 fragments ===
2:00:59.624506 INFO: performing precursor FDR with 47 features
2:00:59.624542 INFO: Decoy channel: -1
2:00:59.624564 INFO: Competetive: True
2:00:59.627127 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:59.628322 WARNING: dropped 1 decoy PSMs due to missing features
2:00:59.650395 INFO: Test AUC: 0.774
2:00:59.650469 INFO: Train AUC: 0.722
2:00:59.650499 INFO: AUC difference: 7.22%
2:00:59.650520 WARNING: AUC difference > 5%. This may indicate overfitting.
2:00:59.827013 INFO: Resetting torch num_threads to 100
2:00:59.827620 INFO: === FDR correction performed with classifier version 7 ===
2:00:59.828288 PROGRESS: ============================= Precursor FDR =============================
2:00:59.828384 PROGRESS: Total precursors accumulated: 449
2:00:59.828446 PROGRESS: Target precursors: 435 (96.88%)
2:00:59.828500 PROGRESS: Decoy precursors: 14 (3.12%)
2:00:59.828548 PROGRESS: 
2:00:59.828592 PROGRESS: Precursor Summary:
2:00:59.829592 PROGRESS: Channel   0:	 0.05 FDR:   435; 0.01 FDR:   371; 0.001 FDR:   322
2:00:59.829684 PROGRESS: 
2:00:59.829739 PROGRESS: Protein Summary:
2:00:59.830925 PROGRESS: Channel   0:	 0.05 FDR:   419; 0.01 FDR:   359; 0.001 FDR:   311
2:00:59.831020 PROGRESS: =========================================================================
2:00:59.833804 INFO: fragments_df: keeping 3057 of 17517 [sum(precursor_idx_mask)=6872 sum(mass_error_mask)=17517 stop_rank=3057
2:00:59.838768 INFO: calibration group: precursor, fitting rt estimator 
2:00:59.943700 INFO: calibration group: fragment, fitting mz estimator 
2:01:00.284402 INFO: Using score_cutoff 44.26787998580933 (fac=0.99, q=1)
2:01:00.284819 INFO: calibration group: precursor, predicting mz
2:01:00.284912 WARNING: mz prediction was skipped as it has not been fitted yet
2:01:00.284943 INFO: calibration group: precursor, predicting rt
2:01:00.286492 INFO: calibration group: fragment, predicting mz
2:01:00.288656 INFO: === checking if optimization conditions were reached ===
2:01:00.288756 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2:01:00.290383 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 4.7963.
2:01:00.290437 INFO: ==============================================
2:01:00.290534 INFO: Starting optimization step 5.
2:01:00.290600 PROGRESS: === Extracting elution groups 0 to 600 ===
2:01:00.290657 PROGRESS: Extracting batch of 1163 precursors
2:01:00.291575 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:01:00.291622 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:00.291652 INFO: FWHM in RT is 2.30 seconds, sigma is 0.30
2:01:00.291675 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:01:00.291828 INFO: Starting candidate selection
2:01:00.406193 INFO: Starting candidate scoring
2:01:00.448708 INFO: Finished candidate processing
2:01:00.448795 INFO: Collecting candidate features
2:01:00.457251 WARNING: intensity_correlation has 1 NaNs ( 0.04 % out of 2269)
2:01:00.460194 INFO: Collecting fragment features
2:01:00.464031 INFO: Finished candidate scoring
2:01:00.465645 PROGRESS: === Extracted 2269 precursors and 17500 fragments ===
2:01:00.465927 INFO: performing precursor FDR with 47 features
2:01:00.465963 INFO: Decoy channel: -1
2:01:00.465985 INFO: Competetive: True
2:01:00.468574 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:00.469755 WARNING: dropped 1 decoy PSMs due to missing features
2:01:00.491020 INFO: Test AUC: 0.730
2:01:00.491088 INFO: Train AUC: 0.729
2:01:00.491118 INFO: AUC difference: 0.12%
2:01:00.667736 INFO: Resetting torch num_threads to 100
2:01:00.668347 INFO: === FDR correction performed with classifier version 7 ===
2:01:00.668986 PROGRESS: ============================= Precursor FDR =============================
2:01:00.669079 PROGRESS: Total precursors accumulated: 449
2:01:00.669141 PROGRESS: Target precursors: 435 (96.88%)
2:01:00.669194 PROGRESS: Decoy precursors: 14 (3.12%)
2:01:00.669243 PROGRESS: 
2:01:00.669288 PROGRESS: Precursor Summary:
2:01:00.670302 PROGRESS: Channel   0:	 0.05 FDR:   435; 0.01 FDR:   368; 0.001 FDR:   324
2:01:00.670405 PROGRESS: 
2:01:00.670463 PROGRESS: Protein Summary:
2:01:00.671659 PROGRESS: Channel   0:	 0.05 FDR:   419; 0.01 FDR:   356; 0.001 FDR:   313
2:01:00.671760 PROGRESS: =========================================================================
2:01:00.674587 INFO: fragments_df: keeping 3036 of 17500 [sum(precursor_idx_mask)=6830 sum(mass_error_mask)=17500 stop_rank=3036
2:01:00.679660 INFO: calibration group: precursor, fitting rt estimator 
2:01:00.784914 INFO: calibration group: fragment, fitting mz estimator 
2:01:01.125036 INFO: Using score_cutoff 44.95232485313415 (fac=0.99, q=1)
2:01:01.125455 INFO: calibration group: precursor, predicting mz
2:01:01.125543 WARNING: mz prediction was skipped as it has not been fitted yet
2:01:01.125575 INFO: calibration group: precursor, predicting rt
2:01:01.127133 INFO: calibration group: fragment, predicting mz
2:01:01.129269 INFO: === checking if optimization conditions were reached ===
2:01:01.129373 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2:01:01.130348 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 4.7963 found after 6 searches.
2:01:01.130397 INFO: ==============================================
2:01:01.130484 PROGRESS: Optimization finished for rt_error.
2:01:01.135113 INFO: calibration group: precursor, predicting mz
2:01:01.135225 WARNING: mz prediction was skipped as it has not been fitted yet
2:01:01.135255 INFO: calibration group: precursor, predicting rt
2:01:01.136534 INFO: calibration group: fragment, predicting mz
2:01:01.164652 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:01:01.164806 PROGRESS: ==============================================
2:01:01.165206 PROGRESS: ms2_error      : 6.7411
2:01:01.165268 PROGRESS: rt_error       : 4.7963
2:01:01.165317 PROGRESS: ==============================================
2:01:01.165882 INFO: calibration group: precursor, predicting mz
2:01:01.165975 WARNING: mz prediction was skipped as it has not been fitted yet
2:01:01.166003 INFO: calibration group: precursor, predicting rt
2:01:01.300372 INFO: calibration group: fragment, predicting mz
2:01:01.656417 PROGRESS: Extracting batch of 238438 precursors
2:01:01.729381 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:01:01.729538 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:01.729576 INFO: FWHM in RT is 2.30 seconds, sigma is 0.30
2:01:01.729600 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:01:01.729841 INFO: Starting candidate selection
2:01:08.177428 INFO: Applying score cutoff of 44.95232485313415
2:01:08.182125 INFO: Removed 287587 precursors with score below cutoff
2:01:08.240317 INFO: Starting candidate scoring
2:01:09.478466 INFO: Finished candidate processing
2:01:09.478582 INFO: Collecting candidate features
2:01:09.766631 INFO: Collecting fragment features
2:01:09.870912 INFO: Finished candidate scoring
2:01:09.965587 INFO: === FDR correction performed with classifier version 13 ===
2:01:09.966196 INFO: performing precursor FDR with 47 features
2:01:09.966238 INFO: Decoy channel: -1
2:01:09.966261 INFO: Competetive: True
2:01:10.020611 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:10.041021 WARNING: FDR calculation for 139376 target and 41537 decoy PSMs
2:01:10.041158 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:01:13.560422 INFO: Test AUC: 0.917
2:01:13.560574 INFO: Train AUC: 0.917
2:01:13.560606 INFO: AUC difference: 0.01%
2:01:13.771178 INFO: Resetting torch num_threads to 100
2:01:13.790550 INFO: Removing fragments below FDR threshold
2:01:13.844869 PROGRESS: ============================= Precursor FDR =============================
2:01:13.845464 PROGRESS: Total precursors accumulated: 96,169
2:01:13.845536 PROGRESS: Target precursors: 95,217 (99.01%)
2:01:13.845589 PROGRESS: Decoy precursors: 952 (0.99%)
2:01:13.845635 PROGRESS: 
2:01:13.845684 PROGRESS: Precursor Summary:
2:01:13.888071 PROGRESS: Channel   0:	 0.05 FDR: 95,217; 0.01 FDR: 95,217; 0.001 FDR: 86,385
2:01:13.888414 PROGRESS: 
2:01:13.888487 PROGRESS: Protein Summary:
2:01:13.955527 PROGRESS: Channel   0:	 0.05 FDR: 10,243; 0.01 FDR: 10,243; 0.001 FDR: 9,386
2:01:13.955829 PROGRESS: =========================================================================
2:01:14.652100 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:01:14.674601 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:01:14.674786 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant
2:01:14.674864 INFO: Creating folder run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/figures
2:01:14.675857 INFO: Initializing RawFileManager
2:01:24.526451 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
2:01:24.530869 INFO: Determining DIA cycle
2:01:24.547282 INFO: Found cycle with start 0.00 min and length 300.
2:01:24.714708 INFO: RT (min)            : 0.0 - 26.9
2:01:24.714806 INFO: RT duration (sec)   : 1611.2
2:01:24.714835 INFO: RT duration (min)   : 26.9
2:01:24.714860 INFO: Cycle len (scans)   : 300
2:01:24.714879 INFO: Cycle len (sec)     : 1.65
2:01:24.714898 INFO: Number of cycles    : 978
2:01:24.714916 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:01:24.763557 INFO: Initializing CalibrationManager
2:01:24.763893 INFO: Loading calibration config
2:01:24.764523 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed'], 'function': LOESSRegression()}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed'], 'function': LOESSRegression(n_kernels=2)}], 'name': 'precursor'}]
2:01:24.764634 INFO: Calibration group :fragment, found 1 estimator(s)
2:01:24.764727 INFO: Calibration group :precursor, found 3 estimator(s)
2:01:24.764804 INFO: Disabling ion mobility calibration
2:01:24.764831 INFO: removed mobility estimator from group precursor
2:01:24.764989 INFO: Initializing OptimizationManager
2:01:24.765102 INFO: initial parameter: ms1_error = 30
2:01:24.765165 INFO: initial parameter: ms2_error = 30
2:01:24.765216 INFO: initial parameter: rt_error = 805.611083984375
2:01:24.765260 INFO: initial parameter: mobility_error = 0.1
2:01:24.765306 INFO: initial parameter: column_type = library
2:01:24.765348 INFO: initial parameter: num_candidates = 1
2:01:24.765388 INFO: initial parameter: classifier_version = -1
2:01:24.765428 INFO: initial parameter: fwhm_rt = 5
2:01:24.765469 INFO: initial parameter: fwhm_mobility = 0.01
2:01:24.765509 INFO: initial parameter: score_cutoff = 0
2:01:24.765580 INFO: Initializing TimingManager
2:01:24.765638 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:01:24.765751 INFO: FDRManager not loaded from disk.
2:01:24.765775 INFO: Initializing FDRManager
2:01:24.765815 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
2:01:24.802967 PROGRESS: 123,909 target precursors potentially observable (0 removed)
2:01:24.856581 PROGRESS: Starting initial search for precursors.
2:01:24.864949 INFO: Starting optimization step 0.
2:01:24.865128 PROGRESS: === Extracting elution groups 0 to 200 ===
2:01:24.865206 PROGRESS: Extracting batch of 392 precursors
2:01:24.866253 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:01:24.866305 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:24.866346 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:01:24.866370 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:01:24.866650 INFO: Starting candidate selection
2:01:24.995353 INFO: Starting candidate scoring
2:01:25.031403 INFO: Finished candidate processing
2:01:25.031485 INFO: Collecting candidate features
2:01:25.040624 INFO: Collecting fragment features
2:01:25.042616 INFO: Finished candidate scoring
2:01:25.043324 PROGRESS: === Extracted 392 precursors and 4290 fragments ===
2:01:25.043604 INFO: performing precursor FDR with 47 features
2:01:25.043640 INFO: Decoy channel: -1
2:01:25.043664 INFO: Competetive: True
2:01:25.044711 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:25.064545 INFO: Test AUC: 0.367
2:01:25.064617 INFO: Train AUC: 0.327
2:01:25.064646 INFO: AUC difference: 12.27%
2:01:25.064669 WARNING: AUC difference > 5%. This may indicate overfitting.
2:01:25.234718 INFO: Resetting torch num_threads to 100
2:01:25.235278 INFO: === FDR correction performed with classifier version -1 ===
2:01:25.235931 PROGRESS: ============================= Precursor FDR =============================
2:01:25.236022 PROGRESS: Total precursors accumulated: 200
2:01:25.236082 PROGRESS: Target precursors: 62 (31.00%)
2:01:25.236283 PROGRESS: Decoy precursors: 138 (69.00%)
2:01:25.236337 PROGRESS: 
2:01:25.236383 PROGRESS: Precursor Summary:
2:01:25.237244 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:01:25.237331 PROGRESS: 
2:01:25.237386 PROGRESS: Protein Summary:
2:01:25.238283 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:01:25.238368 PROGRESS: =========================================================================
2:01:25.242114 INFO: Starting optimization step 1.
2:01:25.242218 PROGRESS: === Extracting elution groups 200 to 600 ===
2:01:25.242281 PROGRESS: Extracting batch of 771 precursors
2:01:25.243043 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:01:25.243088 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:25.243119 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:01:25.243140 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:01:25.243303 INFO: Starting candidate selection
2:01:25.376794 INFO: Starting candidate scoring
2:01:25.416219 INFO: Finished candidate processing
2:01:25.416301 INFO: Collecting candidate features
2:01:25.425327 INFO: Collecting fragment features
2:01:25.427752 INFO: Finished candidate scoring
2:01:25.429791 PROGRESS: === Extracted 1163 precursors and 12646 fragments ===
2:01:25.430539 INFO: performing precursor FDR with 47 features
2:01:25.430582 INFO: Decoy channel: -1
2:01:25.430605 INFO: Competetive: True
2:01:25.433431 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:25.456041 INFO: Test AUC: 0.322
2:01:25.456115 INFO: Train AUC: 0.310
2:01:25.456144 INFO: AUC difference: 3.84%
2:01:25.640380 INFO: Resetting torch num_threads to 100
2:01:25.641040 INFO: === FDR correction performed with classifier version -1 ===
2:01:25.641725 PROGRESS: ============================= Precursor FDR =============================
2:01:25.641822 PROGRESS: Total precursors accumulated: 600
2:01:25.641883 PROGRESS: Target precursors: 183 (30.50%)
2:01:25.641934 PROGRESS: Decoy precursors: 417 (69.50%)
2:01:25.641981 PROGRESS: 
2:01:25.642026 PROGRESS: Precursor Summary:
2:01:25.642896 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:01:25.642984 PROGRESS: 
2:01:25.643038 PROGRESS: Protein Summary:
2:01:25.643968 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:01:25.644057 PROGRESS: =========================================================================
2:01:25.648830 INFO: Starting optimization step 2.
2:01:25.648937 PROGRESS: === Extracting elution groups 600 to 1400 ===
2:01:25.648998 PROGRESS: Extracting batch of 1538 precursors
2:01:25.649841 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:01:25.649889 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:25.649919 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:01:25.649940 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:01:25.650099 INFO: Starting candidate selection
2:01:25.810148 INFO: Starting candidate scoring
2:01:25.849510 INFO: Finished candidate processing
2:01:25.849591 INFO: Collecting candidate features
2:01:25.859964 INFO: Collecting fragment features
2:01:25.863533 INFO: Finished candidate scoring
2:01:25.866410 PROGRESS: === Extracted 2701 precursors and 29370 fragments ===
2:01:25.867343 INFO: performing precursor FDR with 47 features
2:01:25.867386 INFO: Decoy channel: -1
2:01:25.867409 INFO: Competetive: True
2:01:25.870574 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:25.910063 INFO: Test AUC: 0.331
2:01:25.910163 INFO: Train AUC: 0.320
2:01:25.910193 INFO: AUC difference: 3.20%
2:01:26.085352 INFO: Resetting torch num_threads to 100
2:01:26.086110 INFO: === FDR correction performed with classifier version -1 ===
2:01:26.086990 PROGRESS: ============================= Precursor FDR =============================
2:01:26.087086 PROGRESS: Total precursors accumulated: 1,400
2:01:26.087150 PROGRESS: Target precursors: 473 (33.79%)
2:01:26.087201 PROGRESS: Decoy precursors: 927 (66.21%)
2:01:26.087255 PROGRESS: 
2:01:26.087300 PROGRESS: Precursor Summary:
2:01:26.088167 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:01:26.088271 PROGRESS: 
2:01:26.088336 PROGRESS: Protein Summary:
2:01:26.089295 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:01:26.089384 PROGRESS: =========================================================================
2:01:26.096001 INFO: Starting optimization step 3.
2:01:26.096136 PROGRESS: === Extracting elution groups 1400 to 3000 ===
2:01:26.096211 PROGRESS: Extracting batch of 3065 precursors
2:01:26.097436 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:01:26.097484 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:26.097514 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:01:26.097536 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:01:26.097716 INFO: Starting candidate selection
2:01:26.365589 INFO: Starting candidate scoring
2:01:26.408117 INFO: Finished candidate processing
2:01:26.408207 INFO: Collecting candidate features
2:01:26.420824 INFO: Collecting fragment features
2:01:26.424550 INFO: Finished candidate scoring
2:01:26.428986 PROGRESS: === Extracted 5766 precursors and 62584 fragments ===
2:01:26.430203 INFO: performing precursor FDR with 47 features
2:01:26.430247 INFO: Decoy channel: -1
2:01:26.430271 INFO: Competetive: True
2:01:26.433980 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:26.466054 INFO: Test AUC: 0.347
2:01:26.466146 INFO: Train AUC: 0.326
2:01:26.466174 INFO: AUC difference: 6.39%
2:01:26.466197 WARNING: AUC difference > 5%. This may indicate overfitting.
2:01:26.639789 INFO: Resetting torch num_threads to 100
2:01:26.640592 INFO: === FDR correction performed with classifier version -1 ===
2:01:26.641298 PROGRESS: ============================= Precursor FDR =============================
2:01:26.641392 PROGRESS: Total precursors accumulated: 1
2:01:26.641454 PROGRESS: Target precursors: 1 (100.00%)
2:01:26.641505 PROGRESS: Decoy precursors: 0 (0.00%)
2:01:26.641551 PROGRESS: 
2:01:26.641598 PROGRESS: Precursor Summary:
2:01:26.642529 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:01:26.642618 PROGRESS: 
2:01:26.642674 PROGRESS: Protein Summary:
2:01:26.643693 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:01:26.643787 PROGRESS: =========================================================================
2:01:26.653407 INFO: Starting optimization step 4.
2:01:26.653539 PROGRESS: === Extracting elution groups 3000 to 6200 ===
2:01:26.653605 PROGRESS: Extracting batch of 6167 precursors
2:01:26.654997 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:01:26.655045 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:26.655075 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:01:26.655096 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:01:26.655260 INFO: Starting candidate selection
2:01:27.082973 INFO: Starting candidate scoring
2:01:27.133049 INFO: Finished candidate processing
2:01:27.133150 INFO: Collecting candidate features
2:01:27.150676 INFO: Collecting fragment features
2:01:27.156368 INFO: Finished candidate scoring
2:01:27.163396 PROGRESS: === Extracted 11933 precursors and 129351 fragments ===
2:01:27.165263 INFO: performing precursor FDR with 47 features
2:01:27.165323 INFO: Decoy channel: -1
2:01:27.165347 INFO: Competetive: True
2:01:27.170656 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:27.217748 INFO: Test AUC: 0.329
2:01:27.217855 INFO: Train AUC: 0.322
2:01:27.217885 INFO: AUC difference: 2.07%
2:01:27.391806 INFO: Resetting torch num_threads to 100
2:01:27.392793 INFO: === FDR correction performed with classifier version -1 ===
2:01:27.393485 PROGRESS: ============================= Precursor FDR =============================
2:01:27.393579 PROGRESS: Total precursors accumulated: 1
2:01:27.393642 PROGRESS: Target precursors: 1 (100.00%)
2:01:27.393694 PROGRESS: Decoy precursors: 0 (0.00%)
2:01:27.393750 PROGRESS: 
2:01:27.393796 PROGRESS: Precursor Summary:
2:01:27.394732 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:01:27.394822 PROGRESS: 
2:01:27.394877 PROGRESS: Protein Summary:
2:01:27.395896 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:01:27.395988 PROGRESS: =========================================================================
2:01:27.411497 INFO: Starting optimization step 5.
2:01:27.411736 PROGRESS: === Extracting elution groups 6200 to 12600 ===
2:01:27.411804 PROGRESS: Extracting batch of 12312 precursors
2:01:27.414242 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:01:27.414302 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:27.414333 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:01:27.414355 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:01:27.414531 INFO: Starting candidate selection
2:01:28.207851 INFO: Starting candidate scoring
2:01:28.294758 INFO: Finished candidate processing
2:01:28.294873 INFO: Collecting candidate features
2:01:28.322236 INFO: Collecting fragment features
2:01:28.331915 INFO: Finished candidate scoring
2:01:28.344464 PROGRESS: === Extracted 24245 precursors and 263266 fragments ===
2:01:28.347725 INFO: performing precursor FDR with 47 features
2:01:28.347798 INFO: Decoy channel: -1
2:01:28.347825 INFO: Competetive: True
2:01:28.356646 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:28.658939 INFO: Test AUC: 0.795
2:01:28.659081 INFO: Train AUC: 0.794
2:01:28.659111 INFO: AUC difference: 0.10%
2:01:28.847328 INFO: Resetting torch num_threads to 100
2:01:28.848755 INFO: === FDR correction performed with classifier version -1 ===
2:01:28.849795 PROGRESS: ============================= Precursor FDR =============================
2:01:28.849887 PROGRESS: Total precursors accumulated: 4,256
2:01:28.849948 PROGRESS: Target precursors: 3,976 (93.42%)
2:01:28.850001 PROGRESS: Decoy precursors: 280 (6.58%)
2:01:28.850048 PROGRESS: 
2:01:28.850096 PROGRESS: Precursor Summary:
2:01:28.851014 PROGRESS: Channel   0:	 0.05 FDR:    12; 0.01 FDR:    12; 0.001 FDR:    12
2:01:28.851103 PROGRESS: 
2:01:28.851160 PROGRESS: Protein Summary:
2:01:28.852157 PROGRESS: Channel   0:	 0.05 FDR:    11; 0.01 FDR:    11; 0.001 FDR:    11
2:01:28.852255 PROGRESS: =========================================================================
2:01:28.873519 INFO: Starting optimization step 6.
2:01:28.873813 PROGRESS: === Extracting elution groups 12600 to 25400 ===
2:01:28.873884 PROGRESS: Extracting batch of 24645 precursors
2:01:28.878815 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:01:28.878890 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:28.878923 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:01:28.878945 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:01:28.879143 INFO: Starting candidate selection
2:01:30.315794 INFO: Starting candidate scoring
2:01:30.490325 INFO: Finished candidate processing
2:01:30.490441 INFO: Collecting candidate features
2:01:30.543679 INFO: Collecting fragment features
2:01:30.558340 INFO: Finished candidate scoring
2:01:30.579948 PROGRESS: === Extracted 48890 precursors and 531079 fragments ===
2:01:30.586339 INFO: performing precursor FDR with 47 features
2:01:30.586430 INFO: Decoy channel: -1
2:01:30.586459 INFO: Competetive: True
2:01:30.603201 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:31.247733 INFO: Test AUC: 0.824
2:01:31.247875 INFO: Train AUC: 0.824
2:01:31.247905 INFO: AUC difference: 0.01%
2:01:31.444060 INFO: Resetting torch num_threads to 100
2:01:31.446236 INFO: === FDR correction performed with classifier version -1 ===
2:01:31.448425 PROGRESS: ============================= Precursor FDR =============================
2:01:31.448532 PROGRESS: Total precursors accumulated: 14,558
2:01:31.448593 PROGRESS: Target precursors: 13,824 (94.96%)
2:01:31.448645 PROGRESS: Decoy precursors: 734 (5.04%)
2:01:31.448690 PROGRESS: 
2:01:31.448734 PROGRESS: Precursor Summary:
2:01:31.452771 PROGRESS: Channel   0:	 0.05 FDR: 13,665; 0.01 FDR: 10,256; 0.001 FDR: 6,677
2:01:31.452886 PROGRESS: 
2:01:31.452943 PROGRESS: Protein Summary:
2:01:31.458868 PROGRESS: Channel   0:	 0.05 FDR: 5,526; 0.01 FDR: 4,287; 0.001 FDR: 3,176
2:01:31.458992 PROGRESS: =========================================================================
2:01:31.511877 INFO: fragments_df: keeping 5000 of 531079 [sum(precursor_idx_mask)=116144 sum(mass_error_mask)=531079 stop_rank=5000
2:01:31.520368 INFO: calibration group: precursor, fitting rt estimator 
2:01:33.395694 INFO: calibration group: fragment, fitting mz estimator 
2:01:34.016986 INFO: Using score_cutoff 58.405721357345584 (fac=0.99, q=1)
2:01:34.017570 INFO: calibration group: precursor, predicting mz
2:01:34.017660 WARNING: mz prediction was skipped as it has not been fitted yet
2:01:34.017690 INFO: calibration group: precursor, predicting rt
2:01:34.019241 INFO: calibration group: fragment, predicting mz
2:01:34.021384 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:01:34.021504 INFO: Starting optimization step 7.
2:01:34.021584 PROGRESS: === Extracting elution groups 0 to 600 ===
2:01:34.021660 PROGRESS: Extracting batch of 1163 precursors
2:01:34.022674 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:01:34.022729 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:34.022764 INFO: FWHM in RT is 3.04 seconds, sigma is 0.39
2:01:34.022787 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:01:34.022957 INFO: Starting candidate selection
2:01:34.176780 INFO: Starting candidate scoring
2:01:34.217149 INFO: Finished candidate processing
2:01:34.217241 INFO: Collecting candidate features
2:01:34.228535 INFO: Collecting fragment features
2:01:34.232712 INFO: Finished candidate scoring
2:01:34.234305 PROGRESS: === Extracted 2326 precursors and 25011 fragments ===
2:01:34.234584 INFO: performing precursor FDR with 47 features
2:01:34.234621 INFO: Decoy channel: -1
2:01:34.234643 INFO: Competetive: True
2:01:34.237243 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:34.259636 INFO: Test AUC: 0.678
2:01:34.259714 INFO: Train AUC: 0.708
2:01:34.259745 INFO: AUC difference: 4.13%
2:01:34.436538 INFO: Resetting torch num_threads to 100
2:01:34.437172 INFO: === FDR correction performed with classifier version 6 ===
2:01:34.437805 PROGRESS: ============================= Precursor FDR =============================
2:01:34.437897 PROGRESS: Total precursors accumulated: 344
2:01:34.437957 PROGRESS: Target precursors: 324 (94.19%)
2:01:34.438012 PROGRESS: Decoy precursors: 20 (5.81%)
2:01:34.438059 PROGRESS: 
2:01:34.438102 PROGRESS: Precursor Summary:
2:01:34.439079 PROGRESS: Channel   0:	 0.05 FDR:   316; 0.01 FDR:   208; 0.001 FDR:   149
2:01:34.439168 PROGRESS: 
2:01:34.439224 PROGRESS: Protein Summary:
2:01:34.440352 PROGRESS: Channel   0:	 0.05 FDR:   304; 0.01 FDR:   199; 0.001 FDR:   149
2:01:34.440446 PROGRESS: =========================================================================
2:01:34.443999 INFO: fragments_df: keeping 2180 of 25011 [sum(precursor_idx_mask)=4665 sum(mass_error_mask)=25011 stop_rank=2180
2:01:34.449621 INFO: calibration group: precursor, fitting rt estimator 
2:01:34.546301 INFO: calibration group: fragment, fitting mz estimator 
2:01:34.786964 INFO: Using score_cutoff 61.4286362651825 (fac=0.99, q=1)
2:01:34.787390 INFO: calibration group: precursor, predicting mz
2:01:34.787476 WARNING: mz prediction was skipped as it has not been fitted yet
2:01:34.787505 INFO: calibration group: precursor, predicting rt
2:01:34.789097 INFO: calibration group: fragment, predicting mz
2:01:34.791215 INFO: === checking if optimization conditions were reached ===
2:01:34.792495 PROGRESS: ❌ ms2_error      : 15.0038 > 6.7411 or insufficient steps taken.
2:01:34.792547 INFO: ==============================================
2:01:34.792633 INFO: Starting optimization step 8.
2:01:34.792697 PROGRESS: === Extracting elution groups 0 to 600 ===
2:01:34.792768 PROGRESS: Extracting batch of 1163 precursors
2:01:34.793697 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:01:34.793743 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:34.793772 INFO: FWHM in RT is 2.88 seconds, sigma is 0.37
2:01:34.793794 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:01:34.793954 INFO: Starting candidate selection
2:01:34.944976 INFO: Starting candidate scoring
2:01:34.985561 INFO: Finished candidate processing
2:01:34.985663 INFO: Collecting candidate features
2:01:34.997262 INFO: Collecting fragment features
2:01:35.001250 INFO: Finished candidate scoring
2:01:35.002905 PROGRESS: === Extracted 2326 precursors and 23477 fragments ===
2:01:35.003206 INFO: performing precursor FDR with 47 features
2:01:35.003244 INFO: Decoy channel: -1
2:01:35.003268 INFO: Competetive: True
2:01:35.005842 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:35.028280 INFO: Test AUC: 0.737
2:01:35.028387 INFO: Train AUC: 0.716
2:01:35.028417 INFO: AUC difference: 2.87%
2:01:35.200578 INFO: Resetting torch num_threads to 100
2:01:35.201186 INFO: === FDR correction performed with classifier version 7 ===
2:01:35.201823 PROGRESS: ============================= Precursor FDR =============================
2:01:35.201917 PROGRESS: Total precursors accumulated: 422
2:01:35.201982 PROGRESS: Target precursors: 408 (96.68%)
2:01:35.202035 PROGRESS: Decoy precursors: 14 (3.32%)
2:01:35.202083 PROGRESS: 
2:01:35.202130 PROGRESS: Precursor Summary:
2:01:35.203110 PROGRESS: Channel   0:	 0.05 FDR:   408; 0.01 FDR:   320; 0.001 FDR:   249
2:01:35.203201 PROGRESS: 
2:01:35.203258 PROGRESS: Protein Summary:
2:01:35.204450 PROGRESS: Channel   0:	 0.05 FDR:   391; 0.01 FDR:   310; 0.001 FDR:   243
2:01:35.204545 PROGRESS: =========================================================================
2:01:35.207686 INFO: fragments_df: keeping 2994 of 23477 [sum(precursor_idx_mask)=6836 sum(mass_error_mask)=23477 stop_rank=2994
2:01:35.212648 INFO: calibration group: precursor, fitting rt estimator 
2:01:35.311929 INFO: calibration group: fragment, fitting mz estimator 
2:01:35.643222 INFO: Using score_cutoff 50.611226206970215 (fac=0.99, q=1)
2:01:35.643651 INFO: calibration group: precursor, predicting mz
2:01:35.643738 WARNING: mz prediction was skipped as it has not been fitted yet
2:01:35.643769 INFO: calibration group: precursor, predicting rt
2:01:35.645318 INFO: calibration group: fragment, predicting mz
2:01:35.647449 INFO: === checking if optimization conditions were reached ===
2:01:35.648764 PROGRESS: ❌ ms2_error      : 8.4365 > 6.7411 or insufficient steps taken.
2:01:35.648817 INFO: ==============================================
2:01:35.648904 INFO: Starting optimization step 9.
2:01:35.648969 PROGRESS: === Extracting elution groups 0 to 600 ===
2:01:35.649025 PROGRESS: Extracting batch of 1163 precursors
2:01:35.649941 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:01:35.649988 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:35.650019 INFO: FWHM in RT is 2.67 seconds, sigma is 0.34
2:01:35.650042 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:01:35.650202 INFO: Starting candidate selection
2:01:35.799763 INFO: Starting candidate scoring
2:01:35.841615 INFO: Finished candidate processing
2:01:35.841697 INFO: Collecting candidate features
2:01:35.852969 INFO: Collecting fragment features
2:01:35.857187 INFO: Finished candidate scoring
2:01:35.858820 PROGRESS: === Extracted 2326 precursors and 21238 fragments ===
2:01:35.859102 INFO: performing precursor FDR with 47 features
2:01:35.859138 INFO: Decoy channel: -1
2:01:35.859160 INFO: Competetive: True
2:01:35.861705 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:35.883807 INFO: Test AUC: 0.700
2:01:35.883880 INFO: Train AUC: 0.720
2:01:35.883909 INFO: AUC difference: 2.78%
2:01:36.056262 INFO: Resetting torch num_threads to 100
2:01:36.056877 INFO: === FDR correction performed with classifier version 8 ===
2:01:36.057521 PROGRESS: ============================= Precursor FDR =============================
2:01:36.057621 PROGRESS: Total precursors accumulated: 428
2:01:36.057687 PROGRESS: Target precursors: 412 (96.26%)
2:01:36.057746 PROGRESS: Decoy precursors: 16 (3.74%)
2:01:36.057795 PROGRESS: 
2:01:36.057842 PROGRESS: Precursor Summary:
2:01:36.058837 PROGRESS: Channel   0:	 0.05 FDR:   412; 0.01 FDR:   314; 0.001 FDR:   186
2:01:36.058927 PROGRESS: 
2:01:36.058983 PROGRESS: Protein Summary:
2:01:36.060126 PROGRESS: Channel   0:	 0.05 FDR:   396; 0.01 FDR:   305; 0.001 FDR:   182
2:01:36.060216 PROGRESS: =========================================================================
2:01:36.063166 INFO: fragments_df: keeping 2979 of 21238 [sum(precursor_idx_mask)=6317 sum(mass_error_mask)=21238 stop_rank=2979
2:01:36.068429 INFO: calibration group: precursor, fitting rt estimator 
2:01:36.171973 INFO: calibration group: fragment, fitting mz estimator 
2:01:36.507855 INFO: Using score_cutoff 48.9956362323761 (fac=0.99, q=1)
2:01:36.508284 INFO: calibration group: precursor, predicting mz
2:01:36.508372 WARNING: mz prediction was skipped as it has not been fitted yet
2:01:36.508403 INFO: calibration group: precursor, predicting rt
2:01:36.509956 INFO: calibration group: fragment, predicting mz
2:01:36.512094 INFO: === checking if optimization conditions were reached ===
2:01:36.513434 PROGRESS: ✅ ms2_error      : 6.7411 <= 6.7411
2:01:36.513489 INFO: ==============================================
2:01:36.513577 PROGRESS: Optimization finished for ms2_error.
2:01:36.518255 INFO: calibration group: precursor, predicting mz
2:01:36.518363 WARNING: mz prediction was skipped as it has not been fitted yet
2:01:36.518396 INFO: calibration group: precursor, predicting rt
2:01:36.519656 INFO: calibration group: fragment, predicting mz
2:01:36.521765 INFO: Starting optimization step 0.
2:01:36.521871 PROGRESS: === Extracting elution groups 0 to 600 ===
2:01:36.521935 PROGRESS: Extracting batch of 1163 precursors
2:01:36.522747 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:01:36.522797 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:36.522828 INFO: FWHM in RT is 2.41 seconds, sigma is 0.31
2:01:36.522851 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:01:36.523014 INFO: Starting candidate selection
2:01:36.672908 INFO: Starting candidate scoring
2:01:36.715683 INFO: Finished candidate processing
2:01:36.715768 INFO: Collecting candidate features
2:01:36.726825 INFO: Collecting fragment features
2:01:36.730815 INFO: Finished candidate scoring
2:01:36.732475 PROGRESS: === Extracted 2326 precursors and 20113 fragments ===
2:01:36.732759 INFO: performing precursor FDR with 47 features
2:01:36.732795 INFO: Decoy channel: -1
2:01:36.732818 INFO: Competetive: True
2:01:36.735312 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:36.758153 INFO: Test AUC: 0.725
2:01:36.758225 INFO: Train AUC: 0.718
2:01:36.758255 INFO: AUC difference: 0.91%
2:01:36.930932 INFO: Resetting torch num_threads to 100
2:01:36.931542 INFO: === FDR correction performed with classifier version 9 ===
2:01:36.932188 PROGRESS: ============================= Precursor FDR =============================
2:01:36.932294 PROGRESS: Total precursors accumulated: 442
2:01:36.932359 PROGRESS: Target precursors: 425 (96.15%)
2:01:36.932412 PROGRESS: Decoy precursors: 17 (3.85%)
2:01:36.932459 PROGRESS: 
2:01:36.932503 PROGRESS: Precursor Summary:
2:01:36.933486 PROGRESS: Channel   0:	 0.05 FDR:   425; 0.01 FDR:   320; 0.001 FDR:   182
2:01:36.933576 PROGRESS: 
2:01:36.933634 PROGRESS: Protein Summary:
2:01:36.934786 PROGRESS: Channel   0:	 0.05 FDR:   407; 0.01 FDR:   310; 0.001 FDR:   178
2:01:36.934881 PROGRESS: =========================================================================
2:01:36.937723 INFO: fragments_df: keeping 3007 of 20113 [sum(precursor_idx_mask)=6186 sum(mass_error_mask)=20113 stop_rank=3007
2:01:36.942667 INFO: calibration group: precursor, fitting rt estimator 
2:01:37.037210 INFO: calibration group: fragment, fitting mz estimator 
2:01:37.371432 INFO: Using score_cutoff 40.94627050209046 (fac=0.99, q=1)
2:01:37.371852 INFO: calibration group: precursor, predicting mz
2:01:37.371938 WARNING: mz prediction was skipped as it has not been fitted yet
2:01:37.371969 INFO: calibration group: precursor, predicting rt
2:01:37.373519 INFO: calibration group: fragment, predicting mz
2:01:37.375674 INFO: === checking if optimization conditions were reached ===
2:01:37.375779 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2:01:37.377215 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 226.2794.
2:01:37.377270 INFO: ==============================================
2:01:37.377355 INFO: Starting optimization step 1.
2:01:37.377420 PROGRESS: === Extracting elution groups 0 to 600 ===
2:01:37.377477 PROGRESS: Extracting batch of 1163 precursors
2:01:37.378366 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:01:37.378414 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:37.378444 INFO: FWHM in RT is 2.31 seconds, sigma is 0.30
2:01:37.378466 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:01:37.378621 INFO: Starting candidate selection
2:01:37.513922 INFO: Starting candidate scoring
2:01:37.557186 INFO: Finished candidate processing
2:01:37.557269 INFO: Collecting candidate features
2:01:37.568479 INFO: Collecting fragment features
2:01:37.572486 INFO: Finished candidate scoring
2:01:37.574053 PROGRESS: === Extracted 2325 precursors and 19851 fragments ===
2:01:37.574345 INFO: performing precursor FDR with 47 features
2:01:37.574380 INFO: Decoy channel: -1
2:01:37.574402 INFO: Competetive: True
2:01:37.576953 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:37.599141 INFO: Test AUC: 0.758
2:01:37.599214 INFO: Train AUC: 0.723
2:01:37.599243 INFO: AUC difference: 4.84%
2:01:37.771147 INFO: Resetting torch num_threads to 100
2:01:37.771763 INFO: === FDR correction performed with classifier version 9 ===
2:01:37.772430 PROGRESS: ============================= Precursor FDR =============================
2:01:37.772526 PROGRESS: Total precursors accumulated: 439
2:01:37.772588 PROGRESS: Target precursors: 420 (95.67%)
2:01:37.772641 PROGRESS: Decoy precursors: 19 (4.33%)
2:01:37.772690 PROGRESS: 
2:01:37.772736 PROGRESS: Precursor Summary:
2:01:37.773745 PROGRESS: Channel   0:	 0.05 FDR:   420; 0.01 FDR:   318; 0.001 FDR:   215
2:01:37.773839 PROGRESS: 
2:01:37.773896 PROGRESS: Protein Summary:
2:01:37.775068 PROGRESS: Channel   0:	 0.05 FDR:   402; 0.01 FDR:   308; 0.001 FDR:   209
2:01:37.775164 PROGRESS: =========================================================================
2:01:37.778013 INFO: fragments_df: keeping 2965 of 19851 [sum(precursor_idx_mask)=6154 sum(mass_error_mask)=19851 stop_rank=2965
2:01:37.782995 INFO: calibration group: precursor, fitting rt estimator 
2:01:37.887346 INFO: calibration group: fragment, fitting mz estimator 
2:01:38.218317 INFO: Using score_cutoff 46.43694361038208 (fac=0.99, q=1)
2:01:38.218738 INFO: calibration group: precursor, predicting mz
2:01:38.218827 WARNING: mz prediction was skipped as it has not been fitted yet
2:01:38.218858 INFO: calibration group: precursor, predicting rt
2:01:38.220424 INFO: calibration group: fragment, predicting mz
2:01:38.222587 INFO: === checking if optimization conditions were reached ===
2:01:38.222693 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2:01:38.224220 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 18.2463.
2:01:38.224281 INFO: ==============================================
2:01:38.224369 INFO: Starting optimization step 2.
2:01:38.224433 PROGRESS: === Extracting elution groups 0 to 600 ===
2:01:38.224491 PROGRESS: Extracting batch of 1163 precursors
2:01:38.225400 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:01:38.225449 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:38.225480 INFO: FWHM in RT is 2.30 seconds, sigma is 0.30
2:01:38.225511 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:01:38.225687 INFO: Starting candidate selection
2:01:38.351352 INFO: Starting candidate scoring
2:01:38.393138 INFO: Finished candidate processing
2:01:38.393222 INFO: Collecting candidate features
2:01:38.401660 WARNING: intensity_correlation has 2 NaNs ( 0.09 % out of 2259)
2:01:38.405435 INFO: Collecting fragment features
2:01:38.409437 INFO: Finished candidate scoring
2:01:38.411044 PROGRESS: === Extracted 2259 precursors and 17445 fragments ===
2:01:38.411325 INFO: performing precursor FDR with 47 features
2:01:38.411361 INFO: Decoy channel: -1
2:01:38.411382 INFO: Competetive: True
2:01:38.413882 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:38.415049 WARNING: dropped 2 decoy PSMs due to missing features
2:01:38.439337 INFO: Test AUC: 0.703
2:01:38.439411 INFO: Train AUC: 0.735
2:01:38.439440 INFO: AUC difference: 4.37%
2:01:38.611772 INFO: Resetting torch num_threads to 100
2:01:38.612385 INFO: === FDR correction performed with classifier version 9 ===
2:01:38.613047 PROGRESS: ============================= Precursor FDR =============================
2:01:38.613143 PROGRESS: Total precursors accumulated: 453
2:01:38.613204 PROGRESS: Target precursors: 433 (95.58%)
2:01:38.613256 PROGRESS: Decoy precursors: 20 (4.42%)
2:01:38.613304 PROGRESS: 
2:01:38.613354 PROGRESS: Precursor Summary:
2:01:38.614338 PROGRESS: Channel   0:	 0.05 FDR:   433; 0.01 FDR:   225; 0.001 FDR:   150
2:01:38.614428 PROGRESS: 
2:01:38.614483 PROGRESS: Protein Summary:
2:01:38.615614 PROGRESS: Channel   0:	 0.05 FDR:   415; 0.01 FDR:   220; 0.001 FDR:   147
2:01:38.615708 PROGRESS: =========================================================================
2:01:38.618207 INFO: fragments_df: keeping 2175 of 17445 [sum(precursor_idx_mask)=4213 sum(mass_error_mask)=17445 stop_rank=2175
2:01:38.623223 INFO: calibration group: precursor, fitting rt estimator 
2:01:38.715434 INFO: calibration group: fragment, fitting mz estimator 
2:01:38.961113 INFO: Using score_cutoff 49.29337541656494 (fac=0.99, q=1)
2:01:38.961518 INFO: calibration group: precursor, predicting mz
2:01:38.961606 WARNING: mz prediction was skipped as it has not been fitted yet
2:01:38.961637 INFO: calibration group: precursor, predicting rt
2:01:38.963229 INFO: calibration group: fragment, predicting mz
2:01:38.965395 INFO: === checking if optimization conditions were reached ===
2:01:38.965502 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2:01:38.966496 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 226.2794 found after 3 searches.
2:01:38.966545 INFO: ==============================================
2:01:38.966630 PROGRESS: Optimization finished for rt_error.
2:01:38.971574 INFO: calibration group: precursor, predicting mz
2:01:38.971691 WARNING: mz prediction was skipped as it has not been fitted yet
2:01:38.971720 INFO: calibration group: precursor, predicting rt
2:01:38.973030 INFO: calibration group: fragment, predicting mz
2:01:39.001013 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:01:39.001171 PROGRESS: ==============================================
2:01:39.001240 PROGRESS: ms2_error      : 6.7411
2:01:39.001297 PROGRESS: rt_error       : 226.2794
2:01:39.001345 PROGRESS: ==============================================
2:01:39.001862 INFO: calibration group: precursor, predicting mz
2:01:39.001945 WARNING: mz prediction was skipped as it has not been fitted yet
2:01:39.001975 INFO: calibration group: precursor, predicting rt
2:01:39.131887 INFO: calibration group: fragment, predicting mz
2:01:39.484856 PROGRESS: Extracting batch of 238438 precursors
2:01:39.542136 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
2:01:39.542319 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:39.542381 INFO: FWHM in RT is 2.30 seconds, sigma is 0.30
2:01:39.542407 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:01:39.542682 INFO: Starting candidate selection
2:01:49.154543 INFO: Applying score cutoff of 46.43694361038208
2:01:49.160748 INFO: Removed 209409 precursors with score below cutoff
2:01:49.240328 INFO: Starting candidate scoring
2:01:51.073186 INFO: Finished candidate processing
2:01:51.073356 INFO: Collecting candidate features
2:01:51.476106 INFO: Collecting fragment features
2:01:51.634845 INFO: Finished candidate scoring
2:01:51.762182 INFO: === FDR correction performed with classifier version 11 ===
2:01:51.762876 INFO: performing precursor FDR with 47 features
2:01:51.762920 INFO: Decoy channel: -1
2:01:51.762944 INFO: Competetive: True
2:01:51.840825 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:51.870125 WARNING: FDR calculation for 168823 target and 98644 decoy PSMs
2:01:51.870287 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:01:57.373718 INFO: Test AUC: 0.853
2:01:57.373868 INFO: Train AUC: 0.853
2:01:57.373900 INFO: AUC difference: 0.03%
2:01:57.631355 INFO: Resetting torch num_threads to 100
2:01:57.651374 INFO: Removing fragments below FDR threshold
2:01:57.714134 PROGRESS: ============================= Precursor FDR =============================
2:01:57.714440 PROGRESS: Total precursors accumulated: 94,936
2:01:57.714509 PROGRESS: Target precursors: 93,997 (99.01%)
2:01:57.714563 PROGRESS: Decoy precursors: 939 (0.99%)
2:01:57.714610 PROGRESS: 
2:01:57.714654 PROGRESS: Precursor Summary:
2:01:57.755664 PROGRESS: Channel   0:	 0.05 FDR: 93,997; 0.01 FDR: 93,997; 0.001 FDR: 85,358
2:01:57.755995 PROGRESS: 
2:01:57.756079 PROGRESS: Protein Summary:
2:01:57.823512 PROGRESS: Channel   0:	 0.05 FDR: 10,197; 0.01 FDR: 10,197; 0.001 FDR: 9,239
2:01:57.823809 PROGRESS: =========================================================================
2:01:58.507607 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:01:59.063113 PROGRESS: Processing search outputs
2:01:59.063265 PROGRESS: Performing protein grouping and FDR
2:01:59.063299 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:01:59.130585 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:01:59.205507 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:01:59.273874 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:01:59.342052 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:01:59.412115 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:01:59.480606 INFO: Building combined output
2:01:59.664155 INFO: Performing protein inference
2:02:00.262639 INFO: Inference strategy: library. Using library grouping for protein inference
2:02:00.266731 INFO: Performing protein FDR
2:02:10.846597 INFO: Normalizing q-values using 11,589 targets and 3,332 decoys
2:02:10.854728 INFO: Test AUC: 0.962
2:02:10.854805 INFO: Train AUC: 0.959
2:02:10.854841 INFO: AUC difference: 0.32%
2:02:11.915568 PROGRESS: ================ Protein FDR =================
2:02:11.915738 PROGRESS: Unique protein groups in output
2:02:11.915769 PROGRESS:   1% protein FDR: 9,767
2:02:11.915790 PROGRESS: 
2:02:11.915808 PROGRESS: Unique precursor in output
2:02:11.915827 PROGRESS:   1% protein FDR: 111,571
2:02:11.915849 PROGRESS: ================================================
2:02:12.050640 PROGRESS: Building search statistics
2:02:12.271951 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
2:02:12.272213 INFO: Initializing OptimizationManager
2:02:12.272538 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
2:02:12.272630 INFO: Initializing CalibrationManager
2:02:12.272880 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
2:02:12.272968 INFO: Initializing RawFileManager
2:02:12.320232 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
2:02:12.320655 INFO: Initializing OptimizationManager
2:02:12.320907 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
2:02:12.320985 INFO: Initializing CalibrationManager
2:02:12.321208 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
2:02:12.321287 INFO: Initializing RawFileManager
2:02:12.368533 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
2:02:12.368717 INFO: Initializing OptimizationManager
2:02:12.368938 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
2:02:12.369028 INFO: Initializing CalibrationManager
2:02:12.369251 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
2:02:12.369328 INFO: Initializing RawFileManager
2:02:12.416531 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
2:02:12.416756 INFO: Initializing OptimizationManager
2:02:12.416991 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
2:02:12.417071 INFO: Initializing CalibrationManager
2:02:12.417301 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
2:02:12.417389 INFO: Initializing RawFileManager
2:02:12.463142 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
2:02:12.463362 INFO: Initializing OptimizationManager
2:02:12.463599 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
2:02:12.463681 INFO: Initializing CalibrationManager
2:02:12.463908 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
2:02:12.463982 INFO: Initializing RawFileManager
2:02:12.510173 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
2:02:12.510403 INFO: Initializing OptimizationManager
2:02:12.510631 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
2:02:12.510710 INFO: Initializing CalibrationManager
2:02:12.510922 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
2:02:12.510999 INFO: Initializing RawFileManager
2:02:12.514565 INFO: Writing stat output to disk
2:02:12.514638 INFO: Saving run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/stat.tsv to disk
2:02:12.532529 PROGRESS: Building internal statistics
2:02:12.532911 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
2:02:12.532975 INFO: Initializing TimingManager
2:02:12.533455 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
2:02:12.533498 INFO: Initializing TimingManager
2:02:12.533685 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
2:02:12.533725 INFO: Initializing TimingManager
2:02:12.533893 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
2:02:12.533931 INFO: Initializing TimingManager
2:02:12.534100 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
2:02:12.534136 INFO: Initializing TimingManager
2:02:12.534301 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
2:02:12.534336 INFO: Initializing TimingManager
2:02:12.534818 INFO: Writing internal output to disk
2:02:12.534865 INFO: Saving run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/internal.tsv to disk
2:02:12.535491 PROGRESS: Performing label free quantification
2:02:12.704450 INFO: Accumulating fragment data
2:02:12.704630 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:02:12.820888 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:02:14.331313 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:02:15.862644 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:02:17.310664 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:02:18.789690 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:02:20.523658 PROGRESS: Performing label free quantification on the precursor level
2:02:20.523816 INFO: Filtering fragments by quality
2:02:20.889627 INFO: Performing label-free quantification using directLFQ
2:02:21.955058 INFO: 111571 lfq-groups total
2:03:36.688662 INFO: using 100 processes
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2:04:54.033269 INFO: Writing precursor output to disk
2:04:54.033626 INFO: Saving run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/precursor.matrix.tsv to disk
2:04:54.615310 PROGRESS: Performing label free quantification on the pg level
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2:05:55.902038 INFO: lfq-object 8200
2:05:55.954411 INFO: lfq-object 8300
2:05:55.990840 INFO: lfq-object 8400
2:05:56.034556 INFO: lfq-object 8500
2:05:56.058691 INFO: lfq-object 8600
2:05:56.105202 INFO: lfq-object 8700
2:05:56.157685 INFO: lfq-object 8800
2:05:56.195369 INFO: lfq-object 8900
2:05:56.226069 INFO: lfq-object 9000
2:05:56.286301 INFO: lfq-object 9100
2:05:56.315873 INFO: lfq-object 9200
2:05:56.385610 INFO: lfq-object 9300
2:05:56.425080 INFO: lfq-object 9400
2:05:56.459718 INFO: lfq-object 9500
2:05:56.499416 INFO: lfq-object 9600
2:05:56.546938 INFO: lfq-object 9700
2:06:00.132543 INFO: Writing pg output to disk
2:06:00.132760 INFO: Saving run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/pg.matrix.tsv to disk
2:06:00.476464 INFO: Writing psm output to disk
2:06:00.476625 INFO: Saving run_output_Astral/alphadia_1.10.4_Notransfer_calibrationSet_new_bounds/precursors.tsv to disk
2:06:29.181970 PROGRESS: Building spectral library
2:06:29.384205 INFO: Building MBR spectral library
2:06:29.384388 INFO: Running MbrLibraryBuilder
2:06:29.739364 INFO: MBR spectral library contains 111,571 precursors, 9,767 proteins
2:06:29.739554 INFO: Writing MBR spectral library to disk
2:06:30.578888 PROGRESS: =================== Search Finished ===================
2:06:30.642102 WARNING: WARNING: Temp mmap arrays were written to /tmp/temp_mmap_5i92rf15. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 614,125,113,344
