0:00:00.000057 INFO: Output directory: /home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet, cwd: /home/robbe/ProteoBench_diaPASEF.
0:00:00.000173 INFO: User provided config file: config_alphadia110_default_Astral.yaml.
0:00:00.000206 INFO: User provided config dict: {}.
0:00:00.014167 PROGRESS:           _      _         ___ ___   _   
0:00:00.014236 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.014265 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.014287 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.014311 PROGRESS:            |_|                           
0:00:00.014335 PROGRESS: 
0:00:00.014355 PROGRESS: version: 1.10.4-dev0
0:00:00.014382 INFO: hostname: thestral
0:00:00.014429 INFO: date: 2025-06-27 14:40:02
0:00:00.014451 INFO: ================ AlphaX Environment ===============
0:00:00.014470 INFO: alphatims       : 1.0.8
0:00:00.014490 INFO: alpharaw        : 0.4.5
0:00:00.014507 INFO: alphabase       : 1.5.0
0:00:00.014524 INFO: alphapeptdeep   : 1.3.0
0:00:00.014541 INFO: directlfq       : 0.2.19
0:00:00.014558 INFO: ===================================================
0:00:00.014575 INFO: ================= Pip Environment =================
0:00:00.102636 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
0:00:00.102743 INFO: ===================================================
0:00:00.102784 INFO: Running step 'library'
0:00:00.102896 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:00:00.114412 INFO: loading additional config provided via CLI
0:00:00.114478 INFO: loading additional config provided via CLI parameters
0:00:00.114733 INFO: Updating config with 'user defined'
0:00:00.114821 INFO: Updating config with 'user defined (cli)'
0:00:00.114845 INFO: Updating config with 'multistep search'
0:00:00.114881 INFO: ├──version: 1
0:00:00.114907 INFO: ├──workflow_name: None
0:00:00.114931 INFO: [32;20m├──output_directory: run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library [multistep search, default: None][0m
0:00:00.114951 INFO: ├──library_path: None
0:00:00.114971 INFO: ├──raw_paths:
0:00:00.114991 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
0:00:00.115011 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
0:00:00.115029 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
0:00:00.115051 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
0:00:00.115069 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
0:00:00.115088 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
0:00:00.115106 INFO: ├──fasta_paths:
0:00:00.115125 INFO: │   [32;20m- ./ProteoBenchFASTA_DDAQuantification.fasta [user defined (cli), default: None][0m
0:00:00.115145 INFO: ├──quant_directory: None
0:00:00.115163 INFO: ├──general
0:00:00.115185 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
0:00:00.115203 INFO: │   ├──transfer_step_enabled: False
0:00:00.115222 INFO: │   ├──mbr_step_enabled: True
0:00:00.115241 INFO: │   ├──reuse_calibration: False
0:00:00.115259 INFO: │   ├──reuse_quant: False
0:00:00.115277 INFO: │   ├──astral_ms1: False
0:00:00.115295 INFO: │   ├──log_level: INFO
0:00:00.115313 INFO: │   ├──mmap_detector_events: False
0:00:00.115333 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
0:00:00.115352 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.115370 INFO: │   ├──save_mbr_library: True
0:00:00.115387 INFO: │   └──save_figures: True
0:00:00.115405 INFO: ├──library_loading
0:00:00.115427 INFO: │   └──rt_heuristic: 180
0:00:00.115446 INFO: ├──library_prediction
0:00:00.115465 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.115483 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.115502 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.115520 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
0:00:00.115538 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.115556 INFO: │   ├──missed_cleavages: 1
0:00:00.115577 INFO: │   ├──precursor_len:
0:00:00.115595 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.115614 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.115631 INFO: │   ├──precursor_charge:
0:00:00.115649 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.115667 INFO: │   │   [32;20m- 4[0m
0:00:00.115685 INFO: │   ├──precursor_mz:
0:00:00.115703 INFO: │   │   [32;20m- 400[0m
0:00:00.115723 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
0:00:00.115741 INFO: │   ├──fragment_mz:
0:00:00.115759 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
0:00:00.115784 INFO: │   │   [32;20m- 2000[0m
0:00:00.115803 INFO: │   ├──nce: 25
0:00:00.115819 INFO: │   ├──fragment_types:
0:00:00.115838 INFO: │   │   [32;20m- b[0m
0:00:00.115855 INFO: │   │   [32;20m- y[0m
0:00:00.115871 INFO: │   ├──max_fragment_charge: 2
0:00:00.115889 INFO: │   [32;20m├──instrument: Astral [user defined, default: Lumos][0m
0:00:00.115908 INFO: │   ├──peptdeep_model_path: None
0:00:00.115925 INFO: │   └──peptdeep_model_type: generic
0:00:00.115943 INFO: ├──custom_modifications:
0:00:00.115961 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.115979 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.115999 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.116017 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.116035 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.116053 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.116072 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.116090 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.116108 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.116125 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.116143 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.116161 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.116179 INFO: │   ├──name: Label:13C(12)@K
0:00:00.116196 INFO: │   └──composition: C(12)
0:00:00.116212 INFO: ├──search
0:00:00.116230 INFO: │   [32;20m├──target_ms1_tolerance: 0 [user defined, default: 5][0m
0:00:00.116249 INFO: │   [32;20m├──target_ms2_tolerance: 0 [user defined, default: 10][0m
0:00:00.116268 INFO: │   ├──target_rt_tolerance: 0
0:00:00.116285 INFO: │   ├──target_mobility_tolerance: 0
0:00:00.116302 INFO: │   ├──quant_window: 3
0:00:00.116321 INFO: │   [32;20m├──target_num_candidates: 2 [user defined, default: 3][0m
0:00:00.116338 INFO: │   ├──channel_filter: 
0:00:00.116356 INFO: │   ├──exclude_shared_ions: True
0:00:00.116373 INFO: │   ├──compete_for_fragments: True
0:00:00.116391 INFO: │   ├──quant_all: True
0:00:00.116409 INFO: │   ├──top_k_fragments: 12
0:00:00.116427 INFO: │   ├──experimental_xic: True
0:00:00.116444 INFO: │   └──optimized_peak_group_score: False
0:00:00.116461 INFO: ├──calibration
0:00:00.116480 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 8000][0m
0:00:00.116498 INFO: │   ├──optimization_lock_target: 200
0:00:00.116516 INFO: │   ├──max_steps: 20
0:00:00.116534 INFO: │   ├──min_steps: 2
0:00:00.116551 INFO: │   ├──max_skips: 1
0:00:00.116569 INFO: │   ├──norm_rt_mode: linear
0:00:00.116587 INFO: │   ├──max_fragments: 5000
0:00:00.116609 INFO: │   └──min_correlation: 0.7
0:00:00.116627 INFO: ├──search_initial
0:00:00.116644 INFO: │   ├──initial_num_candidates: 1
0:00:00.116663 INFO: │   ├──initial_ms1_tolerance: 30
0:00:00.116681 INFO: │   ├──initial_ms2_tolerance: 30
0:00:00.116699 INFO: │   ├──initial_mobility_tolerance: 0.1
0:00:00.116718 INFO: │   └──initial_rt_tolerance: 0.5
0:00:00.116737 INFO: ├──selection_config
0:00:00.116756 INFO: │   ├──peak_len_rt: 10.0
0:00:00.116775 INFO: │   ├──sigma_scale_rt: 0.5
0:00:00.116794 INFO: │   ├──peak_len_mobility: 0.01
0:00:00.116811 INFO: │   ├──sigma_scale_mobility: 1.0
0:00:00.116830 INFO: │   ├──top_k_precursors: 3
0:00:00.116848 INFO: │   ├──kernel_size: 30
0:00:00.116866 INFO: │   ├──f_mobility: 1.0
0:00:00.116884 INFO: │   ├──f_rt: 0.99
0:00:00.116902 INFO: │   ├──center_fraction: 0.5
0:00:00.116921 INFO: │   ├──min_size_mobility: 8
0:00:00.116940 INFO: │   ├──min_size_rt: 3
0:00:00.116959 INFO: │   ├──max_size_mobility: 20
0:00:00.116977 INFO: │   ├──max_size_rt: 15
0:00:00.116996 INFO: │   ├──group_channels: False
0:00:00.117019 INFO: │   ├──use_weighted_score: True
0:00:00.117037 INFO: │   ├──join_close_candidates: False
0:00:00.117057 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
0:00:00.117077 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
0:00:00.117094 INFO: ├──scoring_config
0:00:00.117112 INFO: │   ├──score_grouped: False
0:00:00.117130 INFO: │   ├──top_k_isotopes: 3
0:00:00.117147 INFO: │   ├──reference_channel: -1
0:00:00.117166 INFO: │   ├──precursor_mz_tolerance: 10
0:00:00.117183 INFO: │   └──fragment_mz_tolerance: 15
0:00:00.117200 INFO: ├──library_multiplexing
0:00:00.117218 INFO: │   ├──enabled: False
0:00:00.117235 INFO: │   ├──input_channel: 0
0:00:00.117254 INFO: │   └──multiplex_mapping:
0:00:00.117271 INFO: ├──multiplexing
0:00:00.117288 INFO: │   ├──enabled: False
0:00:00.117305 INFO: │   ├──target_channels: 4,8
0:00:00.117322 INFO: │   ├──decoy_channel: 12
0:00:00.117340 INFO: │   ├──reference_channel: 0
0:00:00.117358 INFO: │   └──competetive_scoring: True
0:00:00.117374 INFO: ├──fdr
0:00:00.117393 INFO: │   ├──fdr: 0.01
0:00:00.117411 INFO: │   ├──group_level: proteins
0:00:00.117429 INFO: │   ├──inference_strategy: heuristic
0:00:00.117447 INFO: │   ├──competetive_scoring: True
0:00:00.117464 INFO: │   ├──keep_decoys: False
0:00:00.117481 INFO: │   ├──channel_wise_fdr: False
0:00:00.117499 INFO: │   ├──enable_two_step_classifier: False
0:00:00.117518 INFO: │   ├──two_step_classifier_max_iterations: 5
0:00:00.117536 INFO: │   └──enable_nn_hyperparameter_tuning: False
0:00:00.117553 INFO: ├──search_output
0:00:00.117572 INFO: │   ├──file_format: tsv
0:00:00.117590 INFO: │   ├──peptide_level_lfq: False
0:00:00.117608 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
0:00:00.117625 INFO: │   ├──min_k_fragments: 12
0:00:00.117643 INFO: │   ├──min_correlation: 0.9
0:00:00.117661 INFO: │   ├──num_samples_quadratic: 50
0:00:00.117678 INFO: │   ├──min_nonnan: 3
0:00:00.117696 INFO: │   ├──normalize_lfq: True
0:00:00.117713 INFO: │   └──save_fragment_quant_matrix: False
0:00:00.117730 INFO: ├──optimization
0:00:00.117748 INFO: │   ├──order_of_optimization: None
0:00:00.117766 INFO: │   ├──ms2_error
0:00:00.117783 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.117801 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.117820 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.117839 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.117857 INFO: │   │   ├──try_narrower_values: True
0:00:00.117874 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.117892 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.117911 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.117929 INFO: │   ├──ms1_error
0:00:00.117947 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.117966 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.117984 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.118003 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.118020 INFO: │   │   ├──try_narrower_values: False
0:00:00.118039 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.118057 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.118075 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.118093 INFO: │   ├──mobility_error
0:00:00.118111 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.118129 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.118147 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.118165 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.119094 INFO: │   │   ├──try_narrower_values: False
0:00:00.119121 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.119139 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.119157 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.119174 INFO: │   └──rt_error
0:00:00.119193 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.119212 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.119230 INFO: │       ├──automatic_update_percentile_range: 0.99
0:00:00.119249 INFO: │       ├──automatic_update_factor: 1.1
0:00:00.119266 INFO: │       ├──try_narrower_values: True
0:00:00.119284 INFO: │       ├──maximal_decrease: 0.2
0:00:00.119301 INFO: │       ├──favour_narrower_optimum: True
0:00:00.119318 INFO: │       └──maximum_decrease_from_maximum: 0.1
0:00:00.119337 INFO: ├──optimization_manager
0:00:00.119354 INFO: │   ├──fwhm_rt: 5
0:00:00.119372 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.119390 INFO: │   └──score_cutoff: 0
0:00:00.119409 INFO: ├──transfer_library
0:00:00.119426 INFO: │   ├──enabled: False
0:00:00.119443 INFO: │   ├──fragment_types:
0:00:00.119460 INFO: │   │   [32;20m- b[0m
0:00:00.119477 INFO: │   │   [32;20m- y[0m
0:00:00.119495 INFO: │   ├──max_charge: 2
0:00:00.119513 INFO: │   ├──top_k_samples: 3
0:00:00.119530 INFO: │   ├──norm_delta_max: True
0:00:00.119548 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.119566 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.119584 INFO: └──transfer_learning
0:00:00.119601 INFO:     ├──enabled: False
0:00:00.119619 INFO:     ├──batch_size: 2000
0:00:00.119636 INFO:     ├──max_lr: 0.0001
0:00:00.119654 INFO:     ├──train_fraction: 0.7
0:00:00.119673 INFO:     ├──validation_fraction: 0.2
0:00:00.119691 INFO:     ├──test_fraction: 0.1
0:00:00.119708 INFO:     ├──test_interval: 1
0:00:00.119725 INFO:     ├──lr_patience: 3
0:00:00.119743 INFO:     [32;20m├──epochs: 20 [user defined, default: 51][0m
0:00:00.119762 INFO:     ├──warmup_epochs: 5
0:00:00.119780 INFO:     ├──nce: 25
0:00:00.119797 INFO:     [32;20m└──instrument: Astral [user defined, default: Lumos][0m
0:00:00.124581 INFO: Registering 7 custom modifications
0:00:00.153389 PROGRESS: No library provided. Building library from fasta files.
0:00:00.153491 INFO: Running FastaDigest
0:00:01.012670 INFO: Digesting fasta file
0:00:08.495810 INFO: Adding modifications
0:01:39.472211 INFO: Removing non-canonical amino acids
0:01:45.312808 INFO: Fasta library contains 5,215,079 precursors
0:01:45.313293 PROGRESS: Predicting library properties.
0:01:45.313367 INFO: Running PeptDeepPrediction
0:01:45.313451 INFO: Device set to cpu
0:01:46.211288 INFO: Loading PeptDeep models of type generic
0:01:46.966742 INFO: Predicting RT, MS2 and mobility
0:01:46.966908 INFO: Using multiprocessing with 100 processes ...
0:01:47.313157 INFO: Predicting rt,ms2,mobility ...
0:09:38.642512 INFO: Adding fragment mz information
0:09:38.922314 INFO: Adding fragment intensity information
0:09:39.203269 INFO: Adding precursor information
0:09:39.602314 INFO: Running PrecursorInitializer
0:09:39.648255 INFO: Running AnnotateFasta
0:09:39.814920 INFO: Dropping decoys from input library before annotation
0:10:06.231242 INFO: Running IsotopeGenerator
0:10:25.681916 INFO: Running RTNormalization
0:10:25.682394 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:10:25.682491 INFO: Saving library to run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/speclib.hdf
0:10:57.428898 INFO: Running DecoyGenerator
0:12:44.916429 INFO: Running FlattenLibrary
0:13:14.050648 INFO: Running InitFlatColumns
0:13:14.307243 INFO: Running LogFlatLibraryStats
0:13:14.307420 INFO: ============ Library Stats ============
0:13:14.307470 INFO: Number of precursors: 10,400,392
0:13:15.993826 INFO: 	thereof targets:5,215,079
0:13:15.994043 INFO: 	thereof decoys: 5,185,313
0:13:16.067271 INFO: Number of elution groups: 5,215,079
0:13:16.067397 INFO: 	average size: 1.99
0:13:16.405511 INFO: Number of proteins: 117,993
0:13:16.431158 INFO: Number of channels: 1 ([0])
0:13:16.431341 INFO: Isotopes Distribution for 4 isotopes
0:13:16.431370 INFO: =======================================
0:13:16.440298 INFO: Searching 6 files:
0:13:16.440366 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
0:13:16.440389 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
0:13:16.440410 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
0:13:16.440427 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
0:13:16.440444 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
0:13:16.440460 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
0:13:16.440477 INFO: Using 1 fasta files:
0:13:16.440498 INFO:   ./ProteoBenchFASTA_DDAQuantification.fasta
0:13:16.440521 INFO: Using library: None
0:13:16.440540 INFO: Saving output to: run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library
0:13:16.440573 PROGRESS: Starting Search Workflows
0:13:16.440680 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:13:16.440753 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant
0:13:16.440838 INFO: Creating folder run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/figures
0:13:16.441737 INFO: Initializing RawFileManager
0:13:27.870350 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.
0:13:27.875504 INFO: Determining DIA cycle
0:13:28.296323 INFO: Found cycle with start 0.00 min and length 300.
0:13:28.461676 INFO: RT (min)            : 0.0 - 26.9
0:13:28.461768 INFO: RT duration (sec)   : 1611.2
0:13:28.461795 INFO: RT duration (min)   : 26.9
0:13:28.461818 INFO: Cycle len (scans)   : 300
0:13:28.461838 INFO: Cycle len (sec)     : 1.65
0:13:28.461857 INFO: Number of cycles    : 977
0:13:28.461876 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:13:29.796887 INFO: Initializing CalibrationManager
0:13:29.797164 INFO: Loading calibration config
0:13:29.797270 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'}]
0:13:29.797338 INFO: Calibration group :fragment, found 1 estimator(s)
0:13:29.797449 INFO: Calibration group :precursor, found 3 estimator(s)
0:13:29.797521 INFO: Disabling ion mobility calibration
0:13:29.797551 INFO: removed mobility estimator from group precursor
0:13:29.797698 INFO: Initializing OptimizationManager
0:13:29.797814 INFO: initial parameter: ms1_error = 30
0:13:29.797870 INFO: initial parameter: ms2_error = 30
0:13:29.797929 INFO: initial parameter: rt_error = 805.5992431640625
0:13:29.797979 INFO: initial parameter: mobility_error = 0.1
0:13:29.798021 INFO: initial parameter: column_type = library
0:13:29.798063 INFO: initial parameter: num_candidates = 1
0:13:29.798103 INFO: initial parameter: classifier_version = -1
0:13:29.798154 INFO: initial parameter: fwhm_rt = 5
0:13:29.798198 INFO: initial parameter: fwhm_mobility = 0.01
0:13:29.798241 INFO: initial parameter: score_cutoff = 0
0:13:29.798311 INFO: Initializing TimingManager
0:13:29.798375 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:13:29.798499 INFO: FDRManager not loaded from disk.
0:13:29.798526 INFO: Initializing FDRManager
0:13:29.798565 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:13:31.278617 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
0:13:33.119405 PROGRESS: Starting initial search for precursors.
0:13:34.302144 INFO: Starting optimization step 0.
0:13:34.302357 PROGRESS: === Extracting elution groups 0 to 200 ===
0:13:34.302426 PROGRESS: Extracting batch of 395 precursors
0:13:35.722807 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:13:35.722919 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:13:35.722959 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:13:35.722982 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:13:39.166921 INFO: Starting candidate selection
0:14:58.648479 INFO: Starting candidate scoring
0:22:31.262436 INFO: Finished candidate processing
0:22:31.262828 INFO: Collecting candidate features
0:22:31.855115 INFO: Collecting fragment features
0:22:33.664382 INFO: Finished candidate scoring
0:22:33.666434 PROGRESS: === Extracted 395 precursors and 3928 fragments ===
0:22:33.666839 INFO: performing precursor FDR with 47 features
0:22:33.666880 INFO: Decoy channel: -1
0:22:33.666902 INFO: Competetive: True
0:22:33.668036 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:37.324998 INFO: Test AUC: 0.435
0:22:37.325171 INFO: Train AUC: 0.529
0:22:37.325242 INFO: AUC difference: 17.79%
0:22:37.325301 WARNING: AUC difference > 5%. This may indicate overfitting.
0:22:37.615254 INFO: Resetting torch num_threads to 100
0:22:37.615842 INFO: === FDR correction performed with classifier version -1 ===
0:22:37.616463 PROGRESS: ============================= Precursor FDR =============================
0:22:37.616551 PROGRESS: Total precursors accumulated: 1
0:22:37.616610 PROGRESS: Target precursors: 1 (100.00%)
0:22:37.616660 PROGRESS: Decoy precursors: 0 (0.00%)
0:22:37.616707 PROGRESS: 
0:22:37.616750 PROGRESS: Precursor Summary:
0:22:37.617699 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:22:37.617785 PROGRESS: 
0:22:37.617840 PROGRESS: Protein Summary:
0:22:37.618862 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:22:37.618952 PROGRESS: =========================================================================
0:22:37.680976 INFO: Starting optimization step 1.
0:22:37.681167 PROGRESS: === Extracting elution groups 200 to 600 ===
0:22:37.681242 PROGRESS: Extracting batch of 790 precursors
0:22:37.682285 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:22:37.682335 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:37.682370 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:22:37.682392 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:22:37.682592 INFO: Starting candidate selection
0:22:37.814527 INFO: Starting candidate scoring
0:22:37.853377 INFO: Finished candidate processing
0:22:37.853456 INFO: Collecting candidate features
0:22:37.861962 INFO: Collecting fragment features
0:22:37.864105 INFO: Finished candidate scoring
0:22:37.866039 PROGRESS: === Extracted 1183 precursors and 11893 fragments ===
0:22:37.866767 INFO: performing precursor FDR with 47 features
0:22:37.866812 INFO: Decoy channel: -1
0:22:37.866843 INFO: Competetive: True
0:22:37.869427 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:39.258996 INFO: Test AUC: 0.471
0:22:39.259543 INFO: Train AUC: 0.526
0:22:39.259639 INFO: AUC difference: 10.43%
0:22:39.259706 WARNING: AUC difference > 5%. This may indicate overfitting.
0:22:40.074550 INFO: Resetting torch num_threads to 100
0:22:40.075239 INFO: === FDR correction performed with classifier version -1 ===
0:22:40.075888 PROGRESS: ============================= Precursor FDR =============================
0:22:40.075985 PROGRESS: Total precursors accumulated: 599
0:22:40.076063 PROGRESS: Target precursors: 311 (51.92%)
0:22:40.076134 PROGRESS: Decoy precursors: 288 (48.08%)
0:22:40.076197 PROGRESS: 
0:22:40.076255 PROGRESS: Precursor Summary:
0:22:40.077144 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:40.077240 PROGRESS: 
0:22:40.077311 PROGRESS: Protein Summary:
0:22:40.078263 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:40.078361 PROGRESS: =========================================================================
0:22:40.140373 INFO: Starting optimization step 2.
0:22:40.140576 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:22:40.140657 PROGRESS: Extracting batch of 1585 precursors
0:22:40.141559 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:22:40.141607 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:40.141648 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:22:40.141677 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:22:40.141867 INFO: Starting candidate selection
0:22:40.298193 INFO: Starting candidate scoring
0:22:40.335405 INFO: Finished candidate processing
0:22:40.335483 INFO: Collecting candidate features
0:22:40.345983 INFO: Collecting fragment features
0:22:40.348642 INFO: Finished candidate scoring
0:22:40.351403 PROGRESS: === Extracted 2762 precursors and 27938 fragments ===
0:22:40.352257 INFO: performing precursor FDR with 47 features
0:22:40.352300 INFO: Decoy channel: -1
0:22:40.352324 INFO: Competetive: True
0:22:40.355355 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:40.395000 INFO: Test AUC: 0.495
0:22:40.395073 INFO: Train AUC: 0.512
0:22:40.395103 INFO: AUC difference: 3.44%
0:22:40.567547 INFO: Resetting torch num_threads to 100
0:22:40.568273 INFO: === FDR correction performed with classifier version -1 ===
0:22:40.568996 PROGRESS: ============================= Precursor FDR =============================
0:22:40.569087 PROGRESS: Total precursors accumulated: 1,396
0:22:40.569144 PROGRESS: Target precursors: 722 (51.72%)
0:22:40.569194 PROGRESS: Decoy precursors: 674 (48.28%)
0:22:40.569241 PROGRESS: 
0:22:40.569285 PROGRESS: Precursor Summary:
0:22:40.570134 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:40.570224 PROGRESS: 
0:22:40.570277 PROGRESS: Protein Summary:
0:22:40.571201 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:40.571289 PROGRESS: =========================================================================
0:22:40.638280 INFO: Starting optimization step 3.
0:22:40.638478 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:22:40.638546 PROGRESS: Extracting batch of 3157 precursors
0:22:40.639604 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:22:40.639652 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:40.639684 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:22:40.639706 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:22:40.639870 INFO: Starting candidate selection
0:22:40.881344 INFO: Starting candidate scoring
0:22:40.920797 INFO: Finished candidate processing
0:22:40.920886 INFO: Collecting candidate features
0:22:40.933808 INFO: Collecting fragment features
0:22:40.937320 INFO: Finished candidate scoring
0:22:40.941677 PROGRESS: === Extracted 5917 precursors and 60170 fragments ===
0:22:40.942904 INFO: performing precursor FDR with 47 features
0:22:40.942950 INFO: Decoy channel: -1
0:22:40.942973 INFO: Competetive: True
0:22:40.946689 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:40.998795 INFO: Test AUC: 0.505
0:22:40.998885 INFO: Train AUC: 0.509
0:22:40.998914 INFO: AUC difference: 0.74%
0:22:41.173089 INFO: Resetting torch num_threads to 100
0:22:41.173980 INFO: === FDR correction performed with classifier version -1 ===
0:22:41.175329 PROGRESS: ============================= Precursor FDR =============================
0:22:41.175422 PROGRESS: Total precursors accumulated: 2,995
0:22:41.175481 PROGRESS: Target precursors: 1,550 (51.75%)
0:22:41.175533 PROGRESS: Decoy precursors: 1,445 (48.25%)
0:22:41.175580 PROGRESS: 
0:22:41.175624 PROGRESS: Precursor Summary:
0:22:41.176497 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:41.176588 PROGRESS: 
0:22:41.176642 PROGRESS: Protein Summary:
0:22:41.177572 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:41.177659 PROGRESS: =========================================================================
0:22:41.252881 INFO: Starting optimization step 4.
0:22:41.253092 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:22:41.253160 PROGRESS: Extracting batch of 6336 precursors
0:22:41.254616 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:22:41.254665 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:41.254699 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:22:41.254721 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:22:41.254888 INFO: Starting candidate selection
0:22:41.730661 INFO: Starting candidate scoring
0:22:41.779809 INFO: Finished candidate processing
0:22:41.779919 INFO: Collecting candidate features
0:22:41.797725 INFO: Collecting fragment features
0:22:41.803722 INFO: Finished candidate scoring
0:22:41.814249 PROGRESS: === Extracted 12238 precursors and 124737 fragments ===
0:22:41.816161 INFO: performing precursor FDR with 47 features
0:22:41.816222 INFO: Decoy channel: -1
0:22:41.816248 INFO: Competetive: True
0:22:41.822509 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:41.927472 INFO: Test AUC: 0.498
0:22:41.927577 INFO: Train AUC: 0.509
0:22:41.927606 INFO: AUC difference: 2.29%
0:22:42.106275 INFO: Resetting torch num_threads to 100
0:22:42.107487 INFO: === FDR correction performed with classifier version -1 ===
0:22:42.108769 PROGRESS: ============================= Precursor FDR =============================
0:22:42.108864 PROGRESS: Total precursors accumulated: 6,188
0:22:42.108922 PROGRESS: Target precursors: 3,207 (51.83%)
0:22:42.108972 PROGRESS: Decoy precursors: 2,981 (48.17%)
0:22:42.109017 PROGRESS: 
0:22:42.109060 PROGRESS: Precursor Summary:
0:22:42.109947 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:42.110035 PROGRESS: 
0:22:42.110089 PROGRESS: Protein Summary:
0:22:42.111062 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:42.111151 PROGRESS: =========================================================================
0:22:42.199349 INFO: Starting optimization step 5.
0:22:42.199575 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:22:42.199643 PROGRESS: Extracting batch of 12662 precursors
0:22:42.201999 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:22:42.202051 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:42.202084 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:22:42.202106 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:22:42.202274 INFO: Starting candidate selection
0:22:43.142503 INFO: Starting candidate scoring
0:22:43.241166 INFO: Finished candidate processing
0:22:43.241294 INFO: Collecting candidate features
0:22:43.270645 INFO: Collecting fragment features
0:22:43.280317 INFO: Finished candidate scoring
0:22:43.387478 PROGRESS: === Extracted 24888 precursors and 253951 fragments ===
0:22:43.391539 INFO: performing precursor FDR with 47 features
0:22:43.391638 INFO: Decoy channel: -1
0:22:43.391673 INFO: Competetive: True
0:22:43.406096 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:43.798657 INFO: Test AUC: 0.528
0:22:43.798803 INFO: Train AUC: 0.538
0:22:43.798833 INFO: AUC difference: 1.80%
0:22:43.997463 INFO: Resetting torch num_threads to 100
0:22:43.999820 INFO: === FDR correction performed with classifier version -1 ===
0:22:44.000551 PROGRESS: ============================= Precursor FDR =============================
0:22:44.000646 PROGRESS: Total precursors accumulated: 1
0:22:44.000706 PROGRESS: Target precursors: 1 (100.00%)
0:22:44.000757 PROGRESS: Decoy precursors: 0 (0.00%)
0:22:44.000805 PROGRESS: 
0:22:44.000850 PROGRESS: Precursor Summary:
0:22:44.001783 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:22:44.001870 PROGRESS: 
0:22:44.001923 PROGRESS: Protein Summary:
0:22:44.002945 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:22:44.003035 PROGRESS: =========================================================================
0:22:44.131703 INFO: Starting optimization step 6.
0:22:44.131953 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:22:44.132036 PROGRESS: Extracting batch of 25287 precursors
0:22:44.138615 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:22:44.138681 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:44.138719 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:22:44.138742 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:22:44.138997 INFO: Starting candidate selection
0:22:45.668597 INFO: Starting candidate scoring
0:22:45.810117 INFO: Finished candidate processing
0:22:45.810218 INFO: Collecting candidate features
0:22:45.870664 INFO: Collecting fragment features
0:22:45.888461 INFO: Finished candidate scoring
0:22:45.921126 PROGRESS: === Extracted 50105 precursors and 511328 fragments ===
0:22:45.928296 INFO: performing precursor FDR with 47 features
0:22:45.928368 INFO: Decoy channel: -1
0:22:45.928393 INFO: Competetive: True
0:22:45.951848 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:46.783674 INFO: Test AUC: 0.556
0:22:46.783796 INFO: Train AUC: 0.574
0:22:46.783827 INFO: AUC difference: 3.21%
0:22:46.980376 INFO: Resetting torch num_threads to 100
0:22:46.983554 INFO: === FDR correction performed with classifier version -1 ===
0:22:46.984157 PROGRESS: ============================= Precursor FDR =============================
0:22:46.984245 PROGRESS: Total precursors accumulated: 189
0:22:46.984307 PROGRESS: Target precursors: 173 (91.53%)
0:22:46.984360 PROGRESS: Decoy precursors: 16 (8.47%)
0:22:46.984407 PROGRESS: 
0:22:46.984452 PROGRESS: Precursor Summary:
0:22:46.985341 PROGRESS: Channel   0:	 0.05 FDR:   125; 0.01 FDR:    41; 0.001 FDR:    41
0:22:46.985427 PROGRESS: 
0:22:46.985482 PROGRESS: Protein Summary:
0:22:46.986471 PROGRESS: Channel   0:	 0.05 FDR:   124; 0.01 FDR:    41; 0.001 FDR:    41
0:22:46.986557 PROGRESS: =========================================================================
0:22:47.146819 INFO: Starting optimization step 7.
0:22:47.147073 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:22:47.147152 PROGRESS: Extracting batch of 50588 precursors
0:22:47.159881 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:22:47.160000 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:47.160034 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:22:47.160057 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:22:47.160292 INFO: Starting candidate selection
0:22:50.200647 INFO: Starting candidate scoring
0:22:50.507326 INFO: Finished candidate processing
0:22:50.507429 INFO: Collecting candidate features
0:22:50.618249 INFO: Collecting fragment features
0:22:50.652299 INFO: Finished candidate scoring
0:22:50.703635 PROGRESS: === Extracted 100596 precursors and 1027529 fragments ===
0:22:50.715569 INFO: performing precursor FDR with 47 features
0:22:50.715667 INFO: Decoy channel: -1
0:22:50.715699 INFO: Competetive: True
0:22:50.762272 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:52.488572 INFO: Test AUC: 0.565
0:22:52.488699 INFO: Train AUC: 0.583
0:22:52.488734 INFO: AUC difference: 3.16%
0:22:52.699145 INFO: Resetting torch num_threads to 100
0:22:52.706042 INFO: === FDR correction performed with classifier version -1 ===
0:22:52.706800 PROGRESS: ============================= Precursor FDR =============================
0:22:52.706930 PROGRESS: Total precursors accumulated: 533
0:22:52.707005 PROGRESS: Target precursors: 488 (91.56%)
0:22:52.707074 PROGRESS: Decoy precursors: 45 (8.44%)
0:22:52.707136 PROGRESS: 
0:22:52.707196 PROGRESS: Precursor Summary:
0:22:52.708210 PROGRESS: Channel   0:	 0.05 FDR:   372; 0.01 FDR:   273; 0.001 FDR:     1
0:22:52.708311 PROGRESS: 
0:22:52.708378 PROGRESS: Protein Summary:
0:22:52.709520 PROGRESS: Channel   0:	 0.05 FDR:   355; 0.01 FDR:   262; 0.001 FDR:     1
0:22:52.709620 PROGRESS: =========================================================================
0:22:52.786146 INFO: fragments_df: keeping 2545 of 1027529 [sum(precursor_idx_mask)=3112 sum(mass_error_mask)=1027529 stop_rank=2545
0:22:53.023151 INFO: calibration group: precursor, fitting rt estimator 
0:22:53.164627 INFO: calibration group: fragment, fitting mz estimator 
0:22:53.505604 INFO: Using score_cutoff 72.4306366241455 (fac=0.99, q=1)
0:22:53.506167 INFO: calibration group: precursor, predicting mz
0:22:53.506266 WARNING: mz prediction was skipped as it has not been fitted yet
0:22:53.506304 INFO: calibration group: precursor, predicting rt
0:22:53.571084 INFO: calibration group: fragment, predicting mz
0:22:53.720832 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:22:53.721145 INFO: Starting optimization step 8.
0:22:53.721239 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:22:53.721318 PROGRESS: Extracting batch of 100800 precursors
0:22:53.861288 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:22:53.861417 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:53.861467 INFO: FWHM in RT is 3.03 seconds, sigma is 0.39
0:22:53.861499 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:22:53.861734 INFO: Starting candidate selection
0:22:58.520829 INFO: Starting candidate scoring
0:22:59.886718 INFO: Finished candidate processing
0:22:59.886819 INFO: Collecting candidate features
0:23:00.252691 INFO: Collecting fragment features
0:23:00.394303 INFO: Finished candidate scoring
0:23:00.523871 PROGRESS: === Extracted 201192 precursors and 2029779 fragments ===
0:23:00.524304 INFO: performing precursor FDR with 47 features
0:23:00.524345 INFO: Decoy channel: -1
0:23:00.524369 INFO: Competetive: True
0:23:00.590910 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:04.026824 INFO: Test AUC: 0.567
0:23:04.026954 INFO: Train AUC: 0.586
0:23:04.026984 INFO: AUC difference: 3.21%
0:23:04.254983 INFO: Resetting torch num_threads to 100
0:23:04.261184 INFO: === FDR correction performed with classifier version 7 ===
0:23:04.261925 PROGRESS: ============================= Precursor FDR =============================
0:23:04.262033 PROGRESS: Total precursors accumulated: 604
0:23:04.262094 PROGRESS: Target precursors: 552 (91.39%)
0:23:04.262157 PROGRESS: Decoy precursors: 52 (8.61%)
0:23:04.262206 PROGRESS: 
0:23:04.262251 PROGRESS: Precursor Summary:
0:23:04.263277 PROGRESS: Channel   0:	 0.05 FDR:   462; 0.01 FDR:   374; 0.001 FDR:   148
0:23:04.263371 PROGRESS: 
0:23:04.263425 PROGRESS: Protein Summary:
0:23:04.264607 PROGRESS: Channel   0:	 0.05 FDR:   437; 0.01 FDR:   357; 0.001 FDR:   143
0:23:04.264698 PROGRESS: =========================================================================
0:23:04.400701 INFO: fragments_df: keeping 4128 of 2029779 [sum(precursor_idx_mask)=8368 sum(mass_error_mask)=2029779 stop_rank=4128
0:23:04.618638 INFO: calibration group: precursor, fitting rt estimator 
0:23:04.745331 INFO: calibration group: fragment, fitting mz estimator 
0:23:05.285905 INFO: Using score_cutoff 62.08099544792175 (fac=0.99, q=1)
0:23:05.286335 INFO: calibration group: precursor, predicting mz
0:23:05.286424 WARNING: mz prediction was skipped as it has not been fitted yet
0:23:05.286457 INFO: calibration group: precursor, predicting rt
0:23:05.347032 INFO: calibration group: fragment, predicting mz
0:23:05.500641 INFO: === checking if optimization conditions were reached ===
0:23:05.500945 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:23:05.503595 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 24.9604.
0:23:05.503661 INFO: ==============================================
0:23:05.503767 INFO: Starting optimization step 9.
0:23:05.503840 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:23:05.503918 PROGRESS: Extracting batch of 100800 precursors
0:23:05.543342 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:23:05.543485 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:23:05.543529 INFO: FWHM in RT is 2.92 seconds, sigma is 0.38
0:23:05.543558 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:23:05.543850 INFO: Starting candidate selection
0:23:11.207928 INFO: Starting candidate scoring
0:23:12.564501 INFO: Finished candidate processing
0:23:12.564640 INFO: Collecting candidate features
0:23:12.916609 INFO: Collecting fragment features
0:23:13.054680 INFO: Finished candidate scoring
0:23:13.163869 PROGRESS: === Extracted 201191 precursors and 1968240 fragments ===
0:23:13.164274 INFO: performing precursor FDR with 47 features
0:23:13.164315 INFO: Decoy channel: -1
0:23:13.164339 INFO: Competetive: True
0:23:13.222992 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:17.056193 INFO: Test AUC: 0.563
0:23:17.056419 INFO: Train AUC: 0.583
0:23:17.056457 INFO: AUC difference: 3.41%
0:23:17.304328 INFO: Resetting torch num_threads to 100
0:23:17.321474 INFO: === FDR correction performed with classifier version 7 ===
0:23:17.322713 PROGRESS: ============================= Precursor FDR =============================
0:23:17.322817 PROGRESS: Total precursors accumulated: 639
0:23:17.322880 PROGRESS: Target precursors: 587 (91.86%)
0:23:17.322932 PROGRESS: Decoy precursors: 52 (8.14%)
0:23:17.322979 PROGRESS: 
0:23:17.323025 PROGRESS: Precursor Summary:
0:23:17.324133 PROGRESS: Channel   0:	 0.05 FDR:   508; 0.01 FDR:   412; 0.001 FDR:   338
0:23:17.324224 PROGRESS: 
0:23:17.324280 PROGRESS: Protein Summary:
0:23:17.325505 PROGRESS: Channel   0:	 0.05 FDR:   481; 0.01 FDR:   390; 0.001 FDR:   322
0:23:17.325595 PROGRESS: =========================================================================
0:23:17.454723 INFO: fragments_df: keeping 4453 of 1968240 [sum(precursor_idx_mask)=9226 sum(mass_error_mask)=1968240 stop_rank=4453
0:23:17.631425 INFO: calibration group: precursor, fitting rt estimator 
0:23:17.769266 INFO: calibration group: fragment, fitting mz estimator 
0:23:18.360454 INFO: Using score_cutoff 59.513329175949096 (fac=0.99, q=1)
0:23:18.360947 INFO: calibration group: precursor, predicting mz
0:23:18.361037 WARNING: mz prediction was skipped as it has not been fitted yet
0:23:18.361068 INFO: calibration group: precursor, predicting rt
0:23:18.392266 INFO: calibration group: fragment, predicting mz
0:23:18.460026 INFO: === checking if optimization conditions were reached ===
0:23:18.460420 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:23:18.463487 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 21.0284.
0:23:18.463549 INFO: ==============================================
0:23:18.463655 INFO: Starting optimization step 10.
0:23:18.463735 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:23:18.463815 PROGRESS: Extracting batch of 50212 precursors
0:23:18.480155 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:23:18.480303 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:23:18.480355 INFO: FWHM in RT is 2.87 seconds, sigma is 0.37
0:23:18.480394 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:23:18.480762 INFO: Starting candidate selection
0:23:20.855231 INFO: Starting candidate scoring
0:23:21.569050 INFO: Finished candidate processing
0:23:21.569176 INFO: Collecting candidate features
0:23:21.796013 INFO: Collecting fragment features
0:23:21.864063 INFO: Finished candidate scoring
0:23:21.929091 PROGRESS: === Extracted 100210 precursors and 960007 fragments ===
0:23:21.929511 INFO: performing precursor FDR with 47 features
0:23:21.929552 INFO: Decoy channel: -1
0:23:21.929575 INFO: Competetive: True
0:23:21.959508 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:23.651939 INFO: Test AUC: 0.559
0:23:23.652079 INFO: Train AUC: 0.585
0:23:23.652110 INFO: AUC difference: 4.38%
0:23:23.858777 INFO: Resetting torch num_threads to 100
0:23:23.861683 INFO: === FDR correction performed with classifier version 7 ===
0:23:23.862345 PROGRESS: ============================= Precursor FDR =============================
0:23:23.862436 PROGRESS: Total precursors accumulated: 315
0:23:23.862494 PROGRESS: Target precursors: 286 (90.79%)
0:23:23.862748 PROGRESS: Decoy precursors: 29 (9.21%)
0:23:23.862808 PROGRESS: 
0:23:23.862857 PROGRESS: Precursor Summary:
0:23:23.863813 PROGRESS: Channel   0:	 0.05 FDR:   225; 0.01 FDR:   182; 0.001 FDR:   178
0:23:23.863905 PROGRESS: 
0:23:23.863963 PROGRESS: Protein Summary:
0:23:23.865025 PROGRESS: Channel   0:	 0.05 FDR:   216; 0.01 FDR:   177; 0.001 FDR:   173
0:23:23.865114 PROGRESS: =========================================================================
0:23:23.989241 INFO: calibration group: precursor, predicting mz
0:23:23.989516 WARNING: mz prediction was skipped as it has not been fitted yet
0:23:23.989551 INFO: calibration group: precursor, predicting rt
0:23:24.021346 INFO: calibration group: fragment, predicting mz
0:23:24.087667 INFO: === skipping optimization until target number of precursors are found ===
0:23:24.087977 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:23:24.088059 INFO: Starting optimization step 11.
0:23:24.088136 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:23:24.088207 PROGRESS: Extracting batch of 50588 precursors
0:23:24.105650 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:23:24.105802 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:23:24.105844 INFO: FWHM in RT is 2.87 seconds, sigma is 0.37
0:23:24.105874 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:23:24.106142 INFO: Starting candidate selection
0:23:26.587177 INFO: Starting candidate scoring
0:23:27.267141 INFO: Finished candidate processing
0:23:27.267286 INFO: Collecting candidate features
0:23:27.463069 INFO: Collecting fragment features
0:23:27.547101 INFO: Finished candidate scoring
0:23:27.719734 PROGRESS: === Extracted 201191 precursors and 1928083 fragments ===
0:23:27.742073 INFO: performing precursor FDR with 47 features
0:23:27.742197 INFO: Decoy channel: -1
0:23:27.742234 INFO: Competetive: True
0:23:27.835948 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:31.696053 INFO: Test AUC: 0.563
0:23:31.696175 INFO: Train AUC: 0.584
0:23:31.696207 INFO: AUC difference: 3.64%
0:23:31.949455 INFO: Resetting torch num_threads to 100
0:23:31.957426 INFO: === FDR correction performed with classifier version 7 ===
0:23:31.958195 PROGRESS: ============================= Precursor FDR =============================
0:23:31.958302 PROGRESS: Total precursors accumulated: 690
0:23:31.958362 PROGRESS: Target precursors: 630 (91.30%)
0:23:31.958412 PROGRESS: Decoy precursors: 60 (8.70%)
0:23:31.958458 PROGRESS: 
0:23:31.958500 PROGRESS: Precursor Summary:
0:23:31.959581 PROGRESS: Channel   0:	 0.05 FDR:   521; 0.01 FDR:   387; 0.001 FDR:   346
0:23:31.959678 PROGRESS: 
0:23:31.959738 PROGRESS: Protein Summary:
0:23:31.960976 PROGRESS: Channel   0:	 0.05 FDR:   496; 0.01 FDR:   370; 0.001 FDR:   331
0:23:31.961069 PROGRESS: =========================================================================
0:23:32.107040 INFO: fragments_df: keeping 4255 of 1928083 [sum(precursor_idx_mask)=8556 sum(mass_error_mask)=1928083 stop_rank=4255
0:23:32.317214 INFO: calibration group: precursor, fitting rt estimator 
0:23:32.434758 INFO: calibration group: fragment, fitting mz estimator 
0:23:32.937214 INFO: Using score_cutoff 60.79233161315918 (fac=0.99, q=1)
0:23:32.937750 INFO: calibration group: precursor, predicting mz
0:23:32.937850 WARNING: mz prediction was skipped as it has not been fitted yet
0:23:32.937882 INFO: calibration group: precursor, predicting rt
0:23:32.999577 INFO: calibration group: fragment, predicting mz
0:23:33.147714 INFO: === checking if optimization conditions were reached ===
0:23:33.148141 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
0:23:33.151442 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 18.2264.
0:23:33.151506 INFO: ==============================================
0:23:33.151621 INFO: Starting optimization step 12.
0:23:33.151712 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:23:33.151815 PROGRESS: Extracting batch of 100800 precursors
0:23:33.184238 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:23:33.184399 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:23:33.184452 INFO: FWHM in RT is 2.88 seconds, sigma is 0.37
0:23:33.184477 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:23:33.184872 INFO: Starting candidate selection
0:23:38.026885 INFO: Starting candidate scoring
0:23:39.393870 INFO: Finished candidate processing
0:23:39.394124 INFO: Collecting candidate features
0:23:39.806019 INFO: Collecting fragment features
0:23:39.986638 INFO: Finished candidate scoring
0:23:40.127518 PROGRESS: === Extracted 201191 precursors and 1875879 fragments ===
0:23:40.128227 INFO: performing precursor FDR with 47 features
0:23:40.128271 INFO: Decoy channel: -1
0:23:40.128297 INFO: Competetive: True
0:23:40.209593 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:44.803400 INFO: Test AUC: 0.565
0:23:44.803601 INFO: Train AUC: 0.584
0:23:44.803636 INFO: AUC difference: 3.24%
0:23:45.047493 INFO: Resetting torch num_threads to 100
0:23:45.053066 INFO: === FDR correction performed with classifier version 7 ===
0:23:45.053916 PROGRESS: ============================= Precursor FDR =============================
0:23:45.054030 PROGRESS: Total precursors accumulated: 747
0:23:45.054090 PROGRESS: Target precursors: 683 (91.43%)
0:23:45.054145 PROGRESS: Decoy precursors: 64 (8.57%)
0:23:45.054193 PROGRESS: 
0:23:45.054239 PROGRESS: Precursor Summary:
0:23:45.055355 PROGRESS: Channel   0:	 0.05 FDR:   551; 0.01 FDR:   430; 0.001 FDR:   381
0:23:45.055454 PROGRESS: 
0:23:45.055516 PROGRESS: Protein Summary:
0:23:45.056787 PROGRESS: Channel   0:	 0.05 FDR:   519; 0.01 FDR:   408; 0.001 FDR:   367
0:23:45.056878 PROGRESS: =========================================================================
0:23:45.190922 INFO: fragments_df: keeping 4633 of 1875879 [sum(precursor_idx_mask)=9449 sum(mass_error_mask)=1875879 stop_rank=4633
0:23:45.369647 INFO: calibration group: precursor, fitting rt estimator 
0:23:45.485113 INFO: calibration group: fragment, fitting mz estimator 
0:23:46.048867 INFO: Using score_cutoff 61.93629258041381 (fac=0.99, q=1)
0:23:46.049465 INFO: calibration group: precursor, predicting mz
0:23:46.049562 WARNING: mz prediction was skipped as it has not been fitted yet
0:23:46.049597 INFO: calibration group: precursor, predicting rt
0:23:46.083133 INFO: calibration group: fragment, predicting mz
0:23:46.158117 INFO: === checking if optimization conditions were reached ===
0:23:46.158486 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
0:23:46.161584 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 16.0668.
0:23:46.161647 INFO: ==============================================
0:23:46.161755 INFO: Starting optimization step 13.
0:23:46.161827 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:23:46.161910 PROGRESS: Extracting batch of 50212 precursors
0:23:46.181247 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:23:46.181382 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:23:46.181427 INFO: FWHM in RT is 2.81 seconds, sigma is 0.36
0:23:46.181451 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:23:46.181879 INFO: Starting candidate selection
0:23:48.555545 INFO: Starting candidate scoring
0:23:49.201100 INFO: Finished candidate processing
0:23:49.201193 INFO: Collecting candidate features
0:23:49.388309 INFO: Collecting fragment features
0:23:49.452405 INFO: Finished candidate scoring
0:23:49.508223 PROGRESS: === Extracted 100210 precursors and 911899 fragments ===
0:23:49.508599 INFO: performing precursor FDR with 47 features
0:23:49.508639 INFO: Decoy channel: -1
0:23:49.508662 INFO: Competetive: True
0:23:49.538319 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:51.255492 INFO: Test AUC: 0.562
0:23:51.255623 INFO: Train AUC: 0.583
0:23:51.255653 INFO: AUC difference: 3.60%
0:23:51.459204 INFO: Resetting torch num_threads to 100
0:23:51.462160 INFO: === FDR correction performed with classifier version 7 ===
0:23:51.462822 PROGRESS: ============================= Precursor FDR =============================
0:23:51.462920 PROGRESS: Total precursors accumulated: 383
0:23:51.462979 PROGRESS: Target precursors: 350 (91.38%)
0:23:51.463029 PROGRESS: Decoy precursors: 33 (8.62%)
0:23:51.463074 PROGRESS: 
0:23:51.463117 PROGRESS: Precursor Summary:
0:23:51.464051 PROGRESS: Channel   0:	 0.05 FDR:   322; 0.01 FDR:   208; 0.001 FDR:   155
0:23:51.464139 PROGRESS: 
0:23:51.464194 PROGRESS: Protein Summary:
0:23:51.465289 PROGRESS: Channel   0:	 0.05 FDR:   307; 0.01 FDR:   199; 0.001 FDR:   152
0:23:51.465378 PROGRESS: =========================================================================
0:23:51.525809 INFO: fragments_df: keeping 2279 of 911899 [sum(precursor_idx_mask)=4529 sum(mass_error_mask)=911899 stop_rank=2279
0:23:51.653648 INFO: calibration group: precursor, fitting rt estimator 
0:23:51.760097 INFO: calibration group: fragment, fitting mz estimator 
0:23:52.015536 INFO: Using score_cutoff 63.72845150070191 (fac=0.99, q=1)
0:23:52.016005 INFO: calibration group: precursor, predicting mz
0:23:52.016091 WARNING: mz prediction was skipped as it has not been fitted yet
0:23:52.016124 INFO: calibration group: precursor, predicting rt
0:23:52.047754 INFO: calibration group: fragment, predicting mz
0:23:52.114442 INFO: === checking if optimization conditions were reached ===
0:23:52.114799 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
0:23:52.117272 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 14.2869.
0:23:52.117332 INFO: ==============================================
0:23:52.117424 INFO: Starting optimization step 14.
0:23:52.117491 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:23:52.117554 PROGRESS: Extracting batch of 50212 precursors
0:23:52.136523 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:23:52.136682 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:23:52.136717 INFO: FWHM in RT is 2.74 seconds, sigma is 0.35
0:23:52.136741 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:23:52.137006 INFO: Starting candidate selection
0:23:54.757068 INFO: Starting candidate scoring
0:23:55.406476 INFO: Finished candidate processing
0:23:55.406661 INFO: Collecting candidate features
0:23:55.601574 INFO: Collecting fragment features
0:23:55.680690 INFO: Finished candidate scoring
0:23:55.738531 PROGRESS: === Extracted 100208 precursors and 885697 fragments ===
0:23:55.739108 INFO: performing precursor FDR with 47 features
0:23:55.739149 INFO: Decoy channel: -1
0:23:55.739172 INFO: Competetive: True
0:23:55.771729 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:57.376755 INFO: Test AUC: 0.558
0:23:57.376875 INFO: Train AUC: 0.586
0:23:57.376905 INFO: AUC difference: 4.84%
0:23:57.587665 INFO: Resetting torch num_threads to 100
0:23:57.590579 INFO: === FDR correction performed with classifier version 7 ===
0:23:57.591219 PROGRESS: ============================= Precursor FDR =============================
0:23:57.591308 PROGRESS: Total precursors accumulated: 352
0:23:57.591369 PROGRESS: Target precursors: 321 (91.19%)
0:23:57.591430 PROGRESS: Decoy precursors: 31 (8.81%)
0:23:57.591477 PROGRESS: 
0:23:57.591522 PROGRESS: Precursor Summary:
0:23:57.592470 PROGRESS: Channel   0:	 0.05 FDR:   271; 0.01 FDR:   143; 0.001 FDR:   130
0:23:57.592561 PROGRESS: 
0:23:57.592614 PROGRESS: Protein Summary:
0:23:57.593666 PROGRESS: Channel   0:	 0.05 FDR:   256; 0.01 FDR:   139; 0.001 FDR:   128
0:23:57.593754 PROGRESS: =========================================================================
0:23:57.757027 INFO: calibration group: precursor, predicting mz
0:23:57.757269 WARNING: mz prediction was skipped as it has not been fitted yet
0:23:57.757303 INFO: calibration group: precursor, predicting rt
0:23:57.788721 INFO: calibration group: fragment, predicting mz
0:23:57.850727 INFO: === skipping optimization until target number of precursors are found ===
0:23:57.851028 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:23:57.851110 INFO: Starting optimization step 15.
0:23:57.851189 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:23:57.851274 PROGRESS: Extracting batch of 50588 precursors
0:23:57.868956 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:23:57.869086 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:23:57.869139 INFO: FWHM in RT is 2.74 seconds, sigma is 0.35
0:23:57.869172 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:23:57.869487 INFO: Starting candidate selection
0:24:00.440087 INFO: Starting candidate scoring
0:24:01.112339 INFO: Finished candidate processing
0:24:01.112457 INFO: Collecting candidate features
0:24:01.340892 INFO: Collecting fragment features
0:24:01.412340 INFO: Finished candidate scoring
0:24:01.544678 PROGRESS: === Extracted 201188 precursors and 1778432 fragments ===
0:24:01.574137 INFO: performing precursor FDR with 47 features
0:24:01.574315 INFO: Decoy channel: -1
0:24:01.574347 INFO: Competetive: True
0:24:01.697375 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:05.974261 INFO: Test AUC: 0.559
0:24:05.974457 INFO: Train AUC: 0.583
0:24:05.974487 INFO: AUC difference: 4.15%
0:24:06.221827 INFO: Resetting torch num_threads to 100
0:24:06.231816 INFO: === FDR correction performed with classifier version 7 ===
0:24:06.232639 PROGRESS: ============================= Precursor FDR =============================
0:24:06.232753 PROGRESS: Total precursors accumulated: 800
0:24:06.232813 PROGRESS: Target precursors: 729 (91.12%)
0:24:06.233318 PROGRESS: Decoy precursors: 71 (8.88%)
0:24:06.233380 PROGRESS: 
0:24:06.233425 PROGRESS: Precursor Summary:
0:24:06.234514 PROGRESS: Channel   0:	 0.05 FDR:   580; 0.01 FDR:   425; 0.001 FDR:   278
0:24:06.235323 PROGRESS: 
0:24:06.235397 PROGRESS: Protein Summary:
0:24:06.236664 PROGRESS: Channel   0:	 0.05 FDR:   547; 0.01 FDR:   401; 0.001 FDR:   268
0:24:06.236754 PROGRESS: =========================================================================
0:24:06.382313 INFO: fragments_df: keeping 4605 of 1778432 [sum(precursor_idx_mask)=9247 sum(mass_error_mask)=1778432 stop_rank=4605
0:24:06.545063 INFO: calibration group: precursor, fitting rt estimator 
0:24:06.664412 INFO: calibration group: fragment, fitting mz estimator 
0:24:07.225952 INFO: Using score_cutoff 63.067561015319825 (fac=0.99, q=1)
0:24:07.226474 INFO: calibration group: precursor, predicting mz
0:24:07.226567 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:07.226610 INFO: calibration group: precursor, predicting rt
0:24:07.263069 INFO: calibration group: fragment, predicting mz
0:24:07.342585 INFO: === checking if optimization conditions were reached ===
0:24:07.342948 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
0:24:07.346005 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 12.4153.
0:24:07.346066 INFO: ==============================================
0:24:07.346168 INFO: Starting optimization step 16.
0:24:07.346243 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:07.346334 PROGRESS: Extracting batch of 50212 precursors
0:24:07.364563 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:24:07.364711 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:07.364751 INFO: FWHM in RT is 2.66 seconds, sigma is 0.34
0:24:07.364774 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:24:07.365141 INFO: Starting candidate selection
0:24:09.809026 INFO: Starting candidate scoring
0:24:10.429293 INFO: Finished candidate processing
0:24:10.429465 INFO: Collecting candidate features
0:24:10.583590 INFO: Collecting fragment features
0:24:10.645416 INFO: Finished candidate scoring
0:24:10.696119 PROGRESS: === Extracted 100199 precursors and 854287 fragments ===
0:24:10.696472 INFO: performing precursor FDR with 47 features
0:24:10.696512 INFO: Decoy channel: -1
0:24:10.696535 INFO: Competetive: True
0:24:10.724118 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:12.367698 INFO: Test AUC: 0.560
0:24:12.367818 INFO: Train AUC: 0.581
0:24:12.367847 INFO: AUC difference: 3.57%
0:24:12.589723 INFO: Resetting torch num_threads to 100
0:24:12.600420 INFO: === FDR correction performed with classifier version 7 ===
0:24:12.601080 PROGRESS: ============================= Precursor FDR =============================
0:24:12.601168 PROGRESS: Total precursors accumulated: 360
0:24:12.601229 PROGRESS: Target precursors: 328 (91.11%)
0:24:12.601280 PROGRESS: Decoy precursors: 32 (8.89%)
0:24:12.601328 PROGRESS: 
0:24:12.601370 PROGRESS: Precursor Summary:
0:24:12.602317 PROGRESS: Channel   0:	 0.05 FDR:   290; 0.01 FDR:   209; 0.001 FDR:   127
0:24:12.602405 PROGRESS: 
0:24:12.602461 PROGRESS: Protein Summary:
0:24:12.603546 PROGRESS: Channel   0:	 0.05 FDR:   275; 0.01 FDR:   197; 0.001 FDR:   125
0:24:12.603637 PROGRESS: =========================================================================
0:24:12.663766 INFO: fragments_df: keeping 2273 of 854287 [sum(precursor_idx_mask)=4497 sum(mass_error_mask)=854287 stop_rank=2273
0:24:12.837869 INFO: calibration group: precursor, fitting rt estimator 
0:24:13.864426 INFO: calibration group: fragment, fitting mz estimator 
0:24:14.164455 INFO: Using score_cutoff 63.100019558715815 (fac=0.99, q=1)
0:24:14.164907 INFO: calibration group: precursor, predicting mz
0:24:14.165000 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:14.165032 INFO: calibration group: precursor, predicting rt
0:24:14.197719 INFO: calibration group: fragment, predicting mz
0:24:14.264702 INFO: === checking if optimization conditions were reached ===
0:24:14.265009 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
0:24:14.267582 PROGRESS: ❌ ms2_error      : optimization incomplete after 7 search(es). Will search with parameter 10.4832.
0:24:14.267647 INFO: ==============================================
0:24:14.267747 INFO: Starting optimization step 17.
0:24:14.267825 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:14.267906 PROGRESS: Extracting batch of 50212 precursors
0:24:14.296592 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:24:14.296715 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:14.296762 INFO: FWHM in RT is 2.64 seconds, sigma is 0.34
0:24:14.296792 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:24:14.297156 INFO: Starting candidate selection
0:24:16.850806 INFO: Starting candidate scoring
0:24:17.550782 INFO: Finished candidate processing
0:24:17.550937 INFO: Collecting candidate features
0:24:17.750401 INFO: Collecting fragment features
0:24:17.811038 INFO: Finished candidate scoring
0:24:17.866012 PROGRESS: === Extracted 100195 precursors and 816228 fragments ===
0:24:17.866376 INFO: performing precursor FDR with 47 features
0:24:17.866415 INFO: Decoy channel: -1
0:24:17.866439 INFO: Competetive: True
0:24:17.896444 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:19.588186 INFO: Test AUC: 0.565
0:24:19.588305 INFO: Train AUC: 0.578
0:24:19.588334 INFO: AUC difference: 2.34%
0:24:19.790619 INFO: Resetting torch num_threads to 100
0:24:19.793524 INFO: === FDR correction performed with classifier version 7 ===
0:24:19.794166 PROGRESS: ============================= Precursor FDR =============================
0:24:19.794256 PROGRESS: Total precursors accumulated: 376
0:24:19.794313 PROGRESS: Target precursors: 341 (90.69%)
0:24:19.794368 PROGRESS: Decoy precursors: 35 (9.31%)
0:24:19.794414 PROGRESS: 
0:24:19.794457 PROGRESS: Precursor Summary:
0:24:19.795401 PROGRESS: Channel   0:	 0.05 FDR:   294; 0.01 FDR:   217; 0.001 FDR:    67
0:24:19.795491 PROGRESS: 
0:24:19.795545 PROGRESS: Protein Summary:
0:24:19.796604 PROGRESS: Channel   0:	 0.05 FDR:   277; 0.01 FDR:   207; 0.001 FDR:    67
0:24:19.796692 PROGRESS: =========================================================================
0:24:19.851008 INFO: fragments_df: keeping 2310 of 816228 [sum(precursor_idx_mask)=4579 sum(mass_error_mask)=816228 stop_rank=2310
0:24:19.978392 INFO: calibration group: precursor, fitting rt estimator 
0:24:20.091430 INFO: calibration group: fragment, fitting mz estimator 
0:24:20.395936 INFO: Using score_cutoff 58.393551914978026 (fac=0.99, q=1)
0:24:20.396315 INFO: calibration group: precursor, predicting mz
0:24:20.396398 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:20.396431 INFO: calibration group: precursor, predicting rt
0:24:20.427713 INFO: calibration group: fragment, predicting mz
0:24:20.492248 INFO: === checking if optimization conditions were reached ===
0:24:20.492517 PROGRESS: === Optimization of ms2_error has been performed 8 time(s); minimum number is 2 ===
0:24:20.494956 PROGRESS: ❌ ms2_error      : optimization incomplete after 8 search(es). Will search with parameter 9.3449.
0:24:20.495022 INFO: ==============================================
0:24:20.495126 INFO: Starting optimization step 18.
0:24:20.495200 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:20.495268 PROGRESS: Extracting batch of 50212 precursors
0:24:20.512127 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:24:20.512260 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:20.512299 INFO: FWHM in RT is 2.60 seconds, sigma is 0.34
0:24:20.512327 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:24:20.512555 INFO: Starting candidate selection
0:24:22.948983 INFO: Starting candidate scoring
0:24:23.580594 INFO: Finished candidate processing
0:24:23.580720 INFO: Collecting candidate features
0:24:23.741609 INFO: Collecting fragment features
0:24:23.802744 INFO: Finished candidate scoring
0:24:23.890686 PROGRESS: === Extracted 100188 precursors and 795250 fragments ===
0:24:23.891057 INFO: performing precursor FDR with 47 features
0:24:23.891098 INFO: Decoy channel: -1
0:24:23.891124 INFO: Competetive: True
0:24:23.926859 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:25.624679 INFO: Test AUC: 0.566
0:24:25.624870 INFO: Train AUC: 0.580
0:24:25.624902 INFO: AUC difference: 2.29%
0:24:25.847746 INFO: Resetting torch num_threads to 100
0:24:25.850724 INFO: === FDR correction performed with classifier version 7 ===
0:24:25.851402 PROGRESS: ============================= Precursor FDR =============================
0:24:25.851496 PROGRESS: Total precursors accumulated: 384
0:24:25.851554 PROGRESS: Target precursors: 351 (91.41%)
0:24:25.851604 PROGRESS: Decoy precursors: 33 (8.59%)
0:24:25.851651 PROGRESS: 
0:24:25.851695 PROGRESS: Precursor Summary:
0:24:25.852667 PROGRESS: Channel   0:	 0.05 FDR:   308; 0.01 FDR:   250; 0.001 FDR:    70
0:24:25.852758 PROGRESS: 
0:24:25.852813 PROGRESS: Protein Summary:
0:24:25.853899 PROGRESS: Channel   0:	 0.05 FDR:   291; 0.01 FDR:   237; 0.001 FDR:    69
0:24:25.853986 PROGRESS: =========================================================================
0:24:25.906935 INFO: fragments_df: keeping 2598 of 795250 [sum(precursor_idx_mask)=5198 sum(mass_error_mask)=795250 stop_rank=2598
0:24:26.049564 INFO: calibration group: precursor, fitting rt estimator 
0:24:26.168283 INFO: calibration group: fragment, fitting mz estimator 
0:24:26.508473 INFO: Using score_cutoff 56.68270114059448 (fac=0.99, q=1)
0:24:26.508927 INFO: calibration group: precursor, predicting mz
0:24:26.509012 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:26.509045 INFO: calibration group: precursor, predicting rt
0:24:26.540365 INFO: calibration group: fragment, predicting mz
0:24:26.612915 INFO: === checking if optimization conditions were reached ===
0:24:26.613199 PROGRESS: === Optimization of ms2_error has been performed 9 time(s); minimum number is 2 ===
0:24:26.615887 PROGRESS: ❌ ms2_error      : optimization incomplete after 9 search(es). Will search with parameter 8.4655.
0:24:26.615949 INFO: ==============================================
0:24:26.616057 INFO: Starting optimization step 19.
0:24:26.616131 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:26.616209 PROGRESS: Extracting batch of 50212 precursors
0:24:26.634293 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:24:26.634412 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:26.634456 INFO: FWHM in RT is 2.56 seconds, sigma is 0.33
0:24:26.634484 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:24:26.634835 INFO: Starting candidate selection
0:24:29.135740 INFO: Starting candidate scoring
0:24:29.840627 INFO: Finished candidate processing
0:24:29.840763 INFO: Collecting candidate features
0:24:30.024128 INFO: Collecting fragment features
0:24:30.095190 INFO: Finished candidate scoring
0:24:30.157266 PROGRESS: === Extracted 100172 precursors and 769582 fragments ===
0:24:30.157763 INFO: performing precursor FDR with 47 features
0:24:30.157804 INFO: Decoy channel: -1
0:24:30.157829 INFO: Competetive: True
0:24:30.200710 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:32.307794 INFO: Test AUC: 0.560
0:24:32.307959 INFO: Train AUC: 0.581
0:24:32.307990 INFO: AUC difference: 3.68%
0:24:32.517019 INFO: Resetting torch num_threads to 100
0:24:32.521544 INFO: === FDR correction performed with classifier version 7 ===
0:24:32.522308 PROGRESS: ============================= Precursor FDR =============================
0:24:32.522408 PROGRESS: Total precursors accumulated: 381
0:24:32.522470 PROGRESS: Target precursors: 347 (91.08%)
0:24:32.522527 PROGRESS: Decoy precursors: 34 (8.92%)
0:24:32.522576 PROGRESS: 
0:24:32.522628 PROGRESS: Precursor Summary:
0:24:32.523612 PROGRESS: Channel   0:	 0.05 FDR:   267; 0.01 FDR:    86; 0.001 FDR:    86
0:24:32.523705 PROGRESS: 
0:24:32.523762 PROGRESS: Protein Summary:
0:24:32.524829 PROGRESS: Channel   0:	 0.05 FDR:   254; 0.01 FDR:    86; 0.001 FDR:    86
0:24:32.524947 PROGRESS: =========================================================================
0:24:32.832006 INFO: calibration group: precursor, predicting mz
0:24:32.832357 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:32.832396 INFO: calibration group: precursor, predicting rt
0:24:32.865001 INFO: calibration group: fragment, predicting mz
0:24:32.935350 INFO: === skipping optimization until target number of precursors are found ===
0:24:32.935721 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:24:32.935780 WARNING: Optimization did not converge within the maximum number of steps, which is 20.
0:24:32.935914 INFO: Starting optimization step 0.
0:24:32.935986 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:24:32.936054 PROGRESS: Extracting batch of 50588 precursors
0:24:32.952220 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:24:32.952376 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:32.952412 INFO: FWHM in RT is 2.56 seconds, sigma is 0.33
0:24:32.952435 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:24:32.952708 INFO: Starting candidate selection
0:24:35.483025 INFO: Starting candidate scoring
0:24:36.128560 INFO: Finished candidate processing
0:24:36.128740 INFO: Collecting candidate features
0:24:36.395421 INFO: Collecting fragment features
0:24:36.512868 INFO: Finished candidate scoring
0:24:36.726440 PROGRESS: === Extracted 201124 precursors and 1544679 fragments ===
0:24:36.749495 INFO: performing precursor FDR with 47 features
0:24:36.749618 INFO: Decoy channel: -1
0:24:36.749645 INFO: Competetive: True
0:24:36.842203 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:40.494552 INFO: Test AUC: 0.562
0:24:40.494680 INFO: Train AUC: 0.582
0:24:40.494711 INFO: AUC difference: 3.39%
0:24:40.741899 INFO: Resetting torch num_threads to 100
0:24:40.750257 INFO: === FDR correction performed with classifier version 7 ===
0:24:40.751154 PROGRESS: ============================= Precursor FDR =============================
0:24:40.751272 PROGRESS: Total precursors accumulated: 909
0:24:40.751335 PROGRESS: Target precursors: 830 (91.31%)
0:24:40.751386 PROGRESS: Decoy precursors: 79 (8.69%)
0:24:40.751432 PROGRESS: 
0:24:40.751475 PROGRESS: Precursor Summary:
0:24:40.752626 PROGRESS: Channel   0:	 0.05 FDR:   683; 0.01 FDR:   564; 0.001 FDR:   239
0:24:40.752723 PROGRESS: 
0:24:40.752778 PROGRESS: Protein Summary:
0:24:40.754073 PROGRESS: Channel   0:	 0.05 FDR:   635; 0.01 FDR:   528; 0.001 FDR:   232
0:24:40.754173 PROGRESS: =========================================================================
0:24:40.868773 INFO: fragments_df: keeping 5000 of 1544679 [sum(precursor_idx_mask)=11708 sum(mass_error_mask)=1544679 stop_rank=5000
0:24:41.014314 INFO: calibration group: precursor, fitting rt estimator 
0:24:41.153877 INFO: calibration group: fragment, fitting mz estimator 
0:24:41.837470 INFO: Using score_cutoff 50.960692611694334 (fac=0.99, q=1)
0:24:41.837886 INFO: calibration group: precursor, predicting mz
0:24:41.837971 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:41.838003 INFO: calibration group: precursor, predicting rt
0:24:41.869484 INFO: calibration group: fragment, predicting mz
0:24:41.937095 INFO: === checking if optimization conditions were reached ===
0:24:41.937378 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:24:41.939701 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 226.5031.
0:24:41.939764 INFO: ==============================================
0:24:41.939871 INFO: Starting optimization step 1.
0:24:41.939944 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:41.940025 PROGRESS: Extracting batch of 50212 precursors
0:24:41.958112 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:24:41.958241 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:41.958285 INFO: FWHM in RT is 2.48 seconds, sigma is 0.32
0:24:41.958313 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:24:41.958594 INFO: Starting candidate selection
0:24:43.652165 INFO: Starting candidate scoring
0:24:44.292713 INFO: Finished candidate processing
0:24:44.292891 INFO: Collecting candidate features
0:24:44.512462 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 99731)
0:24:44.519676 INFO: Collecting fragment features
0:24:44.578735 INFO: Finished candidate scoring
0:24:44.687397 PROGRESS: === Extracted 99731 precursors and 716134 fragments ===
0:24:44.687871 INFO: performing precursor FDR with 47 features
0:24:44.687912 INFO: Decoy channel: -1
0:24:44.687943 INFO: Competetive: True
0:24:44.794729 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:44.832047 WARNING: dropped 1 target PSMs due to missing features
0:24:44.832218 WARNING: dropped 1 decoy PSMs due to missing features
0:24:47.333147 INFO: Test AUC: 0.552
0:24:47.333328 INFO: Train AUC: 0.574
0:24:47.333359 INFO: AUC difference: 3.70%
0:24:47.551374 INFO: Resetting torch num_threads to 100
0:24:47.555557 INFO: === FDR correction performed with classifier version 7 ===
0:24:47.556287 PROGRESS: ============================= Precursor FDR =============================
0:24:47.556384 PROGRESS: Total precursors accumulated: 380
0:24:47.556443 PROGRESS: Target precursors: 347 (91.32%)
0:24:47.556493 PROGRESS: Decoy precursors: 33 (8.68%)
0:24:47.556547 PROGRESS: 
0:24:47.556593 PROGRESS: Precursor Summary:
0:24:47.557533 PROGRESS: Channel   0:	 0.05 FDR:   299; 0.01 FDR:   229; 0.001 FDR:   131
0:24:47.557822 PROGRESS: 
0:24:47.557885 PROGRESS: Protein Summary:
0:24:47.558988 PROGRESS: Channel   0:	 0.05 FDR:   281; 0.01 FDR:   218; 0.001 FDR:   131
0:24:47.559084 PROGRESS: =========================================================================
0:24:47.609095 INFO: fragments_df: keeping 2383 of 716134 [sum(precursor_idx_mask)=4694 sum(mass_error_mask)=716134 stop_rank=2383
0:24:47.765032 INFO: calibration group: precursor, fitting rt estimator 
0:24:47.883287 INFO: calibration group: fragment, fitting mz estimator 
0:24:48.203535 INFO: Using score_cutoff 51.48614731750488 (fac=0.99, q=1)
0:24:48.203996 INFO: calibration group: precursor, predicting mz
0:24:48.204083 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:48.204115 INFO: calibration group: precursor, predicting rt
0:24:48.237897 INFO: calibration group: fragment, predicting mz
0:24:48.308902 INFO: === checking if optimization conditions were reached ===
0:24:48.309199 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:24:48.311514 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 89.7058.
0:24:48.311575 INFO: ==============================================
0:24:48.311681 INFO: Starting optimization step 2.
0:24:48.311757 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:48.311839 PROGRESS: Extracting batch of 50212 precursors
0:24:48.334031 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:24:48.334153 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:48.334199 INFO: FWHM in RT is 2.55 seconds, sigma is 0.33
0:24:48.334230 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:24:48.334521 INFO: Starting candidate selection
0:24:49.847754 INFO: Starting candidate scoring
0:24:50.487441 INFO: Finished candidate processing
0:24:50.487537 INFO: Collecting candidate features
0:24:50.650002 WARNING: intensity_correlation has 17 NaNs ( 0.02 % out of 98087)
0:24:50.656624 INFO: Collecting fragment features
0:24:50.710012 INFO: Finished candidate scoring
0:24:50.774321 PROGRESS: === Extracted 98087 precursors and 616168 fragments ===
0:24:50.774729 INFO: performing precursor FDR with 47 features
0:24:50.774770 INFO: Decoy channel: -1
0:24:50.774792 INFO: Competetive: True
0:24:50.812968 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:50.836377 WARNING: dropped 9 target PSMs due to missing features
0:24:50.836497 WARNING: dropped 8 decoy PSMs due to missing features
0:24:52.550975 INFO: Test AUC: 0.551
0:24:52.551104 INFO: Train AUC: 0.569
0:24:52.551134 INFO: AUC difference: 3.10%
0:24:52.760164 INFO: Resetting torch num_threads to 100
0:24:52.763787 INFO: === FDR correction performed with classifier version 7 ===
0:24:52.764467 PROGRESS: ============================= Precursor FDR =============================
0:24:52.764555 PROGRESS: Total precursors accumulated: 485
0:24:52.764613 PROGRESS: Target precursors: 445 (91.75%)
0:24:52.764662 PROGRESS: Decoy precursors: 40 (8.25%)
0:24:52.764706 PROGRESS: 
0:24:52.764749 PROGRESS: Precursor Summary:
0:24:52.765724 PROGRESS: Channel   0:	 0.05 FDR:   383; 0.01 FDR:   310; 0.001 FDR:   159
0:24:52.765813 PROGRESS: 
0:24:52.765867 PROGRESS: Protein Summary:
0:24:52.767007 PROGRESS: Channel   0:	 0.05 FDR:   363; 0.01 FDR:   292; 0.001 FDR:   155
0:24:52.767096 PROGRESS: =========================================================================
0:24:52.807452 INFO: fragments_df: keeping 2934 of 616168 [sum(precursor_idx_mask)=6202 sum(mass_error_mask)=616168 stop_rank=2934
0:24:52.938646 INFO: calibration group: precursor, fitting rt estimator 
0:24:53.061929 INFO: calibration group: fragment, fitting mz estimator 
0:24:53.455831 INFO: Using score_cutoff 47.74825862731933 (fac=0.99, q=1)
0:24:53.456241 INFO: calibration group: precursor, predicting mz
0:24:53.456324 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:53.456365 INFO: calibration group: precursor, predicting rt
0:24:53.487875 INFO: calibration group: fragment, predicting mz
0:24:53.556116 INFO: === checking if optimization conditions were reached ===
0:24:53.556392 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:24:53.558786 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 78.9906.
0:24:53.558852 INFO: ==============================================
0:24:53.558951 INFO: Starting optimization step 3.
0:24:53.559028 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:53.559101 PROGRESS: Extracting batch of 50212 precursors
0:24:53.579206 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:24:53.579334 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:53.579374 INFO: FWHM in RT is 2.47 seconds, sigma is 0.32
0:24:53.579405 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:24:53.579635 INFO: Starting candidate selection
0:24:55.477545 INFO: Starting candidate scoring
0:24:56.093210 INFO: Finished candidate processing
0:24:56.093346 INFO: Collecting candidate features
0:24:56.251473 WARNING: intensity_correlation has 20 NaNs ( 0.02 % out of 97692)
0:24:56.257960 INFO: Collecting fragment features
0:24:56.311832 INFO: Finished candidate scoring
0:24:56.379036 PROGRESS: === Extracted 97692 precursors and 606423 fragments ===
0:24:56.379421 INFO: performing precursor FDR with 47 features
0:24:56.379457 INFO: Decoy channel: -1
0:24:56.379478 INFO: Competetive: True
0:24:56.419777 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:56.447022 WARNING: dropped 10 target PSMs due to missing features
0:24:56.447140 WARNING: dropped 10 decoy PSMs due to missing features
0:24:58.258811 INFO: Test AUC: 0.545
0:24:58.259035 INFO: Train AUC: 0.572
0:24:58.259068 INFO: AUC difference: 4.62%
0:24:58.482950 INFO: Resetting torch num_threads to 100
0:24:58.486635 INFO: === FDR correction performed with classifier version 7 ===
0:24:58.487354 PROGRESS: ============================= Precursor FDR =============================
0:24:58.487450 PROGRESS: Total precursors accumulated: 492
0:24:58.487508 PROGRESS: Target precursors: 450 (91.46%)
0:24:58.487558 PROGRESS: Decoy precursors: 42 (8.54%)
0:24:58.487607 PROGRESS: 
0:24:58.487650 PROGRESS: Precursor Summary:
0:24:58.488635 PROGRESS: Channel   0:	 0.05 FDR:   369; 0.01 FDR:   311; 0.001 FDR:   142
0:24:58.488731 PROGRESS: 
0:24:58.488785 PROGRESS: Protein Summary:
0:24:58.489897 PROGRESS: Channel   0:	 0.05 FDR:   350; 0.01 FDR:   293; 0.001 FDR:   139
0:24:58.489983 PROGRESS: =========================================================================
0:24:58.534791 INFO: fragments_df: keeping 2946 of 606423 [sum(precursor_idx_mask)=6231 sum(mass_error_mask)=606423 stop_rank=2946
0:24:58.693546 INFO: calibration group: precursor, fitting rt estimator 
0:24:58.820845 INFO: calibration group: fragment, fitting mz estimator 
0:24:59.216201 INFO: Using score_cutoff 49.30755341720581 (fac=0.99, q=1)
0:24:59.216614 INFO: calibration group: precursor, predicting mz
0:24:59.216699 WARNING: mz prediction was skipped as it has not been fitted yet
0:24:59.216730 INFO: calibration group: precursor, predicting rt
0:24:59.248474 INFO: calibration group: fragment, predicting mz
0:24:59.326176 INFO: === checking if optimization conditions were reached ===
0:24:59.326556 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:24:59.329001 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 74.6870.
0:24:59.329062 INFO: ==============================================
0:24:59.329167 INFO: Starting optimization step 4.
0:24:59.329240 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:59.329315 PROGRESS: Extracting batch of 50212 precursors
0:24:59.346264 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:24:59.346407 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:59.347353 INFO: FWHM in RT is 2.44 seconds, sigma is 0.31
0:24:59.347390 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:24:59.347743 INFO: Starting candidate selection
0:25:01.325769 INFO: Starting candidate scoring
0:25:01.979548 INFO: Finished candidate processing
0:25:01.979704 INFO: Collecting candidate features
0:25:02.148392 WARNING: intensity_correlation has 21 NaNs ( 0.02 % out of 97614)
0:25:02.154912 INFO: Collecting fragment features
0:25:02.213331 INFO: Finished candidate scoring
0:25:02.272444 PROGRESS: === Extracted 97614 precursors and 602578 fragments ===
0:25:02.272808 INFO: performing precursor FDR with 47 features
0:25:02.272848 INFO: Decoy channel: -1
0:25:02.272871 INFO: Competetive: True
0:25:02.308647 INFO: Setting torch num_threads to 2 for FDR classification task
0:25:02.331057 WARNING: dropped 9 target PSMs due to missing features
0:25:02.331177 WARNING: dropped 12 decoy PSMs due to missing features
0:25:04.024444 INFO: Test AUC: 0.549
0:25:04.024562 INFO: Train AUC: 0.570
0:25:04.024599 INFO: AUC difference: 3.69%
0:25:04.242152 INFO: Resetting torch num_threads to 100
0:25:04.245635 INFO: === FDR correction performed with classifier version 7 ===
0:25:04.246318 PROGRESS: ============================= Precursor FDR =============================
0:25:04.246408 PROGRESS: Total precursors accumulated: 483
0:25:04.246468 PROGRESS: Target precursors: 440 (91.10%)
0:25:04.246520 PROGRESS: Decoy precursors: 43 (8.90%)
0:25:04.246565 PROGRESS: 
0:25:04.246616 PROGRESS: Precursor Summary:
0:25:04.247609 PROGRESS: Channel   0:	 0.05 FDR:   370; 0.01 FDR:   325; 0.001 FDR:   307
0:25:04.247696 PROGRESS: 
0:25:04.247753 PROGRESS: Protein Summary:
0:25:04.248907 PROGRESS: Channel   0:	 0.05 FDR:   351; 0.01 FDR:   308; 0.001 FDR:   291
0:25:04.248994 PROGRESS: =========================================================================
0:25:04.291675 INFO: fragments_df: keeping 3049 of 602578 [sum(precursor_idx_mask)=6486 sum(mass_error_mask)=602578 stop_rank=3049
0:25:04.422033 INFO: calibration group: precursor, fitting rt estimator 
0:25:04.550204 INFO: calibration group: fragment, fitting mz estimator 
0:25:04.958428 INFO: Using score_cutoff 47.254952334594726 (fac=0.99, q=1)
0:25:04.958841 INFO: calibration group: precursor, predicting mz
0:25:04.958931 WARNING: mz prediction was skipped as it has not been fitted yet
0:25:04.958962 INFO: calibration group: precursor, predicting rt
0:25:04.990830 INFO: calibration group: fragment, predicting mz
0:25:05.057251 INFO: === checking if optimization conditions were reached ===
0:25:05.057490 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:25:05.059602 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 70.5415.
0:25:05.059658 INFO: ==============================================
0:25:05.059746 INFO: Starting optimization step 5.
0:25:05.059811 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:25:05.059868 PROGRESS: Extracting batch of 50212 precursors
0:25:05.078103 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:25:05.078206 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:25:05.078239 INFO: FWHM in RT is 2.45 seconds, sigma is 0.32
0:25:05.078263 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:25:05.078450 INFO: Starting candidate selection
0:25:07.136179 INFO: Starting candidate scoring
0:25:07.787634 INFO: Finished candidate processing
0:25:07.787788 INFO: Collecting candidate features
0:25:07.978257 WARNING: intensity_correlation has 16 NaNs ( 0.02 % out of 97656)
0:25:07.986585 INFO: Collecting fragment features
0:25:08.044407 INFO: Finished candidate scoring
0:25:08.111487 PROGRESS: === Extracted 97656 precursors and 602295 fragments ===
0:25:08.111928 INFO: performing precursor FDR with 47 features
0:25:08.111967 INFO: Decoy channel: -1
0:25:08.111996 INFO: Competetive: True
0:25:08.160050 INFO: Setting torch num_threads to 2 for FDR classification task
0:25:08.181162 WARNING: dropped 6 target PSMs due to missing features
0:25:08.181291 WARNING: dropped 10 decoy PSMs due to missing features
0:25:09.883934 INFO: Test AUC: 0.556
0:25:09.884073 INFO: Train AUC: 0.568
0:25:09.884103 INFO: AUC difference: 2.08%
0:25:10.101122 INFO: Resetting torch num_threads to 100
0:25:10.104978 INFO: === FDR correction performed with classifier version 7 ===
0:25:10.105715 PROGRESS: ============================= Precursor FDR =============================
0:25:10.105806 PROGRESS: Total precursors accumulated: 475
0:25:10.105868 PROGRESS: Target precursors: 434 (91.37%)
0:25:10.105922 PROGRESS: Decoy precursors: 41 (8.63%)
0:25:10.105969 PROGRESS: 
0:25:10.106012 PROGRESS: Precursor Summary:
0:25:10.107018 PROGRESS: Channel   0:	 0.05 FDR:   348; 0.01 FDR:   308; 0.001 FDR:   214
0:25:10.107120 PROGRESS: 
0:25:10.107177 PROGRESS: Protein Summary:
0:25:10.108398 PROGRESS: Channel   0:	 0.05 FDR:   331; 0.01 FDR:   292; 0.001 FDR:   203
0:25:10.108490 PROGRESS: =========================================================================
0:25:10.150756 INFO: fragments_df: keeping 2933 of 602295 [sum(precursor_idx_mask)=6131 sum(mass_error_mask)=602295 stop_rank=2933
0:25:10.287231 INFO: calibration group: precursor, fitting rt estimator 
0:25:11.539137 INFO: calibration group: fragment, fitting mz estimator 
0:25:11.935792 INFO: Using score_cutoff 39.98853270263672 (fac=0.99, q=1)
0:25:11.936193 INFO: calibration group: precursor, predicting mz
0:25:11.936278 WARNING: mz prediction was skipped as it has not been fitted yet
0:25:11.936311 INFO: calibration group: precursor, predicting rt
0:25:11.967783 INFO: calibration group: fragment, predicting mz
0:25:12.029893 INFO: === checking if optimization conditions were reached ===
0:25:12.030164 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:25:12.032561 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 71.9818.
0:25:12.032630 INFO: ==============================================
0:25:12.032739 INFO: Starting optimization step 6.
0:25:12.032823 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:25:12.032904 PROGRESS: Extracting batch of 50212 precursors
0:25:12.055162 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:25:12.055301 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:25:12.055346 INFO: FWHM in RT is 2.46 seconds, sigma is 0.32
0:25:12.055376 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:25:12.055648 INFO: Starting candidate selection
0:25:14.058690 INFO: Starting candidate scoring
0:25:14.685313 INFO: Finished candidate processing
0:25:14.685409 INFO: Collecting candidate features
0:25:14.835993 WARNING: intensity_correlation has 18 NaNs ( 0.02 % out of 97646)
0:25:14.842825 INFO: Collecting fragment features
0:25:14.894891 INFO: Finished candidate scoring
0:25:14.958266 PROGRESS: === Extracted 97646 precursors and 603039 fragments ===
0:25:14.958743 INFO: performing precursor FDR with 47 features
0:25:14.958788 INFO: Decoy channel: -1
0:25:14.958812 INFO: Competetive: True
0:25:14.993047 INFO: Setting torch num_threads to 2 for FDR classification task
0:25:15.014541 WARNING: dropped 7 target PSMs due to missing features
0:25:15.014732 WARNING: dropped 11 decoy PSMs due to missing features
0:25:17.079319 INFO: Test AUC: 0.555
0:25:17.079529 INFO: Train AUC: 0.566
0:25:17.079561 INFO: AUC difference: 2.06%
0:25:17.305321 INFO: Resetting torch num_threads to 100
0:25:17.309413 INFO: === FDR correction performed with classifier version 7 ===
0:25:17.310198 PROGRESS: ============================= Precursor FDR =============================
0:25:17.310298 PROGRESS: Total precursors accumulated: 506
0:25:17.310357 PROGRESS: Target precursors: 460 (90.91%)
0:25:17.310406 PROGRESS: Decoy precursors: 46 (9.09%)
0:25:17.310455 PROGRESS: 
0:25:17.310499 PROGRESS: Precursor Summary:
0:25:17.311518 PROGRESS: Channel   0:	 0.05 FDR:   382; 0.01 FDR:   319; 0.001 FDR:   288
0:25:17.311612 PROGRESS: 
0:25:17.311674 PROGRESS: Protein Summary:
0:25:17.312850 PROGRESS: Channel   0:	 0.05 FDR:   363; 0.01 FDR:   303; 0.001 FDR:   273
0:25:17.312941 PROGRESS: =========================================================================
0:25:17.357767 INFO: fragments_df: keeping 2989 of 603039 [sum(precursor_idx_mask)=6379 sum(mass_error_mask)=603039 stop_rank=2989
0:25:17.528091 INFO: calibration group: precursor, fitting rt estimator 
0:25:17.657144 INFO: calibration group: fragment, fitting mz estimator 
0:25:18.059846 INFO: Using score_cutoff 47.83683753890991 (fac=0.99, q=1)
0:25:18.060283 INFO: calibration group: precursor, predicting mz
0:25:18.060369 WARNING: mz prediction was skipped as it has not been fitted yet
0:25:18.060402 INFO: calibration group: precursor, predicting rt
0:25:18.091711 INFO: calibration group: fragment, predicting mz
0:25:18.162195 INFO: === checking if optimization conditions were reached ===
0:25:18.162516 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:25:18.164171 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 70.5415 found after 7 searches.
0:25:18.164232 INFO: ==============================================
0:25:18.164339 PROGRESS: Optimization finished for rt_error.
0:25:18.305033 INFO: calibration group: precursor, predicting mz
0:25:18.305279 WARNING: mz prediction was skipped as it has not been fitted yet
0:25:18.305314 INFO: calibration group: precursor, predicting rt
0:25:18.336645 INFO: calibration group: fragment, predicting mz
0:25:18.437572 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:25:18.437800 PROGRESS: ==============================================
0:25:18.437885 PROGRESS: ms2_error      : 8.4655
0:25:18.437948 PROGRESS: rt_error       : 70.5415
0:25:18.438006 PROGRESS: ==============================================
0:25:18.439827 INFO: calibration group: precursor, predicting mz
0:25:18.439955 WARNING: mz prediction was skipped as it has not been fitted yet
0:25:18.439993 INFO: calibration group: precursor, predicting rt
0:25:24.943110 INFO: calibration group: fragment, predicting mz
0:25:39.251734 PROGRESS: Extracting batch of 10183864 precursors
0:25:41.922381 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:25:41.922525 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:25:41.922567 INFO: FWHM in RT is 2.46 seconds, sigma is 0.32
0:25:41.922591 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:25:41.923479 INFO: Starting candidate selection
0:32:03.366509 INFO: Applying score cutoff of 39.98853270263672
0:32:03.570743 INFO: Removed 15246770 precursors with score below cutoff
0:32:05.778481 INFO: Starting candidate scoring
0:32:41.308611 INFO: Finished candidate processing
0:32:41.308920 INFO: Collecting candidate features
0:32:52.187640 WARNING: intensity_correlation has 7 NaNs ( 0.00 % out of 5058857)
0:32:52.355057 INFO: Collecting fragment features
0:32:56.151072 INFO: Finished candidate scoring
0:33:01.732260 INFO: === FDR correction performed with classifier version 25 ===
0:33:01.734576 INFO: performing precursor FDR with 47 features
0:33:01.734654 INFO: Decoy channel: -1
0:33:01.734684 INFO: Competetive: True
0:33:03.190612 INFO: Setting torch num_threads to 2 for FDR classification task
0:33:04.112062 WARNING: dropped 2 target PSMs due to missing features
0:33:04.112200 WARNING: dropped 5 decoy PSMs due to missing features
0:34:34.600075 INFO: Test AUC: 0.604
0:34:34.600307 INFO: Train AUC: 0.613
0:34:34.600342 INFO: AUC difference: 1.36%
0:34:36.120208 INFO: Resetting torch num_threads to 100
0:34:36.416477 INFO: Removing fragments below FDR threshold
0:34:36.873013 PROGRESS: ============================= Precursor FDR =============================
0:34:36.873319 PROGRESS: Total precursors accumulated: 77,099
0:34:36.873387 PROGRESS: Target precursors: 76,336 (99.01%)
0:34:36.873440 PROGRESS: Decoy precursors: 763 (0.99%)
0:34:36.873490 PROGRESS: 
0:34:36.873537 PROGRESS: Precursor Summary:
0:34:36.906379 PROGRESS: Channel   0:	 0.05 FDR: 76,336; 0.01 FDR: 76,336; 0.001 FDR: 52,138
0:34:36.906656 PROGRESS: 
0:34:36.906722 PROGRESS: Protein Summary:
0:34:36.956633 PROGRESS: Channel   0:	 0.05 FDR: 11,756; 0.01 FDR: 11,756; 0.001 FDR: 9,030
0:34:36.956875 PROGRESS: =========================================================================
0:34:37.663515 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:34:38.154729 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:34:38.154935 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant
0:34:38.155032 INFO: Creating folder run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/figures
0:34:38.156061 INFO: Initializing RawFileManager
0:34:49.848059 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.
0:34:49.852599 INFO: Determining DIA cycle
0:34:49.868985 INFO: Found cycle with start 0.00 min and length 300.
0:34:50.034555 INFO: RT (min)            : 0.0 - 26.9
0:34:50.034651 INFO: RT duration (sec)   : 1611.2
0:34:50.034682 INFO: RT duration (min)   : 26.9
0:34:50.034705 INFO: Cycle len (scans)   : 300
0:34:50.034725 INFO: Cycle len (sec)     : 1.65
0:34:50.034743 INFO: Number of cycles    : 978
0:34:50.034761 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:34:51.356614 INFO: Initializing CalibrationManager
0:34:51.357041 INFO: Loading calibration config
0:34:51.358863 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'}]
0:34:51.358970 INFO: Calibration group :fragment, found 1 estimator(s)
0:34:51.359060 INFO: Calibration group :precursor, found 3 estimator(s)
0:34:51.359149 INFO: Disabling ion mobility calibration
0:34:51.359179 INFO: removed mobility estimator from group precursor
0:34:51.359524 INFO: Initializing OptimizationManager
0:34:51.359644 INFO: initial parameter: ms1_error = 30
0:34:51.359706 INFO: initial parameter: ms2_error = 30
0:34:51.359758 INFO: initial parameter: rt_error = 805.6019897460938
0:34:51.359803 INFO: initial parameter: mobility_error = 0.1
0:34:51.359848 INFO: initial parameter: column_type = library
0:34:51.359890 INFO: initial parameter: num_candidates = 1
0:34:51.359934 INFO: initial parameter: classifier_version = -1
0:34:51.359976 INFO: initial parameter: fwhm_rt = 5
0:34:51.360017 INFO: initial parameter: fwhm_mobility = 0.01
0:34:51.360058 INFO: initial parameter: score_cutoff = 0
0:34:51.360127 INFO: Initializing TimingManager
0:34:51.360199 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:34:51.360327 INFO: FDRManager not loaded from disk.
0:34:51.360351 INFO: Initializing FDRManager
0:34:51.360391 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:34:52.637798 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
0:34:54.453214 PROGRESS: Starting initial search for precursors.
0:34:54.672705 INFO: Starting optimization step 0.
0:34:54.672911 PROGRESS: === Extracting elution groups 0 to 200 ===
0:34:54.672984 PROGRESS: Extracting batch of 395 precursors
0:34:54.673969 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:34:54.674014 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:34:54.674048 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:34:54.674070 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:34:54.674350 INFO: Starting candidate selection
0:34:54.855470 INFO: Starting candidate scoring
0:34:54.891710 INFO: Finished candidate processing
0:34:54.891802 INFO: Collecting candidate features
0:34:54.900553 INFO: Collecting fragment features
0:34:54.902588 INFO: Finished candidate scoring
0:34:54.903411 PROGRESS: === Extracted 395 precursors and 3921 fragments ===
0:34:54.903682 INFO: performing precursor FDR with 47 features
0:34:54.903718 INFO: Decoy channel: -1
0:34:54.903741 INFO: Competetive: True
0:34:54.904729 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:54.922129 INFO: Test AUC: 0.522
0:34:54.922193 INFO: Train AUC: 0.481
0:34:54.922222 INFO: AUC difference: 8.55%
0:34:54.922245 WARNING: AUC difference > 5%. This may indicate overfitting.
0:34:55.096783 INFO: Resetting torch num_threads to 100
0:34:55.097310 INFO: === FDR correction performed with classifier version -1 ===
0:34:55.097925 PROGRESS: ============================= Precursor FDR =============================
0:34:55.098016 PROGRESS: Total precursors accumulated: 10
0:34:55.098076 PROGRESS: Target precursors: 10 (100.00%)
0:34:55.098128 PROGRESS: Decoy precursors: 0 (0.00%)
0:34:55.098173 PROGRESS: 
0:34:55.098218 PROGRESS: Precursor Summary:
0:34:55.099161 PROGRESS: Channel   0:	 0.05 FDR:    10; 0.01 FDR:    10; 0.001 FDR:    10
0:34:55.099253 PROGRESS: 
0:34:55.099309 PROGRESS: Protein Summary:
0:34:55.100320 PROGRESS: Channel   0:	 0.05 FDR:    10; 0.01 FDR:    10; 0.001 FDR:    10
0:34:55.100417 PROGRESS: =========================================================================
0:34:55.155747 INFO: Starting optimization step 1.
0:34:55.155921 PROGRESS: === Extracting elution groups 200 to 600 ===
0:34:55.155989 PROGRESS: Extracting batch of 790 precursors
0:34:55.156815 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:34:55.156867 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:34:55.156898 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:34:55.156919 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:34:55.157081 INFO: Starting candidate selection
0:34:55.318731 INFO: Starting candidate scoring
0:34:55.353215 INFO: Finished candidate processing
0:34:55.353288 INFO: Collecting candidate features
0:34:55.362093 INFO: Collecting fragment features
0:34:55.364408 INFO: Finished candidate scoring
0:34:55.366293 PROGRESS: === Extracted 1183 precursors and 11881 fragments ===
0:34:55.367015 INFO: performing precursor FDR with 47 features
0:34:55.367058 INFO: Decoy channel: -1
0:34:55.367082 INFO: Competetive: True
0:34:55.369789 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:55.387928 INFO: Test AUC: 0.491
0:34:55.387990 INFO: Train AUC: 0.496
0:34:55.388020 INFO: AUC difference: 1.05%
0:34:55.560050 INFO: Resetting torch num_threads to 100
0:34:55.560649 INFO: === FDR correction performed with classifier version -1 ===
0:34:55.561274 PROGRESS: ============================= Precursor FDR =============================
0:34:55.561365 PROGRESS: Total precursors accumulated: 1
0:34:55.561426 PROGRESS: Target precursors: 1 (100.00%)
0:34:55.561478 PROGRESS: Decoy precursors: 0 (0.00%)
0:34:55.561524 PROGRESS: 
0:34:55.561570 PROGRESS: Precursor Summary:
0:34:55.562495 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:34:55.562582 PROGRESS: 
0:34:55.562654 PROGRESS: Protein Summary:
0:34:55.563668 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:34:55.563766 PROGRESS: =========================================================================
0:34:55.620945 INFO: Starting optimization step 2.
0:34:55.621130 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:34:55.621199 PROGRESS: Extracting batch of 1585 precursors
0:34:55.622468 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:34:55.622521 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:34:55.622551 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:34:55.622572 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:34:55.622750 INFO: Starting candidate selection
0:34:55.803255 INFO: Starting candidate scoring
0:34:55.840778 INFO: Finished candidate processing
0:34:55.840857 INFO: Collecting candidate features
0:34:55.850878 INFO: Collecting fragment features
0:34:55.854309 INFO: Finished candidate scoring
0:34:55.857255 PROGRESS: === Extracted 2762 precursors and 27874 fragments ===
0:34:55.858226 INFO: performing precursor FDR with 47 features
0:34:55.858270 INFO: Decoy channel: -1
0:34:55.858296 INFO: Competetive: True
0:34:55.861429 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:55.899782 INFO: Test AUC: 0.513
0:34:55.899860 INFO: Train AUC: 0.491
0:34:55.899892 INFO: AUC difference: 4.49%
0:34:56.067200 INFO: Resetting torch num_threads to 100
0:34:56.067966 INFO: === FDR correction performed with classifier version -1 ===
0:34:56.068711 PROGRESS: ============================= Precursor FDR =============================
0:34:56.068806 PROGRESS: Total precursors accumulated: 1,396
0:34:56.068872 PROGRESS: Target precursors: 684 (49.00%)
0:34:56.068931 PROGRESS: Decoy precursors: 712 (51.00%)
0:34:56.068984 PROGRESS: 
0:34:56.069036 PROGRESS: Precursor Summary:
0:34:56.069924 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:34:56.070017 PROGRESS: 
0:34:56.070079 PROGRESS: Protein Summary:
0:34:56.071061 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:34:56.071156 PROGRESS: =========================================================================
0:34:56.131196 INFO: Starting optimization step 3.
0:34:56.131396 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:34:56.131470 PROGRESS: Extracting batch of 3157 precursors
0:34:56.132691 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:34:56.132749 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:34:56.132785 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:34:56.132810 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:34:56.132979 INFO: Starting candidate selection
0:34:56.376041 INFO: Starting candidate scoring
0:34:56.415052 INFO: Finished candidate processing
0:34:56.415139 INFO: Collecting candidate features
0:34:56.428069 INFO: Collecting fragment features
0:34:56.432255 INFO: Finished candidate scoring
0:34:56.436438 PROGRESS: === Extracted 5917 precursors and 59981 fragments ===
0:34:56.438622 INFO: performing precursor FDR with 47 features
0:34:56.438675 INFO: Decoy channel: -1
0:34:56.438702 INFO: Competetive: True
0:34:56.442652 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:56.495020 INFO: Test AUC: 0.485
0:34:56.495116 INFO: Train AUC: 0.492
0:34:56.495148 INFO: AUC difference: 1.55%
0:34:56.665378 INFO: Resetting torch num_threads to 100
0:34:56.666284 INFO: === FDR correction performed with classifier version -1 ===
0:34:56.667235 PROGRESS: ============================= Precursor FDR =============================
0:34:56.667336 PROGRESS: Total precursors accumulated: 2,995
0:34:56.667403 PROGRESS: Target precursors: 1,462 (48.81%)
0:34:56.667460 PROGRESS: Decoy precursors: 1,533 (51.19%)
0:34:56.667515 PROGRESS: 
0:34:56.667568 PROGRESS: Precursor Summary:
0:34:56.668468 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:34:56.668562 PROGRESS: 
0:34:56.668623 PROGRESS: Protein Summary:
0:34:56.669576 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:34:56.669669 PROGRESS: =========================================================================
0:34:56.733738 INFO: Starting optimization step 4.
0:34:56.733937 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:34:56.734015 PROGRESS: Extracting batch of 6336 precursors
0:34:56.735632 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:34:56.735687 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:34:56.735723 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:34:56.735748 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:34:56.735914 INFO: Starting candidate selection
0:34:57.077247 INFO: Starting candidate scoring
0:34:57.124949 INFO: Finished candidate processing
0:34:57.125041 INFO: Collecting candidate features
0:34:57.143657 INFO: Collecting fragment features
0:34:57.150529 INFO: Finished candidate scoring
0:34:57.157897 PROGRESS: === Extracted 12238 precursors and 124540 fragments ===
0:34:57.159722 INFO: performing precursor FDR with 47 features
0:34:57.159778 INFO: Decoy channel: -1
0:34:57.159801 INFO: Competetive: True
0:34:57.165715 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:57.249583 INFO: Test AUC: 0.504
0:34:57.249692 INFO: Train AUC: 0.492
0:34:57.249723 INFO: AUC difference: 2.55%
0:34:57.427002 INFO: Resetting torch num_threads to 100
0:34:57.428231 INFO: === FDR correction performed with classifier version -1 ===
0:34:57.429534 PROGRESS: ============================= Precursor FDR =============================
0:34:57.429628 PROGRESS: Total precursors accumulated: 6,188
0:34:57.429710 PROGRESS: Target precursors: 3,088 (49.90%)
0:34:57.429780 PROGRESS: Decoy precursors: 3,100 (50.10%)
0:34:57.429850 PROGRESS: 
0:34:57.429921 PROGRESS: Precursor Summary:
0:34:57.431100 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:34:57.431200 PROGRESS: 
0:34:57.431258 PROGRESS: Protein Summary:
0:34:57.432341 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:34:57.432443 PROGRESS: =========================================================================
0:34:57.505473 INFO: Starting optimization step 5.
0:34:57.505685 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:34:57.505753 PROGRESS: Extracting batch of 12662 precursors
0:34:57.508248 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:34:57.508299 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:34:57.508331 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:34:57.508351 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:34:57.508515 INFO: Starting candidate selection
0:34:58.341501 INFO: Starting candidate scoring
0:34:58.449672 INFO: Finished candidate processing
0:34:58.449769 INFO: Collecting candidate features
0:34:58.478112 INFO: Collecting fragment features
0:34:58.490688 INFO: Finished candidate scoring
0:34:58.504245 PROGRESS: === Extracted 24888 precursors and 253561 fragments ===
0:34:58.507576 INFO: performing precursor FDR with 47 features
0:34:58.507646 INFO: Decoy channel: -1
0:34:58.507670 INFO: Competetive: True
0:34:58.516823 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:58.782081 INFO: Test AUC: 0.521
0:34:58.782186 INFO: Train AUC: 0.525
0:34:58.782215 INFO: AUC difference: 0.73%
0:34:58.963013 INFO: Resetting torch num_threads to 100
0:34:58.964712 INFO: === FDR correction performed with classifier version -1 ===
0:34:58.965375 PROGRESS: ============================= Precursor FDR =============================
0:34:58.965469 PROGRESS: Total precursors accumulated: 1
0:34:58.965528 PROGRESS: Target precursors: 1 (100.00%)
0:34:58.965580 PROGRESS: Decoy precursors: 0 (0.00%)
0:34:58.965627 PROGRESS: 
0:34:58.965673 PROGRESS: Precursor Summary:
0:34:58.966611 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:34:58.966699 PROGRESS: 
0:34:58.966754 PROGRESS: Protein Summary:
0:34:58.967788 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:34:58.967877 PROGRESS: =========================================================================
0:34:59.056749 INFO: Starting optimization step 6.
0:34:59.056997 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:34:59.057067 PROGRESS: Extracting batch of 25287 precursors
0:34:59.062697 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:34:59.062783 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:34:59.062818 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:34:59.062839 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:34:59.063025 INFO: Starting candidate selection
0:35:00.656402 INFO: Starting candidate scoring
0:35:00.842124 INFO: Finished candidate processing
0:35:00.842259 INFO: Collecting candidate features
0:35:00.899355 INFO: Collecting fragment features
0:35:00.920008 INFO: Finished candidate scoring
0:35:00.969037 PROGRESS: === Extracted 50105 precursors and 510557 fragments ===
0:35:00.978664 INFO: performing precursor FDR with 47 features
0:35:00.978803 INFO: Decoy channel: -1
0:35:00.978829 INFO: Competetive: True
0:35:01.007455 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:01.994352 INFO: Test AUC: 0.563
0:35:01.994515 INFO: Train AUC: 0.571
0:35:01.994546 INFO: AUC difference: 1.36%
0:35:02.198936 INFO: Resetting torch num_threads to 100
0:35:02.203700 INFO: === FDR correction performed with classifier version -1 ===
0:35:02.204418 PROGRESS: ============================= Precursor FDR =============================
0:35:02.204518 PROGRESS: Total precursors accumulated: 178
0:35:02.204579 PROGRESS: Target precursors: 162 (91.01%)
0:35:02.204631 PROGRESS: Decoy precursors: 16 (8.99%)
0:35:02.204677 PROGRESS: 
0:35:02.204721 PROGRESS: Precursor Summary:
0:35:02.205681 PROGRESS: Channel   0:	 0.05 FDR:   136; 0.01 FDR:    66; 0.001 FDR:    66
0:35:02.205776 PROGRESS: 
0:35:02.205832 PROGRESS: Protein Summary:
0:35:02.206884 PROGRESS: Channel   0:	 0.05 FDR:   135; 0.01 FDR:    66; 0.001 FDR:    66
0:35:02.206983 PROGRESS: =========================================================================
0:35:02.366886 INFO: Starting optimization step 7.
0:35:02.367232 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:35:02.367335 PROGRESS: Extracting batch of 50588 precursors
0:35:02.384987 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:35:02.385144 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:02.385180 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:35:02.385203 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:35:02.385475 INFO: Starting candidate selection
0:35:05.624479 INFO: Starting candidate scoring
0:35:05.971811 INFO: Finished candidate processing
0:35:05.971911 INFO: Collecting candidate features
0:35:06.063533 INFO: Collecting fragment features
0:35:06.101302 INFO: Finished candidate scoring
0:35:06.191803 PROGRESS: === Extracted 100595 precursors and 1025422 fragments ===
0:35:06.204181 INFO: performing precursor FDR with 47 features
0:35:06.204270 INFO: Decoy channel: -1
0:35:06.204297 INFO: Competetive: True
0:35:06.246104 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:07.952628 INFO: Test AUC: 0.560
0:35:07.952752 INFO: Train AUC: 0.580
0:35:07.952781 INFO: AUC difference: 3.47%
0:35:08.161018 INFO: Resetting torch num_threads to 100
0:35:08.166397 INFO: === FDR correction performed with classifier version -1 ===
0:35:08.167129 PROGRESS: ============================= Precursor FDR =============================
0:35:08.167233 PROGRESS: Total precursors accumulated: 493
0:35:08.167295 PROGRESS: Target precursors: 451 (91.48%)
0:35:08.167352 PROGRESS: Decoy precursors: 42 (8.52%)
0:35:08.167401 PROGRESS: 
0:35:08.167449 PROGRESS: Precursor Summary:
0:35:08.168441 PROGRESS: Channel   0:	 0.05 FDR:   381; 0.01 FDR:   257; 0.001 FDR:   211
0:35:08.168533 PROGRESS: 
0:35:08.168589 PROGRESS: Protein Summary:
0:35:08.169741 PROGRESS: Channel   0:	 0.05 FDR:   362; 0.01 FDR:   245; 0.001 FDR:   202
0:35:08.169837 PROGRESS: =========================================================================
0:35:08.241844 INFO: fragments_df: keeping 2410 of 1025422 [sum(precursor_idx_mask)=2956 sum(mass_error_mask)=1025422 stop_rank=2410
0:35:08.447787 INFO: calibration group: precursor, fitting rt estimator 
0:35:08.612276 INFO: calibration group: fragment, fitting mz estimator 
0:35:08.928467 INFO: Using score_cutoff 75.22741230468749 (fac=0.99, q=1)
0:35:08.928880 INFO: calibration group: precursor, predicting mz
0:35:08.928972 WARNING: mz prediction was skipped as it has not been fitted yet
0:35:08.929002 INFO: calibration group: precursor, predicting rt
0:35:08.990606 INFO: calibration group: fragment, predicting mz
0:35:09.142132 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:35:09.142433 INFO: Starting optimization step 8.
0:35:09.142514 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:35:09.142598 PROGRESS: Extracting batch of 100800 precursors
0:35:09.177179 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:35:09.177320 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:09.177366 INFO: FWHM in RT is 3.12 seconds, sigma is 0.40
0:35:09.177394 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:35:09.177686 INFO: Starting candidate selection
0:35:13.972386 INFO: Starting candidate scoring
0:35:15.423821 INFO: Finished candidate processing
0:35:15.424028 INFO: Collecting candidate features
0:35:15.811238 INFO: Collecting fragment features
0:35:15.950954 INFO: Finished candidate scoring
0:35:16.062953 PROGRESS: === Extracted 201192 precursors and 2026574 fragments ===
0:35:16.063491 INFO: performing precursor FDR with 47 features
0:35:16.063529 INFO: Decoy channel: -1
0:35:16.063552 INFO: Competetive: True
0:35:16.136626 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:19.599567 INFO: Test AUC: 0.571
0:35:19.599685 INFO: Train AUC: 0.585
0:35:19.599715 INFO: AUC difference: 2.42%
0:35:19.836139 INFO: Resetting torch num_threads to 100
0:35:19.841641 INFO: === FDR correction performed with classifier version 7 ===
0:35:19.842422 PROGRESS: ============================= Precursor FDR =============================
0:35:19.842525 PROGRESS: Total precursors accumulated: 585
0:35:19.842591 PROGRESS: Target precursors: 535 (91.45%)
0:35:19.842657 PROGRESS: Decoy precursors: 50 (8.55%)
0:35:19.842703 PROGRESS: 
0:35:19.842746 PROGRESS: Precursor Summary:
0:35:19.843724 PROGRESS: Channel   0:	 0.05 FDR:   369; 0.01 FDR:   289; 0.001 FDR:     1
0:35:19.843814 PROGRESS: 
0:35:19.843869 PROGRESS: Protein Summary:
0:35:19.844965 PROGRESS: Channel   0:	 0.05 FDR:   355; 0.01 FDR:   277; 0.001 FDR:     1
0:35:19.845060 PROGRESS: =========================================================================
0:35:19.979894 INFO: fragments_df: keeping 3391 of 2026574 [sum(precursor_idx_mask)=6506 sum(mass_error_mask)=2026574 stop_rank=3391
0:35:20.184294 INFO: calibration group: precursor, fitting rt estimator 
0:35:20.308038 INFO: calibration group: fragment, fitting mz estimator 
0:35:20.764680 INFO: Using score_cutoff 73.68407729187011 (fac=0.99, q=1)
0:35:20.765104 INFO: calibration group: precursor, predicting mz
0:35:20.765192 WARNING: mz prediction was skipped as it has not been fitted yet
0:35:20.765222 INFO: calibration group: precursor, predicting rt
0:35:20.826926 INFO: calibration group: fragment, predicting mz
0:35:20.977190 INFO: === checking if optimization conditions were reached ===
0:35:20.977476 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:35:20.979920 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 24.6139.
0:35:20.979982 INFO: ==============================================
0:35:20.980091 INFO: Starting optimization step 9.
0:35:20.980166 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:35:20.980245 PROGRESS: Extracting batch of 100800 precursors
0:35:21.014530 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:35:21.014677 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:21.014724 INFO: FWHM in RT is 3.10 seconds, sigma is 0.40
0:35:21.014753 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:35:21.015071 INFO: Starting candidate selection
0:35:25.608568 INFO: Starting candidate scoring
0:35:26.927335 INFO: Finished candidate processing
0:35:26.927431 INFO: Collecting candidate features
0:35:27.245027 INFO: Collecting fragment features
0:35:27.374024 INFO: Finished candidate scoring
0:35:27.487301 PROGRESS: === Extracted 201189 precursors and 1965834 fragments ===
0:35:27.487672 INFO: performing precursor FDR with 47 features
0:35:27.487708 INFO: Decoy channel: -1
0:35:27.487730 INFO: Competetive: True
0:35:27.549219 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:31.217500 INFO: Test AUC: 0.563
0:35:31.217697 INFO: Train AUC: 0.584
0:35:31.217727 INFO: AUC difference: 3.70%
0:35:31.449838 INFO: Resetting torch num_threads to 100
0:35:31.455556 INFO: === FDR correction performed with classifier version 7 ===
0:35:31.456382 PROGRESS: ============================= Precursor FDR =============================
0:35:31.456486 PROGRESS: Total precursors accumulated: 610
0:35:31.456545 PROGRESS: Target precursors: 557 (91.31%)
0:35:31.456596 PROGRESS: Decoy precursors: 53 (8.69%)
0:35:31.456642 PROGRESS: 
0:35:31.456686 PROGRESS: Precursor Summary:
0:35:31.457741 PROGRESS: Channel   0:	 0.05 FDR:   484; 0.01 FDR:   349; 0.001 FDR:   283
0:35:31.457832 PROGRESS: 
0:35:31.457886 PROGRESS: Protein Summary:
0:35:31.459114 PROGRESS: Channel   0:	 0.05 FDR:   456; 0.01 FDR:   330; 0.001 FDR:   269
0:35:31.459205 PROGRESS: =========================================================================
0:35:31.592548 INFO: fragments_df: keeping 3914 of 1965834 [sum(precursor_idx_mask)=7816 sum(mass_error_mask)=1965834 stop_rank=3914
0:35:31.819137 INFO: calibration group: precursor, fitting rt estimator 
0:35:31.940425 INFO: calibration group: fragment, fitting mz estimator 
0:35:32.447533 INFO: Using score_cutoff 68.2788525238037 (fac=0.99, q=1)
0:35:32.447943 INFO: calibration group: precursor, predicting mz
0:35:32.448032 WARNING: mz prediction was skipped as it has not been fitted yet
0:35:32.448062 INFO: calibration group: precursor, predicting rt
0:35:32.510168 INFO: calibration group: fragment, predicting mz
0:35:32.661568 INFO: === checking if optimization conditions were reached ===
0:35:32.661847 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:35:32.664586 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 19.2857.
0:35:32.664648 INFO: ==============================================
0:35:32.664760 INFO: Starting optimization step 10.
0:35:32.664836 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:35:32.664917 PROGRESS: Extracting batch of 100800 precursors
0:35:32.700434 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:35:32.700565 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:32.700611 INFO: FWHM in RT is 2.84 seconds, sigma is 0.37
0:35:32.700639 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:35:32.700950 INFO: Starting candidate selection
0:35:37.371761 INFO: Starting candidate scoring
0:35:38.819830 INFO: Finished candidate processing
0:35:38.819923 INFO: Collecting candidate features
0:35:39.136127 INFO: Collecting fragment features
0:35:39.255881 INFO: Finished candidate scoring
0:35:39.346411 PROGRESS: === Extracted 201185 precursors and 1887402 fragments ===
0:35:39.346792 INFO: performing precursor FDR with 47 features
0:35:39.346830 INFO: Decoy channel: -1
0:35:39.346853 INFO: Competetive: True
0:35:39.406850 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:42.970405 INFO: Test AUC: 0.566
0:35:42.970596 INFO: Train AUC: 0.580
0:35:42.970636 INFO: AUC difference: 2.41%
0:35:44.490835 INFO: Resetting torch num_threads to 100
0:35:44.496249 INFO: === FDR correction performed with classifier version 7 ===
0:35:44.497049 PROGRESS: ============================= Precursor FDR =============================
0:35:44.497158 PROGRESS: Total precursors accumulated: 728
0:35:44.497225 PROGRESS: Target precursors: 664 (91.21%)
0:35:44.497285 PROGRESS: Decoy precursors: 64 (8.79%)
0:35:44.497332 PROGRESS: 
0:35:44.497377 PROGRESS: Precursor Summary:
0:35:44.498440 PROGRESS: Channel   0:	 0.05 FDR:   519; 0.01 FDR:   429; 0.001 FDR:   242
0:35:44.498534 PROGRESS: 
0:35:44.498589 PROGRESS: Protein Summary:
0:35:44.499809 PROGRESS: Channel   0:	 0.05 FDR:   488; 0.01 FDR:   405; 0.001 FDR:   230
0:35:44.499901 PROGRESS: =========================================================================
0:35:44.622670 INFO: fragments_df: keeping 4671 of 1887402 [sum(precursor_idx_mask)=9527 sum(mass_error_mask)=1887402 stop_rank=4671
0:35:44.773482 INFO: calibration group: precursor, fitting rt estimator 
0:35:44.903677 INFO: calibration group: fragment, fitting mz estimator 
0:35:45.530424 INFO: Using score_cutoff 65.44539898681641 (fac=0.99, q=1)
0:35:45.530825 INFO: calibration group: precursor, predicting mz
0:35:45.530911 WARNING: mz prediction was skipped as it has not been fitted yet
0:35:45.530942 INFO: calibration group: precursor, predicting rt
0:35:45.562000 INFO: calibration group: fragment, predicting mz
0:35:45.635485 INFO: === checking if optimization conditions were reached ===
0:35:45.635749 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
0:35:45.638516 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 16.5109.
0:35:45.638577 INFO: ==============================================
0:35:45.638695 INFO: Starting optimization step 11.
0:35:45.638769 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:35:45.638852 PROGRESS: Extracting batch of 50212 precursors
0:35:45.655321 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:35:45.655431 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:45.655472 INFO: FWHM in RT is 2.69 seconds, sigma is 0.35
0:35:45.655500 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:35:45.655754 INFO: Starting candidate selection
0:35:48.136399 INFO: Starting candidate scoring
0:35:48.870712 INFO: Finished candidate processing
0:35:48.870807 INFO: Collecting candidate features
0:35:49.075114 INFO: Collecting fragment features
0:35:49.160553 INFO: Finished candidate scoring
0:35:49.215158 PROGRESS: === Extracted 100205 precursors and 907623 fragments ===
0:35:49.215636 INFO: performing precursor FDR with 47 features
0:35:49.215677 INFO: Decoy channel: -1
0:35:49.215702 INFO: Competetive: True
0:35:49.259299 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:51.405626 INFO: Test AUC: 0.566
0:35:51.405826 INFO: Train AUC: 0.579
0:35:51.405861 INFO: AUC difference: 2.22%
0:35:51.616812 INFO: Resetting torch num_threads to 100
0:35:51.634669 INFO: === FDR correction performed with classifier version 7 ===
0:35:51.635521 PROGRESS: ============================= Precursor FDR =============================
0:35:51.635629 PROGRESS: Total precursors accumulated: 360
0:35:51.635690 PROGRESS: Target precursors: 329 (91.39%)
0:35:51.635743 PROGRESS: Decoy precursors: 31 (8.61%)
0:35:51.635792 PROGRESS: 
0:35:51.635837 PROGRESS: Precursor Summary:
0:35:51.636820 PROGRESS: Channel   0:	 0.05 FDR:   269; 0.01 FDR:   148; 0.001 FDR:   135
0:35:51.636917 PROGRESS: 
0:35:51.636973 PROGRESS: Protein Summary:
0:35:51.638057 PROGRESS: Channel   0:	 0.05 FDR:   259; 0.01 FDR:   144; 0.001 FDR:   133
0:35:51.638151 PROGRESS: =========================================================================
0:35:51.863471 INFO: calibration group: precursor, predicting mz
0:35:51.863852 WARNING: mz prediction was skipped as it has not been fitted yet
0:35:51.863896 INFO: calibration group: precursor, predicting rt
0:35:51.899973 INFO: calibration group: fragment, predicting mz
0:35:51.976173 INFO: === skipping optimization until target number of precursors are found ===
0:35:51.976564 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:35:51.976653 INFO: Starting optimization step 12.
0:35:51.976732 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:35:51.976838 PROGRESS: Extracting batch of 50588 precursors
0:35:51.997279 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:35:51.997434 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:51.997475 INFO: FWHM in RT is 2.69 seconds, sigma is 0.35
0:35:51.997500 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:35:51.997830 INFO: Starting candidate selection
0:35:54.495840 INFO: Starting candidate scoring
0:35:55.151745 INFO: Finished candidate processing
0:35:55.151849 INFO: Collecting candidate features
0:35:55.308582 INFO: Collecting fragment features
0:35:55.375219 INFO: Finished candidate scoring
0:35:55.470577 PROGRESS: === Extracted 201183 precursors and 1821657 fragments ===
0:35:55.490885 INFO: performing precursor FDR with 47 features
0:35:55.491007 INFO: Decoy channel: -1
0:35:55.491033 INFO: Competetive: True
0:35:55.571584 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:58.813328 INFO: Test AUC: 0.560
0:35:58.813447 INFO: Train AUC: 0.583
0:35:58.813476 INFO: AUC difference: 3.97%
0:35:59.044591 INFO: Resetting torch num_threads to 100
0:35:59.054165 INFO: === FDR correction performed with classifier version 7 ===
0:35:59.054955 PROGRESS: ============================= Precursor FDR =============================
0:35:59.055067 PROGRESS: Total precursors accumulated: 756
0:35:59.055129 PROGRESS: Target precursors: 693 (91.67%)
0:35:59.055182 PROGRESS: Decoy precursors: 63 (8.33%)
0:35:59.055229 PROGRESS: 
0:35:59.055273 PROGRESS: Precursor Summary:
0:35:59.056330 PROGRESS: Channel   0:	 0.05 FDR:   524; 0.01 FDR:   359; 0.001 FDR:   230
0:35:59.056432 PROGRESS: 
0:35:59.056489 PROGRESS: Protein Summary:
0:35:59.057715 PROGRESS: Channel   0:	 0.05 FDR:   496; 0.01 FDR:   339; 0.001 FDR:   222
0:35:59.057814 PROGRESS: =========================================================================
0:35:59.187974 INFO: fragments_df: keeping 4029 of 1821657 [sum(precursor_idx_mask)=7944 sum(mass_error_mask)=1821657 stop_rank=4029
0:35:59.383798 INFO: calibration group: precursor, fitting rt estimator 
0:35:59.522492 INFO: calibration group: fragment, fitting mz estimator 
0:36:00.047531 INFO: Using score_cutoff 70.20212496185302 (fac=0.99, q=1)
0:36:00.047936 INFO: calibration group: precursor, predicting mz
0:36:00.048023 WARNING: mz prediction was skipped as it has not been fitted yet
0:36:00.048054 INFO: calibration group: precursor, predicting rt
0:36:00.110261 INFO: calibration group: fragment, predicting mz
0:36:00.261058 INFO: === checking if optimization conditions were reached ===
0:36:00.261351 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
0:36:00.264131 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 14.9518.
0:36:00.264199 INFO: ==============================================
0:36:00.264302 INFO: Starting optimization step 13.
0:36:00.264377 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:36:00.264446 PROGRESS: Extracting batch of 100800 precursors
0:36:00.298138 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:36:00.298281 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:36:00.298323 INFO: FWHM in RT is 2.76 seconds, sigma is 0.36
0:36:00.298353 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:36:00.298640 INFO: Starting candidate selection
0:36:05.256673 INFO: Starting candidate scoring
0:36:06.590685 INFO: Finished candidate processing
0:36:06.590824 INFO: Collecting candidate features
0:36:07.073969 INFO: Collecting fragment features
0:36:07.233118 INFO: Finished candidate scoring
0:36:07.450548 PROGRESS: === Extracted 201177 precursors and 1768774 fragments ===
0:36:07.451145 INFO: performing precursor FDR with 47 features
0:36:07.451186 INFO: Decoy channel: -1
0:36:07.451210 INFO: Competetive: True
0:36:07.556612 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:12.242319 INFO: Test AUC: 0.563
0:36:12.242493 INFO: Train AUC: 0.582
0:36:12.242541 INFO: AUC difference: 3.24%
0:36:12.483155 INFO: Resetting torch num_threads to 100
0:36:12.491751 INFO: === FDR correction performed with classifier version 7 ===
0:36:12.492740 PROGRESS: ============================= Precursor FDR =============================
0:36:12.492864 PROGRESS: Total precursors accumulated: 811
0:36:12.492928 PROGRESS: Target precursors: 740 (91.25%)
0:36:12.492978 PROGRESS: Decoy precursors: 71 (8.75%)
0:36:12.493025 PROGRESS: 
0:36:12.493070 PROGRESS: Precursor Summary:
0:36:12.494201 PROGRESS: Channel   0:	 0.05 FDR:   584; 0.01 FDR:   388; 0.001 FDR:   251
0:36:12.494301 PROGRESS: 
0:36:12.494357 PROGRESS: Protein Summary:
0:36:12.495656 PROGRESS: Channel   0:	 0.05 FDR:   545; 0.01 FDR:   368; 0.001 FDR:   240
0:36:12.495759 PROGRESS: =========================================================================
0:36:12.623686 INFO: fragments_df: keeping 4274 of 1768774 [sum(precursor_idx_mask)=8465 sum(mass_error_mask)=1768774 stop_rank=4274
0:36:12.933685 INFO: calibration group: precursor, fitting rt estimator 
0:36:13.045303 INFO: calibration group: fragment, fitting mz estimator 
0:36:13.550372 INFO: Using score_cutoff 64.93008809509277 (fac=0.99, q=1)
0:36:13.550905 INFO: calibration group: precursor, predicting mz
0:36:13.551002 WARNING: mz prediction was skipped as it has not been fitted yet
0:36:13.551034 INFO: calibration group: precursor, predicting rt
0:36:13.614414 INFO: calibration group: fragment, predicting mz
0:36:13.774466 INFO: === checking if optimization conditions were reached ===
0:36:13.774847 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
0:36:13.777806 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 13.1496.
0:36:13.777864 INFO: ==============================================
0:36:13.777967 INFO: Starting optimization step 14.
0:36:13.778045 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:36:13.778123 PROGRESS: Extracting batch of 100800 precursors
0:36:13.924531 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:36:13.924714 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:36:13.924760 INFO: FWHM in RT is 2.62 seconds, sigma is 0.34
0:36:13.924786 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:36:13.925146 INFO: Starting candidate selection
0:36:18.810343 INFO: Starting candidate scoring
0:36:20.136091 INFO: Finished candidate processing
0:36:20.136188 INFO: Collecting candidate features
0:36:20.438847 INFO: Collecting fragment features
0:36:20.560815 INFO: Finished candidate scoring
0:36:20.680387 PROGRESS: === Extracted 201176 precursors and 1740081 fragments ===
0:36:20.680834 INFO: performing precursor FDR with 47 features
0:36:20.680873 INFO: Decoy channel: -1
0:36:20.680897 INFO: Competetive: True
0:36:20.750175 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:24.159020 INFO: Test AUC: 0.568
0:36:24.159143 INFO: Train AUC: 0.580
0:36:24.159172 INFO: AUC difference: 2.20%
0:36:24.388854 INFO: Resetting torch num_threads to 100
0:36:24.394796 INFO: === FDR correction performed with classifier version 7 ===
0:36:24.395569 PROGRESS: ============================= Precursor FDR =============================
0:36:24.395672 PROGRESS: Total precursors accumulated: 789
0:36:24.395730 PROGRESS: Target precursors: 724 (91.76%)
0:36:24.395780 PROGRESS: Decoy precursors: 65 (8.24%)
0:36:24.395826 PROGRESS: 
0:36:24.395868 PROGRESS: Precursor Summary:
0:36:24.396912 PROGRESS: Channel   0:	 0.05 FDR:   613; 0.01 FDR:   367; 0.001 FDR:   236
0:36:24.397012 PROGRESS: 
0:36:24.397067 PROGRESS: Protein Summary:
0:36:24.398287 PROGRESS: Channel   0:	 0.05 FDR:   574; 0.01 FDR:   347; 0.001 FDR:   228
0:36:24.398379 PROGRESS: =========================================================================
0:36:24.515269 INFO: fragments_df: keeping 4042 of 1740081 [sum(precursor_idx_mask)=7952 sum(mass_error_mask)=1740081 stop_rank=4042
0:36:24.715813 INFO: calibration group: precursor, fitting rt estimator 
0:36:24.844203 INFO: calibration group: fragment, fitting mz estimator 
0:36:25.366129 INFO: Using score_cutoff 63.93759224853516 (fac=0.99, q=1)
0:36:25.366535 INFO: calibration group: precursor, predicting mz
0:36:25.366633 WARNING: mz prediction was skipped as it has not been fitted yet
0:36:25.366669 INFO: calibration group: precursor, predicting rt
0:36:25.436765 INFO: calibration group: fragment, predicting mz
0:36:25.620330 INFO: === checking if optimization conditions were reached ===
0:36:25.620628 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
0:36:25.623385 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 11.5025.
0:36:25.623449 INFO: ==============================================
0:36:25.623556 INFO: Starting optimization step 15.
0:36:25.623633 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:36:25.623716 PROGRESS: Extracting batch of 100800 precursors
0:36:25.659257 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:36:25.659393 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:36:25.659437 INFO: FWHM in RT is 2.65 seconds, sigma is 0.34
0:36:25.659466 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:36:25.659746 INFO: Starting candidate selection
0:36:30.556070 INFO: Starting candidate scoring
0:36:32.005775 INFO: Finished candidate processing
0:36:32.005873 INFO: Collecting candidate features
0:36:32.320465 INFO: Collecting fragment features
0:36:32.454469 INFO: Finished candidate scoring
0:36:32.542048 PROGRESS: === Extracted 201159 precursors and 1670889 fragments ===
0:36:32.542477 INFO: performing precursor FDR with 47 features
0:36:32.542514 INFO: Decoy channel: -1
0:36:32.542535 INFO: Competetive: True
0:36:32.611354 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:36.051140 INFO: Test AUC: 0.564
0:36:36.051260 INFO: Train AUC: 0.582
0:36:36.051291 INFO: AUC difference: 3.06%
0:36:36.281176 INFO: Resetting torch num_threads to 100
0:36:36.287077 INFO: === FDR correction performed with classifier version 7 ===
0:36:36.287853 PROGRESS: ============================= Precursor FDR =============================
0:36:36.287958 PROGRESS: Total precursors accumulated: 870
0:36:36.288018 PROGRESS: Target precursors: 797 (91.61%)
0:36:36.288076 PROGRESS: Decoy precursors: 73 (8.39%)
0:36:36.288122 PROGRESS: 
0:36:36.288167 PROGRESS: Precursor Summary:
0:36:36.289251 PROGRESS: Channel   0:	 0.05 FDR:   686; 0.01 FDR:   375; 0.001 FDR:   251
0:36:36.289344 PROGRESS: 
0:36:36.289400 PROGRESS: Protein Summary:
0:36:36.290638 PROGRESS: Channel   0:	 0.05 FDR:   641; 0.01 FDR:   355; 0.001 FDR:   241
0:36:36.290734 PROGRESS: =========================================================================
0:36:36.400932 INFO: fragments_df: keeping 4098 of 1670889 [sum(precursor_idx_mask)=8120 sum(mass_error_mask)=1670889 stop_rank=4098
0:36:36.603747 INFO: calibration group: precursor, fitting rt estimator 
0:36:36.724320 INFO: calibration group: fragment, fitting mz estimator 
0:36:37.251360 INFO: Using score_cutoff 65.17869855194091 (fac=0.99, q=1)
0:36:37.251756 INFO: calibration group: precursor, predicting mz
0:36:37.251843 WARNING: mz prediction was skipped as it has not been fitted yet
0:36:37.251872 INFO: calibration group: precursor, predicting rt
0:36:37.320226 INFO: calibration group: fragment, predicting mz
0:36:37.468982 INFO: === checking if optimization conditions were reached ===
0:36:37.469263 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
0:36:37.472131 PROGRESS: ❌ ms2_error      : optimization incomplete after 7 search(es). Will search with parameter 9.8718.
0:36:37.472194 INFO: ==============================================
0:36:37.472304 INFO: Starting optimization step 16.
0:36:37.472381 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:36:37.472463 PROGRESS: Extracting batch of 100800 precursors
0:36:37.509734 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:36:37.509870 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:36:37.509935 INFO: FWHM in RT is 2.58 seconds, sigma is 0.33
0:36:37.509968 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:36:37.510271 INFO: Starting candidate selection
0:36:42.418725 INFO: Starting candidate scoring
0:36:43.868234 INFO: Finished candidate processing
0:36:43.868418 INFO: Collecting candidate features
0:36:44.193418 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 201131)
0:36:44.203158 INFO: Collecting fragment features
0:36:44.316950 INFO: Finished candidate scoring
0:36:44.415184 PROGRESS: === Extracted 201131 precursors and 1583142 fragments ===
0:36:44.415641 INFO: performing precursor FDR with 47 features
0:36:44.415680 INFO: Decoy channel: -1
0:36:44.415705 INFO: Competetive: True
0:36:44.481960 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:44.510114 WARNING: dropped 1 target PSMs due to missing features
0:36:47.878926 INFO: Test AUC: 0.567
0:36:47.879258 INFO: Train AUC: 0.580
0:36:47.879291 INFO: AUC difference: 2.29%
0:36:48.108878 INFO: Resetting torch num_threads to 100
0:36:48.114722 INFO: === FDR correction performed with classifier version 7 ===
0:36:48.115520 PROGRESS: ============================= Precursor FDR =============================
0:36:48.115631 PROGRESS: Total precursors accumulated: 947
0:36:48.115692 PROGRESS: Target precursors: 869 (91.76%)
0:36:48.115743 PROGRESS: Decoy precursors: 78 (8.24%)
0:36:48.115789 PROGRESS: 
0:36:48.115833 PROGRESS: Precursor Summary:
0:36:48.116916 PROGRESS: Channel   0:	 0.05 FDR:   715; 0.01 FDR:   429; 0.001 FDR:   297
0:36:48.117019 PROGRESS: 
0:36:48.117076 PROGRESS: Protein Summary:
0:36:48.118339 PROGRESS: Channel   0:	 0.05 FDR:   666; 0.01 FDR:   407; 0.001 FDR:   284
0:36:48.118433 PROGRESS: =========================================================================
0:36:48.223104 INFO: fragments_df: keeping 4537 of 1583142 [sum(precursor_idx_mask)=9107 sum(mass_error_mask)=1583142 stop_rank=4537
0:36:48.354760 INFO: calibration group: precursor, fitting rt estimator 
0:36:48.490331 INFO: calibration group: fragment, fitting mz estimator 
0:36:49.086495 INFO: Using score_cutoff 63.445092929077155 (fac=0.99, q=1)
0:36:49.086909 INFO: calibration group: precursor, predicting mz
0:36:49.087000 WARNING: mz prediction was skipped as it has not been fitted yet
0:36:49.087030 INFO: calibration group: precursor, predicting rt
0:36:49.117901 INFO: calibration group: fragment, predicting mz
0:36:49.190428 INFO: === checking if optimization conditions were reached ===
0:36:49.190781 PROGRESS: === Optimization of ms2_error has been performed 8 time(s); minimum number is 2 ===
0:36:49.193719 PROGRESS: ❌ ms2_error      : optimization incomplete after 8 search(es). Will search with parameter 8.3647.
0:36:49.193775 INFO: ==============================================
0:36:49.193879 INFO: Starting optimization step 17.
0:36:49.193949 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:36:49.194028 PROGRESS: Extracting batch of 50212 precursors
0:36:49.212649 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:36:49.212790 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:36:49.212831 INFO: FWHM in RT is 2.52 seconds, sigma is 0.33
0:36:49.212855 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:36:49.213177 INFO: Starting candidate selection
0:36:51.667817 INFO: Starting candidate scoring
0:36:52.393095 INFO: Finished candidate processing
0:36:52.393191 INFO: Collecting candidate features
0:36:52.534804 INFO: Collecting fragment features
0:36:52.593464 INFO: Finished candidate scoring
0:36:52.634624 PROGRESS: === Extracted 100177 precursors and 765949 fragments ===
0:36:52.635001 INFO: performing precursor FDR with 47 features
0:36:52.635037 INFO: Decoy channel: -1
0:36:52.635061 INFO: Competetive: True
0:36:52.663350 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:54.208826 INFO: Test AUC: 0.557
0:36:54.208956 INFO: Train AUC: 0.584
0:36:54.208993 INFO: AUC difference: 4.52%
0:36:54.410008 INFO: Resetting torch num_threads to 100
0:36:54.413464 INFO: === FDR correction performed with classifier version 7 ===
0:36:54.414148 PROGRESS: ============================= Precursor FDR =============================
0:36:54.414249 PROGRESS: Total precursors accumulated: 380
0:36:54.414309 PROGRESS: Target precursors: 347 (91.32%)
0:36:54.414360 PROGRESS: Decoy precursors: 33 (8.68%)
0:36:54.414407 PROGRESS: 
0:36:54.414453 PROGRESS: Precursor Summary:
0:36:54.415444 PROGRESS: Channel   0:	 0.05 FDR:   310; 0.01 FDR:   155; 0.001 FDR:   118
0:36:54.415537 PROGRESS: 
0:36:54.415592 PROGRESS: Protein Summary:
0:36:54.416666 PROGRESS: Channel   0:	 0.05 FDR:   293; 0.01 FDR:   150; 0.001 FDR:   117
0:36:54.416759 PROGRESS: =========================================================================
0:36:54.543699 INFO: calibration group: precursor, predicting mz
0:36:54.543927 WARNING: mz prediction was skipped as it has not been fitted yet
0:36:54.543961 INFO: calibration group: precursor, predicting rt
0:36:54.574981 INFO: calibration group: fragment, predicting mz
0:36:54.636479 INFO: === skipping optimization until target number of precursors are found ===
0:36:54.636767 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:36:54.636838 INFO: Starting optimization step 18.
0:36:54.636918 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:36:54.637004 PROGRESS: Extracting batch of 50588 precursors
0:36:54.654156 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:36:54.654277 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:36:54.654317 INFO: FWHM in RT is 2.52 seconds, sigma is 0.33
0:36:54.654347 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:36:54.654579 INFO: Starting candidate selection
0:36:57.127595 INFO: Starting candidate scoring
0:36:57.782876 INFO: Finished candidate processing
0:36:57.782977 INFO: Collecting candidate features
0:36:57.954415 INFO: Collecting fragment features
0:36:58.020909 INFO: Finished candidate scoring
0:36:58.137130 PROGRESS: === Extracted 201140 precursors and 1536868 fragments ===
0:36:58.159207 INFO: performing precursor FDR with 47 features
0:36:58.159327 INFO: Decoy channel: -1
0:36:58.159353 INFO: Competetive: True
0:36:58.260589 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:01.503340 INFO: Test AUC: 0.564
0:37:01.503540 INFO: Train AUC: 0.582
0:37:01.503571 INFO: AUC difference: 2.99%
0:37:01.734250 INFO: Resetting torch num_threads to 100
0:37:01.745901 INFO: === FDR correction performed with classifier version 7 ===
0:37:01.746758 PROGRESS: ============================= Precursor FDR =============================
0:37:01.746858 PROGRESS: Total precursors accumulated: 901
0:37:01.746919 PROGRESS: Target precursors: 824 (91.45%)
0:37:01.746971 PROGRESS: Decoy precursors: 77 (8.55%)
0:37:01.747017 PROGRESS: 
0:37:01.747062 PROGRESS: Precursor Summary:
0:37:01.748159 PROGRESS: Channel   0:	 0.05 FDR:   681; 0.01 FDR:   372; 0.001 FDR:   285
0:37:01.748250 PROGRESS: 
0:37:01.748308 PROGRESS: Protein Summary:
0:37:01.749546 PROGRESS: Channel   0:	 0.05 FDR:   632; 0.01 FDR:   353; 0.001 FDR:   272
0:37:01.749643 PROGRESS: =========================================================================
0:37:01.875189 INFO: fragments_df: keeping 4089 of 1536868 [sum(precursor_idx_mask)=7891 sum(mass_error_mask)=1536868 stop_rank=4089
0:37:02.091267 INFO: calibration group: precursor, fitting rt estimator 
0:37:02.217735 INFO: calibration group: fragment, fitting mz estimator 
0:37:02.756522 INFO: Using score_cutoff 60.582604744720456 (fac=0.99, q=1)
0:37:02.756917 INFO: calibration group: precursor, predicting mz
0:37:02.757004 WARNING: mz prediction was skipped as it has not been fitted yet
0:37:02.757034 INFO: calibration group: precursor, predicting rt
0:37:02.819205 INFO: calibration group: fragment, predicting mz
0:37:02.963053 INFO: === checking if optimization conditions were reached ===
0:37:02.963313 PROGRESS: === Optimization of ms2_error has been performed 9 time(s); minimum number is 2 ===
0:37:02.965707 PROGRESS: ❌ ms2_error      : optimization incomplete after 9 search(es). Will search with parameter 7.5070.
0:37:02.965760 INFO: ==============================================
0:37:02.965855 INFO: Starting optimization step 19.
0:37:02.965922 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:37:02.965992 PROGRESS: Extracting batch of 100800 precursors
0:37:02.990925 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:37:02.991046 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:37:02.991084 INFO: FWHM in RT is 2.54 seconds, sigma is 0.33
0:37:02.991106 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:37:02.991361 INFO: Starting candidate selection
0:37:07.719068 INFO: Starting candidate scoring
0:37:09.158088 INFO: Finished candidate processing
0:37:09.158186 INFO: Collecting candidate features
0:37:09.444655 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 201108)
0:37:09.454309 INFO: Collecting fragment features
0:37:09.565697 INFO: Finished candidate scoring
0:37:09.696119 PROGRESS: === Extracted 201108 precursors and 1480423 fragments ===
0:37:09.696492 INFO: performing precursor FDR with 47 features
0:37:09.696528 INFO: Decoy channel: -1
0:37:09.696550 INFO: Competetive: True
0:37:09.751248 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:09.784988 WARNING: dropped 1 target PSMs due to missing features
0:37:13.002923 INFO: Test AUC: 0.564
0:37:13.003052 INFO: Train AUC: 0.578
0:37:13.003081 INFO: AUC difference: 2.37%
0:37:13.231344 INFO: Resetting torch num_threads to 100
0:37:13.237289 INFO: === FDR correction performed with classifier version 7 ===
0:37:13.238077 PROGRESS: ============================= Precursor FDR =============================
0:37:13.238193 PROGRESS: Total precursors accumulated: 910
0:37:13.238254 PROGRESS: Target precursors: 832 (91.43%)
0:37:13.238308 PROGRESS: Decoy precursors: 78 (8.57%)
0:37:13.238354 PROGRESS: 
0:37:13.238398 PROGRESS: Precursor Summary:
0:37:13.239424 PROGRESS: Channel   0:	 0.05 FDR:   664; 0.01 FDR:   303; 0.001 FDR:     0
0:37:13.239519 PROGRESS: 
0:37:13.239575 PROGRESS: Protein Summary:
0:37:13.240751 PROGRESS: Channel   0:	 0.05 FDR:   615; 0.01 FDR:   287; 0.001 FDR:     0
0:37:13.240844 PROGRESS: =========================================================================
0:37:13.340658 INFO: fragments_df: keeping 3426 of 1480423 [sum(precursor_idx_mask)=6374 sum(mass_error_mask)=1480423 stop_rank=3426
0:37:13.536958 INFO: calibration group: precursor, fitting rt estimator 
0:37:13.653261 INFO: calibration group: fragment, fitting mz estimator 
0:37:14.097309 INFO: Using score_cutoff 61.06054176177978 (fac=0.99, q=1)
0:37:14.097682 INFO: calibration group: precursor, predicting mz
0:37:14.097764 WARNING: mz prediction was skipped as it has not been fitted yet
0:37:14.097793 INFO: calibration group: precursor, predicting rt
0:37:14.159687 INFO: calibration group: fragment, predicting mz
0:37:14.308489 INFO: === checking if optimization conditions were reached ===
0:37:14.308770 PROGRESS: === Optimization of ms2_error has been performed 10 time(s); minimum number is 2 ===
0:37:14.311383 PROGRESS: ❌ ms2_error      : optimization incomplete after 10 search(es). Will search with parameter 6.3338.
0:37:14.311447 INFO: ==============================================
0:37:14.311551 WARNING: Optimization did not converge within the maximum number of steps, which is 20.
0:37:14.311683 INFO: Starting optimization step 0.
0:37:14.311765 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:37:14.311840 PROGRESS: Extracting batch of 100800 precursors
0:37:14.345788 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:37:14.345927 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:37:14.345970 INFO: FWHM in RT is 2.54 seconds, sigma is 0.33
0:37:14.346002 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:37:14.346249 INFO: Starting candidate selection
0:37:19.187746 INFO: Starting candidate scoring
0:37:20.636330 INFO: Finished candidate processing
0:37:20.636487 INFO: Collecting candidate features
0:37:21.058794 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 201059)
0:37:21.068638 INFO: Collecting fragment features
0:37:21.183064 INFO: Finished candidate scoring
0:37:21.271548 PROGRESS: === Extracted 201059 precursors and 1418704 fragments ===
0:37:21.271976 INFO: performing precursor FDR with 47 features
0:37:21.272015 INFO: Decoy channel: -1
0:37:21.272039 INFO: Competetive: True
0:37:21.338762 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:21.379655 WARNING: dropped 1 target PSMs due to missing features
0:37:21.379779 WARNING: dropped 1 decoy PSMs due to missing features
0:37:24.528921 INFO: Test AUC: 0.566
0:37:24.529045 INFO: Train AUC: 0.581
0:37:24.529075 INFO: AUC difference: 2.66%
0:37:24.762079 INFO: Resetting torch num_threads to 100
0:37:24.768147 INFO: === FDR correction performed with classifier version 7 ===
0:37:24.768958 PROGRESS: ============================= Precursor FDR =============================
0:37:24.769069 PROGRESS: Total precursors accumulated: 1,004
0:37:24.769130 PROGRESS: Target precursors: 918 (91.43%)
0:37:24.769183 PROGRESS: Decoy precursors: 86 (8.57%)
0:37:24.769231 PROGRESS: 
0:37:24.769276 PROGRESS: Precursor Summary:
0:37:24.770401 PROGRESS: Channel   0:	 0.05 FDR:   770; 0.01 FDR:   506; 0.001 FDR:   270
0:37:24.770498 PROGRESS: 
0:37:24.770556 PROGRESS: Protein Summary:
0:37:24.771847 PROGRESS: Channel   0:	 0.05 FDR:   715; 0.01 FDR:   473; 0.001 FDR:   257
0:37:24.772114 PROGRESS: =========================================================================
0:37:24.865073 INFO: fragments_df: keeping 5000 of 1418704 [sum(precursor_idx_mask)=10369 sum(mass_error_mask)=1418704 stop_rank=5000
0:37:24.998667 INFO: calibration group: precursor, fitting rt estimator 
0:37:25.128823 INFO: calibration group: fragment, fitting mz estimator 
0:37:25.810109 INFO: Using score_cutoff 55.277671028137206 (fac=0.99, q=1)
0:37:25.810512 INFO: calibration group: precursor, predicting mz
0:37:25.810606 WARNING: mz prediction was skipped as it has not been fitted yet
0:37:25.810637 INFO: calibration group: precursor, predicting rt
0:37:25.841494 INFO: calibration group: fragment, predicting mz
0:37:25.909469 INFO: === checking if optimization conditions were reached ===
0:37:25.909759 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:37:25.912016 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 178.1404.
0:37:25.912078 INFO: ==============================================
0:37:25.912184 INFO: Starting optimization step 1.
0:37:25.912262 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:37:25.912341 PROGRESS: Extracting batch of 50212 precursors
0:37:25.929391 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:37:25.929510 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:37:25.929554 INFO: FWHM in RT is 2.44 seconds, sigma is 0.31
0:37:25.929584 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:37:25.929854 INFO: Starting candidate selection
0:37:27.457646 INFO: Starting candidate scoring
0:37:28.109081 INFO: Finished candidate processing
0:37:28.109202 INFO: Collecting candidate features
0:37:28.287789 WARNING: intensity_correlation has 5 NaNs ( 0.01 % out of 99148)
0:37:28.297611 INFO: Collecting fragment features
0:37:28.353034 INFO: Finished candidate scoring
0:37:28.416593 PROGRESS: === Extracted 99148 precursors and 628282 fragments ===
0:37:28.417058 INFO: performing precursor FDR with 47 features
0:37:28.417098 INFO: Decoy channel: -1
0:37:28.417123 INFO: Competetive: True
0:37:28.467024 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:28.493121 WARNING: dropped 3 target PSMs due to missing features
0:37:28.493283 WARNING: dropped 2 decoy PSMs due to missing features
0:37:30.539985 INFO: Test AUC: 0.561
0:37:30.540208 INFO: Train AUC: 0.574
0:37:30.540241 INFO: AUC difference: 2.24%
0:37:30.747719 INFO: Resetting torch num_threads to 100
0:37:30.751720 INFO: === FDR correction performed with classifier version 7 ===
0:37:30.753087 PROGRESS: ============================= Precursor FDR =============================
0:37:30.753198 PROGRESS: Total precursors accumulated: 425
0:37:30.753259 PROGRESS: Target precursors: 387 (91.06%)
0:37:30.753310 PROGRESS: Decoy precursors: 38 (8.94%)
0:37:30.753356 PROGRESS: 
0:37:30.753399 PROGRESS: Precursor Summary:
0:37:30.754389 PROGRESS: Channel   0:	 0.05 FDR:   328; 0.01 FDR:   234; 0.001 FDR:   142
0:37:30.754483 PROGRESS: 
0:37:30.754538 PROGRESS: Protein Summary:
0:37:30.755646 PROGRESS: Channel   0:	 0.05 FDR:   314; 0.01 FDR:   225; 0.001 FDR:   138
0:37:30.755740 PROGRESS: =========================================================================
0:37:30.798877 INFO: fragments_df: keeping 2340 of 628282 [sum(precursor_idx_mask)=4768 sum(mass_error_mask)=628282 stop_rank=2340
0:37:30.941749 INFO: calibration group: precursor, fitting rt estimator 
0:37:31.057667 INFO: calibration group: fragment, fitting mz estimator 
0:37:31.370991 INFO: Using score_cutoff 56.942775769042974 (fac=0.99, q=1)
0:37:31.371421 INFO: calibration group: precursor, predicting mz
0:37:31.371510 WARNING: mz prediction was skipped as it has not been fitted yet
0:37:31.371542 INFO: calibration group: precursor, predicting rt
0:37:31.402860 INFO: calibration group: fragment, predicting mz
0:37:31.468238 INFO: === checking if optimization conditions were reached ===
0:37:31.468529 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:37:31.470750 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 89.5610.
0:37:31.470811 INFO: ==============================================
0:37:31.470934 INFO: Starting optimization step 2.
0:37:31.471014 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:37:31.471095 PROGRESS: Extracting batch of 50212 precursors
0:37:31.489112 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:37:31.489232 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:37:31.489274 INFO: FWHM in RT is 2.53 seconds, sigma is 0.33
0:37:31.489301 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:37:31.489601 INFO: Starting candidate selection
0:37:33.466807 INFO: Starting candidate scoring
0:37:34.105360 INFO: Finished candidate processing
0:37:34.105517 INFO: Collecting candidate features
0:37:34.247513 WARNING: intensity_correlation has 20 NaNs ( 0.02 % out of 97333)
0:37:34.255941 INFO: Collecting fragment features
0:37:34.304529 INFO: Finished candidate scoring
0:37:34.344854 PROGRESS: === Extracted 97333 precursors and 558885 fragments ===
0:37:34.345233 INFO: performing precursor FDR with 47 features
0:37:34.345270 INFO: Decoy channel: -1
0:37:34.345292 INFO: Competetive: True
0:37:34.376240 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:34.393934 WARNING: dropped 9 target PSMs due to missing features
0:37:34.394063 WARNING: dropped 11 decoy PSMs due to missing features
0:37:35.828424 INFO: Test AUC: 0.550
0:37:35.828554 INFO: Train AUC: 0.571
0:37:35.828583 INFO: AUC difference: 3.73%
0:37:36.027481 INFO: Resetting torch num_threads to 100
0:37:36.030777 INFO: === FDR correction performed with classifier version 7 ===
0:37:36.031471 PROGRESS: ============================= Precursor FDR =============================
0:37:36.031572 PROGRESS: Total precursors accumulated: 552
0:37:36.031637 PROGRESS: Target precursors: 504 (91.30%)
0:37:36.031690 PROGRESS: Decoy precursors: 48 (8.70%)
0:37:36.031737 PROGRESS: 
0:37:36.031781 PROGRESS: Precursor Summary:
0:37:36.032777 PROGRESS: Channel   0:	 0.05 FDR:   405; 0.01 FDR:   267; 0.001 FDR:   151
0:37:36.032869 PROGRESS: 
0:37:36.032926 PROGRESS: Protein Summary:
0:37:36.034058 PROGRESS: Channel   0:	 0.05 FDR:   385; 0.01 FDR:   257; 0.001 FDR:   146
0:37:36.034629 PROGRESS: =========================================================================
0:37:36.073632 INFO: fragments_df: keeping 2585 of 558885 [sum(precursor_idx_mask)=5322 sum(mass_error_mask)=558885 stop_rank=2585
0:37:36.200556 INFO: calibration group: precursor, fitting rt estimator 
0:37:36.303407 INFO: calibration group: fragment, fitting mz estimator 
0:37:36.585012 INFO: Using score_cutoff 53.69659407806396 (fac=0.99, q=1)
0:37:36.585402 INFO: calibration group: precursor, predicting mz
0:37:36.585494 WARNING: mz prediction was skipped as it has not been fitted yet
0:37:36.585525 INFO: calibration group: precursor, predicting rt
0:37:36.617067 INFO: calibration group: fragment, predicting mz
0:37:36.682595 INFO: === checking if optimization conditions were reached ===
0:37:36.682839 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:37:36.684752 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 82.2035.
0:37:36.684806 INFO: ==============================================
0:37:36.684896 INFO: Starting optimization step 3.
0:37:36.684961 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:37:36.685020 PROGRESS: Extracting batch of 50212 precursors
0:37:36.696886 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:37:36.696994 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:37:36.697026 INFO: FWHM in RT is 2.45 seconds, sigma is 0.32
0:37:36.697049 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:37:36.697236 INFO: Starting candidate selection
0:37:38.657187 INFO: Starting candidate scoring
0:37:39.290883 INFO: Finished candidate processing
0:37:39.290976 INFO: Collecting candidate features
0:37:39.425606 WARNING: intensity_correlation has 20 NaNs ( 0.02 % out of 97347)
0:37:39.434501 INFO: Collecting fragment features
0:37:39.479422 INFO: Finished candidate scoring
0:37:39.523376 PROGRESS: === Extracted 97347 precursors and 558634 fragments ===
0:37:39.523750 INFO: performing precursor FDR with 47 features
0:37:39.523787 INFO: Decoy channel: -1
0:37:39.523812 INFO: Competetive: True
0:37:39.549824 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:39.567631 WARNING: dropped 10 target PSMs due to missing features
0:37:39.567757 WARNING: dropped 10 decoy PSMs due to missing features
0:37:41.104284 INFO: Test AUC: 0.548
0:37:41.104491 INFO: Train AUC: 0.570
0:37:41.104522 INFO: AUC difference: 3.93%
0:37:41.307652 INFO: Resetting torch num_threads to 100
0:37:41.311081 INFO: === FDR correction performed with classifier version 7 ===
0:37:41.311828 PROGRESS: ============================= Precursor FDR =============================
0:37:41.311934 PROGRESS: Total precursors accumulated: 546
0:37:41.311995 PROGRESS: Target precursors: 500 (91.58%)
0:37:41.312049 PROGRESS: Decoy precursors: 46 (8.42%)
0:37:41.312096 PROGRESS: 
0:37:41.312141 PROGRESS: Precursor Summary:
0:37:41.313146 PROGRESS: Channel   0:	 0.05 FDR:   434; 0.01 FDR:   267; 0.001 FDR:   137
0:37:41.313238 PROGRESS: 
0:37:41.313293 PROGRESS: Protein Summary:
0:37:41.314441 PROGRESS: Channel   0:	 0.05 FDR:   409; 0.01 FDR:   255; 0.001 FDR:   132
0:37:41.314536 PROGRESS: =========================================================================
0:37:41.353177 INFO: fragments_df: keeping 2586 of 558634 [sum(precursor_idx_mask)=5346 sum(mass_error_mask)=558634 stop_rank=2586
0:37:41.492606 INFO: calibration group: precursor, fitting rt estimator 
0:37:41.626017 INFO: calibration group: fragment, fitting mz estimator 
0:37:41.965273 INFO: Using score_cutoff 56.46781414489746 (fac=0.99, q=1)
0:37:41.965710 INFO: calibration group: precursor, predicting mz
0:37:41.965809 WARNING: mz prediction was skipped as it has not been fitted yet
0:37:41.965839 INFO: calibration group: precursor, predicting rt
0:37:42.004877 INFO: calibration group: fragment, predicting mz
0:37:42.074819 INFO: === checking if optimization conditions were reached ===
0:37:42.075109 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:37:42.077485 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 80.5586.
0:37:42.077561 INFO: ==============================================
0:37:42.077677 INFO: Starting optimization step 4.
0:37:42.077755 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:37:42.077834 PROGRESS: Extracting batch of 50212 precursors
0:37:42.096234 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:37:42.096340 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:37:42.096382 INFO: FWHM in RT is 2.46 seconds, sigma is 0.32
0:37:42.096410 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:37:42.096696 INFO: Starting candidate selection
0:37:45.622071 INFO: Starting candidate scoring
0:37:46.267514 INFO: Finished candidate processing
0:37:46.267644 INFO: Collecting candidate features
0:37:46.412063 WARNING: intensity_correlation has 17 NaNs ( 0.02 % out of 97318)
0:37:46.420143 INFO: Collecting fragment features
0:37:46.468171 INFO: Finished candidate scoring
0:37:46.506444 PROGRESS: === Extracted 97318 precursors and 558731 fragments ===
0:37:46.506829 INFO: performing precursor FDR with 47 features
0:37:46.506868 INFO: Decoy channel: -1
0:37:46.506891 INFO: Competetive: True
0:37:46.537438 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:46.554837 WARNING: dropped 11 target PSMs due to missing features
0:37:46.554960 WARNING: dropped 6 decoy PSMs due to missing features
0:37:47.931935 INFO: Test AUC: 0.550
0:37:47.932057 INFO: Train AUC: 0.571
0:37:47.932086 INFO: AUC difference: 3.60%
0:37:48.132517 INFO: Resetting torch num_threads to 100
0:37:48.135866 INFO: === FDR correction performed with classifier version 7 ===
0:37:48.136584 PROGRESS: ============================= Precursor FDR =============================
0:37:48.136684 PROGRESS: Total precursors accumulated: 557
0:37:48.136742 PROGRESS: Target precursors: 509 (91.38%)
0:37:48.136793 PROGRESS: Decoy precursors: 48 (8.62%)
0:37:48.136839 PROGRESS: 
0:37:48.136883 PROGRESS: Precursor Summary:
0:37:48.137869 PROGRESS: Channel   0:	 0.05 FDR:   414; 0.01 FDR:   271; 0.001 FDR:   175
0:37:48.137959 PROGRESS: 
0:37:48.138013 PROGRESS: Protein Summary:
0:37:48.139157 PROGRESS: Channel   0:	 0.05 FDR:   393; 0.01 FDR:   259; 0.001 FDR:   168
0:37:48.139259 PROGRESS: =========================================================================
0:37:48.177350 INFO: fragments_df: keeping 2609 of 558731 [sum(precursor_idx_mask)=5392 sum(mass_error_mask)=558731 stop_rank=2609
0:37:48.305193 INFO: calibration group: precursor, fitting rt estimator 
0:37:48.424739 INFO: calibration group: fragment, fitting mz estimator 
0:37:48.773751 INFO: Using score_cutoff 53.959914047241206 (fac=0.99, q=1)
0:37:48.774121 INFO: calibration group: precursor, predicting mz
0:37:48.774208 WARNING: mz prediction was skipped as it has not been fitted yet
0:37:48.774239 INFO: calibration group: precursor, predicting rt
0:37:48.804992 INFO: calibration group: fragment, predicting mz
0:37:48.868321 INFO: === checking if optimization conditions were reached ===
0:37:48.868590 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:37:48.869921 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 80.5586 found after 5 searches.
0:37:48.869982 INFO: ==============================================
0:37:48.870086 PROGRESS: Optimization finished for rt_error.
0:37:49.004884 INFO: calibration group: precursor, predicting mz
0:37:49.005133 WARNING: mz prediction was skipped as it has not been fitted yet
0:37:49.005165 INFO: calibration group: precursor, predicting rt
0:37:49.036302 INFO: calibration group: fragment, predicting mz
0:37:49.129452 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:37:49.129690 PROGRESS: ==============================================
0:37:49.129769 PROGRESS: ms2_error      : 6.3338
0:37:49.129835 PROGRESS: rt_error       : 80.5586
0:37:49.129893 PROGRESS: ==============================================
0:37:49.130524 INFO: calibration group: precursor, predicting mz
0:37:49.130662 WARNING: mz prediction was skipped as it has not been fitted yet
0:37:49.130707 INFO: calibration group: precursor, predicting rt
0:37:55.743100 INFO: calibration group: fragment, predicting mz
0:38:10.589212 PROGRESS: Extracting batch of 10183864 precursors
0:38:12.834337 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:38:12.834468 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:38:12.834506 INFO: FWHM in RT is 2.45 seconds, sigma is 0.32
0:38:12.834530 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:38:12.834916 INFO: Starting candidate selection
0:44:41.497464 INFO: Applying score cutoff of 53.959914047241206
0:44:41.564646 INFO: Removed 19367956 precursors with score below cutoff
0:44:43.760875 INFO: Starting candidate scoring
0:44:50.875082 INFO: Finished candidate processing
0:44:50.875287 INFO: Collecting candidate features
0:44:54.260670 INFO: Collecting fragment features
0:44:55.296316 INFO: Finished candidate scoring
0:44:56.460582 INFO: === FDR correction performed with classifier version 24 ===
0:44:56.462078 INFO: performing precursor FDR with 47 features
0:44:56.462132 INFO: Decoy channel: -1
0:44:56.462156 INFO: Competetive: True
0:44:56.761740 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:56.886505 WARNING: FDR calculation for 499479 target and 438217 decoy PSMs
0:44:56.886646 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
0:45:12.883702 INFO: Test AUC: 0.666
0:45:12.883911 INFO: Train AUC: 0.673
0:45:12.883945 INFO: AUC difference: 1.09%
0:45:13.311600 INFO: Resetting torch num_threads to 100
0:45:13.347157 INFO: Removing fragments below FDR threshold
0:45:13.486002 PROGRESS: ============================= Precursor FDR =============================
0:45:13.486275 PROGRESS: Total precursors accumulated: 75,571
0:45:13.486360 PROGRESS: Target precursors: 74,823 (99.01%)
0:45:13.486412 PROGRESS: Decoy precursors: 748 (0.99%)
0:45:13.486461 PROGRESS: 
0:45:13.486508 PROGRESS: Precursor Summary:
0:45:13.516967 PROGRESS: Channel   0:	 0.05 FDR: 74,823; 0.01 FDR: 74,823; 0.001 FDR: 52,092
0:45:13.517210 PROGRESS: 
0:45:13.517276 PROGRESS: Protein Summary:
0:45:13.560256 PROGRESS: Channel   0:	 0.05 FDR: 11,325; 0.01 FDR: 11,325; 0.001 FDR: 8,778
0:45:13.560488 PROGRESS: =========================================================================
0:45:14.152464 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:45:14.601529 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:45:14.601693 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant
0:45:14.601771 INFO: Creating folder run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/figures
0:45:14.602507 INFO: Initializing RawFileManager
0:45:25.040378 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.
0:45:25.045203 INFO: Determining DIA cycle
0:45:25.060621 INFO: Found cycle with start 0.00 min and length 300.
0:45:25.227428 INFO: RT (min)            : 0.0 - 26.9
0:45:25.227554 INFO: RT duration (sec)   : 1611.2
0:45:25.227583 INFO: RT duration (min)   : 26.9
0:45:25.227607 INFO: Cycle len (scans)   : 300
0:45:25.227627 INFO: Cycle len (sec)     : 1.65
0:45:25.227645 INFO: Number of cycles    : 977
0:45:25.227663 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:45:26.587175 INFO: Initializing CalibrationManager
0:45:26.587604 INFO: Loading calibration config
0:45:26.588264 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'}]
0:45:26.588380 INFO: Calibration group :fragment, found 1 estimator(s)
0:45:26.588469 INFO: Calibration group :precursor, found 3 estimator(s)
0:45:26.588557 INFO: Disabling ion mobility calibration
0:45:26.588585 INFO: removed mobility estimator from group precursor
0:45:26.588923 INFO: Initializing OptimizationManager
0:45:26.589039 INFO: initial parameter: ms1_error = 30
0:45:26.589101 INFO: initial parameter: ms2_error = 30
0:45:26.589154 INFO: initial parameter: rt_error = 805.6004638671875
0:45:26.589199 INFO: initial parameter: mobility_error = 0.1
0:45:26.589240 INFO: initial parameter: column_type = library
0:45:26.589283 INFO: initial parameter: num_candidates = 1
0:45:26.589325 INFO: initial parameter: classifier_version = -1
0:45:26.589364 INFO: initial parameter: fwhm_rt = 5
0:45:26.589406 INFO: initial parameter: fwhm_mobility = 0.01
0:45:26.589445 INFO: initial parameter: score_cutoff = 0
0:45:26.589516 INFO: Initializing TimingManager
0:45:26.589581 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:45:26.589728 INFO: FDRManager not loaded from disk.
0:45:26.589751 INFO: Initializing FDRManager
0:45:26.589794 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:45:27.903536 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
0:45:29.766841 PROGRESS: Starting initial search for precursors.
0:45:29.983288 INFO: Starting optimization step 0.
0:45:29.983507 PROGRESS: === Extracting elution groups 0 to 200 ===
0:45:29.983583 PROGRESS: Extracting batch of 395 precursors
0:45:29.984583 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:29.984628 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:29.984664 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:45:29.984688 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:45:29.984949 INFO: Starting candidate selection
0:45:30.128627 INFO: Starting candidate scoring
0:45:30.163481 INFO: Finished candidate processing
0:45:30.163553 INFO: Collecting candidate features
0:45:30.171772 INFO: Collecting fragment features
0:45:30.173808 INFO: Finished candidate scoring
0:45:30.174579 PROGRESS: === Extracted 395 precursors and 3918 fragments ===
0:45:30.174851 INFO: performing precursor FDR with 47 features
0:45:30.174887 INFO: Decoy channel: -1
0:45:30.174910 INFO: Competetive: True
0:45:30.175887 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:30.194608 INFO: Test AUC: 0.432
0:45:30.194671 INFO: Train AUC: 0.450
0:45:30.194699 INFO: AUC difference: 4.10%
0:45:30.365722 INFO: Resetting torch num_threads to 100
0:45:30.366184 INFO: === FDR correction performed with classifier version -1 ===
0:45:30.366770 PROGRESS: ============================= Precursor FDR =============================
0:45:30.366864 PROGRESS: Total precursors accumulated: 200
0:45:30.366924 PROGRESS: Target precursors: 98 (49.00%)
0:45:30.366982 PROGRESS: Decoy precursors: 102 (51.00%)
0:45:30.367029 PROGRESS: 
0:45:30.367073 PROGRESS: Precursor Summary:
0:45:30.367903 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:45:30.367988 PROGRESS: 
0:45:30.368048 PROGRESS: Protein Summary:
0:45:30.368950 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:45:30.369045 PROGRESS: =========================================================================
0:45:30.424080 INFO: Starting optimization step 1.
0:45:30.424223 PROGRESS: === Extracting elution groups 200 to 600 ===
0:45:30.424291 PROGRESS: Extracting batch of 790 precursors
0:45:30.425070 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:30.425116 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:30.425146 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:45:30.425168 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:45:30.425323 INFO: Starting candidate selection
0:45:30.564200 INFO: Starting candidate scoring
0:45:30.600327 INFO: Finished candidate processing
0:45:30.600400 INFO: Collecting candidate features
0:45:30.608892 INFO: Collecting fragment features
0:45:30.611187 INFO: Finished candidate scoring
0:45:30.613201 PROGRESS: === Extracted 1183 precursors and 11924 fragments ===
0:45:30.613950 INFO: performing precursor FDR with 47 features
0:45:30.613994 INFO: Decoy channel: -1
0:45:30.614017 INFO: Competetive: True
0:45:30.616762 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:30.647610 INFO: Test AUC: 0.538
0:45:30.647673 INFO: Train AUC: 0.489
0:45:30.647702 INFO: AUC difference: 9.93%
0:45:30.647723 WARNING: AUC difference > 5%. This may indicate overfitting.
0:45:30.820838 INFO: Resetting torch num_threads to 100
0:45:30.821380 INFO: === FDR correction performed with classifier version -1 ===
0:45:30.822018 PROGRESS: ============================= Precursor FDR =============================
0:45:30.822114 PROGRESS: Total precursors accumulated: 599
0:45:30.822176 PROGRESS: Target precursors: 317 (52.92%)
0:45:30.822230 PROGRESS: Decoy precursors: 282 (47.08%)
0:45:30.822275 PROGRESS: 
0:45:30.822320 PROGRESS: Precursor Summary:
0:45:30.823183 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:45:30.823273 PROGRESS: 
0:45:30.823328 PROGRESS: Protein Summary:
0:45:30.824237 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:45:30.824325 PROGRESS: =========================================================================
0:45:30.881389 INFO: Starting optimization step 2.
0:45:30.881519 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:45:30.881583 PROGRESS: Extracting batch of 1585 precursors
0:45:30.882472 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:30.882519 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:30.882550 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:45:30.882572 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:45:30.882747 INFO: Starting candidate selection
0:45:31.044515 INFO: Starting candidate scoring
0:45:31.082335 INFO: Finished candidate processing
0:45:31.082412 INFO: Collecting candidate features
0:45:31.092466 INFO: Collecting fragment features
0:45:31.095645 INFO: Finished candidate scoring
0:45:31.099025 PROGRESS: === Extracted 2762 precursors and 27968 fragments ===
0:45:31.100087 INFO: performing precursor FDR with 47 features
0:45:31.100135 INFO: Decoy channel: -1
0:45:31.100159 INFO: Competetive: True
0:45:31.103271 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:31.132862 INFO: Test AUC: 0.493
0:45:31.132935 INFO: Train AUC: 0.516
0:45:31.132964 INFO: AUC difference: 4.45%
0:45:31.302320 INFO: Resetting torch num_threads to 100
0:45:31.302980 INFO: === FDR correction performed with classifier version -1 ===
0:45:31.303742 PROGRESS: ============================= Precursor FDR =============================
0:45:31.303841 PROGRESS: Total precursors accumulated: 1,396
0:45:31.303901 PROGRESS: Target precursors: 752 (53.87%)
0:45:31.303953 PROGRESS: Decoy precursors: 644 (46.13%)
0:45:31.303998 PROGRESS: 
0:45:31.304042 PROGRESS: Precursor Summary:
0:45:31.304903 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:45:31.304991 PROGRESS: 
0:45:31.305046 PROGRESS: Protein Summary:
0:45:31.305971 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:45:31.306068 PROGRESS: =========================================================================
0:45:31.365386 INFO: Starting optimization step 3.
0:45:31.365521 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:45:31.365586 PROGRESS: Extracting batch of 3157 precursors
0:45:31.366609 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:31.366656 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:31.366687 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:45:31.366711 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:45:31.366861 INFO: Starting candidate selection
0:45:31.592522 INFO: Starting candidate scoring
0:45:31.632742 INFO: Finished candidate processing
0:45:31.632821 INFO: Collecting candidate features
0:45:31.645515 INFO: Collecting fragment features
0:45:31.649513 INFO: Finished candidate scoring
0:45:31.654329 PROGRESS: === Extracted 5917 precursors and 60162 fragments ===
0:45:31.655600 INFO: performing precursor FDR with 47 features
0:45:31.655646 INFO: Decoy channel: -1
0:45:31.655670 INFO: Competetive: True
0:45:31.659788 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:31.710464 INFO: Test AUC: 0.496
0:45:31.710557 INFO: Train AUC: 0.522
0:45:31.710585 INFO: AUC difference: 4.94%
0:45:31.880534 INFO: Resetting torch num_threads to 100
0:45:31.881326 INFO: === FDR correction performed with classifier version -1 ===
0:45:31.882275 PROGRESS: ============================= Precursor FDR =============================
0:45:31.882375 PROGRESS: Total precursors accumulated: 2,995
0:45:31.882434 PROGRESS: Target precursors: 1,592 (53.16%)
0:45:31.882487 PROGRESS: Decoy precursors: 1,403 (46.84%)
0:45:31.882534 PROGRESS: 
0:45:31.882579 PROGRESS: Precursor Summary:
0:45:31.883480 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:45:31.883569 PROGRESS: 
0:45:31.883626 PROGRESS: Protein Summary:
0:45:31.884555 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:45:31.884646 PROGRESS: =========================================================================
0:45:31.948911 INFO: Starting optimization step 4.
0:45:31.949057 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:45:31.949123 PROGRESS: Extracting batch of 6336 precursors
0:45:31.950676 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:31.950725 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:31.950756 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:45:31.950778 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:45:31.950932 INFO: Starting candidate selection
0:45:32.395158 INFO: Starting candidate scoring
0:45:32.444046 INFO: Finished candidate processing
0:45:32.444139 INFO: Collecting candidate features
0:45:32.462210 INFO: Collecting fragment features
0:45:32.468165 INFO: Finished candidate scoring
0:45:32.475892 PROGRESS: === Extracted 12238 precursors and 124731 fragments ===
0:45:32.477636 INFO: performing precursor FDR with 47 features
0:45:32.477692 INFO: Decoy channel: -1
0:45:32.477717 INFO: Competetive: True
0:45:32.483322 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:32.533088 INFO: Test AUC: 0.512
0:45:32.533184 INFO: Train AUC: 0.508
0:45:32.533215 INFO: AUC difference: 0.74%
0:45:32.708857 INFO: Resetting torch num_threads to 100
0:45:32.710006 INFO: === FDR correction performed with classifier version -1 ===
0:45:32.710652 PROGRESS: ============================= Precursor FDR =============================
0:45:32.710749 PROGRESS: Total precursors accumulated: 1
0:45:32.710807 PROGRESS: Target precursors: 1 (100.00%)
0:45:32.710857 PROGRESS: Decoy precursors: 0 (0.00%)
0:45:32.710904 PROGRESS: 
0:45:32.710946 PROGRESS: Precursor Summary:
0:45:32.711871 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:45:32.711960 PROGRESS: 
0:45:32.712015 PROGRESS: Protein Summary:
0:45:32.713020 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:45:32.713108 PROGRESS: =========================================================================
0:45:32.784126 INFO: Starting optimization step 5.
0:45:32.784324 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:45:32.784392 PROGRESS: Extracting batch of 12662 precursors
0:45:32.786805 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:32.786855 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:32.786885 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:45:32.786906 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:45:32.787068 INFO: Starting candidate selection
0:45:33.599430 INFO: Starting candidate scoring
0:45:33.684402 INFO: Finished candidate processing
0:45:33.684500 INFO: Collecting candidate features
0:45:33.712523 INFO: Collecting fragment features
0:45:33.723190 INFO: Finished candidate scoring
0:45:33.735949 PROGRESS: === Extracted 24888 precursors and 253836 fragments ===
0:45:33.739407 INFO: performing precursor FDR with 47 features
0:45:33.739482 INFO: Decoy channel: -1
0:45:33.739506 INFO: Competetive: True
0:45:33.749061 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:34.002157 INFO: Test AUC: 0.543
0:45:34.002276 INFO: Train AUC: 0.556
0:45:34.002306 INFO: AUC difference: 2.24%
0:45:34.183455 INFO: Resetting torch num_threads to 100
0:45:34.185344 INFO: === FDR correction performed with classifier version -1 ===
0:45:34.185982 PROGRESS: ============================= Precursor FDR =============================
0:45:34.186080 PROGRESS: Total precursors accumulated: 2
0:45:34.186141 PROGRESS: Target precursors: 2 (100.00%)
0:45:34.186194 PROGRESS: Decoy precursors: 0 (0.00%)
0:45:34.186242 PROGRESS: 
0:45:34.186286 PROGRESS: Precursor Summary:
0:45:34.187236 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
0:45:34.187328 PROGRESS: 
0:45:34.187385 PROGRESS: Protein Summary:
0:45:34.188396 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
0:45:34.188486 PROGRESS: =========================================================================
0:45:34.276334 INFO: Starting optimization step 6.
0:45:34.276567 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:45:34.276638 PROGRESS: Extracting batch of 25287 precursors
0:45:34.282187 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:34.282252 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:34.282283 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:45:34.282305 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:45:34.282481 INFO: Starting candidate selection
0:45:35.837965 INFO: Starting candidate scoring
0:45:36.002823 INFO: Finished candidate processing
0:45:36.004067 INFO: Collecting candidate features
0:45:36.050357 INFO: Collecting fragment features
0:45:36.067905 INFO: Finished candidate scoring
0:45:36.091382 PROGRESS: === Extracted 50105 precursors and 511312 fragments ===
0:45:36.097356 INFO: performing precursor FDR with 47 features
0:45:36.097442 INFO: Decoy channel: -1
0:45:36.097467 INFO: Competetive: True
0:45:36.115511 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:36.834457 INFO: Test AUC: 0.562
0:45:36.834581 INFO: Train AUC: 0.575
0:45:36.834620 INFO: AUC difference: 2.13%
0:45:37.023092 INFO: Resetting torch num_threads to 100
0:45:37.026375 INFO: === FDR correction performed with classifier version -1 ===
0:45:37.027004 PROGRESS: ============================= Precursor FDR =============================
0:45:37.027097 PROGRESS: Total precursors accumulated: 190
0:45:37.027156 PROGRESS: Target precursors: 174 (91.58%)
0:45:37.027207 PROGRESS: Decoy precursors: 16 (8.42%)
0:45:37.027254 PROGRESS: 
0:45:37.027299 PROGRESS: Precursor Summary:
0:45:37.028209 PROGRESS: Channel   0:	 0.05 FDR:   163; 0.01 FDR:   119; 0.001 FDR:    74
0:45:37.028297 PROGRESS: 
0:45:37.028353 PROGRESS: Protein Summary:
0:45:37.029367 PROGRESS: Channel   0:	 0.05 FDR:   159; 0.01 FDR:   115; 0.001 FDR:    73
0:45:37.029459 PROGRESS: =========================================================================
0:45:37.149528 INFO: Starting optimization step 7.
0:45:37.150178 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:45:37.150256 PROGRESS: Extracting batch of 50588 precursors
0:45:37.161616 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:37.161729 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:37.161762 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:45:37.161784 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:45:37.161981 INFO: Starting candidate selection
0:45:40.194966 INFO: Starting candidate scoring
0:45:40.534587 INFO: Finished candidate processing
0:45:40.534740 INFO: Collecting candidate features
0:45:40.620879 INFO: Collecting fragment features
0:45:40.654338 INFO: Finished candidate scoring
0:45:40.708794 PROGRESS: === Extracted 100596 precursors and 1027092 fragments ===
0:45:40.720560 INFO: performing precursor FDR with 47 features
0:45:40.720654 INFO: Decoy channel: -1
0:45:40.720680 INFO: Competetive: True
0:45:40.758415 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:42.400581 INFO: Test AUC: 0.564
0:45:42.400701 INFO: Train AUC: 0.585
0:45:42.400729 INFO: AUC difference: 3.50%
0:45:42.595891 INFO: Resetting torch num_threads to 100
0:45:42.626443 INFO: === FDR correction performed with classifier version -1 ===
0:45:42.630780 PROGRESS: ============================= Precursor FDR =============================
0:45:42.630907 PROGRESS: Total precursors accumulated: 546
0:45:42.630970 PROGRESS: Target precursors: 499 (91.39%)
0:45:42.631022 PROGRESS: Decoy precursors: 47 (8.61%)
0:45:42.631073 PROGRESS: 
0:45:42.631118 PROGRESS: Precursor Summary:
0:45:42.632133 PROGRESS: Channel   0:	 0.05 FDR:   428; 0.01 FDR:   349; 0.001 FDR:   276
0:45:42.632225 PROGRESS: 
0:45:42.632280 PROGRESS: Protein Summary:
0:45:42.633459 PROGRESS: Channel   0:	 0.05 FDR:   406; 0.01 FDR:   331; 0.001 FDR:   265
0:45:42.633550 PROGRESS: =========================================================================
0:45:42.718412 INFO: fragments_df: keeping 3079 of 1027092 [sum(precursor_idx_mask)=3998 sum(mass_error_mask)=1027092 stop_rank=3079
0:45:42.953298 INFO: calibration group: precursor, fitting rt estimator 
0:45:43.099146 INFO: calibration group: fragment, fitting mz estimator 
0:45:43.494570 INFO: Using score_cutoff 68.64962788696289 (fac=0.99, q=1)
0:45:43.495007 INFO: calibration group: precursor, predicting mz
0:45:43.495093 WARNING: mz prediction was skipped as it has not been fitted yet
0:45:43.495125 INFO: calibration group: precursor, predicting rt
0:45:43.558504 INFO: calibration group: fragment, predicting mz
0:45:43.712006 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:45:43.712311 INFO: Starting optimization step 8.
0:45:43.712392 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:45:43.712478 PROGRESS: Extracting batch of 100800 precursors
0:45:43.749308 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:43.749445 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:43.749487 INFO: FWHM in RT is 2.97 seconds, sigma is 0.38
0:45:43.749515 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:45:43.749789 INFO: Starting candidate selection
0:45:48.449429 INFO: Starting candidate scoring
0:45:49.772254 INFO: Finished candidate processing
0:45:49.772355 INFO: Collecting candidate features
0:45:50.072629 INFO: Collecting fragment features
0:45:50.200001 INFO: Finished candidate scoring
0:45:50.375777 PROGRESS: === Extracted 201192 precursors and 2026423 fragments ===
0:45:50.376196 INFO: performing precursor FDR with 47 features
0:45:50.376234 INFO: Decoy channel: -1
0:45:50.376258 INFO: Competetive: True
0:45:50.433513 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:53.652150 INFO: Test AUC: 0.567
0:45:53.652270 INFO: Train AUC: 0.589
0:45:53.652301 INFO: AUC difference: 3.66%
0:45:53.874943 INFO: Resetting torch num_threads to 100
0:45:53.880856 INFO: === FDR correction performed with classifier version 7 ===
0:45:53.881808 PROGRESS: ============================= Precursor FDR =============================
0:45:53.881925 PROGRESS: Total precursors accumulated: 643
0:45:53.881993 PROGRESS: Target precursors: 590 (91.76%)
0:45:53.882049 PROGRESS: Decoy precursors: 53 (8.24%)
0:45:53.882096 PROGRESS: 
0:45:53.882142 PROGRESS: Precursor Summary:
0:45:53.883205 PROGRESS: Channel   0:	 0.05 FDR:   507; 0.01 FDR:   363; 0.001 FDR:   236
0:45:53.883299 PROGRESS: 
0:45:53.883356 PROGRESS: Protein Summary:
0:45:53.884546 PROGRESS: Channel   0:	 0.05 FDR:   478; 0.01 FDR:   346; 0.001 FDR:   228
0:45:53.884641 PROGRESS: =========================================================================
0:45:54.017588 INFO: fragments_df: keeping 4043 of 2026423 [sum(precursor_idx_mask)=8170 sum(mass_error_mask)=2026423 stop_rank=4043
0:45:54.215813 INFO: calibration group: precursor, fitting rt estimator 
0:45:54.342025 INFO: calibration group: fragment, fitting mz estimator 
0:45:54.868867 INFO: Using score_cutoff 66.4492435180664 (fac=0.99, q=1)
0:45:54.869258 INFO: calibration group: precursor, predicting mz
0:45:54.869348 WARNING: mz prediction was skipped as it has not been fitted yet
0:45:54.869381 INFO: calibration group: precursor, predicting rt
0:45:54.933738 INFO: calibration group: fragment, predicting mz
0:45:55.083674 INFO: === checking if optimization conditions were reached ===
0:45:55.083959 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:45:55.086505 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 24.3142.
0:45:55.086566 INFO: ==============================================
0:45:55.086680 INFO: Starting optimization step 9.
0:45:55.086757 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:45:55.086837 PROGRESS: Extracting batch of 100800 precursors
0:45:55.122545 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:45:55.122690 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:45:55.122733 INFO: FWHM in RT is 2.92 seconds, sigma is 0.38
0:45:55.122760 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:45:55.123035 INFO: Starting candidate selection
0:45:59.803286 INFO: Starting candidate scoring
0:46:01.136892 INFO: Finished candidate processing
0:46:01.136988 INFO: Collecting candidate features
0:46:01.472917 INFO: Collecting fragment features
0:46:01.603543 INFO: Finished candidate scoring
0:46:01.781577 PROGRESS: === Extracted 201191 precursors and 1966547 fragments ===
0:46:01.782027 INFO: performing precursor FDR with 47 features
0:46:01.782068 INFO: Decoy channel: -1
0:46:01.782091 INFO: Competetive: True
0:46:01.850049 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:05.213319 INFO: Test AUC: 0.562
0:46:05.213491 INFO: Train AUC: 0.584
0:46:05.213522 INFO: AUC difference: 3.78%
0:46:05.443184 INFO: Resetting torch num_threads to 100
0:46:05.449178 INFO: === FDR correction performed with classifier version 7 ===
0:46:05.449952 PROGRESS: ============================= Precursor FDR =============================
0:46:05.450048 PROGRESS: Total precursors accumulated: 633
0:46:05.450107 PROGRESS: Target precursors: 583 (92.10%)
0:46:05.450157 PROGRESS: Decoy precursors: 50 (7.90%)
0:46:05.450204 PROGRESS: 
0:46:05.450248 PROGRESS: Precursor Summary:
0:46:05.451265 PROGRESS: Channel   0:	 0.05 FDR:   455; 0.01 FDR:   378; 0.001 FDR:   278
0:46:05.451356 PROGRESS: 
0:46:05.451415 PROGRESS: Protein Summary:
0:46:05.452602 PROGRESS: Channel   0:	 0.05 FDR:   430; 0.01 FDR:   359; 0.001 FDR:   266
0:46:05.452695 PROGRESS: =========================================================================
0:46:05.588695 INFO: fragments_df: keeping 4194 of 1966547 [sum(precursor_idx_mask)=8426 sum(mass_error_mask)=1966547 stop_rank=4194
0:46:05.793749 INFO: calibration group: precursor, fitting rt estimator 
0:46:05.916850 INFO: calibration group: fragment, fitting mz estimator 
0:46:06.457668 INFO: Using score_cutoff 59.75900034370422 (fac=0.99, q=1)
0:46:06.458076 INFO: calibration group: precursor, predicting mz
0:46:06.458163 WARNING: mz prediction was skipped as it has not been fitted yet
0:46:06.458201 INFO: calibration group: precursor, predicting rt
0:46:06.520607 INFO: calibration group: fragment, predicting mz
0:46:06.670912 INFO: === checking if optimization conditions were reached ===
0:46:06.671200 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:46:06.673921 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 20.6662.
0:46:06.673983 INFO: ==============================================
0:46:06.674093 INFO: Starting optimization step 10.
0:46:06.674168 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:46:06.674249 PROGRESS: Extracting batch of 100800 precursors
0:46:06.709370 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:46:06.709500 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:46:06.709545 INFO: FWHM in RT is 2.84 seconds, sigma is 0.37
0:46:06.709574 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:46:06.709915 INFO: Starting candidate selection
0:46:11.357366 INFO: Starting candidate scoring
0:46:12.802991 INFO: Finished candidate processing
0:46:12.803088 INFO: Collecting candidate features
0:46:13.113758 INFO: Collecting fragment features
0:46:13.227182 INFO: Finished candidate scoring
0:46:13.320595 PROGRESS: === Extracted 201187 precursors and 1907989 fragments ===
0:46:13.320952 INFO: performing precursor FDR with 47 features
0:46:13.320990 INFO: Decoy channel: -1
0:46:13.321015 INFO: Competetive: True
0:46:13.375858 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:16.831394 INFO: Test AUC: 0.562
0:46:16.831589 INFO: Train AUC: 0.584
0:46:16.831620 INFO: AUC difference: 3.78%
0:46:17.065667 INFO: Resetting torch num_threads to 100
0:46:17.070991 INFO: === FDR correction performed with classifier version 7 ===
0:46:17.071755 PROGRESS: ============================= Precursor FDR =============================
0:46:17.071870 PROGRESS: Total precursors accumulated: 705
0:46:17.071937 PROGRESS: Target precursors: 648 (91.91%)
0:46:17.071990 PROGRESS: Decoy precursors: 57 (8.09%)
0:46:17.072036 PROGRESS: 
0:46:17.072081 PROGRESS: Precursor Summary:
0:46:17.073115 PROGRESS: Channel   0:	 0.05 FDR:   546; 0.01 FDR:   420; 0.001 FDR:   278
0:46:17.073207 PROGRESS: 
0:46:17.073265 PROGRESS: Protein Summary:
0:46:17.074477 PROGRESS: Channel   0:	 0.05 FDR:   508; 0.01 FDR:   399; 0.001 FDR:   268
0:46:17.074569 PROGRESS: =========================================================================
0:46:17.204202 INFO: fragments_df: keeping 4498 of 1907989 [sum(precursor_idx_mask)=9220 sum(mass_error_mask)=1907989 stop_rank=4498
0:46:17.358904 INFO: calibration group: precursor, fitting rt estimator 
0:46:17.486044 INFO: calibration group: fragment, fitting mz estimator 
0:46:18.076851 INFO: Using score_cutoff 60.41996643562317 (fac=0.99, q=1)
0:46:18.077250 INFO: calibration group: precursor, predicting mz
0:46:18.077337 WARNING: mz prediction was skipped as it has not been fitted yet
0:46:18.077366 INFO: calibration group: precursor, predicting rt
0:46:18.108317 INFO: calibration group: fragment, predicting mz
0:46:18.176424 INFO: === checking if optimization conditions were reached ===
0:46:18.176703 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
0:46:18.179501 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 17.0227.
0:46:18.179564 INFO: ==============================================
0:46:18.179677 INFO: Starting optimization step 11.
0:46:18.179752 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:46:18.179842 PROGRESS: Extracting batch of 50212 precursors
0:46:18.197304 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:46:18.197423 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:46:18.197467 INFO: FWHM in RT is 2.84 seconds, sigma is 0.37
0:46:18.197497 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:46:18.197786 INFO: Starting candidate selection
0:46:20.577908 INFO: Starting candidate scoring
0:46:21.236780 INFO: Finished candidate processing
0:46:21.236945 INFO: Collecting candidate features
0:46:21.385105 INFO: Collecting fragment features
0:46:21.456021 INFO: Finished candidate scoring
0:46:21.502642 PROGRESS: === Extracted 100209 precursors and 922462 fragments ===
0:46:21.503018 INFO: performing precursor FDR with 47 features
0:46:21.503055 INFO: Decoy channel: -1
0:46:21.503077 INFO: Competetive: True
0:46:21.538793 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:23.070521 INFO: Test AUC: 0.558
0:46:23.070650 INFO: Train AUC: 0.584
0:46:23.070680 INFO: AUC difference: 4.42%
0:46:23.269115 INFO: Resetting torch num_threads to 100
0:46:23.272440 INFO: === FDR correction performed with classifier version 7 ===
0:46:23.273100 PROGRESS: ============================= Precursor FDR =============================
0:46:23.273199 PROGRESS: Total precursors accumulated: 389
0:46:23.273259 PROGRESS: Target precursors: 354 (91.00%)
0:46:23.273311 PROGRESS: Decoy precursors: 35 (9.00%)
0:46:23.273358 PROGRESS: 
0:46:23.273401 PROGRESS: Precursor Summary:
0:46:23.274341 PROGRESS: Channel   0:	 0.05 FDR:   251; 0.01 FDR:   169; 0.001 FDR:   154
0:46:23.274433 PROGRESS: 
0:46:23.274486 PROGRESS: Protein Summary:
0:46:23.275546 PROGRESS: Channel   0:	 0.05 FDR:   241; 0.01 FDR:   164; 0.001 FDR:   150
0:46:23.275639 PROGRESS: =========================================================================
0:46:23.398896 INFO: calibration group: precursor, predicting mz
0:46:23.399164 WARNING: mz prediction was skipped as it has not been fitted yet
0:46:23.399198 INFO: calibration group: precursor, predicting rt
0:46:23.430543 INFO: calibration group: fragment, predicting mz
0:46:23.498406 INFO: === skipping optimization until target number of precursors are found ===
0:46:23.498720 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:46:23.498794 INFO: Starting optimization step 12.
0:46:23.498873 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:46:23.498948 PROGRESS: Extracting batch of 50588 precursors
0:46:23.516056 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:46:23.516180 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:46:23.516220 INFO: FWHM in RT is 2.84 seconds, sigma is 0.37
0:46:23.516251 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:46:23.516480 INFO: Starting candidate selection
0:46:25.913926 INFO: Starting candidate scoring
0:46:26.585933 INFO: Finished candidate processing
0:46:26.586084 INFO: Collecting candidate features
0:46:26.770063 INFO: Collecting fragment features
0:46:26.846421 INFO: Finished candidate scoring
0:46:26.945647 PROGRESS: === Extracted 201190 precursors and 1852469 fragments ===
0:46:26.967458 INFO: performing precursor FDR with 47 features
0:46:26.967590 INFO: Decoy channel: -1
0:46:26.967617 INFO: Competetive: True
0:46:27.042685 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:30.376261 INFO: Test AUC: 0.563
0:46:30.376458 INFO: Train AUC: 0.582
0:46:30.376490 INFO: AUC difference: 3.14%
0:46:30.603853 INFO: Resetting torch num_threads to 100
0:46:30.614909 INFO: === FDR correction performed with classifier version 7 ===
0:46:30.615699 PROGRESS: ============================= Precursor FDR =============================
0:46:30.615799 PROGRESS: Total precursors accumulated: 831
0:46:30.615864 PROGRESS: Target precursors: 759 (91.34%)
0:46:30.615915 PROGRESS: Decoy precursors: 72 (8.66%)
0:46:30.615961 PROGRESS: 
0:46:30.616006 PROGRESS: Precursor Summary:
0:46:30.617030 PROGRESS: Channel   0:	 0.05 FDR:   576; 0.01 FDR:   404; 0.001 FDR:   346
0:46:30.617129 PROGRESS: 
0:46:30.617187 PROGRESS: Protein Summary:
0:46:30.618413 PROGRESS: Channel   0:	 0.05 FDR:   538; 0.01 FDR:   382; 0.001 FDR:   327
0:46:30.618506 PROGRESS: =========================================================================
0:46:30.755344 INFO: fragments_df: keeping 4435 of 1852469 [sum(precursor_idx_mask)=8878 sum(mass_error_mask)=1852469 stop_rank=4435
0:46:30.909946 INFO: calibration group: precursor, fitting rt estimator 
0:46:31.034278 INFO: calibration group: fragment, fitting mz estimator 
0:46:31.619952 INFO: Using score_cutoff 65.09200308151246 (fac=0.99, q=1)
0:46:31.620350 INFO: calibration group: precursor, predicting mz
0:46:31.620438 WARNING: mz prediction was skipped as it has not been fitted yet
0:46:31.620469 INFO: calibration group: precursor, predicting rt
0:46:31.651536 INFO: calibration group: fragment, predicting mz
0:46:31.719750 INFO: === checking if optimization conditions were reached ===
0:46:31.720026 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
0:46:31.722868 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 15.1040.
0:46:31.722930 INFO: ==============================================
0:46:31.723040 INFO: Starting optimization step 13.
0:46:31.723116 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:46:31.723200 PROGRESS: Extracting batch of 50212 precursors
0:46:31.740576 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:46:31.740698 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:46:31.740745 INFO: FWHM in RT is 2.76 seconds, sigma is 0.36
0:46:31.740774 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:46:31.741066 INFO: Starting candidate selection
0:46:34.224662 INFO: Starting candidate scoring
0:46:34.865260 INFO: Finished candidate processing
0:46:34.865429 INFO: Collecting candidate features
0:46:35.009990 INFO: Collecting fragment features
0:46:35.071672 INFO: Finished candidate scoring
0:46:35.114757 PROGRESS: === Extracted 100206 precursors and 898343 fragments ===
0:46:35.115127 INFO: performing precursor FDR with 47 features
0:46:35.115165 INFO: Decoy channel: -1
0:46:35.115189 INFO: Competetive: True
0:46:35.148766 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:36.562471 INFO: Test AUC: 0.560
0:46:36.562606 INFO: Train AUC: 0.584
0:46:36.562639 INFO: AUC difference: 3.99%
0:46:36.760946 INFO: Resetting torch num_threads to 100
0:46:36.764289 INFO: === FDR correction performed with classifier version 7 ===
0:46:36.764953 PROGRESS: ============================= Precursor FDR =============================
0:46:36.765052 PROGRESS: Total precursors accumulated: 379
0:46:36.765114 PROGRESS: Target precursors: 344 (90.77%)
0:46:36.765167 PROGRESS: Decoy precursors: 35 (9.23%)
0:46:36.765213 PROGRESS: 
0:46:36.765259 PROGRESS: Precursor Summary:
0:46:36.766215 PROGRESS: Channel   0:	 0.05 FDR:   276; 0.01 FDR:   151; 0.001 FDR:   132
0:46:36.766307 PROGRESS: 
0:46:36.766365 PROGRESS: Protein Summary:
0:46:36.767444 PROGRESS: Channel   0:	 0.05 FDR:   265; 0.01 FDR:   147; 0.001 FDR:   129
0:46:36.767537 PROGRESS: =========================================================================
0:46:36.890257 INFO: calibration group: precursor, predicting mz
0:46:36.890505 WARNING: mz prediction was skipped as it has not been fitted yet
0:46:36.890539 INFO: calibration group: precursor, predicting rt
0:46:36.921952 INFO: calibration group: fragment, predicting mz
0:46:36.988668 INFO: === skipping optimization until target number of precursors are found ===
0:46:36.988941 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:46:36.989013 INFO: Starting optimization step 14.
0:46:36.989089 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:46:36.989176 PROGRESS: Extracting batch of 50588 precursors
0:46:37.006381 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:46:37.006498 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:46:37.006537 INFO: FWHM in RT is 2.76 seconds, sigma is 0.36
0:46:37.006566 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:46:37.006802 INFO: Starting candidate selection
0:46:39.457803 INFO: Starting candidate scoring
0:46:40.106754 INFO: Finished candidate processing
0:46:40.106874 INFO: Collecting candidate features
0:46:40.253194 INFO: Collecting fragment features
0:46:40.309744 INFO: Finished candidate scoring
0:46:40.398421 PROGRESS: === Extracted 201186 precursors and 1803816 fragments ===
0:46:40.419060 INFO: performing precursor FDR with 47 features
0:46:40.419186 INFO: Decoy channel: -1
0:46:40.419212 INFO: Competetive: True
0:46:40.490859 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:43.788165 INFO: Test AUC: 0.558
0:46:43.788360 INFO: Train AUC: 0.585
0:46:43.788391 INFO: AUC difference: 4.54%
0:46:44.017603 INFO: Resetting torch num_threads to 100
0:46:44.028297 INFO: === FDR correction performed with classifier version 7 ===
0:46:44.029086 PROGRESS: ============================= Precursor FDR =============================
0:46:44.029184 PROGRESS: Total precursors accumulated: 802
0:46:44.029242 PROGRESS: Target precursors: 734 (91.52%)
0:46:44.029294 PROGRESS: Decoy precursors: 68 (8.48%)
0:46:44.029342 PROGRESS: 
0:46:44.029387 PROGRESS: Precursor Summary:
0:46:44.030408 PROGRESS: Channel   0:	 0.05 FDR:   603; 0.01 FDR:   448; 0.001 FDR:   265
0:46:44.030497 PROGRESS: 
0:46:44.030552 PROGRESS: Protein Summary:
0:46:44.031779 PROGRESS: Channel   0:	 0.05 FDR:   560; 0.01 FDR:   423; 0.001 FDR:   252
0:46:44.031873 PROGRESS: =========================================================================
0:46:44.169839 INFO: fragments_df: keeping 4764 of 1803816 [sum(precursor_idx_mask)=9746 sum(mass_error_mask)=1803816 stop_rank=4764
0:46:44.319966 INFO: calibration group: precursor, fitting rt estimator 
0:46:44.445027 INFO: calibration group: fragment, fitting mz estimator 
0:46:45.078062 INFO: Using score_cutoff 61.491721196365354 (fac=0.99, q=1)
0:46:45.078468 INFO: calibration group: precursor, predicting mz
0:46:45.078556 WARNING: mz prediction was skipped as it has not been fitted yet
0:46:45.078586 INFO: calibration group: precursor, predicting rt
0:46:45.109622 INFO: calibration group: fragment, predicting mz
0:46:45.178197 INFO: === checking if optimization conditions were reached ===
0:46:45.178446 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
0:46:45.180876 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 13.6269.
0:46:45.180931 INFO: ==============================================
0:46:45.181035 INFO: Starting optimization step 15.
0:46:45.181112 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:46:45.181188 PROGRESS: Extracting batch of 50212 precursors
0:46:45.193689 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:46:45.193805 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:46:45.193849 INFO: FWHM in RT is 2.69 seconds, sigma is 0.35
0:46:45.193877 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:46:45.194130 INFO: Starting candidate selection
0:46:47.621483 INFO: Starting candidate scoring
0:46:48.362652 INFO: Finished candidate processing
0:46:48.362788 INFO: Collecting candidate features
0:46:48.554252 INFO: Collecting fragment features
0:46:48.626208 INFO: Finished candidate scoring
0:46:48.688615 PROGRESS: === Extracted 100199 precursors and 868380 fragments ===
0:46:48.689109 INFO: performing precursor FDR with 47 features
0:46:48.689149 INFO: Decoy channel: -1
0:46:48.689174 INFO: Competetive: True
0:46:48.741444 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:50.789256 INFO: Test AUC: 0.566
0:46:50.789421 INFO: Train AUC: 0.583
0:46:50.789453 INFO: AUC difference: 2.76%
0:46:50.996172 INFO: Resetting torch num_threads to 100
0:46:51.001536 INFO: === FDR correction performed with classifier version 7 ===
0:46:51.002392 PROGRESS: ============================= Precursor FDR =============================
0:46:51.002505 PROGRESS: Total precursors accumulated: 452
0:46:51.002574 PROGRESS: Target precursors: 412 (91.15%)
0:46:51.002642 PROGRESS: Decoy precursors: 40 (8.85%)
0:46:51.002692 PROGRESS: 
0:46:51.002737 PROGRESS: Precursor Summary:
0:46:51.003811 PROGRESS: Channel   0:	 0.05 FDR:   318; 0.01 FDR:   219; 0.001 FDR:   169
0:46:51.003905 PROGRESS: 
0:46:51.003971 PROGRESS: Protein Summary:
0:46:51.005120 PROGRESS: Channel   0:	 0.05 FDR:   304; 0.01 FDR:   212; 0.001 FDR:   164
0:46:51.005212 PROGRESS: =========================================================================
0:46:51.062831 INFO: fragments_df: keeping 2380 of 868380 [sum(precursor_idx_mask)=4709 sum(mass_error_mask)=868380 stop_rank=2380
0:46:51.235806 INFO: calibration group: precursor, fitting rt estimator 
0:46:51.330122 INFO: calibration group: fragment, fitting mz estimator 
0:46:51.597704 INFO: Using score_cutoff 59.354102300262454 (fac=0.99, q=1)
0:46:51.598181 INFO: calibration group: precursor, predicting mz
0:46:51.598286 WARNING: mz prediction was skipped as it has not been fitted yet
0:46:51.598319 INFO: calibration group: precursor, predicting rt
0:46:51.631389 INFO: calibration group: fragment, predicting mz
0:46:51.701009 INFO: === checking if optimization conditions were reached ===
0:46:51.701312 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
0:46:51.703901 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 11.6971.
0:46:51.703966 INFO: ==============================================
0:46:51.704065 INFO: Starting optimization step 16.
0:46:51.704136 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:46:51.704211 PROGRESS: Extracting batch of 50212 precursors
0:46:51.720932 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:46:51.721066 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:46:51.721101 INFO: FWHM in RT is 2.65 seconds, sigma is 0.34
0:46:51.721124 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:46:51.721394 INFO: Starting candidate selection
0:46:54.270980 INFO: Starting candidate scoring
0:46:54.945938 INFO: Finished candidate processing
0:46:54.946101 INFO: Collecting candidate features
0:46:55.159495 INFO: Collecting fragment features
0:46:55.247277 INFO: Finished candidate scoring
0:46:55.315924 PROGRESS: === Extracted 100195 precursors and 834162 fragments ===
0:46:55.316515 INFO: performing precursor FDR with 47 features
0:46:55.316554 INFO: Decoy channel: -1
0:46:55.316578 INFO: Competetive: True
0:46:55.370030 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:57.470488 INFO: Test AUC: 0.560
0:46:57.470668 INFO: Train AUC: 0.580
0:46:57.470700 INFO: AUC difference: 3.38%
0:47:00.792808 INFO: Resetting torch num_threads to 100
0:47:00.798005 INFO: === FDR correction performed with classifier version 7 ===
0:47:00.798894 PROGRESS: ============================= Precursor FDR =============================
0:47:00.799013 PROGRESS: Total precursors accumulated: 427
0:47:00.799076 PROGRESS: Target precursors: 393 (92.04%)
0:47:00.799129 PROGRESS: Decoy precursors: 34 (7.96%)
0:47:00.799179 PROGRESS: 
0:47:00.799225 PROGRESS: Precursor Summary:
0:47:00.800243 PROGRESS: Channel   0:	 0.05 FDR:   317; 0.01 FDR:   223; 0.001 FDR:   151
0:47:00.800338 PROGRESS: 
0:47:00.800395 PROGRESS: Protein Summary:
0:47:00.801554 PROGRESS: Channel   0:	 0.05 FDR:   301; 0.01 FDR:   214; 0.001 FDR:   148
0:47:00.801645 PROGRESS: =========================================================================
0:47:00.857801 INFO: fragments_df: keeping 2415 of 834162 [sum(precursor_idx_mask)=4747 sum(mass_error_mask)=834162 stop_rank=2415
0:47:01.049614 INFO: calibration group: precursor, fitting rt estimator 
0:47:01.158842 INFO: calibration group: fragment, fitting mz estimator 
0:47:01.468472 INFO: Using score_cutoff 60.48857627105713 (fac=0.99, q=1)
0:47:01.468854 INFO: calibration group: precursor, predicting mz
0:47:01.468940 WARNING: mz prediction was skipped as it has not been fitted yet
0:47:01.468971 INFO: calibration group: precursor, predicting rt
0:47:01.500228 INFO: calibration group: fragment, predicting mz
0:47:01.577273 INFO: === checking if optimization conditions were reached ===
0:47:01.577614 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
0:47:01.581022 PROGRESS: ❌ ms2_error      : optimization incomplete after 7 search(es). Will search with parameter 9.3966.
0:47:01.581216 INFO: ==============================================
0:47:01.581398 INFO: Starting optimization step 17.
0:47:01.581478 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:47:01.581548 PROGRESS: Extracting batch of 50212 precursors
0:47:01.598276 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:47:01.598400 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:47:01.598442 INFO: FWHM in RT is 2.62 seconds, sigma is 0.34
0:47:01.598469 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:47:01.598742 INFO: Starting candidate selection
0:47:04.094301 INFO: Starting candidate scoring
0:47:04.816169 INFO: Finished candidate processing
0:47:04.816266 INFO: Collecting candidate features
0:47:04.966187 INFO: Collecting fragment features
0:47:05.027941 INFO: Finished candidate scoring
0:47:05.072301 PROGRESS: === Extracted 100182 precursors and 793785 fragments ===
0:47:05.072703 INFO: performing precursor FDR with 47 features
0:47:05.072750 INFO: Decoy channel: -1
0:47:05.072773 INFO: Competetive: True
0:47:05.103293 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:06.779012 INFO: Test AUC: 0.564
0:47:06.779163 INFO: Train AUC: 0.581
0:47:06.779194 INFO: AUC difference: 3.09%
0:47:06.985903 INFO: Resetting torch num_threads to 100
0:47:06.989679 INFO: === FDR correction performed with classifier version 7 ===
0:47:06.990398 PROGRESS: ============================= Precursor FDR =============================
0:47:06.990767 PROGRESS: Total precursors accumulated: 450
0:47:06.990837 PROGRESS: Target precursors: 412 (91.56%)
0:47:06.990887 PROGRESS: Decoy precursors: 38 (8.44%)
0:47:06.990932 PROGRESS: 
0:47:06.990978 PROGRESS: Precursor Summary:
0:47:06.991995 PROGRESS: Channel   0:	 0.05 FDR:   347; 0.01 FDR:   231; 0.001 FDR:   216
0:47:06.992084 PROGRESS: 
0:47:06.992139 PROGRESS: Protein Summary:
0:47:06.993264 PROGRESS: Channel   0:	 0.05 FDR:   330; 0.01 FDR:   224; 0.001 FDR:   210
0:47:06.993355 PROGRESS: =========================================================================
0:47:07.055040 INFO: fragments_df: keeping 2441 of 793785 [sum(precursor_idx_mask)=4885 sum(mass_error_mask)=793785 stop_rank=2441
0:47:07.196380 INFO: calibration group: precursor, fitting rt estimator 
0:47:07.308857 INFO: calibration group: fragment, fitting mz estimator 
0:47:07.629592 INFO: Using score_cutoff 60.65076399993896 (fac=0.99, q=1)
0:47:07.630000 INFO: calibration group: precursor, predicting mz
0:47:07.630089 WARNING: mz prediction was skipped as it has not been fitted yet
0:47:07.630118 INFO: calibration group: precursor, predicting rt
0:47:07.661427 INFO: calibration group: fragment, predicting mz
0:47:07.727028 INFO: === checking if optimization conditions were reached ===
0:47:07.727309 PROGRESS: === Optimization of ms2_error has been performed 8 time(s); minimum number is 2 ===
0:47:07.729815 PROGRESS: ❌ ms2_error      : optimization incomplete after 8 search(es). Will search with parameter 8.1649.
0:47:07.729876 INFO: ==============================================
0:47:07.729985 INFO: Starting optimization step 18.
0:47:07.730065 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:47:07.730160 PROGRESS: Extracting batch of 50212 precursors
0:47:07.748367 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:47:07.748489 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:47:07.748533 INFO: FWHM in RT is 2.59 seconds, sigma is 0.33
0:47:07.748563 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:47:07.748850 INFO: Starting candidate selection
0:47:10.263679 INFO: Starting candidate scoring
0:47:10.991748 INFO: Finished candidate processing
0:47:10.991882 INFO: Collecting candidate features
0:47:11.179291 INFO: Collecting fragment features
0:47:11.273865 INFO: Finished candidate scoring
0:47:11.332347 PROGRESS: === Extracted 100182 precursors and 770196 fragments ===
0:47:11.332931 INFO: performing precursor FDR with 47 features
0:47:11.332986 INFO: Decoy channel: -1
0:47:11.333012 INFO: Competetive: True
0:47:11.399728 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:13.459125 INFO: Test AUC: 0.565
0:47:13.459299 INFO: Train AUC: 0.579
0:47:13.459330 INFO: AUC difference: 2.36%
0:47:13.663421 INFO: Resetting torch num_threads to 100
0:47:13.668628 INFO: === FDR correction performed with classifier version 7 ===
0:47:13.669455 PROGRESS: ============================= Precursor FDR =============================
0:47:13.669565 PROGRESS: Total precursors accumulated: 499
0:47:13.669626 PROGRESS: Target precursors: 455 (91.18%)
0:47:13.669679 PROGRESS: Decoy precursors: 44 (8.82%)
0:47:13.669724 PROGRESS: 
0:47:13.669769 PROGRESS: Precursor Summary:
0:47:13.671980 PROGRESS: Channel   0:	 0.05 FDR:   346; 0.01 FDR:   248; 0.001 FDR:   207
0:47:13.672086 PROGRESS: 
0:47:13.672140 PROGRESS: Protein Summary:
0:47:13.673311 PROGRESS: Channel   0:	 0.05 FDR:   332; 0.01 FDR:   238; 0.001 FDR:   201
0:47:13.673405 PROGRESS: =========================================================================
0:47:13.725023 INFO: fragments_df: keeping 2582 of 770196 [sum(precursor_idx_mask)=5157 sum(mass_error_mask)=770196 stop_rank=2582
0:47:13.906499 INFO: calibration group: precursor, fitting rt estimator 
0:47:14.025076 INFO: calibration group: fragment, fitting mz estimator 
0:47:14.366594 INFO: Using score_cutoff 57.211444730758664 (fac=0.99, q=1)
0:47:14.367067 INFO: calibration group: precursor, predicting mz
0:47:14.367157 WARNING: mz prediction was skipped as it has not been fitted yet
0:47:14.367188 INFO: calibration group: precursor, predicting rt
0:47:14.398689 INFO: calibration group: fragment, predicting mz
0:47:14.470985 INFO: === checking if optimization conditions were reached ===
0:47:14.471358 PROGRESS: === Optimization of ms2_error has been performed 9 time(s); minimum number is 2 ===
0:47:14.473836 PROGRESS: ❌ ms2_error      : optimization incomplete after 9 search(es). Will search with parameter 7.5452.
0:47:14.473893 INFO: ==============================================
0:47:14.473989 INFO: Starting optimization step 19.
0:47:14.474060 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:47:14.474119 PROGRESS: Extracting batch of 50212 precursors
0:47:14.490987 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:47:14.491140 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:47:14.491175 INFO: FWHM in RT is 2.50 seconds, sigma is 0.32
0:47:14.491198 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:47:14.491525 INFO: Starting candidate selection
0:47:16.962998 INFO: Starting candidate scoring
0:47:17.620381 INFO: Finished candidate processing
0:47:17.620533 INFO: Collecting candidate features
0:47:17.783290 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 100147)
0:47:17.791580 INFO: Collecting fragment features
0:47:17.843703 INFO: Finished candidate scoring
0:47:17.885154 PROGRESS: === Extracted 100147 precursors and 739549 fragments ===
0:47:17.885535 INFO: performing precursor FDR with 47 features
0:47:17.885572 INFO: Decoy channel: -1
0:47:17.885596 INFO: Competetive: True
0:47:17.915255 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:17.932043 WARNING: dropped 1 target PSMs due to missing features
0:47:19.574270 INFO: Test AUC: 0.561
0:47:19.574382 INFO: Train AUC: 0.580
0:47:19.574412 INFO: AUC difference: 3.19%
0:47:19.779243 INFO: Resetting torch num_threads to 100
0:47:19.782618 INFO: === FDR correction performed with classifier version 7 ===
0:47:19.783296 PROGRESS: ============================= Precursor FDR =============================
0:47:19.783399 PROGRESS: Total precursors accumulated: 485
0:47:19.783459 PROGRESS: Target precursors: 440 (90.72%)
0:47:19.783510 PROGRESS: Decoy precursors: 45 (9.28%)
0:47:19.783557 PROGRESS: 
0:47:19.783602 PROGRESS: Precursor Summary:
0:47:19.784630 PROGRESS: Channel   0:	 0.05 FDR:   381; 0.01 FDR:   235; 0.001 FDR:   168
0:47:19.784724 PROGRESS: 
0:47:19.784780 PROGRESS: Protein Summary:
0:47:19.785973 PROGRESS: Channel   0:	 0.05 FDR:   361; 0.01 FDR:   227; 0.001 FDR:   164
0:47:19.786068 PROGRESS: =========================================================================
0:47:19.833192 INFO: fragments_df: keeping 2442 of 739549 [sum(precursor_idx_mask)=4842 sum(mass_error_mask)=739549 stop_rank=2442
0:47:19.959564 INFO: calibration group: precursor, fitting rt estimator 
0:47:20.064233 INFO: calibration group: fragment, fitting mz estimator 
0:47:20.332261 INFO: Using score_cutoff 60.4585072265625 (fac=0.99, q=1)
0:47:20.332688 INFO: calibration group: precursor, predicting mz
0:47:20.332776 WARNING: mz prediction was skipped as it has not been fitted yet
0:47:20.332808 INFO: calibration group: precursor, predicting rt
0:47:20.364429 INFO: calibration group: fragment, predicting mz
0:47:20.430542 INFO: === checking if optimization conditions were reached ===
0:47:20.430927 PROGRESS: === Optimization of ms2_error has been performed 10 time(s); minimum number is 2 ===
0:47:20.433802 PROGRESS: ❌ ms2_error      : optimization incomplete after 10 search(es). Will search with parameter 6.1929.
0:47:20.433865 INFO: ==============================================
0:47:20.433962 WARNING: Optimization did not converge within the maximum number of steps, which is 20.
0:47:20.434997 INFO: Starting optimization step 0.
0:47:20.435086 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:47:20.435157 PROGRESS: Extracting batch of 50212 precursors
0:47:20.458909 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:47:20.459084 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:47:20.459126 INFO: FWHM in RT is 2.54 seconds, sigma is 0.33
0:47:20.459155 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:47:20.459476 INFO: Starting candidate selection
0:47:23.001812 INFO: Starting candidate scoring
0:47:23.643614 INFO: Finished candidate processing
0:47:23.643707 INFO: Collecting candidate features
0:47:23.799742 INFO: Collecting fragment features
0:47:23.856494 INFO: Finished candidate scoring
0:47:23.900401 PROGRESS: === Extracted 100141 precursors and 710440 fragments ===
0:47:23.900864 INFO: performing precursor FDR with 47 features
0:47:23.900903 INFO: Decoy channel: -1
0:47:23.900928 INFO: Competetive: True
0:47:23.936282 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:25.576310 INFO: Test AUC: 0.556
0:47:25.576467 INFO: Train AUC: 0.585
0:47:25.576498 INFO: AUC difference: 5.04%
0:47:25.576520 WARNING: AUC difference > 5%. This may indicate overfitting.
0:47:25.781842 INFO: Resetting torch num_threads to 100
0:47:25.785279 INFO: === FDR correction performed with classifier version 7 ===
0:47:25.786009 PROGRESS: ============================= Precursor FDR =============================
0:47:25.786108 PROGRESS: Total precursors accumulated: 468
0:47:25.786168 PROGRESS: Target precursors: 425 (90.81%)
0:47:25.786223 PROGRESS: Decoy precursors: 43 (9.19%)
0:47:25.786270 PROGRESS: 
0:47:25.786314 PROGRESS: Precursor Summary:
0:47:25.787329 PROGRESS: Channel   0:	 0.05 FDR:   356; 0.01 FDR:   273; 0.001 FDR:   175
0:47:25.787420 PROGRESS: 
0:47:25.787474 PROGRESS: Protein Summary:
0:47:25.788621 PROGRESS: Channel   0:	 0.05 FDR:   337; 0.01 FDR:   260; 0.001 FDR:   170
0:47:25.788719 PROGRESS: =========================================================================
0:47:25.837164 INFO: fragments_df: keeping 2765 of 710440 [sum(precursor_idx_mask)=5516 sum(mass_error_mask)=710440 stop_rank=2765
0:47:25.973499 INFO: calibration group: precursor, fitting rt estimator 
0:47:26.096071 INFO: calibration group: fragment, fitting mz estimator 
0:47:26.459800 INFO: Using score_cutoff 53.611619581604 (fac=0.99, q=1)
0:47:26.460236 INFO: calibration group: precursor, predicting mz
0:47:26.460329 WARNING: mz prediction was skipped as it has not been fitted yet
0:47:26.460360 INFO: calibration group: precursor, predicting rt
0:47:26.491953 INFO: calibration group: fragment, predicting mz
0:47:26.560933 INFO: === checking if optimization conditions were reached ===
0:47:26.561232 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:47:26.563414 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 206.4080.
0:47:26.563474 INFO: ==============================================
0:47:26.563582 INFO: Starting optimization step 1.
0:47:26.563656 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:47:26.563742 PROGRESS: Extracting batch of 50212 precursors
0:47:26.580841 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:47:26.580968 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:47:26.581012 INFO: FWHM in RT is 2.45 seconds, sigma is 0.32
0:47:26.581042 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:47:26.581366 INFO: Starting candidate selection
0:47:28.617387 INFO: Starting candidate scoring
0:47:29.336996 INFO: Finished candidate processing
0:47:29.337094 INFO: Collecting candidate features
0:47:29.474670 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 99396)
0:47:29.481115 INFO: Collecting fragment features
0:47:29.530724 INFO: Finished candidate scoring
0:47:29.573049 PROGRESS: === Extracted 99396 precursors and 643700 fragments ===
0:47:29.573423 INFO: performing precursor FDR with 47 features
0:47:29.573460 INFO: Decoy channel: -1
0:47:29.573484 INFO: Competetive: True
0:47:29.607906 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:29.623680 WARNING: dropped 1 decoy PSMs due to missing features
0:47:31.095627 INFO: Test AUC: 0.546
0:47:31.095749 INFO: Train AUC: 0.576
0:47:31.095779 INFO: AUC difference: 5.26%
0:47:31.095799 WARNING: AUC difference > 5%. This may indicate overfitting.
0:47:31.300247 INFO: Resetting torch num_threads to 100
0:47:31.303297 INFO: === FDR correction performed with classifier version 7 ===
0:47:31.303944 PROGRESS: ============================= Precursor FDR =============================
0:47:31.304033 PROGRESS: Total precursors accumulated: 506
0:47:31.304092 PROGRESS: Target precursors: 459 (90.71%)
0:47:31.304143 PROGRESS: Decoy precursors: 47 (9.29%)
0:47:31.304188 PROGRESS: 
0:47:31.304233 PROGRESS: Precursor Summary:
0:47:31.305199 PROGRESS: Channel   0:	 0.05 FDR:   385; 0.01 FDR:   271; 0.001 FDR:   185
0:47:31.305286 PROGRESS: 
0:47:31.305339 PROGRESS: Protein Summary:
0:47:31.306476 PROGRESS: Channel   0:	 0.05 FDR:   367; 0.01 FDR:   257; 0.001 FDR:   180
0:47:31.306563 PROGRESS: =========================================================================
0:47:31.349600 INFO: fragments_df: keeping 2716 of 643700 [sum(precursor_idx_mask)=5469 sum(mass_error_mask)=643700 stop_rank=2716
0:47:31.488051 INFO: calibration group: precursor, fitting rt estimator 
0:47:31.606094 INFO: calibration group: fragment, fitting mz estimator 
0:47:31.962294 INFO: Using score_cutoff 48.04285545730591 (fac=0.99, q=1)
0:47:31.962680 INFO: calibration group: precursor, predicting mz
0:47:31.962765 WARNING: mz prediction was skipped as it has not been fitted yet
0:47:31.962794 INFO: calibration group: precursor, predicting rt
0:47:31.993794 INFO: calibration group: fragment, predicting mz
0:47:32.059059 INFO: === checking if optimization conditions were reached ===
0:47:32.059349 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:47:32.061572 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 96.5926.
0:47:32.061634 INFO: ==============================================
0:47:32.061746 INFO: Starting optimization step 2.
0:47:32.061820 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:47:32.061887 PROGRESS: Extracting batch of 50212 precursors
0:47:32.078667 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:47:32.078791 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:47:32.078829 INFO: FWHM in RT is 2.46 seconds, sigma is 0.32
0:47:32.078857 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:47:32.079088 INFO: Starting candidate selection
0:47:33.685133 INFO: Starting candidate scoring
0:47:34.319071 INFO: Finished candidate processing
0:47:34.319260 INFO: Collecting candidate features
0:47:34.455199 WARNING: intensity_correlation has 17 NaNs ( 0.02 % out of 97656)
0:47:34.464960 INFO: Collecting fragment features
0:47:34.509970 INFO: Finished candidate scoring
0:47:34.551559 PROGRESS: === Extracted 97656 precursors and 570245 fragments ===
0:47:34.551937 INFO: performing precursor FDR with 47 features
0:47:34.551974 INFO: Decoy channel: -1
0:47:34.551997 INFO: Competetive: True
0:47:34.583206 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:34.601286 WARNING: dropped 11 target PSMs due to missing features
0:47:34.601413 WARNING: dropped 6 decoy PSMs due to missing features
0:47:36.014058 INFO: Test AUC: 0.548
0:47:36.014185 INFO: Train AUC: 0.572
0:47:36.014215 INFO: AUC difference: 4.10%
0:47:36.215870 INFO: Resetting torch num_threads to 100
0:47:36.218905 INFO: === FDR correction performed with classifier version 7 ===
0:47:36.219554 PROGRESS: ============================= Precursor FDR =============================
0:47:36.219645 PROGRESS: Total precursors accumulated: 552
0:47:36.219705 PROGRESS: Target precursors: 504 (91.30%)
0:47:36.219757 PROGRESS: Decoy precursors: 48 (8.70%)
0:47:36.219805 PROGRESS: 
0:47:36.219850 PROGRESS: Precursor Summary:
0:47:36.220836 PROGRESS: Channel   0:	 0.05 FDR:   390; 0.01 FDR:   286; 0.001 FDR:   189
0:47:36.220926 PROGRESS: 
0:47:36.220981 PROGRESS: Protein Summary:
0:47:36.222119 PROGRESS: Channel   0:	 0.05 FDR:   371; 0.01 FDR:   272; 0.001 FDR:   184
0:47:36.222218 PROGRESS: =========================================================================
0:47:36.261597 INFO: fragments_df: keeping 2784 of 570245 [sum(precursor_idx_mask)=5699 sum(mass_error_mask)=570245 stop_rank=2784
0:47:36.385392 INFO: calibration group: precursor, fitting rt estimator 
0:47:36.559076 INFO: calibration group: fragment, fitting mz estimator 
0:47:36.927278 INFO: Using score_cutoff 48.88493440246582 (fac=0.99, q=1)
0:47:36.927660 INFO: calibration group: precursor, predicting mz
0:47:36.927745 WARNING: mz prediction was skipped as it has not been fitted yet
0:47:36.927774 INFO: calibration group: precursor, predicting rt
0:47:36.960491 INFO: calibration group: fragment, predicting mz
0:47:37.034794 INFO: === checking if optimization conditions were reached ===
0:47:37.035244 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:47:37.038058 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 86.6575.
0:47:37.038121 INFO: ==============================================
0:47:37.038240 INFO: Starting optimization step 3.
0:47:37.038321 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:47:37.038397 PROGRESS: Extracting batch of 50212 precursors
0:47:37.062614 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:47:37.062771 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:47:37.062812 INFO: FWHM in RT is 2.41 seconds, sigma is 0.31
0:47:37.062842 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:47:37.063148 INFO: Starting candidate selection
0:47:39.551109 INFO: Starting candidate scoring
0:47:40.260748 INFO: Finished candidate processing
0:47:40.261012 INFO: Collecting candidate features
0:47:40.437996 WARNING: intensity_correlation has 16 NaNs ( 0.02 % out of 97268)
0:47:40.446040 INFO: Collecting fragment features
0:47:40.500825 INFO: Finished candidate scoring
0:47:40.544427 PROGRESS: === Extracted 97268 precursors and 560223 fragments ===
0:47:40.544904 INFO: performing precursor FDR with 47 features
0:47:40.544942 INFO: Decoy channel: -1
0:47:40.544966 INFO: Competetive: True
0:47:40.586991 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:40.604822 WARNING: dropped 8 target PSMs due to missing features
0:47:40.604947 WARNING: dropped 8 decoy PSMs due to missing features
0:47:42.041920 INFO: Test AUC: 0.561
0:47:42.042058 INFO: Train AUC: 0.567
0:47:42.042089 INFO: AUC difference: 1.04%
0:47:42.241567 INFO: Resetting torch num_threads to 100
0:47:42.244766 INFO: === FDR correction performed with classifier version 7 ===
0:47:42.245516 PROGRESS: ============================= Precursor FDR =============================
0:47:42.245607 PROGRESS: Total precursors accumulated: 591
0:47:42.245665 PROGRESS: Target precursors: 538 (91.03%)
0:47:42.245718 PROGRESS: Decoy precursors: 53 (8.97%)
0:47:42.245764 PROGRESS: 
0:47:42.245807 PROGRESS: Precursor Summary:
0:47:42.246796 PROGRESS: Channel   0:	 0.05 FDR:   424; 0.01 FDR:   314; 0.001 FDR:   243
0:47:42.246887 PROGRESS: 
0:47:42.246942 PROGRESS: Protein Summary:
0:47:42.248080 PROGRESS: Channel   0:	 0.05 FDR:   402; 0.01 FDR:   299; 0.001 FDR:   231
0:47:42.248171 PROGRESS: =========================================================================
0:47:42.286402 INFO: fragments_df: keeping 2962 of 560223 [sum(precursor_idx_mask)=6206 sum(mass_error_mask)=560223 stop_rank=2962
0:47:42.414213 INFO: calibration group: precursor, fitting rt estimator 
0:47:42.535720 INFO: calibration group: fragment, fitting mz estimator 
0:47:42.923997 INFO: Using score_cutoff 53.411243904876706 (fac=0.99, q=1)
0:47:42.924422 INFO: calibration group: precursor, predicting mz
0:47:42.924511 WARNING: mz prediction was skipped as it has not been fitted yet
0:47:42.924541 INFO: calibration group: precursor, predicting rt
0:47:42.955305 INFO: calibration group: fragment, predicting mz
0:47:43.023856 INFO: === checking if optimization conditions were reached ===
0:47:43.024162 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:47:43.026489 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 78.9000.
0:47:43.026548 INFO: ==============================================
0:47:43.026682 INFO: Starting optimization step 4.
0:47:43.026761 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:47:43.026842 PROGRESS: Extracting batch of 50212 precursors
0:47:43.043887 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:47:43.044009 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:47:43.044053 INFO: FWHM in RT is 2.38 seconds, sigma is 0.31
0:47:43.044081 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:47:43.044394 INFO: Starting candidate selection
0:47:44.908641 INFO: Starting candidate scoring
0:47:45.550246 INFO: Finished candidate processing
0:47:45.550377 INFO: Collecting candidate features
0:47:45.683427 WARNING: intensity_correlation has 23 NaNs ( 0.02 % out of 96889)
0:47:45.689869 INFO: Collecting fragment features
0:47:45.735144 INFO: Finished candidate scoring
0:47:45.779350 PROGRESS: === Extracted 96889 precursors and 552120 fragments ===
0:47:45.779748 INFO: performing precursor FDR with 47 features
0:47:45.779787 INFO: Decoy channel: -1
0:47:45.779811 INFO: Competetive: True
0:47:45.815748 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:45.832831 WARNING: dropped 13 target PSMs due to missing features
0:47:45.832953 WARNING: dropped 10 decoy PSMs due to missing features
0:47:47.314199 INFO: Test AUC: 0.550
0:47:47.314321 INFO: Train AUC: 0.570
0:47:47.314351 INFO: AUC difference: 3.39%
0:47:47.510581 INFO: Resetting torch num_threads to 100
0:47:47.513986 INFO: === FDR correction performed with classifier version 7 ===
0:47:47.514647 PROGRESS: ============================= Precursor FDR =============================
0:47:47.514739 PROGRESS: Total precursors accumulated: 528
0:47:47.514797 PROGRESS: Target precursors: 481 (91.10%)
0:47:47.514847 PROGRESS: Decoy precursors: 47 (8.90%)
0:47:47.514893 PROGRESS: 
0:47:47.514937 PROGRESS: Precursor Summary:
0:47:47.515924 PROGRESS: Channel   0:	 0.05 FDR:   416; 0.01 FDR:   326; 0.001 FDR:   248
0:47:47.516012 PROGRESS: 
0:47:47.516067 PROGRESS: Protein Summary:
0:47:47.517214 PROGRESS: Channel   0:	 0.05 FDR:   395; 0.01 FDR:   311; 0.001 FDR:   237
0:47:47.517311 PROGRESS: =========================================================================
0:47:47.556025 INFO: fragments_df: keeping 3049 of 552120 [sum(precursor_idx_mask)=6401 sum(mass_error_mask)=552120 stop_rank=3049
0:47:47.686002 INFO: calibration group: precursor, fitting rt estimator 
0:47:47.812325 INFO: calibration group: fragment, fitting mz estimator 
0:47:48.212601 INFO: Using score_cutoff 46.41587642669678 (fac=0.99, q=1)
0:47:48.212972 INFO: calibration group: precursor, predicting mz
0:47:48.213057 WARNING: mz prediction was skipped as it has not been fitted yet
0:47:48.213087 INFO: calibration group: precursor, predicting rt
0:47:48.243846 INFO: calibration group: fragment, predicting mz
0:47:48.308940 INFO: === checking if optimization conditions were reached ===
0:47:48.309225 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:47:48.311563 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 70.9516.
0:47:48.311626 INFO: ==============================================
0:47:48.311728 INFO: Starting optimization step 5.
0:47:48.311803 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:47:48.311872 PROGRESS: Extracting batch of 50212 precursors
0:47:48.328605 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:47:48.328728 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:47:48.328767 INFO: FWHM in RT is 2.40 seconds, sigma is 0.31
0:47:48.328796 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:47:48.329039 INFO: Starting candidate selection
0:47:50.262037 INFO: Starting candidate scoring
0:47:50.901690 INFO: Finished candidate processing
0:47:50.901887 INFO: Collecting candidate features
0:47:51.157161 WARNING: intensity_correlation has 22 NaNs ( 0.02 % out of 96776)
0:47:51.163943 INFO: Collecting fragment features
0:47:51.225680 INFO: Finished candidate scoring
0:47:51.280729 PROGRESS: === Extracted 96776 precursors and 549090 fragments ===
0:47:51.281224 INFO: performing precursor FDR with 47 features
0:47:51.281262 INFO: Decoy channel: -1
0:47:51.281287 INFO: Competetive: True
0:47:51.319018 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:51.337855 WARNING: dropped 11 target PSMs due to missing features
0:47:51.337980 WARNING: dropped 11 decoy PSMs due to missing features
0:47:52.845845 INFO: Test AUC: 0.551
0:47:52.845972 INFO: Train AUC: 0.569
0:47:52.846003 INFO: AUC difference: 3.17%
0:47:53.045830 INFO: Resetting torch num_threads to 100
0:47:53.048815 INFO: === FDR correction performed with classifier version 7 ===
0:47:53.049502 PROGRESS: ============================= Precursor FDR =============================
0:47:53.049594 PROGRESS: Total precursors accumulated: 564
0:47:53.049654 PROGRESS: Target precursors: 513 (90.96%)
0:47:53.049706 PROGRESS: Decoy precursors: 51 (9.04%)
0:47:53.049753 PROGRESS: 
0:47:53.049799 PROGRESS: Precursor Summary:
0:47:53.050791 PROGRESS: Channel   0:	 0.05 FDR:   434; 0.01 FDR:   336; 0.001 FDR:   253
0:47:53.050883 PROGRESS: 
0:47:53.050940 PROGRESS: Protein Summary:
0:47:53.052084 PROGRESS: Channel   0:	 0.05 FDR:   408; 0.01 FDR:   319; 0.001 FDR:   243
0:47:53.052174 PROGRESS: =========================================================================
0:47:53.091143 INFO: fragments_df: keeping 3107 of 549090 [sum(precursor_idx_mask)=6600 sum(mass_error_mask)=549090 stop_rank=3107
0:47:53.217936 INFO: calibration group: precursor, fitting rt estimator 
0:47:53.346975 INFO: calibration group: fragment, fitting mz estimator 
0:47:53.753326 INFO: Using score_cutoff 46.783590820312504 (fac=0.99, q=1)
0:47:53.753728 INFO: calibration group: precursor, predicting mz
0:47:53.753817 WARNING: mz prediction was skipped as it has not been fitted yet
0:47:53.753848 INFO: calibration group: precursor, predicting rt
0:47:53.784802 INFO: calibration group: fragment, predicting mz
0:47:53.853622 INFO: === checking if optimization conditions were reached ===
0:47:53.853946 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:47:53.856319 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 70.0247.
0:47:53.856389 INFO: ==============================================
0:47:53.856497 INFO: Starting optimization step 6.
0:47:53.856574 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:47:53.856652 PROGRESS: Extracting batch of 50212 precursors
0:47:53.874782 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:47:53.874901 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:47:53.874945 INFO: FWHM in RT is 2.37 seconds, sigma is 0.31
0:47:53.874974 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:47:53.875263 INFO: Starting candidate selection
0:47:55.805640 INFO: Starting candidate scoring
0:47:56.439929 INFO: Finished candidate processing
0:47:56.440016 INFO: Collecting candidate features
0:47:56.574040 WARNING: intensity_correlation has 20 NaNs ( 0.02 % out of 96782)
0:47:56.582323 INFO: Collecting fragment features
0:47:56.630321 INFO: Finished candidate scoring
0:47:56.709543 PROGRESS: === Extracted 96782 precursors and 549021 fragments ===
0:47:56.709915 INFO: performing precursor FDR with 47 features
0:47:56.709952 INFO: Decoy channel: -1
0:47:56.709975 INFO: Competetive: True
0:47:56.740230 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:56.760064 WARNING: dropped 7 target PSMs due to missing features
0:47:56.760188 WARNING: dropped 13 decoy PSMs due to missing features
0:47:58.162514 INFO: Test AUC: 0.549
0:47:58.162640 INFO: Train AUC: 0.569
0:47:58.162674 INFO: AUC difference: 3.47%
0:47:58.358954 INFO: Resetting torch num_threads to 100
0:47:58.362163 INFO: === FDR correction performed with classifier version 7 ===
0:47:58.362914 PROGRESS: ============================= Precursor FDR =============================
0:47:58.363021 PROGRESS: Total precursors accumulated: 559
0:47:58.363081 PROGRESS: Target precursors: 506 (90.52%)
0:47:58.363133 PROGRESS: Decoy precursors: 53 (9.48%)
0:47:58.363177 PROGRESS: 
0:47:58.363226 PROGRESS: Precursor Summary:
0:47:58.364251 PROGRESS: Channel   0:	 0.05 FDR:   411; 0.01 FDR:   338; 0.001 FDR:   240
0:47:58.364347 PROGRESS: 
0:47:58.364407 PROGRESS: Protein Summary:
0:47:58.365582 PROGRESS: Channel   0:	 0.05 FDR:   390; 0.01 FDR:   323; 0.001 FDR:   231
0:47:58.365682 PROGRESS: =========================================================================
0:47:58.403069 INFO: fragments_df: keeping 3079 of 549021 [sum(precursor_idx_mask)=6625 sum(mass_error_mask)=549021 stop_rank=3079
0:47:58.528427 INFO: calibration group: precursor, fitting rt estimator 
0:47:58.649427 INFO: calibration group: fragment, fitting mz estimator 
0:47:59.057742 INFO: Using score_cutoff 43.20333843612671 (fac=0.99, q=1)
0:47:59.058128 INFO: calibration group: precursor, predicting mz
0:47:59.058215 WARNING: mz prediction was skipped as it has not been fitted yet
0:47:59.058246 INFO: calibration group: precursor, predicting rt
0:47:59.089114 INFO: calibration group: fragment, predicting mz
0:47:59.157377 INFO: === checking if optimization conditions were reached ===
0:47:59.157705 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:47:59.159754 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 70.0247 found after 7 searches.
0:47:59.159934 INFO: ==============================================
0:47:59.160129 PROGRESS: Optimization finished for rt_error.
0:47:59.305250 INFO: calibration group: precursor, predicting mz
0:47:59.305504 WARNING: mz prediction was skipped as it has not been fitted yet
0:47:59.305536 INFO: calibration group: precursor, predicting rt
0:47:59.336436 INFO: calibration group: fragment, predicting mz
0:47:59.432035 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:47:59.432269 PROGRESS: ==============================================
0:47:59.432359 PROGRESS: ms2_error      : 6.1929
0:47:59.432429 PROGRESS: rt_error       : 70.0247
0:47:59.432486 PROGRESS: ==============================================
0:47:59.433677 INFO: calibration group: precursor, predicting mz
0:47:59.433805 WARNING: mz prediction was skipped as it has not been fitted yet
0:47:59.433851 INFO: calibration group: precursor, predicting rt
0:48:05.927038 INFO: calibration group: fragment, predicting mz
0:48:20.344697 PROGRESS: Extracting batch of 10183864 precursors
0:48:22.618305 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:48:22.618438 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:48:22.618478 INFO: FWHM in RT is 2.37 seconds, sigma is 0.31
0:48:22.618502 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:48:22.618905 INFO: Starting candidate selection
0:54:45.985349 INFO: Applying score cutoff of 43.20333843612671
0:54:46.112501 INFO: Removed 17562954 precursors with score below cutoff
0:54:48.321248 INFO: Starting candidate scoring
0:55:07.580019 INFO: Finished candidate processing
0:55:07.580318 INFO: Collecting candidate features
0:55:14.316545 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 2734576)
0:55:14.404576 INFO: Collecting fragment features
0:55:16.671147 INFO: Finished candidate scoring
0:55:19.793183 INFO: === FDR correction performed with classifier version 26 ===
0:55:19.795824 INFO: performing precursor FDR with 47 features
0:55:19.795871 INFO: Decoy channel: -1
0:55:19.795902 INFO: Competetive: True
0:55:20.608911 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:21.042953 WARNING: dropped 3 target PSMs due to missing features
0:56:08.765669 INFO: Test AUC: 0.631
0:56:08.765884 INFO: Train AUC: 0.635
0:56:08.765918 INFO: AUC difference: 0.64%
0:56:09.660729 INFO: Resetting torch num_threads to 100
0:56:09.734879 INFO: Removing fragments below FDR threshold
0:56:09.996514 PROGRESS: ============================= Precursor FDR =============================
0:56:09.996791 PROGRESS: Total precursors accumulated: 78,832
0:56:09.996859 PROGRESS: Target precursors: 78,052 (99.01%)
0:56:09.996914 PROGRESS: Decoy precursors: 780 (0.99%)
0:56:09.996961 PROGRESS: 
0:56:09.997007 PROGRESS: Precursor Summary:
0:56:10.028104 PROGRESS: Channel   0:	 0.05 FDR: 78,052; 0.01 FDR: 78,052; 0.001 FDR: 55,305
0:56:10.028348 PROGRESS: 
0:56:10.028414 PROGRESS: Protein Summary:
0:56:10.073819 PROGRESS: Channel   0:	 0.05 FDR: 11,736; 0.01 FDR: 11,736; 0.001 FDR: 9,178
0:56:10.074049 PROGRESS: =========================================================================
0:56:10.707319 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:56:11.114717 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:56:11.114877 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant
0:56:11.114956 INFO: Creating folder run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/figures
0:56:11.115697 INFO: Initializing RawFileManager
0:56:22.294304 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.
0:56:22.298650 INFO: Determining DIA cycle
0:56:22.315034 INFO: Found cycle with start 0.00 min and length 300.
0:56:22.484728 INFO: RT (min)            : 0.0 - 26.9
0:56:22.484815 INFO: RT duration (sec)   : 1611.2
0:56:22.484842 INFO: RT duration (min)   : 26.9
0:56:22.484867 INFO: Cycle len (scans)   : 300
0:56:22.484889 INFO: Cycle len (sec)     : 1.65
0:56:22.484911 INFO: Number of cycles    : 977
0:56:22.484931 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:56:23.796729 INFO: Initializing CalibrationManager
0:56:23.796992 INFO: Loading calibration config
0:56:23.797587 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'}]
0:56:23.797696 INFO: Calibration group :fragment, found 1 estimator(s)
0:56:23.797786 INFO: Calibration group :precursor, found 3 estimator(s)
0:56:23.797863 INFO: Disabling ion mobility calibration
0:56:23.797890 INFO: removed mobility estimator from group precursor
0:56:23.798019 INFO: Initializing OptimizationManager
0:56:23.798129 INFO: initial parameter: ms1_error = 30
0:56:23.798188 INFO: initial parameter: ms2_error = 30
0:56:23.798239 INFO: initial parameter: rt_error = 805.5982666015625
0:56:23.798287 INFO: initial parameter: mobility_error = 0.1
0:56:23.798329 INFO: initial parameter: column_type = library
0:56:23.798371 INFO: initial parameter: num_candidates = 1
0:56:23.798414 INFO: initial parameter: classifier_version = -1
0:56:23.798457 INFO: initial parameter: fwhm_rt = 5
0:56:23.798499 INFO: initial parameter: fwhm_mobility = 0.01
0:56:23.798543 INFO: initial parameter: score_cutoff = 0
0:56:23.798636 INFO: Initializing TimingManager
0:56:23.798708 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:56:23.798849 INFO: FDRManager not loaded from disk.
0:56:23.798873 INFO: Initializing FDRManager
0:56:23.798918 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:56:25.071206 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
0:56:26.891599 PROGRESS: Starting initial search for precursors.
0:56:27.106778 INFO: Starting optimization step 0.
0:56:27.106988 PROGRESS: === Extracting elution groups 0 to 200 ===
0:56:27.107064 PROGRESS: Extracting batch of 395 precursors
0:56:27.108047 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:56:27.108096 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:56:27.108131 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:56:27.108154 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:56:27.108416 INFO: Starting candidate selection
0:56:27.275875 INFO: Starting candidate scoring
0:56:27.312557 INFO: Finished candidate processing
0:56:27.312625 INFO: Collecting candidate features
0:56:27.321038 INFO: Collecting fragment features
0:56:27.323068 INFO: Finished candidate scoring
0:56:27.323862 PROGRESS: === Extracted 395 precursors and 3958 fragments ===
0:56:27.324121 INFO: performing precursor FDR with 47 features
0:56:27.324157 INFO: Decoy channel: -1
0:56:27.324180 INFO: Competetive: True
0:56:27.325178 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:27.345162 INFO: Test AUC: 0.404
0:56:27.345223 INFO: Train AUC: 0.494
0:56:27.345251 INFO: AUC difference: 18.24%
0:56:27.345272 WARNING: AUC difference > 5%. This may indicate overfitting.
0:56:27.518040 INFO: Resetting torch num_threads to 100
0:56:27.518567 INFO: === FDR correction performed with classifier version -1 ===
0:56:27.519172 PROGRESS: ============================= Precursor FDR =============================
0:56:27.519266 PROGRESS: Total precursors accumulated: 200
0:56:27.519325 PROGRESS: Target precursors: 93 (46.50%)
0:56:27.519377 PROGRESS: Decoy precursors: 107 (53.50%)
0:56:27.519427 PROGRESS: 
0:56:27.519471 PROGRESS: Precursor Summary:
0:56:27.520308 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:56:27.520395 PROGRESS: 
0:56:27.520450 PROGRESS: Protein Summary:
0:56:27.521354 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:56:27.521456 PROGRESS: =========================================================================
0:56:27.576333 INFO: Starting optimization step 1.
0:56:27.576515 PROGRESS: === Extracting elution groups 200 to 600 ===
0:56:27.576582 PROGRESS: Extracting batch of 790 precursors
0:56:27.577391 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:56:27.577438 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:56:27.577470 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:56:27.577494 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:56:27.577649 INFO: Starting candidate selection
0:56:27.725540 INFO: Starting candidate scoring
0:56:27.762433 INFO: Finished candidate processing
0:56:27.762496 INFO: Collecting candidate features
0:56:27.770972 INFO: Collecting fragment features
0:56:27.773401 INFO: Finished candidate scoring
0:56:27.775452 PROGRESS: === Extracted 1183 precursors and 12041 fragments ===
0:56:27.776187 INFO: performing precursor FDR with 47 features
0:56:27.776229 INFO: Decoy channel: -1
0:56:27.776253 INFO: Competetive: True
0:56:27.778904 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:27.799833 INFO: Test AUC: 0.560
0:56:27.799898 INFO: Train AUC: 0.491
0:56:27.799926 INFO: AUC difference: 13.93%
0:56:27.799946 WARNING: AUC difference > 5%. This may indicate overfitting.
0:56:27.971672 INFO: Resetting torch num_threads to 100
0:56:27.972292 INFO: === FDR correction performed with classifier version -1 ===
0:56:27.972938 PROGRESS: ============================= Precursor FDR =============================
0:56:27.973032 PROGRESS: Total precursors accumulated: 599
0:56:27.973091 PROGRESS: Target precursors: 305 (50.92%)
0:56:27.973143 PROGRESS: Decoy precursors: 294 (49.08%)
0:56:27.973188 PROGRESS: 
0:56:27.973231 PROGRESS: Precursor Summary:
0:56:27.974088 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:56:27.974177 PROGRESS: 
0:56:27.974232 PROGRESS: Protein Summary:
0:56:27.975176 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:56:27.975269 PROGRESS: =========================================================================
0:56:28.032236 INFO: Starting optimization step 2.
0:56:28.032416 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:56:28.032484 PROGRESS: Extracting batch of 1585 precursors
0:56:28.033367 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:56:28.033413 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:56:28.033444 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:56:28.033466 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:56:28.033620 INFO: Starting candidate selection
0:56:28.204112 INFO: Starting candidate scoring
0:56:28.241978 INFO: Finished candidate processing
0:56:28.242059 INFO: Collecting candidate features
0:56:28.251945 INFO: Collecting fragment features
0:56:28.255504 INFO: Finished candidate scoring
0:56:28.258458 PROGRESS: === Extracted 2762 precursors and 28214 fragments ===
0:56:28.259429 INFO: performing precursor FDR with 47 features
0:56:28.259472 INFO: Decoy channel: -1
0:56:28.259496 INFO: Competetive: True
0:56:28.262610 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:28.284460 INFO: Test AUC: 0.471
0:56:28.284528 INFO: Train AUC: 0.499
0:56:28.284557 INFO: AUC difference: 5.68%
0:56:28.284579 WARNING: AUC difference > 5%. This may indicate overfitting.
0:56:28.457906 INFO: Resetting torch num_threads to 100
0:56:28.458622 INFO: === FDR correction performed with classifier version -1 ===
0:56:28.459279 PROGRESS: ============================= Precursor FDR =============================
0:56:28.459374 PROGRESS: Total precursors accumulated: 1
0:56:28.459439 PROGRESS: Target precursors: 1 (100.00%)
0:56:28.459492 PROGRESS: Decoy precursors: 0 (0.00%)
0:56:28.459541 PROGRESS: 
0:56:28.459587 PROGRESS: Precursor Summary:
0:56:28.460521 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:56:28.460610 PROGRESS: 
0:56:28.460665 PROGRESS: Protein Summary:
0:56:28.461695 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:56:28.461785 PROGRESS: =========================================================================
0:56:28.521014 INFO: Starting optimization step 3.
0:56:28.521208 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:56:28.521275 PROGRESS: Extracting batch of 3157 precursors
0:56:28.522338 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:56:28.522387 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:56:28.522418 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:56:28.522440 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:56:28.522606 INFO: Starting candidate selection
0:56:28.742822 INFO: Starting candidate scoring
0:56:28.782611 INFO: Finished candidate processing
0:56:28.782696 INFO: Collecting candidate features
0:56:28.795544 INFO: Collecting fragment features
0:56:28.799546 INFO: Finished candidate scoring
0:56:28.803653 PROGRESS: === Extracted 5917 precursors and 60638 fragments ===
0:56:28.804922 INFO: performing precursor FDR with 47 features
0:56:28.804965 INFO: Decoy channel: -1
0:56:28.804988 INFO: Competetive: True
0:56:28.808837 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:28.839967 INFO: Test AUC: 0.516
0:56:28.840050 INFO: Train AUC: 0.497
0:56:28.840080 INFO: AUC difference: 3.89%
0:56:29.017533 INFO: Resetting torch num_threads to 100
0:56:29.018410 INFO: === FDR correction performed with classifier version -1 ===
0:56:29.019073 PROGRESS: ============================= Precursor FDR =============================
0:56:29.019170 PROGRESS: Total precursors accumulated: 2
0:56:29.019228 PROGRESS: Target precursors: 2 (100.00%)
0:56:29.019280 PROGRESS: Decoy precursors: 0 (0.00%)
0:56:29.019325 PROGRESS: 
0:56:29.019368 PROGRESS: Precursor Summary:
0:56:29.020300 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
0:56:29.020387 PROGRESS: 
0:56:29.020443 PROGRESS: Protein Summary:
0:56:29.021482 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
0:56:29.021572 PROGRESS: =========================================================================
0:56:29.084738 INFO: Starting optimization step 4.
0:56:29.084953 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:56:29.085022 PROGRESS: Extracting batch of 6336 precursors
0:56:29.086576 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:56:29.086632 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:56:29.086663 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:56:29.086684 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:56:29.086842 INFO: Starting candidate selection
0:56:29.538746 INFO: Starting candidate scoring
0:56:29.595637 INFO: Finished candidate processing
0:56:29.595759 INFO: Collecting candidate features
0:56:29.616970 INFO: Collecting fragment features
0:56:29.624192 INFO: Finished candidate scoring
0:56:29.633892 PROGRESS: === Extracted 12238 precursors and 125614 fragments ===
0:56:29.636067 INFO: performing precursor FDR with 47 features
0:56:29.636137 INFO: Decoy channel: -1
0:56:29.636164 INFO: Competetive: True
0:56:29.643049 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:29.746030 INFO: Test AUC: 0.489
0:56:29.746171 INFO: Train AUC: 0.502
0:56:29.746200 INFO: AUC difference: 2.73%
0:56:29.930631 INFO: Resetting torch num_threads to 100
0:56:29.932450 INFO: === FDR correction performed with classifier version -1 ===
0:56:29.933944 PROGRESS: ============================= Precursor FDR =============================
0:56:29.934051 PROGRESS: Total precursors accumulated: 6,187
0:56:29.934115 PROGRESS: Target precursors: 3,143 (50.80%)
0:56:29.934170 PROGRESS: Decoy precursors: 3,044 (49.20%)
0:56:29.934216 PROGRESS: 
0:56:29.934262 PROGRESS: Precursor Summary:
0:56:29.935199 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:56:29.935299 PROGRESS: 
0:56:29.935355 PROGRESS: Protein Summary:
0:56:29.936331 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:56:29.936432 PROGRESS: =========================================================================
0:56:30.015651 INFO: Starting optimization step 5.
0:56:30.015969 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:56:30.016040 PROGRESS: Extracting batch of 12662 precursors
0:56:30.019451 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:56:30.019515 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:56:30.019551 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:56:30.019574 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:56:30.019789 INFO: Starting candidate selection
0:56:30.852174 INFO: Starting candidate scoring
0:56:30.934963 INFO: Finished candidate processing
0:56:30.935057 INFO: Collecting candidate features
0:56:30.964978 INFO: Collecting fragment features
0:56:30.974820 INFO: Finished candidate scoring
0:56:30.987486 PROGRESS: === Extracted 24888 precursors and 255777 fragments ===
0:56:30.990866 INFO: performing precursor FDR with 47 features
0:56:30.990946 INFO: Decoy channel: -1
0:56:30.990971 INFO: Competetive: True
0:56:31.000603 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:31.255538 INFO: Test AUC: 0.535
0:56:31.255645 INFO: Train AUC: 0.543
0:56:31.255676 INFO: AUC difference: 1.56%
0:56:31.441409 INFO: Resetting torch num_threads to 100
0:56:31.443074 INFO: === FDR correction performed with classifier version -1 ===
0:56:31.443679 PROGRESS: ============================= Precursor FDR =============================
0:56:31.443771 PROGRESS: Total precursors accumulated: 29
0:56:31.443833 PROGRESS: Target precursors: 27 (93.10%)
0:56:31.443885 PROGRESS: Decoy precursors: 2 (6.90%)
0:56:31.443933 PROGRESS: 
0:56:31.443979 PROGRESS: Precursor Summary:
0:56:31.444850 PROGRESS: Channel   0:	 0.05 FDR:    21; 0.01 FDR:    14; 0.001 FDR:    14
0:56:31.444942 PROGRESS: 
0:56:31.444996 PROGRESS: Protein Summary:
0:56:31.445944 PROGRESS: Channel   0:	 0.05 FDR:    21; 0.01 FDR:    14; 0.001 FDR:    14
0:56:31.446034 PROGRESS: =========================================================================
0:56:31.532640 INFO: Starting optimization step 6.
0:56:31.532883 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:56:31.532951 PROGRESS: Extracting batch of 25287 precursors
0:56:31.539514 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:56:31.539575 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:56:31.539607 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:56:31.539629 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:56:31.539807 INFO: Starting candidate selection
0:56:33.109642 INFO: Starting candidate scoring
0:56:33.268459 INFO: Finished candidate processing
0:56:33.268557 INFO: Collecting candidate features
0:56:33.314823 INFO: Collecting fragment features
0:56:33.331545 INFO: Finished candidate scoring
0:56:33.354291 PROGRESS: === Extracted 50105 precursors and 515237 fragments ===
0:56:33.360379 INFO: performing precursor FDR with 47 features
0:56:33.360458 INFO: Decoy channel: -1
0:56:33.360483 INFO: Competetive: True
0:56:33.379366 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:34.129527 INFO: Test AUC: 0.561
0:56:34.129648 INFO: Train AUC: 0.578
0:56:34.129677 INFO: AUC difference: 2.79%
0:56:34.324655 INFO: Resetting torch num_threads to 100
0:56:34.327359 INFO: === FDR correction performed with classifier version -1 ===
0:56:34.327953 PROGRESS: ============================= Precursor FDR =============================
0:56:34.328048 PROGRESS: Total precursors accumulated: 184
0:56:34.328107 PROGRESS: Target precursors: 168 (91.30%)
0:56:34.328159 PROGRESS: Decoy precursors: 16 (8.70%)
0:56:34.328208 PROGRESS: 
0:56:34.328253 PROGRESS: Precursor Summary:
0:56:34.329147 PROGRESS: Channel   0:	 0.05 FDR:   141; 0.01 FDR:    58; 0.001 FDR:    58
0:56:34.329235 PROGRESS: 
0:56:34.329294 PROGRESS: Protein Summary:
0:56:34.330290 PROGRESS: Channel   0:	 0.05 FDR:   138; 0.01 FDR:    57; 0.001 FDR:    57
0:56:34.330382 PROGRESS: =========================================================================
0:56:34.449219 INFO: Starting optimization step 7.
0:56:34.449463 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:56:34.449548 PROGRESS: Extracting batch of 50588 precursors
0:56:34.460230 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:56:34.460333 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:56:34.460366 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:56:34.460390 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:56:34.460586 INFO: Starting candidate selection
0:56:37.546317 INFO: Starting candidate scoring
0:56:37.912522 INFO: Finished candidate processing
0:56:37.912654 INFO: Collecting candidate features
0:56:38.021212 INFO: Collecting fragment features
0:56:38.062880 INFO: Finished candidate scoring
0:56:38.134400 PROGRESS: === Extracted 100596 precursors and 1035394 fragments ===
0:56:38.156092 INFO: performing precursor FDR with 47 features
0:56:38.156216 INFO: Decoy channel: -1
0:56:38.156244 INFO: Competetive: True
0:56:38.214427 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:40.585815 INFO: Test AUC: 0.561
0:56:40.585982 INFO: Train AUC: 0.588
0:56:40.586013 INFO: AUC difference: 4.68%
0:56:40.800972 INFO: Resetting torch num_threads to 100
0:56:40.856884 INFO: === FDR correction performed with classifier version -1 ===
0:56:40.857833 PROGRESS: ============================= Precursor FDR =============================
0:56:40.857936 PROGRESS: Total precursors accumulated: 562
0:56:40.857997 PROGRESS: Target precursors: 514 (91.46%)
0:56:40.858048 PROGRESS: Decoy precursors: 48 (8.54%)
0:56:40.858096 PROGRESS: 
0:56:40.858139 PROGRESS: Precursor Summary:
0:56:40.859193 PROGRESS: Channel   0:	 0.05 FDR:   450; 0.01 FDR:   272; 0.001 FDR:   224
0:56:40.859295 PROGRESS: 
0:56:40.859351 PROGRESS: Protein Summary:
0:56:40.860563 PROGRESS: Channel   0:	 0.05 FDR:   420; 0.01 FDR:   256; 0.001 FDR:   214
0:56:40.860658 PROGRESS: =========================================================================
0:56:40.954101 INFO: fragments_df: keeping 2577 of 1035394 [sum(precursor_idx_mask)=3116 sum(mass_error_mask)=1035394 stop_rank=2577
0:56:41.252407 INFO: calibration group: precursor, fitting rt estimator 
0:56:41.355314 INFO: calibration group: fragment, fitting mz estimator 
0:56:41.641044 INFO: Using score_cutoff 71.81972054901124 (fac=0.99, q=1)
0:56:41.641591 INFO: calibration group: precursor, predicting mz
0:56:41.641685 WARNING: mz prediction was skipped as it has not been fitted yet
0:56:41.641717 INFO: calibration group: precursor, predicting rt
0:56:41.708911 INFO: calibration group: fragment, predicting mz
0:56:41.863755 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:56:41.864104 INFO: Starting optimization step 8.
0:56:41.864182 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:56:41.864267 PROGRESS: Extracting batch of 100800 precursors
0:56:41.898359 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:56:41.898529 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:56:41.898568 INFO: FWHM in RT is 3.03 seconds, sigma is 0.39
0:56:41.898592 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:56:41.898976 INFO: Starting candidate selection
0:56:46.737460 INFO: Starting candidate scoring
0:56:48.053476 INFO: Finished candidate processing
0:56:48.053613 INFO: Collecting candidate features
0:56:48.443781 INFO: Collecting fragment features
0:56:48.587125 INFO: Finished candidate scoring
0:56:48.717447 PROGRESS: === Extracted 201192 precursors and 2046511 fragments ===
0:56:48.718292 INFO: performing precursor FDR with 47 features
0:56:48.718337 INFO: Decoy channel: -1
0:56:48.718363 INFO: Competetive: True
0:56:48.803096 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:53.185930 INFO: Test AUC: 0.563
0:56:53.186097 INFO: Train AUC: 0.594
0:56:53.186135 INFO: AUC difference: 5.29%
0:56:53.186163 WARNING: AUC difference > 5%. This may indicate overfitting.
0:56:53.425019 INFO: Resetting torch num_threads to 100
0:56:53.433211 INFO: === FDR correction performed with classifier version 7 ===
0:56:53.434100 PROGRESS: ============================= Precursor FDR =============================
0:56:53.434200 PROGRESS: Total precursors accumulated: 659
0:56:53.434277 PROGRESS: Target precursors: 603 (91.50%)
0:56:53.434337 PROGRESS: Decoy precursors: 56 (8.50%)
0:56:53.434391 PROGRESS: 
0:56:53.434443 PROGRESS: Precursor Summary:
0:56:53.435552 PROGRESS: Channel   0:	 0.05 FDR:   458; 0.01 FDR:   344; 0.001 FDR:   236
0:56:53.435654 PROGRESS: 
0:56:53.435717 PROGRESS: Protein Summary:
0:56:53.436953 PROGRESS: Channel   0:	 0.05 FDR:   427; 0.01 FDR:   323; 0.001 FDR:   224
0:56:53.437049 PROGRESS: =========================================================================
0:56:53.570420 INFO: fragments_df: keeping 3941 of 2046511 [sum(precursor_idx_mask)=7725 sum(mass_error_mask)=2046511 stop_rank=3941
0:56:53.847609 INFO: calibration group: precursor, fitting rt estimator 
0:56:53.960980 INFO: calibration group: fragment, fitting mz estimator 
0:56:54.419378 INFO: Using score_cutoff 69.34005975723267 (fac=0.99, q=1)
0:56:54.419884 INFO: calibration group: precursor, predicting mz
0:56:54.419978 WARNING: mz prediction was skipped as it has not been fitted yet
0:56:54.420010 INFO: calibration group: precursor, predicting rt
0:56:54.483095 INFO: calibration group: fragment, predicting mz
0:56:54.644017 INFO: === checking if optimization conditions were reached ===
0:56:54.644371 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
0:56:54.646945 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 23.2638.
0:56:54.647007 INFO: ==============================================
0:56:54.647103 INFO: Starting optimization step 9.
0:56:54.647171 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:56:54.647232 PROGRESS: Extracting batch of 100800 precursors
0:56:54.681076 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:56:54.681251 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:56:54.681291 INFO: FWHM in RT is 3.00 seconds, sigma is 0.39
0:56:54.681317 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:56:54.681655 INFO: Starting candidate selection
0:56:59.674224 INFO: Starting candidate scoring
0:57:01.027046 INFO: Finished candidate processing
0:57:01.027140 INFO: Collecting candidate features
0:57:01.340905 INFO: Collecting fragment features
0:57:01.459015 INFO: Finished candidate scoring
0:57:01.541989 PROGRESS: === Extracted 201191 precursors and 1976041 fragments ===
0:57:01.542464 INFO: performing precursor FDR with 47 features
0:57:01.542503 INFO: Decoy channel: -1
0:57:01.542527 INFO: Competetive: True
0:57:01.609817 INFO: Setting torch num_threads to 2 for FDR classification task
0:57:04.942345 INFO: Test AUC: 0.565
0:57:04.942467 INFO: Train AUC: 0.584
0:57:04.942497 INFO: AUC difference: 3.29%
0:57:05.173404 INFO: Resetting torch num_threads to 100
0:57:05.178795 INFO: === FDR correction performed with classifier version 7 ===
0:57:05.179569 PROGRESS: ============================= Precursor FDR =============================
0:57:05.179677 PROGRESS: Total precursors accumulated: 746
0:57:05.179739 PROGRESS: Target precursors: 679 (91.02%)
0:57:05.179797 PROGRESS: Decoy precursors: 67 (8.98%)
0:57:05.179844 PROGRESS: 
0:57:05.179888 PROGRESS: Precursor Summary:
0:57:05.180978 PROGRESS: Channel   0:	 0.05 FDR:   544; 0.01 FDR:   385; 0.001 FDR:   319
0:57:05.181072 PROGRESS: 
0:57:05.181128 PROGRESS: Protein Summary:
0:57:05.182333 PROGRESS: Channel   0:	 0.05 FDR:   512; 0.01 FDR:   363; 0.001 FDR:   300
0:57:05.182430 PROGRESS: =========================================================================
0:57:05.315808 INFO: fragments_df: keeping 4305 of 1976041 [sum(precursor_idx_mask)=8643 sum(mass_error_mask)=1976041 stop_rank=4305
0:57:05.511950 INFO: calibration group: precursor, fitting rt estimator 
0:57:05.636370 INFO: calibration group: fragment, fitting mz estimator 
0:57:06.200659 INFO: Using score_cutoff 69.10178156433105 (fac=0.99, q=1)
0:57:06.201061 INFO: calibration group: precursor, predicting mz
0:57:06.201150 WARNING: mz prediction was skipped as it has not been fitted yet
0:57:06.201182 INFO: calibration group: precursor, predicting rt
0:57:06.264245 INFO: calibration group: fragment, predicting mz
0:57:06.414539 INFO: === checking if optimization conditions were reached ===
0:57:06.414836 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
0:57:06.417618 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 19.0177.
0:57:06.417679 INFO: ==============================================
0:57:06.417792 INFO: Starting optimization step 10.
0:57:06.417866 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:57:06.417943 PROGRESS: Extracting batch of 100800 precursors
0:57:06.451269 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:57:06.451403 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:57:06.451448 INFO: FWHM in RT is 2.89 seconds, sigma is 0.37
0:57:06.451477 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:57:06.451768 INFO: Starting candidate selection
0:57:13.737195 INFO: Starting candidate scoring
0:57:15.078435 INFO: Finished candidate processing
0:57:15.078529 INFO: Collecting candidate features
0:57:15.392695 INFO: Collecting fragment features
0:57:15.510628 INFO: Finished candidate scoring
0:57:15.597429 PROGRESS: === Extracted 201191 precursors and 1914399 fragments ===
0:57:15.597859 INFO: performing precursor FDR with 47 features
0:57:15.597897 INFO: Decoy channel: -1
0:57:15.597919 INFO: Competetive: True
0:57:15.675354 INFO: Setting torch num_threads to 2 for FDR classification task
0:57:18.997579 INFO: Test AUC: 0.568
0:57:18.997699 INFO: Train AUC: 0.584
0:57:18.997729 INFO: AUC difference: 2.68%
0:57:19.229919 INFO: Resetting torch num_threads to 100
0:57:19.235149 INFO: === FDR correction performed with classifier version 7 ===
0:57:19.235922 PROGRESS: ============================= Precursor FDR =============================
0:57:19.236025 PROGRESS: Total precursors accumulated: 780
0:57:19.236092 PROGRESS: Target precursors: 709 (90.90%)
0:57:19.236147 PROGRESS: Decoy precursors: 71 (9.10%)
0:57:19.236193 PROGRESS: 
0:57:19.236238 PROGRESS: Precursor Summary:
0:57:19.237306 PROGRESS: Channel   0:	 0.05 FDR:   601; 0.01 FDR:   356; 0.001 FDR:   305
0:57:19.237400 PROGRESS: 
0:57:19.237456 PROGRESS: Protein Summary:
0:57:19.238707 PROGRESS: Channel   0:	 0.05 FDR:   562; 0.01 FDR:   334; 0.001 FDR:   287
0:57:19.238803 PROGRESS: =========================================================================
0:57:19.366928 INFO: fragments_df: keeping 4082 of 1914399 [sum(precursor_idx_mask)=7908 sum(mass_error_mask)=1914399 stop_rank=4082
0:57:19.562425 INFO: calibration group: precursor, fitting rt estimator 
0:57:19.683631 INFO: calibration group: fragment, fitting mz estimator 
0:57:20.223353 INFO: Using score_cutoff 69.26764893722533 (fac=0.99, q=1)
0:57:20.223761 INFO: calibration group: precursor, predicting mz
0:57:20.223851 WARNING: mz prediction was skipped as it has not been fitted yet
0:57:20.223881 INFO: calibration group: precursor, predicting rt
0:57:20.285652 INFO: calibration group: fragment, predicting mz
0:57:20.435169 INFO: === checking if optimization conditions were reached ===
0:57:20.435448 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
0:57:20.438177 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 16.6651.
0:57:20.438237 INFO: ==============================================
0:57:20.438344 INFO: Starting optimization step 11.
0:57:20.438420 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:57:20.438503 PROGRESS: Extracting batch of 100800 precursors
0:57:20.472057 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:57:20.472191 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:57:20.472255 INFO: FWHM in RT is 2.81 seconds, sigma is 0.36
0:57:20.472285 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:57:20.472579 INFO: Starting candidate selection
0:57:25.330749 INFO: Starting candidate scoring
0:57:26.643576 INFO: Finished candidate processing
0:57:26.643713 INFO: Collecting candidate features
0:57:27.045305 INFO: Collecting fragment features
0:57:27.178214 INFO: Finished candidate scoring
0:57:27.297857 PROGRESS: === Extracted 201186 precursors and 1849234 fragments ===
0:57:27.298343 INFO: performing precursor FDR with 47 features
0:57:27.298384 INFO: Decoy channel: -1
0:57:27.298409 INFO: Competetive: True
0:57:27.394166 INFO: Setting torch num_threads to 2 for FDR classification task
0:57:31.703246 INFO: Test AUC: 0.565
0:57:31.703446 INFO: Train AUC: 0.585
0:57:31.703479 INFO: AUC difference: 3.31%
0:57:31.938640 INFO: Resetting torch num_threads to 100
0:57:31.944498 INFO: === FDR correction performed with classifier version 7 ===
0:57:31.945283 PROGRESS: ============================= Precursor FDR =============================
0:57:31.945395 PROGRESS: Total precursors accumulated: 773
0:57:31.945457 PROGRESS: Target precursors: 706 (91.33%)
0:57:31.945510 PROGRESS: Decoy precursors: 67 (8.67%)
0:57:31.945562 PROGRESS: 
0:57:31.945609 PROGRESS: Precursor Summary:
0:57:31.946720 PROGRESS: Channel   0:	 0.05 FDR:   605; 0.01 FDR:   450; 0.001 FDR:   301
0:57:31.946821 PROGRESS: 
0:57:31.946880 PROGRESS: Protein Summary:
0:57:31.948140 PROGRESS: Channel   0:	 0.05 FDR:   565; 0.01 FDR:   421; 0.001 FDR:   283
0:57:31.948235 PROGRESS: =========================================================================
0:57:32.067649 INFO: fragments_df: keeping 4842 of 1849234 [sum(precursor_idx_mask)=9849 sum(mass_error_mask)=1849234 stop_rank=4842
0:57:32.223895 INFO: calibration group: precursor, fitting rt estimator 
0:57:32.352384 INFO: calibration group: fragment, fitting mz estimator 
0:57:33.003350 INFO: Using score_cutoff 56.722867585372924 (fac=0.99, q=1)
0:57:33.003835 INFO: calibration group: precursor, predicting mz
0:57:33.003926 WARNING: mz prediction was skipped as it has not been fitted yet
0:57:33.003956 INFO: calibration group: precursor, predicting rt
0:57:33.035009 INFO: calibration group: fragment, predicting mz
0:57:33.097483 INFO: === checking if optimization conditions were reached ===
0:57:33.097759 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
0:57:33.100750 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 14.1417.
0:57:33.100816 INFO: ==============================================
0:57:33.100925 INFO: Starting optimization step 12.
0:57:33.101002 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:57:33.101080 PROGRESS: Extracting batch of 50212 precursors
0:57:33.118105 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:57:33.118228 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:57:33.118273 INFO: FWHM in RT is 2.76 seconds, sigma is 0.36
0:57:33.118302 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:57:33.118613 INFO: Starting candidate selection
0:57:35.555773 INFO: Starting candidate scoring
0:57:36.215782 INFO: Finished candidate processing
0:57:36.215945 INFO: Collecting candidate features
0:57:36.364423 INFO: Collecting fragment features
0:57:36.418081 INFO: Finished candidate scoring
0:57:36.455139 PROGRESS: === Extracted 100207 precursors and 895592 fragments ===
0:57:36.455509 INFO: performing precursor FDR with 47 features
0:57:36.455547 INFO: Decoy channel: -1
0:57:36.455570 INFO: Competetive: True
0:57:36.490427 INFO: Setting torch num_threads to 2 for FDR classification task
0:57:37.996053 INFO: Test AUC: 0.565
0:57:37.996177 INFO: Train AUC: 0.587
0:57:37.996206 INFO: AUC difference: 3.74%
0:57:38.201327 INFO: Resetting torch num_threads to 100
0:57:38.204614 INFO: === FDR correction performed with classifier version 7 ===
0:57:38.205275 PROGRESS: ============================= Precursor FDR =============================
0:57:38.205380 PROGRESS: Total precursors accumulated: 370
0:57:38.205446 PROGRESS: Target precursors: 337 (91.08%)
0:57:38.205500 PROGRESS: Decoy precursors: 33 (8.92%)
0:57:38.205546 PROGRESS: 
0:57:38.205589 PROGRESS: Precursor Summary:
0:57:38.206558 PROGRESS: Channel   0:	 0.05 FDR:   303; 0.01 FDR:   146; 0.001 FDR:   123
0:57:38.206661 PROGRESS: 
0:57:38.206718 PROGRESS: Protein Summary:
0:57:38.207807 PROGRESS: Channel   0:	 0.05 FDR:   290; 0.01 FDR:   142; 0.001 FDR:   120
0:57:38.207900 PROGRESS: =========================================================================
0:57:38.330087 INFO: calibration group: precursor, predicting mz
0:57:38.330337 WARNING: mz prediction was skipped as it has not been fitted yet
0:57:38.330373 INFO: calibration group: precursor, predicting rt
0:57:38.361534 INFO: calibration group: fragment, predicting mz
0:57:38.428037 INFO: === skipping optimization until target number of precursors are found ===
0:57:38.428328 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:57:38.428401 INFO: Starting optimization step 13.
0:57:38.428477 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:57:38.428547 PROGRESS: Extracting batch of 50588 precursors
0:57:38.445100 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:57:38.445218 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:57:38.445258 INFO: FWHM in RT is 2.76 seconds, sigma is 0.36
0:57:38.445287 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:57:38.445525 INFO: Starting candidate selection
0:57:40.902813 INFO: Starting candidate scoring
0:57:41.655970 INFO: Finished candidate processing
0:57:41.656065 INFO: Collecting candidate features
0:57:41.822836 INFO: Collecting fragment features
0:57:41.876024 INFO: Finished candidate scoring
0:57:41.955223 PROGRESS: === Extracted 201186 precursors and 1798531 fragments ===
0:57:41.975906 INFO: performing precursor FDR with 47 features
0:57:41.976030 INFO: Decoy channel: -1
0:57:41.976055 INFO: Competetive: True
0:57:42.051094 INFO: Setting torch num_threads to 2 for FDR classification task
0:57:45.298528 INFO: Test AUC: 0.567
0:57:45.300361 INFO: Train AUC: 0.585
0:57:45.300398 INFO: AUC difference: 3.13%
0:57:45.534068 INFO: Resetting torch num_threads to 100
0:57:45.544777 INFO: === FDR correction performed with classifier version 7 ===
0:57:45.545538 PROGRESS: ============================= Precursor FDR =============================
0:57:45.545630 PROGRESS: Total precursors accumulated: 841
0:57:45.545690 PROGRESS: Target precursors: 766 (91.08%)
0:57:45.545740 PROGRESS: Decoy precursors: 75 (8.92%)
0:57:45.545787 PROGRESS: 
0:57:45.545830 PROGRESS: Precursor Summary:
0:57:45.546884 PROGRESS: Channel   0:	 0.05 FDR:   570; 0.01 FDR:   457; 0.001 FDR:   299
0:57:45.546980 PROGRESS: 
0:57:45.547037 PROGRESS: Protein Summary:
0:57:45.548295 PROGRESS: Channel   0:	 0.05 FDR:   533; 0.01 FDR:   428; 0.001 FDR:   283
0:57:45.548392 PROGRESS: =========================================================================
0:57:45.676769 INFO: fragments_df: keeping 4923 of 1798531 [sum(precursor_idx_mask)=9934 sum(mass_error_mask)=1798531 stop_rank=4923
0:57:45.813411 INFO: calibration group: precursor, fitting rt estimator 
0:57:45.942867 INFO: calibration group: fragment, fitting mz estimator 
0:57:46.602569 INFO: Using score_cutoff 66.88939018249512 (fac=0.99, q=1)
0:57:46.602970 INFO: calibration group: precursor, predicting mz
0:57:46.603056 WARNING: mz prediction was skipped as it has not been fitted yet
0:57:46.603087 INFO: calibration group: precursor, predicting rt
0:57:46.634451 INFO: calibration group: fragment, predicting mz
0:57:46.700420 INFO: === checking if optimization conditions were reached ===
0:57:46.700681 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
0:57:46.703645 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 12.4363.
0:57:46.703724 INFO: ==============================================
0:57:46.703869 INFO: Starting optimization step 14.
0:57:46.703947 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:57:46.704015 PROGRESS: Extracting batch of 50212 precursors
0:57:46.785149 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:57:46.785264 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:57:46.785300 INFO: FWHM in RT is 2.73 seconds, sigma is 0.35
0:57:46.785323 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:57:46.785527 INFO: Starting candidate selection
0:57:49.252077 INFO: Starting candidate scoring
0:57:49.966123 INFO: Finished candidate processing
0:57:49.966252 INFO: Collecting candidate features
0:57:50.157406 INFO: Collecting fragment features
0:57:50.222807 INFO: Finished candidate scoring
0:57:50.283407 PROGRESS: === Extracted 100205 precursors and 863781 fragments ===
0:57:50.283942 INFO: performing precursor FDR with 47 features
0:57:50.283980 INFO: Decoy channel: -1
0:57:50.284004 INFO: Competetive: True
0:57:50.341117 INFO: Setting torch num_threads to 2 for FDR classification task
0:57:52.458276 INFO: Test AUC: 0.568
0:57:52.458452 INFO: Train AUC: 0.587
0:57:52.458482 INFO: AUC difference: 3.33%
0:57:52.670561 INFO: Resetting torch num_threads to 100
0:57:52.674970 INFO: === FDR correction performed with classifier version 7 ===
0:57:52.675766 PROGRESS: ============================= Precursor FDR =============================
0:57:52.675857 PROGRESS: Total precursors accumulated: 402
0:57:52.675916 PROGRESS: Target precursors: 367 (91.29%)
0:57:52.675966 PROGRESS: Decoy precursors: 35 (8.71%)
0:57:52.676012 PROGRESS: 
0:57:52.676056 PROGRESS: Precursor Summary:
0:57:52.677053 PROGRESS: Channel   0:	 0.05 FDR:   313; 0.01 FDR:   184; 0.001 FDR:   129
0:57:52.677151 PROGRESS: 
0:57:52.677209 PROGRESS: Protein Summary:
0:57:52.678356 PROGRESS: Channel   0:	 0.05 FDR:   302; 0.01 FDR:   178; 0.001 FDR:   126
0:57:52.678458 PROGRESS: =========================================================================
0:57:52.880335 INFO: calibration group: precursor, predicting mz
0:57:52.880728 WARNING: mz prediction was skipped as it has not been fitted yet
0:57:52.880764 INFO: calibration group: precursor, predicting rt
0:57:52.913393 INFO: calibration group: fragment, predicting mz
0:57:52.982526 INFO: === skipping optimization until target number of precursors are found ===
0:57:52.982903 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
0:57:52.982982 INFO: Starting optimization step 15.
0:57:52.983053 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:57:52.983129 PROGRESS: Extracting batch of 50588 precursors
0:57:53.000891 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:57:53.001041 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:57:53.001082 INFO: FWHM in RT is 2.73 seconds, sigma is 0.35
0:57:53.001105 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:57:53.001447 INFO: Starting candidate selection
0:57:55.462881 INFO: Starting candidate scoring
0:57:56.127814 INFO: Finished candidate processing
0:57:56.127913 INFO: Collecting candidate features
0:57:56.273816 INFO: Collecting fragment features
0:57:56.326872 INFO: Finished candidate scoring
0:57:56.411624 PROGRESS: === Extracted 201183 precursors and 1734614 fragments ===
0:57:56.431542 INFO: performing precursor FDR with 47 features
0:57:56.431666 INFO: Decoy channel: -1
0:57:56.431691 INFO: Competetive: True
0:57:56.510764 INFO: Setting torch num_threads to 2 for FDR classification task
0:57:59.785103 INFO: Test AUC: 0.565
0:57:59.785220 INFO: Train AUC: 0.585
0:57:59.785251 INFO: AUC difference: 3.34%
0:58:00.015742 INFO: Resetting torch num_threads to 100
0:58:00.023942 INFO: === FDR correction performed with classifier version 7 ===
0:58:00.024746 PROGRESS: ============================= Precursor FDR =============================
0:58:00.024847 PROGRESS: Total precursors accumulated: 838
0:58:00.024916 PROGRESS: Target precursors: 765 (91.29%)
0:58:00.024972 PROGRESS: Decoy precursors: 73 (8.71%)
0:58:00.025028 PROGRESS: 
0:58:00.025074 PROGRESS: Precursor Summary:
0:58:00.026129 PROGRESS: Channel   0:	 0.05 FDR:   641; 0.01 FDR:   419; 0.001 FDR:   300
0:58:00.026219 PROGRESS: 
0:58:00.026275 PROGRESS: Protein Summary:
0:58:00.027518 PROGRESS: Channel   0:	 0.05 FDR:   602; 0.01 FDR:   393; 0.001 FDR:   283
0:58:00.027613 PROGRESS: =========================================================================
0:58:00.149426 INFO: fragments_df: keeping 4616 of 1734614 [sum(precursor_idx_mask)=9082 sum(mass_error_mask)=1734614 stop_rank=4616
0:58:00.278218 INFO: calibration group: precursor, fitting rt estimator 
0:58:00.413338 INFO: calibration group: fragment, fitting mz estimator 
0:58:01.026132 INFO: Using score_cutoff 66.70650242614747 (fac=0.99, q=1)
0:58:01.026540 INFO: calibration group: precursor, predicting mz
0:58:01.026638 WARNING: mz prediction was skipped as it has not been fitted yet
0:58:01.026669 INFO: calibration group: precursor, predicting rt
0:58:01.058900 INFO: calibration group: fragment, predicting mz
0:58:01.128563 INFO: === checking if optimization conditions were reached ===
0:58:01.129537 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
0:58:01.132751 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 10.2250.
0:58:01.132818 INFO: ==============================================
0:58:01.132929 INFO: Starting optimization step 16.
0:58:01.133013 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:58:01.133097 PROGRESS: Extracting batch of 50212 precursors
0:58:01.149232 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:58:01.149342 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:58:01.149381 INFO: FWHM in RT is 2.69 seconds, sigma is 0.35
0:58:01.149411 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:58:01.149636 INFO: Starting candidate selection
0:58:03.735889 INFO: Starting candidate scoring
0:58:04.408112 INFO: Finished candidate processing
0:58:04.408962 INFO: Collecting candidate features
0:58:04.608844 INFO: Collecting fragment features
0:58:04.688523 INFO: Finished candidate scoring
0:58:04.743648 PROGRESS: === Extracted 100207 precursors and 826940 fragments ===
0:58:04.744232 INFO: performing precursor FDR with 47 features
0:58:04.744296 INFO: Decoy channel: -1
0:58:04.744321 INFO: Competetive: True
0:58:04.801198 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:06.885102 INFO: Test AUC: 0.568
0:58:06.885273 INFO: Train AUC: 0.588
0:58:06.885305 INFO: AUC difference: 3.44%
0:58:07.095444 INFO: Resetting torch num_threads to 100
0:58:07.099838 INFO: === FDR correction performed with classifier version 7 ===
0:58:07.100620 PROGRESS: ============================= Precursor FDR =============================
0:58:07.100718 PROGRESS: Total precursors accumulated: 428
0:58:07.100779 PROGRESS: Target precursors: 390 (91.12%)
0:58:07.100830 PROGRESS: Decoy precursors: 38 (8.88%)
0:58:07.100875 PROGRESS: 
0:58:07.100920 PROGRESS: Precursor Summary:
0:58:07.101910 PROGRESS: Channel   0:	 0.05 FDR:   309; 0.01 FDR:   218; 0.001 FDR:   166
0:58:07.102007 PROGRESS: 
0:58:07.102061 PROGRESS: Protein Summary:
0:58:07.103196 PROGRESS: Channel   0:	 0.05 FDR:   298; 0.01 FDR:   208; 0.001 FDR:   161
0:58:07.103292 PROGRESS: =========================================================================
0:58:07.157457 INFO: fragments_df: keeping 2352 of 826940 [sum(precursor_idx_mask)=4639 sum(mass_error_mask)=826940 stop_rank=2352
0:58:07.321916 INFO: calibration group: precursor, fitting rt estimator 
0:58:07.426589 INFO: calibration group: fragment, fitting mz estimator 
0:58:07.691901 INFO: Using score_cutoff 66.37886538848878 (fac=0.99, q=1)
0:58:07.692425 INFO: calibration group: precursor, predicting mz
0:58:07.692518 WARNING: mz prediction was skipped as it has not been fitted yet
0:58:07.692550 INFO: calibration group: precursor, predicting rt
0:58:07.723886 INFO: calibration group: fragment, predicting mz
0:58:07.787805 INFO: === checking if optimization conditions were reached ===
0:58:07.788180 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
0:58:07.790738 PROGRESS: ❌ ms2_error      : optimization incomplete after 7 search(es). Will search with parameter 8.2079.
0:58:07.790803 INFO: ==============================================
0:58:07.790914 INFO: Starting optimization step 17.
0:58:07.790988 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:58:07.791060 PROGRESS: Extracting batch of 50212 precursors
0:58:07.808204 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:58:07.808351 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:58:07.808392 INFO: FWHM in RT is 2.58 seconds, sigma is 0.33
0:58:07.808414 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:58:07.808740 INFO: Starting candidate selection
0:58:10.284345 INFO: Starting candidate scoring
0:58:10.929984 INFO: Finished candidate processing
0:58:10.930080 INFO: Collecting candidate features
0:58:11.079360 INFO: Collecting fragment features
0:58:11.129046 INFO: Finished candidate scoring
0:58:11.167846 PROGRESS: === Extracted 100198 precursors and 779095 fragments ===
0:58:11.168208 INFO: performing precursor FDR with 47 features
0:58:11.168246 INFO: Decoy channel: -1
0:58:11.168269 INFO: Competetive: True
0:58:11.196261 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:12.776435 INFO: Test AUC: 0.570
0:58:12.776559 INFO: Train AUC: 0.585
0:58:12.776587 INFO: AUC difference: 2.50%
0:58:12.978478 INFO: Resetting torch num_threads to 100
0:58:12.981268 INFO: === FDR correction performed with classifier version 7 ===
0:58:12.981908 PROGRESS: ============================= Precursor FDR =============================
0:58:12.982007 PROGRESS: Total precursors accumulated: 443
0:58:12.982066 PROGRESS: Target precursors: 404 (91.20%)
0:58:12.982117 PROGRESS: Decoy precursors: 39 (8.80%)
0:58:12.982162 PROGRESS: 
0:58:12.982205 PROGRESS: Precursor Summary:
0:58:12.983159 PROGRESS: Channel   0:	 0.05 FDR:   301; 0.01 FDR:   213; 0.001 FDR:   161
0:58:12.983249 PROGRESS: 
0:58:12.983302 PROGRESS: Protein Summary:
0:58:12.984369 PROGRESS: Channel   0:	 0.05 FDR:   290; 0.01 FDR:   205; 0.001 FDR:   156
0:58:12.984459 PROGRESS: =========================================================================
0:58:13.034775 INFO: fragments_df: keeping 2330 of 779095 [sum(precursor_idx_mask)=4464 sum(mass_error_mask)=779095 stop_rank=2330
0:58:13.155521 INFO: calibration group: precursor, fitting rt estimator 
0:58:13.269572 INFO: calibration group: fragment, fitting mz estimator 
0:58:13.582781 INFO: Using score_cutoff 67.26342818298339 (fac=0.99, q=1)
0:58:13.583163 INFO: calibration group: precursor, predicting mz
0:58:13.583248 WARNING: mz prediction was skipped as it has not been fitted yet
0:58:13.583279 INFO: calibration group: precursor, predicting rt
0:58:13.614689 INFO: calibration group: fragment, predicting mz
0:58:13.678782 INFO: === checking if optimization conditions were reached ===
0:58:13.679010 PROGRESS: === Optimization of ms2_error has been performed 8 time(s); minimum number is 2 ===
0:58:13.681037 PROGRESS: ❌ ms2_error      : optimization incomplete after 8 search(es). Will search with parameter 7.2704.
0:58:13.681092 INFO: ==============================================
0:58:13.681193 INFO: Starting optimization step 18.
0:58:13.681267 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:58:13.681345 PROGRESS: Extracting batch of 50212 precursors
0:58:13.692810 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:58:13.692924 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:58:13.692964 INFO: FWHM in RT is 2.58 seconds, sigma is 0.33
0:58:13.692991 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:58:13.693186 INFO: Starting candidate selection
0:58:16.299633 INFO: Starting candidate scoring
0:58:17.022482 INFO: Finished candidate processing
0:58:17.022673 INFO: Collecting candidate features
0:58:17.212224 INFO: Collecting fragment features
0:58:17.286254 INFO: Finished candidate scoring
0:58:17.324762 PROGRESS: === Extracted 100181 precursors and 750480 fragments ===
0:58:17.325237 INFO: performing precursor FDR with 47 features
0:58:17.325275 INFO: Decoy channel: -1
0:58:17.325301 INFO: Competetive: True
0:58:17.364777 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:18.933386 INFO: Test AUC: 0.561
0:58:18.933522 INFO: Train AUC: 0.585
0:58:18.933551 INFO: AUC difference: 4.09%
0:58:19.139487 INFO: Resetting torch num_threads to 100
0:58:19.142411 INFO: === FDR correction performed with classifier version 7 ===
0:58:19.143081 PROGRESS: ============================= Precursor FDR =============================
0:58:19.143177 PROGRESS: Total precursors accumulated: 425
0:58:19.143236 PROGRESS: Target precursors: 386 (90.82%)
0:58:19.143288 PROGRESS: Decoy precursors: 39 (9.18%)
0:58:19.143334 PROGRESS: 
0:58:19.143379 PROGRESS: Precursor Summary:
0:58:19.144332 PROGRESS: Channel   0:	 0.05 FDR:   290; 0.01 FDR:   229; 0.001 FDR:   108
0:58:19.144424 PROGRESS: 
0:58:19.144478 PROGRESS: Protein Summary:
0:58:19.145557 PROGRESS: Channel   0:	 0.05 FDR:   279; 0.01 FDR:   221; 0.001 FDR:   106
0:58:19.145649 PROGRESS: =========================================================================
0:58:19.195318 INFO: fragments_df: keeping 2437 of 750480 [sum(precursor_idx_mask)=4724 sum(mass_error_mask)=750480 stop_rank=2437
0:58:19.319752 INFO: calibration group: precursor, fitting rt estimator 
0:58:19.466745 INFO: calibration group: fragment, fitting mz estimator 
0:58:19.791347 INFO: Using score_cutoff 65.1529982208252 (fac=0.99, q=1)
0:58:19.791751 INFO: calibration group: precursor, predicting mz
0:58:19.791839 WARNING: mz prediction was skipped as it has not been fitted yet
0:58:19.791870 INFO: calibration group: precursor, predicting rt
0:58:19.822888 INFO: calibration group: fragment, predicting mz
0:58:19.896586 INFO: === checking if optimization conditions were reached ===
0:58:19.896832 PROGRESS: === Optimization of ms2_error has been performed 9 time(s); minimum number is 2 ===
0:58:19.898972 PROGRESS: ❌ ms2_error      : optimization incomplete after 9 search(es). Will search with parameter 6.5850.
0:58:19.899028 INFO: ==============================================
0:58:19.899124 INFO: Starting optimization step 19.
0:58:19.899191 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:58:19.899258 PROGRESS: Extracting batch of 50212 precursors
0:58:19.911229 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:58:19.911322 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:58:19.911359 INFO: FWHM in RT is 2.52 seconds, sigma is 0.33
0:58:19.911382 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:58:19.911613 INFO: Starting candidate selection
0:58:22.345359 INFO: Starting candidate scoring
0:58:22.996469 INFO: Finished candidate processing
0:58:22.996569 INFO: Collecting candidate features
0:58:23.140936 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 100155)
0:58:23.149392 INFO: Collecting fragment features
0:58:23.197472 INFO: Finished candidate scoring
0:58:23.236466 PROGRESS: === Extracted 100155 precursors and 714971 fragments ===
0:58:23.236835 INFO: performing precursor FDR with 47 features
0:58:23.236871 INFO: Decoy channel: -1
0:58:23.236894 INFO: Competetive: True
0:58:23.265472 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:23.279740 WARNING: dropped 1 decoy PSMs due to missing features
0:58:24.857971 INFO: Test AUC: 0.561
0:58:24.858096 INFO: Train AUC: 0.585
0:58:24.858126 INFO: AUC difference: 4.03%
0:58:25.063931 INFO: Resetting torch num_threads to 100
0:58:25.066833 INFO: === FDR correction performed with classifier version 7 ===
0:58:25.067490 PROGRESS: ============================= Precursor FDR =============================
0:58:25.067589 PROGRESS: Total precursors accumulated: 432
0:58:25.067649 PROGRESS: Target precursors: 395 (91.44%)
0:58:25.067700 PROGRESS: Decoy precursors: 37 (8.56%)
0:58:25.067745 PROGRESS: 
0:58:25.067788 PROGRESS: Precursor Summary:
0:58:25.068751 PROGRESS: Channel   0:	 0.05 FDR:   311; 0.01 FDR:   232; 0.001 FDR:   157
0:58:25.068846 PROGRESS: 
0:58:25.068902 PROGRESS: Protein Summary:
0:58:25.069978 PROGRESS: Channel   0:	 0.05 FDR:   300; 0.01 FDR:   224; 0.001 FDR:   150
0:58:25.070072 PROGRESS: =========================================================================
0:58:25.118720 INFO: fragments_df: keeping 2358 of 714971 [sum(precursor_idx_mask)=4685 sum(mass_error_mask)=714971 stop_rank=2358
0:58:25.242199 INFO: calibration group: precursor, fitting rt estimator 
0:58:25.363253 INFO: calibration group: fragment, fitting mz estimator 
0:58:25.675600 INFO: Using score_cutoff 52.66123317718506 (fac=0.99, q=1)
0:58:25.675992 INFO: calibration group: precursor, predicting mz
0:58:25.676081 WARNING: mz prediction was skipped as it has not been fitted yet
0:58:25.676111 INFO: calibration group: precursor, predicting rt
0:58:25.706963 INFO: calibration group: fragment, predicting mz
0:58:25.771744 INFO: === checking if optimization conditions were reached ===
0:58:25.772012 PROGRESS: === Optimization of ms2_error has been performed 10 time(s); minimum number is 2 ===
0:58:25.774417 PROGRESS: ❌ ms2_error      : optimization incomplete after 10 search(es). Will search with parameter 5.6035.
0:58:25.774481 INFO: ==============================================
0:58:25.774578 WARNING: Optimization did not converge within the maximum number of steps, which is 20.
0:58:25.775572 INFO: Starting optimization step 0.
0:58:25.775659 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:58:25.775730 PROGRESS: Extracting batch of 50212 precursors
0:58:25.792262 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:58:25.792379 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:58:25.792416 INFO: FWHM in RT is 2.48 seconds, sigma is 0.32
0:58:25.792444 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:58:25.792673 INFO: Starting candidate selection
0:58:28.329444 INFO: Starting candidate scoring
0:58:28.974129 INFO: Finished candidate processing
0:58:28.974265 INFO: Collecting candidate features
0:58:29.112190 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 100098)
0:58:29.122047 INFO: Collecting fragment features
0:58:29.170636 INFO: Finished candidate scoring
0:58:29.209755 PROGRESS: === Extracted 100098 precursors and 675961 fragments ===
0:58:29.210118 INFO: performing precursor FDR with 47 features
0:58:29.210156 INFO: Decoy channel: -1
0:58:29.210179 INFO: Competetive: True
0:58:29.242023 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:29.257969 WARNING: dropped 2 decoy PSMs due to missing features
0:58:30.863784 INFO: Test AUC: 0.560
0:58:30.863959 INFO: Train AUC: 0.582
0:58:30.863989 INFO: AUC difference: 3.69%
0:58:31.069605 INFO: Resetting torch num_threads to 100
0:58:31.072570 INFO: === FDR correction performed with classifier version 7 ===
0:58:31.073243 PROGRESS: ============================= Precursor FDR =============================
0:58:31.073343 PROGRESS: Total precursors accumulated: 405
0:58:31.073406 PROGRESS: Target precursors: 370 (91.36%)
0:58:31.073458 PROGRESS: Decoy precursors: 35 (8.64%)
0:58:31.073506 PROGRESS: 
0:58:31.073549 PROGRESS: Precursor Summary:
0:58:31.074515 PROGRESS: Channel   0:	 0.05 FDR:   304; 0.01 FDR:   221; 0.001 FDR:   151
0:58:31.074611 PROGRESS: 
0:58:31.074667 PROGRESS: Protein Summary:
0:58:31.075777 PROGRESS: Channel   0:	 0.05 FDR:   292; 0.01 FDR:   213; 0.001 FDR:   147
0:58:31.075877 PROGRESS: =========================================================================
0:58:31.120117 INFO: fragments_df: keeping 2295 of 675961 [sum(precursor_idx_mask)=4429 sum(mass_error_mask)=675961 stop_rank=2295
0:58:31.260688 INFO: calibration group: precursor, fitting rt estimator 
0:58:31.376204 INFO: calibration group: fragment, fitting mz estimator 
0:58:31.674146 INFO: Using score_cutoff 60.24028848266602 (fac=0.99, q=1)
0:58:31.674549 INFO: calibration group: precursor, predicting mz
0:58:31.674652 WARNING: mz prediction was skipped as it has not been fitted yet
0:58:31.674692 INFO: calibration group: precursor, predicting rt
0:58:31.706058 INFO: calibration group: fragment, predicting mz
0:58:31.775571 INFO: === checking if optimization conditions were reached ===
0:58:31.775848 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:58:31.777933 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 83.5432.
0:58:31.777995 INFO: ==============================================
0:58:31.778105 INFO: Starting optimization step 1.
0:58:31.778181 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:58:31.778264 PROGRESS: Extracting batch of 50212 precursors
0:58:31.795475 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:58:31.795599 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:58:31.795645 INFO: FWHM in RT is 2.48 seconds, sigma is 0.32
0:58:31.795676 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:58:31.795972 INFO: Starting candidate selection
0:58:33.775814 INFO: Starting candidate scoring
0:58:34.471581 INFO: Finished candidate processing
0:58:34.471714 INFO: Collecting candidate features
0:58:34.646957 WARNING: intensity_correlation has 23 NaNs ( 0.02 % out of 96534)
0:58:34.647315 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 96534)
0:58:34.653837 INFO: Collecting fragment features
0:58:34.704911 INFO: Finished candidate scoring
0:58:34.803526 PROGRESS: === Extracted 96534 precursors and 533674 fragments ===
0:58:34.804049 INFO: performing precursor FDR with 47 features
0:58:34.804089 INFO: Decoy channel: -1
0:58:34.804113 INFO: Competetive: True
0:58:34.850963 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:34.876512 WARNING: dropped 10 target PSMs due to missing features
0:58:34.876680 WARNING: dropped 13 decoy PSMs due to missing features
0:58:36.974010 INFO: Test AUC: 0.549
0:58:36.974175 INFO: Train AUC: 0.577
0:58:36.974208 INFO: AUC difference: 4.90%
0:58:37.180495 INFO: Resetting torch num_threads to 100
0:58:37.184903 INFO: === FDR correction performed with classifier version 7 ===
0:58:37.185714 PROGRESS: ============================= Precursor FDR =============================
0:58:37.185817 PROGRESS: Total precursors accumulated: 484
0:58:37.185878 PROGRESS: Target precursors: 441 (91.12%)
0:58:37.185930 PROGRESS: Decoy precursors: 43 (8.88%)
0:58:37.185977 PROGRESS: 
0:58:37.186021 PROGRESS: Precursor Summary:
0:58:37.187062 PROGRESS: Channel   0:	 0.05 FDR:   401; 0.01 FDR:   245; 0.001 FDR:   155
0:58:37.187158 PROGRESS: 
0:58:37.187214 PROGRESS: Protein Summary:
0:58:37.188369 PROGRESS: Channel   0:	 0.05 FDR:   381; 0.01 FDR:   235; 0.001 FDR:   151
0:58:37.188463 PROGRESS: =========================================================================
0:58:37.225989 INFO: fragments_df: keeping 2451 of 533674 [sum(precursor_idx_mask)=4815 sum(mass_error_mask)=533674 stop_rank=2451
0:58:37.391679 INFO: calibration group: precursor, fitting rt estimator 
0:58:37.494403 INFO: calibration group: fragment, fitting mz estimator 
0:58:37.763529 INFO: Using score_cutoff 60.71165619049073 (fac=0.99, q=1)
0:58:37.764024 INFO: calibration group: precursor, predicting mz
0:58:37.764119 WARNING: mz prediction was skipped as it has not been fitted yet
0:58:37.764151 INFO: calibration group: precursor, predicting rt
0:58:37.796278 INFO: calibration group: fragment, predicting mz
0:58:37.867308 INFO: === checking if optimization conditions were reached ===
0:58:37.867663 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:58:37.870056 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 75.7355.
0:58:37.870124 INFO: ==============================================
0:58:37.870256 INFO: Starting optimization step 2.
0:58:37.870337 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:58:37.870402 PROGRESS: Extracting batch of 50212 precursors
0:58:37.887554 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:58:37.887711 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:58:37.887747 INFO: FWHM in RT is 2.45 seconds, sigma is 0.32
0:58:37.887771 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:58:37.888050 INFO: Starting candidate selection
0:58:40.001940 INFO: Starting candidate scoring
0:58:40.643799 INFO: Finished candidate processing
0:58:40.644003 INFO: Collecting candidate features
0:58:40.837425 WARNING: intensity_correlation has 35 NaNs ( 0.04 % out of 96011)
0:58:41.505077 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 96011)
0:58:41.513811 INFO: Collecting fragment features
0:58:41.568051 INFO: Finished candidate scoring
0:58:41.626197 PROGRESS: === Extracted 96011 precursors and 523534 fragments ===
0:58:41.626798 INFO: performing precursor FDR with 47 features
0:58:41.626839 INFO: Decoy channel: -1
0:58:41.626863 INFO: Competetive: True
0:58:41.679802 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:41.705586 WARNING: dropped 13 target PSMs due to missing features
0:58:41.705749 WARNING: dropped 22 decoy PSMs due to missing features
0:58:43.662577 INFO: Test AUC: 0.553
0:58:43.662756 INFO: Train AUC: 0.575
0:58:43.662787 INFO: AUC difference: 3.80%
0:58:43.878250 INFO: Resetting torch num_threads to 100
0:58:43.882668 INFO: === FDR correction performed with classifier version 7 ===
0:58:43.883484 PROGRESS: ============================= Precursor FDR =============================
0:58:43.883586 PROGRESS: Total precursors accumulated: 495
0:58:43.883647 PROGRESS: Target precursors: 452 (91.31%)
0:58:43.883700 PROGRESS: Decoy precursors: 43 (8.69%)
0:58:43.883753 PROGRESS: 
0:58:43.883800 PROGRESS: Precursor Summary:
0:58:43.884836 PROGRESS: Channel   0:	 0.05 FDR:   385; 0.01 FDR:   271; 0.001 FDR:   248
0:58:43.884928 PROGRESS: 
0:58:43.884982 PROGRESS: Protein Summary:
0:58:43.886166 PROGRESS: Channel   0:	 0.05 FDR:   366; 0.01 FDR:   259; 0.001 FDR:   238
0:58:43.886272 PROGRESS: =========================================================================
0:58:43.922508 INFO: fragments_df: keeping 2646 of 523534 [sum(precursor_idx_mask)=5305 sum(mass_error_mask)=523534 stop_rank=2646
0:58:44.088623 INFO: calibration group: precursor, fitting rt estimator 
0:58:44.205028 INFO: calibration group: fragment, fitting mz estimator 
0:58:44.497163 INFO: Using score_cutoff 55.18901688766479 (fac=0.99, q=1)
0:58:44.497689 INFO: calibration group: precursor, predicting mz
0:58:44.497781 WARNING: mz prediction was skipped as it has not been fitted yet
0:58:44.497813 INFO: calibration group: precursor, predicting rt
0:58:44.530224 INFO: calibration group: fragment, predicting mz
0:58:44.600057 INFO: === checking if optimization conditions were reached ===
0:58:44.600415 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:58:44.602820 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 64.4231.
0:58:44.602879 INFO: ==============================================
0:58:44.602980 INFO: Starting optimization step 3.
0:58:44.603050 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:58:44.603123 PROGRESS: Extracting batch of 50212 precursors
0:58:44.619731 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:58:44.619883 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:58:44.619925 INFO: FWHM in RT is 2.41 seconds, sigma is 0.31
0:58:44.619949 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:58:44.620270 INFO: Starting candidate selection
0:58:46.285415 INFO: Starting candidate scoring
0:58:46.974579 INFO: Finished candidate processing
0:58:46.974689 INFO: Collecting candidate features
0:58:47.109052 WARNING: intensity_correlation has 56 NaNs ( 0.06 % out of 95334)
0:58:47.109345 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 95334)
0:58:47.115459 INFO: Collecting fragment features
0:58:47.156272 INFO: Finished candidate scoring
0:58:47.195307 PROGRESS: === Extracted 95334 precursors and 510234 fragments ===
0:58:47.195847 INFO: performing precursor FDR with 47 features
0:58:47.195885 INFO: Decoy channel: -1
0:58:47.195907 INFO: Competetive: True
0:58:47.223544 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:47.241054 WARNING: dropped 28 target PSMs due to missing features
0:58:47.241163 WARNING: dropped 28 decoy PSMs due to missing features
0:58:48.670048 INFO: Test AUC: 0.543
0:58:48.670167 INFO: Train AUC: 0.576
0:58:48.670198 INFO: AUC difference: 5.80%
0:58:48.670220 WARNING: AUC difference > 5%. This may indicate overfitting.
0:58:48.871106 INFO: Resetting torch num_threads to 100
0:58:48.873999 INFO: === FDR correction performed with classifier version 7 ===
0:58:48.874693 PROGRESS: ============================= Precursor FDR =============================
0:58:48.874787 PROGRESS: Total precursors accumulated: 522
0:58:48.874846 PROGRESS: Target precursors: 478 (91.57%)
0:58:48.874897 PROGRESS: Decoy precursors: 44 (8.43%)
0:58:48.874943 PROGRESS: 
0:58:48.874986 PROGRESS: Precursor Summary:
0:58:48.875961 PROGRESS: Channel   0:	 0.05 FDR:   393; 0.01 FDR:   280; 0.001 FDR:   250
0:58:48.876047 PROGRESS: 
0:58:48.876100 PROGRESS: Protein Summary:
0:58:48.877235 PROGRESS: Channel   0:	 0.05 FDR:   374; 0.01 FDR:   269; 0.001 FDR:   241
0:58:48.877322 PROGRESS: =========================================================================
0:58:48.913306 INFO: fragments_df: keeping 2675 of 510234 [sum(precursor_idx_mask)=5441 sum(mass_error_mask)=510234 stop_rank=2675
0:58:49.036813 INFO: calibration group: precursor, fitting rt estimator 
0:58:49.161243 INFO: calibration group: fragment, fitting mz estimator 
0:58:49.510887 INFO: Using score_cutoff 54.51202402267457 (fac=0.99, q=1)
0:58:49.511279 INFO: calibration group: precursor, predicting mz
0:58:49.511362 WARNING: mz prediction was skipped as it has not been fitted yet
0:58:49.511390 INFO: calibration group: precursor, predicting rt
0:58:49.542583 INFO: calibration group: fragment, predicting mz
0:58:49.607528 INFO: === checking if optimization conditions were reached ===
0:58:49.607820 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:58:49.610159 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 64.1095.
0:58:49.610218 INFO: ==============================================
0:58:49.610336 INFO: Starting optimization step 4.
0:58:49.610411 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:58:49.610479 PROGRESS: Extracting batch of 50212 precursors
0:58:49.627252 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:58:49.627368 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:58:49.627405 INFO: FWHM in RT is 2.40 seconds, sigma is 0.31
0:58:49.627431 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:58:49.627659 INFO: Starting candidate selection
0:58:51.317694 INFO: Starting candidate scoring
0:58:52.012530 INFO: Finished candidate processing
0:58:52.012715 INFO: Collecting candidate features
0:58:52.212543 WARNING: intensity_correlation has 48 NaNs ( 0.05 % out of 95341)
0:58:52.212920 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 95341)
0:58:52.219488 INFO: Collecting fragment features
0:58:52.272092 INFO: Finished candidate scoring
0:58:52.334596 PROGRESS: === Extracted 95341 precursors and 510234 fragments ===
0:58:52.335153 INFO: performing precursor FDR with 47 features
0:58:52.335194 INFO: Decoy channel: -1
0:58:52.335223 INFO: Competetive: True
0:58:52.366005 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:52.385829 WARNING: dropped 23 target PSMs due to missing features
0:58:52.385952 WARNING: dropped 25 decoy PSMs due to missing features
0:58:53.844593 INFO: Test AUC: 0.554
0:58:53.844733 INFO: Train AUC: 0.574
0:58:53.844764 INFO: AUC difference: 3.34%
0:58:54.055587 INFO: Resetting torch num_threads to 100
0:58:54.058429 INFO: === FDR correction performed with classifier version 7 ===
0:58:54.059123 PROGRESS: ============================= Precursor FDR =============================
0:58:54.059228 PROGRESS: Total precursors accumulated: 509
0:58:54.059288 PROGRESS: Target precursors: 466 (91.55%)
0:58:54.059340 PROGRESS: Decoy precursors: 43 (8.45%)
0:58:54.059387 PROGRESS: 
0:58:54.059429 PROGRESS: Precursor Summary:
0:58:54.060409 PROGRESS: Channel   0:	 0.05 FDR:   384; 0.01 FDR:   250; 0.001 FDR:   158
0:58:54.060500 PROGRESS: 
0:58:54.060555 PROGRESS: Protein Summary:
0:58:54.061676 PROGRESS: Channel   0:	 0.05 FDR:   365; 0.01 FDR:   240; 0.001 FDR:   152
0:58:54.061775 PROGRESS: =========================================================================
0:58:54.097300 INFO: fragments_df: keeping 2435 of 510234 [sum(precursor_idx_mask)=4896 sum(mass_error_mask)=510234 stop_rank=2435
0:58:54.219997 INFO: calibration group: precursor, fitting rt estimator 
0:58:54.339939 INFO: calibration group: fragment, fitting mz estimator 
0:58:54.658785 INFO: Using score_cutoff 56.75191080551148 (fac=0.99, q=1)
0:58:54.659199 INFO: calibration group: precursor, predicting mz
0:58:54.659288 WARNING: mz prediction was skipped as it has not been fitted yet
0:58:54.659319 INFO: calibration group: precursor, predicting rt
0:58:54.690910 INFO: calibration group: fragment, predicting mz
0:58:54.757135 INFO: === checking if optimization conditions were reached ===
0:58:54.757415 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:58:54.758844 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 64.4231 found after 5 searches.
0:58:54.758903 INFO: ==============================================
0:58:54.759008 PROGRESS: Optimization finished for rt_error.
0:58:54.893011 INFO: calibration group: precursor, predicting mz
0:58:54.893250 WARNING: mz prediction was skipped as it has not been fitted yet
0:58:54.893283 INFO: calibration group: precursor, predicting rt
0:58:54.924972 INFO: calibration group: fragment, predicting mz
0:58:55.021618 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:58:55.021851 PROGRESS: ==============================================
0:58:55.021933 PROGRESS: ms2_error      : 5.6035
0:58:55.021999 PROGRESS: rt_error       : 64.4231
0:58:55.022054 PROGRESS: ==============================================
0:58:55.023052 INFO: calibration group: precursor, predicting mz
0:58:55.023178 WARNING: mz prediction was skipped as it has not been fitted yet
0:58:55.023214 INFO: calibration group: precursor, predicting rt
0:59:01.654485 INFO: calibration group: fragment, predicting mz
0:59:17.043914 PROGRESS: Extracting batch of 10183864 precursors
0:59:19.244713 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
0:59:19.244844 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:59:19.244893 INFO: FWHM in RT is 2.40 seconds, sigma is 0.31
0:59:19.244918 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:59:19.245290 INFO: Starting candidate selection
1:04:37.168547 INFO: Applying score cutoff of 54.51202402267457
1:04:37.211983 INFO: Removed 19722285 precursors with score below cutoff
1:04:39.381921 INFO: Starting candidate scoring
1:04:43.835243 INFO: Finished candidate processing
1:04:43.835392 INFO: Collecting candidate features
1:04:47.692588 INFO: Collecting fragment features
1:04:48.498454 INFO: Finished candidate scoring
1:04:49.281825 INFO: === FDR correction performed with classifier version 23 ===
1:04:49.282791 INFO: performing precursor FDR with 47 features
1:04:49.282843 INFO: Decoy channel: -1
1:04:49.282872 INFO: Competetive: True
1:04:49.495517 INFO: Setting torch num_threads to 2 for FDR classification task
1:04:49.590883 WARNING: FDR calculation for 312523 target and 241745 decoy PSMs
1:04:49.591017 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1:05:00.131005 INFO: Test AUC: 0.705
1:05:00.131135 INFO: Train AUC: 0.713
1:05:00.131168 INFO: AUC difference: 1.20%
1:05:00.521214 INFO: Resetting torch num_threads to 100
1:05:00.558304 INFO: Removing fragments below FDR threshold
1:05:00.654237 PROGRESS: ============================= Precursor FDR =============================
1:05:00.654478 PROGRESS: Total precursors accumulated: 71,535
1:05:00.654546 PROGRESS: Target precursors: 70,827 (99.01%)
1:05:00.654614 PROGRESS: Decoy precursors: 708 (0.99%)
1:05:00.654670 PROGRESS: 
1:05:00.654719 PROGRESS: Precursor Summary:
1:05:00.690950 PROGRESS: Channel   0:	 0.05 FDR: 70,827; 0.01 FDR: 70,827; 0.001 FDR: 49,347
1:05:00.691190 PROGRESS: 
1:05:00.691255 PROGRESS: Protein Summary:
1:05:00.743260 PROGRESS: Channel   0:	 0.05 FDR: 10,866; 0.01 FDR: 10,866; 0.001 FDR: 8,466
1:05:00.743480 PROGRESS: =========================================================================
1:05:01.356717 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:05:01.891201 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:05:01.891361 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant
1:05:01.891439 INFO: Creating folder run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/figures
1:05:01.892128 INFO: Initializing RawFileManager
1:05:11.940752 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.
1:05:11.947905 INFO: Determining DIA cycle
1:05:11.964288 INFO: Found cycle with start 0.00 min and length 300.
1:05:12.142008 INFO: RT (min)            : 0.0 - 26.9
1:05:12.142098 INFO: RT duration (sec)   : 1611.2
1:05:12.142126 INFO: RT duration (min)   : 26.9
1:05:12.142150 INFO: Cycle len (scans)   : 300
1:05:12.142170 INFO: Cycle len (sec)     : 1.65
1:05:12.142189 INFO: Number of cycles    : 977
1:05:12.142209 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:05:13.571005 INFO: Initializing CalibrationManager
1:05:13.571291 INFO: Loading calibration config
1:05:13.571895 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'}]
1:05:13.571989 INFO: Calibration group :fragment, found 1 estimator(s)
1:05:13.572073 INFO: Calibration group :precursor, found 3 estimator(s)
1:05:13.572164 INFO: Disabling ion mobility calibration
1:05:13.572193 INFO: removed mobility estimator from group precursor
1:05:13.572333 INFO: Initializing OptimizationManager
1:05:13.572446 INFO: initial parameter: ms1_error = 30
1:05:13.572511 INFO: initial parameter: ms2_error = 30
1:05:13.572563 INFO: initial parameter: rt_error = 805.6002197265625
1:05:13.572608 INFO: initial parameter: mobility_error = 0.1
1:05:13.572651 INFO: initial parameter: column_type = library
1:05:13.572693 INFO: initial parameter: num_candidates = 1
1:05:13.572734 INFO: initial parameter: classifier_version = -1
1:05:13.572775 INFO: initial parameter: fwhm_rt = 5
1:05:13.572818 INFO: initial parameter: fwhm_mobility = 0.01
1:05:13.572860 INFO: initial parameter: score_cutoff = 0
1:05:13.572934 INFO: Initializing TimingManager
1:05:13.573000 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:05:13.573141 INFO: FDRManager not loaded from disk.
1:05:13.573165 INFO: Initializing FDRManager
1:05:13.573211 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:05:15.078901 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
1:05:17.462835 PROGRESS: Starting initial search for precursors.
1:05:17.682861 INFO: Starting optimization step 0.
1:05:17.683079 PROGRESS: === Extracting elution groups 0 to 200 ===
1:05:17.683152 PROGRESS: Extracting batch of 395 precursors
1:05:17.684598 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:05:17.684650 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:05:17.684690 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:05:17.684716 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:05:17.684997 INFO: Starting candidate selection
1:05:17.834857 INFO: Starting candidate scoring
1:05:17.871006 INFO: Finished candidate processing
1:05:17.871078 INFO: Collecting candidate features
1:05:17.880521 INFO: Collecting fragment features
1:05:17.882674 INFO: Finished candidate scoring
1:05:17.883694 PROGRESS: === Extracted 395 precursors and 3960 fragments ===
1:05:17.883965 INFO: performing precursor FDR with 47 features
1:05:17.884000 INFO: Decoy channel: -1
1:05:17.884024 INFO: Competetive: True
1:05:17.885014 INFO: Setting torch num_threads to 2 for FDR classification task
1:05:17.903562 INFO: Test AUC: 0.483
1:05:17.903624 INFO: Train AUC: 0.497
1:05:17.903654 INFO: AUC difference: 2.92%
1:05:18.080145 INFO: Resetting torch num_threads to 100
1:05:18.080686 INFO: === FDR correction performed with classifier version -1 ===
1:05:18.081341 PROGRESS: ============================= Precursor FDR =============================
1:05:18.081435 PROGRESS: Total precursors accumulated: 8
1:05:18.081496 PROGRESS: Target precursors: 8 (100.00%)
1:05:18.081549 PROGRESS: Decoy precursors: 0 (0.00%)
1:05:18.081595 PROGRESS: 
1:05:18.081640 PROGRESS: Precursor Summary:
1:05:18.082577 PROGRESS: Channel   0:	 0.05 FDR:     8; 0.01 FDR:     8; 0.001 FDR:     8
1:05:18.082677 PROGRESS: 
1:05:18.082734 PROGRESS: Protein Summary:
1:05:18.083744 PROGRESS: Channel   0:	 0.05 FDR:     8; 0.01 FDR:     8; 0.001 FDR:     8
1:05:18.083834 PROGRESS: =========================================================================
1:05:18.144351 INFO: Starting optimization step 1.
1:05:18.144534 PROGRESS: === Extracting elution groups 200 to 600 ===
1:05:18.144602 PROGRESS: Extracting batch of 790 precursors
1:05:18.145443 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:05:18.145494 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:05:18.145526 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:05:18.145550 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:05:18.145724 INFO: Starting candidate selection
1:05:18.284267 INFO: Starting candidate scoring
1:05:18.319537 INFO: Finished candidate processing
1:05:18.319610 INFO: Collecting candidate features
1:05:18.328612 INFO: Collecting fragment features
1:05:18.331098 INFO: Finished candidate scoring
1:05:18.333093 PROGRESS: === Extracted 1183 precursors and 11994 fragments ===
1:05:18.333830 INFO: performing precursor FDR with 47 features
1:05:18.333872 INFO: Decoy channel: -1
1:05:18.333896 INFO: Competetive: True
1:05:18.336654 INFO: Setting torch num_threads to 2 for FDR classification task
1:05:18.358745 INFO: Test AUC: 0.510
1:05:18.358814 INFO: Train AUC: 0.491
1:05:18.358846 INFO: AUC difference: 3.98%
1:05:18.537803 INFO: Resetting torch num_threads to 100
1:05:18.541463 INFO: === FDR correction performed with classifier version -1 ===
1:05:18.542211 PROGRESS: ============================= Precursor FDR =============================
1:05:18.542303 PROGRESS: Total precursors accumulated: 599
1:05:18.542361 PROGRESS: Target precursors: 289 (48.25%)
1:05:18.542413 PROGRESS: Decoy precursors: 310 (51.75%)
1:05:18.542459 PROGRESS: 
1:05:18.542511 PROGRESS: Precursor Summary:
1:05:18.543397 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:05:18.543487 PROGRESS: 
1:05:18.543542 PROGRESS: Protein Summary:
1:05:18.544487 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:05:18.544580 PROGRESS: =========================================================================
1:05:18.616342 INFO: Starting optimization step 2.
1:05:18.616544 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:05:18.616610 PROGRESS: Extracting batch of 1585 precursors
1:05:18.617570 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:05:18.617617 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:05:18.617648 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:05:18.617669 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:05:18.617834 INFO: Starting candidate selection
1:05:18.800188 INFO: Starting candidate scoring
1:05:18.842247 INFO: Finished candidate processing
1:05:18.842369 INFO: Collecting candidate features
1:05:18.855533 INFO: Collecting fragment features
1:05:18.860205 INFO: Finished candidate scoring
1:05:18.866066 PROGRESS: === Extracted 2762 precursors and 28103 fragments ===
1:05:18.867498 INFO: performing precursor FDR with 47 features
1:05:18.867548 INFO: Decoy channel: -1
1:05:18.867574 INFO: Competetive: True
1:05:18.872540 INFO: Setting torch num_threads to 2 for FDR classification task
1:05:18.915107 INFO: Test AUC: 0.521
1:05:18.915213 INFO: Train AUC: 0.497
1:05:18.915243 INFO: AUC difference: 4.87%
1:05:19.102362 INFO: Resetting torch num_threads to 100
1:05:19.104743 INFO: === FDR correction performed with classifier version -1 ===
1:05:19.106730 PROGRESS: ============================= Precursor FDR =============================
1:05:19.106915 PROGRESS: Total precursors accumulated: 1,396
1:05:19.107006 PROGRESS: Target precursors: 715 (51.22%)
1:05:19.107058 PROGRESS: Decoy precursors: 681 (48.78%)
1:05:19.107109 PROGRESS: 
1:05:19.107156 PROGRESS: Precursor Summary:
1:05:19.108257 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:05:19.108389 PROGRESS: 
1:05:19.108454 PROGRESS: Protein Summary:
1:05:19.109596 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:05:19.109724 PROGRESS: =========================================================================
1:05:19.202484 INFO: Starting optimization step 3.
1:05:19.202793 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:05:19.202868 PROGRESS: Extracting batch of 3157 precursors
1:05:19.204264 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:05:19.204313 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:05:19.204351 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:05:19.204374 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:05:19.204624 INFO: Starting candidate selection
1:05:19.493197 INFO: Starting candidate scoring
1:05:19.548974 INFO: Finished candidate processing
1:05:19.549095 INFO: Collecting candidate features
1:05:19.572238 INFO: Collecting fragment features
1:05:19.579154 INFO: Finished candidate scoring
1:05:19.586644 PROGRESS: === Extracted 5917 precursors and 60443 fragments ===
1:05:19.588281 INFO: performing precursor FDR with 47 features
1:05:19.588327 INFO: Decoy channel: -1
1:05:19.588353 INFO: Competetive: True
1:05:19.595683 INFO: Setting torch num_threads to 2 for FDR classification task
1:05:19.665587 INFO: Test AUC: 0.532
1:05:19.665708 INFO: Train AUC: 0.491
1:05:19.665737 INFO: AUC difference: 8.28%
1:05:19.665759 WARNING: AUC difference > 5%. This may indicate overfitting.
1:05:19.851096 INFO: Resetting torch num_threads to 100
1:05:19.852593 INFO: === FDR correction performed with classifier version -1 ===
1:05:19.853781 PROGRESS: ============================= Precursor FDR =============================
1:05:19.853885 PROGRESS: Total precursors accumulated: 2,995
1:05:19.853948 PROGRESS: Target precursors: 1,505 (50.25%)
1:05:19.854002 PROGRESS: Decoy precursors: 1,490 (49.75%)
1:05:19.854059 PROGRESS: 
1:05:19.854105 PROGRESS: Precursor Summary:
1:05:19.855029 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:05:19.855120 PROGRESS: 
1:05:19.855176 PROGRESS: Protein Summary:
1:05:19.856129 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:05:19.856221 PROGRESS: =========================================================================
1:05:19.946635 INFO: Starting optimization step 4.
1:05:19.946922 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:05:19.946995 PROGRESS: Extracting batch of 6336 precursors
1:05:19.948859 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:05:19.948910 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:05:19.948944 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:05:19.948967 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:05:19.949211 INFO: Starting candidate selection
1:05:20.461864 INFO: Starting candidate scoring
1:05:20.515365 INFO: Finished candidate processing
1:05:20.515489 INFO: Collecting candidate features
1:05:20.542735 INFO: Collecting fragment features
1:05:20.548371 INFO: Finished candidate scoring
1:05:20.555483 PROGRESS: === Extracted 12238 precursors and 125442 fragments ===
1:05:20.557291 INFO: performing precursor FDR with 47 features
1:05:20.557336 INFO: Decoy channel: -1
1:05:20.557360 INFO: Competetive: True
1:05:20.562979 INFO: Setting torch num_threads to 2 for FDR classification task
1:05:20.618382 INFO: Test AUC: 0.491
1:05:20.618483 INFO: Train AUC: 0.502
1:05:20.618512 INFO: AUC difference: 2.17%
1:05:20.800220 INFO: Resetting torch num_threads to 100
1:05:20.801514 INFO: === FDR correction performed with classifier version -1 ===
1:05:20.802197 PROGRESS: ============================= Precursor FDR =============================
1:05:20.802290 PROGRESS: Total precursors accumulated: 2
1:05:20.802349 PROGRESS: Target precursors: 2 (100.00%)
1:05:20.802400 PROGRESS: Decoy precursors: 0 (0.00%)
1:05:20.802447 PROGRESS: 
1:05:20.802491 PROGRESS: Precursor Summary:
1:05:20.803433 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:05:20.803524 PROGRESS: 
1:05:20.803581 PROGRESS: Protein Summary:
1:05:20.804607 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:05:20.804697 PROGRESS: =========================================================================
1:05:20.945382 INFO: Starting optimization step 5.
1:05:20.945626 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:05:20.945702 PROGRESS: Extracting batch of 12662 precursors
1:05:20.948212 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:05:20.948264 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:05:20.948296 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:05:20.948318 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:05:20.948494 INFO: Starting candidate selection
1:05:21.795671 INFO: Starting candidate scoring
1:05:21.885464 INFO: Finished candidate processing
1:05:21.885574 INFO: Collecting candidate features
1:05:21.914744 INFO: Collecting fragment features
1:05:21.925164 INFO: Finished candidate scoring
1:05:21.939937 PROGRESS: === Extracted 24888 precursors and 255331 fragments ===
1:05:21.943340 INFO: performing precursor FDR with 47 features
1:05:21.943408 INFO: Decoy channel: -1
1:05:21.943435 INFO: Competetive: True
1:05:21.953582 INFO: Setting torch num_threads to 2 for FDR classification task
1:05:22.236605 INFO: Test AUC: 0.516
1:05:22.236729 INFO: Train AUC: 0.521
1:05:22.236760 INFO: AUC difference: 0.95%
1:05:22.417460 INFO: Resetting torch num_threads to 100
1:05:22.419289 INFO: === FDR correction performed with classifier version -1 ===
1:05:22.419950 PROGRESS: ============================= Precursor FDR =============================
1:05:22.420045 PROGRESS: Total precursors accumulated: 2
1:05:22.420106 PROGRESS: Target precursors: 2 (100.00%)
1:05:22.420159 PROGRESS: Decoy precursors: 0 (0.00%)
1:05:22.420205 PROGRESS: 
1:05:22.420250 PROGRESS: Precursor Summary:
1:05:22.421179 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:05:22.421275 PROGRESS: 
1:05:22.421332 PROGRESS: Protein Summary:
1:05:22.422334 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:05:22.422426 PROGRESS: =========================================================================
1:05:22.610580 INFO: Starting optimization step 6.
1:05:22.610845 PROGRESS: === Extracting elution groups 12600 to 25400 ===
1:05:22.610916 PROGRESS: Extracting batch of 25287 precursors
1:05:22.617241 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:05:22.617313 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:05:22.617346 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:05:22.617369 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:05:22.617558 INFO: Starting candidate selection
1:05:24.214937 INFO: Starting candidate scoring
1:05:24.405375 INFO: Finished candidate processing
1:05:24.405480 INFO: Collecting candidate features
1:05:24.452248 INFO: Collecting fragment features
1:05:24.468821 INFO: Finished candidate scoring
1:05:24.494594 PROGRESS: === Extracted 50105 precursors and 514418 fragments ===
1:05:24.501118 INFO: performing precursor FDR with 47 features
1:05:24.501200 INFO: Decoy channel: -1
1:05:24.501226 INFO: Competetive: True
1:05:24.520046 INFO: Setting torch num_threads to 2 for FDR classification task
1:05:25.295306 INFO: Test AUC: 0.540
1:05:25.295439 INFO: Train AUC: 0.563
1:05:25.295470 INFO: AUC difference: 3.99%
1:05:25.487957 INFO: Resetting torch num_threads to 100
1:05:25.490738 INFO: === FDR correction performed with classifier version -1 ===
1:05:25.491374 PROGRESS: ============================= Precursor FDR =============================
1:05:25.491470 PROGRESS: Total precursors accumulated: 56
1:05:25.491530 PROGRESS: Target precursors: 51 (91.07%)
1:05:25.491582 PROGRESS: Decoy precursors: 5 (8.93%)
1:05:25.491627 PROGRESS: 
1:05:25.491672 PROGRESS: Precursor Summary:
1:05:25.492517 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:05:25.492607 PROGRESS: 
1:05:25.492663 PROGRESS: Protein Summary:
1:05:25.493587 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:05:25.493684 PROGRESS: =========================================================================
1:05:25.740842 INFO: Starting optimization step 7.
1:05:25.741116 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1:05:25.741197 PROGRESS: Extracting batch of 50588 precursors
1:05:25.752994 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:05:25.753109 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:05:25.753144 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:05:25.753167 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:05:25.753379 INFO: Starting candidate selection
1:05:28.869595 INFO: Starting candidate scoring
1:05:29.198038 INFO: Finished candidate processing
1:05:29.198180 INFO: Collecting candidate features
1:05:29.287686 INFO: Collecting fragment features
1:05:29.319565 INFO: Finished candidate scoring
1:05:29.375889 PROGRESS: === Extracted 100596 precursors and 1033935 fragments ===
1:05:29.388293 INFO: performing precursor FDR with 47 features
1:05:29.388395 INFO: Decoy channel: -1
1:05:29.388424 INFO: Competetive: True
1:05:29.428423 INFO: Setting torch num_threads to 2 for FDR classification task
1:05:31.132993 INFO: Test AUC: 0.558
1:05:31.133130 INFO: Train AUC: 0.578
1:05:31.133161 INFO: AUC difference: 3.48%
1:05:31.345457 INFO: Resetting torch num_threads to 100
1:05:31.350591 INFO: === FDR correction performed with classifier version -1 ===
1:05:31.351342 PROGRESS: ============================= Precursor FDR =============================
1:05:31.351437 PROGRESS: Total precursors accumulated: 486
1:05:31.351498 PROGRESS: Target precursors: 444 (91.36%)
1:05:31.351552 PROGRESS: Decoy precursors: 42 (8.64%)
1:05:31.351599 PROGRESS: 
1:05:31.351644 PROGRESS: Precursor Summary:
1:05:31.352618 PROGRESS: Channel   0:	 0.05 FDR:   351; 0.01 FDR:   204; 0.001 FDR:   185
1:05:31.352724 PROGRESS: 
1:05:31.352779 PROGRESS: Protein Summary:
1:05:31.353920 PROGRESS: Channel   0:	 0.05 FDR:   335; 0.01 FDR:   199; 0.001 FDR:   180
1:05:31.354018 PROGRESS: =========================================================================
1:05:31.428555 INFO: fragments_df: keeping 2022 of 1033935 [sum(precursor_idx_mask)=2377 sum(mass_error_mask)=1033935 stop_rank=2022
1:05:31.624144 INFO: calibration group: precursor, fitting rt estimator 
1:05:31.740450 INFO: calibration group: fragment, fitting mz estimator 
1:05:32.015271 INFO: Using score_cutoff 75.39497753906251 (fac=0.99, q=1)
1:05:32.015712 INFO: calibration group: precursor, predicting mz
1:05:32.015802 WARNING: mz prediction was skipped as it has not been fitted yet
1:05:32.015831 INFO: calibration group: precursor, predicting rt
1:05:32.087134 INFO: calibration group: fragment, predicting mz
1:05:32.234127 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:05:32.234440 INFO: Starting optimization step 8.
1:05:32.234522 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:05:32.234592 PROGRESS: Extracting batch of 100800 precursors
1:05:32.270458 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:05:32.270621 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:05:32.270661 INFO: FWHM in RT is 3.00 seconds, sigma is 0.39
1:05:32.270688 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:05:32.270941 INFO: Starting candidate selection
1:05:37.333293 INFO: Starting candidate scoring
1:05:38.706308 INFO: Finished candidate processing
1:05:38.706536 INFO: Collecting candidate features
1:05:39.116692 INFO: Collecting fragment features
1:05:39.244725 INFO: Finished candidate scoring
1:05:39.356362 PROGRESS: === Extracted 201192 precursors and 2043171 fragments ===
1:05:39.356900 INFO: performing precursor FDR with 47 features
1:05:39.356944 INFO: Decoy channel: -1
1:05:39.356969 INFO: Competetive: True
1:05:39.429584 INFO: Setting torch num_threads to 2 for FDR classification task
1:05:42.756715 INFO: Test AUC: 0.569
1:05:42.756848 INFO: Train AUC: 0.583
1:05:42.756878 INFO: AUC difference: 2.48%
1:05:42.990333 INFO: Resetting torch num_threads to 100
1:05:42.995780 INFO: === FDR correction performed with classifier version 7 ===
1:05:42.996580 PROGRESS: ============================= Precursor FDR =============================
1:05:42.996677 PROGRESS: Total precursors accumulated: 594
1:05:42.996743 PROGRESS: Target precursors: 543 (91.41%)
1:05:42.996796 PROGRESS: Decoy precursors: 51 (8.59%)
1:05:42.996848 PROGRESS: 
1:05:42.996894 PROGRESS: Precursor Summary:
1:05:42.997926 PROGRESS: Channel   0:	 0.05 FDR:   405; 0.01 FDR:   245; 0.001 FDR:   233
1:05:42.998016 PROGRESS: 
1:05:42.998070 PROGRESS: Protein Summary:
1:05:42.999230 PROGRESS: Channel   0:	 0.05 FDR:   383; 0.01 FDR:   238; 0.001 FDR:   228
1:05:42.999325 PROGRESS: =========================================================================
1:05:43.135807 INFO: fragments_df: keeping 2954 of 2043171 [sum(precursor_idx_mask)=5594 sum(mass_error_mask)=2043171 stop_rank=2954
1:05:43.335904 INFO: calibration group: precursor, fitting rt estimator 
1:05:43.453659 INFO: calibration group: fragment, fitting mz estimator 
1:05:43.844258 INFO: Using score_cutoff 77.23546572875976 (fac=0.99, q=1)
1:05:43.844696 INFO: calibration group: precursor, predicting mz
1:05:43.844784 WARNING: mz prediction was skipped as it has not been fitted yet
1:05:43.844813 INFO: calibration group: precursor, predicting rt
1:05:43.906968 INFO: calibration group: fragment, predicting mz
1:05:44.059437 INFO: === checking if optimization conditions were reached ===
1:05:44.059727 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
1:05:44.062197 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 22.7412.
1:05:44.062258 INFO: ==============================================
1:05:44.062372 INFO: Starting optimization step 9.
1:05:44.062448 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:05:44.062542 PROGRESS: Extracting batch of 100800 precursors
1:05:44.096905 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:05:44.097047 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:05:44.097095 INFO: FWHM in RT is 2.98 seconds, sigma is 0.38
1:05:44.097127 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:05:44.097433 INFO: Starting candidate selection
1:05:48.702915 INFO: Starting candidate scoring
1:05:50.022427 INFO: Finished candidate processing
1:05:50.022536 INFO: Collecting candidate features
1:05:50.333769 INFO: Collecting fragment features
1:05:50.445636 INFO: Finished candidate scoring
1:05:50.538346 PROGRESS: === Extracted 201190 precursors and 1958454 fragments ===
1:05:50.538742 INFO: performing precursor FDR with 47 features
1:05:50.538783 INFO: Decoy channel: -1
1:05:50.538807 INFO: Competetive: True
1:05:50.594696 INFO: Setting torch num_threads to 2 for FDR classification task
1:05:53.876690 INFO: Test AUC: 0.563
1:05:53.876825 INFO: Train AUC: 0.581
1:05:53.876856 INFO: AUC difference: 3.05%
1:05:54.110890 INFO: Resetting torch num_threads to 100
1:05:54.166674 INFO: === FDR correction performed with classifier version 7 ===
1:05:54.167537 PROGRESS: ============================= Precursor FDR =============================
1:05:54.167651 PROGRESS: Total precursors accumulated: 650
1:05:54.167728 PROGRESS: Target precursors: 595 (91.54%)
1:05:54.167792 PROGRESS: Decoy precursors: 55 (8.46%)
1:05:54.167840 PROGRESS: 
1:05:54.167885 PROGRESS: Precursor Summary:
1:05:54.168941 PROGRESS: Channel   0:	 0.05 FDR:   462; 0.01 FDR:   267; 0.001 FDR:   229
1:05:54.169038 PROGRESS: 
1:05:54.169096 PROGRESS: Protein Summary:
1:05:54.170275 PROGRESS: Channel   0:	 0.05 FDR:   434; 0.01 FDR:   258; 0.001 FDR:   222
1:05:54.170373 PROGRESS: =========================================================================
1:05:54.308765 INFO: fragments_df: keeping 3143 of 1958454 [sum(precursor_idx_mask)=6010 sum(mass_error_mask)=1958454 stop_rank=3143
1:05:54.538427 INFO: calibration group: precursor, fitting rt estimator 
1:05:54.658779 INFO: calibration group: fragment, fitting mz estimator 
1:05:55.069511 INFO: Using score_cutoff 76.86574100189208 (fac=0.99, q=1)
1:05:55.069929 INFO: calibration group: precursor, predicting mz
1:05:55.070015 WARNING: mz prediction was skipped as it has not been fitted yet
1:05:55.070046 INFO: calibration group: precursor, predicting rt
1:05:55.133659 INFO: calibration group: fragment, predicting mz
1:05:55.283345 INFO: === checking if optimization conditions were reached ===
1:05:55.283666 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
1:05:55.286511 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 17.4004.
1:05:55.286577 INFO: ==============================================
1:05:55.286703 INFO: Starting optimization step 10.
1:05:55.286793 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:05:55.286878 PROGRESS: Extracting batch of 100800 precursors
1:05:55.337971 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:05:55.338102 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:05:55.338140 INFO: FWHM in RT is 2.87 seconds, sigma is 0.37
1:05:55.338165 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:05:55.338432 INFO: Starting candidate selection
1:06:00.247416 INFO: Starting candidate scoring
1:06:01.731297 INFO: Finished candidate processing
1:06:01.731411 INFO: Collecting candidate features
1:06:02.122365 INFO: Collecting fragment features
1:06:02.247098 INFO: Finished candidate scoring
1:06:02.344797 PROGRESS: === Extracted 201189 precursors and 1870042 fragments ===
1:06:02.345350 INFO: performing precursor FDR with 47 features
1:06:02.345392 INFO: Decoy channel: -1
1:06:02.345416 INFO: Competetive: True
1:06:02.406700 INFO: Setting torch num_threads to 2 for FDR classification task
1:06:05.871017 INFO: Test AUC: 0.566
1:06:05.871158 INFO: Train AUC: 0.579
1:06:05.871202 INFO: AUC difference: 2.17%
1:06:09.096557 INFO: Resetting torch num_threads to 100
1:06:09.127414 INFO: === FDR correction performed with classifier version 7 ===
1:06:09.128535 PROGRESS: ============================= Precursor FDR =============================
1:06:09.128658 PROGRESS: Total precursors accumulated: 698
1:06:09.128727 PROGRESS: Target precursors: 637 (91.26%)
1:06:09.128784 PROGRESS: Decoy precursors: 61 (8.74%)
1:06:09.128833 PROGRESS: 
1:06:09.128878 PROGRESS: Precursor Summary:
1:06:09.130064 PROGRESS: Channel   0:	 0.05 FDR:   503; 0.01 FDR:   371; 0.001 FDR:   220
1:06:09.130161 PROGRESS: 
1:06:09.130219 PROGRESS: Protein Summary:
1:06:09.131500 PROGRESS: Channel   0:	 0.05 FDR:   472; 0.01 FDR:   350; 0.001 FDR:   213
1:06:09.131602 PROGRESS: =========================================================================
1:06:09.268158 INFO: fragments_df: keeping 4196 of 1870042 [sum(precursor_idx_mask)=8146 sum(mass_error_mask)=1870042 stop_rank=4196
1:06:09.513326 INFO: calibration group: precursor, fitting rt estimator 
1:06:09.659110 INFO: calibration group: fragment, fitting mz estimator 
1:06:10.213661 INFO: Using score_cutoff 71.93478735351562 (fac=0.99, q=1)
1:06:10.214113 INFO: calibration group: precursor, predicting mz
1:06:10.214204 WARNING: mz prediction was skipped as it has not been fitted yet
1:06:10.214235 INFO: calibration group: precursor, predicting rt
1:06:10.280142 INFO: calibration group: fragment, predicting mz
1:06:10.432768 INFO: === checking if optimization conditions were reached ===
1:06:10.433064 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
1:06:10.436058 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 14.9107.
1:06:10.436123 INFO: ==============================================
1:06:10.436248 INFO: Starting optimization step 11.
1:06:10.436326 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:06:10.436417 PROGRESS: Extracting batch of 100800 precursors
1:06:10.472900 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:06:10.473133 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:06:10.473183 INFO: FWHM in RT is 2.81 seconds, sigma is 0.36
1:06:10.473214 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:06:10.473712 INFO: Starting candidate selection
1:06:15.383321 INFO: Starting candidate scoring
1:06:16.888607 INFO: Finished candidate processing
1:06:16.888713 INFO: Collecting candidate features
1:06:17.205827 INFO: Collecting fragment features
1:06:17.333698 INFO: Finished candidate scoring
1:06:17.446455 PROGRESS: === Extracted 201181 precursors and 1792788 fragments ===
1:06:17.446865 INFO: performing precursor FDR with 47 features
1:06:17.446905 INFO: Decoy channel: -1
1:06:17.446928 INFO: Competetive: True
1:06:17.515269 INFO: Setting torch num_threads to 2 for FDR classification task
1:06:21.152979 INFO: Test AUC: 0.565
1:06:21.153119 INFO: Train AUC: 0.579
1:06:21.153149 INFO: AUC difference: 2.36%
1:06:21.391296 INFO: Resetting torch num_threads to 100
1:06:21.397914 INFO: === FDR correction performed with classifier version 7 ===
1:06:21.398737 PROGRESS: ============================= Precursor FDR =============================
1:06:21.398852 PROGRESS: Total precursors accumulated: 765
1:06:21.398919 PROGRESS: Target precursors: 697 (91.11%)
1:06:21.398972 PROGRESS: Decoy precursors: 68 (8.89%)
1:06:21.399018 PROGRESS: 
1:06:21.399061 PROGRESS: Precursor Summary:
1:06:21.400173 PROGRESS: Channel   0:	 0.05 FDR:   599; 0.01 FDR:   402; 0.001 FDR:   256
1:06:21.400269 PROGRESS: 
1:06:21.400329 PROGRESS: Protein Summary:
1:06:21.401576 PROGRESS: Channel   0:	 0.05 FDR:   561; 0.01 FDR:   381; 0.001 FDR:   248
1:06:21.401669 PROGRESS: =========================================================================
1:06:21.521477 INFO: fragments_df: keeping 4462 of 1792788 [sum(precursor_idx_mask)=8719 sum(mass_error_mask)=1792788 stop_rank=4462
1:06:21.664928 INFO: calibration group: precursor, fitting rt estimator 
1:06:21.796154 INFO: calibration group: fragment, fitting mz estimator 
1:06:22.337845 INFO: Using score_cutoff 64.86781655731201 (fac=0.99, q=1)
1:06:22.338319 INFO: calibration group: precursor, predicting mz
1:06:22.338411 WARNING: mz prediction was skipped as it has not been fitted yet
1:06:22.338450 INFO: calibration group: precursor, predicting rt
1:06:22.369669 INFO: calibration group: fragment, predicting mz
1:06:22.448178 INFO: === checking if optimization conditions were reached ===
1:06:22.448518 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
1:06:22.451527 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 12.2337.
1:06:22.451609 INFO: ==============================================
1:06:22.451754 INFO: Starting optimization step 12.
1:06:22.451836 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:06:22.451905 PROGRESS: Extracting batch of 50212 precursors
1:06:22.658780 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:06:22.659083 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:06:22.659158 INFO: FWHM in RT is 2.71 seconds, sigma is 0.35
1:06:22.659188 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:06:22.659621 INFO: Starting candidate selection
1:06:25.137842 INFO: Starting candidate scoring
1:06:25.829080 INFO: Finished candidate processing
1:06:25.829213 INFO: Collecting candidate features
1:06:26.061739 INFO: Collecting fragment features
1:06:26.132468 INFO: Finished candidate scoring
1:06:26.191459 PROGRESS: === Extracted 100207 precursors and 863039 fragments ===
1:06:26.192177 INFO: performing precursor FDR with 47 features
1:06:26.192220 INFO: Decoy channel: -1
1:06:26.192245 INFO: Competetive: True
1:06:26.237518 INFO: Setting torch num_threads to 2 for FDR classification task
1:06:27.978986 INFO: Test AUC: 0.559
1:06:27.979115 INFO: Train AUC: 0.579
1:06:27.979147 INFO: AUC difference: 3.42%
1:06:28.184868 INFO: Resetting torch num_threads to 100
1:06:28.188040 INFO: === FDR correction performed with classifier version 7 ===
1:06:28.188705 PROGRESS: ============================= Precursor FDR =============================
1:06:28.188802 PROGRESS: Total precursors accumulated: 419
1:06:28.188872 PROGRESS: Target precursors: 381 (90.93%)
1:06:28.188930 PROGRESS: Decoy precursors: 38 (9.07%)
1:06:28.188980 PROGRESS: 
1:06:28.189025 PROGRESS: Precursor Summary:
1:06:28.190009 PROGRESS: Channel   0:	 0.05 FDR:   284; 0.01 FDR:   218; 0.001 FDR:   178
1:06:28.190104 PROGRESS: 
1:06:28.190162 PROGRESS: Protein Summary:
1:06:28.191281 PROGRESS: Channel   0:	 0.05 FDR:   273; 0.01 FDR:   211; 0.001 FDR:   173
1:06:28.191375 PROGRESS: =========================================================================
1:06:28.250757 INFO: fragments_df: keeping 2341 of 863039 [sum(precursor_idx_mask)=4685 sum(mass_error_mask)=863039 stop_rank=2341
1:06:28.377012 INFO: calibration group: precursor, fitting rt estimator 
1:06:28.522040 INFO: calibration group: fragment, fitting mz estimator 
1:06:28.774753 INFO: Using score_cutoff 58.52189525756835 (fac=0.99, q=1)
1:06:28.775170 INFO: calibration group: precursor, predicting mz
1:06:28.775259 WARNING: mz prediction was skipped as it has not been fitted yet
1:06:28.775290 INFO: calibration group: precursor, predicting rt
1:06:28.806827 INFO: calibration group: fragment, predicting mz
1:06:28.882746 INFO: === checking if optimization conditions were reached ===
1:06:28.883044 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
1:06:28.885579 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 11.0283.
1:06:28.885642 INFO: ==============================================
1:06:28.885748 INFO: Starting optimization step 13.
1:06:28.885824 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:06:28.885919 PROGRESS: Extracting batch of 50212 precursors
1:06:28.905120 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:06:28.905239 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:06:28.905300 INFO: FWHM in RT is 2.68 seconds, sigma is 0.35
1:06:28.905333 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:06:28.905599 INFO: Starting candidate selection
1:06:31.344932 INFO: Starting candidate scoring
1:06:32.068243 INFO: Finished candidate processing
1:06:32.068344 INFO: Collecting candidate features
1:06:32.232469 INFO: Collecting fragment features
1:06:32.291568 INFO: Finished candidate scoring
1:06:32.337148 PROGRESS: === Extracted 100207 precursors and 845361 fragments ===
1:06:32.337516 INFO: performing precursor FDR with 47 features
1:06:32.337554 INFO: Decoy channel: -1
1:06:32.337577 INFO: Competetive: True
1:06:32.369400 INFO: Setting torch num_threads to 2 for FDR classification task
1:06:34.270344 INFO: Test AUC: 0.566
1:06:34.270530 INFO: Train AUC: 0.579
1:06:34.270561 INFO: AUC difference: 2.37%
1:06:34.479254 INFO: Resetting torch num_threads to 100
1:06:34.482611 INFO: === FDR correction performed with classifier version 7 ===
1:06:34.483320 PROGRESS: ============================= Precursor FDR =============================
1:06:34.483423 PROGRESS: Total precursors accumulated: 426
1:06:34.483482 PROGRESS: Target precursors: 387 (90.85%)
1:06:34.483534 PROGRESS: Decoy precursors: 39 (9.15%)
1:06:34.483584 PROGRESS: 
1:06:34.483628 PROGRESS: Precursor Summary:
1:06:34.484810 PROGRESS: Channel   0:	 0.05 FDR:   304; 0.01 FDR:   232; 0.001 FDR:   211
1:06:34.484912 PROGRESS: 
1:06:34.484968 PROGRESS: Protein Summary:
1:06:34.486085 PROGRESS: Channel   0:	 0.05 FDR:   294; 0.01 FDR:   223; 0.001 FDR:   203
1:06:34.486179 PROGRESS: =========================================================================
1:06:34.543201 INFO: fragments_df: keeping 2440 of 845361 [sum(precursor_idx_mask)=4962 sum(mass_error_mask)=845361 stop_rank=2440
1:06:34.691477 INFO: calibration group: precursor, fitting rt estimator 
1:06:34.804732 INFO: calibration group: fragment, fitting mz estimator 
1:06:35.119245 INFO: Using score_cutoff 49.59165819740295 (fac=0.99, q=1)
1:06:35.119669 INFO: calibration group: precursor, predicting mz
1:06:35.119763 WARNING: mz prediction was skipped as it has not been fitted yet
1:06:35.119796 INFO: calibration group: precursor, predicting rt
1:06:35.152189 INFO: calibration group: fragment, predicting mz
1:06:35.226628 INFO: === checking if optimization conditions were reached ===
1:06:35.226924 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
1:06:35.229552 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 10.6338.
1:06:35.229614 INFO: ==============================================
1:06:35.229724 INFO: Starting optimization step 14.
1:06:35.229803 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:06:35.229883 PROGRESS: Extracting batch of 50212 precursors
1:06:35.248658 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:06:35.248779 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:06:35.248824 INFO: FWHM in RT is 2.66 seconds, sigma is 0.34
1:06:35.248852 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:06:35.249147 INFO: Starting candidate selection
1:06:37.762537 INFO: Starting candidate scoring
1:06:38.431782 INFO: Finished candidate processing
1:06:38.431881 INFO: Collecting candidate features
1:06:38.601126 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 100193)
1:06:38.609674 INFO: Collecting fragment features
1:06:38.674779 INFO: Finished candidate scoring
1:06:38.716536 PROGRESS: === Extracted 100193 precursors and 822734 fragments ===
1:06:38.716928 INFO: performing precursor FDR with 47 features
1:06:38.716968 INFO: Decoy channel: -1
1:06:38.716991 INFO: Competetive: True
1:06:38.748235 INFO: Setting torch num_threads to 2 for FDR classification task
1:06:38.764779 WARNING: dropped 1 decoy PSMs due to missing features
1:06:40.536779 INFO: Test AUC: 0.569
1:06:40.536907 INFO: Train AUC: 0.579
1:06:40.536937 INFO: AUC difference: 1.72%
1:06:40.740822 INFO: Resetting torch num_threads to 100
1:06:40.744058 INFO: === FDR correction performed with classifier version 7 ===
1:06:40.744722 PROGRESS: ============================= Precursor FDR =============================
1:06:40.744822 PROGRESS: Total precursors accumulated: 431
1:06:40.744890 PROGRESS: Target precursors: 393 (91.18%)
1:06:40.744946 PROGRESS: Decoy precursors: 38 (8.82%)
1:06:40.744993 PROGRESS: 
1:06:40.745038 PROGRESS: Precursor Summary:
1:06:40.745995 PROGRESS: Channel   0:	 0.05 FDR:   326; 0.01 FDR:   228; 0.001 FDR:   203
1:06:40.746089 PROGRESS: 
1:06:40.746144 PROGRESS: Protein Summary:
1:06:40.747261 PROGRESS: Channel   0:	 0.05 FDR:   316; 0.01 FDR:   219; 0.001 FDR:   196
1:06:40.747355 PROGRESS: =========================================================================
1:06:40.801364 INFO: fragments_df: keeping 2389 of 822734 [sum(precursor_idx_mask)=4878 sum(mass_error_mask)=822734 stop_rank=2389
1:06:40.931993 INFO: calibration group: precursor, fitting rt estimator 
1:06:41.046848 INFO: calibration group: fragment, fitting mz estimator 
1:06:41.362346 INFO: Using score_cutoff 56.71627214241028 (fac=0.99, q=1)
1:06:41.362757 INFO: calibration group: precursor, predicting mz
1:06:41.362847 WARNING: mz prediction was skipped as it has not been fitted yet
1:06:41.362880 INFO: calibration group: precursor, predicting rt
1:06:41.395026 INFO: calibration group: fragment, predicting mz
1:06:41.471869 INFO: === checking if optimization conditions were reached ===
1:06:41.472145 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
1:06:41.473255 PROGRESS: ✅ ms2_error      : optimization complete. Optimal parameter 11.0283 found after 7 searches.
1:06:41.473312 INFO: ==============================================
1:06:41.473415 PROGRESS: Optimization finished for ms2_error.
1:06:41.607860 INFO: calibration group: precursor, predicting mz
1:06:41.608130 WARNING: mz prediction was skipped as it has not been fitted yet
1:06:41.608165 INFO: calibration group: precursor, predicting rt
1:06:41.640379 INFO: calibration group: fragment, predicting mz
1:06:41.739408 INFO: Starting optimization step 0.
1:06:41.739655 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:06:41.739737 PROGRESS: Extracting batch of 50212 precursors
1:06:41.758097 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:06:41.758201 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:06:41.758240 INFO: FWHM in RT is 2.66 seconds, sigma is 0.34
1:06:41.758268 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:06:41.758485 INFO: Starting candidate selection
1:06:44.192992 INFO: Starting candidate scoring
1:06:44.855958 INFO: Finished candidate processing
1:06:44.856061 INFO: Collecting candidate features
1:06:45.002423 INFO: Collecting fragment features
1:06:45.057637 INFO: Finished candidate scoring
1:06:45.097730 PROGRESS: === Extracted 100206 precursors and 844945 fragments ===
1:06:45.098119 INFO: performing precursor FDR with 47 features
1:06:45.098158 INFO: Decoy channel: -1
1:06:45.098182 INFO: Competetive: True
1:06:45.126850 INFO: Setting torch num_threads to 2 for FDR classification task
1:06:46.892751 INFO: Test AUC: 0.572
1:06:46.892936 INFO: Train AUC: 0.591
1:06:46.892966 INFO: AUC difference: 3.18%
1:06:47.102702 INFO: Resetting torch num_threads to 100
1:06:47.127881 INFO: === FDR correction performed with classifier version 13 ===
1:06:47.128736 PROGRESS: ============================= Precursor FDR =============================
1:06:47.128866 PROGRESS: Total precursors accumulated: 450
1:06:47.128929 PROGRESS: Target precursors: 409 (90.89%)
1:06:47.128982 PROGRESS: Decoy precursors: 41 (9.11%)
1:06:47.129030 PROGRESS: 
1:06:47.129078 PROGRESS: Precursor Summary:
1:06:47.130075 PROGRESS: Channel   0:	 0.05 FDR:   335; 0.01 FDR:   247; 0.001 FDR:   190
1:06:47.130169 PROGRESS: 
1:06:47.130235 PROGRESS: Protein Summary:
1:06:47.131369 PROGRESS: Channel   0:	 0.05 FDR:   324; 0.01 FDR:   239; 0.001 FDR:   184
1:06:47.131476 PROGRESS: =========================================================================
1:06:47.189421 INFO: fragments_df: keeping 2591 of 844945 [sum(precursor_idx_mask)=5300 sum(mass_error_mask)=844945 stop_rank=2591
1:06:47.370555 INFO: calibration group: precursor, fitting rt estimator 
1:06:47.490071 INFO: calibration group: fragment, fitting mz estimator 
1:06:47.828030 INFO: Using score_cutoff 59.81550505142212 (fac=0.99, q=1)
1:06:47.828542 INFO: calibration group: precursor, predicting mz
1:06:47.828636 WARNING: mz prediction was skipped as it has not been fitted yet
1:06:47.828665 INFO: calibration group: precursor, predicting rt
1:06:47.861352 INFO: calibration group: fragment, predicting mz
1:06:47.939034 INFO: === checking if optimization conditions were reached ===
1:06:47.939310 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:06:47.941228 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 212.3225.
1:06:47.941289 INFO: ==============================================
1:06:47.941389 INFO: Starting optimization step 1.
1:06:47.941463 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:06:47.941538 PROGRESS: Extracting batch of 50212 precursors
1:06:47.955025 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:06:47.955118 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:06:47.955165 INFO: FWHM in RT is 2.66 seconds, sigma is 0.34
1:06:47.955190 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:06:47.955485 INFO: Starting candidate selection
1:06:50.027389 INFO: Starting candidate scoring
1:06:50.827547 INFO: Finished candidate processing
1:06:50.827646 INFO: Collecting candidate features
1:06:50.991458 INFO: Collecting fragment features
1:06:51.043943 INFO: Finished candidate scoring
1:06:51.094268 PROGRESS: === Extracted 99848 precursors and 782117 fragments ===
1:06:51.094682 INFO: performing precursor FDR with 47 features
1:06:51.094722 INFO: Decoy channel: -1
1:06:51.094745 INFO: Competetive: True
1:06:51.126174 INFO: Setting torch num_threads to 2 for FDR classification task
1:06:52.692974 INFO: Test AUC: 0.560
1:06:52.693099 INFO: Train AUC: 0.580
1:06:52.693130 INFO: AUC difference: 3.56%
1:06:52.895850 INFO: Resetting torch num_threads to 100
1:06:52.898971 INFO: === FDR correction performed with classifier version 13 ===
1:06:52.899654 PROGRESS: ============================= Precursor FDR =============================
1:06:52.899751 PROGRESS: Total precursors accumulated: 479
1:06:52.899814 PROGRESS: Target precursors: 438 (91.44%)
1:06:52.899866 PROGRESS: Decoy precursors: 41 (8.56%)
1:06:52.899919 PROGRESS: 
1:06:52.899965 PROGRESS: Precursor Summary:
1:06:52.900957 PROGRESS: Channel   0:	 0.05 FDR:   402; 0.01 FDR:   234; 0.001 FDR:   198
1:06:52.901052 PROGRESS: 
1:06:52.901114 PROGRESS: Protein Summary:
1:06:52.902237 PROGRESS: Channel   0:	 0.05 FDR:   385; 0.01 FDR:   226; 0.001 FDR:   191
1:06:52.902330 PROGRESS: =========================================================================
1:06:52.956297 INFO: fragments_df: keeping 2428 of 782117 [sum(precursor_idx_mask)=5036 sum(mass_error_mask)=782117 stop_rank=2428
1:06:53.082648 INFO: calibration group: precursor, fitting rt estimator 
1:06:53.203452 INFO: calibration group: fragment, fitting mz estimator 
1:06:53.517663 INFO: Using score_cutoff 63.5971088596344 (fac=0.99, q=1)
1:06:53.518075 INFO: calibration group: precursor, predicting mz
1:06:53.518163 WARNING: mz prediction was skipped as it has not been fitted yet
1:06:53.518194 INFO: calibration group: precursor, predicting rt
1:06:53.553757 INFO: calibration group: fragment, predicting mz
1:06:53.621882 INFO: === checking if optimization conditions were reached ===
1:06:53.622171 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:06:53.624321 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 102.3163.
1:06:53.624383 INFO: ==============================================
1:06:53.624486 INFO: Starting optimization step 2.
1:06:53.624575 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:06:53.624640 PROGRESS: Extracting batch of 50212 precursors
1:06:53.640749 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:06:53.640858 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:06:53.640900 INFO: FWHM in RT is 2.69 seconds, sigma is 0.35
1:06:53.640930 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:06:53.641154 INFO: Starting candidate selection
1:06:55.583516 INFO: Starting candidate scoring
1:06:56.248404 INFO: Finished candidate processing
1:06:56.248539 INFO: Collecting candidate features
1:06:56.420838 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 99012)
1:06:56.430317 INFO: Collecting fragment features
1:06:56.487838 INFO: Finished candidate scoring
1:06:56.554253 PROGRESS: === Extracted 99012 precursors and 703446 fragments ===
1:06:56.554757 INFO: performing precursor FDR with 47 features
1:06:56.554798 INFO: Decoy channel: -1
1:06:56.554824 INFO: Competetive: True
1:06:56.596502 INFO: Setting torch num_threads to 2 for FDR classification task
1:06:56.623221 WARNING: dropped 1 target PSMs due to missing features
1:06:56.623402 WARNING: dropped 2 decoy PSMs due to missing features
1:06:58.864839 INFO: Test AUC: 0.557
1:06:58.865030 INFO: Train AUC: 0.575
1:06:58.865063 INFO: AUC difference: 3.12%
1:06:59.076412 INFO: Resetting torch num_threads to 100
1:06:59.080453 INFO: === FDR correction performed with classifier version 13 ===
1:06:59.081210 PROGRESS: ============================= Precursor FDR =============================
1:06:59.081314 PROGRESS: Total precursors accumulated: 475
1:06:59.081372 PROGRESS: Target precursors: 431 (90.74%)
1:06:59.081428 PROGRESS: Decoy precursors: 44 (9.26%)
1:06:59.081501 PROGRESS: 
1:06:59.081562 PROGRESS: Precursor Summary:
1:06:59.082639 PROGRESS: Channel   0:	 0.05 FDR:   370; 0.01 FDR:   250; 0.001 FDR:   196
1:06:59.082742 PROGRESS: 
1:06:59.082828 PROGRESS: Protein Summary:
1:06:59.084047 PROGRESS: Channel   0:	 0.05 FDR:   356; 0.01 FDR:   241; 0.001 FDR:   189
1:06:59.084142 PROGRESS: =========================================================================
1:06:59.132782 INFO: fragments_df: keeping 2509 of 703446 [sum(precursor_idx_mask)=5280 sum(mass_error_mask)=703446 stop_rank=2509
1:06:59.281625 INFO: calibration group: precursor, fitting rt estimator 
1:06:59.405792 INFO: calibration group: fragment, fitting mz estimator 
1:06:59.729342 INFO: Using score_cutoff 56.29670831909179 (fac=0.99, q=1)
1:06:59.729829 INFO: calibration group: precursor, predicting mz
1:06:59.729920 WARNING: mz prediction was skipped as it has not been fitted yet
1:06:59.729950 INFO: calibration group: precursor, predicting rt
1:06:59.761942 INFO: calibration group: fragment, predicting mz
1:06:59.831737 INFO: === checking if optimization conditions were reached ===
1:06:59.832062 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:06:59.834561 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 81.4565.
1:06:59.834635 INFO: ==============================================
1:06:59.834746 INFO: Starting optimization step 3.
1:06:59.834826 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:06:59.834906 PROGRESS: Extracting batch of 50212 precursors
1:06:59.855278 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:06:59.855392 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:06:59.855436 INFO: FWHM in RT is 2.67 seconds, sigma is 0.34
1:06:59.855464 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:06:59.855758 INFO: Starting candidate selection
1:07:01.835716 INFO: Starting candidate scoring
1:07:02.531760 INFO: Finished candidate processing
1:07:02.531966 INFO: Collecting candidate features
1:07:02.704639 WARNING: intensity_correlation has 9 NaNs ( 0.01 % out of 98679)
1:07:02.716872 INFO: Collecting fragment features
1:07:02.774458 INFO: Finished candidate scoring
1:07:02.838082 PROGRESS: === Extracted 98679 precursors and 691764 fragments ===
1:07:02.838613 INFO: performing precursor FDR with 47 features
1:07:02.838656 INFO: Decoy channel: -1
1:07:02.838684 INFO: Competetive: True
1:07:02.875596 INFO: Setting torch num_threads to 2 for FDR classification task
1:07:02.897906 WARNING: dropped 7 target PSMs due to missing features
1:07:02.898084 WARNING: dropped 2 decoy PSMs due to missing features
1:07:04.851625 INFO: Test AUC: 0.554
1:07:04.851794 INFO: Train AUC: 0.575
1:07:04.851826 INFO: AUC difference: 3.65%
1:07:05.073454 INFO: Resetting torch num_threads to 100
1:07:05.077241 INFO: === FDR correction performed with classifier version 13 ===
1:07:05.078272 PROGRESS: ============================= Precursor FDR =============================
1:07:05.078381 PROGRESS: Total precursors accumulated: 460
1:07:05.078443 PROGRESS: Target precursors: 417 (90.65%)
1:07:05.078497 PROGRESS: Decoy precursors: 43 (9.35%)
1:07:05.078543 PROGRESS: 
1:07:05.078588 PROGRESS: Precursor Summary:
1:07:05.079668 PROGRESS: Channel   0:	 0.05 FDR:   341; 0.01 FDR:   255; 0.001 FDR:   230
1:07:05.079766 PROGRESS: 
1:07:05.079825 PROGRESS: Protein Summary:
1:07:05.081002 PROGRESS: Channel   0:	 0.05 FDR:   331; 0.01 FDR:   248; 0.001 FDR:   223
1:07:05.081099 PROGRESS: =========================================================================
1:07:05.129111 INFO: fragments_df: keeping 2556 of 691764 [sum(precursor_idx_mask)=5371 sum(mass_error_mask)=691764 stop_rank=2556
1:07:05.287710 INFO: calibration group: precursor, fitting rt estimator 
1:07:05.393331 INFO: calibration group: fragment, fitting mz estimator 
1:07:05.672871 INFO: Using score_cutoff 63.2103385597229 (fac=0.99, q=1)
1:07:05.673351 INFO: calibration group: precursor, predicting mz
1:07:05.673440 WARNING: mz prediction was skipped as it has not been fitted yet
1:07:05.673473 INFO: calibration group: precursor, predicting rt
1:07:05.705932 INFO: calibration group: fragment, predicting mz
1:07:05.775904 INFO: === checking if optimization conditions were reached ===
1:07:05.776243 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:07:05.778552 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 79.2097.
1:07:05.778624 INFO: ==============================================
1:07:05.778720 INFO: Starting optimization step 4.
1:07:05.778792 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:07:05.778857 PROGRESS: Extracting batch of 50212 precursors
1:07:05.793576 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:07:05.793712 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:07:05.793747 INFO: FWHM in RT is 2.66 seconds, sigma is 0.34
1:07:05.793771 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:07:05.794049 INFO: Starting candidate selection
1:07:07.868977 INFO: Starting candidate scoring
1:07:08.529433 INFO: Finished candidate processing
1:07:08.529532 INFO: Collecting candidate features
1:07:08.681817 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 98550)
1:07:08.690198 INFO: Collecting fragment features
1:07:08.740287 INFO: Finished candidate scoring
1:07:08.788890 PROGRESS: === Extracted 98550 precursors and 686682 fragments ===
1:07:08.789254 INFO: performing precursor FDR with 47 features
1:07:08.789291 INFO: Decoy channel: -1
1:07:08.789314 INFO: Competetive: True
1:07:08.823486 INFO: Setting torch num_threads to 2 for FDR classification task
1:07:08.845685 WARNING: dropped 1 target PSMs due to missing features
1:07:08.845807 WARNING: dropped 2 decoy PSMs due to missing features
1:07:10.638825 INFO: Test AUC: 0.553
1:07:10.638986 INFO: Train AUC: 0.577
1:07:10.639017 INFO: AUC difference: 4.21%
1:07:10.853908 INFO: Resetting torch num_threads to 100
1:07:10.857815 INFO: === FDR correction performed with classifier version 13 ===
1:07:10.858673 PROGRESS: ============================= Precursor FDR =============================
1:07:10.858775 PROGRESS: Total precursors accumulated: 485
1:07:10.858836 PROGRESS: Target precursors: 440 (90.72%)
1:07:10.858897 PROGRESS: Decoy precursors: 45 (9.28%)
1:07:10.858944 PROGRESS: 
1:07:10.858988 PROGRESS: Precursor Summary:
1:07:10.860035 PROGRESS: Channel   0:	 0.05 FDR:   375; 0.01 FDR:   265; 0.001 FDR:   228
1:07:10.860127 PROGRESS: 
1:07:10.860694 PROGRESS: Protein Summary:
1:07:10.861883 PROGRESS: Channel   0:	 0.05 FDR:   362; 0.01 FDR:   256; 0.001 FDR:   221
1:07:10.861974 PROGRESS: =========================================================================
1:07:10.907897 INFO: fragments_df: keeping 2618 of 686682 [sum(precursor_idx_mask)=5566 sum(mass_error_mask)=686682 stop_rank=2618
1:07:11.055436 INFO: calibration group: precursor, fitting rt estimator 
1:07:11.178257 INFO: calibration group: fragment, fitting mz estimator 
1:07:11.515959 INFO: Using score_cutoff 56.36392200164795 (fac=0.99, q=1)
1:07:11.516401 INFO: calibration group: precursor, predicting mz
1:07:11.516490 WARNING: mz prediction was skipped as it has not been fitted yet
1:07:11.516522 INFO: calibration group: precursor, predicting rt
1:07:11.548578 INFO: calibration group: fragment, predicting mz
1:07:11.619526 INFO: === checking if optimization conditions were reached ===
1:07:11.619819 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1:07:11.621425 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 79.2097 found after 5 searches.
1:07:11.621483 INFO: ==============================================
1:07:11.621594 PROGRESS: Optimization finished for rt_error.
1:07:11.760548 INFO: calibration group: precursor, predicting mz
1:07:11.760796 WARNING: mz prediction was skipped as it has not been fitted yet
1:07:11.760829 INFO: calibration group: precursor, predicting rt
1:07:11.792936 INFO: calibration group: fragment, predicting mz
1:07:11.893659 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:07:11.893890 PROGRESS: ==============================================
1:07:11.893972 PROGRESS: ms2_error      : 11.0283
1:07:11.894037 PROGRESS: rt_error       : 79.2097
1:07:11.894107 PROGRESS: ==============================================
1:07:11.896080 INFO: calibration group: precursor, predicting mz
1:07:11.896216 WARNING: mz prediction was skipped as it has not been fitted yet
1:07:11.896253 INFO: calibration group: precursor, predicting rt
1:07:18.604493 INFO: calibration group: fragment, predicting mz
1:07:33.931159 PROGRESS: Extracting batch of 10183864 precursors
1:07:36.398257 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:07:36.398392 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:07:36.398431 INFO: FWHM in RT is 2.66 seconds, sigma is 0.34
1:07:36.398455 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:07:36.398849 INFO: Starting candidate selection
1:14:15.504440 INFO: Applying score cutoff of 56.36392200164795
1:14:15.595392 INFO: Removed 18740535 precursors with score below cutoff
1:14:17.783388 INFO: Starting candidate scoring
1:14:29.166236 INFO: Finished candidate processing
1:14:29.166368 INFO: Collecting candidate features
1:14:33.776884 INFO: Collecting fragment features
1:14:35.319850 INFO: Finished candidate scoring
1:14:36.551065 INFO: === FDR correction performed with classifier version 19 ===
1:14:36.556343 INFO: performing precursor FDR with 47 features
1:14:36.556416 INFO: Decoy channel: -1
1:14:36.556443 INFO: Competetive: True
1:14:37.029053 INFO: Setting torch num_threads to 2 for FDR classification task
1:14:37.239977 WARNING: FDR calculation for 825925 target and 742166 decoy PSMs
1:14:37.240107 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1:15:04.760355 INFO: Test AUC: 0.628
1:15:04.760568 INFO: Train AUC: 0.632
1:15:04.760601 INFO: AUC difference: 0.54%
1:15:05.334256 INFO: Resetting torch num_threads to 100
1:15:05.385737 INFO: Removing fragments below FDR threshold
1:15:05.583025 PROGRESS: ============================= Precursor FDR =============================
1:15:05.583321 PROGRESS: Total precursors accumulated: 71,390
1:15:05.583403 PROGRESS: Target precursors: 70,684 (99.01%)
1:15:05.583456 PROGRESS: Decoy precursors: 706 (0.99%)
1:15:05.583502 PROGRESS: 
1:15:05.583548 PROGRESS: Precursor Summary:
1:15:05.612461 PROGRESS: Channel   0:	 0.05 FDR: 70,684; 0.01 FDR: 70,684; 0.001 FDR: 48,812
1:15:05.612716 PROGRESS: 
1:15:05.612784 PROGRESS: Protein Summary:
1:15:05.653693 PROGRESS: Channel   0:	 0.05 FDR: 10,707; 0.01 FDR: 10,707; 0.001 FDR: 8,275
1:15:05.653922 PROGRESS: =========================================================================
1:15:06.244276 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:15:06.665259 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:15:06.665431 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant
1:15:06.665506 INFO: Creating folder run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/figures
1:15:06.666243 INFO: Initializing RawFileManager
1:15:19.047495 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.
1:15:19.052934 INFO: Determining DIA cycle
1:15:19.068615 INFO: Found cycle with start 0.00 min and length 300.
1:15:19.478147 INFO: RT (min)            : 0.0 - 26.9
1:15:19.478273 INFO: RT duration (sec)   : 1611.2
1:15:19.478301 INFO: RT duration (min)   : 26.9
1:15:19.478324 INFO: Cycle len (scans)   : 300
1:15:19.478347 INFO: Cycle len (sec)     : 1.65
1:15:19.478373 INFO: Number of cycles    : 978
1:15:19.478392 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:15:21.709325 INFO: Initializing CalibrationManager
1:15:21.709610 INFO: Loading calibration config
1:15:21.710230 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'}]
1:15:21.710324 INFO: Calibration group :fragment, found 1 estimator(s)
1:15:21.710415 INFO: Calibration group :precursor, found 3 estimator(s)
1:15:21.710499 INFO: Disabling ion mobility calibration
1:15:21.710528 INFO: removed mobility estimator from group precursor
1:15:21.710713 INFO: Initializing OptimizationManager
1:15:21.710831 INFO: initial parameter: ms1_error = 30
1:15:21.710899 INFO: initial parameter: ms2_error = 30
1:15:21.710953 INFO: initial parameter: rt_error = 805.611083984375
1:15:21.711004 INFO: initial parameter: mobility_error = 0.1
1:15:21.711051 INFO: initial parameter: column_type = library
1:15:21.711097 INFO: initial parameter: num_candidates = 1
1:15:21.711140 INFO: initial parameter: classifier_version = -1
1:15:21.711181 INFO: initial parameter: fwhm_rt = 5
1:15:21.711229 INFO: initial parameter: fwhm_mobility = 0.01
1:15:21.711270 INFO: initial parameter: score_cutoff = 0
1:15:21.711341 INFO: Initializing TimingManager
1:15:21.711417 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:15:21.711577 INFO: FDRManager not loaded from disk.
1:15:21.711610 INFO: Initializing FDRManager
1:15:21.711653 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:15:23.253022 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
1:15:25.082266 PROGRESS: Starting initial search for precursors.
1:15:25.300666 INFO: Starting optimization step 0.
1:15:25.300893 PROGRESS: === Extracting elution groups 0 to 200 ===
1:15:25.300971 PROGRESS: Extracting batch of 395 precursors
1:15:25.302464 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:15:25.302516 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:15:25.302550 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:15:25.302572 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:15:25.302870 INFO: Starting candidate selection
1:15:25.454551 INFO: Starting candidate scoring
1:15:25.493447 INFO: Finished candidate processing
1:15:25.493516 INFO: Collecting candidate features
1:15:25.502422 INFO: Collecting fragment features
1:15:25.504583 INFO: Finished candidate scoring
1:15:25.505592 PROGRESS: === Extracted 395 precursors and 3952 fragments ===
1:15:25.505867 INFO: performing precursor FDR with 47 features
1:15:25.505903 INFO: Decoy channel: -1
1:15:25.505926 INFO: Competetive: True
1:15:25.506949 INFO: Setting torch num_threads to 2 for FDR classification task
1:15:25.526660 INFO: Test AUC: 0.593
1:15:25.526724 INFO: Train AUC: 0.534
1:15:25.526752 INFO: AUC difference: 11.13%
1:15:25.526772 WARNING: AUC difference > 5%. This may indicate overfitting.
1:15:25.697758 INFO: Resetting torch num_threads to 100
1:15:25.698287 INFO: === FDR correction performed with classifier version -1 ===
1:15:25.698917 PROGRESS: ============================= Precursor FDR =============================
1:15:25.699015 PROGRESS: Total precursors accumulated: 200
1:15:25.699076 PROGRESS: Target precursors: 112 (56.00%)
1:15:25.699128 PROGRESS: Decoy precursors: 88 (44.00%)
1:15:25.699174 PROGRESS: 
1:15:25.699219 PROGRESS: Precursor Summary:
1:15:25.700059 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:15:25.700147 PROGRESS: 
1:15:25.700202 PROGRESS: Protein Summary:
1:15:25.701108 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:15:25.701198 PROGRESS: =========================================================================
1:15:25.756270 INFO: Starting optimization step 1.
1:15:25.756456 PROGRESS: === Extracting elution groups 200 to 600 ===
1:15:25.756523 PROGRESS: Extracting batch of 790 precursors
1:15:25.757351 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:15:25.757403 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:15:25.757435 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:15:25.757457 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:15:25.757617 INFO: Starting candidate selection
1:15:25.902850 INFO: Starting candidate scoring
1:15:25.940736 INFO: Finished candidate processing
1:15:25.940800 INFO: Collecting candidate features
1:15:25.949801 INFO: Collecting fragment features
1:15:25.952226 INFO: Finished candidate scoring
1:15:25.954137 PROGRESS: === Extracted 1183 precursors and 12006 fragments ===
1:15:25.954871 INFO: performing precursor FDR with 47 features
1:15:25.954917 INFO: Decoy channel: -1
1:15:25.954940 INFO: Competetive: True
1:15:25.957726 INFO: Setting torch num_threads to 2 for FDR classification task
1:15:25.979877 INFO: Test AUC: 0.548
1:15:25.979944 INFO: Train AUC: 0.490
1:15:25.979972 INFO: AUC difference: 11.79%
1:15:25.979995 WARNING: AUC difference > 5%. This may indicate overfitting.
1:15:26.149211 INFO: Resetting torch num_threads to 100
1:15:26.149832 INFO: === FDR correction performed with classifier version -1 ===
1:15:26.150482 PROGRESS: ============================= Precursor FDR =============================
1:15:26.150581 PROGRESS: Total precursors accumulated: 599
1:15:26.150655 PROGRESS: Target precursors: 297 (49.58%)
1:15:26.150708 PROGRESS: Decoy precursors: 302 (50.42%)
1:15:26.150762 PROGRESS: 
1:15:26.150808 PROGRESS: Precursor Summary:
1:15:26.151668 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:15:26.151757 PROGRESS: 
1:15:26.151812 PROGRESS: Protein Summary:
1:15:26.152743 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:15:26.152831 PROGRESS: =========================================================================
1:15:26.210268 INFO: Starting optimization step 2.
1:15:26.210452 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:15:26.210520 PROGRESS: Extracting batch of 1585 precursors
1:15:26.211491 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:15:26.211543 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:15:26.211574 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:15:26.211595 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:15:26.211755 INFO: Starting candidate selection
1:15:26.368963 INFO: Starting candidate scoring
1:15:26.408301 INFO: Finished candidate processing
1:15:26.408382 INFO: Collecting candidate features
1:15:26.418758 INFO: Collecting fragment features
1:15:26.421929 INFO: Finished candidate scoring
1:15:26.424944 PROGRESS: === Extracted 2762 precursors and 28154 fragments ===
1:15:26.425937 INFO: performing precursor FDR with 47 features
1:15:26.425983 INFO: Decoy channel: -1
1:15:26.426006 INFO: Competetive: True
1:15:26.429255 INFO: Setting torch num_threads to 2 for FDR classification task
1:15:26.468365 INFO: Test AUC: 0.516
1:15:26.468443 INFO: Train AUC: 0.505
1:15:26.468473 INFO: AUC difference: 2.18%
1:15:26.641117 INFO: Resetting torch num_threads to 100
1:15:26.641839 INFO: === FDR correction performed with classifier version -1 ===
1:15:26.642623 PROGRESS: ============================= Precursor FDR =============================
1:15:26.642720 PROGRESS: Total precursors accumulated: 1,396
1:15:26.642781 PROGRESS: Target precursors: 705 (50.50%)
1:15:26.642834 PROGRESS: Decoy precursors: 691 (49.50%)
1:15:26.642880 PROGRESS: 
1:15:26.642924 PROGRESS: Precursor Summary:
1:15:26.643798 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:15:26.643890 PROGRESS: 
1:15:26.643945 PROGRESS: Protein Summary:
1:15:26.644865 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:15:26.644953 PROGRESS: =========================================================================
1:15:26.704878 INFO: Starting optimization step 3.
1:15:26.705063 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:15:26.705134 PROGRESS: Extracting batch of 3157 precursors
1:15:26.706403 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:15:26.706458 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:15:26.706491 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:15:26.706515 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:15:26.706691 INFO: Starting candidate selection
1:15:26.921897 INFO: Starting candidate scoring
1:15:26.962282 INFO: Finished candidate processing
1:15:26.962368 INFO: Collecting candidate features
1:15:26.975118 INFO: Collecting fragment features
1:15:26.979559 INFO: Finished candidate scoring
1:15:26.984452 PROGRESS: === Extracted 5917 precursors and 60557 fragments ===
1:15:26.985839 INFO: performing precursor FDR with 47 features
1:15:26.985886 INFO: Decoy channel: -1
1:15:26.985909 INFO: Competetive: True
1:15:26.990439 INFO: Setting torch num_threads to 2 for FDR classification task
1:15:27.023474 INFO: Test AUC: 0.491
1:15:27.023553 INFO: Train AUC: 0.516
1:15:27.023582 INFO: AUC difference: 4.93%
1:15:27.196025 INFO: Resetting torch num_threads to 100
1:15:27.196898 INFO: === FDR correction performed with classifier version -1 ===
1:15:27.197545 PROGRESS: ============================= Precursor FDR =============================
1:15:27.197640 PROGRESS: Total precursors accumulated: 1
1:15:27.197701 PROGRESS: Target precursors: 1 (100.00%)
1:15:27.197752 PROGRESS: Decoy precursors: 0 (0.00%)
1:15:27.197798 PROGRESS: 
1:15:27.197842 PROGRESS: Precursor Summary:
1:15:27.198792 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:15:27.198884 PROGRESS: 
1:15:27.198946 PROGRESS: Protein Summary:
1:15:27.199966 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:15:27.200058 PROGRESS: =========================================================================
1:15:27.263822 INFO: Starting optimization step 4.
1:15:27.264021 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:15:27.264091 PROGRESS: Extracting batch of 6336 precursors
1:15:27.265696 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:15:27.265743 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:15:27.265773 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:15:27.265794 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:15:27.265952 INFO: Starting candidate selection
1:15:27.705597 INFO: Starting candidate scoring
1:15:27.755306 INFO: Finished candidate processing
1:15:27.755392 INFO: Collecting candidate features
1:15:27.774370 INFO: Collecting fragment features
1:15:27.780240 INFO: Finished candidate scoring
1:15:27.789434 PROGRESS: === Extracted 12238 precursors and 125525 fragments ===
1:15:27.791430 INFO: performing precursor FDR with 47 features
1:15:27.791486 INFO: Decoy channel: -1
1:15:27.791511 INFO: Competetive: True
1:15:27.797263 INFO: Setting torch num_threads to 2 for FDR classification task
1:15:27.886228 INFO: Test AUC: 0.533
1:15:27.886341 INFO: Train AUC: 0.506
1:15:27.886370 INFO: AUC difference: 5.30%
1:15:27.886391 WARNING: AUC difference > 5%. This may indicate overfitting.
1:15:28.061595 INFO: Resetting torch num_threads to 100
1:15:28.062844 INFO: === FDR correction performed with classifier version -1 ===
1:15:28.064174 PROGRESS: ============================= Precursor FDR =============================
1:15:28.064274 PROGRESS: Total precursors accumulated: 6,188
1:15:28.064334 PROGRESS: Target precursors: 3,203 (51.76%)
1:15:28.064384 PROGRESS: Decoy precursors: 2,985 (48.24%)
1:15:28.064430 PROGRESS: 
1:15:28.064474 PROGRESS: Precursor Summary:
1:15:28.065367 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:15:28.065459 PROGRESS: 
1:15:28.065515 PROGRESS: Protein Summary:
1:15:28.066476 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:15:28.066566 PROGRESS: =========================================================================
1:15:28.139314 INFO: Starting optimization step 5.
1:15:28.139526 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:15:28.139594 PROGRESS: Extracting batch of 12662 precursors
1:15:28.142161 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:15:28.142213 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:15:28.142246 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:15:28.142270 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:15:28.142440 INFO: Starting candidate selection
1:15:28.989678 INFO: Starting candidate scoring
1:15:29.072774 INFO: Finished candidate processing
1:15:29.072874 INFO: Collecting candidate features
1:15:29.100913 INFO: Collecting fragment features
1:15:29.110983 INFO: Finished candidate scoring
1:15:29.123517 PROGRESS: === Extracted 24888 precursors and 255444 fragments ===
1:15:29.126402 INFO: performing precursor FDR with 47 features
1:15:29.126464 INFO: Decoy channel: -1
1:15:29.126489 INFO: Competetive: True
1:15:29.136529 INFO: Setting torch num_threads to 2 for FDR classification task
1:15:29.405016 INFO: Test AUC: 0.532
1:15:29.405135 INFO: Train AUC: 0.548
1:15:29.405165 INFO: AUC difference: 2.98%
1:15:29.589054 INFO: Resetting torch num_threads to 100
1:15:29.590766 INFO: === FDR correction performed with classifier version -1 ===
1:15:29.591368 PROGRESS: ============================= Precursor FDR =============================
1:15:29.591460 PROGRESS: Total precursors accumulated: 14
1:15:29.591519 PROGRESS: Target precursors: 13 (92.86%)
1:15:29.591572 PROGRESS: Decoy precursors: 1 (7.14%)
1:15:29.591617 PROGRESS: 
1:15:29.591674 PROGRESS: Precursor Summary:
1:15:29.592523 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:15:29.592611 PROGRESS: 
1:15:29.592665 PROGRESS: Protein Summary:
1:15:29.593590 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:15:29.593678 PROGRESS: =========================================================================
1:15:29.682369 INFO: Starting optimization step 6.
1:15:29.682629 PROGRESS: === Extracting elution groups 12600 to 25400 ===
1:15:29.682703 PROGRESS: Extracting batch of 25287 precursors
1:15:29.687926 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:15:29.687985 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:15:29.688017 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:15:29.688039 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:15:29.688214 INFO: Starting candidate selection
1:15:31.242371 INFO: Starting candidate scoring
1:15:31.437510 INFO: Finished candidate processing
1:15:31.437644 INFO: Collecting candidate features
1:15:31.495601 INFO: Collecting fragment features
1:15:31.515265 INFO: Finished candidate scoring
1:15:31.548144 PROGRESS: === Extracted 50105 precursors and 514376 fragments ===
1:15:31.557393 INFO: performing precursor FDR with 47 features
1:15:31.557487 INFO: Decoy channel: -1
1:15:31.557515 INFO: Competetive: True
1:15:31.582502 INFO: Setting torch num_threads to 2 for FDR classification task
1:15:32.567956 INFO: Test AUC: 0.554
1:15:32.568124 INFO: Train AUC: 0.574
1:15:32.568154 INFO: AUC difference: 3.33%
1:15:32.767522 INFO: Resetting torch num_threads to 100
1:15:32.771834 INFO: === FDR correction performed with classifier version -1 ===
1:15:32.772552 PROGRESS: ============================= Precursor FDR =============================
1:15:32.772652 PROGRESS: Total precursors accumulated: 211
1:15:32.772711 PROGRESS: Target precursors: 193 (91.47%)
1:15:32.772762 PROGRESS: Decoy precursors: 18 (8.53%)
1:15:32.772810 PROGRESS: 
1:15:32.772856 PROGRESS: Precursor Summary:
1:15:32.773813 PROGRESS: Channel   0:	 0.05 FDR:   103; 0.01 FDR:    68; 0.001 FDR:    68
1:15:32.773905 PROGRESS: 
1:15:32.773961 PROGRESS: Protein Summary:
1:15:32.775015 PROGRESS: Channel   0:	 0.05 FDR:   102; 0.01 FDR:    67; 0.001 FDR:    67
1:15:32.775112 PROGRESS: =========================================================================
1:15:32.932006 INFO: Starting optimization step 7.
1:15:32.932372 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1:15:32.932466 PROGRESS: Extracting batch of 50588 precursors
1:15:32.948023 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:15:32.948165 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:15:32.948206 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:15:32.948235 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:15:32.948512 INFO: Starting candidate selection
1:15:36.078585 INFO: Starting candidate scoring
1:15:36.405340 INFO: Finished candidate processing
1:15:36.405438 INFO: Collecting candidate features
1:15:36.491706 INFO: Collecting fragment features
1:15:36.523263 INFO: Finished candidate scoring
1:15:36.575102 PROGRESS: === Extracted 100596 precursors and 1033687 fragments ===
1:15:36.586846 INFO: performing precursor FDR with 47 features
1:15:36.586932 INFO: Decoy channel: -1
1:15:36.586957 INFO: Competetive: True
1:15:36.625910 INFO: Setting torch num_threads to 2 for FDR classification task
1:15:38.377429 INFO: Test AUC: 0.568
1:15:38.377551 INFO: Train AUC: 0.586
1:15:38.377582 INFO: AUC difference: 2.93%
1:15:38.577645 INFO: Resetting torch num_threads to 100
1:15:38.582970 INFO: === FDR correction performed with classifier version -1 ===
1:15:38.583703 PROGRESS: ============================= Precursor FDR =============================
1:15:38.583804 PROGRESS: Total precursors accumulated: 564
1:15:38.583864 PROGRESS: Target precursors: 519 (92.02%)
1:15:38.583915 PROGRESS: Decoy precursors: 45 (7.98%)
1:15:38.583961 PROGRESS: 
1:15:38.584005 PROGRESS: Precursor Summary:
1:15:38.584994 PROGRESS: Channel   0:	 0.05 FDR:   430; 0.01 FDR:   272; 0.001 FDR:   211
1:15:38.585094 PROGRESS: 
1:15:38.585149 PROGRESS: Protein Summary:
1:15:38.586320 PROGRESS: Channel   0:	 0.05 FDR:   407; 0.01 FDR:   260; 0.001 FDR:   200
1:15:38.586413 PROGRESS: =========================================================================
1:15:38.660587 INFO: fragments_df: keeping 2542 of 1033687 [sum(precursor_idx_mask)=3165 sum(mass_error_mask)=1033687 stop_rank=2542
1:15:38.856753 INFO: calibration group: precursor, fitting rt estimator 
1:15:38.957260 INFO: calibration group: fragment, fitting mz estimator 
1:15:39.230346 INFO: Using score_cutoff 75.50110721282958 (fac=0.99, q=1)
1:15:39.230768 INFO: calibration group: precursor, predicting mz
1:15:39.230856 WARNING: mz prediction was skipped as it has not been fitted yet
1:15:39.230886 INFO: calibration group: precursor, predicting rt
1:15:39.295792 INFO: calibration group: fragment, predicting mz
1:15:39.457638 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:15:39.457948 INFO: Starting optimization step 8.
1:15:39.458031 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:15:39.458102 PROGRESS: Extracting batch of 100800 precursors
1:15:39.492180 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:15:39.492321 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:15:39.492358 INFO: FWHM in RT is 2.92 seconds, sigma is 0.38
1:15:39.492386 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:15:39.492630 INFO: Starting candidate selection
1:15:44.563995 INFO: Starting candidate scoring
1:15:46.113523 INFO: Finished candidate processing
1:15:46.113736 INFO: Collecting candidate features
1:15:46.456694 INFO: Collecting fragment features
1:15:46.582612 INFO: Finished candidate scoring
1:15:46.696147 PROGRESS: === Extracted 201192 precursors and 2041799 fragments ===
1:15:46.696615 INFO: performing precursor FDR with 47 features
1:15:46.696654 INFO: Decoy channel: -1
1:15:46.696678 INFO: Competetive: True
1:15:46.753085 INFO: Setting torch num_threads to 2 for FDR classification task
1:15:50.001090 INFO: Test AUC: 0.572
1:15:50.001211 INFO: Train AUC: 0.586
1:15:50.001240 INFO: AUC difference: 2.49%
1:15:50.228595 INFO: Resetting torch num_threads to 100
1:15:50.233938 INFO: === FDR correction performed with classifier version 7 ===
1:15:50.234741 PROGRESS: ============================= Precursor FDR =============================
1:15:50.234847 PROGRESS: Total precursors accumulated: 586
1:15:50.234919 PROGRESS: Target precursors: 535 (91.30%)
1:15:50.234977 PROGRESS: Decoy precursors: 51 (8.70%)
1:15:50.235023 PROGRESS: 
1:15:50.235066 PROGRESS: Precursor Summary:
1:15:50.236117 PROGRESS: Channel   0:	 0.05 FDR:   445; 0.01 FDR:   252; 0.001 FDR:   215
1:15:50.236207 PROGRESS: 
1:15:50.236263 PROGRESS: Protein Summary:
1:15:50.237412 PROGRESS: Channel   0:	 0.05 FDR:   418; 0.01 FDR:   240; 0.001 FDR:   205
1:15:50.237506 PROGRESS: =========================================================================
1:15:50.375342 INFO: fragments_df: keeping 3041 of 2041799 [sum(precursor_idx_mask)=5766 sum(mass_error_mask)=2041799 stop_rank=3041
1:15:50.572157 INFO: calibration group: precursor, fitting rt estimator 
1:15:50.693385 INFO: calibration group: fragment, fitting mz estimator 
1:15:51.093547 INFO: Using score_cutoff 78.88550981369018 (fac=0.99, q=1)
1:15:51.093978 INFO: calibration group: precursor, predicting mz
1:15:51.094066 WARNING: mz prediction was skipped as it has not been fitted yet
1:15:51.094094 INFO: calibration group: precursor, predicting rt
1:15:51.159320 INFO: calibration group: fragment, predicting mz
1:15:51.308604 INFO: === checking if optimization conditions were reached ===
1:15:51.308890 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 2 ===
1:15:51.310967 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 23.4443.
1:15:51.311029 INFO: ==============================================
1:15:51.311150 INFO: Starting optimization step 9.
1:15:51.311248 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:15:51.311337 PROGRESS: Extracting batch of 100800 precursors
1:15:51.334299 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:15:51.334423 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:15:51.334471 INFO: FWHM in RT is 2.89 seconds, sigma is 0.37
1:15:51.334502 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:15:51.334778 INFO: Starting candidate selection
1:15:56.196111 INFO: Starting candidate scoring
1:15:57.514528 INFO: Finished candidate processing
1:15:57.514678 INFO: Collecting candidate features
1:15:57.931524 INFO: Collecting fragment features
1:15:58.078328 INFO: Finished candidate scoring
1:15:58.226342 PROGRESS: === Extracted 201191 precursors and 1969489 fragments ===
1:15:58.226833 INFO: performing precursor FDR with 47 features
1:15:58.226876 INFO: Decoy channel: -1
1:15:58.226901 INFO: Competetive: True
1:15:58.310155 INFO: Setting torch num_threads to 2 for FDR classification task
1:16:02.832530 INFO: Test AUC: 0.559
1:16:02.832742 INFO: Train AUC: 0.584
1:16:02.832776 INFO: AUC difference: 4.35%
1:16:03.066231 INFO: Resetting torch num_threads to 100
1:16:03.072167 INFO: === FDR correction performed with classifier version 7 ===
1:16:03.072977 PROGRESS: ============================= Precursor FDR =============================
1:16:03.073091 PROGRESS: Total precursors accumulated: 655
1:16:03.073151 PROGRESS: Target precursors: 597 (91.15%)
1:16:03.073204 PROGRESS: Decoy precursors: 58 (8.85%)
1:16:03.073252 PROGRESS: 
1:16:03.073297 PROGRESS: Precursor Summary:
1:16:03.074319 PROGRESS: Channel   0:	 0.05 FDR:   471; 0.01 FDR:   305; 0.001 FDR:     1
1:16:03.074413 PROGRESS: 
1:16:03.074468 PROGRESS: Protein Summary:
1:16:03.075610 PROGRESS: Channel   0:	 0.05 FDR:   437; 0.01 FDR:   292; 0.001 FDR:     1
1:16:03.075707 PROGRESS: =========================================================================
1:16:03.205026 INFO: fragments_df: keeping 3632 of 1969489 [sum(precursor_idx_mask)=6875 sum(mass_error_mask)=1969489 stop_rank=3632
1:16:03.425495 INFO: calibration group: precursor, fitting rt estimator 
1:16:03.541588 INFO: calibration group: fragment, fitting mz estimator 
1:16:04.010227 INFO: Using score_cutoff 74.04914885559081 (fac=0.99, q=1)
1:16:04.010659 INFO: calibration group: precursor, predicting mz
1:16:04.010749 WARNING: mz prediction was skipped as it has not been fitted yet
1:16:04.010780 INFO: calibration group: precursor, predicting rt
1:16:04.075532 INFO: calibration group: fragment, predicting mz
1:16:04.229286 INFO: === checking if optimization conditions were reached ===
1:16:04.229542 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 2 ===
1:16:04.231821 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 18.8494.
1:16:04.231877 INFO: ==============================================
1:16:04.231975 INFO: Starting optimization step 10.
1:16:04.232043 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:16:04.232109 PROGRESS: Extracting batch of 100800 precursors
1:16:04.255066 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:16:04.255187 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:16:04.255225 INFO: FWHM in RT is 2.81 seconds, sigma is 0.36
1:16:04.255247 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:16:04.255517 INFO: Starting candidate selection
1:16:09.035884 INFO: Starting candidate scoring
1:16:10.481278 INFO: Finished candidate processing
1:16:10.481412 INFO: Collecting candidate features
1:16:10.895669 INFO: Collecting fragment features
1:16:11.043071 INFO: Finished candidate scoring
1:16:11.185701 PROGRESS: === Extracted 201191 precursors and 1886699 fragments ===
1:16:11.186208 INFO: performing precursor FDR with 47 features
1:16:11.186247 INFO: Decoy channel: -1
1:16:11.186271 INFO: Competetive: True
1:16:11.270468 INFO: Setting torch num_threads to 2 for FDR classification task
1:16:15.816659 INFO: Test AUC: 0.557
1:16:15.816864 INFO: Train AUC: 0.582
1:16:15.816896 INFO: AUC difference: 4.30%
1:16:16.049115 INFO: Resetting torch num_threads to 100
1:16:16.054457 INFO: === FDR correction performed with classifier version 7 ===
1:16:16.055268 PROGRESS: ============================= Precursor FDR =============================
1:16:16.055381 PROGRESS: Total precursors accumulated: 719
1:16:16.055453 PROGRESS: Target precursors: 655 (91.10%)
1:16:16.055510 PROGRESS: Decoy precursors: 64 (8.90%)
1:16:16.055561 PROGRESS: 
1:16:16.055607 PROGRESS: Precursor Summary:
1:16:16.056651 PROGRESS: Channel   0:	 0.05 FDR:   534; 0.01 FDR:   274; 0.001 FDR:   228
1:16:16.056748 PROGRESS: 
1:16:16.056803 PROGRESS: Protein Summary:
1:16:16.057985 PROGRESS: Channel   0:	 0.05 FDR:   501; 0.01 FDR:   261; 0.001 FDR:   217
1:16:16.058077 PROGRESS: =========================================================================
1:16:16.183440 INFO: fragments_df: keeping 3269 of 1886699 [sum(precursor_idx_mask)=6162 sum(mass_error_mask)=1886699 stop_rank=3269
1:16:16.408476 INFO: calibration group: precursor, fitting rt estimator 
1:16:16.527177 INFO: calibration group: fragment, fitting mz estimator 
1:16:16.956486 INFO: Using score_cutoff 74.51430383605957 (fac=0.99, q=1)
1:16:16.956908 INFO: calibration group: precursor, predicting mz
1:16:16.956998 WARNING: mz prediction was skipped as it has not been fitted yet
1:16:16.957028 INFO: calibration group: precursor, predicting rt
1:16:17.021353 INFO: calibration group: fragment, predicting mz
1:16:17.169551 INFO: === checking if optimization conditions were reached ===
1:16:17.169803 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 2 ===
1:16:17.172107 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 14.7035.
1:16:17.172164 INFO: ==============================================
1:16:17.172261 INFO: Starting optimization step 11.
1:16:17.172329 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:16:17.172406 PROGRESS: Extracting batch of 100800 precursors
1:16:17.195382 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:16:17.195502 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:16:17.195540 INFO: FWHM in RT is 2.75 seconds, sigma is 0.35
1:16:17.195564 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:16:17.195816 INFO: Starting candidate selection
1:16:22.072063 INFO: Starting candidate scoring
1:16:23.520036 INFO: Finished candidate processing
1:16:23.521048 INFO: Collecting candidate features
1:16:23.939319 INFO: Collecting fragment features
1:16:24.080044 INFO: Finished candidate scoring
1:16:24.205377 PROGRESS: === Extracted 201183 precursors and 1790761 fragments ===
1:16:24.205774 INFO: performing precursor FDR with 47 features
1:16:24.205812 INFO: Decoy channel: -1
1:16:24.205837 INFO: Competetive: True
1:16:24.259677 INFO: Setting torch num_threads to 2 for FDR classification task
1:16:27.785754 INFO: Test AUC: 0.560
1:16:27.786259 INFO: Train AUC: 0.582
1:16:27.786296 INFO: AUC difference: 3.71%
1:16:28.020856 INFO: Resetting torch num_threads to 100
1:16:28.047523 INFO: === FDR correction performed with classifier version 7 ===
1:16:28.048477 PROGRESS: ============================= Precursor FDR =============================
1:16:28.048588 PROGRESS: Total precursors accumulated: 773
1:16:28.048650 PROGRESS: Target precursors: 703 (90.94%)
1:16:28.048706 PROGRESS: Decoy precursors: 70 (9.06%)
1:16:28.048753 PROGRESS: 
1:16:28.048798 PROGRESS: Precursor Summary:
1:16:28.049886 PROGRESS: Channel   0:	 0.05 FDR:   625; 0.01 FDR:   467; 0.001 FDR:   182
1:16:28.049987 PROGRESS: 
1:16:28.050045 PROGRESS: Protein Summary:
1:16:28.051303 PROGRESS: Channel   0:	 0.05 FDR:   577; 0.01 FDR:   442; 0.001 FDR:   174
1:16:28.051400 PROGRESS: =========================================================================
1:16:28.171605 INFO: fragments_df: keeping 5000 of 1790761 [sum(precursor_idx_mask)=10179 sum(mass_error_mask)=1790761 stop_rank=5000
1:16:28.330364 INFO: calibration group: precursor, fitting rt estimator 
1:16:28.460731 INFO: calibration group: fragment, fitting mz estimator 
1:16:29.135583 INFO: Using score_cutoff 62.318775325012204 (fac=0.99, q=1)
1:16:29.136026 INFO: calibration group: precursor, predicting mz
1:16:29.136116 WARNING: mz prediction was skipped as it has not been fitted yet
1:16:29.136145 INFO: calibration group: precursor, predicting rt
1:16:29.168269 INFO: calibration group: fragment, predicting mz
1:16:29.238441 INFO: === checking if optimization conditions were reached ===
1:16:29.238695 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 2 ===
1:16:29.241204 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 12.3822.
1:16:29.241258 INFO: ==============================================
1:16:29.241357 INFO: Starting optimization step 12.
1:16:29.241428 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:16:29.241498 PROGRESS: Extracting batch of 50212 precursors
1:16:29.254271 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:16:29.254374 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:16:29.254412 INFO: FWHM in RT is 2.62 seconds, sigma is 0.34
1:16:29.254435 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:16:29.254695 INFO: Starting candidate selection
1:16:31.689255 INFO: Starting candidate scoring
1:16:32.344210 INFO: Finished candidate processing
1:16:32.344377 INFO: Collecting candidate features
1:16:32.491705 INFO: Collecting fragment features
1:16:32.545917 INFO: Finished candidate scoring
1:16:32.586986 PROGRESS: === Extracted 100203 precursors and 860655 fragments ===
1:16:32.587361 INFO: performing precursor FDR with 47 features
1:16:32.587399 INFO: Decoy channel: -1
1:16:32.587423 INFO: Competetive: True
1:16:32.615689 INFO: Setting torch num_threads to 2 for FDR classification task
1:16:34.090712 INFO: Test AUC: 0.560
1:16:34.090839 INFO: Train AUC: 0.581
1:16:34.090870 INFO: AUC difference: 3.55%
1:16:34.295988 INFO: Resetting torch num_threads to 100
1:16:34.298836 INFO: === FDR correction performed with classifier version 7 ===
1:16:34.299486 PROGRESS: ============================= Precursor FDR =============================
1:16:34.299581 PROGRESS: Total precursors accumulated: 357
1:16:34.299648 PROGRESS: Target precursors: 326 (91.32%)
1:16:34.299704 PROGRESS: Decoy precursors: 31 (8.68%)
1:16:34.299752 PROGRESS: 
1:16:34.299796 PROGRESS: Precursor Summary:
1:16:34.300735 PROGRESS: Channel   0:	 0.05 FDR:   282; 0.01 FDR:   171; 0.001 FDR:   171
1:16:34.300824 PROGRESS: 
1:16:34.300879 PROGRESS: Protein Summary:
1:16:34.301957 PROGRESS: Channel   0:	 0.05 FDR:   269; 0.01 FDR:   167; 0.001 FDR:   167
1:16:34.302049 PROGRESS: =========================================================================
1:16:34.425097 INFO: calibration group: precursor, predicting mz
1:16:34.425341 WARNING: mz prediction was skipped as it has not been fitted yet
1:16:34.425374 INFO: calibration group: precursor, predicting rt
1:16:34.457989 INFO: calibration group: fragment, predicting mz
1:16:34.528732 INFO: === skipping optimization until target number of precursors are found ===
1:16:34.529002 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
1:16:34.529072 INFO: Starting optimization step 13.
1:16:34.529150 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1:16:34.529218 PROGRESS: Extracting batch of 50588 precursors
1:16:34.545424 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:16:34.545540 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:16:34.545578 INFO: FWHM in RT is 2.62 seconds, sigma is 0.34
1:16:34.545606 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:16:34.545836 INFO: Starting candidate selection
1:16:36.986951 INFO: Starting candidate scoring
1:16:37.704483 INFO: Finished candidate processing
1:16:37.704616 INFO: Collecting candidate features
1:16:37.885621 INFO: Collecting fragment features
1:16:37.966486 INFO: Finished candidate scoring
1:16:38.094613 PROGRESS: === Extracted 201181 precursors and 1727339 fragments ===
1:16:38.127735 INFO: performing precursor FDR with 47 features
1:16:38.127920 INFO: Decoy channel: -1
1:16:38.127946 INFO: Competetive: True
1:16:38.237526 INFO: Setting torch num_threads to 2 for FDR classification task
1:16:42.884833 INFO: Test AUC: 0.564
1:16:42.885011 INFO: Train AUC: 0.582
1:16:42.885044 INFO: AUC difference: 3.12%
1:16:43.121758 INFO: Resetting torch num_threads to 100
1:16:43.130931 INFO: === FDR correction performed with classifier version 7 ===
1:16:43.131759 PROGRESS: ============================= Precursor FDR =============================
1:16:43.131876 PROGRESS: Total precursors accumulated: 840
1:16:43.131936 PROGRESS: Target precursors: 767 (91.31%)
1:16:43.131989 PROGRESS: Decoy precursors: 73 (8.69%)
1:16:43.132037 PROGRESS: 
1:16:43.132083 PROGRESS: Precursor Summary:
1:16:43.133176 PROGRESS: Channel   0:	 0.05 FDR:   653; 0.01 FDR:   453; 0.001 FDR:     1
1:16:43.133271 PROGRESS: 
1:16:43.133326 PROGRESS: Protein Summary:
1:16:43.134562 PROGRESS: Channel   0:	 0.05 FDR:   603; 0.01 FDR:   427; 0.001 FDR:     1
1:16:43.134668 PROGRESS: =========================================================================
1:16:43.267745 INFO: fragments_df: keeping 4956 of 1727339 [sum(precursor_idx_mask)=9841 sum(mass_error_mask)=1727339 stop_rank=4956
1:16:43.417136 INFO: calibration group: precursor, fitting rt estimator 
1:16:43.549153 INFO: calibration group: fragment, fitting mz estimator 
1:16:44.211734 INFO: Using score_cutoff 60.38921447753906 (fac=0.99, q=1)
1:16:44.212201 INFO: calibration group: precursor, predicting mz
1:16:44.212293 WARNING: mz prediction was skipped as it has not been fitted yet
1:16:44.212323 INFO: calibration group: precursor, predicting rt
1:16:44.244659 INFO: calibration group: fragment, predicting mz
1:16:44.313737 INFO: === checking if optimization conditions were reached ===
1:16:44.314023 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 2 ===
1:16:44.317042 PROGRESS: ❌ ms2_error      : optimization incomplete after 5 search(es). Will search with parameter 11.2649.
1:16:44.317107 INFO: ==============================================
1:16:44.317219 INFO: Starting optimization step 14.
1:16:44.317296 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:16:44.317376 PROGRESS: Extracting batch of 50212 precursors
1:16:44.332260 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:16:44.332367 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:16:44.332405 INFO: FWHM in RT is 2.58 seconds, sigma is 0.33
1:16:44.332427 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:16:44.332666 INFO: Starting candidate selection
1:16:46.763957 INFO: Starting candidate scoring
1:16:47.483159 INFO: Finished candidate processing
1:16:47.483254 INFO: Collecting candidate features
1:16:47.634264 INFO: Collecting fragment features
1:16:47.685999 INFO: Finished candidate scoring
1:16:47.733280 PROGRESS: === Extracted 100205 precursors and 842471 fragments ===
1:16:47.733682 INFO: performing precursor FDR with 47 features
1:16:47.733719 INFO: Decoy channel: -1
1:16:47.733746 INFO: Competetive: True
1:16:47.762956 INFO: Setting torch num_threads to 2 for FDR classification task
1:16:49.405133 INFO: Test AUC: 0.562
1:16:49.405254 INFO: Train AUC: 0.584
1:16:49.405289 INFO: AUC difference: 3.86%
1:16:49.607494 INFO: Resetting torch num_threads to 100
1:16:49.610487 INFO: === FDR correction performed with classifier version 7 ===
1:16:49.611169 PROGRESS: ============================= Precursor FDR =============================
1:16:49.611276 PROGRESS: Total precursors accumulated: 363
1:16:49.611349 PROGRESS: Target precursors: 332 (91.46%)
1:16:49.611414 PROGRESS: Decoy precursors: 31 (8.54%)
1:16:49.611472 PROGRESS: 
1:16:49.611530 PROGRESS: Precursor Summary:
1:16:49.612500 PROGRESS: Channel   0:	 0.05 FDR:   264; 0.01 FDR:   155; 0.001 FDR:   139
1:16:49.612604 PROGRESS: 
1:16:49.612672 PROGRESS: Protein Summary:
1:16:49.613801 PROGRESS: Channel   0:	 0.05 FDR:   252; 0.01 FDR:   150; 0.001 FDR:   135
1:16:49.613904 PROGRESS: =========================================================================
1:16:49.736898 INFO: calibration group: precursor, predicting mz
1:16:49.737165 WARNING: mz prediction was skipped as it has not been fitted yet
1:16:49.737207 INFO: calibration group: precursor, predicting rt
1:16:49.769548 INFO: calibration group: fragment, predicting mz
1:16:49.836273 INFO: === skipping optimization until target number of precursors are found ===
1:16:49.836543 PROGRESS: === Optimization of ms2_error has been skipped 1 time(s); maximum number is 1 ===
1:16:49.836608 INFO: Starting optimization step 15.
1:16:49.836687 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1:16:49.836756 PROGRESS: Extracting batch of 50588 precursors
1:16:49.853221 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:16:49.853334 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:16:49.853373 INFO: FWHM in RT is 2.58 seconds, sigma is 0.33
1:16:49.853401 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:16:49.853633 INFO: Starting candidate selection
1:16:52.304065 INFO: Starting candidate scoring
1:16:52.952964 INFO: Finished candidate processing
1:16:52.953097 INFO: Collecting candidate features
1:16:53.138018 INFO: Collecting fragment features
1:16:53.200447 INFO: Finished candidate scoring
1:16:53.327818 PROGRESS: === Extracted 201182 precursors and 1691150 fragments ===
1:16:53.360177 INFO: performing precursor FDR with 47 features
1:16:53.360363 INFO: Decoy channel: -1
1:16:53.360390 INFO: Competetive: True
1:16:53.465443 INFO: Setting torch num_threads to 2 for FDR classification task
1:16:58.642959 INFO: Test AUC: 0.562
1:16:58.643172 INFO: Train AUC: 0.584
1:16:58.643208 INFO: AUC difference: 3.79%
1:16:58.875904 INFO: Resetting torch num_threads to 100
1:16:58.885627 INFO: === FDR correction performed with classifier version 7 ===
1:16:58.886442 PROGRESS: ============================= Precursor FDR =============================
1:16:58.886561 PROGRESS: Total precursors accumulated: 857
1:16:58.886645 PROGRESS: Target precursors: 785 (91.60%)
1:16:58.886711 PROGRESS: Decoy precursors: 72 (8.40%)
1:16:58.886768 PROGRESS: 
1:16:58.886824 PROGRESS: Precursor Summary:
1:16:58.887951 PROGRESS: Channel   0:	 0.05 FDR:   633; 0.01 FDR:   435; 0.001 FDR:   272
1:16:58.888054 PROGRESS: 
1:16:58.888115 PROGRESS: Protein Summary:
1:16:58.889380 PROGRESS: Channel   0:	 0.05 FDR:   583; 0.01 FDR:   411; 0.001 FDR:   257
1:16:58.889480 PROGRESS: =========================================================================
1:16:59.017886 INFO: fragments_df: keeping 4756 of 1691150 [sum(precursor_idx_mask)=9405 sum(mass_error_mask)=1691150 stop_rank=4756
1:16:59.167239 INFO: calibration group: precursor, fitting rt estimator 
1:16:59.293313 INFO: calibration group: fragment, fitting mz estimator 
1:16:59.924903 INFO: Using score_cutoff 62.91312208786011 (fac=0.99, q=1)
1:16:59.925326 INFO: calibration group: precursor, predicting mz
1:16:59.925416 WARNING: mz prediction was skipped as it has not been fitted yet
1:16:59.925447 INFO: calibration group: precursor, predicting rt
1:16:59.958278 INFO: calibration group: fragment, predicting mz
1:17:00.026682 INFO: === checking if optimization conditions were reached ===
1:17:00.026968 PROGRESS: === Optimization of ms2_error has been performed 6 time(s); minimum number is 2 ===
1:17:00.029887 PROGRESS: ❌ ms2_error      : optimization incomplete after 6 search(es). Will search with parameter 9.9998.
1:17:00.029950 INFO: ==============================================
1:17:00.030064 INFO: Starting optimization step 16.
1:17:00.030139 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:17:00.030234 PROGRESS: Extracting batch of 50212 precursors
1:17:00.048198 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:17:00.048313 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:17:00.048360 INFO: FWHM in RT is 2.56 seconds, sigma is 0.33
1:17:00.048407 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:17:00.048692 INFO: Starting candidate selection
1:17:02.458683 INFO: Starting candidate scoring
1:17:03.119293 INFO: Finished candidate processing
1:17:03.119460 INFO: Collecting candidate features
1:17:03.271712 INFO: Collecting fragment features
1:17:03.322127 INFO: Finished candidate scoring
1:17:03.365881 PROGRESS: === Extracted 100189 precursors and 796996 fragments ===
1:17:03.366248 INFO: performing precursor FDR with 47 features
1:17:03.366285 INFO: Decoy channel: -1
1:17:03.366307 INFO: Competetive: True
1:17:03.394453 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:04.837369 INFO: Test AUC: 0.564
1:17:04.837495 INFO: Train AUC: 0.583
1:17:04.837524 INFO: AUC difference: 3.26%
1:17:05.039677 INFO: Resetting torch num_threads to 100
1:17:05.042523 INFO: === FDR correction performed with classifier version 7 ===
1:17:05.043194 PROGRESS: ============================= Precursor FDR =============================
1:17:05.043297 PROGRESS: Total precursors accumulated: 437
1:17:05.043355 PROGRESS: Target precursors: 398 (91.08%)
1:17:05.043407 PROGRESS: Decoy precursors: 39 (8.92%)
1:17:05.043458 PROGRESS: 
1:17:05.043501 PROGRESS: Precursor Summary:
1:17:05.044481 PROGRESS: Channel   0:	 0.05 FDR:   314; 0.01 FDR:   237; 0.001 FDR:   142
1:17:05.044572 PROGRESS: 
1:17:05.044632 PROGRESS: Protein Summary:
1:17:05.045727 PROGRESS: Channel   0:	 0.05 FDR:   301; 0.01 FDR:   226; 0.001 FDR:   139
1:17:05.045823 PROGRESS: =========================================================================
1:17:05.099233 INFO: fragments_df: keeping 2488 of 796996 [sum(precursor_idx_mask)=5043 sum(mass_error_mask)=796996 stop_rank=2488
1:17:05.222725 INFO: calibration group: precursor, fitting rt estimator 
1:17:05.320123 INFO: calibration group: fragment, fitting mz estimator 
1:17:05.594415 INFO: Using score_cutoff 55.69716993255615 (fac=0.99, q=1)
1:17:05.594807 INFO: calibration group: precursor, predicting mz
1:17:05.594897 WARNING: mz prediction was skipped as it has not been fitted yet
1:17:05.594928 INFO: calibration group: precursor, predicting rt
1:17:05.627288 INFO: calibration group: fragment, predicting mz
1:17:05.695075 INFO: === checking if optimization conditions were reached ===
1:17:05.695303 PROGRESS: === Optimization of ms2_error has been performed 7 time(s); minimum number is 2 ===
1:17:05.697390 PROGRESS: ❌ ms2_error      : optimization incomplete after 7 search(es). Will search with parameter 8.1373.
1:17:05.697445 INFO: ==============================================
1:17:05.697536 INFO: Starting optimization step 17.
1:17:05.697601 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:17:05.697660 PROGRESS: Extracting batch of 50212 precursors
1:17:05.709299 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:17:05.709406 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:17:05.709439 INFO: FWHM in RT is 2.48 seconds, sigma is 0.32
1:17:05.709461 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:17:05.709709 INFO: Starting candidate selection
1:17:08.181402 INFO: Starting candidate scoring
1:17:08.817755 INFO: Finished candidate processing
1:17:08.817859 INFO: Collecting candidate features
1:17:08.966774 INFO: Collecting fragment features
1:17:09.016633 INFO: Finished candidate scoring
1:17:09.061179 PROGRESS: === Extracted 100195 precursors and 775109 fragments ===
1:17:09.061536 INFO: performing precursor FDR with 47 features
1:17:09.061573 INFO: Decoy channel: -1
1:17:09.061596 INFO: Competetive: True
1:17:09.089437 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:10.645315 INFO: Test AUC: 0.555
1:17:10.645439 INFO: Train AUC: 0.585
1:17:10.645469 INFO: AUC difference: 5.12%
1:17:10.645492 WARNING: AUC difference > 5%. This may indicate overfitting.
1:17:10.849950 INFO: Resetting torch num_threads to 100
1:17:10.852803 INFO: === FDR correction performed with classifier version 7 ===
1:17:10.853460 PROGRESS: ============================= Precursor FDR =============================
1:17:10.853569 PROGRESS: Total precursors accumulated: 446
1:17:10.853631 PROGRESS: Target precursors: 404 (90.58%)
1:17:10.853683 PROGRESS: Decoy precursors: 42 (9.42%)
1:17:10.853730 PROGRESS: 
1:17:10.853773 PROGRESS: Precursor Summary:
1:17:10.854768 PROGRESS: Channel   0:	 0.05 FDR:   341; 0.01 FDR:   220; 0.001 FDR:   145
1:17:10.854862 PROGRESS: 
1:17:10.854916 PROGRESS: Protein Summary:
1:17:10.856020 PROGRESS: Channel   0:	 0.05 FDR:   326; 0.01 FDR:   210; 0.001 FDR:   143
1:17:10.856113 PROGRESS: =========================================================================
1:17:10.907379 INFO: fragments_df: keeping 2365 of 775109 [sum(precursor_idx_mask)=4651 sum(mass_error_mask)=775109 stop_rank=2365
1:17:11.030919 INFO: calibration group: precursor, fitting rt estimator 
1:17:11.147788 INFO: calibration group: fragment, fitting mz estimator 
1:17:11.469414 INFO: Using score_cutoff 56.5950090763092 (fac=0.99, q=1)
1:17:11.469809 INFO: calibration group: precursor, predicting mz
1:17:11.469896 WARNING: mz prediction was skipped as it has not been fitted yet
1:17:11.469929 INFO: calibration group: precursor, predicting rt
1:17:11.502456 INFO: calibration group: fragment, predicting mz
1:17:11.573599 INFO: === checking if optimization conditions were reached ===
1:17:11.573869 PROGRESS: === Optimization of ms2_error has been performed 8 time(s); minimum number is 2 ===
1:17:11.576404 PROGRESS: ❌ ms2_error      : optimization incomplete after 8 search(es). Will search with parameter 7.5688.
1:17:11.576469 INFO: ==============================================
1:17:11.576586 INFO: Starting optimization step 18.
1:17:11.576665 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:17:11.576749 PROGRESS: Extracting batch of 50212 precursors
1:17:11.591211 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:17:11.591320 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:17:11.591353 INFO: FWHM in RT is 2.47 seconds, sigma is 0.32
1:17:11.591376 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:17:11.591567 INFO: Starting candidate selection
1:17:14.119209 INFO: Starting candidate scoring
1:17:14.843214 INFO: Finished candidate processing
1:17:14.843323 INFO: Collecting candidate features
1:17:14.995426 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 100169)
1:17:15.004487 INFO: Collecting fragment features
1:17:15.055564 INFO: Finished candidate scoring
1:17:15.103685 PROGRESS: === Extracted 100169 precursors and 745084 fragments ===
1:17:15.104138 INFO: performing precursor FDR with 47 features
1:17:15.104176 INFO: Decoy channel: -1
1:17:15.104201 INFO: Competetive: True
1:17:15.132762 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:15.147902 WARNING: dropped 1 target PSMs due to missing features
1:17:16.613317 INFO: Test AUC: 0.560
1:17:16.613461 INFO: Train AUC: 0.583
1:17:16.613492 INFO: AUC difference: 3.85%
1:17:16.823108 INFO: Resetting torch num_threads to 100
1:17:16.826084 INFO: === FDR correction performed with classifier version 7 ===
1:17:16.826757 PROGRESS: ============================= Precursor FDR =============================
1:17:16.826855 PROGRESS: Total precursors accumulated: 484
1:17:16.826915 PROGRESS: Target precursors: 440 (90.91%)
1:17:16.826967 PROGRESS: Decoy precursors: 44 (9.09%)
1:17:16.827014 PROGRESS: 
1:17:16.827060 PROGRESS: Precursor Summary:
1:17:16.828019 PROGRESS: Channel   0:	 0.05 FDR:   373; 0.01 FDR:   220; 0.001 FDR:   143
1:17:16.828109 PROGRESS: 
1:17:16.828165 PROGRESS: Protein Summary:
1:17:16.829274 PROGRESS: Channel   0:	 0.05 FDR:   358; 0.01 FDR:   211; 0.001 FDR:   139
1:17:16.829370 PROGRESS: =========================================================================
1:17:16.879241 INFO: fragments_df: keeping 2367 of 745084 [sum(precursor_idx_mask)=4564 sum(mass_error_mask)=745084 stop_rank=2367
1:17:17.002076 INFO: calibration group: precursor, fitting rt estimator 
1:17:17.111820 INFO: calibration group: fragment, fitting mz estimator 
1:17:17.424212 INFO: Using score_cutoff 55.87506867713928 (fac=0.99, q=1)
1:17:17.424626 INFO: calibration group: precursor, predicting mz
1:17:17.424715 WARNING: mz prediction was skipped as it has not been fitted yet
1:17:17.424746 INFO: calibration group: precursor, predicting rt
1:17:17.457083 INFO: calibration group: fragment, predicting mz
1:17:17.526064 INFO: === checking if optimization conditions were reached ===
1:17:17.526306 PROGRESS: === Optimization of ms2_error has been performed 9 time(s); minimum number is 2 ===
1:17:17.528401 PROGRESS: ❌ ms2_error      : optimization incomplete after 9 search(es). Will search with parameter 6.4981.
1:17:17.528455 INFO: ==============================================
1:17:17.528553 INFO: Starting optimization step 19.
1:17:17.528620 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:17:17.528688 PROGRESS: Extracting batch of 50212 precursors
1:17:17.540618 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:17:17.540720 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:17:17.540758 INFO: FWHM in RT is 2.47 seconds, sigma is 0.32
1:17:17.540780 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:17:17.541012 INFO: Starting candidate selection
1:17:20.004350 INFO: Starting candidate scoring
1:17:20.678930 INFO: Finished candidate processing
1:17:20.679027 INFO: Collecting candidate features
1:17:20.823180 INFO: Collecting fragment features
1:17:20.871533 INFO: Finished candidate scoring
1:17:20.928184 PROGRESS: === Extracted 100161 precursors and 712707 fragments ===
1:17:20.928569 INFO: performing precursor FDR with 47 features
1:17:20.928606 INFO: Decoy channel: -1
1:17:20.928630 INFO: Competetive: True
1:17:20.954448 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:22.473607 INFO: Test AUC: 0.567
1:17:22.473734 INFO: Train AUC: 0.581
1:17:22.473763 INFO: AUC difference: 2.48%
1:17:22.679764 INFO: Resetting torch num_threads to 100
1:17:22.682663 INFO: === FDR correction performed with classifier version 7 ===
1:17:22.683316 PROGRESS: ============================= Precursor FDR =============================
1:17:22.683419 PROGRESS: Total precursors accumulated: 458
1:17:22.683480 PROGRESS: Target precursors: 418 (91.27%)
1:17:22.683533 PROGRESS: Decoy precursors: 40 (8.73%)
1:17:22.683580 PROGRESS: 
1:17:22.683624 PROGRESS: Precursor Summary:
1:17:22.684617 PROGRESS: Channel   0:	 0.05 FDR:   370; 0.01 FDR:   250; 0.001 FDR:   178
1:17:22.684710 PROGRESS: 
1:17:22.684766 PROGRESS: Protein Summary:
1:17:22.685879 PROGRESS: Channel   0:	 0.05 FDR:   356; 0.01 FDR:   239; 0.001 FDR:   173
1:17:22.685972 PROGRESS: =========================================================================
1:17:22.734104 INFO: fragments_df: keeping 2563 of 712707 [sum(precursor_idx_mask)=5094 sum(mass_error_mask)=712707 stop_rank=2563
1:17:22.859084 INFO: calibration group: precursor, fitting rt estimator 
1:17:22.975937 INFO: calibration group: fragment, fitting mz estimator 
1:17:23.315106 INFO: Using score_cutoff 54.369874103164676 (fac=0.99, q=1)
1:17:23.315483 INFO: calibration group: precursor, predicting mz
1:17:23.315567 WARNING: mz prediction was skipped as it has not been fitted yet
1:17:23.315597 INFO: calibration group: precursor, predicting rt
1:17:23.347963 INFO: calibration group: fragment, predicting mz
1:17:23.417082 INFO: === checking if optimization conditions were reached ===
1:17:23.417316 PROGRESS: === Optimization of ms2_error has been performed 10 time(s); minimum number is 2 ===
1:17:23.419399 PROGRESS: ❌ ms2_error      : optimization incomplete after 10 search(es). Will search with parameter 5.8637.
1:17:23.419456 INFO: ==============================================
1:17:23.419541 WARNING: Optimization did not converge within the maximum number of steps, which is 20.
1:17:23.419648 INFO: Starting optimization step 0.
1:17:23.419713 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:17:23.419769 PROGRESS: Extracting batch of 50212 precursors
1:17:23.431609 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:17:23.431716 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:17:23.431763 INFO: FWHM in RT is 2.37 seconds, sigma is 0.31
1:17:23.431786 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:17:23.432019 INFO: Starting candidate selection
1:17:25.833705 INFO: Starting candidate scoring
1:17:26.480478 INFO: Finished candidate processing
1:17:26.480666 INFO: Collecting candidate features
1:17:26.689374 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 100074)
1:17:26.699069 INFO: Collecting fragment features
1:17:26.772697 INFO: Finished candidate scoring
1:17:26.837506 PROGRESS: === Extracted 100074 precursors and 670310 fragments ===
1:17:26.837886 INFO: performing precursor FDR with 47 features
1:17:26.837922 INFO: Decoy channel: -1
1:17:26.837947 INFO: Competetive: True
1:17:26.879168 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:26.902581 WARNING: dropped 3 target PSMs due to missing features
1:17:26.902709 WARNING: dropped 1 decoy PSMs due to missing features
1:17:28.262241 INFO: Test AUC: 0.559
1:17:28.262435 INFO: Train AUC: 0.581
1:17:28.262465 INFO: AUC difference: 3.67%
1:17:28.470381 INFO: Resetting torch num_threads to 100
1:17:28.473310 INFO: === FDR correction performed with classifier version 7 ===
1:17:28.474010 PROGRESS: ============================= Precursor FDR =============================
1:17:28.474115 PROGRESS: Total precursors accumulated: 482
1:17:28.474175 PROGRESS: Target precursors: 440 (91.29%)
1:17:28.474225 PROGRESS: Decoy precursors: 42 (8.71%)
1:17:28.474277 PROGRESS: 
1:17:28.474321 PROGRESS: Precursor Summary:
1:17:28.475305 PROGRESS: Channel   0:	 0.05 FDR:   349; 0.01 FDR:   243; 0.001 FDR:   165
1:17:28.475399 PROGRESS: 
1:17:28.475455 PROGRESS: Protein Summary:
1:17:28.476556 PROGRESS: Channel   0:	 0.05 FDR:   333; 0.01 FDR:   233; 0.001 FDR:   161
1:17:28.476656 PROGRESS: =========================================================================
1:17:28.521624 INFO: fragments_df: keeping 2501 of 670310 [sum(precursor_idx_mask)=4892 sum(mass_error_mask)=670310 stop_rank=2501
1:17:28.653473 INFO: calibration group: precursor, fitting rt estimator 
1:17:28.766707 INFO: calibration group: fragment, fitting mz estimator 
1:17:29.094840 INFO: Using score_cutoff 57.43170164108276 (fac=0.99, q=1)
1:17:29.095258 INFO: calibration group: precursor, predicting mz
1:17:29.095347 WARNING: mz prediction was skipped as it has not been fitted yet
1:17:29.095377 INFO: calibration group: precursor, predicting rt
1:17:29.127801 INFO: calibration group: fragment, predicting mz
1:17:29.197991 INFO: === checking if optimization conditions were reached ===
1:17:29.198293 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:17:29.200391 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 104.7874.
1:17:29.200454 INFO: ==============================================
1:17:29.200563 INFO: Starting optimization step 1.
1:17:29.200641 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:17:29.200721 PROGRESS: Extracting batch of 50212 precursors
1:17:29.218304 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:17:29.218428 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:17:29.218471 INFO: FWHM in RT is 2.34 seconds, sigma is 0.30
1:17:29.218498 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:17:29.218809 INFO: Starting candidate selection
1:17:34.504449 INFO: Starting candidate scoring
1:17:35.144895 INFO: Finished candidate processing
1:17:35.145032 INFO: Collecting candidate features
1:17:35.284215 WARNING: intensity_correlation has 38 NaNs ( 0.04 % out of 96914)
1:17:35.290642 INFO: Collecting fragment features
1:17:35.333381 INFO: Finished candidate scoring
1:17:35.375761 PROGRESS: === Extracted 96914 precursors and 541931 fragments ===
1:17:35.376124 INFO: performing precursor FDR with 47 features
1:17:35.376160 INFO: Decoy channel: -1
1:17:35.376183 INFO: Competetive: True
1:17:35.402950 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:35.420331 WARNING: dropped 19 target PSMs due to missing features
1:17:35.420457 WARNING: dropped 19 decoy PSMs due to missing features
1:17:36.774751 INFO: Test AUC: 0.552
1:17:36.774871 INFO: Train AUC: 0.570
1:17:36.774900 INFO: AUC difference: 3.11%
1:17:36.980965 INFO: Resetting torch num_threads to 100
1:17:36.984735 INFO: === FDR correction performed with classifier version 7 ===
1:17:36.986107 PROGRESS: ============================= Precursor FDR =============================
1:17:36.986206 PROGRESS: Total precursors accumulated: 518
1:17:36.986265 PROGRESS: Target precursors: 474 (91.51%)
1:17:36.986320 PROGRESS: Decoy precursors: 44 (8.49%)
1:17:36.986367 PROGRESS: 
1:17:36.986411 PROGRESS: Precursor Summary:
1:17:36.987407 PROGRESS: Channel   0:	 0.05 FDR:   395; 0.01 FDR:   272; 0.001 FDR:   167
1:17:36.987502 PROGRESS: 
1:17:36.987559 PROGRESS: Protein Summary:
1:17:36.988683 PROGRESS: Channel   0:	 0.05 FDR:   375; 0.01 FDR:   262; 0.001 FDR:   162
1:17:36.988776 PROGRESS: =========================================================================
1:17:37.028097 INFO: fragments_df: keeping 2676 of 541931 [sum(precursor_idx_mask)=5389 sum(mass_error_mask)=541931 stop_rank=2676
1:17:37.181096 INFO: calibration group: precursor, fitting rt estimator 
1:17:37.295044 INFO: calibration group: fragment, fitting mz estimator 
1:17:37.647067 INFO: Using score_cutoff 54.15372109451294 (fac=0.99, q=1)
1:17:37.647447 INFO: calibration group: precursor, predicting mz
1:17:37.647534 WARNING: mz prediction was skipped as it has not been fitted yet
1:17:37.647565 INFO: calibration group: precursor, predicting rt
1:17:37.679744 INFO: calibration group: fragment, predicting mz
1:17:37.752199 INFO: === checking if optimization conditions were reached ===
1:17:37.752434 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:17:37.754292 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 72.7293.
1:17:37.754347 INFO: ==============================================
1:17:37.754454 INFO: Starting optimization step 2.
1:17:37.754521 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:17:37.754581 PROGRESS: Extracting batch of 50212 precursors
1:17:37.811085 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:17:37.811192 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:17:37.811230 INFO: FWHM in RT is 2.31 seconds, sigma is 0.30
1:17:37.811256 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:17:37.811448 INFO: Starting candidate selection
1:17:39.266475 INFO: Starting candidate scoring
1:17:39.959950 INFO: Finished candidate processing
1:17:39.960053 INFO: Collecting candidate features
1:17:40.104347 WARNING: intensity_correlation has 45 NaNs ( 0.05 % out of 95692)
1:17:40.114227 INFO: Collecting fragment features
1:17:40.157345 INFO: Finished candidate scoring
1:17:40.198382 PROGRESS: === Extracted 95692 precursors and 516880 fragments ===
1:17:40.198829 INFO: performing precursor FDR with 47 features
1:17:40.198870 INFO: Decoy channel: -1
1:17:40.198894 INFO: Competetive: True
1:17:40.224901 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:40.242481 WARNING: dropped 22 target PSMs due to missing features
1:17:40.242610 WARNING: dropped 23 decoy PSMs due to missing features
1:17:41.648610 INFO: Test AUC: 0.546
1:17:41.648731 INFO: Train AUC: 0.576
1:17:41.648762 INFO: AUC difference: 5.20%
1:17:41.648784 WARNING: AUC difference > 5%. This may indicate overfitting.
1:17:41.851685 INFO: Resetting torch num_threads to 100
1:17:41.854517 INFO: === FDR correction performed with classifier version 7 ===
1:17:41.855211 PROGRESS: ============================= Precursor FDR =============================
1:17:41.855308 PROGRESS: Total precursors accumulated: 531
1:17:41.855369 PROGRESS: Target precursors: 487 (91.71%)
1:17:41.855420 PROGRESS: Decoy precursors: 44 (8.29%)
1:17:41.855467 PROGRESS: 
1:17:41.855512 PROGRESS: Precursor Summary:
1:17:41.856520 PROGRESS: Channel   0:	 0.05 FDR:   417; 0.01 FDR:   351; 0.001 FDR:   282
1:17:41.856620 PROGRESS: 
1:17:41.856676 PROGRESS: Protein Summary:
1:17:41.857853 PROGRESS: Channel   0:	 0.05 FDR:   395; 0.01 FDR:   334; 0.001 FDR:   271
1:17:41.857962 PROGRESS: =========================================================================
1:17:41.893353 INFO: fragments_df: keeping 3141 of 516880 [sum(precursor_idx_mask)=6768 sum(mass_error_mask)=516880 stop_rank=3141
1:17:42.017751 INFO: calibration group: precursor, fitting rt estimator 
1:17:42.144701 INFO: calibration group: fragment, fitting mz estimator 
1:17:42.552315 INFO: Using score_cutoff 44.5724232673645 (fac=0.99, q=1)
1:17:42.552721 INFO: calibration group: precursor, predicting mz
1:17:42.552809 WARNING: mz prediction was skipped as it has not been fitted yet
1:17:42.552839 INFO: calibration group: precursor, predicting rt
1:17:42.585608 INFO: calibration group: fragment, predicting mz
1:17:42.656166 INFO: === checking if optimization conditions were reached ===
1:17:42.656445 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:17:42.658799 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 74.9789.
1:17:42.658861 INFO: ==============================================
1:17:42.658968 INFO: Starting optimization step 3.
1:17:42.659042 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:17:42.659118 PROGRESS: Extracting batch of 50212 precursors
1:17:42.673990 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:17:42.674104 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:17:42.674140 INFO: FWHM in RT is 2.25 seconds, sigma is 0.29
1:17:42.674162 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:17:42.674389 INFO: Starting candidate selection
1:17:44.110339 INFO: Starting candidate scoring
1:17:44.736173 INFO: Finished candidate processing
1:17:44.736310 INFO: Collecting candidate features
1:17:44.868403 WARNING: intensity_correlation has 47 NaNs ( 0.05 % out of 96042)
1:17:44.877095 INFO: Collecting fragment features
1:17:44.918652 INFO: Finished candidate scoring
1:17:44.956573 PROGRESS: === Extracted 96042 precursors and 520735 fragments ===
1:17:44.956943 INFO: performing precursor FDR with 47 features
1:17:44.956980 INFO: Decoy channel: -1
1:17:44.957003 INFO: Competetive: True
1:17:44.982936 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:44.999621 WARNING: dropped 22 target PSMs due to missing features
1:17:44.999745 WARNING: dropped 25 decoy PSMs due to missing features
1:17:46.813123 INFO: Test AUC: 0.553
1:17:46.813686 INFO: Train AUC: 0.571
1:17:46.813720 INFO: AUC difference: 3.28%
1:17:47.016040 INFO: Resetting torch num_threads to 100
1:17:47.019176 INFO: === FDR correction performed with classifier version 7 ===
1:17:47.019855 PROGRESS: ============================= Precursor FDR =============================
1:17:47.019951 PROGRESS: Total precursors accumulated: 527
1:17:47.020015 PROGRESS: Target precursors: 483 (91.65%)
1:17:47.020069 PROGRESS: Decoy precursors: 44 (8.35%)
1:17:47.020116 PROGRESS: 
1:17:47.020159 PROGRESS: Precursor Summary:
1:17:47.021172 PROGRESS: Channel   0:	 0.05 FDR:   418; 0.01 FDR:   344; 0.001 FDR:   282
1:17:47.021263 PROGRESS: 
1:17:47.021320 PROGRESS: Protein Summary:
1:17:47.022485 PROGRESS: Channel   0:	 0.05 FDR:   396; 0.01 FDR:   327; 0.001 FDR:   271
1:17:47.022578 PROGRESS: =========================================================================
1:17:47.059443 INFO: fragments_df: keeping 3080 of 520735 [sum(precursor_idx_mask)=6640 sum(mass_error_mask)=520735 stop_rank=3080
1:17:47.180471 INFO: calibration group: precursor, fitting rt estimator 
1:17:47.302133 INFO: calibration group: fragment, fitting mz estimator 
1:17:47.703617 INFO: Using score_cutoff 46.18787241439819 (fac=0.99, q=1)
1:17:47.703999 INFO: calibration group: precursor, predicting mz
1:17:47.704085 WARNING: mz prediction was skipped as it has not been fitted yet
1:17:47.704114 INFO: calibration group: precursor, predicting rt
1:17:47.736931 INFO: calibration group: fragment, predicting mz
1:17:47.808342 INFO: === checking if optimization conditions were reached ===
1:17:47.808573 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:17:47.809698 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 72.7293 found after 4 searches.
1:17:47.809749 INFO: ==============================================
1:17:47.810420 PROGRESS: Optimization finished for rt_error.
1:17:47.929113 INFO: calibration group: precursor, predicting mz
1:17:47.929356 WARNING: mz prediction was skipped as it has not been fitted yet
1:17:47.929390 INFO: calibration group: precursor, predicting rt
1:17:47.962420 INFO: calibration group: fragment, predicting mz
1:17:48.060389 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:17:48.060589 PROGRESS: ==============================================
1:17:48.060663 PROGRESS: ms2_error      : 5.8637
1:17:48.060719 PROGRESS: rt_error       : 72.7293
1:17:48.060769 PROGRESS: ==============================================
1:17:48.061456 INFO: calibration group: precursor, predicting mz
1:17:48.061541 WARNING: mz prediction was skipped as it has not been fitted yet
1:17:48.061569 INFO: calibration group: precursor, predicting rt
1:17:54.944551 INFO: calibration group: fragment, predicting mz
1:18:10.556035 PROGRESS: Extracting batch of 10183864 precursors
1:18:12.769251 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:18:12.769383 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:18:12.769422 INFO: FWHM in RT is 2.25 seconds, sigma is 0.29
1:18:12.769445 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:18:12.769822 INFO: Starting candidate selection
1:22:53.922537 INFO: Applying score cutoff of 44.5724232673645
1:22:54.029079 INFO: Removed 18222377 precursors with score below cutoff
1:22:56.206314 INFO: Starting candidate scoring
1:23:11.129072 INFO: Finished candidate processing
1:23:11.129362 INFO: Collecting candidate features
1:23:16.776856 WARNING: intensity_correlation has 6 NaNs ( 0.00 % out of 2073935)
1:23:16.844515 INFO: Collecting fragment features
1:23:18.636899 INFO: Finished candidate scoring
1:23:20.676033 INFO: === FDR correction performed with classifier version 22 ===
1:23:20.679042 INFO: performing precursor FDR with 47 features
1:23:20.679111 INFO: Decoy channel: -1
1:23:20.679138 INFO: Competetive: True
1:23:21.295105 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:21.682768 WARNING: dropped 5 target PSMs due to missing features
1:23:21.682901 WARNING: dropped 1 decoy PSMs due to missing features
1:23:56.912118 INFO: Test AUC: 0.627
1:23:56.912338 INFO: Train AUC: 0.632
1:23:56.912373 INFO: AUC difference: 0.79%
1:23:57.628072 INFO: Resetting torch num_threads to 100
1:23:57.687809 INFO: Removing fragments below FDR threshold
1:23:57.901232 PROGRESS: ============================= Precursor FDR =============================
1:23:57.901514 PROGRESS: Total precursors accumulated: 77,843
1:23:57.901587 PROGRESS: Target precursors: 77,073 (99.01%)
1:23:57.901641 PROGRESS: Decoy precursors: 770 (0.99%)
1:23:57.901691 PROGRESS: 
1:23:57.901738 PROGRESS: Precursor Summary:
1:23:57.933139 PROGRESS: Channel   0:	 0.05 FDR: 77,073; 0.01 FDR: 77,073; 0.001 FDR: 56,644
1:23:57.933374 PROGRESS: 
1:23:57.933438 PROGRESS: Protein Summary:
1:23:57.977641 PROGRESS: Channel   0:	 0.05 FDR: 11,373; 0.01 FDR: 11,373; 0.001 FDR: 8,996
1:23:57.977874 PROGRESS: =========================================================================
1:23:58.586332 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:24:21.857835 PROGRESS: Processing search outputs
1:24:21.858064 PROGRESS: Performing protein grouping and FDR
1:24:21.858106 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:24:21.911951 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:24:21.940656 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:24:21.967707 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:24:22.004589 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:24:22.047170 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:24:22.094835 INFO: Building combined output
1:24:22.485243 INFO: Performing protein inference
1:24:22.963028 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
1:24:53.663056 INFO: Performing protein FDR
1:24:58.345090 INFO: Normalizing q-values using 15,627 targets and 3,547 decoys
1:24:58.356907 INFO: Test AUC: 0.877
1:24:58.356966 INFO: Train AUC: 0.873
1:24:58.356996 INFO: AUC difference: 0.48%
1:24:58.963129 PROGRESS: ================ Protein FDR =================
1:24:58.963267 PROGRESS: Unique protein groups in output
1:24:58.963296 PROGRESS:   1% protein FDR: 9,923
1:24:58.963318 PROGRESS: 
1:24:58.963336 PROGRESS: Unique precursor in output
1:24:58.963354 PROGRESS:   1% protein FDR: 110,515
1:24:58.963373 PROGRESS: ================================================
1:24:59.034770 PROGRESS: Building search statistics
1:24:59.152642 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
1:24:59.152853 INFO: Initializing OptimizationManager
1:24:59.153133 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
1:24:59.153219 INFO: Initializing CalibrationManager
1:24:59.153444 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
1:24:59.153522 INFO: Initializing RawFileManager
1:24:59.186182 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
1:24:59.186373 INFO: Initializing OptimizationManager
1:24:59.186586 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
1:24:59.186677 INFO: Initializing CalibrationManager
1:24:59.186863 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
1:24:59.186939 INFO: Initializing RawFileManager
1:24:59.222784 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
1:24:59.222933 INFO: Initializing OptimizationManager
1:24:59.223133 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
1:24:59.223214 INFO: Initializing CalibrationManager
1:24:59.223397 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
1:24:59.223475 INFO: Initializing RawFileManager
1:24:59.255716 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
1:24:59.255905 INFO: Initializing OptimizationManager
1:24:59.256110 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
1:24:59.256187 INFO: Initializing CalibrationManager
1:24:59.256377 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
1:24:59.256449 INFO: Initializing RawFileManager
1:24:59.288429 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
1:24:59.289165 INFO: Initializing OptimizationManager
1:24:59.289391 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
1:24:59.289471 INFO: Initializing CalibrationManager
1:24:59.289676 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
1:24:59.289753 INFO: Initializing RawFileManager
1:24:59.322966 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
1:24:59.323111 INFO: Initializing OptimizationManager
1:24:59.323303 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
1:24:59.323376 INFO: Initializing CalibrationManager
1:24:59.323575 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
1:24:59.323650 INFO: Initializing RawFileManager
1:24:59.326621 INFO: Writing stat output to disk
1:24:59.326702 INFO: Saving run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/stat.tsv to disk
1:24:59.335825 PROGRESS: Building internal statistics
1:24:59.336131 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
1:24:59.336177 INFO: Initializing TimingManager
1:24:59.336543 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
1:24:59.336590 INFO: Initializing TimingManager
1:24:59.336779 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
1:24:59.336819 INFO: Initializing TimingManager
1:24:59.336987 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
1:24:59.337024 INFO: Initializing TimingManager
1:24:59.337179 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
1:24:59.337214 INFO: Initializing TimingManager
1:24:59.337369 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
1:24:59.337405 INFO: Initializing TimingManager
1:24:59.337801 INFO: Writing internal output to disk
1:24:59.337847 INFO: Saving run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/internal.tsv to disk
1:24:59.338345 PROGRESS: Performing label free quantification
1:24:59.425249 INFO: Accumulating fragment data
1:24:59.425404 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:24:59.669590 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:25:00.835792 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:25:02.026689 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:25:03.316588 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:25:04.639583 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:25:06.297005 PROGRESS: Performing label free quantification on the precursor level
1:25:06.297137 INFO: Filtering fragments by quality
1:25:06.634379 INFO: Performing label-free quantification using directLFQ
1:25:08.285328 INFO: 110515 lfq-groups total
1:25:50.785919 INFO: using 100 processes
1:25:50.987998 INFO: lfq-object 0
1:25:51.077725 INFO: lfq-object 300
1:25:51.080817 INFO: lfq-object 100
1:25:51.169540 INFO: lfq-object 600
1:25:51.177205 INFO: lfq-object 400
1:25:51.192812 INFO: lfq-object 200
1:25:51.275666 INFO: lfq-object 700
1:25:51.280467 INFO: lfq-object 500
1:25:51.282710 INFO: lfq-object 900
1:25:51.338668 INFO: lfq-object 1400
1:25:51.349069 INFO: lfq-object 1200
1:25:51.375800 INFO: lfq-object 800
1:25:51.384944 INFO: lfq-object 1000
1:25:51.429107 INFO: lfq-object 1700
1:25:51.436049 INFO: lfq-object 1500
1:25:51.449270 INFO: lfq-object 1300
1:25:51.484227 INFO: lfq-object 1100
1:25:51.527884 INFO: lfq-object 1800
1:25:51.535437 INFO: lfq-object 1600
1:25:51.547282 INFO: lfq-object 2000
1:25:51.629058 INFO: lfq-object 1900
1:25:51.653541 INFO: lfq-object 2100
1:25:51.701387 INFO: lfq-object 2300
1:25:51.753115 INFO: lfq-object 2200
1:25:51.766688 INFO: lfq-object 2500
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1:25:52.057605 INFO: lfq-object 3100
1:25:52.092281 INFO: lfq-object 3000
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1:25:52.224453 INFO: lfq-object 3400
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1:25:52.698304 INFO: lfq-object 5000
1:25:52.698905 INFO: lfq-object 4800
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1:25:53.137870 INFO: lfq-object 6000
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1:25:53.385068 INFO: lfq-object 7000
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1:25:53.472789 INFO: lfq-object 7300
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1:26:55.788472 INFO: lfq-object 108700
1:26:55.813765 INFO: lfq-object 108900
1:26:55.888587 INFO: lfq-object 108800
1:26:55.913348 INFO: lfq-object 109000
1:26:55.931008 INFO: lfq-object 109200
1:26:56.009452 INFO: lfq-object 109100
1:26:56.030984 INFO: lfq-object 109300
1:26:56.068453 INFO: lfq-object 109500
1:26:56.118990 INFO: lfq-object 109700
1:26:56.130785 INFO: lfq-object 109400
1:26:56.167322 INFO: lfq-object 109600
1:26:56.209395 INFO: lfq-object 109800
1:26:56.260389 INFO: lfq-object 110000
1:26:56.309525 INFO: lfq-object 109900
1:26:56.359442 INFO: lfq-object 110100
1:26:56.401160 INFO: lfq-object 110300
1:26:56.458448 INFO: lfq-object 110200
1:26:56.498393 INFO: lfq-object 110400
1:26:56.605518 INFO: lfq-object 110500
1:27:02.063122 INFO: Writing precursor output to disk
1:27:02.063538 INFO: Saving run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/precursor.matrix.tsv to disk
1:27:02.533751 PROGRESS: Performing label free quantification on the pg level
1:27:02.533863 INFO: Filtering fragments by quality
1:27:02.927295 INFO: Performing label-free quantification using directLFQ
1:27:03.271648 INFO: 9923 lfq-groups total
1:27:27.518436 INFO: using 100 processes
1:27:27.622704 INFO: lfq-object 0
1:27:27.651998 INFO: lfq-object 100
1:27:27.687801 INFO: lfq-object 200
1:27:27.718322 INFO: lfq-object 300
1:27:27.771914 INFO: lfq-object 400
1:27:27.801787 INFO: lfq-object 500
1:27:27.834513 INFO: lfq-object 600
1:27:27.872008 INFO: lfq-object 700
1:27:27.936668 INFO: lfq-object 900
1:27:27.990026 INFO: lfq-object 1000
1:27:28.054361 INFO: lfq-object 1100
1:27:28.083729 INFO: lfq-object 800
1:27:28.111929 INFO: lfq-object 1200
1:27:28.175882 INFO: lfq-object 1300
1:27:28.201715 INFO: lfq-object 1400
1:27:28.241199 INFO: lfq-object 1500
1:27:28.305161 INFO: lfq-object 1600
1:27:28.341286 INFO: lfq-object 1700
1:27:28.383050 INFO: lfq-object 1800
1:27:28.442557 INFO: lfq-object 1900
1:27:28.486306 INFO: lfq-object 2000
1:27:28.531241 INFO: lfq-object 2100
1:27:28.586741 INFO: lfq-object 2200
1:27:28.640496 INFO: lfq-object 2300
1:27:28.675806 INFO: lfq-object 2400
1:27:28.699719 INFO: lfq-object 2500
1:27:28.731563 INFO: lfq-object 2600
1:27:28.768881 INFO: lfq-object 2700
1:27:28.806738 INFO: lfq-object 2800
1:27:28.845716 INFO: lfq-object 2900
1:27:28.891253 INFO: lfq-object 3000
1:27:28.954452 INFO: lfq-object 3100
1:27:28.997764 INFO: lfq-object 3200
1:27:29.041899 INFO: lfq-object 3300
1:27:29.107395 INFO: lfq-object 3400
1:27:29.177700 INFO: lfq-object 3500
1:27:29.227407 INFO: lfq-object 3600
1:27:29.269965 INFO: lfq-object 3700
1:27:29.325347 INFO: lfq-object 3800
1:27:29.349917 INFO: lfq-object 3900
1:27:29.395987 INFO: lfq-object 4000
1:27:29.435394 INFO: lfq-object 4100
1:27:29.475420 INFO: lfq-object 4200
1:27:29.527571 INFO: lfq-object 4300
1:27:29.574617 INFO: lfq-object 4400
1:27:29.629900 INFO: lfq-object 4500
1:27:29.667941 INFO: lfq-object 4600
1:27:29.720651 INFO: lfq-object 4700
1:27:29.767353 INFO: lfq-object 4800
1:27:29.816221 INFO: lfq-object 4900
1:27:29.846730 INFO: lfq-object 5000
1:27:29.882142 INFO: lfq-object 5100
1:27:29.916205 INFO: lfq-object 5200
1:27:29.967428 INFO: lfq-object 5300
1:27:29.998285 INFO: lfq-object 5400
1:27:30.037721 INFO: lfq-object 5500
1:27:30.086327 INFO: lfq-object 5600
1:27:30.125822 INFO: lfq-object 5700
1:27:30.167909 INFO: lfq-object 5800
1:27:30.203958 INFO: lfq-object 5900
1:27:30.238778 INFO: lfq-object 6000
1:27:30.279561 INFO: lfq-object 6100
1:27:30.324413 INFO: lfq-object 6200
1:27:30.359430 INFO: lfq-object 6300
1:27:30.399383 INFO: lfq-object 6400
1:27:30.426776 INFO: lfq-object 6500
1:27:30.459860 INFO: lfq-object 6600
1:27:30.497206 INFO: lfq-object 6700
1:27:30.541771 INFO: lfq-object 6800
1:27:30.581147 INFO: lfq-object 6900
1:27:30.628076 INFO: lfq-object 7000
1:27:30.682505 INFO: lfq-object 7100
1:27:30.744436 INFO: lfq-object 7200
1:27:30.771963 INFO: lfq-object 7300
1:27:30.817246 INFO: lfq-object 7400
1:27:30.868043 INFO: lfq-object 7500
1:27:30.907328 INFO: lfq-object 7600
1:27:30.933990 INFO: lfq-object 7700
1:27:30.969060 INFO: lfq-object 7800
1:27:31.007226 INFO: lfq-object 7900
1:27:31.053241 INFO: lfq-object 8000
1:27:31.080109 INFO: lfq-object 8100
1:27:31.136725 INFO: lfq-object 8200
1:27:31.164312 INFO: lfq-object 8300
1:27:31.198104 INFO: lfq-object 8400
1:27:31.244679 INFO: lfq-object 8500
1:27:31.288275 INFO: lfq-object 8600
1:27:31.320289 INFO: lfq-object 8700
1:27:31.360386 INFO: lfq-object 8800
1:27:31.398098 INFO: lfq-object 8900
1:27:31.434335 INFO: lfq-object 9000
1:27:31.494188 INFO: lfq-object 9100
1:27:31.546015 INFO: lfq-object 9200
1:27:31.609560 INFO: lfq-object 9300
1:27:31.671272 INFO: lfq-object 9400
1:27:31.717886 INFO: lfq-object 9500
1:27:31.747301 INFO: lfq-object 9600
1:27:31.782077 INFO: lfq-object 9700
1:27:31.809972 INFO: lfq-object 9800
1:27:31.844692 INFO: lfq-object 9900
1:27:33.657065 INFO: Writing pg output to disk
1:27:33.657283 INFO: Saving run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/pg.matrix.tsv to disk
1:27:33.921192 INFO: Writing psm output to disk
1:27:33.921320 INFO: Saving run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/precursors.tsv to disk
1:27:55.914153 PROGRESS: Building spectral library
1:27:56.036050 INFO: Building MBR spectral library
1:27:56.036189 INFO: Running MbrLibraryBuilder
1:27:57.897133 INFO: MBR spectral library contains 110,515 precursors, 9,923 proteins
1:27:57.897279 INFO: Writing MBR spectral library to disk
1:27:59.111681 PROGRESS: =================== Search Finished ===================
1:28:00.217541 INFO: Running step 'mbr'
1:28:00.220417 INFO: Extracted extra_config from previous step: defaultdict(<class 'dict'>, {'search': {'target_ms1_tolerance': 30.0, 'target_ms2_tolerance': 6.2633305}})
1:28:00.220576 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
1:28:00.232034 INFO: loading additional config provided via CLI
1:28:00.232106 INFO: loading additional config provided via CLI parameters
1:28:00.232368 INFO: Updating config with 'user defined'
1:28:00.232463 INFO: Updating config with 'user defined (cli)'
1:28:00.232488 INFO: Updating config with 'multistep search'
1:28:00.232530 INFO: ├──version: 1
1:28:00.232556 INFO: ├──workflow_name: None
1:28:00.232578 INFO: [32;20m├──output_directory: run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet [multistep search, default: None][0m
1:28:00.232598 INFO: [32;20m├──library_path: run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/speclib.mbr.hdf [multistep search, default: None][0m
1:28:00.232619 INFO: ├──raw_paths:
1:28:00.232640 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
1:28:00.232661 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
1:28:00.232679 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
1:28:00.232698 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
1:28:00.232720 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
1:28:00.232738 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
1:28:00.232755 INFO: ├──fasta_paths:
1:28:00.232776 INFO: ├──quant_directory: None
1:28:00.232794 INFO: ├──general
1:28:00.232819 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
1:28:00.232839 INFO: │   ├──transfer_step_enabled: False
1:28:00.232870 INFO: │   ├──mbr_step_enabled: True
1:28:00.232889 INFO: │   ├──reuse_calibration: False
1:28:00.232908 INFO: │   ├──reuse_quant: False
1:28:00.232927 INFO: │   ├──astral_ms1: False
1:28:00.232945 INFO: │   ├──log_level: INFO
1:28:00.232963 INFO: │   ├──mmap_detector_events: False
1:28:00.232983 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
1:28:00.233001 INFO: │   ├──save_library: True
1:28:00.233019 INFO: │   ├──save_mbr_library: True
1:28:00.233037 INFO: │   └──save_figures: True
1:28:00.233054 INFO: ├──library_loading
1:28:00.233074 INFO: │   └──rt_heuristic: 180
1:28:00.233091 INFO: ├──library_prediction
1:28:00.233109 INFO: │   ├──enabled: False
1:28:00.233129 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
1:28:00.233147 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
1:28:00.233164 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
1:28:00.233183 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
1:28:00.233201 INFO: │   ├──missed_cleavages: 1
1:28:00.233217 INFO: │   ├──precursor_len:
1:28:00.233235 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
1:28:00.233254 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
1:28:00.233272 INFO: │   ├──precursor_charge:
1:28:00.233291 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
1:28:00.233308 INFO: │   │   [32;20m- 4[0m
1:28:00.233325 INFO: │   ├──precursor_mz:
1:28:00.233344 INFO: │   │   [32;20m- 400[0m
1:28:00.233361 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
1:28:00.233379 INFO: │   ├──fragment_mz:
1:28:00.233397 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
1:28:00.233414 INFO: │   │   [32;20m- 2000[0m
1:28:00.233431 INFO: │   ├──nce: 25
1:28:00.233449 INFO: │   ├──fragment_types:
1:28:00.233466 INFO: │   │   [32;20m- b[0m
1:28:00.233484 INFO: │   │   [32;20m- y[0m
1:28:00.233503 INFO: │   ├──max_fragment_charge: 2
1:28:00.233521 INFO: │   [32;20m├──instrument: Astral [user defined, default: Lumos][0m
1:28:00.233539 INFO: │   ├──peptdeep_model_path: None
1:28:00.233558 INFO: │   └──peptdeep_model_type: generic
1:28:00.233576 INFO: ├──custom_modifications:
1:28:00.233595 INFO: │   ├──name: Dimethyl:d12@K
1:28:00.233613 INFO: │   └──composition: H(-2)2H(8)13C(2)
1:28:00.233633 INFO: │   ├──name: Dimethyl:d12@Any_N-term
1:28:00.233651 INFO: │   └──composition: H(-2)2H(8)13C(2)
1:28:00.233669 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
1:28:00.233685 INFO: │   └──composition: H(-2)2H(8)13C(2)
1:28:00.233704 INFO: │   ├──name: mTRAQ:d12@K
1:28:00.233722 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
1:28:00.233739 INFO: │   ├──name: mTRAQ:d12@Any_N-term
1:28:00.233757 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
1:28:00.233775 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
1:28:00.233791 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
1:28:00.233809 INFO: │   ├──name: Label:13C(12)@K
1:28:00.233827 INFO: │   └──composition: C(12)
1:28:00.233844 INFO: ├──search
1:28:00.233866 INFO: │   [32;20m├──target_ms1_tolerance: 30.0 [multistep search, default: 5][0m
1:28:00.233885 INFO: │   [32;20m├──target_ms2_tolerance: 6.2633305 [multistep search, default: 10][0m
1:28:00.233903 INFO: │   ├──target_rt_tolerance: 0
1:28:00.233921 INFO: │   ├──target_mobility_tolerance: 0
1:28:00.233939 INFO: │   ├──quant_window: 3
1:28:00.233956 INFO: │   [32;20m├──target_num_candidates: 2 [user defined, default: 3][0m
1:28:00.233975 INFO: │   ├──channel_filter: 
1:28:00.233991 INFO: │   ├──exclude_shared_ions: True
1:28:00.234008 INFO: │   ├──compete_for_fragments: True
1:28:00.234032 INFO: │   ├──quant_all: True
1:28:00.234052 INFO: │   ├──top_k_fragments: 12
1:28:00.234070 INFO: │   ├──experimental_xic: True
1:28:00.234089 INFO: │   └──optimized_peak_group_score: False
1:28:00.234105 INFO: ├──calibration
1:28:00.234125 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 8000][0m
1:28:00.234143 INFO: │   ├──optimization_lock_target: 200
1:28:00.234160 INFO: │   ├──max_steps: 20
1:28:00.234180 INFO: │   ├──min_steps: 2
1:28:00.234197 INFO: │   ├──max_skips: 1
1:28:00.234215 INFO: │   ├──norm_rt_mode: linear
1:28:00.234233 INFO: │   ├──max_fragments: 5000
1:28:00.234255 INFO: │   └──min_correlation: 0.7
1:28:00.234272 INFO: ├──search_initial
1:28:00.234291 INFO: │   ├──initial_num_candidates: 1
1:28:00.234308 INFO: │   ├──initial_ms1_tolerance: 30
1:28:00.234325 INFO: │   ├──initial_ms2_tolerance: 30
1:28:00.234345 INFO: │   ├──initial_mobility_tolerance: 0.1
1:28:00.234364 INFO: │   └──initial_rt_tolerance: 0.5
1:28:00.234383 INFO: ├──selection_config
1:28:00.234403 INFO: │   ├──peak_len_rt: 10.0
1:28:00.234422 INFO: │   ├──sigma_scale_rt: 0.5
1:28:00.234440 INFO: │   ├──peak_len_mobility: 0.01
1:28:00.234458 INFO: │   ├──sigma_scale_mobility: 1.0
1:28:00.234476 INFO: │   ├──top_k_precursors: 3
1:28:00.234493 INFO: │   ├──kernel_size: 30
1:28:00.234512 INFO: │   ├──f_mobility: 1.0
1:28:00.234529 INFO: │   ├──f_rt: 0.99
1:28:00.234547 INFO: │   ├──center_fraction: 0.5
1:28:00.234565 INFO: │   ├──min_size_mobility: 8
1:28:00.234582 INFO: │   ├──min_size_rt: 3
1:28:00.234605 INFO: │   ├──max_size_mobility: 20
1:28:00.234626 INFO: │   ├──max_size_rt: 15
1:28:00.234643 INFO: │   ├──group_channels: False
1:28:00.234661 INFO: │   ├──use_weighted_score: True
1:28:00.234680 INFO: │   ├──join_close_candidates: False
1:28:00.234698 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
1:28:00.234716 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
1:28:00.234735 INFO: ├──scoring_config
1:28:00.234753 INFO: │   ├──score_grouped: False
1:28:00.234771 INFO: │   ├──top_k_isotopes: 3
1:28:00.234789 INFO: │   ├──reference_channel: -1
1:28:00.234808 INFO: │   ├──precursor_mz_tolerance: 10
1:28:00.234826 INFO: │   └──fragment_mz_tolerance: 15
1:28:00.234845 INFO: ├──library_multiplexing
1:28:00.234862 INFO: │   ├──enabled: False
1:28:00.234880 INFO: │   ├──input_channel: 0
1:28:00.234899 INFO: │   └──multiplex_mapping:
1:28:00.234916 INFO: ├──multiplexing
1:28:00.234935 INFO: │   ├──enabled: False
1:28:00.234952 INFO: │   ├──target_channels: 4,8
1:28:00.234970 INFO: │   ├──decoy_channel: 12
1:28:00.234988 INFO: │   ├──reference_channel: 0
1:28:00.235006 INFO: │   └──competetive_scoring: True
1:28:00.235023 INFO: ├──fdr
1:28:00.235042 INFO: │   ├──fdr: 0.01
1:28:00.235060 INFO: │   ├──group_level: proteins
1:28:00.235078 INFO: │   [32;20m├──inference_strategy: library [multistep search, default: heuristic][0m
1:28:00.235098 INFO: │   ├──competetive_scoring: True
1:28:00.235115 INFO: │   ├──keep_decoys: False
1:28:00.235132 INFO: │   ├──channel_wise_fdr: False
1:28:00.235151 INFO: │   ├──enable_two_step_classifier: False
1:28:00.235169 INFO: │   ├──two_step_classifier_max_iterations: 5
1:28:00.235187 INFO: │   └──enable_nn_hyperparameter_tuning: False
1:28:00.235205 INFO: ├──search_output
1:28:00.235224 INFO: │   ├──file_format: tsv
1:28:00.235242 INFO: │   ├──peptide_level_lfq: False
1:28:00.235263 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
1:28:00.235280 INFO: │   ├──min_k_fragments: 12
1:28:00.235305 INFO: │   ├──min_correlation: 0.9
1:28:00.235324 INFO: │   ├──num_samples_quadratic: 50
1:28:00.235342 INFO: │   ├──min_nonnan: 3
1:28:00.235360 INFO: │   ├──normalize_lfq: True
1:28:00.235378 INFO: │   └──save_fragment_quant_matrix: False
1:28:00.235395 INFO: ├──optimization
1:28:00.235413 INFO: │   ├──order_of_optimization: None
1:28:00.235430 INFO: │   ├──ms2_error
1:28:00.235449 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1:28:00.235467 INFO: │   │   ├──targeted_update_factor: 1.0
1:28:00.235486 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1:28:00.235504 INFO: │   │   ├──automatic_update_factor: 1.1
1:28:00.235524 INFO: │   │   ├──try_narrower_values: True
1:28:00.235542 INFO: │   │   ├──maximal_decrease: 0.5
1:28:00.235560 INFO: │   │   ├──favour_narrower_optimum: False
1:28:00.235579 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1:28:00.235597 INFO: │   ├──ms1_error
1:28:00.235615 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1:28:00.235634 INFO: │   │   ├──targeted_update_factor: 1.0
1:28:00.235652 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1:28:00.235670 INFO: │   │   ├──automatic_update_factor: 1.1
1:28:00.235687 INFO: │   │   ├──try_narrower_values: False
1:28:00.235704 INFO: │   │   ├──maximal_decrease: 0.2
1:28:00.235722 INFO: │   │   ├──favour_narrower_optimum: False
1:28:00.235740 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1:28:00.235756 INFO: │   ├──mobility_error
1:28:00.235774 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1:28:00.235793 INFO: │   │   ├──targeted_update_factor: 1.0
1:28:00.235811 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1:28:00.235829 INFO: │   │   ├──automatic_update_factor: 1.1
1:28:00.235848 INFO: │   │   ├──try_narrower_values: False
1:28:00.235866 INFO: │   │   ├──maximal_decrease: 0.2
1:28:00.235885 INFO: │   │   ├──favour_narrower_optimum: False
1:28:00.235904 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1:28:00.235922 INFO: │   └──rt_error
1:28:00.235940 INFO: │       ├──targeted_update_percentile_range: 0.95
1:28:00.235959 INFO: │       ├──targeted_update_factor: 1.0
1:28:00.235977 INFO: │       ├──automatic_update_percentile_range: 0.99
1:28:00.235995 INFO: │       ├──automatic_update_factor: 1.1
1:28:00.236014 INFO: │       ├──try_narrower_values: True
1:28:00.236031 INFO: │       ├──maximal_decrease: 0.2
1:28:00.236048 INFO: │       ├──favour_narrower_optimum: True
1:28:00.236067 INFO: │       └──maximum_decrease_from_maximum: 0.1
1:28:00.236084 INFO: ├──optimization_manager
1:28:00.236102 INFO: │   ├──fwhm_rt: 5
1:28:00.236121 INFO: │   ├──fwhm_mobility: 0.01
1:28:00.236139 INFO: │   └──score_cutoff: 0
1:28:00.236157 INFO: ├──transfer_library
1:28:00.236174 INFO: │   ├──enabled: False
1:28:00.236191 INFO: │   ├──fragment_types:
1:28:00.236209 INFO: │   │   [32;20m- b[0m
1:28:00.236227 INFO: │   │   [32;20m- y[0m
1:28:00.236245 INFO: │   ├──max_charge: 2
1:28:00.236264 INFO: │   ├──top_k_samples: 3
1:28:00.236282 INFO: │   ├──norm_delta_max: True
1:28:00.236299 INFO: │   ├──precursor_correlation_cutoff: 0.5
1:28:00.236318 INFO: │   └──fragment_correlation_ratio: 0.75
1:28:00.236335 INFO: └──transfer_learning
1:28:00.236353 INFO:     ├──enabled: False
1:28:00.236371 INFO:     ├──batch_size: 2000
1:28:00.236389 INFO:     ├──max_lr: 0.0001
1:28:00.236406 INFO:     ├──train_fraction: 0.7
1:28:00.236425 INFO:     ├──validation_fraction: 0.2
1:28:00.236442 INFO:     ├──test_fraction: 0.1
1:28:00.236459 INFO:     ├──test_interval: 1
1:28:00.236482 INFO:     ├──lr_patience: 3
1:28:00.236500 INFO:     [32;20m├──epochs: 20 [user defined, default: 51][0m
1:28:00.236517 INFO:     ├──warmup_epochs: 5
1:28:00.236535 INFO:     ├──nce: 25
1:28:00.236552 INFO:     [32;20m└──instrument: Astral [user defined, default: Lumos][0m
1:28:00.242544 INFO: Registering 7 custom modifications
1:28:00.258669 INFO: Running DynamicLoader
1:28:00.258751 INFO: Loading .hdf library from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/speclib.mbr.hdf
1:28:00.778831 INFO: Running PrecursorInitializer
1:28:00.779002 INFO: Running AnnotateFasta
1:28:00.779297 INFO: Dropping decoys from input library before annotation
1:28:00.801539 INFO: Running IsotopeGenerator
1:28:00.801789 WARNING: Input library already contains isotope information. Skipping isotope generation. 
 Please note that isotope generation outside of alphabase is not supported.
1:28:00.801834 INFO: Running RTNormalization
1:28:00.805676 INFO: Saving library to run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/speclib.hdf
1:28:01.584561 INFO: Running DecoyGenerator
1:28:12.518147 INFO: Running FlattenLibrary
1:28:13.453605 INFO: Running InitFlatColumns
1:28:13.460564 INFO: Running LogFlatLibraryStats
1:28:13.460675 INFO: ============ Library Stats ============
1:28:13.460705 INFO: Number of precursors: 221,011
1:28:13.505844 INFO: 	thereof targets:110,515
1:28:13.505981 INFO: 	thereof decoys: 110,496
1:28:13.507976 INFO: Number of elution groups: 110,515
1:28:13.508019 INFO: 	average size: 2.00
1:28:13.516238 INFO: Number of proteins: 9,923
1:28:13.517016 INFO: Number of channels: 1 ([0])
1:28:13.517114 INFO: Isotopes Distribution for 4 isotopes
1:28:13.517140 INFO: =======================================
1:28:13.517275 INFO: Searching 6 files:
1:28:13.517305 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
1:28:13.517325 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
1:28:13.517345 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
1:28:13.517363 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
1:28:13.517380 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
1:28:13.517396 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
1:28:13.517414 INFO: Using 0 fasta files:
1:28:13.517431 INFO: Using library: run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/library/speclib.mbr.hdf
1:28:13.517449 INFO: Saving output to: run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet
1:28:13.517485 PROGRESS: Starting Search Workflows
1:28:13.517556 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:28:13.517611 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant
1:28:13.517676 INFO: Creating folder run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/figures
1:28:13.518408 INFO: Initializing RawFileManager
1:28:24.107362 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.
1:28:24.111412 INFO: Determining DIA cycle
1:28:24.127899 INFO: Found cycle with start 0.00 min and length 300.
1:28:24.292337 INFO: RT (min)            : 0.0 - 26.9
1:28:24.292434 INFO: RT duration (sec)   : 1611.2
1:28:24.292463 INFO: RT duration (min)   : 26.9
1:28:24.292485 INFO: Cycle len (scans)   : 300
1:28:24.292505 INFO: Cycle len (sec)     : 1.65
1:28:24.292524 INFO: Number of cycles    : 977
1:28:24.292542 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:28:24.323936 INFO: Initializing CalibrationManager
1:28:24.324209 INFO: Loading calibration config
1:28:24.324700 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'}]
1:28:24.324802 INFO: Calibration group :fragment, found 1 estimator(s)
1:28:24.324888 INFO: Calibration group :precursor, found 3 estimator(s)
1:28:24.324964 INFO: Disabling ion mobility calibration
1:28:24.324993 INFO: removed mobility estimator from group precursor
1:28:24.325119 INFO: Initializing OptimizationManager
1:28:24.325223 INFO: initial parameter: ms1_error = 30
1:28:24.325279 INFO: initial parameter: ms2_error = 30
1:28:24.325325 INFO: initial parameter: rt_error = 805.5992431640625
1:28:24.325368 INFO: initial parameter: mobility_error = 0.1
1:28:24.325408 INFO: initial parameter: column_type = library
1:28:24.325448 INFO: initial parameter: num_candidates = 1
1:28:24.325488 INFO: initial parameter: classifier_version = -1
1:28:24.325528 INFO: initial parameter: fwhm_rt = 5
1:28:24.325567 INFO: initial parameter: fwhm_mobility = 0.01
1:28:24.325605 INFO: initial parameter: score_cutoff = 0
1:28:24.325661 INFO: Initializing TimingManager
1:28:24.325715 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:28:24.325814 INFO: FDRManager not loaded from disk.
1:28:24.325838 INFO: Initializing FDRManager
1:28:24.325872 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:28:24.360040 PROGRESS: 110,515 target precursors potentially observable (0 removed)
1:28:24.419622 PROGRESS: Starting initial search for precursors.
1:28:24.426553 INFO: Starting optimization step 0.
1:28:24.426667 PROGRESS: === Extracting elution groups 0 to 200 ===
1:28:24.426838 PROGRESS: Extracting batch of 400 precursors
1:28:24.427716 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:28:24.427763 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:28:24.427799 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:28:24.427820 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:28:24.428067 INFO: Starting candidate selection
1:28:24.552942 INFO: Starting candidate scoring
1:28:24.586260 INFO: Finished candidate processing
1:28:24.586330 INFO: Collecting candidate features
1:28:24.594469 INFO: Collecting fragment features
1:28:24.596670 INFO: Finished candidate scoring
1:28:24.597406 PROGRESS: === Extracted 400 precursors and 4426 fragments ===
1:28:24.597658 INFO: performing precursor FDR with 47 features
1:28:24.597694 INFO: Decoy channel: -1
1:28:24.597716 INFO: Competetive: True
1:28:24.598698 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:24.617412 INFO: Test AUC: 0.513
1:28:24.617470 INFO: Train AUC: 0.545
1:28:24.617498 INFO: AUC difference: 5.86%
1:28:24.617519 WARNING: AUC difference > 5%. This may indicate overfitting.
1:28:24.813217 INFO: Resetting torch num_threads to 100
1:28:24.813649 INFO: === FDR correction performed with classifier version -1 ===
1:28:24.814234 PROGRESS: ============================= Precursor FDR =============================
1:28:24.814322 PROGRESS: Total precursors accumulated: 200
1:28:24.814379 PROGRESS: Target precursors: 113 (56.50%)
1:28:24.814429 PROGRESS: Decoy precursors: 87 (43.50%)
1:28:24.814473 PROGRESS: 
1:28:24.814516 PROGRESS: Precursor Summary:
1:28:24.815339 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:28:24.815426 PROGRESS: 
1:28:24.815487 PROGRESS: Protein Summary:
1:28:24.816373 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:28:24.816455 PROGRESS: =========================================================================
1:28:24.820149 INFO: Starting optimization step 1.
1:28:24.820249 PROGRESS: === Extracting elution groups 200 to 600 ===
1:28:24.820310 PROGRESS: Extracting batch of 797 precursors
1:28:24.821058 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:28:24.821102 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:28:24.821132 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:28:24.821152 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:28:24.821295 INFO: Starting candidate selection
1:28:24.950297 INFO: Starting candidate scoring
1:28:24.984997 INFO: Finished candidate processing
1:28:24.985068 INFO: Collecting candidate features
1:28:24.993729 INFO: Collecting fragment features
1:28:24.996162 INFO: Finished candidate scoring
1:28:24.998352 PROGRESS: === Extracted 1197 precursors and 13189 fragments ===
1:28:24.999104 INFO: performing precursor FDR with 47 features
1:28:24.999147 INFO: Decoy channel: -1
1:28:24.999171 INFO: Competetive: True
1:28:25.002032 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:25.033505 INFO: Test AUC: 0.535
1:28:25.033568 INFO: Train AUC: 0.510
1:28:25.033598 INFO: AUC difference: 5.02%
1:28:25.033620 WARNING: AUC difference > 5%. This may indicate overfitting.
1:28:25.200549 INFO: Resetting torch num_threads to 100
1:28:25.201020 INFO: === FDR correction performed with classifier version -1 ===
1:28:25.201704 PROGRESS: ============================= Precursor FDR =============================
1:28:25.201796 PROGRESS: Total precursors accumulated: 600
1:28:25.201855 PROGRESS: Target precursors: 318 (53.00%)
1:28:25.201905 PROGRESS: Decoy precursors: 282 (47.00%)
1:28:25.201952 PROGRESS: 
1:28:25.201998 PROGRESS: Precursor Summary:
1:28:25.202851 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:28:25.202938 PROGRESS: 
1:28:25.202992 PROGRESS: Protein Summary:
1:28:25.203895 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:28:25.203979 PROGRESS: =========================================================================
1:28:25.208630 INFO: Starting optimization step 2.
1:28:25.208734 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:28:25.208796 PROGRESS: Extracting batch of 1592 precursors
1:28:25.209640 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:28:25.209686 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:28:25.209717 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:28:25.209739 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:28:25.209886 INFO: Starting candidate selection
1:28:25.385663 INFO: Starting candidate scoring
1:28:25.422404 INFO: Finished candidate processing
1:28:25.422483 INFO: Collecting candidate features
1:28:25.432508 INFO: Collecting fragment features
1:28:25.435552 INFO: Finished candidate scoring
1:28:25.438858 PROGRESS: === Extracted 2789 precursors and 30756 fragments ===
1:28:25.439924 INFO: performing precursor FDR with 47 features
1:28:25.439969 INFO: Decoy channel: -1
1:28:25.439999 INFO: Competetive: True
1:28:25.443862 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:25.483769 INFO: Test AUC: 0.489
1:28:25.483848 INFO: Train AUC: 0.503
1:28:25.483884 INFO: AUC difference: 2.64%
1:28:25.654941 INFO: Resetting torch num_threads to 100
1:28:25.655610 INFO: === FDR correction performed with classifier version -1 ===
1:28:25.656398 PROGRESS: ============================= Precursor FDR =============================
1:28:25.656500 PROGRESS: Total precursors accumulated: 1,400
1:28:25.656577 PROGRESS: Target precursors: 694 (49.57%)
1:28:25.656648 PROGRESS: Decoy precursors: 706 (50.43%)
1:28:25.656712 PROGRESS: 
1:28:25.656770 PROGRESS: Precursor Summary:
1:28:25.657664 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:28:25.657759 PROGRESS: 
1:28:25.658370 PROGRESS: Protein Summary:
1:28:25.659357 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:28:25.659457 PROGRESS: =========================================================================
1:28:25.666157 INFO: Starting optimization step 3.
1:28:25.666273 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:28:25.666353 PROGRESS: Extracting batch of 3186 precursors
1:28:25.667622 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:28:25.667670 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:28:25.667712 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:28:25.667740 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:28:25.667917 INFO: Starting candidate selection
1:28:25.921731 INFO: Starting candidate scoring
1:28:25.963197 INFO: Finished candidate processing
1:28:25.963287 INFO: Collecting candidate features
1:28:25.976580 INFO: Collecting fragment features
1:28:25.980947 INFO: Finished candidate scoring
1:28:25.986134 PROGRESS: === Extracted 5975 precursors and 65974 fragments ===
1:28:25.987521 INFO: performing precursor FDR with 47 features
1:28:25.987567 INFO: Decoy channel: -1
1:28:25.987591 INFO: Competetive: True
1:28:25.991327 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:26.043084 INFO: Test AUC: 0.533
1:28:26.043176 INFO: Train AUC: 0.495
1:28:26.043205 INFO: AUC difference: 7.73%
1:28:26.043226 WARNING: AUC difference > 5%. This may indicate overfitting.
1:28:26.213919 INFO: Resetting torch num_threads to 100
1:28:26.214664 INFO: === FDR correction performed with classifier version -1 ===
1:28:26.215601 PROGRESS: ============================= Precursor FDR =============================
1:28:26.215696 PROGRESS: Total precursors accumulated: 2,999
1:28:26.215757 PROGRESS: Target precursors: 1,509 (50.32%)
1:28:26.215807 PROGRESS: Decoy precursors: 1,490 (49.68%)
1:28:26.215856 PROGRESS: 
1:28:26.215901 PROGRESS: Precursor Summary:
1:28:26.216788 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:28:26.216875 PROGRESS: 
1:28:26.216930 PROGRESS: Protein Summary:
1:28:26.217872 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:28:26.217958 PROGRESS: =========================================================================
1:28:26.229225 INFO: Starting optimization step 4.
1:28:26.229340 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:28:26.229401 PROGRESS: Extracting batch of 6377 precursors
1:28:26.230876 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:28:26.230924 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:28:26.230955 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:28:26.230977 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:28:26.231138 INFO: Starting candidate selection
1:28:26.662844 INFO: Starting candidate scoring
1:28:26.710384 INFO: Finished candidate processing
1:28:26.710475 INFO: Collecting candidate features
1:28:26.728253 INFO: Collecting fragment features
1:28:26.736084 INFO: Finished candidate scoring
1:28:26.747123 PROGRESS: === Extracted 12352 precursors and 136131 fragments ===
1:28:26.748887 INFO: performing precursor FDR with 47 features
1:28:26.748945 INFO: Decoy channel: -1
1:28:26.748971 INFO: Competetive: True
1:28:26.754533 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:26.804148 INFO: Test AUC: 0.506
1:28:26.804246 INFO: Train AUC: 0.498
1:28:26.804278 INFO: AUC difference: 1.55%
1:28:26.984207 INFO: Resetting torch num_threads to 100
1:28:26.989983 INFO: === FDR correction performed with classifier version -1 ===
1:28:26.990678 PROGRESS: ============================= Precursor FDR =============================
1:28:26.990781 PROGRESS: Total precursors accumulated: 1
1:28:26.990840 PROGRESS: Target precursors: 1 (100.00%)
1:28:26.990891 PROGRESS: Decoy precursors: 0 (0.00%)
1:28:26.990938 PROGRESS: 
1:28:26.990983 PROGRESS: Precursor Summary:
1:28:26.991920 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:28:26.992014 PROGRESS: 
1:28:26.992069 PROGRESS: Protein Summary:
1:28:26.993088 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:28:26.993173 PROGRESS: =========================================================================
1:28:27.013872 INFO: Starting optimization step 5.
1:28:27.014059 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:28:27.014128 PROGRESS: Extracting batch of 12745 precursors
1:28:27.016787 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:28:27.016837 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:28:27.016873 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:28:27.016895 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:28:27.017082 INFO: Starting candidate selection
1:28:27.833445 INFO: Starting candidate scoring
1:28:27.924158 INFO: Finished candidate processing
1:28:27.924258 INFO: Collecting candidate features
1:28:27.953954 INFO: Collecting fragment features
1:28:27.964564 INFO: Finished candidate scoring
1:28:27.979548 PROGRESS: === Extracted 25097 precursors and 276601 fragments ===
1:28:27.982516 INFO: performing precursor FDR with 47 features
1:28:27.982588 INFO: Decoy channel: -1
1:28:27.982625 INFO: Competetive: True
1:28:27.993360 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:28.369249 INFO: Test AUC: 0.812
1:28:28.369365 INFO: Train AUC: 0.815
1:28:28.369397 INFO: AUC difference: 0.36%
1:28:28.557694 INFO: Resetting torch num_threads to 100
1:28:28.559282 INFO: === FDR correction performed with classifier version -1 ===
1:28:28.560872 PROGRESS: ============================= Precursor FDR =============================
1:28:28.560975 PROGRESS: Total precursors accumulated: 7,106
1:28:28.561037 PROGRESS: Target precursors: 6,711 (94.44%)
1:28:28.561087 PROGRESS: Decoy precursors: 395 (5.56%)
1:28:28.561136 PROGRESS: 
1:28:28.561184 PROGRESS: Precursor Summary:
1:28:28.562838 PROGRESS: Channel   0:	 0.05 FDR: 6,450; 0.01 FDR:    10; 0.001 FDR:    10
1:28:28.562939 PROGRESS: 
1:28:28.562995 PROGRESS: Protein Summary:
1:28:28.565068 PROGRESS: Channel   0:	 0.05 FDR: 3,547; 0.01 FDR:    10; 0.001 FDR:    10
1:28:28.565161 PROGRESS: =========================================================================
1:28:28.586877 INFO: Starting optimization step 6.
1:28:28.587114 PROGRESS: === Extracting elution groups 12600 to 25400 ===
1:28:28.587192 PROGRESS: Extracting batch of 25486 precursors
1:28:28.592805 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:28:28.592868 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:28:28.592903 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:28:28.592927 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:28:28.593149 INFO: Starting candidate selection
1:28:30.104060 INFO: Starting candidate scoring
1:28:30.255256 INFO: Finished candidate processing
1:28:30.255357 INFO: Collecting candidate features
1:28:30.298910 INFO: Collecting fragment features
1:28:30.314397 INFO: Finished candidate scoring
1:28:30.338299 PROGRESS: === Extracted 50583 precursors and 557391 fragments ===
1:28:30.347836 INFO: performing precursor FDR with 47 features
1:28:30.347905 INFO: Decoy channel: -1
1:28:30.347930 INFO: Competetive: True
1:28:30.365578 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:31.158362 INFO: Test AUC: 0.827
1:28:31.158485 INFO: Train AUC: 0.833
1:28:31.158514 INFO: AUC difference: 0.70%
1:28:31.350362 INFO: Resetting torch num_threads to 100
1:28:31.353122 INFO: === FDR correction performed with classifier version -1 ===
1:28:31.356219 PROGRESS: ============================= Precursor FDR =============================
1:28:31.356339 PROGRESS: Total precursors accumulated: 15,943
1:28:31.356401 PROGRESS: Target precursors: 15,000 (94.09%)
1:28:31.356451 PROGRESS: Decoy precursors: 943 (5.91%)
1:28:31.356498 PROGRESS: 
1:28:31.356543 PROGRESS: Precursor Summary:
1:28:31.358346 PROGRESS: Channel   0:	 0.05 FDR: 6,723; 0.01 FDR:     0; 0.001 FDR:     0
1:28:31.358440 PROGRESS: 
1:28:31.358496 PROGRESS: Protein Summary:
1:28:31.360603 PROGRESS: Channel   0:	 0.05 FDR: 3,687; 0.01 FDR:     0; 0.001 FDR:     0
1:28:31.360695 PROGRESS: =========================================================================
1:28:31.397119 INFO: Starting optimization step 7.
1:28:31.397361 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1:28:31.397441 PROGRESS: Extracting batch of 50998 precursors
1:28:31.408317 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:28:31.408436 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:28:31.408469 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:28:31.408491 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:28:31.408705 INFO: Starting candidate selection
1:28:34.358286 INFO: Starting candidate scoring
1:28:34.668773 INFO: Finished candidate processing
1:28:34.668914 INFO: Collecting candidate features
1:28:34.750849 INFO: Collecting fragment features
1:28:34.779687 INFO: Finished candidate scoring
1:28:34.831999 PROGRESS: === Extracted 101581 precursors and 1119482 fragments ===
1:28:34.843470 INFO: performing precursor FDR with 47 features
1:28:34.843593 INFO: Decoy channel: -1
1:28:34.843621 INFO: Competetive: True
1:28:34.877260 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:36.547696 INFO: Test AUC: 0.846
1:28:36.547821 INFO: Train AUC: 0.849
1:28:36.547852 INFO: AUC difference: 0.32%
1:28:36.751715 INFO: Resetting torch num_threads to 100
1:28:36.758792 INFO: === FDR correction performed with classifier version -1 ===
1:28:36.764448 PROGRESS: ============================= Precursor FDR =============================
1:28:36.764604 PROGRESS: Total precursors accumulated: 33,040
1:28:36.764665 PROGRESS: Target precursors: 31,444 (95.17%)
1:28:36.764715 PROGRESS: Decoy precursors: 1,596 (4.83%)
1:28:36.764765 PROGRESS: 
1:28:36.764813 PROGRESS: Precursor Summary:
1:28:36.769253 PROGRESS: Channel   0:	 0.05 FDR: 31,367; 0.01 FDR:     0; 0.001 FDR:     0
1:28:36.769375 PROGRESS: 
1:28:36.769431 PROGRESS: Protein Summary:
1:28:36.775574 PROGRESS: Channel   0:	 0.05 FDR: 7,478; 0.01 FDR:     0; 0.001 FDR:     0
1:28:36.775699 PROGRESS: =========================================================================
1:28:36.859698 INFO: Starting optimization step 8.
1:28:36.859960 PROGRESS: === Extracting elution groups 51000 to 102200 ===
1:28:36.860036 PROGRESS: Extracting batch of 101953 precursors
1:28:36.883522 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:28:36.883645 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:28:36.883681 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:28:36.883703 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:28:36.883936 INFO: Starting candidate selection
1:28:42.942013 INFO: Starting candidate scoring
1:28:43.658640 INFO: Finished candidate processing
1:28:43.658742 INFO: Collecting candidate features
1:28:43.825077 INFO: Collecting fragment features
1:28:43.898201 INFO: Finished candidate scoring
1:28:44.010134 PROGRESS: === Extracted 203534 precursors and 2242462 fragments ===
1:28:44.044072 INFO: performing precursor FDR with 47 features
1:28:44.044201 INFO: Decoy channel: -1
1:28:44.044227 INFO: Competetive: True
1:28:44.122001 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:47.645368 INFO: Test AUC: 0.865
1:28:47.645487 INFO: Train AUC: 0.868
1:28:47.645516 INFO: AUC difference: 0.45%
1:28:47.880014 INFO: Resetting torch num_threads to 100
1:28:47.890571 INFO: === FDR correction performed with classifier version -1 ===
1:28:47.905520 PROGRESS: ============================= Precursor FDR =============================
1:28:47.905725 PROGRESS: Total precursors accumulated: 69,936
1:28:47.905789 PROGRESS: Target precursors: 67,388 (96.36%)
1:28:47.905842 PROGRESS: Decoy precursors: 2,548 (3.64%)
1:28:47.905889 PROGRESS: 
1:28:47.905938 PROGRESS: Precursor Summary:
1:28:47.933713 PROGRESS: Channel   0:	 0.05 FDR: 67,388; 0.01 FDR: 63,259; 0.001 FDR: 51,585
1:28:47.933942 PROGRESS: 
1:28:47.934005 PROGRESS: Protein Summary:
1:28:47.972610 PROGRESS: Channel   0:	 0.05 FDR: 9,136; 0.01 FDR: 8,906; 0.001 FDR: 8,067
1:28:47.972846 PROGRESS: =========================================================================
1:28:48.241404 INFO: fragments_df: keeping 5000 of 2242462 [sum(precursor_idx_mask)=712879 sum(mass_error_mask)=2242462 stop_rank=5000
1:28:48.258649 INFO: calibration group: precursor, fitting rt estimator 
1:29:45.094269 INFO: calibration group: fragment, fitting mz estimator 
1:29:45.785908 INFO: Using score_cutoff 52.5575260848999 (fac=0.99, q=1)
1:29:45.787552 INFO: calibration group: precursor, predicting mz
1:29:45.787646 WARNING: mz prediction was skipped as it has not been fitted yet
1:29:45.787679 INFO: calibration group: precursor, predicting rt
1:29:45.789362 INFO: calibration group: fragment, predicting mz
1:29:45.791624 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:29:45.791757 INFO: Starting optimization step 9.
1:29:45.791831 PROGRESS: === Extracting elution groups 0 to 600 ===
1:29:45.791909 PROGRESS: Extracting batch of 1197 precursors
1:29:45.796119 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:29:45.796171 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:45.796207 INFO: FWHM in RT is 3.01 seconds, sigma is 0.39
1:29:45.796229 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:29:45.796431 INFO: Starting candidate selection
1:29:45.952594 INFO: Starting candidate scoring
1:29:45.991977 INFO: Finished candidate processing
1:29:45.992056 INFO: Collecting candidate features
1:29:46.003009 INFO: Collecting fragment features
1:29:46.006961 INFO: Finished candidate scoring
1:29:46.008695 PROGRESS: === Extracted 2394 precursors and 26090 fragments ===
1:29:46.008967 INFO: performing precursor FDR with 47 features
1:29:46.009005 INFO: Decoy channel: -1
1:29:46.009027 INFO: Competetive: True
1:29:46.012216 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:46.035270 INFO: Test AUC: 0.760
1:29:46.035336 INFO: Train AUC: 0.734
1:29:46.035367 INFO: AUC difference: 3.59%
1:29:46.212043 INFO: Resetting torch num_threads to 100
1:29:46.212630 INFO: === FDR correction performed with classifier version 8 ===
1:29:46.213262 PROGRESS: ============================= Precursor FDR =============================
1:29:46.213358 PROGRESS: Total precursors accumulated: 407
1:29:46.213419 PROGRESS: Target precursors: 391 (96.07%)
1:29:46.213471 PROGRESS: Decoy precursors: 16 (3.93%)
1:29:46.213522 PROGRESS: 
1:29:46.213567 PROGRESS: Precursor Summary:
1:29:46.214627 PROGRESS: Channel   0:	 0.05 FDR:   391; 0.01 FDR:   346; 0.001 FDR:   277
1:29:46.214719 PROGRESS: 
1:29:46.214775 PROGRESS: Protein Summary:
1:29:46.215973 PROGRESS: Channel   0:	 0.05 FDR:   376; 0.01 FDR:   333; 0.001 FDR:   267
1:29:46.216063 PROGRESS: =========================================================================
1:29:46.229537 INFO: fragments_df: keeping 3155 of 26090 [sum(precursor_idx_mask)=7661 sum(mass_error_mask)=26090 stop_rank=3155
1:29:46.239032 INFO: calibration group: precursor, fitting rt estimator 
1:29:46.342529 INFO: calibration group: fragment, fitting mz estimator 
1:29:46.691724 INFO: Using score_cutoff 54.87341794395447 (fac=0.99, q=1)
1:29:46.692102 INFO: calibration group: precursor, predicting mz
1:29:46.692185 WARNING: mz prediction was skipped as it has not been fitted yet
1:29:46.692217 INFO: calibration group: precursor, predicting rt
1:29:46.693791 INFO: calibration group: fragment, predicting mz
1:29:46.696130 INFO: === checking if optimization conditions were reached ===
1:29:46.697538 PROGRESS: ❌ ms2_error      : 15.1095 > 6.2633 or insufficient steps taken.
1:29:46.697591 INFO: ==============================================
1:29:46.697672 INFO: Starting optimization step 10.
1:29:46.697743 PROGRESS: === Extracting elution groups 0 to 600 ===
1:29:46.697801 PROGRESS: Extracting batch of 1197 precursors
1:29:46.698694 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:29:46.698742 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:46.698784 INFO: FWHM in RT is 2.95 seconds, sigma is 0.38
1:29:46.698807 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:29:46.698954 INFO: Starting candidate selection
1:29:46.846789 INFO: Starting candidate scoring
1:29:46.885559 INFO: Finished candidate processing
1:29:46.885638 INFO: Collecting candidate features
1:29:46.896160 INFO: Collecting fragment features
1:29:46.900079 INFO: Finished candidate scoring
1:29:46.901871 PROGRESS: === Extracted 2394 precursors and 24553 fragments ===
1:29:46.902130 INFO: performing precursor FDR with 47 features
1:29:46.902166 INFO: Decoy channel: -1
1:29:46.902188 INFO: Competetive: True
1:29:46.904757 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:46.927638 INFO: Test AUC: 0.725
1:29:46.927704 INFO: Train AUC: 0.767
1:29:46.927733 INFO: AUC difference: 5.48%
1:29:46.927755 WARNING: AUC difference > 5%. This may indicate overfitting.
1:29:47.100726 INFO: Resetting torch num_threads to 100
1:29:47.101289 INFO: === FDR correction performed with classifier version 9 ===
1:29:47.101926 PROGRESS: ============================= Precursor FDR =============================
1:29:47.102015 PROGRESS: Total precursors accumulated: 478
1:29:47.102075 PROGRESS: Target precursors: 461 (96.44%)
1:29:47.102126 PROGRESS: Decoy precursors: 17 (3.56%)
1:29:47.102172 PROGRESS: 
1:29:47.102216 PROGRESS: Precursor Summary:
1:29:47.103227 PROGRESS: Channel   0:	 0.05 FDR:   461; 0.01 FDR:   348; 0.001 FDR:   231
1:29:47.103318 PROGRESS: 
1:29:47.103375 PROGRESS: Protein Summary:
1:29:47.104550 PROGRESS: Channel   0:	 0.05 FDR:   442; 0.01 FDR:   336; 0.001 FDR:   225
1:29:47.104639 PROGRESS: =========================================================================
1:29:47.107866 INFO: fragments_df: keeping 3254 of 24553 [sum(precursor_idx_mask)=7405 sum(mass_error_mask)=24553 stop_rank=3254
1:29:47.112668 INFO: calibration group: precursor, fitting rt estimator 
1:29:47.233196 INFO: calibration group: fragment, fitting mz estimator 
1:29:47.658834 INFO: Using score_cutoff 49.74206105003357 (fac=0.99, q=1)
1:29:47.659216 INFO: calibration group: precursor, predicting mz
1:29:47.659303 WARNING: mz prediction was skipped as it has not been fitted yet
1:29:47.659335 INFO: calibration group: precursor, predicting rt
1:29:47.660909 INFO: calibration group: fragment, predicting mz
1:29:47.663218 INFO: === checking if optimization conditions were reached ===
1:29:47.664601 PROGRESS: ❌ ms2_error      : 8.3917 > 6.2633 or insufficient steps taken.
1:29:47.664654 INFO: ==============================================
1:29:47.664736 INFO: Starting optimization step 11.
1:29:47.664801 PROGRESS: === Extracting elution groups 0 to 600 ===
1:29:47.664857 PROGRESS: Extracting batch of 1197 precursors
1:29:47.665750 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:29:47.665797 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:47.665828 INFO: FWHM in RT is 2.59 seconds, sigma is 0.33
1:29:47.665850 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:29:47.665992 INFO: Starting candidate selection
1:29:47.812345 INFO: Starting candidate scoring
1:29:47.850909 INFO: Finished candidate processing
1:29:47.850988 INFO: Collecting candidate features
1:29:47.861391 INFO: Collecting fragment features
1:29:47.865515 INFO: Finished candidate scoring
1:29:47.867202 PROGRESS: === Extracted 2394 precursors and 22312 fragments ===
1:29:47.867459 INFO: performing precursor FDR with 47 features
1:29:47.867495 INFO: Decoy channel: -1
1:29:47.867517 INFO: Competetive: True
1:29:47.870010 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:47.892537 INFO: Test AUC: 0.772
1:29:47.892602 INFO: Train AUC: 0.748
1:29:47.892632 INFO: AUC difference: 3.19%
1:29:48.065623 INFO: Resetting torch num_threads to 100
1:29:48.066187 INFO: === FDR correction performed with classifier version 10 ===
1:29:48.066820 PROGRESS: ============================= Precursor FDR =============================
1:29:48.066921 PROGRESS: Total precursors accumulated: 505
1:29:48.066987 PROGRESS: Target precursors: 490 (97.03%)
1:29:48.067038 PROGRESS: Decoy precursors: 15 (2.97%)
1:29:48.067085 PROGRESS: 
1:29:48.067128 PROGRESS: Precursor Summary:
1:29:48.068130 PROGRESS: Channel   0:	 0.05 FDR:   490; 0.01 FDR:   413; 0.001 FDR:   245
1:29:48.068218 PROGRESS: 
1:29:48.068273 PROGRESS: Protein Summary:
1:29:48.069443 PROGRESS: Channel   0:	 0.05 FDR:   470; 0.01 FDR:   398; 0.001 FDR:   237
1:29:48.069535 PROGRESS: =========================================================================
1:29:48.072650 INFO: fragments_df: keeping 3630 of 22312 [sum(precursor_idx_mask)=8324 sum(mass_error_mask)=22312 stop_rank=3630
1:29:48.077376 INFO: calibration group: precursor, fitting rt estimator 
1:29:48.197027 INFO: calibration group: fragment, fitting mz estimator 
1:29:48.621946 INFO: Using score_cutoff 41.92472184906006 (fac=0.99, q=1)
1:29:48.622330 INFO: calibration group: precursor, predicting mz
1:29:48.622413 WARNING: mz prediction was skipped as it has not been fitted yet
1:29:48.622443 INFO: calibration group: precursor, predicting rt
1:29:48.624003 INFO: calibration group: fragment, predicting mz
1:29:48.626361 INFO: === checking if optimization conditions were reached ===
1:29:48.627766 PROGRESS: ✅ ms2_error      : 6.2633 <= 6.2633
1:29:48.627818 INFO: ==============================================
1:29:48.627902 PROGRESS: Optimization finished for ms2_error.
1:29:48.632381 INFO: calibration group: precursor, predicting mz
1:29:48.632482 WARNING: mz prediction was skipped as it has not been fitted yet
1:29:48.632517 INFO: calibration group: precursor, predicting rt
1:29:48.633821 INFO: calibration group: fragment, predicting mz
1:29:48.636145 INFO: Starting optimization step 0.
1:29:48.636243 PROGRESS: === Extracting elution groups 0 to 600 ===
1:29:48.636308 PROGRESS: Extracting batch of 1197 precursors
1:29:48.637093 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:29:48.637138 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:48.637168 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
1:29:48.637189 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:29:48.637335 INFO: Starting candidate selection
1:29:48.793692 INFO: Starting candidate scoring
1:29:48.833742 INFO: Finished candidate processing
1:29:48.833818 INFO: Collecting candidate features
1:29:48.845534 INFO: Collecting fragment features
1:29:48.850781 INFO: Finished candidate scoring
1:29:48.852595 PROGRESS: === Extracted 2394 precursors and 21193 fragments ===
1:29:48.852858 INFO: performing precursor FDR with 47 features
1:29:48.852896 INFO: Decoy channel: -1
1:29:48.852922 INFO: Competetive: True
1:29:48.855522 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:48.888047 INFO: Test AUC: 0.718
1:29:48.888119 INFO: Train AUC: 0.752
1:29:48.888149 INFO: AUC difference: 4.55%
1:29:49.061721 INFO: Resetting torch num_threads to 100
1:29:49.062313 INFO: === FDR correction performed with classifier version 11 ===
1:29:49.062956 PROGRESS: ============================= Precursor FDR =============================
1:29:49.063048 PROGRESS: Total precursors accumulated: 493
1:29:49.063109 PROGRESS: Target precursors: 480 (97.36%)
1:29:49.063162 PROGRESS: Decoy precursors: 13 (2.64%)
1:29:49.063210 PROGRESS: 
1:29:49.063256 PROGRESS: Precursor Summary:
1:29:49.064267 PROGRESS: Channel   0:	 0.05 FDR:   480; 0.01 FDR:   417; 0.001 FDR:   314
1:29:49.064356 PROGRESS: 
1:29:49.064418 PROGRESS: Protein Summary:
1:29:49.065642 PROGRESS: Channel   0:	 0.05 FDR:   460; 0.01 FDR:   399; 0.001 FDR:   304
1:29:49.065731 PROGRESS: =========================================================================
1:29:49.068898 INFO: fragments_df: keeping 3713 of 21193 [sum(precursor_idx_mask)=8073 sum(mass_error_mask)=21193 stop_rank=3713
1:29:49.073635 INFO: calibration group: precursor, fitting rt estimator 
1:29:49.206742 INFO: calibration group: fragment, fitting mz estimator 
1:29:49.694470 INFO: Using score_cutoff 38.62322245788574 (fac=0.99, q=1)
1:29:49.694868 INFO: calibration group: precursor, predicting mz
1:29:49.694961 WARNING: mz prediction was skipped as it has not been fitted yet
1:29:49.694994 INFO: calibration group: precursor, predicting rt
1:29:49.696534 INFO: calibration group: fragment, predicting mz
1:29:49.698808 INFO: === checking if optimization conditions were reached ===
1:29:49.698914 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:29:49.700397 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 57.0801.
1:29:49.700447 INFO: ==============================================
1:29:49.700529 INFO: Starting optimization step 1.
1:29:49.700594 PROGRESS: === Extracting elution groups 0 to 600 ===
1:29:49.700650 PROGRESS: Extracting batch of 1197 precursors
1:29:49.701535 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:29:49.701583 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:49.701613 INFO: FWHM in RT is 2.25 seconds, sigma is 0.29
1:29:49.701635 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:29:49.701777 INFO: Starting candidate selection
1:29:49.815249 INFO: Starting candidate scoring
1:29:49.856059 INFO: Finished candidate processing
1:29:49.856144 INFO: Collecting candidate features
1:29:49.867633 INFO: Collecting fragment features
1:29:49.871640 INFO: Finished candidate scoring
1:29:49.873329 PROGRESS: === Extracted 2386 precursors and 19537 fragments ===
1:29:49.873602 INFO: performing precursor FDR with 47 features
1:29:49.873646 INFO: Decoy channel: -1
1:29:49.873674 INFO: Competetive: True
1:29:49.876282 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:49.898773 INFO: Test AUC: 0.750
1:29:49.898842 INFO: Train AUC: 0.726
1:29:49.898881 INFO: AUC difference: 3.29%
1:29:50.069706 INFO: Resetting torch num_threads to 100
1:29:50.070309 INFO: === FDR correction performed with classifier version 11 ===
1:29:50.070952 PROGRESS: ============================= Precursor FDR =============================
1:29:50.071055 PROGRESS: Total precursors accumulated: 474
1:29:50.071130 PROGRESS: Target precursors: 459 (96.84%)
1:29:50.071196 PROGRESS: Decoy precursors: 15 (3.16%)
1:29:50.071256 PROGRESS: 
1:29:50.071313 PROGRESS: Precursor Summary:
1:29:50.072326 PROGRESS: Channel   0:	 0.05 FDR:   459; 0.01 FDR:   338; 0.001 FDR:   210
1:29:50.072423 PROGRESS: 
1:29:50.072491 PROGRESS: Protein Summary:
1:29:50.073667 PROGRESS: Channel   0:	 0.05 FDR:   442; 0.01 FDR:   325; 0.001 FDR:   202
1:29:50.073764 PROGRESS: =========================================================================
1:29:50.076630 INFO: fragments_df: keeping 3062 of 19537 [sum(precursor_idx_mask)=6486 sum(mass_error_mask)=19537 stop_rank=3062
1:29:50.081376 INFO: calibration group: precursor, fitting rt estimator 
1:29:50.177005 INFO: calibration group: fragment, fitting mz estimator 
1:29:50.516290 INFO: Using score_cutoff 41.97396409950256 (fac=0.99, q=1)
1:29:50.516702 INFO: calibration group: precursor, predicting mz
1:29:50.516793 WARNING: mz prediction was skipped as it has not been fitted yet
1:29:50.516830 INFO: calibration group: precursor, predicting rt
1:29:50.518443 INFO: calibration group: fragment, predicting mz
1:29:50.520759 INFO: === checking if optimization conditions were reached ===
1:29:50.520869 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:29:50.522404 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 13.2539.
1:29:50.522457 INFO: ==============================================
1:29:50.522555 INFO: Starting optimization step 2.
1:29:50.522642 PROGRESS: === Extracting elution groups 0 to 600 ===
1:29:50.522719 PROGRESS: Extracting batch of 1197 precursors
1:29:50.523623 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:29:50.523674 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:50.523715 INFO: FWHM in RT is 2.24 seconds, sigma is 0.29
1:29:50.523743 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:29:50.523902 INFO: Starting candidate selection
1:29:50.645513 INFO: Starting candidate scoring
1:29:50.685812 INFO: Finished candidate processing
1:29:50.685890 INFO: Collecting candidate features
1:29:50.697585 INFO: Collecting fragment features
1:29:50.702471 INFO: Finished candidate scoring
1:29:50.704105 PROGRESS: === Extracted 2321 precursors and 18159 fragments ===
1:29:50.704359 INFO: performing precursor FDR with 47 features
1:29:50.704394 INFO: Decoy channel: -1
1:29:50.704416 INFO: Competetive: True
1:29:50.706913 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:50.728204 INFO: Test AUC: 0.731
1:29:50.728266 INFO: Train AUC: 0.749
1:29:50.728296 INFO: AUC difference: 2.45%
1:29:50.900718 INFO: Resetting torch num_threads to 100
1:29:50.901276 INFO: === FDR correction performed with classifier version 11 ===
1:29:50.901878 PROGRESS: ============================= Precursor FDR =============================
1:29:50.901965 PROGRESS: Total precursors accumulated: 288
1:29:50.902023 PROGRESS: Target precursors: 270 (93.75%)
1:29:50.902073 PROGRESS: Decoy precursors: 18 (6.25%)
1:29:50.902120 PROGRESS: 
1:29:50.902163 PROGRESS: Precursor Summary:
1:29:50.903098 PROGRESS: Channel   0:	 0.05 FDR:   107; 0.01 FDR:    44; 0.001 FDR:    44
1:29:50.903188 PROGRESS: 
1:29:50.903250 PROGRESS: Protein Summary:
1:29:50.904250 PROGRESS: Channel   0:	 0.05 FDR:   105; 0.01 FDR:    43; 0.001 FDR:    43
1:29:50.904336 PROGRESS: =========================================================================
1:29:50.910576 INFO: calibration group: precursor, predicting mz
1:29:50.910696 WARNING: mz prediction was skipped as it has not been fitted yet
1:29:50.910739 INFO: calibration group: precursor, predicting rt
1:29:50.912434 INFO: calibration group: fragment, predicting mz
1:29:50.916085 INFO: === skipping optimization until target number of precursors are found ===
1:29:50.916196 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1:29:50.916249 INFO: Starting optimization step 3.
1:29:50.916310 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:29:50.916365 PROGRESS: Extracting batch of 1592 precursors
1:29:50.917222 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:29:50.917269 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:50.917300 INFO: FWHM in RT is 2.24 seconds, sigma is 0.29
1:29:50.917322 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:29:50.917465 INFO: Starting candidate selection
1:29:51.047476 INFO: Starting candidate scoring
1:29:51.088484 INFO: Finished candidate processing
1:29:51.088566 INFO: Collecting candidate features
1:29:51.101401 INFO: Collecting fragment features
1:29:51.105781 INFO: Finished candidate scoring
1:29:51.109840 PROGRESS: === Extracted 5407 precursors and 41847 fragments ===
1:29:51.110887 INFO: performing precursor FDR with 47 features
1:29:51.110935 INFO: Decoy channel: -1
1:29:51.110959 INFO: Competetive: True
1:29:51.114959 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:51.147939 INFO: Test AUC: 0.711
1:29:51.148017 INFO: Train AUC: 0.734
1:29:51.148050 INFO: AUC difference: 3.18%
1:29:51.328582 INFO: Resetting torch num_threads to 100
1:29:51.329318 INFO: === FDR correction performed with classifier version 11 ===
1:29:51.329934 PROGRESS: ============================= Precursor FDR =============================
1:29:51.330022 PROGRESS: Total precursors accumulated: 564
1:29:51.330087 PROGRESS: Target precursors: 524 (92.91%)
1:29:51.330140 PROGRESS: Decoy precursors: 40 (7.09%)
1:29:51.330185 PROGRESS: 
1:29:51.330229 PROGRESS: Precursor Summary:
1:29:51.331173 PROGRESS: Channel   0:	 0.05 FDR:   169; 0.01 FDR:   104; 0.001 FDR:    85
1:29:51.331264 PROGRESS: 
1:29:51.331319 PROGRESS: Protein Summary:
1:29:51.332374 PROGRESS: Channel   0:	 0.05 FDR:   164; 0.01 FDR:   102; 0.001 FDR:    83
1:29:51.332462 PROGRESS: =========================================================================
1:29:51.340152 INFO: calibration group: precursor, predicting mz
1:29:51.340265 WARNING: mz prediction was skipped as it has not been fitted yet
1:29:51.340306 INFO: calibration group: precursor, predicting rt
1:29:51.342999 INFO: calibration group: fragment, predicting mz
1:29:51.348396 INFO: === skipping optimization until target number of precursors are found ===
1:29:51.348505 PROGRESS: === Optimization of rt_error has been skipped 2 time(s); maximum number is 1 ===
1:29:51.348982 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 805.5992 found after 2 searches.
1:29:51.349040 PROGRESS: Optimization finished for rt_error.
1:29:51.353749 INFO: calibration group: precursor, predicting mz
1:29:51.353857 WARNING: mz prediction was skipped as it has not been fitted yet
1:29:51.353890 INFO: calibration group: precursor, predicting rt
1:29:51.355235 INFO: calibration group: fragment, predicting mz
1:29:51.383773 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:29:51.384002 PROGRESS: ==============================================
1:29:51.384080 PROGRESS: ms2_error      : 6.2633
1:29:51.384135 PROGRESS: rt_error       : 805.5992
1:29:51.384194 PROGRESS: ==============================================
1:29:51.385025 INFO: calibration group: precursor, predicting mz
1:29:51.385154 WARNING: mz prediction was skipped as it has not been fitted yet
1:29:51.385185 INFO: calibration group: precursor, predicting rt
1:29:51.520777 INFO: calibration group: fragment, predicting mz
1:29:51.876013 PROGRESS: Extracting batch of 220080 precursors
1:29:51.943546 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:29:51.943672 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:51.943705 INFO: FWHM in RT is 2.25 seconds, sigma is 0.29
1:29:51.943727 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:29:51.943937 INFO: Starting candidate selection
1:30:01.234100 INFO: Applying score cutoff of 38.62322245788574
1:30:01.249476 INFO: Removed 98356 precursors with score below cutoff
1:30:01.356801 INFO: Starting candidate scoring
1:30:03.934141 INFO: Finished candidate processing
1:30:03.934242 INFO: Collecting candidate features
1:30:04.451925 INFO: Collecting fragment features
1:30:04.662905 INFO: Finished candidate scoring
1:30:04.883075 INFO: === FDR correction performed with classifier version 12 ===
1:30:04.885081 INFO: performing precursor FDR with 47 features
1:30:04.885132 INFO: Decoy channel: -1
1:30:04.885157 INFO: Competetive: True
1:30:04.968942 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:05.002841 WARNING: FDR calculation for 191160 target and 150644 decoy PSMs
1:30:05.002969 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1:30:10.952087 INFO: Test AUC: 0.830
1:30:10.952287 INFO: Train AUC: 0.829
1:30:10.952317 INFO: AUC difference: 0.06%
1:30:11.234834 INFO: Resetting torch num_threads to 100
1:30:11.256079 INFO: Removing fragments below FDR threshold
1:30:11.331751 PROGRESS: ============================= Precursor FDR =============================
1:30:11.332025 PROGRESS: Total precursors accumulated: 97,481
1:30:11.332096 PROGRESS: Target precursors: 96,516 (99.01%)
1:30:11.332147 PROGRESS: Decoy precursors: 965 (0.99%)
1:30:11.332193 PROGRESS: 
1:30:11.332238 PROGRESS: Precursor Summary:
1:30:11.373457 PROGRESS: Channel   0:	 0.05 FDR: 96,516; 0.01 FDR: 96,516; 0.001 FDR: 86,693
1:30:11.374181 PROGRESS: 
1:30:11.374273 PROGRESS: Protein Summary:
1:30:11.435290 PROGRESS: Channel   0:	 0.05 FDR: 9,817; 0.01 FDR: 9,817; 0.001 FDR: 9,641
1:30:11.435536 PROGRESS: =========================================================================
1:30:12.120741 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:30:12.151232 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:30:12.151388 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant
1:30:12.151460 INFO: Creating folder run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/figures
1:30:12.152068 INFO: Initializing RawFileManager
1:30:21.913610 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.
1:30:21.918192 INFO: Determining DIA cycle
1:30:21.934584 INFO: Found cycle with start 0.00 min and length 300.
1:30:22.103155 INFO: RT (min)            : 0.0 - 26.9
1:30:22.103252 INFO: RT duration (sec)   : 1611.2
1:30:22.103281 INFO: RT duration (min)   : 26.9
1:30:22.103306 INFO: Cycle len (scans)   : 300
1:30:22.103326 INFO: Cycle len (sec)     : 1.65
1:30:22.103344 INFO: Number of cycles    : 978
1:30:22.103365 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:30:22.153249 INFO: Initializing CalibrationManager
1:30:22.153539 INFO: Loading calibration config
1:30:22.154140 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'}]
1:30:22.154234 INFO: Calibration group :fragment, found 1 estimator(s)
1:30:22.154320 INFO: Calibration group :precursor, found 3 estimator(s)
1:30:22.154407 INFO: Disabling ion mobility calibration
1:30:22.154434 INFO: removed mobility estimator from group precursor
1:30:22.154577 INFO: Initializing OptimizationManager
1:30:22.154704 INFO: initial parameter: ms1_error = 30
1:30:22.154774 INFO: initial parameter: ms2_error = 30
1:30:22.154829 INFO: initial parameter: rt_error = 805.6019897460938
1:30:22.154874 INFO: initial parameter: mobility_error = 0.1
1:30:22.154917 INFO: initial parameter: column_type = library
1:30:22.154960 INFO: initial parameter: num_candidates = 1
1:30:22.155001 INFO: initial parameter: classifier_version = -1
1:30:22.155043 INFO: initial parameter: fwhm_rt = 5
1:30:22.155085 INFO: initial parameter: fwhm_mobility = 0.01
1:30:22.155124 INFO: initial parameter: score_cutoff = 0
1:30:22.155198 INFO: Initializing TimingManager
1:30:22.155268 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:30:22.155416 INFO: FDRManager not loaded from disk.
1:30:22.155443 INFO: Initializing FDRManager
1:30:22.155483 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:30:22.190147 PROGRESS: 110,515 target precursors potentially observable (0 removed)
1:30:22.244898 PROGRESS: Starting initial search for precursors.
1:30:22.252537 INFO: Starting optimization step 0.
1:30:22.252703 PROGRESS: === Extracting elution groups 0 to 200 ===
1:30:22.252781 PROGRESS: Extracting batch of 400 precursors
1:30:22.253789 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:30:22.253839 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:22.253875 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:30:22.253896 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:30:22.254151 INFO: Starting candidate selection
1:30:22.387715 INFO: Starting candidate scoring
1:30:22.424680 INFO: Finished candidate processing
1:30:22.424747 INFO: Collecting candidate features
1:30:22.433092 INFO: Collecting fragment features
1:30:22.435155 INFO: Finished candidate scoring
1:30:22.435897 PROGRESS: === Extracted 400 precursors and 4417 fragments ===
1:30:22.436163 INFO: performing precursor FDR with 47 features
1:30:22.436199 INFO: Decoy channel: -1
1:30:22.436221 INFO: Competetive: True
1:30:22.437208 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:22.455222 INFO: Test AUC: 0.418
1:30:22.455287 INFO: Train AUC: 0.483
1:30:22.455316 INFO: AUC difference: 13.56%
1:30:22.455337 WARNING: AUC difference > 5%. This may indicate overfitting.
1:30:22.631690 INFO: Resetting torch num_threads to 100
1:30:22.632208 INFO: === FDR correction performed with classifier version -1 ===
1:30:22.632829 PROGRESS: ============================= Precursor FDR =============================
1:30:22.632922 PROGRESS: Total precursors accumulated: 3
1:30:22.632982 PROGRESS: Target precursors: 3 (100.00%)
1:30:22.633035 PROGRESS: Decoy precursors: 0 (0.00%)
1:30:22.633083 PROGRESS: 
1:30:22.633128 PROGRESS: Precursor Summary:
1:30:22.634053 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1:30:22.634142 PROGRESS: 
1:30:22.634198 PROGRESS: Protein Summary:
1:30:22.635226 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1:30:22.635318 PROGRESS: =========================================================================
1:30:22.638873 INFO: Starting optimization step 1.
1:30:22.638976 PROGRESS: === Extracting elution groups 200 to 600 ===
1:30:22.639038 PROGRESS: Extracting batch of 797 precursors
1:30:22.639766 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:30:22.639812 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:22.639842 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:30:22.639863 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:30:22.640013 INFO: Starting candidate selection
1:30:22.774143 INFO: Starting candidate scoring
1:30:22.810256 INFO: Finished candidate processing
1:30:22.810324 INFO: Collecting candidate features
1:30:22.819336 INFO: Collecting fragment features
1:30:22.821844 INFO: Finished candidate scoring
1:30:22.823701 PROGRESS: === Extracted 1197 precursors and 13174 fragments ===
1:30:22.824436 INFO: performing precursor FDR with 47 features
1:30:22.824477 INFO: Decoy channel: -1
1:30:22.824501 INFO: Competetive: True
1:30:22.827230 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:22.845932 INFO: Test AUC: 0.495
1:30:22.845991 INFO: Train AUC: 0.459
1:30:22.846019 INFO: AUC difference: 7.71%
1:30:22.846041 WARNING: AUC difference > 5%. This may indicate overfitting.
1:30:23.023942 INFO: Resetting torch num_threads to 100
1:30:23.024516 INFO: === FDR correction performed with classifier version -1 ===
1:30:23.025144 PROGRESS: ============================= Precursor FDR =============================
1:30:23.025236 PROGRESS: Total precursors accumulated: 3
1:30:23.025297 PROGRESS: Target precursors: 3 (100.00%)
1:30:23.025347 PROGRESS: Decoy precursors: 0 (0.00%)
1:30:23.025394 PROGRESS: 
1:30:23.025436 PROGRESS: Precursor Summary:
1:30:23.026364 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1:30:23.026452 PROGRESS: 
1:30:23.026508 PROGRESS: Protein Summary:
1:30:23.027535 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1:30:23.027628 PROGRESS: =========================================================================
1:30:23.032252 INFO: Starting optimization step 2.
1:30:23.032360 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:30:23.032422 PROGRESS: Extracting batch of 1592 precursors
1:30:23.033232 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:30:23.033276 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:23.033307 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:30:23.033328 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:30:23.033475 INFO: Starting candidate selection
1:30:23.187294 INFO: Starting candidate scoring
1:30:23.225203 INFO: Finished candidate processing
1:30:23.225279 INFO: Collecting candidate features
1:30:23.235494 INFO: Collecting fragment features
1:30:23.239408 INFO: Finished candidate scoring
1:30:23.242533 PROGRESS: === Extracted 2789 precursors and 30671 fragments ===
1:30:23.243551 INFO: performing precursor FDR with 47 features
1:30:23.243597 INFO: Decoy channel: -1
1:30:23.243620 INFO: Competetive: True
1:30:23.246992 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:23.286228 INFO: Test AUC: 0.440
1:30:23.286303 INFO: Train AUC: 0.464
1:30:23.286331 INFO: AUC difference: 4.99%
1:30:23.466317 INFO: Resetting torch num_threads to 100
1:30:23.467032 INFO: === FDR correction performed with classifier version -1 ===
1:30:23.467811 PROGRESS: ============================= Precursor FDR =============================
1:30:23.467912 PROGRESS: Total precursors accumulated: 1,400
1:30:23.467974 PROGRESS: Target precursors: 647 (46.21%)
1:30:23.468026 PROGRESS: Decoy precursors: 753 (53.79%)
1:30:23.468071 PROGRESS: 
1:30:23.468114 PROGRESS: Precursor Summary:
1:30:23.468967 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:30:23.469055 PROGRESS: 
1:30:23.469109 PROGRESS: Protein Summary:
1:30:23.470044 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:30:23.470132 PROGRESS: =========================================================================
1:30:23.476381 INFO: Starting optimization step 3.
1:30:23.476489 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:30:23.476550 PROGRESS: Extracting batch of 3186 precursors
1:30:23.477666 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:30:23.477712 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:23.477742 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:30:23.477763 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:30:23.477927 INFO: Starting candidate selection
1:30:23.730776 INFO: Starting candidate scoring
1:30:23.783687 INFO: Finished candidate processing
1:30:23.783798 INFO: Collecting candidate features
1:30:23.799749 INFO: Collecting fragment features
1:30:23.805038 INFO: Finished candidate scoring
1:30:23.810886 PROGRESS: === Extracted 5975 precursors and 65887 fragments ===
1:30:23.812372 INFO: performing precursor FDR with 47 features
1:30:23.812418 INFO: Decoy channel: -1
1:30:23.812442 INFO: Competetive: True
1:30:23.816996 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:23.876238 INFO: Test AUC: 0.465
1:30:23.876359 INFO: Train AUC: 0.455
1:30:23.876390 INFO: AUC difference: 2.18%
1:30:24.061993 INFO: Resetting torch num_threads to 100
1:30:24.063209 INFO: === FDR correction performed with classifier version -1 ===
1:30:24.064265 PROGRESS: ============================= Precursor FDR =============================
1:30:24.064363 PROGRESS: Total precursors accumulated: 3,000
1:30:24.064429 PROGRESS: Target precursors: 1,371 (45.70%)
1:30:24.064483 PROGRESS: Decoy precursors: 1,629 (54.30%)
1:30:24.064530 PROGRESS: 
1:30:24.064576 PROGRESS: Precursor Summary:
1:30:24.065489 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:30:24.065582 PROGRESS: 
1:30:24.065639 PROGRESS: Protein Summary:
1:30:24.066613 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:30:24.066715 PROGRESS: =========================================================================
1:30:24.080538 INFO: Starting optimization step 4.
1:30:24.080690 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:30:24.080759 PROGRESS: Extracting batch of 6377 precursors
1:30:24.082876 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:30:24.082930 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:24.082963 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:30:24.082985 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:30:24.083189 INFO: Starting candidate selection
1:30:24.569951 INFO: Starting candidate scoring
1:30:24.631148 INFO: Finished candidate processing
1:30:24.631275 INFO: Collecting candidate features
1:30:24.653120 INFO: Collecting fragment features
1:30:24.661079 INFO: Finished candidate scoring
1:30:24.670547 PROGRESS: === Extracted 12352 precursors and 135935 fragments ===
1:30:24.672826 INFO: performing precursor FDR with 47 features
1:30:24.672903 INFO: Decoy channel: -1
1:30:24.672929 INFO: Competetive: True
1:30:24.684479 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:24.796674 INFO: Test AUC: 0.470
1:30:24.796814 INFO: Train AUC: 0.453
1:30:24.796844 INFO: AUC difference: 3.80%
1:30:24.984220 INFO: Resetting torch num_threads to 100
1:30:24.985713 INFO: === FDR correction performed with classifier version -1 ===
1:30:24.987212 PROGRESS: ============================= Precursor FDR =============================
1:30:24.987324 PROGRESS: Total precursors accumulated: 6,200
1:30:24.987388 PROGRESS: Target precursors: 2,846 (45.90%)
1:30:24.987447 PROGRESS: Decoy precursors: 3,354 (54.10%)
1:30:24.987496 PROGRESS: 
1:30:24.987543 PROGRESS: Precursor Summary:
1:30:24.988500 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:30:24.988596 PROGRESS: 
1:30:24.988655 PROGRESS: Protein Summary:
1:30:24.989645 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:30:24.989743 PROGRESS: =========================================================================
1:30:25.012311 INFO: Starting optimization step 5.
1:30:25.012537 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:30:25.012609 PROGRESS: Extracting batch of 12745 precursors
1:30:25.015825 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:30:25.015881 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:25.015915 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:30:25.015938 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:30:25.016154 INFO: Starting candidate selection
1:30:25.869409 INFO: Starting candidate scoring
1:30:25.962058 INFO: Finished candidate processing
1:30:25.962159 INFO: Collecting candidate features
1:30:25.990289 INFO: Collecting fragment features
1:30:26.000147 INFO: Finished candidate scoring
1:30:26.013347 PROGRESS: === Extracted 25097 precursors and 276273 fragments ===
1:30:26.016659 INFO: performing precursor FDR with 47 features
1:30:26.016716 INFO: Decoy channel: -1
1:30:26.016741 INFO: Competetive: True
1:30:26.026099 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:26.383187 INFO: Test AUC: 0.821
1:30:26.383299 INFO: Train AUC: 0.815
1:30:26.383328 INFO: AUC difference: 0.79%
1:30:26.573119 INFO: Resetting torch num_threads to 100
1:30:26.574432 INFO: === FDR correction performed with classifier version -1 ===
1:30:26.575764 PROGRESS: ============================= Precursor FDR =============================
1:30:26.575861 PROGRESS: Total precursors accumulated: 7,095
1:30:26.575922 PROGRESS: Target precursors: 6,754 (95.19%)
1:30:26.575974 PROGRESS: Decoy precursors: 341 (4.81%)
1:30:26.576022 PROGRESS: 
1:30:26.576065 PROGRESS: Precursor Summary:
1:30:26.578064 PROGRESS: Channel   0:	 0.05 FDR: 6,730; 0.01 FDR: 4,604; 0.001 FDR:   112
1:30:26.578159 PROGRESS: 
1:30:26.578215 PROGRESS: Protein Summary:
1:30:26.581036 PROGRESS: Channel   0:	 0.05 FDR: 3,687; 0.01 FDR: 2,685; 0.001 FDR:   108
1:30:26.581135 PROGRESS: =========================================================================
1:30:26.608877 INFO: fragments_df: keeping 5000 of 276273 [sum(precursor_idx_mask)=52134 sum(mass_error_mask)=276273 stop_rank=5000
1:30:26.615675 INFO: calibration group: precursor, fitting rt estimator 
1:30:27.244471 INFO: calibration group: fragment, fitting mz estimator 
1:30:27.918292 INFO: Using score_cutoff 58.42108277778626 (fac=0.99, q=1)
1:30:27.918765 INFO: calibration group: precursor, predicting mz
1:30:27.918857 WARNING: mz prediction was skipped as it has not been fitted yet
1:30:27.918888 INFO: calibration group: precursor, predicting rt
1:30:27.920390 INFO: calibration group: fragment, predicting mz
1:30:27.922705 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:30:27.922827 INFO: Starting optimization step 6.
1:30:27.922898 PROGRESS: === Extracting elution groups 0 to 600 ===
1:30:27.922956 PROGRESS: Extracting batch of 1197 precursors
1:30:27.923888 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:30:27.923936 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:27.923966 INFO: FWHM in RT is 2.96 seconds, sigma is 0.38
1:30:27.923989 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:30:27.924148 INFO: Starting candidate selection
1:30:28.075109 INFO: Starting candidate scoring
1:30:28.113728 INFO: Finished candidate processing
1:30:28.113808 INFO: Collecting candidate features
1:30:28.125793 INFO: Collecting fragment features
1:30:28.130060 INFO: Finished candidate scoring
1:30:28.131678 PROGRESS: === Extracted 2394 precursors and 26047 fragments ===
1:30:28.131940 INFO: performing precursor FDR with 47 features
1:30:28.131975 INFO: Decoy channel: -1
1:30:28.131999 INFO: Competetive: True
1:30:28.134481 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:28.156054 INFO: Test AUC: 0.675
1:30:28.156120 INFO: Train AUC: 0.714
1:30:28.156149 INFO: AUC difference: 5.45%
1:30:28.156171 WARNING: AUC difference > 5%. This may indicate overfitting.
1:30:28.334616 INFO: Resetting torch num_threads to 100
1:30:28.335192 INFO: === FDR correction performed with classifier version 5 ===
1:30:28.335809 PROGRESS: ============================= Precursor FDR =============================
1:30:28.335901 PROGRESS: Total precursors accumulated: 380
1:30:28.335959 PROGRESS: Target precursors: 360 (94.74%)
1:30:28.336011 PROGRESS: Decoy precursors: 20 (5.26%)
1:30:28.336064 PROGRESS: 
1:30:28.336111 PROGRESS: Precursor Summary:
1:30:28.337072 PROGRESS: Channel   0:	 0.05 FDR:   353; 0.01 FDR:   244; 0.001 FDR:    58
1:30:28.337162 PROGRESS: 
1:30:28.337217 PROGRESS: Protein Summary:
1:30:28.338289 PROGRESS: Channel   0:	 0.05 FDR:   341; 0.01 FDR:   236; 0.001 FDR:    57
1:30:28.338379 PROGRESS: =========================================================================
1:30:28.341813 INFO: fragments_df: keeping 2482 of 26047 [sum(precursor_idx_mask)=5386 sum(mass_error_mask)=26047 stop_rank=2482
1:30:28.346637 INFO: calibration group: precursor, fitting rt estimator 
1:30:28.442728 INFO: calibration group: fragment, fitting mz estimator 
1:30:28.715914 INFO: Using score_cutoff 57.11229797401428 (fac=0.99, q=1)
1:30:28.716297 INFO: calibration group: precursor, predicting mz
1:30:28.716383 WARNING: mz prediction was skipped as it has not been fitted yet
1:30:28.716414 INFO: calibration group: precursor, predicting rt
1:30:28.717941 INFO: calibration group: fragment, predicting mz
1:30:28.720214 INFO: === checking if optimization conditions were reached ===
1:30:28.721462 PROGRESS: ❌ ms2_error      : 14.6961 > 6.2633 or insufficient steps taken.
1:30:28.721516 INFO: ==============================================
1:30:28.721604 INFO: Starting optimization step 7.
1:30:28.721670 PROGRESS: === Extracting elution groups 0 to 600 ===
1:30:28.721728 PROGRESS: Extracting batch of 1197 precursors
1:30:28.722654 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:30:28.722701 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:28.722732 INFO: FWHM in RT is 2.92 seconds, sigma is 0.38
1:30:28.722753 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:30:28.722898 INFO: Starting candidate selection
1:30:28.870967 INFO: Starting candidate scoring
1:30:28.911676 INFO: Finished candidate processing
1:30:28.911755 INFO: Collecting candidate features
1:30:28.923554 INFO: Collecting fragment features
1:30:28.927818 INFO: Finished candidate scoring
1:30:28.929467 PROGRESS: === Extracted 2394 precursors and 24243 fragments ===
1:30:28.929733 INFO: performing precursor FDR with 47 features
1:30:28.929768 INFO: Decoy channel: -1
1:30:28.929790 INFO: Competetive: True
1:30:28.932321 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:28.954904 INFO: Test AUC: 0.736
1:30:28.954971 INFO: Train AUC: 0.733
1:30:28.955012 INFO: AUC difference: 0.41%
1:30:29.132863 INFO: Resetting torch num_threads to 100
1:30:29.133461 INFO: === FDR correction performed with classifier version 6 ===
1:30:29.134078 PROGRESS: ============================= Precursor FDR =============================
1:30:29.134169 PROGRESS: Total precursors accumulated: 453
1:30:29.134231 PROGRESS: Target precursors: 437 (96.47%)
1:30:29.134283 PROGRESS: Decoy precursors: 16 (3.53%)
1:30:29.134331 PROGRESS: 
1:30:29.134376 PROGRESS: Precursor Summary:
1:30:29.135370 PROGRESS: Channel   0:	 0.05 FDR:   437; 0.01 FDR:   332; 0.001 FDR:   266
1:30:29.135465 PROGRESS: 
1:30:29.135523 PROGRESS: Protein Summary:
1:30:29.136677 PROGRESS: Channel   0:	 0.05 FDR:   420; 0.01 FDR:   321; 0.001 FDR:   257
1:30:29.136768 PROGRESS: =========================================================================
1:30:29.139942 INFO: fragments_df: keeping 3155 of 24243 [sum(precursor_idx_mask)=7019 sum(mass_error_mask)=24243 stop_rank=3155
1:30:29.144801 INFO: calibration group: precursor, fitting rt estimator 
1:30:29.266623 INFO: calibration group: fragment, fitting mz estimator 
1:30:29.686801 INFO: Using score_cutoff 49.921349980545045 (fac=0.99, q=1)
1:30:29.687189 INFO: calibration group: precursor, predicting mz
1:30:29.687277 WARNING: mz prediction was skipped as it has not been fitted yet
1:30:29.687310 INFO: calibration group: precursor, predicting rt
1:30:29.688840 INFO: calibration group: fragment, predicting mz
1:30:29.691254 INFO: === checking if optimization conditions were reached ===
1:30:29.692606 PROGRESS: ❌ ms2_error      : 7.2764 > 6.2633 or insufficient steps taken.
1:30:29.692658 INFO: ==============================================
1:30:29.692744 INFO: Starting optimization step 8.
1:30:29.692809 PROGRESS: === Extracting elution groups 0 to 600 ===
1:30:29.692867 PROGRESS: Extracting batch of 1197 precursors
1:30:29.694065 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:30:29.694112 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:29.694143 INFO: FWHM in RT is 2.60 seconds, sigma is 0.33
1:30:29.694165 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:30:29.694310 INFO: Starting candidate selection
1:30:29.841236 INFO: Starting candidate scoring
1:30:29.883658 INFO: Finished candidate processing
1:30:29.883740 INFO: Collecting candidate features
1:30:29.895695 INFO: Collecting fragment features
1:30:29.900067 INFO: Finished candidate scoring
1:30:29.901823 PROGRESS: === Extracted 2394 precursors and 21807 fragments ===
1:30:29.902095 INFO: performing precursor FDR with 47 features
1:30:29.902131 INFO: Decoy channel: -1
1:30:29.902153 INFO: Competetive: True
1:30:29.904849 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:29.937301 INFO: Test AUC: 0.792
1:30:29.937374 INFO: Train AUC: 0.728
1:30:29.937403 INFO: AUC difference: 8.78%
1:30:29.937424 WARNING: AUC difference > 5%. This may indicate overfitting.
1:30:30.117494 INFO: Resetting torch num_threads to 100
1:30:30.118161 INFO: === FDR correction performed with classifier version 7 ===
1:30:30.118795 PROGRESS: ============================= Precursor FDR =============================
1:30:30.118888 PROGRESS: Total precursors accumulated: 483
1:30:30.118950 PROGRESS: Target precursors: 463 (95.86%)
1:30:30.119003 PROGRESS: Decoy precursors: 20 (4.14%)
1:30:30.119058 PROGRESS: 
1:30:30.119110 PROGRESS: Precursor Summary:
1:30:30.120094 PROGRESS: Channel   0:	 0.05 FDR:   463; 0.01 FDR:   348; 0.001 FDR:   185
1:30:30.120187 PROGRESS: 
1:30:30.120245 PROGRESS: Protein Summary:
1:30:30.121394 PROGRESS: Channel   0:	 0.05 FDR:   445; 0.01 FDR:   335; 0.001 FDR:   180
1:30:30.121486 PROGRESS: =========================================================================
1:30:30.124624 INFO: fragments_df: keeping 3284 of 21807 [sum(precursor_idx_mask)=6949 sum(mass_error_mask)=21807 stop_rank=3284
1:30:30.134768 INFO: calibration group: precursor, fitting rt estimator 
1:30:30.260911 INFO: calibration group: fragment, fitting mz estimator 
1:30:30.700775 INFO: Using score_cutoff 43.38270210456848 (fac=0.99, q=1)
1:30:30.701228 INFO: calibration group: precursor, predicting mz
1:30:30.701319 WARNING: mz prediction was skipped as it has not been fitted yet
1:30:30.701352 INFO: calibration group: precursor, predicting rt
1:30:30.703159 INFO: calibration group: fragment, predicting mz
1:30:30.705476 INFO: === checking if optimization conditions were reached ===
1:30:30.706894 PROGRESS: ✅ ms2_error      : 6.2633 <= 6.2633
1:30:30.706950 INFO: ==============================================
1:30:30.707044 PROGRESS: Optimization finished for ms2_error.
1:30:30.714485 INFO: calibration group: precursor, predicting mz
1:30:30.714597 WARNING: mz prediction was skipped as it has not been fitted yet
1:30:30.714638 INFO: calibration group: precursor, predicting rt
1:30:30.715918 INFO: calibration group: fragment, predicting mz
1:30:30.718174 INFO: Starting optimization step 0.
1:30:30.718270 PROGRESS: === Extracting elution groups 0 to 600 ===
1:30:30.718341 PROGRESS: Extracting batch of 1197 precursors
1:30:30.719331 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:30:30.719377 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:30.719411 INFO: FWHM in RT is 2.38 seconds, sigma is 0.31
1:30:30.719433 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:30:30.719604 INFO: Starting candidate selection
1:30:30.868492 INFO: Starting candidate scoring
1:30:30.910957 INFO: Finished candidate processing
1:30:30.911036 INFO: Collecting candidate features
1:30:30.922353 INFO: Collecting fragment features
1:30:30.927422 INFO: Finished candidate scoring
1:30:30.929050 PROGRESS: === Extracted 2394 precursors and 21072 fragments ===
1:30:30.929334 INFO: performing precursor FDR with 47 features
1:30:30.929369 INFO: Decoy channel: -1
1:30:30.929391 INFO: Competetive: True
1:30:30.932287 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:30.967312 INFO: Test AUC: 0.719
1:30:30.967409 INFO: Train AUC: 0.728
1:30:30.967438 INFO: AUC difference: 1.22%
1:30:31.143272 INFO: Resetting torch num_threads to 100
1:30:31.143853 INFO: === FDR correction performed with classifier version 8 ===
1:30:31.144480 PROGRESS: ============================= Precursor FDR =============================
1:30:31.144574 PROGRESS: Total precursors accumulated: 462
1:30:31.144634 PROGRESS: Target precursors: 443 (95.89%)
1:30:31.144687 PROGRESS: Decoy precursors: 19 (4.11%)
1:30:31.144733 PROGRESS: 
1:30:31.144781 PROGRESS: Precursor Summary:
1:30:31.145779 PROGRESS: Channel   0:	 0.05 FDR:   443; 0.01 FDR:   358; 0.001 FDR:   210
1:30:31.145871 PROGRESS: 
1:30:31.145928 PROGRESS: Protein Summary:
1:30:31.147117 PROGRESS: Channel   0:	 0.05 FDR:   427; 0.01 FDR:   345; 0.001 FDR:   203
1:30:31.147220 PROGRESS: =========================================================================
1:30:31.150217 INFO: fragments_df: keeping 3359 of 21072 [sum(precursor_idx_mask)=7007 sum(mass_error_mask)=21072 stop_rank=3359
1:30:31.155130 INFO: calibration group: precursor, fitting rt estimator 
1:30:31.261924 INFO: calibration group: fragment, fitting mz estimator 
1:30:31.641482 INFO: Using score_cutoff 42.07507904319763 (fac=0.99, q=1)
1:30:31.641908 INFO: calibration group: precursor, predicting mz
1:30:31.641998 WARNING: mz prediction was skipped as it has not been fitted yet
1:30:31.642029 INFO: calibration group: precursor, predicting rt
1:30:31.643583 INFO: calibration group: fragment, predicting mz
1:30:31.645899 INFO: === checking if optimization conditions were reached ===
1:30:31.646012 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:30:31.647525 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 173.1513.
1:30:31.647576 INFO: ==============================================
1:30:31.647663 INFO: Starting optimization step 1.
1:30:31.647732 PROGRESS: === Extracting elution groups 0 to 600 ===
1:30:31.647793 PROGRESS: Extracting batch of 1197 precursors
1:30:31.648773 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:30:31.648819 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:31.648852 INFO: FWHM in RT is 2.28 seconds, sigma is 0.29
1:30:31.648874 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:30:31.649045 INFO: Starting candidate selection
1:30:31.763878 INFO: Starting candidate scoring
1:30:31.804573 INFO: Finished candidate processing
1:30:31.804648 INFO: Collecting candidate features
1:30:31.816129 INFO: Collecting fragment features
1:30:31.820482 INFO: Finished candidate scoring
1:30:31.822148 PROGRESS: === Extracted 2393 precursors and 20583 fragments ===
1:30:31.822418 INFO: performing precursor FDR with 47 features
1:30:31.822454 INFO: Decoy channel: -1
1:30:31.822476 INFO: Competetive: True
1:30:31.825156 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:31.847834 INFO: Test AUC: 0.747
1:30:31.847901 INFO: Train AUC: 0.729
1:30:31.847930 INFO: AUC difference: 2.50%
1:30:32.023807 INFO: Resetting torch num_threads to 100
1:30:32.024383 INFO: === FDR correction performed with classifier version 8 ===
1:30:32.025008 PROGRESS: ============================= Precursor FDR =============================
1:30:32.025098 PROGRESS: Total precursors accumulated: 464
1:30:32.025158 PROGRESS: Target precursors: 443 (95.47%)
1:30:32.025208 PROGRESS: Decoy precursors: 21 (4.53%)
1:30:32.025254 PROGRESS: 
1:30:32.025297 PROGRESS: Precursor Summary:
1:30:32.026309 PROGRESS: Channel   0:	 0.05 FDR:   443; 0.01 FDR:   309; 0.001 FDR:   195
1:30:32.026402 PROGRESS: 
1:30:32.026458 PROGRESS: Protein Summary:
1:30:32.027636 PROGRESS: Channel   0:	 0.05 FDR:   426; 0.01 FDR:   298; 0.001 FDR:   189
1:30:32.027729 PROGRESS: =========================================================================
1:30:32.030566 INFO: fragments_df: keeping 3005 of 20583 [sum(precursor_idx_mask)=6054 sum(mass_error_mask)=20583 stop_rank=3005
1:30:32.036934 INFO: calibration group: precursor, fitting rt estimator 
1:30:32.158291 INFO: calibration group: fragment, fitting mz estimator 
1:30:32.556155 INFO: Using score_cutoff 41.93431640167236 (fac=0.99, q=1)
1:30:32.556542 INFO: calibration group: precursor, predicting mz
1:30:32.556627 WARNING: mz prediction was skipped as it has not been fitted yet
1:30:32.556656 INFO: calibration group: precursor, predicting rt
1:30:32.558195 INFO: calibration group: fragment, predicting mz
1:30:32.560475 INFO: === checking if optimization conditions were reached ===
1:30:32.560576 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:30:32.562070 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 13.4150.
1:30:32.562119 INFO: ==============================================
1:30:32.562212 INFO: Starting optimization step 2.
1:30:32.562280 PROGRESS: === Extracting elution groups 0 to 600 ===
1:30:32.562335 PROGRESS: Extracting batch of 1197 precursors
1:30:32.563236 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:30:32.563282 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:32.563313 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
1:30:32.563334 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:30:32.563478 INFO: Starting candidate selection
1:30:32.674576 INFO: Starting candidate scoring
1:30:32.714903 INFO: Finished candidate processing
1:30:32.714984 INFO: Collecting candidate features
1:30:32.723711 WARNING: intensity_correlation has 2 NaNs ( 0.09 % out of 2309)
1:30:32.726775 INFO: Collecting fragment features
1:30:32.731790 INFO: Finished candidate scoring
1:30:32.733464 PROGRESS: === Extracted 2309 precursors and 18131 fragments ===
1:30:32.733732 INFO: performing precursor FDR with 47 features
1:30:32.733771 INFO: Decoy channel: -1
1:30:32.733796 INFO: Competetive: True
1:30:32.736367 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:32.737577 WARNING: dropped 2 decoy PSMs due to missing features
1:30:32.759703 INFO: Test AUC: 0.768
1:30:32.759767 INFO: Train AUC: 0.762
1:30:32.759809 INFO: AUC difference: 0.80%
1:30:32.932760 INFO: Resetting torch num_threads to 100
1:30:32.933314 INFO: === FDR correction performed with classifier version 8 ===
1:30:32.933940 PROGRESS: ============================= Precursor FDR =============================
1:30:32.934032 PROGRESS: Total precursors accumulated: 508
1:30:32.934092 PROGRESS: Target precursors: 496 (97.64%)
1:30:32.934144 PROGRESS: Decoy precursors: 12 (2.36%)
1:30:32.934195 PROGRESS: 
1:30:32.934240 PROGRESS: Precursor Summary:
1:30:32.935189 PROGRESS: Channel   0:	 0.05 FDR:   496; 0.01 FDR:    13; 0.001 FDR:    13
1:30:32.935287 PROGRESS: 
1:30:32.935342 PROGRESS: Protein Summary:
1:30:32.936401 PROGRESS: Channel   0:	 0.05 FDR:   477; 0.01 FDR:    13; 0.001 FDR:    13
1:30:32.936499 PROGRESS: =========================================================================
1:30:32.944989 INFO: calibration group: precursor, predicting mz
1:30:32.945100 WARNING: mz prediction was skipped as it has not been fitted yet
1:30:32.945131 INFO: calibration group: precursor, predicting rt
1:30:32.946769 INFO: calibration group: fragment, predicting mz
1:30:32.950309 INFO: === skipping optimization until target number of precursors are found ===
1:30:32.950419 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1:30:32.950469 INFO: Starting optimization step 3.
1:30:32.950532 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:30:32.950588 PROGRESS: Extracting batch of 1592 precursors
1:30:32.951486 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:30:32.951530 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:32.951559 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
1:30:32.951581 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:30:32.951730 INFO: Starting candidate selection
1:30:33.080593 INFO: Starting candidate scoring
1:30:33.120916 INFO: Finished candidate processing
1:30:33.120998 INFO: Collecting candidate features
1:30:33.133346 INFO: Collecting fragment features
1:30:33.137562 INFO: Finished candidate scoring
1:30:33.140978 PROGRESS: === Extracted 5393 precursors and 42073 fragments ===
1:30:33.141880 INFO: performing precursor FDR with 47 features
1:30:33.141923 INFO: Decoy channel: -1
1:30:33.141948 INFO: Competetive: True
1:30:33.145521 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:33.147119 WARNING: dropped 2 decoy PSMs due to missing features
1:30:33.188771 INFO: Test AUC: 0.781
1:30:33.188856 INFO: Train AUC: 0.760
1:30:33.188885 INFO: AUC difference: 2.71%
1:30:33.365067 INFO: Resetting torch num_threads to 100
1:30:33.365794 INFO: === FDR correction performed with classifier version 8 ===
1:30:33.366501 PROGRESS: ============================= Precursor FDR =============================
1:30:33.366592 PROGRESS: Total precursors accumulated: 1,191
1:30:33.366666 PROGRESS: Target precursors: 1,157 (97.15%)
1:30:33.366720 PROGRESS: Decoy precursors: 34 (2.85%)
1:30:33.366767 PROGRESS: 
1:30:33.366818 PROGRESS: Precursor Summary:
1:30:33.367875 PROGRESS: Channel   0:	 0.05 FDR: 1,157; 0.01 FDR:   117; 0.001 FDR:    26
1:30:33.367969 PROGRESS: 
1:30:33.368027 PROGRESS: Protein Summary:
1:30:33.369317 PROGRESS: Channel   0:	 0.05 FDR: 1,029; 0.01 FDR:   114; 0.001 FDR:    26
1:30:33.369414 PROGRESS: =========================================================================
1:30:33.379303 INFO: calibration group: precursor, predicting mz
1:30:33.379421 WARNING: mz prediction was skipped as it has not been fitted yet
1:30:33.379452 INFO: calibration group: precursor, predicting rt
1:30:33.381987 INFO: calibration group: fragment, predicting mz
1:30:33.387484 INFO: === skipping optimization until target number of precursors are found ===
1:30:36.810332 PROGRESS: === Optimization of rt_error has been skipped 2 time(s); maximum number is 1 ===
1:30:36.811219 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 805.6020 found after 2 searches.
1:30:36.811291 PROGRESS: Optimization finished for rt_error.
1:30:36.816435 INFO: calibration group: precursor, predicting mz
1:30:36.816544 WARNING: mz prediction was skipped as it has not been fitted yet
1:30:36.816576 INFO: calibration group: precursor, predicting rt
1:30:36.818018 INFO: calibration group: fragment, predicting mz
1:30:36.846084 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:30:36.846226 PROGRESS: ==============================================
1:30:36.846300 PROGRESS: ms2_error      : 6.2633
1:30:36.846357 PROGRESS: rt_error       : 805.6020
1:30:36.846407 PROGRESS: ==============================================
1:30:36.846986 INFO: calibration group: precursor, predicting mz
1:30:36.847091 WARNING: mz prediction was skipped as it has not been fitted yet
1:30:36.847122 INFO: calibration group: precursor, predicting rt
1:30:36.975368 INFO: calibration group: fragment, predicting mz
1:30:37.315742 PROGRESS: Extracting batch of 220080 precursors
1:30:37.383590 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:30:37.383713 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:37.383748 INFO: FWHM in RT is 2.28 seconds, sigma is 0.29
1:30:37.383771 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:30:37.383980 INFO: Starting candidate selection
1:30:46.951907 INFO: Applying score cutoff of 42.07507904319763
1:30:46.960275 INFO: Removed 134522 precursors with score below cutoff
1:30:47.029379 INFO: Starting candidate scoring
1:30:49.341464 INFO: Finished candidate processing
1:30:49.341612 INFO: Collecting candidate features
1:30:49.838073 INFO: Collecting fragment features
1:30:50.030175 INFO: Finished candidate scoring
1:30:50.205689 INFO: === FDR correction performed with classifier version 9 ===
1:30:50.206964 INFO: performing precursor FDR with 47 features
1:30:50.207013 INFO: Decoy channel: -1
1:30:50.207037 INFO: Competetive: True
1:30:50.292145 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:50.322851 WARNING: FDR calculation for 177563 target and 128075 decoy PSMs
1:30:50.322975 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1:30:55.606996 INFO: Test AUC: 0.837
1:30:55.607164 INFO: Train AUC: 0.839
1:30:55.607195 INFO: AUC difference: 0.28%
1:30:55.878931 INFO: Resetting torch num_threads to 100
1:30:55.898703 INFO: Removing fragments below FDR threshold
1:30:55.962321 PROGRESS: ============================= Precursor FDR =============================
1:30:55.962590 PROGRESS: Total precursors accumulated: 95,696
1:30:55.962674 PROGRESS: Target precursors: 94,749 (99.01%)
1:30:55.962736 PROGRESS: Decoy precursors: 947 (0.99%)
1:30:55.962785 PROGRESS: 
1:30:55.962832 PROGRESS: Precursor Summary:
1:30:56.002160 PROGRESS: Channel   0:	 0.05 FDR: 94,749; 0.01 FDR: 94,749; 0.001 FDR: 86,360
1:30:56.002413 PROGRESS: 
1:30:56.002475 PROGRESS: Protein Summary:
1:30:56.062489 PROGRESS: Channel   0:	 0.05 FDR: 9,797; 0.01 FDR: 9,797; 0.001 FDR: 9,629
1:30:56.062749 PROGRESS: =========================================================================
1:30:56.733412 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:30:56.763593 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:30:56.763745 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant
1:30:56.763814 INFO: Creating folder run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/figures
1:30:56.764377 INFO: Initializing RawFileManager
1:31:06.770170 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.
1:31:06.775224 INFO: Determining DIA cycle
1:31:06.790464 INFO: Found cycle with start 0.00 min and length 300.
1:31:06.953629 INFO: RT (min)            : 0.0 - 26.9
1:31:06.953728 INFO: RT duration (sec)   : 1611.2
1:31:06.953777 INFO: RT duration (min)   : 26.9
1:31:06.953803 INFO: Cycle len (scans)   : 300
1:31:06.953822 INFO: Cycle len (sec)     : 1.65
1:31:06.953840 INFO: Number of cycles    : 977
1:31:06.953859 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:31:07.004686 INFO: Initializing CalibrationManager
1:31:07.004978 INFO: Loading calibration config
1:31:07.005586 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'}]
1:31:07.005675 INFO: Calibration group :fragment, found 1 estimator(s)
1:31:07.005764 INFO: Calibration group :precursor, found 3 estimator(s)
1:31:07.005841 INFO: Disabling ion mobility calibration
1:31:07.005869 INFO: removed mobility estimator from group precursor
1:31:07.006012 INFO: Initializing OptimizationManager
1:31:07.006122 INFO: initial parameter: ms1_error = 30
1:31:07.006188 INFO: initial parameter: ms2_error = 30
1:31:07.006237 INFO: initial parameter: rt_error = 805.6004638671875
1:31:07.006286 INFO: initial parameter: mobility_error = 0.1
1:31:07.006329 INFO: initial parameter: column_type = library
1:31:07.006372 INFO: initial parameter: num_candidates = 1
1:31:07.006416 INFO: initial parameter: classifier_version = -1
1:31:07.006458 INFO: initial parameter: fwhm_rt = 5
1:31:07.006499 INFO: initial parameter: fwhm_mobility = 0.01
1:31:07.006540 INFO: initial parameter: score_cutoff = 0
1:31:07.006617 INFO: Initializing TimingManager
1:31:07.006685 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:31:07.006800 INFO: FDRManager not loaded from disk.
1:31:07.006823 INFO: Initializing FDRManager
1:31:07.006859 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:31:07.043017 PROGRESS: 110,515 target precursors potentially observable (0 removed)
1:31:07.094461 PROGRESS: Starting initial search for precursors.
1:31:07.102090 INFO: Starting optimization step 0.
1:31:07.102251 PROGRESS: === Extracting elution groups 0 to 200 ===
1:31:07.102323 PROGRESS: Extracting batch of 400 precursors
1:31:07.103326 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:07.103379 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:07.103414 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:31:07.103437 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:31:07.103698 INFO: Starting candidate selection
1:31:07.232613 INFO: Starting candidate scoring
1:31:07.269248 INFO: Finished candidate processing
1:31:07.269317 INFO: Collecting candidate features
1:31:07.277585 INFO: Collecting fragment features
1:31:07.279590 INFO: Finished candidate scoring
1:31:07.280309 PROGRESS: === Extracted 400 precursors and 4408 fragments ===
1:31:07.280562 INFO: performing precursor FDR with 47 features
1:31:07.280596 INFO: Decoy channel: -1
1:31:07.280619 INFO: Competetive: True
1:31:07.281617 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:07.299636 INFO: Test AUC: 0.523
1:31:07.299696 INFO: Train AUC: 0.448
1:31:07.299727 INFO: AUC difference: 16.69%
1:31:07.299749 WARNING: AUC difference > 5%. This may indicate overfitting.
1:31:07.473958 INFO: Resetting torch num_threads to 100
1:31:07.474499 INFO: === FDR correction performed with classifier version -1 ===
1:31:07.475154 PROGRESS: ============================= Precursor FDR =============================
1:31:07.475246 PROGRESS: Total precursors accumulated: 2
1:31:07.475305 PROGRESS: Target precursors: 2 (100.00%)
1:31:07.475356 PROGRESS: Decoy precursors: 0 (0.00%)
1:31:07.475401 PROGRESS: 
1:31:07.475445 PROGRESS: Precursor Summary:
1:31:07.476373 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:31:07.476460 PROGRESS: 
1:31:07.476518 PROGRESS: Protein Summary:
1:31:07.477543 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:31:07.477632 PROGRESS: =========================================================================
1:31:07.481214 INFO: Starting optimization step 1.
1:31:07.481314 PROGRESS: === Extracting elution groups 200 to 600 ===
1:31:07.481378 PROGRESS: Extracting batch of 797 precursors
1:31:07.482113 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:07.482156 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:07.482186 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:31:07.482208 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:31:07.482358 INFO: Starting candidate selection
1:31:07.615806 INFO: Starting candidate scoring
1:31:07.651140 INFO: Finished candidate processing
1:31:07.651201 INFO: Collecting candidate features
1:31:07.660097 INFO: Collecting fragment features
1:31:07.662702 INFO: Finished candidate scoring
1:31:07.664655 PROGRESS: === Extracted 1197 precursors and 13185 fragments ===
1:31:07.665392 INFO: performing precursor FDR with 47 features
1:31:07.665432 INFO: Decoy channel: -1
1:31:07.665455 INFO: Competetive: True
1:31:07.668174 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:07.700011 INFO: Test AUC: 0.458
1:31:07.700084 INFO: Train AUC: 0.435
1:31:07.700113 INFO: AUC difference: 5.22%
1:31:07.700134 WARNING: AUC difference > 5%. This may indicate overfitting.
1:31:07.868874 INFO: Resetting torch num_threads to 100
1:31:07.869481 INFO: === FDR correction performed with classifier version -1 ===
1:31:07.870140 PROGRESS: ============================= Precursor FDR =============================
1:31:07.870232 PROGRESS: Total precursors accumulated: 600
1:31:07.870292 PROGRESS: Target precursors: 272 (45.33%)
1:31:07.870344 PROGRESS: Decoy precursors: 328 (54.67%)
1:31:07.870391 PROGRESS: 
1:31:07.870435 PROGRESS: Precursor Summary:
1:31:07.871304 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:31:07.871394 PROGRESS: 
1:31:07.871448 PROGRESS: Protein Summary:
1:31:07.872371 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:31:07.872458 PROGRESS: =========================================================================
1:31:07.876980 INFO: Starting optimization step 2.
1:31:07.877088 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:31:07.877154 PROGRESS: Extracting batch of 1592 precursors
1:31:07.877983 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:07.878031 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:07.878061 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:31:07.878083 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:31:07.878232 INFO: Starting candidate selection
1:31:08.033663 INFO: Starting candidate scoring
1:31:08.074348 INFO: Finished candidate processing
1:31:08.074426 INFO: Collecting candidate features
1:31:08.084577 INFO: Collecting fragment features
1:31:08.088444 INFO: Finished candidate scoring
1:31:08.091343 PROGRESS: === Extracted 2789 precursors and 30751 fragments ===
1:31:08.092337 INFO: performing precursor FDR with 47 features
1:31:08.092386 INFO: Decoy channel: -1
1:31:08.092418 INFO: Competetive: True
1:31:08.095575 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:08.118979 INFO: Test AUC: 0.435
1:31:08.119053 INFO: Train AUC: 0.448
1:31:08.119105 INFO: AUC difference: 2.83%
1:31:08.291371 INFO: Resetting torch num_threads to 100
1:31:08.292044 INFO: === FDR correction performed with classifier version -1 ===
1:31:08.292710 PROGRESS: ============================= Precursor FDR =============================
1:31:08.292810 PROGRESS: Total precursors accumulated: 1
1:31:08.292883 PROGRESS: Target precursors: 1 (100.00%)
1:31:08.292948 PROGRESS: Decoy precursors: 0 (0.00%)
1:31:08.293009 PROGRESS: 
1:31:08.293067 PROGRESS: Precursor Summary:
1:31:08.294020 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:31:08.294119 PROGRESS: 
1:31:08.294186 PROGRESS: Protein Summary:
1:31:08.295259 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:31:08.295358 PROGRESS: =========================================================================
1:31:08.301563 INFO: Starting optimization step 3.
1:31:08.301678 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:31:08.301754 PROGRESS: Extracting batch of 3186 precursors
1:31:08.304080 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:08.304127 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:08.304165 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:31:08.304195 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:31:08.304358 INFO: Starting candidate selection
1:31:08.569399 INFO: Starting candidate scoring
1:31:08.611278 INFO: Finished candidate processing
1:31:08.611367 INFO: Collecting candidate features
1:31:08.625581 INFO: Collecting fragment features
1:31:08.629570 INFO: Finished candidate scoring
1:31:08.633617 PROGRESS: === Extracted 5975 precursors and 65912 fragments ===
1:31:08.634839 INFO: performing precursor FDR with 47 features
1:31:08.634881 INFO: Decoy channel: -1
1:31:08.634905 INFO: Competetive: True
1:31:08.638807 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:08.669468 INFO: Test AUC: 0.422
1:31:08.669551 INFO: Train AUC: 0.437
1:31:08.669581 INFO: AUC difference: 3.45%
1:31:08.847620 INFO: Resetting torch num_threads to 100
1:31:08.848379 INFO: === FDR correction performed with classifier version -1 ===
1:31:08.849020 PROGRESS: ============================= Precursor FDR =============================
1:31:08.849108 PROGRESS: Total precursors accumulated: 2
1:31:08.849167 PROGRESS: Target precursors: 2 (100.00%)
1:31:08.849218 PROGRESS: Decoy precursors: 0 (0.00%)
1:31:08.849265 PROGRESS: 
1:31:08.849315 PROGRESS: Precursor Summary:
1:31:08.850230 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:31:08.850319 PROGRESS: 
1:31:08.850375 PROGRESS: Protein Summary:
1:31:08.851414 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:31:08.851503 PROGRESS: =========================================================================
1:31:08.861324 INFO: Starting optimization step 4.
1:31:08.861446 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:31:08.861510 PROGRESS: Extracting batch of 6377 precursors
1:31:08.863022 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:08.863071 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:08.863102 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:31:08.863123 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:31:08.863280 INFO: Starting candidate selection
1:31:09.308122 INFO: Starting candidate scoring
1:31:09.358552 INFO: Finished candidate processing
1:31:09.358657 INFO: Collecting candidate features
1:31:09.375960 INFO: Collecting fragment features
1:31:09.382173 INFO: Finished candidate scoring
1:31:09.389092 PROGRESS: === Extracted 12352 precursors and 135933 fragments ===
1:31:09.390931 INFO: performing precursor FDR with 47 features
1:31:09.390985 INFO: Decoy channel: -1
1:31:09.391009 INFO: Competetive: True
1:31:09.396051 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:09.442826 INFO: Test AUC: 0.436
1:31:09.442924 INFO: Train AUC: 0.428
1:31:09.442954 INFO: AUC difference: 1.94%
1:31:09.620640 INFO: Resetting torch num_threads to 100
1:31:09.621553 INFO: === FDR correction performed with classifier version -1 ===
1:31:09.622203 PROGRESS: ============================= Precursor FDR =============================
1:31:09.622295 PROGRESS: Total precursors accumulated: 1
1:31:09.622355 PROGRESS: Target precursors: 1 (100.00%)
1:31:09.622408 PROGRESS: Decoy precursors: 0 (0.00%)
1:31:09.622454 PROGRESS: 
1:31:09.622499 PROGRESS: Precursor Summary:
1:31:09.623448 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:31:09.623540 PROGRESS: 
1:31:09.623597 PROGRESS: Protein Summary:
1:31:09.624620 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:31:09.624708 PROGRESS: =========================================================================
1:31:09.640551 INFO: Starting optimization step 5.
1:31:09.640717 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:31:09.640784 PROGRESS: Extracting batch of 12745 precursors
1:31:09.643616 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:09.643666 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:09.643699 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:31:09.643721 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:31:09.643883 INFO: Starting candidate selection
1:31:10.440581 INFO: Starting candidate scoring
1:31:10.528699 INFO: Finished candidate processing
1:31:10.528796 INFO: Collecting candidate features
1:31:10.557023 INFO: Collecting fragment features
1:31:10.567224 INFO: Finished candidate scoring
1:31:10.579163 PROGRESS: === Extracted 25097 precursors and 276415 fragments ===
1:31:10.582654 INFO: performing precursor FDR with 47 features
1:31:10.582728 INFO: Decoy channel: -1
1:31:10.582752 INFO: Competetive: True
1:31:10.591153 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:10.998171 INFO: Test AUC: 0.811
1:31:10.998286 INFO: Train AUC: 0.806
1:31:10.998317 INFO: AUC difference: 0.57%
1:31:11.185651 INFO: Resetting torch num_threads to 100
1:31:11.187035 INFO: === FDR correction performed with classifier version -1 ===
1:31:11.188364 PROGRESS: ============================= Precursor FDR =============================
1:31:11.188461 PROGRESS: Total precursors accumulated: 6,887
1:31:11.188522 PROGRESS: Target precursors: 6,557 (95.21%)
1:31:11.188573 PROGRESS: Decoy precursors: 330 (4.79%)
1:31:11.188619 PROGRESS: 
1:31:11.188664 PROGRESS: Precursor Summary:
1:31:11.190855 PROGRESS: Channel   0:	 0.05 FDR: 6,549; 0.01 FDR: 4,470; 0.001 FDR: 2,124
1:31:11.190955 PROGRESS: 
1:31:11.191012 PROGRESS: Protein Summary:
1:31:11.194117 PROGRESS: Channel   0:	 0.05 FDR: 3,595; 0.01 FDR: 2,581; 0.001 FDR: 1,390
1:31:11.194219 PROGRESS: =========================================================================
1:31:11.220669 INFO: fragments_df: keeping 5000 of 276415 [sum(precursor_idx_mask)=50612 sum(mass_error_mask)=276415 stop_rank=5000
1:31:11.227428 INFO: calibration group: precursor, fitting rt estimator 
1:31:15.914515 INFO: calibration group: fragment, fitting mz estimator 
1:31:16.617446 INFO: Using score_cutoff 61.9598757774353 (fac=0.99, q=1)
1:31:16.617963 INFO: calibration group: precursor, predicting mz
1:31:16.618060 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:16.618095 INFO: calibration group: precursor, predicting rt
1:31:16.619909 INFO: calibration group: fragment, predicting mz
1:31:16.622358 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:31:16.622490 INFO: Starting optimization step 6.
1:31:16.622567 PROGRESS: === Extracting elution groups 0 to 600 ===
1:31:16.622638 PROGRESS: Extracting batch of 1197 precursors
1:31:16.626955 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:16.627006 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:16.627039 INFO: FWHM in RT is 3.03 seconds, sigma is 0.39
1:31:16.627062 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:16.627232 INFO: Starting candidate selection
1:31:16.782568 INFO: Starting candidate scoring
1:31:16.821518 INFO: Finished candidate processing
1:31:16.821601 INFO: Collecting candidate features
1:31:16.832765 INFO: Collecting fragment features
1:31:16.836874 INFO: Finished candidate scoring
1:31:16.838632 PROGRESS: === Extracted 2394 precursors and 26080 fragments ===
1:31:16.838917 INFO: performing precursor FDR with 47 features
1:31:16.838954 INFO: Decoy channel: -1
1:31:16.838976 INFO: Competetive: True
1:31:16.842052 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:16.865082 INFO: Test AUC: 0.682
1:31:16.865147 INFO: Train AUC: 0.697
1:31:16.865179 INFO: AUC difference: 2.08%
1:31:17.050318 INFO: Resetting torch num_threads to 100
1:31:17.051298 INFO: === FDR correction performed with classifier version 5 ===
1:31:17.052072 PROGRESS: ============================= Precursor FDR =============================
1:31:17.052167 PROGRESS: Total precursors accumulated: 376
1:31:17.052228 PROGRESS: Target precursors: 356 (94.68%)
1:31:17.052282 PROGRESS: Decoy precursors: 20 (5.32%)
1:31:17.052336 PROGRESS: 
1:31:17.052386 PROGRESS: Precursor Summary:
1:31:17.053393 PROGRESS: Channel   0:	 0.05 FDR:   341; 0.01 FDR:   259; 0.001 FDR:   144
1:31:17.053485 PROGRESS: 
1:31:17.053542 PROGRESS: Protein Summary:
1:31:17.054684 PROGRESS: Channel   0:	 0.05 FDR:   328; 0.01 FDR:   248; 0.001 FDR:   138
1:31:17.054778 PROGRESS: =========================================================================
1:31:17.064047 INFO: fragments_df: keeping 2677 of 26080 [sum(precursor_idx_mask)=5730 sum(mass_error_mask)=26080 stop_rank=2677
1:31:17.075580 INFO: calibration group: precursor, fitting rt estimator 
1:31:17.188042 INFO: calibration group: fragment, fitting mz estimator 
1:31:17.542553 INFO: Using score_cutoff 57.89593030929565 (fac=0.99, q=1)
1:31:17.542977 INFO: calibration group: precursor, predicting mz
1:31:17.543065 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:17.543096 INFO: calibration group: precursor, predicting rt
1:31:17.544647 INFO: calibration group: fragment, predicting mz
1:31:17.546973 INFO: === checking if optimization conditions were reached ===
1:31:17.548286 PROGRESS: ❌ ms2_error      : 14.8008 > 6.2633 or insufficient steps taken.
1:31:17.548337 INFO: ==============================================
1:31:17.548422 INFO: Starting optimization step 7.
1:31:17.548486 PROGRESS: === Extracting elution groups 0 to 600 ===
1:31:17.548549 PROGRESS: Extracting batch of 1197 precursors
1:31:17.549528 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:17.549576 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:17.549609 INFO: FWHM in RT is 3.02 seconds, sigma is 0.39
1:31:17.549631 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:17.549804 INFO: Starting candidate selection
1:31:17.695865 INFO: Starting candidate scoring
1:31:17.734712 INFO: Finished candidate processing
1:31:17.734792 INFO: Collecting candidate features
1:31:17.746055 INFO: Collecting fragment features
1:31:17.750436 INFO: Finished candidate scoring
1:31:17.752201 PROGRESS: === Extracted 2394 precursors and 24233 fragments ===
1:31:17.752463 INFO: performing precursor FDR with 47 features
1:31:17.752499 INFO: Decoy channel: -1
1:31:17.752521 INFO: Competetive: True
1:31:17.755171 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:17.777720 INFO: Test AUC: 0.738
1:31:17.777787 INFO: Train AUC: 0.720
1:31:17.777816 INFO: AUC difference: 2.54%
1:31:17.954556 INFO: Resetting torch num_threads to 100
1:31:17.955174 INFO: === FDR correction performed with classifier version 6 ===
1:31:17.955817 PROGRESS: ============================= Precursor FDR =============================
1:31:17.955911 PROGRESS: Total precursors accumulated: 417
1:31:17.955972 PROGRESS: Target precursors: 406 (97.36%)
1:31:17.956025 PROGRESS: Decoy precursors: 11 (2.64%)
1:31:17.956073 PROGRESS: 
1:31:17.956118 PROGRESS: Precursor Summary:
1:31:17.957102 PROGRESS: Channel   0:	 0.05 FDR:   406; 0.01 FDR:   363; 0.001 FDR:   304
1:31:17.957192 PROGRESS: 
1:31:17.957258 PROGRESS: Protein Summary:
1:31:17.958415 PROGRESS: Channel   0:	 0.05 FDR:   388; 0.01 FDR:   347; 0.001 FDR:   292
1:31:17.958506 PROGRESS: =========================================================================
1:31:17.961801 INFO: fragments_df: keeping 3478 of 24233 [sum(precursor_idx_mask)=7695 sum(mass_error_mask)=24233 stop_rank=3478
1:31:17.966582 INFO: calibration group: precursor, fitting rt estimator 
1:31:18.094290 INFO: calibration group: fragment, fitting mz estimator 
1:31:18.546962 INFO: Using score_cutoff 50.03442945098877 (fac=0.99, q=1)
1:31:18.547427 INFO: calibration group: precursor, predicting mz
1:31:18.547518 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:18.547547 INFO: calibration group: precursor, predicting rt
1:31:18.549234 INFO: calibration group: fragment, predicting mz
1:31:18.551567 INFO: === checking if optimization conditions were reached ===
1:31:18.552954 PROGRESS: ❌ ms2_error      : 7.6368 > 6.2633 or insufficient steps taken.
1:31:18.553008 INFO: ==============================================
1:31:18.553094 INFO: Starting optimization step 8.
1:31:18.553163 PROGRESS: === Extracting elution groups 0 to 600 ===
1:31:18.553224 PROGRESS: Extracting batch of 1197 precursors
1:31:18.554187 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:18.554234 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:18.554266 INFO: FWHM in RT is 2.62 seconds, sigma is 0.34
1:31:18.554288 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:18.554442 INFO: Starting candidate selection
1:31:18.707407 INFO: Starting candidate scoring
1:31:18.746792 INFO: Finished candidate processing
1:31:18.746870 INFO: Collecting candidate features
1:31:18.758031 INFO: Collecting fragment features
1:31:18.762262 INFO: Finished candidate scoring
1:31:18.763987 PROGRESS: === Extracted 2394 precursors and 21858 fragments ===
1:31:18.764255 INFO: performing precursor FDR with 47 features
1:31:18.764290 INFO: Decoy channel: -1
1:31:18.764312 INFO: Competetive: True
1:31:18.766966 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:18.789464 INFO: Test AUC: 0.738
1:31:18.789527 INFO: Train AUC: 0.744
1:31:18.789556 INFO: AUC difference: 0.74%
1:31:18.964373 INFO: Resetting torch num_threads to 100
1:31:18.964944 INFO: === FDR correction performed with classifier version 7 ===
1:31:18.965562 PROGRESS: ============================= Precursor FDR =============================
1:31:18.965653 PROGRESS: Total precursors accumulated: 460
1:31:18.965714 PROGRESS: Target precursors: 450 (97.83%)
1:31:18.965765 PROGRESS: Decoy precursors: 10 (2.17%)
1:31:18.965818 PROGRESS: 
1:31:18.965866 PROGRESS: Precursor Summary:
1:31:18.966860 PROGRESS: Channel   0:	 0.05 FDR:   450; 0.01 FDR:   345; 0.001 FDR:   266
1:31:18.966952 PROGRESS: 
1:31:18.967008 PROGRESS: Protein Summary:
1:31:18.968184 PROGRESS: Channel   0:	 0.05 FDR:   430; 0.01 FDR:   331; 0.001 FDR:   254
1:31:18.968274 PROGRESS: =========================================================================
1:31:18.971336 INFO: fragments_df: keeping 3322 of 21858 [sum(precursor_idx_mask)=6892 sum(mass_error_mask)=21858 stop_rank=3322
1:31:18.976094 INFO: calibration group: precursor, fitting rt estimator 
1:31:19.101124 INFO: calibration group: fragment, fitting mz estimator 
1:31:19.538204 INFO: Using score_cutoff 47.487097787475584 (fac=0.99, q=1)
1:31:19.538585 INFO: calibration group: precursor, predicting mz
1:31:19.538683 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:19.538714 INFO: calibration group: precursor, predicting rt
1:31:19.540241 INFO: calibration group: fragment, predicting mz
1:31:19.542522 INFO: === checking if optimization conditions were reached ===
1:31:19.543885 PROGRESS: ✅ ms2_error      : 6.2633 <= 6.2633
1:31:19.543936 INFO: ==============================================
1:31:19.544022 PROGRESS: Optimization finished for ms2_error.
1:31:19.550150 INFO: calibration group: precursor, predicting mz
1:31:19.550265 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:19.550303 INFO: calibration group: precursor, predicting rt
1:31:19.551596 INFO: calibration group: fragment, predicting mz
1:31:19.553880 INFO: Starting optimization step 0.
1:31:19.553974 PROGRESS: === Extracting elution groups 0 to 600 ===
1:31:19.554037 PROGRESS: Extracting batch of 1197 precursors
1:31:19.554850 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:19.554897 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:19.554926 INFO: FWHM in RT is 2.40 seconds, sigma is 0.31
1:31:19.554948 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:19.555093 INFO: Starting candidate selection
1:31:19.700841 INFO: Starting candidate scoring
1:31:19.741320 INFO: Finished candidate processing
1:31:19.741400 INFO: Collecting candidate features
1:31:19.752685 INFO: Collecting fragment features
1:31:19.757657 INFO: Finished candidate scoring
1:31:19.759367 PROGRESS: === Extracted 2394 precursors and 21195 fragments ===
1:31:19.759639 INFO: performing precursor FDR with 47 features
1:31:19.759676 INFO: Decoy channel: -1
1:31:19.759702 INFO: Competetive: True
1:31:19.762270 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:19.785324 INFO: Test AUC: 0.759
1:31:19.785396 INFO: Train AUC: 0.738
1:31:19.785425 INFO: AUC difference: 2.89%
1:31:19.958941 INFO: Resetting torch num_threads to 100
1:31:19.959493 INFO: === FDR correction performed with classifier version 8 ===
1:31:19.960121 PROGRESS: ============================= Precursor FDR =============================
1:31:19.960213 PROGRESS: Total precursors accumulated: 460
1:31:19.960274 PROGRESS: Target precursors: 449 (97.61%)
1:31:19.960325 PROGRESS: Decoy precursors: 11 (2.39%)
1:31:19.960371 PROGRESS: 
1:31:19.960418 PROGRESS: Precursor Summary:
1:31:19.961430 PROGRESS: Channel   0:	 0.05 FDR:   449; 0.01 FDR:   365; 0.001 FDR:   329
1:31:19.961520 PROGRESS: 
1:31:19.961576 PROGRESS: Protein Summary:
1:31:19.962774 PROGRESS: Channel   0:	 0.05 FDR:   431; 0.01 FDR:   351; 0.001 FDR:   316
1:31:19.962871 PROGRESS: =========================================================================
1:31:19.965876 INFO: fragments_df: keeping 3527 of 21195 [sum(precursor_idx_mask)=7180 sum(mass_error_mask)=21195 stop_rank=3527
1:31:19.970622 INFO: calibration group: precursor, fitting rt estimator 
1:31:20.099381 INFO: calibration group: fragment, fitting mz estimator 
1:31:20.558505 INFO: Using score_cutoff 45.861414944458005 (fac=0.99, q=1)
1:31:20.558900 INFO: calibration group: precursor, predicting mz
1:31:20.558987 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:20.559017 INFO: calibration group: precursor, predicting rt
1:31:20.560538 INFO: calibration group: fragment, predicting mz
1:31:20.562883 INFO: === checking if optimization conditions were reached ===
1:31:20.562990 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:31:20.564435 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 135.3019.
1:31:20.564487 INFO: ==============================================
1:31:20.564576 INFO: Starting optimization step 1.
1:31:20.564641 PROGRESS: === Extracting elution groups 0 to 600 ===
1:31:20.564697 PROGRESS: Extracting batch of 1197 precursors
1:31:20.565576 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:20.565619 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:20.565649 INFO: FWHM in RT is 2.34 seconds, sigma is 0.30
1:31:20.565670 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:20.565815 INFO: Starting candidate selection
1:31:20.678732 INFO: Starting candidate scoring
1:31:20.719490 INFO: Finished candidate processing
1:31:20.719568 INFO: Collecting candidate features
1:31:20.730846 INFO: Collecting fragment features
1:31:20.735049 INFO: Finished candidate scoring
1:31:20.736725 PROGRESS: === Extracted 2393 precursors and 20529 fragments ===
1:31:20.736992 INFO: performing precursor FDR with 47 features
1:31:20.737028 INFO: Decoy channel: -1
1:31:20.737061 INFO: Competetive: True
1:31:20.739685 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:20.761580 INFO: Test AUC: 0.718
1:31:20.761651 INFO: Train AUC: 0.749
1:31:20.761686 INFO: AUC difference: 4.12%
1:31:20.934823 INFO: Resetting torch num_threads to 100
1:31:20.935362 INFO: === FDR correction performed with classifier version 8 ===
1:31:20.936006 PROGRESS: ============================= Precursor FDR =============================
1:31:20.936095 PROGRESS: Total precursors accumulated: 466
1:31:20.936153 PROGRESS: Target precursors: 452 (97.00%)
1:31:20.936204 PROGRESS: Decoy precursors: 14 (3.00%)
1:31:20.936251 PROGRESS: 
1:31:20.936296 PROGRESS: Precursor Summary:
1:31:20.937262 PROGRESS: Channel   0:	 0.05 FDR:   452; 0.01 FDR:   356; 0.001 FDR:   320
1:31:20.937355 PROGRESS: 
1:31:20.937410 PROGRESS: Protein Summary:
1:31:20.938595 PROGRESS: Channel   0:	 0.05 FDR:   433; 0.01 FDR:   342; 0.001 FDR:   307
1:31:20.938695 PROGRESS: =========================================================================
1:31:20.941630 INFO: fragments_df: keeping 3375 of 20529 [sum(precursor_idx_mask)=6973 sum(mass_error_mask)=20529 stop_rank=3375
1:31:20.946644 INFO: calibration group: precursor, fitting rt estimator 
1:31:21.075081 INFO: calibration group: fragment, fitting mz estimator 
1:31:21.517615 INFO: Using score_cutoff 45.75996649360656 (fac=0.99, q=1)
1:31:21.518001 INFO: calibration group: precursor, predicting mz
1:31:21.518087 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:21.518117 INFO: calibration group: precursor, predicting rt
1:31:21.519681 INFO: calibration group: fragment, predicting mz
1:31:21.521998 INFO: === checking if optimization conditions were reached ===
1:31:21.522098 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:31:21.523625 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 31.6010.
1:31:21.523677 INFO: ==============================================
1:31:21.523774 INFO: Starting optimization step 2.
1:31:21.523844 PROGRESS: === Extracting elution groups 0 to 600 ===
1:31:21.523901 PROGRESS: Extracting batch of 1197 precursors
1:31:21.524785 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:21.524832 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:21.524861 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
1:31:21.524884 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:21.525030 INFO: Starting candidate selection
1:31:21.636293 INFO: Starting candidate scoring
1:31:21.676679 INFO: Finished candidate processing
1:31:21.676754 INFO: Collecting candidate features
1:31:21.688813 INFO: Collecting fragment features
1:31:21.693120 INFO: Finished candidate scoring
1:31:21.694807 PROGRESS: === Extracted 2381 precursors and 19133 fragments ===
1:31:21.695069 INFO: performing precursor FDR with 47 features
1:31:21.695105 INFO: Decoy channel: -1
1:31:21.695127 INFO: Competetive: True
1:31:21.697649 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:21.720825 INFO: Test AUC: 0.744
1:31:21.720894 INFO: Train AUC: 0.742
1:31:21.720923 INFO: AUC difference: 0.23%
1:31:21.896101 INFO: Resetting torch num_threads to 100
1:31:21.896664 INFO: === FDR correction performed with classifier version 8 ===
1:31:21.897273 PROGRESS: ============================= Precursor FDR =============================
1:31:21.897369 PROGRESS: Total precursors accumulated: 478
1:31:21.897429 PROGRESS: Target precursors: 466 (97.49%)
1:31:21.897479 PROGRESS: Decoy precursors: 12 (2.51%)
1:31:21.897524 PROGRESS: 
1:31:21.897568 PROGRESS: Precursor Summary:
1:31:21.898589 PROGRESS: Channel   0:	 0.05 FDR:   466; 0.01 FDR:   437; 0.001 FDR:   255
1:31:21.898698 PROGRESS: 
1:31:21.898753 PROGRESS: Protein Summary:
1:31:21.899959 PROGRESS: Channel   0:	 0.05 FDR:   448; 0.01 FDR:   420; 0.001 FDR:   243
1:31:21.900056 PROGRESS: =========================================================================
1:31:21.903091 INFO: fragments_df: keeping 3667 of 19133 [sum(precursor_idx_mask)=8282 sum(mass_error_mask)=19133 stop_rank=3667
1:31:21.907818 INFO: calibration group: precursor, fitting rt estimator 
1:31:22.017167 INFO: calibration group: fragment, fitting mz estimator 
1:31:22.428561 INFO: Using score_cutoff 42.448525144958495 (fac=0.99, q=1)
1:31:22.428953 INFO: calibration group: precursor, predicting mz
1:31:22.429040 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:22.429071 INFO: calibration group: precursor, predicting rt
1:31:22.430588 INFO: calibration group: fragment, predicting mz
1:31:22.432932 INFO: === checking if optimization conditions were reached ===
1:31:22.433033 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:31:22.434677 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 14.3242.
1:31:22.434728 INFO: ==============================================
1:31:22.434816 INFO: Starting optimization step 3.
1:31:22.434881 PROGRESS: === Extracting elution groups 0 to 600 ===
1:31:22.434938 PROGRESS: Extracting batch of 1197 precursors
1:31:22.435802 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:22.435845 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:22.435875 INFO: FWHM in RT is 2.26 seconds, sigma is 0.29
1:31:22.435897 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:22.436038 INFO: Starting candidate selection
1:31:22.549514 INFO: Starting candidate scoring
1:31:22.589577 INFO: Finished candidate processing
1:31:22.589650 INFO: Collecting candidate features
1:31:22.601654 INFO: Collecting fragment features
1:31:22.605793 INFO: Finished candidate scoring
1:31:22.607451 PROGRESS: === Extracted 2311 precursors and 18237 fragments ===
1:31:22.607715 INFO: performing precursor FDR with 47 features
1:31:22.607750 INFO: Decoy channel: -1
1:31:22.607771 INFO: Competetive: True
1:31:22.610295 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:22.634086 INFO: Test AUC: 0.737
1:31:22.634162 INFO: Train AUC: 0.754
1:31:22.634193 INFO: AUC difference: 2.23%
1:31:22.810733 INFO: Resetting torch num_threads to 100
1:31:22.811298 INFO: === FDR correction performed with classifier version 8 ===
1:31:22.811926 PROGRESS: ============================= Precursor FDR =============================
1:31:22.812017 PROGRESS: Total precursors accumulated: 483
1:31:22.812077 PROGRESS: Target precursors: 467 (96.69%)
1:31:22.812127 PROGRESS: Decoy precursors: 16 (3.31%)
1:31:22.812174 PROGRESS: 
1:31:22.812218 PROGRESS: Precursor Summary:
1:31:22.813200 PROGRESS: Channel   0:	 0.05 FDR:   467; 0.01 FDR:   286; 0.001 FDR:   261
1:31:22.813289 PROGRESS: 
1:31:22.813345 PROGRESS: Protein Summary:
1:31:22.814502 PROGRESS: Channel   0:	 0.05 FDR:   449; 0.01 FDR:   275; 0.001 FDR:   250
1:31:22.814590 PROGRESS: =========================================================================
1:31:22.817242 INFO: fragments_df: keeping 2679 of 18237 [sum(precursor_idx_mask)=5384 sum(mass_error_mask)=18237 stop_rank=2679
1:31:22.821981 INFO: calibration group: precursor, fitting rt estimator 
1:31:22.940231 INFO: calibration group: fragment, fitting mz estimator 
1:31:23.293936 INFO: Using score_cutoff 47.738461538314816 (fac=0.99, q=1)
1:31:23.294319 INFO: calibration group: precursor, predicting mz
1:31:23.294403 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:23.294433 INFO: calibration group: precursor, predicting rt
1:31:23.295977 INFO: calibration group: fragment, predicting mz
1:31:23.298239 INFO: === checking if optimization conditions were reached ===
1:31:23.298340 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:31:23.299901 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 9.0763.
1:31:23.299955 INFO: ==============================================
1:31:23.300050 INFO: Starting optimization step 4.
1:31:23.300119 PROGRESS: === Extracting elution groups 0 to 600 ===
1:31:23.300186 PROGRESS: Extracting batch of 1197 precursors
1:31:23.301073 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:23.301117 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:23.301147 INFO: FWHM in RT is 2.36 seconds, sigma is 0.30
1:31:23.301168 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:23.301313 INFO: Starting candidate selection
1:31:23.413574 INFO: Starting candidate scoring
1:31:23.453675 INFO: Finished candidate processing
1:31:23.453751 INFO: Collecting candidate features
1:31:23.465982 INFO: Collecting fragment features
1:31:23.470066 INFO: Finished candidate scoring
1:31:23.471725 PROGRESS: === Extracted 2318 precursors and 18392 fragments ===
1:31:23.471990 INFO: performing precursor FDR with 47 features
1:31:23.472026 INFO: Decoy channel: -1
1:31:23.472048 INFO: Competetive: True
1:31:23.474672 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:23.498146 INFO: Test AUC: 0.755
1:31:23.498218 INFO: Train AUC: 0.744
1:31:23.498249 INFO: AUC difference: 1.50%
1:31:23.672848 INFO: Resetting torch num_threads to 100
1:31:23.673422 INFO: === FDR correction performed with classifier version 8 ===
1:31:23.674044 PROGRESS: ============================= Precursor FDR =============================
1:31:23.674134 PROGRESS: Total precursors accumulated: 490
1:31:23.674195 PROGRESS: Target precursors: 479 (97.76%)
1:31:23.674247 PROGRESS: Decoy precursors: 11 (2.24%)
1:31:23.674293 PROGRESS: 
1:31:23.674338 PROGRESS: Precursor Summary:
1:31:23.675360 PROGRESS: Channel   0:	 0.05 FDR:   479; 0.01 FDR:   357; 0.001 FDR:   268
1:31:23.675454 PROGRESS: 
1:31:23.675511 PROGRESS: Protein Summary:
1:31:23.676680 PROGRESS: Channel   0:	 0.05 FDR:   461; 0.01 FDR:   344; 0.001 FDR:   257
1:31:23.676778 PROGRESS: =========================================================================
1:31:23.679636 INFO: fragments_df: keeping 3161 of 18392 [sum(precursor_idx_mask)=6704 sum(mass_error_mask)=18392 stop_rank=3161
1:31:23.684361 INFO: calibration group: precursor, fitting rt estimator 
1:31:23.808941 INFO: calibration group: fragment, fitting mz estimator 
1:31:24.221773 INFO: Using score_cutoff 45.247578991699214 (fac=0.99, q=1)
1:31:24.222164 INFO: calibration group: precursor, predicting mz
1:31:24.222248 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:24.222277 INFO: calibration group: precursor, predicting rt
1:31:24.223822 INFO: calibration group: fragment, predicting mz
1:31:24.226050 INFO: === checking if optimization conditions were reached ===
1:31:24.226150 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1:31:24.227733 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 6.3632.
1:31:24.227786 INFO: ==============================================
1:31:24.227876 INFO: Starting optimization step 5.
1:31:24.227942 PROGRESS: === Extracting elution groups 0 to 600 ===
1:31:24.227998 PROGRESS: Extracting batch of 1197 precursors
1:31:24.228887 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:24.228932 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:24.228963 INFO: FWHM in RT is 2.32 seconds, sigma is 0.30
1:31:24.228984 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:24.229127 INFO: Starting candidate selection
1:31:24.341207 INFO: Starting candidate scoring
1:31:24.382018 INFO: Finished candidate processing
1:31:24.382092 INFO: Collecting candidate features
1:31:24.393801 INFO: Collecting fragment features
1:31:24.397381 INFO: Finished candidate scoring
1:31:24.399017 PROGRESS: === Extracted 2322 precursors and 18343 fragments ===
1:31:24.399292 INFO: performing precursor FDR with 47 features
1:31:24.399328 INFO: Decoy channel: -1
1:31:24.399353 INFO: Competetive: True
1:31:24.401870 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:24.426462 INFO: Test AUC: 0.759
1:31:24.426535 INFO: Train AUC: 0.744
1:31:24.426567 INFO: AUC difference: 2.04%
1:31:24.601235 INFO: Resetting torch num_threads to 100
1:31:24.601842 INFO: === FDR correction performed with classifier version 8 ===
1:31:24.602468 PROGRESS: ============================= Precursor FDR =============================
1:31:24.602561 PROGRESS: Total precursors accumulated: 492
1:31:24.602630 PROGRESS: Target precursors: 479 (97.36%)
1:31:24.602685 PROGRESS: Decoy precursors: 13 (2.64%)
1:31:24.602731 PROGRESS: 
1:31:24.602776 PROGRESS: Precursor Summary:
1:31:24.603781 PROGRESS: Channel   0:	 0.05 FDR:   479; 0.01 FDR:   428; 0.001 FDR:   257
1:31:24.603872 PROGRESS: 
1:31:24.603928 PROGRESS: Protein Summary:
1:31:24.605114 PROGRESS: Channel   0:	 0.05 FDR:   460; 0.01 FDR:   412; 0.001 FDR:   246
1:31:24.605207 PROGRESS: =========================================================================
1:31:24.608259 INFO: fragments_df: keeping 3553 of 18343 [sum(precursor_idx_mask)=8012 sum(mass_error_mask)=18343 stop_rank=3553
1:31:24.613133 INFO: calibration group: precursor, fitting rt estimator 
1:31:24.741833 INFO: calibration group: fragment, fitting mz estimator 
1:31:25.206251 INFO: Using score_cutoff 43.25708935890198 (fac=0.99, q=1)
1:31:25.206659 INFO: calibration group: precursor, predicting mz
1:31:25.206746 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:25.206777 INFO: calibration group: precursor, predicting rt
1:31:25.208297 INFO: calibration group: fragment, predicting mz
1:31:25.210578 INFO: === checking if optimization conditions were reached ===
1:31:25.210690 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1:31:25.212332 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 7.4851.
1:31:25.212384 INFO: ==============================================
1:31:25.212478 INFO: Starting optimization step 6.
1:31:25.212547 PROGRESS: === Extracting elution groups 0 to 600 ===
1:31:25.212603 PROGRESS: Extracting batch of 1197 precursors
1:31:25.213550 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:25.213596 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:25.213627 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
1:31:25.213650 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:25.213801 INFO: Starting candidate selection
1:31:25.323863 INFO: Starting candidate scoring
1:31:25.366393 INFO: Finished candidate processing
1:31:25.366465 INFO: Collecting candidate features
1:31:25.377659 INFO: Collecting fragment features
1:31:25.381661 INFO: Finished candidate scoring
1:31:25.383390 PROGRESS: === Extracted 2319 precursors and 18309 fragments ===
1:31:25.383658 INFO: performing precursor FDR with 47 features
1:31:25.383694 INFO: Decoy channel: -1
1:31:25.383716 INFO: Competetive: True
1:31:25.386267 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:25.408134 INFO: Test AUC: 0.762
1:31:25.408203 INFO: Train AUC: 0.747
1:31:25.408232 INFO: AUC difference: 2.00%
1:31:25.583307 INFO: Resetting torch num_threads to 100
1:31:25.583871 INFO: === FDR correction performed with classifier version 8 ===
1:31:25.584498 PROGRESS: ============================= Precursor FDR =============================
1:31:25.584588 PROGRESS: Total precursors accumulated: 497
1:31:25.584646 PROGRESS: Target precursors: 482 (96.98%)
1:31:25.584696 PROGRESS: Decoy precursors: 15 (3.02%)
1:31:25.584741 PROGRESS: 
1:31:25.584785 PROGRESS: Precursor Summary:
1:31:25.585775 PROGRESS: Channel   0:	 0.05 FDR:   482; 0.01 FDR:   431; 0.001 FDR:   256
1:31:25.585864 PROGRESS: 
1:31:25.585918 PROGRESS: Protein Summary:
1:31:25.587098 PROGRESS: Channel   0:	 0.05 FDR:   463; 0.01 FDR:   415; 0.001 FDR:   246
1:31:25.587198 PROGRESS: =========================================================================
1:31:25.590122 INFO: fragments_df: keeping 3559 of 18309 [sum(precursor_idx_mask)=8065 sum(mass_error_mask)=18309 stop_rank=3559
1:31:25.594884 INFO: calibration group: precursor, fitting rt estimator 
1:31:25.724272 INFO: calibration group: fragment, fitting mz estimator 
1:31:26.190370 INFO: Using score_cutoff 43.28299494552613 (fac=0.99, q=1)
1:31:26.190770 INFO: calibration group: precursor, predicting mz
1:31:26.190858 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:26.190889 INFO: calibration group: precursor, predicting rt
1:31:26.192406 INFO: calibration group: fragment, predicting mz
1:31:26.194684 INFO: === checking if optimization conditions were reached ===
1:31:26.194786 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1:31:26.196403 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 7.6397.
1:31:26.196454 INFO: ==============================================
1:31:26.196542 INFO: Starting optimization step 7.
1:31:26.196608 PROGRESS: === Extracting elution groups 0 to 600 ===
1:31:26.196665 PROGRESS: Extracting batch of 1197 precursors
1:31:26.197553 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:26.197600 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:26.197631 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
1:31:26.197652 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:26.197797 INFO: Starting candidate selection
1:31:26.307891 INFO: Starting candidate scoring
1:31:26.349274 INFO: Finished candidate processing
1:31:26.349347 INFO: Collecting candidate features
1:31:26.360425 INFO: Collecting fragment features
1:31:26.364487 INFO: Finished candidate scoring
1:31:26.366142 PROGRESS: === Extracted 2321 precursors and 18325 fragments ===
1:31:26.366413 INFO: performing precursor FDR with 47 features
1:31:26.366449 INFO: Decoy channel: -1
1:31:26.366471 INFO: Competetive: True
1:31:26.369004 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:26.391089 INFO: Test AUC: 0.759
1:31:26.391159 INFO: Train AUC: 0.747
1:31:26.391188 INFO: AUC difference: 1.54%
1:31:26.567434 INFO: Resetting torch num_threads to 100
1:31:26.568013 INFO: === FDR correction performed with classifier version 8 ===
1:31:26.568633 PROGRESS: ============================= Precursor FDR =============================
1:31:26.568725 PROGRESS: Total precursors accumulated: 493
1:31:26.568782 PROGRESS: Target precursors: 479 (97.16%)
1:31:26.568832 PROGRESS: Decoy precursors: 14 (2.84%)
1:31:26.568878 PROGRESS: 
1:31:26.568925 PROGRESS: Precursor Summary:
1:31:26.569935 PROGRESS: Channel   0:	 0.05 FDR:   479; 0.01 FDR:   434; 0.001 FDR:   257
1:31:26.570024 PROGRESS: 
1:31:26.570080 PROGRESS: Protein Summary:
1:31:26.571264 PROGRESS: Channel   0:	 0.05 FDR:   461; 0.01 FDR:   418; 0.001 FDR:   246
1:31:26.571357 PROGRESS: =========================================================================
1:31:26.574378 INFO: fragments_df: keeping 3577 of 18325 [sum(precursor_idx_mask)=8115 sum(mass_error_mask)=18325 stop_rank=3577
1:31:26.579169 INFO: calibration group: precursor, fitting rt estimator 
1:31:26.708331 INFO: calibration group: fragment, fitting mz estimator 
1:31:27.177200 INFO: Using score_cutoff 43.30564163360596 (fac=0.99, q=1)
1:31:27.177590 INFO: calibration group: precursor, predicting mz
1:31:27.177674 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:27.177703 INFO: calibration group: precursor, predicting rt
1:31:27.179229 INFO: calibration group: fragment, predicting mz
1:31:27.181555 INFO: === checking if optimization conditions were reached ===
1:31:27.181662 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
1:31:27.182617 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 6.3632 found after 8 searches.
1:31:27.182667 INFO: ==============================================
1:31:27.182754 PROGRESS: Optimization finished for rt_error.
1:31:27.187158 INFO: calibration group: precursor, predicting mz
1:31:27.187262 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:27.187291 INFO: calibration group: precursor, predicting rt
1:31:27.188560 INFO: calibration group: fragment, predicting mz
1:31:27.215988 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:31:27.216137 PROGRESS: ==============================================
1:31:27.216205 PROGRESS: ms2_error      : 6.2633
1:31:27.216262 PROGRESS: rt_error       : 6.3632
1:31:27.216309 PROGRESS: ==============================================
1:31:27.216830 INFO: calibration group: precursor, predicting mz
1:31:27.216917 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:27.216945 INFO: calibration group: precursor, predicting rt
1:31:27.341666 INFO: calibration group: fragment, predicting mz
1:31:27.699505 PROGRESS: Extracting batch of 220080 precursors
1:31:27.763844 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:27.763966 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:27.763999 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
1:31:27.764021 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:27.764224 INFO: Starting candidate selection
1:31:34.089270 INFO: Applying score cutoff of 43.25708935890198
1:31:34.094107 INFO: Removed 250966 precursors with score below cutoff
1:31:34.148809 INFO: Starting candidate scoring
1:31:35.417306 INFO: Finished candidate processing
1:31:35.417444 INFO: Collecting candidate features
1:31:35.774205 INFO: Collecting fragment features
1:31:35.934345 INFO: Finished candidate scoring
1:31:36.087810 INFO: === FDR correction performed with classifier version 14 ===
1:31:36.089204 INFO: performing precursor FDR with 47 features
1:31:36.089243 INFO: Decoy channel: -1
1:31:36.089267 INFO: Competetive: True
1:31:36.168671 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:36.200126 WARNING: FDR calculation for 137035 target and 43685 decoy PSMs
1:31:36.200288 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1:31:40.165250 INFO: Test AUC: 0.927
1:31:40.165452 INFO: Train AUC: 0.927
1:31:40.165483 INFO: AUC difference: 0.05%
1:31:40.390950 INFO: Resetting torch num_threads to 100
1:31:40.409719 INFO: Removing fragments below FDR threshold
1:31:40.468574 PROGRESS: ============================= Precursor FDR =============================
1:31:40.469089 PROGRESS: Total precursors accumulated: 96,378
1:31:40.469160 PROGRESS: Target precursors: 95,424 (99.01%)
1:31:40.469211 PROGRESS: Decoy precursors: 954 (0.99%)
1:31:40.469259 PROGRESS: 
1:31:40.469304 PROGRESS: Precursor Summary:
1:31:40.510367 PROGRESS: Channel   0:	 0.05 FDR: 95,424; 0.01 FDR: 95,424; 0.001 FDR: 86,442
1:31:40.510620 PROGRESS: 
1:31:40.510687 PROGRESS: Protein Summary:
1:31:40.568017 PROGRESS: Channel   0:	 0.05 FDR: 9,829; 0.01 FDR: 9,829; 0.001 FDR: 9,680
1:31:40.568253 PROGRESS: =========================================================================
1:31:41.236892 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:31:41.266402 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:31:41.266554 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant
1:31:41.266628 INFO: Creating folder run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/figures
1:31:41.267154 INFO: Initializing RawFileManager
1:31:53.140247 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.
1:31:53.144365 INFO: Determining DIA cycle
1:31:53.160778 INFO: Found cycle with start 0.00 min and length 300.
1:31:53.330049 INFO: RT (min)            : 0.0 - 26.9
1:31:53.330139 INFO: RT duration (sec)   : 1611.2
1:31:53.330166 INFO: RT duration (min)   : 26.9
1:31:53.330190 INFO: Cycle len (scans)   : 300
1:31:53.330211 INFO: Cycle len (sec)     : 1.65
1:31:53.330229 INFO: Number of cycles    : 977
1:31:53.330249 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:31:53.385552 INFO: Initializing CalibrationManager
1:31:53.385840 INFO: Loading calibration config
1:31:53.386464 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'}]
1:31:53.386554 INFO: Calibration group :fragment, found 1 estimator(s)
1:31:53.386647 INFO: Calibration group :precursor, found 3 estimator(s)
1:31:53.386741 INFO: Disabling ion mobility calibration
1:31:53.386770 INFO: removed mobility estimator from group precursor
1:31:53.386899 INFO: Initializing OptimizationManager
1:31:53.387010 INFO: initial parameter: ms1_error = 30
1:31:53.387069 INFO: initial parameter: ms2_error = 30
1:31:53.387121 INFO: initial parameter: rt_error = 805.5982666015625
1:31:53.387167 INFO: initial parameter: mobility_error = 0.1
1:31:53.387208 INFO: initial parameter: column_type = library
1:31:53.387249 INFO: initial parameter: num_candidates = 1
1:31:53.387289 INFO: initial parameter: classifier_version = -1
1:31:53.387329 INFO: initial parameter: fwhm_rt = 5
1:31:53.387372 INFO: initial parameter: fwhm_mobility = 0.01
1:31:53.387412 INFO: initial parameter: score_cutoff = 0
1:31:53.387482 INFO: Initializing TimingManager
1:31:53.387545 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:31:53.387655 INFO: FDRManager not loaded from disk.
1:31:53.387679 INFO: Initializing FDRManager
1:31:53.387714 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:31:53.425544 PROGRESS: 110,515 target precursors potentially observable (0 removed)
1:31:53.481992 PROGRESS: Starting initial search for precursors.
1:31:53.489343 INFO: Starting optimization step 0.
1:31:53.489511 PROGRESS: === Extracting elution groups 0 to 200 ===
1:31:53.489587 PROGRESS: Extracting batch of 400 precursors
1:31:53.490598 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:53.490659 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:53.490698 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:31:53.490720 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:31:53.490981 INFO: Starting candidate selection
1:31:53.619385 INFO: Starting candidate scoring
1:31:53.655297 INFO: Finished candidate processing
1:31:53.655365 INFO: Collecting candidate features
1:31:53.663754 INFO: Collecting fragment features
1:31:53.665729 INFO: Finished candidate scoring
1:31:53.666491 PROGRESS: === Extracted 400 precursors and 4428 fragments ===
1:31:53.666765 INFO: performing precursor FDR with 47 features
1:31:53.666802 INFO: Decoy channel: -1
1:31:53.666825 INFO: Competetive: True
1:31:53.667820 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:53.687006 INFO: Test AUC: 0.402
1:31:53.687067 INFO: Train AUC: 0.464
1:31:53.687096 INFO: AUC difference: 13.23%
1:31:53.687116 WARNING: AUC difference > 5%. This may indicate overfitting.
1:31:53.861751 INFO: Resetting torch num_threads to 100
1:31:53.862287 INFO: === FDR correction performed with classifier version -1 ===
1:31:53.862915 PROGRESS: ============================= Precursor FDR =============================
1:31:53.863017 PROGRESS: Total precursors accumulated: 200
1:31:53.863078 PROGRESS: Target precursors: 82 (41.00%)
1:31:53.863129 PROGRESS: Decoy precursors: 118 (59.00%)
1:31:53.863178 PROGRESS: 
1:31:53.863225 PROGRESS: Precursor Summary:
1:31:53.864063 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:31:53.864151 PROGRESS: 
1:31:53.864206 PROGRESS: Protein Summary:
1:31:53.865111 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:31:53.865198 PROGRESS: =========================================================================
1:31:53.868847 INFO: Starting optimization step 1.
1:31:53.868952 PROGRESS: === Extracting elution groups 200 to 600 ===
1:31:53.869015 PROGRESS: Extracting batch of 797 precursors
1:31:53.869758 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:53.869802 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:53.869832 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:31:53.869853 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:31:53.870003 INFO: Starting candidate selection
1:31:54.001093 INFO: Starting candidate scoring
1:31:54.037138 INFO: Finished candidate processing
1:31:54.037203 INFO: Collecting candidate features
1:31:54.045935 INFO: Collecting fragment features
1:31:54.048460 INFO: Finished candidate scoring
1:31:54.050428 PROGRESS: === Extracted 1197 precursors and 13224 fragments ===
1:31:54.051184 INFO: performing precursor FDR with 47 features
1:31:54.051229 INFO: Decoy channel: -1
1:31:54.051252 INFO: Competetive: True
1:31:54.053927 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:54.073198 INFO: Test AUC: 0.492
1:31:54.073260 INFO: Train AUC: 0.469
1:31:54.073288 INFO: AUC difference: 5.05%
1:31:54.073313 WARNING: AUC difference > 5%. This may indicate overfitting.
1:31:54.246301 INFO: Resetting torch num_threads to 100
1:31:54.246899 INFO: === FDR correction performed with classifier version -1 ===
1:31:54.247539 PROGRESS: ============================= Precursor FDR =============================
1:31:54.247631 PROGRESS: Total precursors accumulated: 1
1:31:54.247693 PROGRESS: Target precursors: 1 (100.00%)
1:31:54.247746 PROGRESS: Decoy precursors: 0 (0.00%)
1:31:54.247793 PROGRESS: 
1:31:54.247838 PROGRESS: Precursor Summary:
1:31:54.248765 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:31:54.248854 PROGRESS: 
1:31:54.248909 PROGRESS: Protein Summary:
1:31:54.249914 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:31:54.250002 PROGRESS: =========================================================================
1:31:54.254571 INFO: Starting optimization step 2.
1:31:54.254684 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:31:54.254749 PROGRESS: Extracting batch of 1592 precursors
1:31:54.255834 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:54.255880 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:54.255910 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:31:54.255933 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:31:54.256082 INFO: Starting candidate selection
1:31:54.410923 INFO: Starting candidate scoring
1:31:54.450470 INFO: Finished candidate processing
1:31:54.450547 INFO: Collecting candidate features
1:31:54.460629 INFO: Collecting fragment features
1:31:54.464447 INFO: Finished candidate scoring
1:31:54.467321 PROGRESS: === Extracted 2789 precursors and 30844 fragments ===
1:31:54.468304 INFO: performing precursor FDR with 47 features
1:31:54.468347 INFO: Decoy channel: -1
1:31:54.468371 INFO: Competetive: True
1:31:54.471427 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:54.508510 INFO: Test AUC: 0.436
1:31:54.508588 INFO: Train AUC: 0.482
1:31:54.508617 INFO: AUC difference: 9.45%
1:31:54.508638 WARNING: AUC difference > 5%. This may indicate overfitting.
1:31:54.682249 INFO: Resetting torch num_threads to 100
1:31:54.682934 INFO: === FDR correction performed with classifier version -1 ===
1:31:54.683682 PROGRESS: ============================= Precursor FDR =============================
1:31:54.683792 PROGRESS: Total precursors accumulated: 1,400
1:31:54.683853 PROGRESS: Target precursors: 671 (47.93%)
1:31:54.683905 PROGRESS: Decoy precursors: 729 (52.07%)
1:31:54.683955 PROGRESS: 
1:31:54.684000 PROGRESS: Precursor Summary:
1:31:54.684863 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:31:54.684951 PROGRESS: 
1:31:54.685008 PROGRESS: Protein Summary:
1:31:54.685942 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:31:54.686030 PROGRESS: =========================================================================
1:31:54.692132 INFO: Starting optimization step 3.
1:31:54.692237 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:31:54.692299 PROGRESS: Extracting batch of 3186 precursors
1:31:54.693302 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:54.693348 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:54.693378 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:31:54.693400 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:31:54.693550 INFO: Starting candidate selection
1:31:54.944075 INFO: Starting candidate scoring
1:31:54.985165 INFO: Finished candidate processing
1:31:54.985248 INFO: Collecting candidate features
1:31:54.998754 INFO: Collecting fragment features
1:31:55.002803 INFO: Finished candidate scoring
1:31:55.006928 PROGRESS: === Extracted 5975 precursors and 66119 fragments ===
1:31:55.008148 INFO: performing precursor FDR with 47 features
1:31:55.008190 INFO: Decoy channel: -1
1:31:55.008213 INFO: Competetive: True
1:31:55.012082 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:55.064822 INFO: Test AUC: 0.487
1:31:55.064914 INFO: Train AUC: 0.483
1:31:55.064942 INFO: AUC difference: 0.91%
1:31:55.240063 INFO: Resetting torch num_threads to 100
1:31:55.240867 INFO: === FDR correction performed with classifier version -1 ===
1:31:55.241855 PROGRESS: ============================= Precursor FDR =============================
1:31:55.241954 PROGRESS: Total precursors accumulated: 3,000
1:31:55.242017 PROGRESS: Target precursors: 1,455 (48.50%)
1:31:55.242068 PROGRESS: Decoy precursors: 1,545 (51.50%)
1:31:55.242114 PROGRESS: 
1:31:55.242159 PROGRESS: Precursor Summary:
1:31:55.243061 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:31:55.243151 PROGRESS: 
1:31:55.243206 PROGRESS: Protein Summary:
1:31:55.244142 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:31:55.244230 PROGRESS: =========================================================================
1:31:55.253987 INFO: Starting optimization step 4.
1:31:55.254116 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:31:55.254180 PROGRESS: Extracting batch of 6377 precursors
1:31:55.255747 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:55.255797 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:55.255827 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:31:55.255848 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:31:55.256015 INFO: Starting candidate selection
1:31:55.694300 INFO: Starting candidate scoring
1:31:55.745504 INFO: Finished candidate processing
1:31:55.745598 INFO: Collecting candidate features
1:31:55.763211 INFO: Collecting fragment features
1:31:55.770007 INFO: Finished candidate scoring
1:31:55.776684 PROGRESS: === Extracted 12352 precursors and 136421 fragments ===
1:31:55.778352 INFO: performing precursor FDR with 47 features
1:31:55.778397 INFO: Decoy channel: -1
1:31:55.778422 INFO: Competetive: True
1:31:55.783418 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:55.831437 INFO: Test AUC: 0.474
1:31:55.831535 INFO: Train AUC: 0.475
1:31:55.831564 INFO: AUC difference: 0.30%
1:31:56.004716 INFO: Resetting torch num_threads to 100
1:31:56.005651 INFO: === FDR correction performed with classifier version -1 ===
1:31:56.006301 PROGRESS: ============================= Precursor FDR =============================
1:31:56.006406 PROGRESS: Total precursors accumulated: 1
1:31:56.006466 PROGRESS: Target precursors: 1 (100.00%)
1:31:56.006519 PROGRESS: Decoy precursors: 0 (0.00%)
1:31:56.006569 PROGRESS: 
1:31:56.006625 PROGRESS: Precursor Summary:
1:31:56.007567 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:31:56.007654 PROGRESS: 
1:31:56.007711 PROGRESS: Protein Summary:
1:31:56.008744 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:31:56.008831 PROGRESS: =========================================================================
1:31:56.024852 INFO: Starting optimization step 5.
1:31:56.024992 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:31:56.025057 PROGRESS: Extracting batch of 12745 precursors
1:31:56.027546 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:56.027595 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:56.027626 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:31:56.027647 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:31:56.027813 INFO: Starting candidate selection
1:31:56.818733 INFO: Starting candidate scoring
1:31:56.918000 INFO: Finished candidate processing
1:31:56.918100 INFO: Collecting candidate features
1:31:56.946568 INFO: Collecting fragment features
1:31:56.955903 INFO: Finished candidate scoring
1:31:56.968204 PROGRESS: === Extracted 25097 precursors and 277415 fragments ===
1:31:56.971373 INFO: performing precursor FDR with 47 features
1:31:56.971431 INFO: Decoy channel: -1
1:31:56.971458 INFO: Competetive: True
1:31:56.980118 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:57.370459 INFO: Test AUC: 0.824
1:31:57.370581 INFO: Train AUC: 0.822
1:31:57.370624 INFO: AUC difference: 0.17%
1:31:57.556514 INFO: Resetting torch num_threads to 100
1:31:57.557846 INFO: === FDR correction performed with classifier version -1 ===
1:31:57.559304 PROGRESS: ============================= Precursor FDR =============================
1:31:57.559403 PROGRESS: Total precursors accumulated: 7,239
1:31:57.559470 PROGRESS: Target precursors: 6,898 (95.29%)
1:31:57.559528 PROGRESS: Decoy precursors: 341 (4.71%)
1:31:57.559582 PROGRESS: 
1:31:57.559633 PROGRESS: Precursor Summary:
1:31:57.561697 PROGRESS: Channel   0:	 0.05 FDR: 6,898; 0.01 FDR: 3,693; 0.001 FDR:   685
1:31:57.561796 PROGRESS: 
1:31:57.561860 PROGRESS: Protein Summary:
1:31:57.564697 PROGRESS: Channel   0:	 0.05 FDR: 3,694; 0.01 FDR: 2,178; 0.001 FDR:   533
1:31:57.564798 PROGRESS: =========================================================================
1:31:57.589746 INFO: fragments_df: keeping 5000 of 277415 [sum(precursor_idx_mask)=41587 sum(mass_error_mask)=277415 stop_rank=5000
1:31:57.598203 INFO: calibration group: precursor, fitting rt estimator 
1:31:58.032095 INFO: calibration group: fragment, fitting mz estimator 
1:31:58.650625 INFO: Using score_cutoff 57.654665771484375 (fac=0.99, q=1)
1:31:58.651098 INFO: calibration group: precursor, predicting mz
1:31:58.651191 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:58.651224 INFO: calibration group: precursor, predicting rt
1:31:58.653574 INFO: calibration group: fragment, predicting mz
1:31:58.658313 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:31:58.658437 INFO: Starting optimization step 6.
1:31:58.658513 PROGRESS: === Extracting elution groups 0 to 1400 ===
1:31:58.658579 PROGRESS: Extracting batch of 2789 precursors
1:31:58.659776 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:58.659827 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:58.659860 INFO: FWHM in RT is 3.06 seconds, sigma is 0.39
1:31:58.659886 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:58.660039 INFO: Starting candidate selection
1:31:58.893348 INFO: Starting candidate scoring
1:31:58.939305 INFO: Finished candidate processing
1:31:58.939395 INFO: Collecting candidate features
1:31:58.955523 INFO: Collecting fragment features
1:31:58.960500 INFO: Finished candidate scoring
1:31:58.964123 PROGRESS: === Extracted 5578 precursors and 61016 fragments ===
1:31:58.964405 INFO: performing precursor FDR with 47 features
1:31:58.964442 INFO: Decoy channel: -1
1:31:58.964465 INFO: Competetive: True
1:31:58.967735 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:59.008803 INFO: Test AUC: 0.710
1:31:59.008891 INFO: Train AUC: 0.703
1:31:59.008920 INFO: AUC difference: 1.06%
1:31:59.185923 INFO: Resetting torch num_threads to 100
1:31:59.186635 INFO: === FDR correction performed with classifier version 5 ===
1:31:59.187329 PROGRESS: ============================= Precursor FDR =============================
1:31:59.187420 PROGRESS: Total precursors accumulated: 820
1:31:59.187479 PROGRESS: Target precursors: 774 (94.39%)
1:31:59.187531 PROGRESS: Decoy precursors: 46 (5.61%)
1:31:59.187589 PROGRESS: 
1:31:59.187637 PROGRESS: Precursor Summary:
1:31:59.188675 PROGRESS: Channel   0:	 0.05 FDR:   743; 0.01 FDR:   358; 0.001 FDR:   170
1:31:59.188767 PROGRESS: 
1:31:59.188824 PROGRESS: Protein Summary:
1:31:59.190064 PROGRESS: Channel   0:	 0.05 FDR:   682; 0.01 FDR:   331; 0.001 FDR:   160
1:31:59.190158 PROGRESS: =========================================================================
1:31:59.196320 INFO: fragments_df: keeping 4004 of 61016 [sum(precursor_idx_mask)=7905 sum(mass_error_mask)=61016 stop_rank=4004
1:31:59.203421 INFO: calibration group: precursor, fitting rt estimator 
1:31:59.330645 INFO: calibration group: fragment, fitting mz estimator 
1:31:59.858105 INFO: Using score_cutoff 57.69621484909058 (fac=0.99, q=1)
1:31:59.858499 INFO: calibration group: precursor, predicting mz
1:31:59.858582 WARNING: mz prediction was skipped as it has not been fitted yet
1:31:59.858618 INFO: calibration group: precursor, predicting rt
1:31:59.860952 INFO: calibration group: fragment, predicting mz
1:31:59.865759 INFO: === checking if optimization conditions were reached ===
1:31:59.867247 PROGRESS: ❌ ms2_error      : 13.4619 > 6.2633 or insufficient steps taken.
1:31:59.867298 INFO: ==============================================
1:31:59.867386 INFO: Starting optimization step 7.
1:31:59.867451 PROGRESS: === Extracting elution groups 0 to 1400 ===
1:31:59.867507 PROGRESS: Extracting batch of 2789 precursors
1:31:59.868702 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:31:59.868748 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:31:59.868778 INFO: FWHM in RT is 3.00 seconds, sigma is 0.39
1:31:59.868799 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:31:59.868950 INFO: Starting candidate selection
1:32:00.090506 INFO: Starting candidate scoring
1:32:00.137155 INFO: Finished candidate processing
1:32:00.137238 INFO: Collecting candidate features
1:32:00.152867 INFO: Collecting fragment features
1:32:00.157702 INFO: Finished candidate scoring
1:32:00.160661 PROGRESS: === Extracted 5578 precursors and 56267 fragments ===
1:32:00.160937 INFO: performing precursor FDR with 47 features
1:32:00.160972 INFO: Decoy channel: -1
1:32:00.160994 INFO: Competetive: True
1:32:00.164051 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:00.204926 INFO: Test AUC: 0.707
1:32:00.205011 INFO: Train AUC: 0.724
1:32:00.205040 INFO: AUC difference: 2.35%
1:32:00.380256 INFO: Resetting torch num_threads to 100
1:32:00.380923 INFO: === FDR correction performed with classifier version 6 ===
1:32:00.381605 PROGRESS: ============================= Precursor FDR =============================
1:32:00.381698 PROGRESS: Total precursors accumulated: 1,021
1:32:00.381758 PROGRESS: Target precursors: 981 (96.08%)
1:32:00.381813 PROGRESS: Decoy precursors: 40 (3.92%)
1:32:00.381860 PROGRESS: 
1:32:00.381906 PROGRESS: Precursor Summary:
1:32:00.382956 PROGRESS: Channel   0:	 0.05 FDR:   981; 0.01 FDR:   139; 0.001 FDR:   124
1:32:00.383051 PROGRESS: 
1:32:00.383107 PROGRESS: Protein Summary:
1:32:00.384332 PROGRESS: Channel   0:	 0.05 FDR:   886; 0.01 FDR:   131; 0.001 FDR:   117
1:32:00.384426 PROGRESS: =========================================================================
1:32:00.390619 INFO: calibration group: precursor, predicting mz
1:32:00.390733 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:00.390764 INFO: calibration group: precursor, predicting rt
1:32:00.393179 INFO: calibration group: fragment, predicting mz
1:32:00.398430 INFO: === skipping optimization until target number of precursors are found ===
1:32:00.398551 INFO: Starting optimization step 8.
1:32:00.398628 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:32:00.398691 PROGRESS: Extracting batch of 3186 precursors
1:32:00.399768 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:00.399815 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:00.399847 INFO: FWHM in RT is 3.00 seconds, sigma is 0.39
1:32:00.399868 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:00.400017 INFO: Starting candidate selection
1:32:00.633984 INFO: Starting candidate scoring
1:32:00.682549 INFO: Finished candidate processing
1:32:00.682653 INFO: Collecting candidate features
1:32:00.699907 INFO: Collecting fragment features
1:32:00.705448 INFO: Finished candidate scoring
1:32:00.711040 PROGRESS: === Extracted 11950 precursors and 120724 fragments ===
1:32:00.712302 INFO: performing precursor FDR with 47 features
1:32:00.712351 INFO: Decoy channel: -1
1:32:00.712374 INFO: Competetive: True
1:32:00.717277 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:00.777841 INFO: Test AUC: 0.715
1:32:00.777945 INFO: Train AUC: 0.730
1:32:00.777975 INFO: AUC difference: 1.99%
1:32:00.955119 INFO: Resetting torch num_threads to 100
1:32:00.956021 INFO: === FDR correction performed with classifier version 6 ===
1:32:00.956848 PROGRESS: ============================= Precursor FDR =============================
1:32:00.956940 PROGRESS: Total precursors accumulated: 2,218
1:32:00.957000 PROGRESS: Target precursors: 2,125 (95.81%)
1:32:00.957052 PROGRESS: Decoy precursors: 93 (4.19%)
1:32:00.957098 PROGRESS: 
1:32:00.957144 PROGRESS: Precursor Summary:
1:32:00.958378 PROGRESS: Channel   0:	 0.05 FDR: 2,125; 0.01 FDR:   832; 0.001 FDR:   176
1:32:00.958470 PROGRESS: 
1:32:00.958527 PROGRESS: Protein Summary:
1:32:00.960119 PROGRESS: Channel   0:	 0.05 FDR: 1,683; 0.01 FDR:   706; 0.001 FDR:   163
1:32:00.960218 PROGRESS: =========================================================================
1:32:00.971555 INFO: fragments_df: keeping 5000 of 120724 [sum(precursor_idx_mask)=17789 sum(mass_error_mask)=120724 stop_rank=5000
1:32:00.980015 INFO: calibration group: precursor, fitting rt estimator 
1:32:01.134967 INFO: calibration group: fragment, fitting mz estimator 
1:32:01.809652 INFO: Using score_cutoff 49.8210604019165 (fac=0.99, q=1)
1:32:01.810050 INFO: calibration group: precursor, predicting mz
1:32:01.810136 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:01.810168 INFO: calibration group: precursor, predicting rt
1:32:01.812507 INFO: calibration group: fragment, predicting mz
1:32:01.817217 INFO: === checking if optimization conditions were reached ===
1:32:01.818826 PROGRESS: ✅ ms2_error      : 6.2633 <= 6.2633
1:32:01.818879 INFO: ==============================================
1:32:01.818966 PROGRESS: Optimization finished for ms2_error.
1:32:01.826401 INFO: calibration group: precursor, predicting mz
1:32:01.826510 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:01.826542 INFO: calibration group: precursor, predicting rt
1:32:01.828623 INFO: calibration group: fragment, predicting mz
1:32:01.833103 INFO: Starting optimization step 0.
1:32:01.833204 PROGRESS: === Extracting elution groups 0 to 1400 ===
1:32:01.833267 PROGRESS: Extracting batch of 2789 precursors
1:32:01.834302 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:01.834347 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:01.834378 INFO: FWHM in RT is 2.75 seconds, sigma is 0.35
1:32:01.834402 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:01.834550 INFO: Starting candidate selection
1:32:02.047095 INFO: Starting candidate scoring
1:32:02.093317 INFO: Finished candidate processing
1:32:02.093402 INFO: Collecting candidate features
1:32:02.109216 INFO: Collecting fragment features
1:32:02.114243 INFO: Finished candidate scoring
1:32:02.117250 PROGRESS: === Extracted 5578 precursors and 49533 fragments ===
1:32:02.117518 INFO: performing precursor FDR with 47 features
1:32:02.117555 INFO: Decoy channel: -1
1:32:02.117579 INFO: Competetive: True
1:32:02.120740 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:02.153144 INFO: Test AUC: 0.678
1:32:02.153231 INFO: Train AUC: 0.722
1:32:02.153265 INFO: AUC difference: 6.21%
1:32:02.153292 WARNING: AUC difference > 5%. This may indicate overfitting.
1:32:02.330568 INFO: Resetting torch num_threads to 100
1:32:02.331250 INFO: === FDR correction performed with classifier version 8 ===
1:32:02.331947 PROGRESS: ============================= Precursor FDR =============================
1:32:02.332041 PROGRESS: Total precursors accumulated: 1,055
1:32:02.332102 PROGRESS: Target precursors: 1,007 (95.45%)
1:32:02.332155 PROGRESS: Decoy precursors: 48 (4.55%)
1:32:02.332201 PROGRESS: 
1:32:02.332247 PROGRESS: Precursor Summary:
1:32:02.333278 PROGRESS: Channel   0:	 0.05 FDR: 1,007; 0.01 FDR:   115; 0.001 FDR:    50
1:32:02.333368 PROGRESS: 
1:32:02.333425 PROGRESS: Protein Summary:
1:32:02.334644 PROGRESS: Channel   0:	 0.05 FDR:   916; 0.01 FDR:   110; 0.001 FDR:    48
1:32:02.334738 PROGRESS: =========================================================================
1:32:02.343797 INFO: calibration group: precursor, predicting mz
1:32:02.343916 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:02.343950 INFO: calibration group: precursor, predicting rt
1:32:02.346379 INFO: calibration group: fragment, predicting mz
1:32:02.351747 INFO: === skipping optimization until target number of precursors are found ===
1:32:02.351878 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1:32:02.351927 INFO: Starting optimization step 1.
1:32:02.351992 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:32:02.352045 PROGRESS: Extracting batch of 3186 precursors
1:32:02.353148 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:02.353194 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:02.353225 INFO: FWHM in RT is 2.75 seconds, sigma is 0.35
1:32:02.353248 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:02.353395 INFO: Starting candidate selection
1:32:02.594255 INFO: Starting candidate scoring
1:32:02.643273 INFO: Finished candidate processing
1:32:02.643366 INFO: Collecting candidate features
1:32:02.661332 INFO: Collecting fragment features
1:32:02.666623 INFO: Finished candidate scoring
1:32:02.672273 PROGRESS: === Extracted 11950 precursors and 106596 fragments ===
1:32:02.673529 INFO: performing precursor FDR with 47 features
1:32:02.673577 INFO: Decoy channel: -1
1:32:02.673599 INFO: Competetive: True
1:32:02.678909 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:02.741500 INFO: Test AUC: 0.723
1:32:02.741597 INFO: Train AUC: 0.721
1:32:02.741625 INFO: AUC difference: 0.24%
1:32:02.922849 INFO: Resetting torch num_threads to 100
1:32:02.923779 INFO: === FDR correction performed with classifier version 8 ===
1:32:02.924600 PROGRESS: ============================= Precursor FDR =============================
1:32:02.924690 PROGRESS: Total precursors accumulated: 2,292
1:32:02.924747 PROGRESS: Target precursors: 2,181 (95.16%)
1:32:02.924798 PROGRESS: Decoy precursors: 111 (4.84%)
1:32:02.924844 PROGRESS: 
1:32:02.924888 PROGRESS: Precursor Summary:
1:32:02.925989 PROGRESS: Channel   0:	 0.05 FDR: 2,169; 0.01 FDR:     0; 0.001 FDR:     0
1:32:02.926082 PROGRESS: 
1:32:02.926139 PROGRESS: Protein Summary:
1:32:02.927520 PROGRESS: Channel   0:	 0.05 FDR: 1,731; 0.01 FDR:     0; 0.001 FDR:     0
1:32:02.927621 PROGRESS: =========================================================================
1:32:02.937599 INFO: calibration group: precursor, predicting mz
1:32:02.937730 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:02.937762 INFO: calibration group: precursor, predicting rt
1:32:02.942163 INFO: calibration group: fragment, predicting mz
1:32:02.952174 INFO: === skipping optimization until target number of precursors are found ===
1:32:02.952310 PROGRESS: === Optimization of rt_error has been skipped 2 time(s); maximum number is 1 ===
1:32:02.952359 INFO: Starting optimization step 2.
1:32:02.952428 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:32:02.952487 PROGRESS: Extracting batch of 6377 precursors
1:32:02.954217 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:02.954264 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:02.954297 INFO: FWHM in RT is 2.75 seconds, sigma is 0.35
1:32:02.954317 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:02.954464 INFO: Starting candidate selection
1:32:03.324727 INFO: Starting candidate scoring
1:32:03.418607 INFO: Finished candidate processing
1:32:03.418708 INFO: Collecting candidate features
1:32:03.450688 INFO: Collecting fragment features
1:32:03.460735 INFO: Finished candidate scoring
1:32:03.471151 PROGRESS: === Extracted 24703 precursors and 219721 fragments ===
1:32:03.473218 INFO: performing precursor FDR with 47 features
1:32:03.473273 INFO: Decoy channel: -1
1:32:03.473297 INFO: Competetive: True
1:32:03.481330 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:03.786719 INFO: Test AUC: 0.766
1:32:03.786832 INFO: Train AUC: 0.770
1:32:03.786862 INFO: AUC difference: 0.48%
1:32:03.971280 INFO: Resetting torch num_threads to 100
1:32:03.973001 INFO: === FDR correction performed with classifier version 8 ===
1:32:03.974185 PROGRESS: ============================= Precursor FDR =============================
1:32:03.974279 PROGRESS: Total precursors accumulated: 5,121
1:32:03.974339 PROGRESS: Target precursors: 4,964 (96.93%)
1:32:03.974391 PROGRESS: Decoy precursors: 157 (3.07%)
1:32:03.974438 PROGRESS: 
1:32:03.974489 PROGRESS: Precursor Summary:
1:32:03.976285 PROGRESS: Channel   0:	 0.05 FDR: 4,964; 0.01 FDR: 3,702; 0.001 FDR:     6
1:32:03.976387 PROGRESS: 
1:32:03.976442 PROGRESS: Protein Summary:
1:32:03.978874 PROGRESS: Channel   0:	 0.05 FDR: 3,224; 0.01 FDR: 2,513; 0.001 FDR:     6
1:32:03.978977 PROGRESS: =========================================================================
1:32:04.005777 INFO: fragments_df: keeping 5000 of 219721 [sum(precursor_idx_mask)=74047 sum(mass_error_mask)=219721 stop_rank=5000
1:32:04.014607 INFO: calibration group: precursor, fitting rt estimator 
1:32:04.512524 INFO: calibration group: fragment, fitting mz estimator 
1:32:05.195582 INFO: Using score_cutoff 44.85127992668152 (fac=0.99, q=1)
1:32:05.196039 INFO: calibration group: precursor, predicting mz
1:32:05.196129 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:05.196162 INFO: calibration group: precursor, predicting rt
1:32:05.197740 INFO: calibration group: fragment, predicting mz
1:32:05.199874 INFO: === checking if optimization conditions were reached ===
1:32:05.199995 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:32:05.203366 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 32.1906.
1:32:05.203423 INFO: ==============================================
1:32:05.203520 INFO: Starting optimization step 3.
1:32:05.203600 PROGRESS: === Extracting elution groups 0 to 600 ===
1:32:05.203669 PROGRESS: Extracting batch of 1197 precursors
1:32:05.207467 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:05.207519 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:05.207553 INFO: FWHM in RT is 2.36 seconds, sigma is 0.30
1:32:05.207574 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:05.207750 INFO: Starting candidate selection
1:32:05.320538 INFO: Starting candidate scoring
1:32:05.361825 INFO: Finished candidate processing
1:32:05.361919 INFO: Collecting candidate features
1:32:05.373409 INFO: Collecting fragment features
1:32:05.377511 INFO: Finished candidate scoring
1:32:05.379128 PROGRESS: === Extracted 2377 precursors and 19367 fragments ===
1:32:05.379422 INFO: performing precursor FDR with 47 features
1:32:05.379457 INFO: Decoy channel: -1
1:32:05.379480 INFO: Competetive: True
1:32:05.382483 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:05.405920 INFO: Test AUC: 0.755
1:32:05.405988 INFO: Train AUC: 0.744
1:32:05.406018 INFO: AUC difference: 1.51%
1:32:05.580099 INFO: Resetting torch num_threads to 100
1:32:05.580785 INFO: === FDR correction performed with classifier version 8 ===
1:32:05.581457 PROGRESS: ============================= Precursor FDR =============================
1:32:05.581554 PROGRESS: Total precursors accumulated: 496
1:32:05.581623 PROGRESS: Target precursors: 481 (96.98%)
1:32:05.581685 PROGRESS: Decoy precursors: 15 (3.02%)
1:32:05.581738 PROGRESS: 
1:32:05.581787 PROGRESS: Precursor Summary:
1:32:05.582760 PROGRESS: Channel   0:	 0.05 FDR:   481; 0.01 FDR:    12; 0.001 FDR:    12
1:32:05.582860 PROGRESS: 
1:32:05.582925 PROGRESS: Protein Summary:
1:32:05.584011 PROGRESS: Channel   0:	 0.05 FDR:   462; 0.01 FDR:    12; 0.001 FDR:    12
1:32:05.584115 PROGRESS: =========================================================================
1:32:05.594889 INFO: calibration group: precursor, predicting mz
1:32:05.595017 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:05.595052 INFO: calibration group: precursor, predicting rt
1:32:05.596713 INFO: calibration group: fragment, predicting mz
1:32:05.599859 INFO: === skipping optimization until target number of precursors are found ===
1:32:05.599986 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1:32:05.600042 INFO: Starting optimization step 4.
1:32:05.600116 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:32:05.600178 PROGRESS: Extracting batch of 1592 precursors
1:32:05.601108 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:05.601158 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:05.601195 INFO: FWHM in RT is 2.36 seconds, sigma is 0.30
1:32:05.601221 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:05.601402 INFO: Starting candidate selection
1:32:05.730030 INFO: Starting candidate scoring
1:32:05.770554 INFO: Finished candidate processing
1:32:05.770644 INFO: Collecting candidate features
1:32:05.783316 INFO: Collecting fragment features
1:32:05.787387 INFO: Finished candidate scoring
1:32:05.790859 PROGRESS: === Extracted 5543 precursors and 44704 fragments ===
1:32:05.791764 INFO: performing precursor FDR with 47 features
1:32:05.791806 INFO: Decoy channel: -1
1:32:05.791829 INFO: Competetive: True
1:32:05.795475 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:05.828154 INFO: Test AUC: 0.735
1:32:05.828238 INFO: Train AUC: 0.744
1:32:05.828267 INFO: AUC difference: 1.23%
1:32:06.002591 INFO: Resetting torch num_threads to 100
1:32:06.003344 INFO: === FDR correction performed with classifier version 8 ===
1:32:06.004081 PROGRESS: ============================= Precursor FDR =============================
1:32:06.004175 PROGRESS: Total precursors accumulated: 1,141
1:32:06.004237 PROGRESS: Target precursors: 1,101 (96.49%)
1:32:06.004289 PROGRESS: Decoy precursors: 40 (3.51%)
1:32:06.004341 PROGRESS: 
1:32:06.004385 PROGRESS: Precursor Summary:
1:32:06.005395 PROGRESS: Channel   0:	 0.05 FDR: 1,101; 0.01 FDR:    55; 0.001 FDR:    55
1:32:06.005486 PROGRESS: 
1:32:06.005547 PROGRESS: Protein Summary:
1:32:06.006770 PROGRESS: Channel   0:	 0.05 FDR:   988; 0.01 FDR:    52; 0.001 FDR:    52
1:32:06.006865 PROGRESS: =========================================================================
1:32:06.014591 INFO: calibration group: precursor, predicting mz
1:32:06.014713 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:06.014744 INFO: calibration group: precursor, predicting rt
1:32:06.017142 INFO: calibration group: fragment, predicting mz
1:32:06.022244 INFO: === skipping optimization until target number of precursors are found ===
1:32:06.022361 PROGRESS: === Optimization of rt_error has been skipped 2 time(s); maximum number is 1 ===
1:32:06.022409 INFO: Starting optimization step 5.
1:32:06.022470 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:32:06.022526 PROGRESS: Extracting batch of 3186 precursors
1:32:06.023623 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:06.023670 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:06.023701 INFO: FWHM in RT is 2.36 seconds, sigma is 0.30
1:32:06.023724 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:06.023873 INFO: Starting candidate selection
1:32:06.196390 INFO: Starting candidate scoring
1:32:06.245452 INFO: Finished candidate processing
1:32:06.245537 INFO: Collecting candidate features
1:32:06.260158 WARNING: intensity_correlation has 2 NaNs ( 0.03 % out of 6348)
1:32:06.263348 INFO: Collecting fragment features
1:32:06.269382 INFO: Finished candidate scoring
1:32:06.276918 PROGRESS: === Extracted 11891 precursors and 96095 fragments ===
1:32:06.279098 INFO: performing precursor FDR with 47 features
1:32:06.279143 INFO: Decoy channel: -1
1:32:06.279167 INFO: Competetive: True
1:32:06.284756 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:06.286732 WARNING: dropped 2 decoy PSMs due to missing features
1:32:06.353538 INFO: Test AUC: 0.736
1:32:06.353637 INFO: Train AUC: 0.744
1:32:06.353665 INFO: AUC difference: 1.14%
1:32:06.533043 INFO: Resetting torch num_threads to 100
1:32:06.533943 INFO: === FDR correction performed with classifier version 8 ===
1:32:06.534810 PROGRESS: ============================= Precursor FDR =============================
1:32:06.534903 PROGRESS: Total precursors accumulated: 2,449
1:32:06.534964 PROGRESS: Target precursors: 2,359 (96.33%)
1:32:06.535015 PROGRESS: Decoy precursors: 90 (3.67%)
1:32:06.535060 PROGRESS: 
1:32:06.535111 PROGRESS: Precursor Summary:
1:32:06.536225 PROGRESS: Channel   0:	 0.05 FDR: 2,359; 0.01 FDR:     0; 0.001 FDR:     0
1:32:06.536317 PROGRESS: 
1:32:06.536372 PROGRESS: Protein Summary:
1:32:06.537775 PROGRESS: Channel   0:	 0.05 FDR: 1,859; 0.01 FDR:     0; 0.001 FDR:     0
1:32:06.537868 PROGRESS: =========================================================================
1:32:06.548957 INFO: calibration group: precursor, predicting mz
1:32:06.549077 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:06.549108 INFO: calibration group: precursor, predicting rt
1:32:06.553375 INFO: calibration group: fragment, predicting mz
1:32:06.562247 INFO: === skipping optimization until target number of precursors are found ===
1:32:06.562375 PROGRESS: === Optimization of rt_error has been skipped 3 time(s); maximum number is 1 ===
1:32:06.562423 INFO: Starting optimization step 6.
1:32:06.562485 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:32:06.562539 PROGRESS: Extracting batch of 6377 precursors
1:32:06.564178 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:06.564228 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:06.564259 INFO: FWHM in RT is 2.36 seconds, sigma is 0.30
1:32:06.564281 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:06.564430 INFO: Starting candidate selection
1:32:06.855030 INFO: Starting candidate scoring
1:32:06.945752 INFO: Finished candidate processing
1:32:06.945848 INFO: Collecting candidate features
1:32:06.969881 WARNING: intensity_correlation has 2 NaNs ( 0.02 % out of 12663)
1:32:06.973310 INFO: Collecting fragment features
1:32:06.983166 INFO: Finished candidate scoring
1:32:06.993484 PROGRESS: === Extracted 24554 precursors and 197722 fragments ===
1:32:06.995817 INFO: performing precursor FDR with 47 features
1:32:06.995875 INFO: Decoy channel: -1
1:32:06.995900 INFO: Competetive: True
1:32:07.003628 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:07.007686 WARNING: dropped 1 target PSMs due to missing features
1:32:07.007772 WARNING: dropped 3 decoy PSMs due to missing features
1:32:07.294867 INFO: Test AUC: 0.818
1:32:07.294985 INFO: Train AUC: 0.817
1:32:07.295015 INFO: AUC difference: 0.08%
1:32:07.477192 INFO: Resetting torch num_threads to 100
1:32:07.478390 INFO: === FDR correction performed with classifier version 8 ===
1:32:07.479616 PROGRESS: ============================= Precursor FDR =============================
1:32:07.479712 PROGRESS: Total precursors accumulated: 5,487
1:32:07.479771 PROGRESS: Target precursors: 5,404 (98.49%)
1:32:07.479821 PROGRESS: Decoy precursors: 83 (1.51%)
1:32:07.479868 PROGRESS: 
1:32:07.479913 PROGRESS: Precursor Summary:
1:32:07.481891 PROGRESS: Channel   0:	 0.05 FDR: 5,404; 0.01 FDR: 5,031; 0.001 FDR: 1,221
1:32:07.481992 PROGRESS: 
1:32:07.482048 PROGRESS: Protein Summary:
1:32:07.484978 PROGRESS: Channel   0:	 0.05 FDR: 3,462; 0.01 FDR: 3,254; 0.001 FDR:   993
1:32:07.485078 PROGRESS: =========================================================================
1:32:07.511883 INFO: fragments_df: keeping 5000 of 197722 [sum(precursor_idx_mask)=95270 sum(mass_error_mask)=197722 stop_rank=5000
1:32:07.519209 INFO: calibration group: precursor, fitting rt estimator 
1:32:08.221388 INFO: calibration group: fragment, fitting mz estimator 
1:32:08.906494 INFO: Using score_cutoff 38.03505571746826 (fac=0.99, q=1)
1:32:08.906980 INFO: calibration group: precursor, predicting mz
1:32:08.907069 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:08.907099 INFO: calibration group: precursor, predicting rt
1:32:08.908610 INFO: calibration group: fragment, predicting mz
1:32:08.910829 INFO: === checking if optimization conditions were reached ===
1:32:08.910938 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:32:08.914863 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 21.3569.
1:32:08.914919 INFO: ==============================================
1:32:08.915021 INFO: Starting optimization step 7.
1:32:08.915091 PROGRESS: === Extracting elution groups 0 to 600 ===
1:32:08.915147 PROGRESS: Extracting batch of 1197 precursors
1:32:08.916052 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:08.916101 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:08.916131 INFO: FWHM in RT is 2.29 seconds, sigma is 0.29
1:32:08.916152 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:08.916304 INFO: Starting candidate selection
1:32:09.027489 INFO: Starting candidate scoring
1:32:09.066522 INFO: Finished candidate processing
1:32:09.066597 INFO: Collecting candidate features
1:32:09.074944 WARNING: intensity_correlation has 2 NaNs ( 0.09 % out of 2311)
1:32:09.077936 INFO: Collecting fragment features
1:32:09.081941 INFO: Finished candidate scoring
1:32:09.083650 PROGRESS: === Extracted 2311 precursors and 18332 fragments ===
1:32:09.083915 INFO: performing precursor FDR with 47 features
1:32:09.083951 INFO: Decoy channel: -1
1:32:09.083973 INFO: Competetive: True
1:32:09.086507 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:09.087848 WARNING: dropped 1 target PSMs due to missing features
1:32:09.087898 WARNING: dropped 1 decoy PSMs due to missing features
1:32:09.108690 INFO: Test AUC: 0.730
1:32:09.108755 INFO: Train AUC: 0.739
1:32:09.108783 INFO: AUC difference: 1.20%
1:32:09.279163 INFO: Resetting torch num_threads to 100
1:32:09.279734 INFO: === FDR correction performed with classifier version 8 ===
1:32:09.280347 PROGRESS: ============================= Precursor FDR =============================
1:32:09.280437 PROGRESS: Total precursors accumulated: 493
1:32:09.280498 PROGRESS: Target precursors: 479 (97.16%)
1:32:09.280548 PROGRESS: Decoy precursors: 14 (2.84%)
1:32:09.280596 PROGRESS: 
1:32:09.280638 PROGRESS: Precursor Summary:
1:32:09.281564 PROGRESS: Channel   0:	 0.05 FDR:   479; 0.01 FDR:    25; 0.001 FDR:    25
1:32:09.281654 PROGRESS: 
1:32:09.281710 PROGRESS: Protein Summary:
1:32:09.282782 PROGRESS: Channel   0:	 0.05 FDR:   462; 0.01 FDR:    24; 0.001 FDR:    24
1:32:09.282885 PROGRESS: =========================================================================
1:32:09.287907 INFO: calibration group: precursor, predicting mz
1:32:09.288011 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:09.288043 INFO: calibration group: precursor, predicting rt
1:32:09.289642 INFO: calibration group: fragment, predicting mz
1:32:09.292560 INFO: === skipping optimization until target number of precursors are found ===
1:32:09.292676 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1:32:09.292724 INFO: Starting optimization step 8.
1:32:09.292791 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:32:09.292847 PROGRESS: Extracting batch of 1592 precursors
1:32:09.293713 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:09.293759 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:09.293788 INFO: FWHM in RT is 2.29 seconds, sigma is 0.29
1:32:09.293809 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:09.293957 INFO: Starting candidate selection
1:32:09.422750 INFO: Starting candidate scoring
1:32:09.462469 INFO: Finished candidate processing
1:32:09.462552 INFO: Collecting candidate features
1:32:09.471885 WARNING: intensity_correlation has 2 NaNs ( 0.07 % out of 3074)
1:32:09.474833 INFO: Collecting fragment features
1:32:09.479738 INFO: Finished candidate scoring
1:32:09.483113 PROGRESS: === Extracted 5385 precursors and 42330 fragments ===
1:32:09.483990 INFO: performing precursor FDR with 47 features
1:32:09.484032 INFO: Decoy channel: -1
1:32:09.484056 INFO: Competetive: True
1:32:09.487603 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:09.489278 WARNING: dropped 1 target PSMs due to missing features
1:32:09.489328 WARNING: dropped 3 decoy PSMs due to missing features
1:32:09.520532 INFO: Test AUC: 0.740
1:32:09.520616 INFO: Train AUC: 0.740
1:32:09.520647 INFO: AUC difference: 0.04%
1:32:09.692762 INFO: Resetting torch num_threads to 100
1:32:09.693462 INFO: === FDR correction performed with classifier version 8 ===
1:32:09.694158 PROGRESS: ============================= Precursor FDR =============================
1:32:09.694251 PROGRESS: Total precursors accumulated: 1,130
1:32:09.694310 PROGRESS: Target precursors: 1,093 (96.73%)
1:32:09.694362 PROGRESS: Decoy precursors: 37 (3.27%)
1:32:09.694408 PROGRESS: 
1:32:09.694461 PROGRESS: Precursor Summary:
1:32:09.695480 PROGRESS: Channel   0:	 0.05 FDR: 1,093; 0.01 FDR:    52; 0.001 FDR:    52
1:32:09.695573 PROGRESS: 
1:32:09.695630 PROGRESS: Protein Summary:
1:32:09.696842 PROGRESS: Channel   0:	 0.05 FDR:   985; 0.01 FDR:    50; 0.001 FDR:    50
1:32:09.696934 PROGRESS: =========================================================================
1:32:09.703285 INFO: calibration group: precursor, predicting mz
1:32:09.703398 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:09.703431 INFO: calibration group: precursor, predicting rt
1:32:09.705860 INFO: calibration group: fragment, predicting mz
1:32:09.711005 INFO: === skipping optimization until target number of precursors are found ===
1:32:09.711116 PROGRESS: === Optimization of rt_error has been skipped 2 time(s); maximum number is 1 ===
1:32:09.711593 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 32.1906 found after 2 searches.
1:32:09.711651 PROGRESS: Optimization finished for rt_error.
1:32:09.716367 INFO: calibration group: precursor, predicting mz
1:32:09.716474 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:09.716505 INFO: calibration group: precursor, predicting rt
1:32:09.717778 INFO: calibration group: fragment, predicting mz
1:32:09.746758 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:32:09.746901 PROGRESS: ==============================================
1:32:09.746974 PROGRESS: ms2_error      : 6.2633
1:32:09.747031 PROGRESS: rt_error       : 32.1906
1:32:09.747078 PROGRESS: ==============================================
1:32:09.747777 INFO: calibration group: precursor, predicting mz
1:32:09.747881 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:09.747910 INFO: calibration group: precursor, predicting rt
1:32:09.862991 INFO: calibration group: fragment, predicting mz
1:32:10.193762 PROGRESS: Extracting batch of 220080 precursors
1:32:10.257900 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:10.258034 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:10.258069 INFO: FWHM in RT is 2.29 seconds, sigma is 0.29
1:32:10.258092 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:10.258300 INFO: Starting candidate selection
1:32:18.092436 INFO: Applying score cutoff of 38.03505571746826
1:32:18.099636 INFO: Removed 195852 precursors with score below cutoff
1:32:18.168947 INFO: Starting candidate scoring
1:32:20.001163 INFO: Finished candidate processing
1:32:20.001269 INFO: Collecting candidate features
1:32:20.396281 INFO: Collecting fragment features
1:32:20.551466 INFO: Finished candidate scoring
1:32:20.679295 INFO: === FDR correction performed with classifier version 15 ===
1:32:20.680132 INFO: performing precursor FDR with 47 features
1:32:20.680181 INFO: Decoy channel: -1
1:32:20.680202 INFO: Competetive: True
1:32:20.750225 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:20.776388 WARNING: FDR calculation for 163616 target and 80145 decoy PSMs
1:32:20.776561 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1:32:25.084944 INFO: Test AUC: 0.902
1:32:25.085088 INFO: Train AUC: 0.902
1:32:25.085119 INFO: AUC difference: 0.00%
1:32:25.320234 INFO: Resetting torch num_threads to 100
1:32:25.339770 INFO: Removing fragments below FDR threshold
1:32:25.412523 PROGRESS: ============================= Precursor FDR =============================
1:32:25.412798 PROGRESS: Total precursors accumulated: 101,075
1:32:25.412863 PROGRESS: Target precursors: 100,075 (99.01%)
1:32:25.412916 PROGRESS: Decoy precursors: 1,000 (0.99%)
1:32:25.412963 PROGRESS: 
1:32:25.413008 PROGRESS: Precursor Summary:
1:32:25.456681 PROGRESS: Channel   0:	 0.05 FDR: 100,075; 0.01 FDR: 100,075; 0.001 FDR: 88,581
1:32:25.457444 PROGRESS: 
1:32:25.457518 PROGRESS: Protein Summary:
1:32:25.526025 PROGRESS: Channel   0:	 0.05 FDR: 9,868; 0.01 FDR: 9,868; 0.001 FDR: 9,632
1:32:25.526282 PROGRESS: =========================================================================
1:32:26.252815 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:32:26.276377 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:32:26.276531 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant
1:32:26.276599 INFO: Creating folder run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/figures
1:32:26.277221 INFO: Initializing RawFileManager
1:32:36.484449 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.
1:32:36.489515 INFO: Determining DIA cycle
1:32:36.505879 INFO: Found cycle with start 0.00 min and length 300.
1:32:36.678884 INFO: RT (min)            : 0.0 - 26.9
1:32:36.678973 INFO: RT duration (sec)   : 1611.2
1:32:36.679000 INFO: RT duration (min)   : 26.9
1:32:36.679024 INFO: Cycle len (scans)   : 300
1:32:36.679048 INFO: Cycle len (sec)     : 1.65
1:32:36.679069 INFO: Number of cycles    : 977
1:32:36.679089 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:32:36.730622 INFO: Initializing CalibrationManager
1:32:36.730907 INFO: Loading calibration config
1:32:36.731529 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'}]
1:32:36.731630 INFO: Calibration group :fragment, found 1 estimator(s)
1:32:36.731715 INFO: Calibration group :precursor, found 3 estimator(s)
1:32:36.731796 INFO: Disabling ion mobility calibration
1:32:36.731824 INFO: removed mobility estimator from group precursor
1:32:36.731966 INFO: Initializing OptimizationManager
1:32:36.732075 INFO: initial parameter: ms1_error = 30
1:32:36.732134 INFO: initial parameter: ms2_error = 30
1:32:36.732183 INFO: initial parameter: rt_error = 805.6002197265625
1:32:36.732230 INFO: initial parameter: mobility_error = 0.1
1:32:36.732273 INFO: initial parameter: column_type = library
1:32:36.732315 INFO: initial parameter: num_candidates = 1
1:32:36.732356 INFO: initial parameter: classifier_version = -1
1:32:36.732397 INFO: initial parameter: fwhm_rt = 5
1:32:36.732439 INFO: initial parameter: fwhm_mobility = 0.01
1:32:36.732481 INFO: initial parameter: score_cutoff = 0
1:32:36.732553 INFO: Initializing TimingManager
1:32:36.732612 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:32:36.732727 INFO: FDRManager not loaded from disk.
1:32:36.732748 INFO: Initializing FDRManager
1:32:36.732783 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:32:36.768399 PROGRESS: 110,515 target precursors potentially observable (0 removed)
1:32:36.818449 PROGRESS: Starting initial search for precursors.
1:32:36.826156 INFO: Starting optimization step 0.
1:32:36.826309 PROGRESS: === Extracting elution groups 0 to 200 ===
1:32:36.826385 PROGRESS: Extracting batch of 400 precursors
1:32:36.827378 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:36.827429 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:36.827465 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:32:36.827490 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:32:36.827750 INFO: Starting candidate selection
1:32:36.954741 INFO: Starting candidate scoring
1:32:36.989685 INFO: Finished candidate processing
1:32:36.989748 INFO: Collecting candidate features
1:32:36.998086 INFO: Collecting fragment features
1:32:37.000135 INFO: Finished candidate scoring
1:32:37.000890 PROGRESS: === Extracted 400 precursors and 4419 fragments ===
1:32:37.001145 INFO: performing precursor FDR with 47 features
1:32:37.001180 INFO: Decoy channel: -1
1:32:37.001203 INFO: Competetive: True
1:32:37.002174 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:37.020140 INFO: Test AUC: 0.501
1:32:37.020204 INFO: Train AUC: 0.452
1:32:37.020233 INFO: AUC difference: 10.85%
1:32:37.020256 WARNING: AUC difference > 5%. This may indicate overfitting.
1:32:37.192570 INFO: Resetting torch num_threads to 100
1:32:37.193093 INFO: === FDR correction performed with classifier version -1 ===
1:32:37.193724 PROGRESS: ============================= Precursor FDR =============================
1:32:37.193816 PROGRESS: Total precursors accumulated: 1
1:32:37.193878 PROGRESS: Target precursors: 1 (100.00%)
1:32:37.193929 PROGRESS: Decoy precursors: 0 (0.00%)
1:32:37.193974 PROGRESS: 
1:32:37.194019 PROGRESS: Precursor Summary:
1:32:37.194977 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:32:37.195083 PROGRESS: 
1:32:37.195140 PROGRESS: Protein Summary:
1:32:37.196164 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:32:37.196251 PROGRESS: =========================================================================
1:32:37.199958 INFO: Starting optimization step 1.
1:32:37.200063 PROGRESS: === Extracting elution groups 200 to 600 ===
1:32:37.200125 PROGRESS: Extracting batch of 797 precursors
1:32:37.201169 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:37.201216 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:37.201247 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:32:37.201270 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:32:37.201423 INFO: Starting candidate selection
1:32:37.334607 INFO: Starting candidate scoring
1:32:37.370048 INFO: Finished candidate processing
1:32:37.370117 INFO: Collecting candidate features
1:32:37.378947 INFO: Collecting fragment features
1:32:37.381591 INFO: Finished candidate scoring
1:32:37.383461 PROGRESS: === Extracted 1197 precursors and 13226 fragments ===
1:32:37.384197 INFO: performing precursor FDR with 47 features
1:32:37.384239 INFO: Decoy channel: -1
1:32:37.384263 INFO: Competetive: True
1:32:37.386959 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:37.406284 INFO: Test AUC: 0.453
1:32:37.406344 INFO: Train AUC: 0.483
1:32:37.406372 INFO: AUC difference: 6.15%
1:32:37.406393 WARNING: AUC difference > 5%. This may indicate overfitting.
1:32:37.577626 INFO: Resetting torch num_threads to 100
1:32:37.578213 INFO: === FDR correction performed with classifier version -1 ===
1:32:37.578857 PROGRESS: ============================= Precursor FDR =============================
1:32:37.578951 PROGRESS: Total precursors accumulated: 2
1:32:37.579011 PROGRESS: Target precursors: 2 (100.00%)
1:32:37.579062 PROGRESS: Decoy precursors: 0 (0.00%)
1:32:37.579107 PROGRESS: 
1:32:37.579151 PROGRESS: Precursor Summary:
1:32:37.580077 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:32:37.580169 PROGRESS: 
1:32:37.580225 PROGRESS: Protein Summary:
1:32:37.581243 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:32:37.581331 PROGRESS: =========================================================================
1:32:37.585958 INFO: Starting optimization step 2.
1:32:37.586064 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:32:37.586126 PROGRESS: Extracting batch of 1592 precursors
1:32:37.586959 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:37.587007 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:37.587041 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:32:37.587064 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:32:37.587215 INFO: Starting candidate selection
1:32:37.750476 INFO: Starting candidate scoring
1:32:37.789064 INFO: Finished candidate processing
1:32:37.789147 INFO: Collecting candidate features
1:32:37.799173 INFO: Collecting fragment features
1:32:37.802893 INFO: Finished candidate scoring
1:32:37.805668 PROGRESS: === Extracted 2789 precursors and 30839 fragments ===
1:32:37.806676 INFO: performing precursor FDR with 47 features
1:32:37.806720 INFO: Decoy channel: -1
1:32:37.806744 INFO: Competetive: True
1:32:37.809890 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:37.834386 INFO: Test AUC: 0.496
1:32:37.834461 INFO: Train AUC: 0.459
1:32:37.834492 INFO: AUC difference: 8.01%
1:32:37.834517 WARNING: AUC difference > 5%. This may indicate overfitting.
1:32:38.008579 INFO: Resetting torch num_threads to 100
1:32:38.009219 INFO: === FDR correction performed with classifier version -1 ===
1:32:38.009868 PROGRESS: ============================= Precursor FDR =============================
1:32:38.009962 PROGRESS: Total precursors accumulated: 2
1:32:38.010022 PROGRESS: Target precursors: 2 (100.00%)
1:32:38.010076 PROGRESS: Decoy precursors: 0 (0.00%)
1:32:38.010122 PROGRESS: 
1:32:38.010166 PROGRESS: Precursor Summary:
1:32:38.011123 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:32:38.011217 PROGRESS: 
1:32:38.011274 PROGRESS: Protein Summary:
1:32:38.012300 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:32:38.012390 PROGRESS: =========================================================================
1:32:38.018578 INFO: Starting optimization step 3.
1:32:38.018694 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:32:38.018758 PROGRESS: Extracting batch of 3186 precursors
1:32:38.019801 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:38.019848 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:38.019881 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:32:38.019905 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:32:38.020052 INFO: Starting candidate selection
1:32:38.273761 INFO: Starting candidate scoring
1:32:38.316134 INFO: Finished candidate processing
1:32:38.316217 INFO: Collecting candidate features
1:32:38.329306 INFO: Collecting fragment features
1:32:38.333523 INFO: Finished candidate scoring
1:32:38.337584 PROGRESS: === Extracted 5975 precursors and 66147 fragments ===
1:32:38.338836 INFO: performing precursor FDR with 47 features
1:32:38.338881 INFO: Decoy channel: -1
1:32:38.338903 INFO: Competetive: True
1:32:38.342863 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:38.374241 INFO: Test AUC: 0.438
1:32:38.374322 INFO: Train AUC: 0.470
1:32:38.374351 INFO: AUC difference: 6.85%
1:32:38.374371 WARNING: AUC difference > 5%. This may indicate overfitting.
1:32:38.553705 INFO: Resetting torch num_threads to 100
1:32:38.554442 INFO: === FDR correction performed with classifier version -1 ===
1:32:38.555100 PROGRESS: ============================= Precursor FDR =============================
1:32:38.555197 PROGRESS: Total precursors accumulated: 3
1:32:38.555259 PROGRESS: Target precursors: 3 (100.00%)
1:32:38.555313 PROGRESS: Decoy precursors: 0 (0.00%)
1:32:38.555359 PROGRESS: 
1:32:38.555404 PROGRESS: Precursor Summary:
1:32:38.556340 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1:32:38.556431 PROGRESS: 
1:32:38.556487 PROGRESS: Protein Summary:
1:32:38.557513 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1:32:38.557601 PROGRESS: =========================================================================
1:32:38.567641 INFO: Starting optimization step 4.
1:32:38.567760 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:32:38.567823 PROGRESS: Extracting batch of 6377 precursors
1:32:38.569421 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:38.569469 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:38.569502 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:32:38.569523 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:32:38.569678 INFO: Starting candidate selection
1:32:39.003476 INFO: Starting candidate scoring
1:32:39.064298 INFO: Finished candidate processing
1:32:39.064390 INFO: Collecting candidate features
1:32:39.082900 INFO: Collecting fragment features
1:32:39.089483 INFO: Finished candidate scoring
1:32:39.096396 PROGRESS: === Extracted 12352 precursors and 136463 fragments ===
1:32:39.098173 INFO: performing precursor FDR with 47 features
1:32:39.098228 INFO: Decoy channel: -1
1:32:39.098252 INFO: Competetive: True
1:32:39.103738 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:39.150686 INFO: Test AUC: 0.459
1:32:39.150777 INFO: Train AUC: 0.469
1:32:39.150805 INFO: AUC difference: 2.21%
1:32:39.328688 INFO: Resetting torch num_threads to 100
1:32:39.329606 INFO: === FDR correction performed with classifier version -1 ===
1:32:39.330254 PROGRESS: ============================= Precursor FDR =============================
1:32:39.330351 PROGRESS: Total precursors accumulated: 1
1:32:39.330412 PROGRESS: Target precursors: 1 (100.00%)
1:32:39.330463 PROGRESS: Decoy precursors: 0 (0.00%)
1:32:39.330508 PROGRESS: 
1:32:39.330561 PROGRESS: Precursor Summary:
1:32:39.331504 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:32:39.331591 PROGRESS: 
1:32:39.331647 PROGRESS: Protein Summary:
1:32:39.332659 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:32:39.332748 PROGRESS: =========================================================================
1:32:39.348576 INFO: Starting optimization step 5.
1:32:39.348742 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:32:39.348809 PROGRESS: Extracting batch of 12745 precursors
1:32:39.351521 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:39.351574 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:39.351607 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:32:39.351630 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:32:39.351796 INFO: Starting candidate selection
1:32:40.140833 INFO: Starting candidate scoring
1:32:40.228804 INFO: Finished candidate processing
1:32:40.228902 INFO: Collecting candidate features
1:32:40.259026 INFO: Collecting fragment features
1:32:40.269247 INFO: Finished candidate scoring
1:32:40.282310 PROGRESS: === Extracted 25097 precursors and 277338 fragments ===
1:32:40.285761 INFO: performing precursor FDR with 47 features
1:32:40.285838 INFO: Decoy channel: -1
1:32:40.285869 INFO: Competetive: True
1:32:40.295114 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:40.666578 INFO: Test AUC: 0.811
1:32:40.666707 INFO: Train AUC: 0.818
1:32:40.666993 INFO: AUC difference: 0.94%
1:32:40.856520 INFO: Resetting torch num_threads to 100
1:32:40.857888 INFO: === FDR correction performed with classifier version -1 ===
1:32:40.859230 PROGRESS: ============================= Precursor FDR =============================
1:32:40.859337 PROGRESS: Total precursors accumulated: 7,167
1:32:40.859412 PROGRESS: Target precursors: 6,805 (94.95%)
1:32:40.859478 PROGRESS: Decoy precursors: 362 (5.05%)
1:32:40.859538 PROGRESS: 
1:32:40.859596 PROGRESS: Precursor Summary:
1:32:40.861935 PROGRESS: Channel   0:	 0.05 FDR: 6,724; 0.01 FDR: 4,524; 0.001 FDR: 2,449
1:32:40.862050 PROGRESS: 
1:32:40.862120 PROGRESS: Protein Summary:
1:32:40.865392 PROGRESS: Channel   0:	 0.05 FDR: 3,624; 0.01 FDR: 2,563; 0.001 FDR: 1,548
1:32:40.865503 PROGRESS: =========================================================================
1:32:40.892179 INFO: fragments_df: keeping 5000 of 277338 [sum(precursor_idx_mask)=51218 sum(mass_error_mask)=277338 stop_rank=5000
1:32:40.898739 INFO: calibration group: precursor, fitting rt estimator 
1:32:41.511217 INFO: calibration group: fragment, fitting mz estimator 
1:32:42.184323 INFO: Using score_cutoff 59.396573233795166 (fac=0.99, q=1)
1:32:42.184853 INFO: calibration group: precursor, predicting mz
1:32:42.184953 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:42.184992 INFO: calibration group: precursor, predicting rt
1:32:42.186562 INFO: calibration group: fragment, predicting mz
1:32:42.188822 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:32:42.188949 INFO: Starting optimization step 6.
1:32:42.189032 PROGRESS: === Extracting elution groups 0 to 600 ===
1:32:42.189103 PROGRESS: Extracting batch of 1197 precursors
1:32:42.190125 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:42.190172 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:42.190212 INFO: FWHM in RT is 3.04 seconds, sigma is 0.39
1:32:42.190241 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:42.190409 INFO: Starting candidate selection
1:32:42.335708 INFO: Starting candidate scoring
1:32:42.373889 INFO: Finished candidate processing
1:32:42.373962 INFO: Collecting candidate features
1:32:42.385959 INFO: Collecting fragment features
1:32:42.390673 INFO: Finished candidate scoring
1:32:42.392259 PROGRESS: === Extracted 2394 precursors and 26187 fragments ===
1:32:42.392512 INFO: performing precursor FDR with 47 features
1:32:42.392548 INFO: Decoy channel: -1
1:32:42.392569 INFO: Competetive: True
1:32:42.395036 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:42.416423 INFO: Test AUC: 0.689
1:32:42.416489 INFO: Train AUC: 0.700
1:32:42.416518 INFO: AUC difference: 1.53%
1:32:42.595190 INFO: Resetting torch num_threads to 100
1:32:42.595773 INFO: === FDR correction performed with classifier version 5 ===
1:32:42.596381 PROGRESS: ============================= Precursor FDR =============================
1:32:42.596472 PROGRESS: Total precursors accumulated: 373
1:32:42.596529 PROGRESS: Target precursors: 353 (94.64%)
1:32:42.596578 PROGRESS: Decoy precursors: 20 (5.36%)
1:32:42.596630 PROGRESS: 
1:32:42.596676 PROGRESS: Precursor Summary:
1:32:42.597631 PROGRESS: Channel   0:	 0.05 FDR:   347; 0.01 FDR:   167; 0.001 FDR:   167
1:32:42.597721 PROGRESS: 
1:32:42.597775 PROGRESS: Protein Summary:
1:32:42.598899 PROGRESS: Channel   0:	 0.05 FDR:   336; 0.01 FDR:   163; 0.001 FDR:   163
1:32:42.598987 PROGRESS: =========================================================================
1:32:42.603758 INFO: calibration group: precursor, predicting mz
1:32:42.603860 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:42.603890 INFO: calibration group: precursor, predicting rt
1:32:42.605468 INFO: calibration group: fragment, predicting mz
1:32:42.608469 INFO: === skipping optimization until target number of precursors are found ===
1:32:42.608578 INFO: Starting optimization step 7.
1:32:42.608641 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:32:42.608696 PROGRESS: Extracting batch of 1592 precursors
1:32:42.609559 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:42.609603 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:42.609632 INFO: FWHM in RT is 3.04 seconds, sigma is 0.39
1:32:42.609653 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:42.609799 INFO: Starting candidate selection
1:32:42.774209 INFO: Starting candidate scoring
1:32:42.814924 INFO: Finished candidate processing
1:32:42.815012 INFO: Collecting candidate features
1:32:42.827341 INFO: Collecting fragment features
1:32:42.830957 INFO: Finished candidate scoring
1:32:42.834485 PROGRESS: === Extracted 5578 precursors and 61008 fragments ===
1:32:42.835437 INFO: performing precursor FDR with 47 features
1:32:42.835480 INFO: Decoy channel: -1
1:32:42.835504 INFO: Competetive: True
1:32:42.838993 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:42.869242 INFO: Test AUC: 0.700
1:32:42.869324 INFO: Train AUC: 0.694
1:32:42.869354 INFO: AUC difference: 0.86%
1:32:43.050813 INFO: Resetting torch num_threads to 100
1:32:43.051557 INFO: === FDR correction performed with classifier version 5 ===
1:32:43.052249 PROGRESS: ============================= Precursor FDR =============================
1:32:43.052340 PROGRESS: Total precursors accumulated: 809
1:32:43.052400 PROGRESS: Target precursors: 766 (94.68%)
1:32:43.052453 PROGRESS: Decoy precursors: 43 (5.32%)
1:32:43.052502 PROGRESS: 
1:32:43.052547 PROGRESS: Precursor Summary:
1:32:43.053627 PROGRESS: Channel   0:	 0.05 FDR:   734; 0.01 FDR:   561; 0.001 FDR:   369
1:32:43.053719 PROGRESS: 
1:32:43.053776 PROGRESS: Protein Summary:
1:32:43.055112 PROGRESS: Channel   0:	 0.05 FDR:   665; 0.01 FDR:   514; 0.001 FDR:   340
1:32:43.055210 PROGRESS: =========================================================================
1:32:43.061635 INFO: fragments_df: keeping 5000 of 61008 [sum(precursor_idx_mask)=12498 sum(mass_error_mask)=61008 stop_rank=5000
1:32:43.067105 INFO: calibration group: precursor, fitting rt estimator 
1:32:43.207808 INFO: calibration group: fragment, fitting mz estimator 
1:32:43.887713 INFO: Using score_cutoff 59.337639335632325 (fac=0.99, q=1)
1:32:43.888107 INFO: calibration group: precursor, predicting mz
1:32:43.888191 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:43.888221 INFO: calibration group: precursor, predicting rt
1:32:43.889727 INFO: calibration group: fragment, predicting mz
1:32:43.891987 INFO: === checking if optimization conditions were reached ===
1:32:43.893607 PROGRESS: ❌ ms2_error      : 13.4530 > 6.2633 or insufficient steps taken.
1:32:43.893661 INFO: ==============================================
1:32:43.893749 INFO: Starting optimization step 8.
1:32:43.893815 PROGRESS: === Extracting elution groups 0 to 600 ===
1:32:43.893872 PROGRESS: Extracting batch of 1197 precursors
1:32:43.894802 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:43.894849 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:43.894879 INFO: FWHM in RT is 2.97 seconds, sigma is 0.38
1:32:43.894900 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:43.895050 INFO: Starting candidate selection
1:32:44.051608 INFO: Starting candidate scoring
1:32:44.091698 INFO: Finished candidate processing
1:32:44.091776 INFO: Collecting candidate features
1:32:44.102942 INFO: Collecting fragment features
1:32:44.107193 INFO: Finished candidate scoring
1:32:44.108916 PROGRESS: === Extracted 2394 precursors and 24176 fragments ===
1:32:44.109184 INFO: performing precursor FDR with 47 features
1:32:44.109221 INFO: Decoy channel: -1
1:32:44.109244 INFO: Competetive: True
1:32:44.111777 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:44.134108 INFO: Test AUC: 0.742
1:32:44.134177 INFO: Train AUC: 0.726
1:32:44.134207 INFO: AUC difference: 2.30%
1:32:44.310725 INFO: Resetting torch num_threads to 100
1:32:44.311291 INFO: === FDR correction performed with classifier version 7 ===
1:32:44.311912 PROGRESS: ============================= Precursor FDR =============================
1:32:44.312001 PROGRESS: Total precursors accumulated: 433
1:32:44.312062 PROGRESS: Target precursors: 416 (96.07%)
1:32:44.312112 PROGRESS: Decoy precursors: 17 (3.93%)
1:32:44.312161 PROGRESS: 
1:32:44.312210 PROGRESS: Precursor Summary:
1:32:44.313207 PROGRESS: Channel   0:	 0.05 FDR:   416; 0.01 FDR:   306; 0.001 FDR:   211
1:32:44.313301 PROGRESS: 
1:32:44.313357 PROGRESS: Protein Summary:
1:32:44.314487 PROGRESS: Channel   0:	 0.05 FDR:   400; 0.01 FDR:   297; 0.001 FDR:   204
1:32:44.314582 PROGRESS: =========================================================================
1:32:44.317692 INFO: fragments_df: keeping 3083 of 24176 [sum(precursor_idx_mask)=6503 sum(mass_error_mask)=24176 stop_rank=3083
1:32:44.322458 INFO: calibration group: precursor, fitting rt estimator 
1:32:44.438833 INFO: calibration group: fragment, fitting mz estimator 
1:32:44.841084 INFO: Using score_cutoff 52.466987634658814 (fac=0.99, q=1)
1:32:44.841474 INFO: calibration group: precursor, predicting mz
1:32:44.841560 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:44.841589 INFO: calibration group: precursor, predicting rt
1:32:44.843129 INFO: calibration group: fragment, predicting mz
1:32:44.845404 INFO: === checking if optimization conditions were reached ===
1:32:44.846720 PROGRESS: ❌ ms2_error      : 6.7285 > 6.2633 or insufficient steps taken.
1:32:44.846772 INFO: ==============================================
1:32:44.846858 INFO: Starting optimization step 9.
1:32:44.846924 PROGRESS: === Extracting elution groups 0 to 600 ===
1:32:44.846980 PROGRESS: Extracting batch of 1197 precursors
1:32:44.847870 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:44.847915 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:44.847946 INFO: FWHM in RT is 2.63 seconds, sigma is 0.34
1:32:44.847966 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:44.848109 INFO: Starting candidate selection
1:32:44.993895 INFO: Starting candidate scoring
1:32:45.035111 INFO: Finished candidate processing
1:32:45.035191 INFO: Collecting candidate features
1:32:45.046292 INFO: Collecting fragment features
1:32:45.051173 INFO: Finished candidate scoring
1:32:45.052872 PROGRESS: === Extracted 2394 precursors and 21234 fragments ===
1:32:45.053148 INFO: performing precursor FDR with 47 features
1:32:45.053184 INFO: Decoy channel: -1
1:32:45.053207 INFO: Competetive: True
1:32:45.055796 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:45.077819 INFO: Test AUC: 0.736
1:32:45.077886 INFO: Train AUC: 0.724
1:32:45.077915 INFO: AUC difference: 1.68%
1:32:45.248214 INFO: Resetting torch num_threads to 100
1:32:45.248792 INFO: === FDR correction performed with classifier version 8 ===
1:32:45.249402 PROGRESS: ============================= Precursor FDR =============================
1:32:45.249493 PROGRESS: Total precursors accumulated: 450
1:32:45.249552 PROGRESS: Target precursors: 433 (96.22%)
1:32:45.249601 PROGRESS: Decoy precursors: 17 (3.78%)
1:32:45.249650 PROGRESS: 
1:32:45.249692 PROGRESS: Precursor Summary:
1:32:45.250712 PROGRESS: Channel   0:	 0.05 FDR:   433; 0.01 FDR:   326; 0.001 FDR:   217
1:32:45.250804 PROGRESS: 
1:32:45.250861 PROGRESS: Protein Summary:
1:32:45.252018 PROGRESS: Channel   0:	 0.05 FDR:   415; 0.01 FDR:   315; 0.001 FDR:   209
1:32:45.252111 PROGRESS: =========================================================================
1:32:45.255095 INFO: fragments_df: keeping 3164 of 21234 [sum(precursor_idx_mask)=6477 sum(mass_error_mask)=21234 stop_rank=3164
1:32:45.259907 INFO: calibration group: precursor, fitting rt estimator 
1:32:45.383035 INFO: calibration group: fragment, fitting mz estimator 
1:32:45.803659 INFO: Using score_cutoff 43.43094489097595 (fac=0.99, q=1)
1:32:45.804317 INFO: calibration group: precursor, predicting mz
1:32:45.804404 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:45.804437 INFO: calibration group: precursor, predicting rt
1:32:45.805983 INFO: calibration group: fragment, predicting mz
1:32:45.808354 INFO: === checking if optimization conditions were reached ===
1:32:45.809694 PROGRESS: ✅ ms2_error      : 6.2633 <= 6.2633
1:32:45.809745 INFO: ==============================================
1:32:45.809831 PROGRESS: Optimization finished for ms2_error.
1:32:45.815683 INFO: calibration group: precursor, predicting mz
1:32:45.815791 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:45.815820 INFO: calibration group: precursor, predicting rt
1:32:45.817091 INFO: calibration group: fragment, predicting mz
1:32:45.819346 INFO: Starting optimization step 0.
1:32:45.819444 PROGRESS: === Extracting elution groups 0 to 600 ===
1:32:45.819508 PROGRESS: Extracting batch of 1197 precursors
1:32:45.820567 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:45.820611 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:45.820641 INFO: FWHM in RT is 2.41 seconds, sigma is 0.31
1:32:45.820663 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:45.820805 INFO: Starting candidate selection
1:32:45.967832 INFO: Starting candidate scoring
1:32:46.008193 INFO: Finished candidate processing
1:32:46.008269 INFO: Collecting candidate features
1:32:46.019571 INFO: Collecting fragment features
1:32:46.024335 INFO: Finished candidate scoring
1:32:46.026173 PROGRESS: === Extracted 2394 precursors and 21236 fragments ===
1:32:46.026444 INFO: performing precursor FDR with 47 features
1:32:46.026479 INFO: Decoy channel: -1
1:32:46.026501 INFO: Competetive: True
1:32:46.029053 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:46.051926 INFO: Test AUC: 0.752
1:32:46.051990 INFO: Train AUC: 0.722
1:32:46.052018 INFO: AUC difference: 4.15%
1:32:46.226355 INFO: Resetting torch num_threads to 100
1:32:46.226933 INFO: === FDR correction performed with classifier version 9 ===
1:32:46.227544 PROGRESS: ============================= Precursor FDR =============================
1:32:46.227631 PROGRESS: Total precursors accumulated: 449
1:32:46.227688 PROGRESS: Target precursors: 431 (95.99%)
1:32:46.227736 PROGRESS: Decoy precursors: 18 (4.01%)
1:32:46.227779 PROGRESS: 
1:32:46.227828 PROGRESS: Precursor Summary:
1:32:46.228792 PROGRESS: Channel   0:	 0.05 FDR:   431; 0.01 FDR:   311; 0.001 FDR:   212
1:32:46.228882 PROGRESS: 
1:32:46.228935 PROGRESS: Protein Summary:
1:32:46.230056 PROGRESS: Channel   0:	 0.05 FDR:   414; 0.01 FDR:   301; 0.001 FDR:   204
1:32:46.230145 PROGRESS: =========================================================================
1:32:46.233041 INFO: fragments_df: keeping 3113 of 21236 [sum(precursor_idx_mask)=6199 sum(mass_error_mask)=21236 stop_rank=3113
1:32:46.238289 INFO: calibration group: precursor, fitting rt estimator 
1:32:46.337774 INFO: calibration group: fragment, fitting mz estimator 
1:32:46.684389 INFO: Using score_cutoff 45.065777824401856 (fac=0.99, q=1)
1:32:46.684786 INFO: calibration group: precursor, predicting mz
1:32:46.684869 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:46.684898 INFO: calibration group: precursor, predicting rt
1:32:46.686460 INFO: calibration group: fragment, predicting mz
1:32:46.688781 INFO: === checking if optimization conditions were reached ===
1:32:46.688888 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:32:46.690305 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 56.9082.
1:32:46.690355 INFO: ==============================================
1:32:46.690437 INFO: Starting optimization step 1.
1:32:46.690508 PROGRESS: === Extracting elution groups 0 to 600 ===
1:32:46.690572 PROGRESS: Extracting batch of 1197 precursors
1:32:46.691473 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:46.691518 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:46.691547 INFO: FWHM in RT is 2.40 seconds, sigma is 0.31
1:32:46.691568 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:46.691712 INFO: Starting candidate selection
1:32:46.806628 INFO: Starting candidate scoring
1:32:46.846724 INFO: Finished candidate processing
1:32:46.846805 INFO: Collecting candidate features
1:32:46.857867 INFO: Collecting fragment features
1:32:46.862650 INFO: Finished candidate scoring
1:32:46.864362 PROGRESS: === Extracted 2387 precursors and 19786 fragments ===
1:32:46.864633 INFO: performing precursor FDR with 47 features
1:32:46.864671 INFO: Decoy channel: -1
1:32:46.864699 INFO: Competetive: True
1:32:46.867251 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:46.889596 INFO: Test AUC: 0.743
1:32:46.889661 INFO: Train AUC: 0.744
1:32:46.889699 INFO: AUC difference: 0.15%
1:32:47.067167 INFO: Resetting torch num_threads to 100
1:32:47.067797 INFO: === FDR correction performed with classifier version 9 ===
1:32:47.068416 PROGRESS: ============================= Precursor FDR =============================
1:32:47.068513 PROGRESS: Total precursors accumulated: 480
1:32:47.068583 PROGRESS: Target precursors: 461 (96.04%)
1:32:47.068644 PROGRESS: Decoy precursors: 19 (3.96%)
1:32:47.068701 PROGRESS: 
1:32:47.068755 PROGRESS: Precursor Summary:
1:32:47.069730 PROGRESS: Channel   0:	 0.05 FDR:   461; 0.01 FDR:   308; 0.001 FDR:   144
1:32:47.069827 PROGRESS: 
1:32:47.069891 PROGRESS: Protein Summary:
1:32:47.071090 PROGRESS: Channel   0:	 0.05 FDR:   442; 0.01 FDR:   298; 0.001 FDR:   139
1:32:47.071189 PROGRESS: =========================================================================
1:32:47.074074 INFO: fragments_df: keeping 2960 of 19786 [sum(precursor_idx_mask)=6042 sum(mass_error_mask)=19786 stop_rank=2960
1:32:47.082700 INFO: calibration group: precursor, fitting rt estimator 
1:32:47.201026 INFO: calibration group: fragment, fitting mz estimator 
1:32:47.601243 INFO: Using score_cutoff 50.545794678497316 (fac=0.99, q=1)
1:32:47.601672 INFO: calibration group: precursor, predicting mz
1:32:47.601763 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:47.601797 INFO: calibration group: precursor, predicting rt
1:32:47.603416 INFO: calibration group: fragment, predicting mz
1:32:47.605752 INFO: === checking if optimization conditions were reached ===
1:32:47.605868 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:32:47.607471 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 8.1170.
1:32:47.607524 INFO: ==============================================
1:32:47.607626 INFO: Starting optimization step 2.
1:32:47.607718 PROGRESS: === Extracting elution groups 0 to 600 ===
1:32:47.607785 PROGRESS: Extracting batch of 1197 precursors
1:32:47.611129 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:47.611179 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:47.611221 INFO: FWHM in RT is 2.41 seconds, sigma is 0.31
1:32:47.611249 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:47.611421 INFO: Starting candidate selection
1:32:47.725774 INFO: Starting candidate scoring
1:32:47.766485 INFO: Finished candidate processing
1:32:47.766575 INFO: Collecting candidate features
1:32:47.778281 INFO: Collecting fragment features
1:32:47.782189 INFO: Finished candidate scoring
1:32:47.783814 PROGRESS: === Extracted 2335 precursors and 18503 fragments ===
1:32:47.784099 INFO: performing precursor FDR with 47 features
1:32:47.784134 INFO: Decoy channel: -1
1:32:47.784157 INFO: Competetive: True
1:32:47.787082 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:47.809573 INFO: Test AUC: 0.748
1:32:47.809637 INFO: Train AUC: 0.739
1:32:47.809666 INFO: AUC difference: 1.22%
1:32:47.983727 INFO: Resetting torch num_threads to 100
1:32:47.984757 INFO: === FDR correction performed with classifier version 9 ===
1:32:47.985543 PROGRESS: ============================= Precursor FDR =============================
1:32:47.985640 PROGRESS: Total precursors accumulated: 465
1:32:47.985700 PROGRESS: Target precursors: 452 (97.20%)
1:32:47.985753 PROGRESS: Decoy precursors: 13 (2.80%)
1:32:47.985804 PROGRESS: 
1:32:47.985856 PROGRESS: Precursor Summary:
1:32:47.986876 PROGRESS: Channel   0:	 0.05 FDR:   452; 0.01 FDR:   318; 0.001 FDR:   156
1:32:47.986974 PROGRESS: 
1:32:47.987030 PROGRESS: Protein Summary:
1:32:47.988191 PROGRESS: Channel   0:	 0.05 FDR:   433; 0.01 FDR:   308; 0.001 FDR:   151
1:32:47.988284 PROGRESS: =========================================================================
1:32:47.991286 INFO: fragments_df: keeping 2936 of 18503 [sum(precursor_idx_mask)=6093 sum(mass_error_mask)=18503 stop_rank=2936
1:32:47.996532 INFO: calibration group: precursor, fitting rt estimator 
1:32:48.122397 INFO: calibration group: fragment, fitting mz estimator 
1:32:48.515425 INFO: Using score_cutoff 47.69764669761658 (fac=0.99, q=1)
1:32:48.515906 INFO: calibration group: precursor, predicting mz
1:32:48.515997 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:48.516027 INFO: calibration group: precursor, predicting rt
1:32:48.517632 INFO: calibration group: fragment, predicting mz
1:32:48.519917 INFO: === checking if optimization conditions were reached ===
1:32:48.520028 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:32:48.521692 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 5.6269.
1:32:48.521742 INFO: ==============================================
1:32:48.521831 INFO: Starting optimization step 3.
1:32:48.521895 PROGRESS: === Extracting elution groups 0 to 600 ===
1:32:48.521960 PROGRESS: Extracting batch of 1197 precursors
1:32:48.522985 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:48.523031 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:48.523065 INFO: FWHM in RT is 2.40 seconds, sigma is 0.31
1:32:48.523087 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:48.523268 INFO: Starting candidate selection
1:32:48.636825 INFO: Starting candidate scoring
1:32:48.677367 INFO: Finished candidate processing
1:32:48.677443 INFO: Collecting candidate features
1:32:48.689012 INFO: Collecting fragment features
1:32:48.692888 INFO: Finished candidate scoring
1:32:48.694512 PROGRESS: === Extracted 2336 precursors and 18504 fragments ===
1:32:48.694797 INFO: performing precursor FDR with 47 features
1:32:48.694835 INFO: Decoy channel: -1
1:32:48.694858 INFO: Competetive: True
1:32:48.697556 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:48.720958 INFO: Test AUC: 0.762
1:32:48.721021 INFO: Train AUC: 0.740
1:32:48.721064 INFO: AUC difference: 2.90%
1:32:48.891895 INFO: Resetting torch num_threads to 100
1:32:48.892447 INFO: === FDR correction performed with classifier version 9 ===
1:32:48.893054 PROGRESS: ============================= Precursor FDR =============================
1:32:48.893145 PROGRESS: Total precursors accumulated: 462
1:32:48.893204 PROGRESS: Target precursors: 449 (97.19%)
1:32:48.893257 PROGRESS: Decoy precursors: 13 (2.81%)
1:32:48.893303 PROGRESS: 
1:32:48.893347 PROGRESS: Precursor Summary:
1:32:48.894321 PROGRESS: Channel   0:	 0.05 FDR:   449; 0.01 FDR:   312; 0.001 FDR:   153
1:32:48.894409 PROGRESS: 
1:32:48.894464 PROGRESS: Protein Summary:
1:32:48.895616 PROGRESS: Channel   0:	 0.05 FDR:   431; 0.01 FDR:   302; 0.001 FDR:   148
1:32:48.895710 PROGRESS: =========================================================================
1:32:48.898442 INFO: fragments_df: keeping 2897 of 18504 [sum(precursor_idx_mask)=5987 sum(mass_error_mask)=18504 stop_rank=2897
1:32:48.903210 INFO: calibration group: precursor, fitting rt estimator 
1:32:49.022242 INFO: calibration group: fragment, fitting mz estimator 
1:32:49.406320 INFO: Using score_cutoff 47.49256827163696 (fac=0.99, q=1)
1:32:49.406720 INFO: calibration group: precursor, predicting mz
1:32:49.406810 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:49.406842 INFO: calibration group: precursor, predicting rt
1:32:49.408384 INFO: calibration group: fragment, predicting mz
1:32:49.410690 INFO: === checking if optimization conditions were reached ===
1:32:49.410794 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:32:49.412380 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 3.3518.
1:32:49.412434 INFO: ==============================================
1:32:49.412522 INFO: Starting optimization step 4.
1:32:49.412586 PROGRESS: === Extracting elution groups 0 to 600 ===
1:32:49.412641 PROGRESS: Extracting batch of 1197 precursors
1:32:49.413521 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:49.413567 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:49.413597 INFO: FWHM in RT is 2.39 seconds, sigma is 0.31
1:32:49.413619 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:49.413765 INFO: Starting candidate selection
1:32:49.526472 INFO: Starting candidate scoring
1:32:49.566904 INFO: Finished candidate processing
1:32:49.566979 INFO: Collecting candidate features
1:32:49.578114 INFO: Collecting fragment features
1:32:49.581992 INFO: Finished candidate scoring
1:32:49.583722 PROGRESS: === Extracted 2331 precursors and 18350 fragments ===
1:32:49.584005 INFO: performing precursor FDR with 47 features
1:32:49.584041 INFO: Decoy channel: -1
1:32:49.584066 INFO: Competetive: True
1:32:49.586736 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:49.609530 INFO: Test AUC: 0.733
1:32:49.609598 INFO: Train AUC: 0.726
1:32:49.609627 INFO: AUC difference: 0.89%
1:32:49.779323 INFO: Resetting torch num_threads to 100
1:32:49.779890 INFO: === FDR correction performed with classifier version 9 ===
1:32:49.780515 PROGRESS: ============================= Precursor FDR =============================
1:32:49.780606 PROGRESS: Total precursors accumulated: 444
1:32:49.780664 PROGRESS: Target precursors: 430 (96.85%)
1:32:49.780715 PROGRESS: Decoy precursors: 14 (3.15%)
1:32:49.780760 PROGRESS: 
1:32:49.780818 PROGRESS: Precursor Summary:
1:32:49.781792 PROGRESS: Channel   0:	 0.05 FDR:   430; 0.01 FDR:   294; 0.001 FDR:   138
1:32:49.781883 PROGRESS: 
1:32:49.781938 PROGRESS: Protein Summary:
1:32:49.783086 PROGRESS: Channel   0:	 0.05 FDR:   415; 0.01 FDR:   285; 0.001 FDR:   133
1:32:49.783180 PROGRESS: =========================================================================
1:32:49.785853 INFO: fragments_df: keeping 2775 of 18350 [sum(precursor_idx_mask)=5666 sum(mass_error_mask)=18350 stop_rank=2775
1:32:49.790612 INFO: calibration group: precursor, fitting rt estimator 
1:32:49.909287 INFO: calibration group: fragment, fitting mz estimator 
1:32:50.281993 INFO: Using score_cutoff 43.02239881324768 (fac=0.99, q=1)
1:32:50.282385 INFO: calibration group: precursor, predicting mz
1:32:50.282471 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:50.282501 INFO: calibration group: precursor, predicting rt
1:32:50.284053 INFO: calibration group: fragment, predicting mz
1:32:50.286351 INFO: === checking if optimization conditions were reached ===
1:32:50.286462 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1:32:50.288038 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 2.2341.
1:32:50.288092 INFO: ==============================================
1:32:50.288180 INFO: Starting optimization step 5.
1:32:50.288243 PROGRESS: === Extracting elution groups 0 to 600 ===
1:32:50.288297 PROGRESS: Extracting batch of 1197 precursors
1:32:50.289205 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:50.289251 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:50.289282 INFO: FWHM in RT is 2.39 seconds, sigma is 0.31
1:32:50.289304 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:50.289454 INFO: Starting candidate selection
1:32:50.400663 INFO: Starting candidate scoring
1:32:50.442250 INFO: Finished candidate processing
1:32:50.442329 INFO: Collecting candidate features
1:32:50.453719 INFO: Collecting fragment features
1:32:50.457982 INFO: Finished candidate scoring
1:32:50.459582 PROGRESS: === Extracted 2315 precursors and 17934 fragments ===
1:32:50.459847 INFO: performing precursor FDR with 47 features
1:32:50.459884 INFO: Decoy channel: -1
1:32:50.459907 INFO: Competetive: True
1:32:50.462438 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:50.484485 INFO: Test AUC: 0.686
1:32:50.484549 INFO: Train AUC: 0.683
1:32:50.484579 INFO: AUC difference: 0.45%
1:32:50.662783 INFO: Resetting torch num_threads to 100
1:32:50.663372 INFO: === FDR correction performed with classifier version 9 ===
1:32:50.663979 PROGRESS: ============================= Precursor FDR =============================
1:32:50.664070 PROGRESS: Total precursors accumulated: 342
1:32:50.664128 PROGRESS: Target precursors: 324 (94.74%)
1:32:50.664180 PROGRESS: Decoy precursors: 18 (5.26%)
1:32:50.664226 PROGRESS: 
1:32:50.664270 PROGRESS: Precursor Summary:
1:32:50.665206 PROGRESS: Channel   0:	 0.05 FDR:   308; 0.01 FDR:   131; 0.001 FDR:    88
1:32:50.665295 PROGRESS: 
1:32:50.665350 PROGRESS: Protein Summary:
1:32:50.666413 PROGRESS: Channel   0:	 0.05 FDR:   300; 0.01 FDR:   128; 0.001 FDR:    86
1:32:50.666503 PROGRESS: =========================================================================
1:32:50.674739 INFO: calibration group: precursor, predicting mz
1:32:50.674852 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:50.674884 INFO: calibration group: precursor, predicting rt
1:32:50.676516 INFO: calibration group: fragment, predicting mz
1:32:50.679865 INFO: === skipping optimization until target number of precursors are found ===
1:32:50.680011 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1:32:50.680062 INFO: Starting optimization step 6.
1:32:50.680125 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:32:50.680181 PROGRESS: Extracting batch of 1592 precursors
1:32:50.681063 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:50.681636 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:50.681669 INFO: FWHM in RT is 2.39 seconds, sigma is 0.31
1:32:50.681691 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:50.681839 INFO: Starting candidate selection
1:32:50.815663 INFO: Starting candidate scoring
1:32:50.857132 INFO: Finished candidate processing
1:32:50.857214 INFO: Collecting candidate features
1:32:50.870124 INFO: Collecting fragment features
1:32:50.874749 INFO: Finished candidate scoring
1:32:50.878254 PROGRESS: === Extracted 5404 precursors and 41373 fragments ===
1:32:50.879188 INFO: performing precursor FDR with 47 features
1:32:50.879230 INFO: Decoy channel: -1
1:32:50.879254 INFO: Competetive: True
1:32:50.883075 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:50.914671 INFO: Test AUC: 0.691
1:32:50.914755 INFO: Train AUC: 0.685
1:32:50.914783 INFO: AUC difference: 0.88%
1:32:51.094578 INFO: Resetting torch num_threads to 100
1:32:51.095339 INFO: === FDR correction performed with classifier version 9 ===
1:32:51.095991 PROGRESS: ============================= Precursor FDR =============================
1:32:51.096082 PROGRESS: Total precursors accumulated: 765
1:32:51.096140 PROGRESS: Target precursors: 725 (94.77%)
1:32:51.096190 PROGRESS: Decoy precursors: 40 (5.23%)
1:32:51.096236 PROGRESS: 
1:32:51.096279 PROGRESS: Precursor Summary:
1:32:51.097342 PROGRESS: Channel   0:	 0.05 FDR:   682; 0.01 FDR:   403; 0.001 FDR:   171
1:32:51.097435 PROGRESS: 
1:32:51.097490 PROGRESS: Protein Summary:
1:32:51.098746 PROGRESS: Channel   0:	 0.05 FDR:   632; 0.01 FDR:   375; 0.001 FDR:   161
1:32:51.099016 PROGRESS: =========================================================================
1:32:51.103740 INFO: fragments_df: keeping 4083 of 41373 [sum(precursor_idx_mask)=7925 sum(mass_error_mask)=41373 stop_rank=4083
1:32:51.111078 INFO: calibration group: precursor, fitting rt estimator 
1:32:51.236619 INFO: calibration group: fragment, fitting mz estimator 
1:32:51.777978 INFO: Using score_cutoff 46.03328000793457 (fac=0.99, q=1)
1:32:51.778380 INFO: calibration group: precursor, predicting mz
1:32:51.778465 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:51.778493 INFO: calibration group: precursor, predicting rt
1:32:51.780980 INFO: calibration group: fragment, predicting mz
1:32:51.785805 INFO: === checking if optimization conditions were reached ===
1:32:51.785916 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1:32:51.786907 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 3.3518 found after 6 searches.
1:32:51.786958 INFO: ==============================================
1:32:51.787044 PROGRESS: Optimization finished for rt_error.
1:32:51.791774 INFO: calibration group: precursor, predicting mz
1:32:51.791882 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:51.791911 INFO: calibration group: precursor, predicting rt
1:32:51.793207 INFO: calibration group: fragment, predicting mz
1:32:51.821286 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:32:51.821418 PROGRESS: ==============================================
1:32:51.821496 PROGRESS: ms2_error      : 6.2633
1:32:51.821551 PROGRESS: rt_error       : 3.3518
1:32:51.821598 PROGRESS: ==============================================
1:32:51.822186 INFO: calibration group: precursor, predicting mz
1:32:51.822302 WARNING: mz prediction was skipped as it has not been fitted yet
1:32:51.822330 INFO: calibration group: precursor, predicting rt
1:32:51.954170 INFO: calibration group: fragment, predicting mz
1:32:52.301235 PROGRESS: Extracting batch of 220080 precursors
1:32:52.375861 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:32:52.375988 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:52.376020 INFO: FWHM in RT is 2.39 seconds, sigma is 0.31
1:32:52.376042 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:52.376268 INFO: Starting candidate selection
1:33:00.205574 INFO: Applying score cutoff of 43.02239881324768
1:33:00.210647 INFO: Removed 261643 precursors with score below cutoff
1:33:00.277254 INFO: Starting candidate scoring
1:33:01.571198 INFO: Finished candidate processing
1:33:01.571294 INFO: Collecting candidate features
1:33:01.872050 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 169771)
1:33:01.880701 INFO: Collecting fragment features
1:33:01.992666 INFO: Finished candidate scoring
1:33:02.079745 INFO: === FDR correction performed with classifier version 14 ===
1:33:02.080462 INFO: performing precursor FDR with 47 features
1:33:02.080511 INFO: Decoy channel: -1
1:33:02.080533 INFO: Competetive: True
1:33:02.152544 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:02.181485 WARNING: dropped 1 target PSMs due to missing features
1:33:02.181628 WARNING: FDR calculation for 127213 target and 42557 decoy PSMs
1:33:02.181654 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1:33:05.519564 INFO: Test AUC: 0.910
1:33:05.519757 INFO: Train AUC: 0.912
1:33:05.519789 INFO: AUC difference: 0.32%
1:33:10.880960 INFO: Resetting torch num_threads to 100
1:33:10.898851 INFO: Removing fragments below FDR threshold
1:33:10.958440 PROGRESS: ============================= Precursor FDR =============================
1:33:10.958705 PROGRESS: Total precursors accumulated: 85,903
1:33:10.958772 PROGRESS: Target precursors: 85,053 (99.01%)
1:33:10.958826 PROGRESS: Decoy precursors: 850 (0.99%)
1:33:10.958872 PROGRESS: 
1:33:10.958916 PROGRESS: Precursor Summary:
1:33:10.995351 PROGRESS: Channel   0:	 0.05 FDR: 85,053; 0.01 FDR: 85,053; 0.001 FDR: 74,366
1:33:10.995600 PROGRESS: 
1:33:10.995688 PROGRESS: Protein Summary:
1:33:11.048465 PROGRESS: Channel   0:	 0.05 FDR: 9,695; 0.01 FDR: 9,695; 0.001 FDR: 9,370
1:33:11.048730 PROGRESS: =========================================================================
1:33:11.680774 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:33:11.703031 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:33:11.703162 INFO: Quantification results path: run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant
1:33:11.703236 INFO: Creating folder run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/figures
1:33:11.703799 INFO: Initializing RawFileManager
1:33:21.540829 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.
1:33:21.546229 INFO: Determining DIA cycle
1:33:21.562507 INFO: Found cycle with start 0.00 min and length 300.
1:33:21.732414 INFO: RT (min)            : 0.0 - 26.9
1:33:21.732503 INFO: RT duration (sec)   : 1611.2
1:33:21.732530 INFO: RT duration (min)   : 26.9
1:33:21.732552 INFO: Cycle len (scans)   : 300
1:33:21.732571 INFO: Cycle len (sec)     : 1.65
1:33:21.732590 INFO: Number of cycles    : 978
1:33:21.732611 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:33:21.776157 INFO: Initializing CalibrationManager
1:33:21.776446 INFO: Loading calibration config
1:33:21.776856 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'}]
1:33:21.776945 INFO: Calibration group :fragment, found 1 estimator(s)
1:33:21.777014 INFO: Calibration group :precursor, found 3 estimator(s)
1:33:21.777084 INFO: Disabling ion mobility calibration
1:33:21.777111 INFO: removed mobility estimator from group precursor
1:33:21.777232 INFO: Initializing OptimizationManager
1:33:21.777868 INFO: initial parameter: ms1_error = 30
1:33:21.777932 INFO: initial parameter: ms2_error = 30
1:33:21.777982 INFO: initial parameter: rt_error = 805.611083984375
1:33:21.778028 INFO: initial parameter: mobility_error = 0.1
1:33:21.778071 INFO: initial parameter: column_type = library
1:33:21.778111 INFO: initial parameter: num_candidates = 1
1:33:21.778153 INFO: initial parameter: classifier_version = -1
1:33:21.778194 INFO: initial parameter: fwhm_rt = 5
1:33:21.778236 INFO: initial parameter: fwhm_mobility = 0.01
1:33:21.778279 INFO: initial parameter: score_cutoff = 0
1:33:21.778333 INFO: Initializing TimingManager
1:33:21.778387 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:33:21.778457 INFO: FDRManager not loaded from disk.
1:33:21.778479 INFO: Initializing FDRManager
1:33:21.778503 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:33:21.818280 PROGRESS: 110,515 target precursors potentially observable (0 removed)
1:33:21.873848 PROGRESS: Starting initial search for precursors.
1:33:21.881173 INFO: Starting optimization step 0.
1:33:21.881332 PROGRESS: === Extracting elution groups 0 to 200 ===
1:33:21.881401 PROGRESS: Extracting batch of 400 precursors
1:33:21.882339 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:33:21.882391 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:33:21.882426 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:33:21.882448 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:33:21.882662 INFO: Starting candidate selection
1:33:22.018958 INFO: Starting candidate scoring
1:33:22.054822 INFO: Finished candidate processing
1:33:22.054888 INFO: Collecting candidate features
1:33:22.063163 INFO: Collecting fragment features
1:33:22.065228 INFO: Finished candidate scoring
1:33:22.066019 PROGRESS: === Extracted 400 precursors and 4419 fragments ===
1:33:22.066295 INFO: performing precursor FDR with 47 features
1:33:22.066332 INFO: Decoy channel: -1
1:33:22.066355 INFO: Competetive: True
1:33:22.067372 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:22.096852 INFO: Test AUC: 0.531
1:33:22.096921 INFO: Train AUC: 0.465
1:33:22.096950 INFO: AUC difference: 14.23%
1:33:22.096973 WARNING: AUC difference > 5%. This may indicate overfitting.
1:33:22.275362 INFO: Resetting torch num_threads to 100
1:33:22.275900 INFO: === FDR correction performed with classifier version -1 ===
1:33:22.276536 PROGRESS: ============================= Precursor FDR =============================
1:33:22.276629 PROGRESS: Total precursors accumulated: 200
1:33:22.276693 PROGRESS: Target precursors: 92 (46.00%)
1:33:22.276745 PROGRESS: Decoy precursors: 108 (54.00%)
1:33:22.276791 PROGRESS: 
1:33:22.276835 PROGRESS: Precursor Summary:
1:33:22.277688 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:33:22.277775 PROGRESS: 
1:33:22.277831 PROGRESS: Protein Summary:
1:33:22.278763 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:33:22.278856 PROGRESS: =========================================================================
1:33:22.282694 INFO: Starting optimization step 1.
1:33:22.282796 PROGRESS: === Extracting elution groups 200 to 600 ===
1:33:22.282866 PROGRESS: Extracting batch of 797 precursors
1:33:22.283680 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:33:22.283724 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:33:22.283755 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:33:22.283775 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:33:22.283931 INFO: Starting candidate selection
1:33:22.420181 INFO: Starting candidate scoring
1:33:22.457575 INFO: Finished candidate processing
1:33:22.457637 INFO: Collecting candidate features
1:33:22.466546 INFO: Collecting fragment features
1:33:22.468911 INFO: Finished candidate scoring
1:33:22.471051 PROGRESS: === Extracted 1197 precursors and 13210 fragments ===
1:33:22.471817 INFO: performing precursor FDR with 47 features
1:33:22.471859 INFO: Decoy channel: -1
1:33:22.471883 INFO: Competetive: True
1:33:22.474774 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:22.507019 INFO: Test AUC: 0.526
1:33:22.507090 INFO: Train AUC: 0.514
1:33:22.507119 INFO: AUC difference: 2.38%
1:33:22.679666 INFO: Resetting torch num_threads to 100
1:33:22.680292 INFO: === FDR correction performed with classifier version -1 ===
1:33:22.680966 PROGRESS: ============================= Precursor FDR =============================
1:33:22.681058 PROGRESS: Total precursors accumulated: 600
1:33:22.681123 PROGRESS: Target precursors: 310 (51.67%)
1:33:22.681176 PROGRESS: Decoy precursors: 290 (48.33%)
1:33:22.681221 PROGRESS: 
1:33:22.681266 PROGRESS: Precursor Summary:
1:33:22.682122 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:33:22.682210 PROGRESS: 
1:33:22.682265 PROGRESS: Protein Summary:
1:33:22.683216 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:33:22.683306 PROGRESS: =========================================================================
1:33:22.688170 INFO: Starting optimization step 2.
1:33:22.688273 PROGRESS: === Extracting elution groups 600 to 1400 ===
1:33:22.688335 PROGRESS: Extracting batch of 1592 precursors
1:33:22.689165 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:33:22.689210 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:33:22.689241 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:33:22.689263 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:33:22.689414 INFO: Starting candidate selection
1:33:22.857338 INFO: Starting candidate scoring
1:33:22.895034 INFO: Finished candidate processing
1:33:22.895111 INFO: Collecting candidate features
1:33:22.905260 INFO: Collecting fragment features
1:33:22.909814 INFO: Finished candidate scoring
1:33:22.913134 PROGRESS: === Extracted 2789 precursors and 30818 fragments ===
1:33:22.914240 INFO: performing precursor FDR with 47 features
1:33:22.914284 INFO: Decoy channel: -1
1:33:22.914307 INFO: Competetive: True
1:33:22.917863 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:22.957072 INFO: Test AUC: 0.474
1:33:22.957144 INFO: Train AUC: 0.539
1:33:22.957174 INFO: AUC difference: 12.15%
1:33:22.957195 WARNING: AUC difference > 5%. This may indicate overfitting.
1:33:23.137857 INFO: Resetting torch num_threads to 100
1:33:23.138540 INFO: === FDR correction performed with classifier version -1 ===
1:33:23.139292 PROGRESS: ============================= Precursor FDR =============================
1:33:23.139388 PROGRESS: Total precursors accumulated: 1,400
1:33:23.139449 PROGRESS: Target precursors: 728 (52.00%)
1:33:23.139500 PROGRESS: Decoy precursors: 672 (48.00%)
1:33:23.139546 PROGRESS: 
1:33:23.139591 PROGRESS: Precursor Summary:
1:33:23.140461 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:33:23.140552 PROGRESS: 
1:33:23.140609 PROGRESS: Protein Summary:
1:33:23.141542 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:33:23.141634 PROGRESS: =========================================================================
1:33:23.148160 INFO: Starting optimization step 3.
1:33:23.148270 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1:33:23.148333 PROGRESS: Extracting batch of 3186 precursors
1:33:23.149457 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:33:23.149503 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:33:23.149536 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:33:23.149557 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:33:23.149732 INFO: Starting candidate selection
1:33:23.403073 INFO: Starting candidate scoring
1:33:23.443499 INFO: Finished candidate processing
1:33:23.443584 INFO: Collecting candidate features
1:33:23.458103 INFO: Collecting fragment features
1:33:23.462142 INFO: Finished candidate scoring
1:33:23.466267 PROGRESS: === Extracted 5975 precursors and 66083 fragments ===
1:33:23.467502 INFO: performing precursor FDR with 47 features
1:33:23.467546 INFO: Decoy channel: -1
1:33:23.467570 INFO: Competetive: True
1:33:23.471687 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:23.523619 INFO: Test AUC: 0.529
1:33:23.523713 INFO: Train AUC: 0.525
1:33:23.523742 INFO: AUC difference: 0.73%
1:33:23.699367 INFO: Resetting torch num_threads to 100
1:33:23.700316 INFO: === FDR correction performed with classifier version -1 ===
1:33:23.701318 PROGRESS: ============================= Precursor FDR =============================
1:33:23.701414 PROGRESS: Total precursors accumulated: 3,000
1:33:23.701479 PROGRESS: Target precursors: 1,579 (52.63%)
1:33:23.701532 PROGRESS: Decoy precursors: 1,421 (47.37%)
1:33:23.701581 PROGRESS: 
1:33:23.701626 PROGRESS: Precursor Summary:
1:33:23.702513 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:33:23.702611 PROGRESS: 
1:33:23.702671 PROGRESS: Protein Summary:
1:33:23.703630 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:33:23.703719 PROGRESS: =========================================================================
1:33:23.714088 INFO: Starting optimization step 4.
1:33:23.714207 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1:33:23.714274 PROGRESS: Extracting batch of 6377 precursors
1:33:23.715937 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:33:23.715985 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:33:23.716016 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:33:23.716037 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:33:23.716200 INFO: Starting candidate selection
1:33:24.161798 INFO: Starting candidate scoring
1:33:24.212302 INFO: Finished candidate processing
1:33:24.212393 INFO: Collecting candidate features
1:33:24.231686 INFO: Collecting fragment features
1:33:24.239173 INFO: Finished candidate scoring
1:33:24.246159 PROGRESS: === Extracted 12352 precursors and 136406 fragments ===
1:33:24.247991 INFO: performing precursor FDR with 47 features
1:33:24.248050 INFO: Decoy channel: -1
1:33:24.248075 INFO: Competetive: True
1:33:24.253630 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:24.333310 INFO: Test AUC: 0.538
1:33:24.333427 INFO: Train AUC: 0.521
1:33:24.333456 INFO: AUC difference: 3.29%
1:33:24.512972 INFO: Resetting torch num_threads to 100
1:33:24.513941 INFO: === FDR correction performed with classifier version -1 ===
1:33:24.515503 PROGRESS: ============================= Precursor FDR =============================
1:33:24.515599 PROGRESS: Total precursors accumulated: 6,198
1:33:24.515665 PROGRESS: Target precursors: 3,266 (52.69%)
1:33:24.515715 PROGRESS: Decoy precursors: 2,932 (47.31%)
1:33:24.515762 PROGRESS: 
1:33:24.515806 PROGRESS: Precursor Summary:
1:33:24.516723 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:33:24.516813 PROGRESS: 
1:33:24.516868 PROGRESS: Protein Summary:
1:33:24.517837 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:33:24.517925 PROGRESS: =========================================================================
1:33:24.533359 INFO: Starting optimization step 5.
1:33:24.533590 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1:33:24.533659 PROGRESS: Extracting batch of 12745 precursors
1:33:24.536016 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:33:24.536066 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:33:24.536097 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:33:24.536118 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:33:24.536281 INFO: Starting candidate selection
1:33:25.340514 INFO: Starting candidate scoring
1:33:25.449444 INFO: Finished candidate processing
1:33:25.449581 INFO: Collecting candidate features
1:33:25.481492 INFO: Collecting fragment features
1:33:25.492688 INFO: Finished candidate scoring
1:33:25.512985 PROGRESS: === Extracted 25097 precursors and 277278 fragments ===
1:33:25.517524 INFO: performing precursor FDR with 47 features
1:33:25.517628 INFO: Decoy channel: -1
1:33:25.517657 INFO: Competetive: True
1:33:25.531151 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:26.026906 INFO: Test AUC: 0.831
1:33:26.027079 INFO: Train AUC: 0.825
1:33:26.027112 INFO: AUC difference: 0.76%
1:33:26.223579 INFO: Resetting torch num_threads to 100
1:33:26.225611 INFO: === FDR correction performed with classifier version -1 ===
1:33:26.227262 PROGRESS: ============================= Precursor FDR =============================
1:33:26.227369 PROGRESS: Total precursors accumulated: 7,362
1:33:26.227433 PROGRESS: Target precursors: 7,006 (95.16%)
1:33:26.227488 PROGRESS: Decoy precursors: 356 (4.84%)
1:33:26.227536 PROGRESS: 
1:33:26.227581 PROGRESS: Precursor Summary:
1:33:26.229692 PROGRESS: Channel   0:	 0.05 FDR: 6,987; 0.01 FDR: 3,254; 0.001 FDR:   478
1:33:26.229789 PROGRESS: 
1:33:26.229847 PROGRESS: Protein Summary:
1:33:26.232754 PROGRESS: Channel   0:	 0.05 FDR: 3,746; 0.01 FDR: 1,974; 0.001 FDR:   394
1:33:26.232858 PROGRESS: =========================================================================
1:33:26.259989 INFO: fragments_df: keeping 5000 of 277278 [sum(precursor_idx_mask)=37394 sum(mass_error_mask)=277278 stop_rank=5000
1:33:26.271601 INFO: calibration group: precursor, fitting rt estimator 
1:33:26.647863 INFO: calibration group: fragment, fitting mz estimator 
1:33:27.269038 INFO: Using score_cutoff 61.9175661781311 (fac=0.99, q=1)
1:33:27.269597 INFO: calibration group: precursor, predicting mz
1:33:27.269689 WARNING: mz prediction was skipped as it has not been fitted yet
1:33:27.269725 INFO: calibration group: precursor, predicting rt
1:33:27.272323 INFO: calibration group: fragment, predicting mz
1:33:27.277379 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:33:27.277518 INFO: Starting optimization step 6.
1:33:27.277593 PROGRESS: === Extracting elution groups 0 to 1400 ===
1:33:27.277654 PROGRESS: Extracting batch of 2789 precursors
1:33:27.279121 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:33:27.279173 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:33:27.279205 INFO: FWHM in RT is 2.98 seconds, sigma is 0.38
1:33:27.279228 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:33:27.279413 INFO: Starting candidate selection
1:33:27.543533 INFO: Starting candidate scoring
1:33:27.602533 INFO: Finished candidate processing
1:33:27.602668 INFO: Collecting candidate features
1:33:27.621284 INFO: Collecting fragment features
1:33:27.626939 INFO: Finished candidate scoring
1:33:27.632181 PROGRESS: === Extracted 5578 precursors and 60964 fragments ===
1:33:27.632539 INFO: performing precursor FDR with 47 features
1:33:27.632579 INFO: Decoy channel: -1
1:33:27.632603 INFO: Competetive: True
1:33:27.636274 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:27.673638 INFO: Test AUC: 0.712
1:33:27.673751 INFO: Train AUC: 0.698
1:33:27.673782 INFO: AUC difference: 2.12%
1:33:27.859922 INFO: Resetting torch num_threads to 100
1:33:27.860924 INFO: === FDR correction performed with classifier version 5 ===
1:33:27.861706 PROGRESS: ============================= Precursor FDR =============================
1:33:27.861810 PROGRESS: Total precursors accumulated: 785
1:33:27.861871 PROGRESS: Target precursors: 737 (93.89%)
1:33:27.861925 PROGRESS: Decoy precursors: 48 (6.11%)
1:33:27.861979 PROGRESS: 
1:33:27.862026 PROGRESS: Precursor Summary:
1:33:27.863144 PROGRESS: Channel   0:	 0.05 FDR:   673; 0.01 FDR:   350; 0.001 FDR:   136
1:33:27.863248 PROGRESS: 
1:33:27.863306 PROGRESS: Protein Summary:
1:33:27.864566 PROGRESS: Channel   0:	 0.05 FDR:   614; 0.01 FDR:   326; 0.001 FDR:   132
1:33:27.864663 PROGRESS: =========================================================================
1:33:27.871951 INFO: fragments_df: keeping 4079 of 60964 [sum(precursor_idx_mask)=7897 sum(mass_error_mask)=60964 stop_rank=4079
1:33:27.881208 INFO: calibration group: precursor, fitting rt estimator 
1:33:28.001618 INFO: calibration group: fragment, fitting mz estimator 
1:33:28.482183 INFO: Using score_cutoff 65.83029404067993 (fac=0.99, q=1)
1:33:28.482693 INFO: calibration group: precursor, predicting mz
1:33:28.482789 WARNING: mz prediction was skipped as it has not been fitted yet
1:33:28.482821 INFO: calibration group: precursor, predicting rt
1:33:28.485420 INFO: calibration group: fragment, predicting mz
1:33:28.490160 INFO: === checking if optimization conditions were reached ===
1:33:28.491734 PROGRESS: ❌ ms2_error      : 13.1964 > 6.2633 or insufficient steps taken.
1:33:28.491795 INFO: ==============================================
1:33:28.491889 INFO: Starting optimization step 7.
1:33:28.491959 PROGRESS: === Extracting elution groups 0 to 1400 ===
1:33:28.492020 PROGRESS: Extracting batch of 2789 precursors
1:33:28.493506 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:33:28.493555 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:33:28.493588 INFO: FWHM in RT is 2.88 seconds, sigma is 0.37
1:33:28.493612 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:33:28.493799 INFO: Starting candidate selection
1:33:28.766721 INFO: Starting candidate scoring
1:33:28.825513 INFO: Finished candidate processing
1:33:28.825639 INFO: Collecting candidate features
1:33:28.843003 INFO: Collecting fragment features
1:33:28.848515 INFO: Finished candidate scoring
1:33:28.852649 PROGRESS: === Extracted 5578 precursors and 56109 fragments ===
1:33:28.852984 INFO: performing precursor FDR with 47 features
1:33:28.853021 INFO: Decoy channel: -1
1:33:28.853045 INFO: Competetive: True
1:33:28.856642 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:28.894217 INFO: Test AUC: 0.720
1:33:28.894330 INFO: Train AUC: 0.740
1:33:28.894360 INFO: AUC difference: 2.71%
1:33:29.075810 INFO: Resetting torch num_threads to 100
1:33:29.076802 INFO: === FDR correction performed with classifier version 6 ===
1:33:29.077610 PROGRESS: ============================= Precursor FDR =============================
1:33:29.077710 PROGRESS: Total precursors accumulated: 1,015
1:33:29.077771 PROGRESS: Target precursors: 974 (95.96%)
1:33:29.077824 PROGRESS: Decoy precursors: 41 (4.04%)
1:33:29.077871 PROGRESS: 
1:33:29.077919 PROGRESS: Precursor Summary:
1:33:29.079071 PROGRESS: Channel   0:	 0.05 FDR:   974; 0.01 FDR:   548; 0.001 FDR:   396
1:33:29.079169 PROGRESS: 
1:33:29.079227 PROGRESS: Protein Summary:
1:33:29.080613 PROGRESS: Channel   0:	 0.05 FDR:   872; 0.01 FDR:   499; 0.001 FDR:   366
1:33:29.080707 PROGRESS: =========================================================================
1:33:29.086831 INFO: fragments_df: keeping 5000 of 56109 [sum(precursor_idx_mask)=11783 sum(mass_error_mask)=56109 stop_rank=5000
1:33:29.092788 INFO: calibration group: precursor, fitting rt estimator 
1:33:29.223069 INFO: calibration group: fragment, fitting mz estimator 
1:33:29.840452 INFO: Using score_cutoff 55.49070101852417 (fac=0.99, q=1)
1:33:29.840943 INFO: calibration group: precursor, predicting mz
1:33:29.841034 WARNING: mz prediction was skipped as it has not been fitted yet
1:33:29.841066 INFO: calibration group: precursor, predicting rt
1:33:29.843259 INFO: calibration group: fragment, predicting mz
1:33:29.845667 INFO: === checking if optimization conditions were reached ===
1:33:29.847353 PROGRESS: ✅ ms2_error      : 6.2633 <= 6.2633
1:33:29.847409 INFO: ==============================================
1:33:29.847504 PROGRESS: Optimization finished for ms2_error.
1:33:29.853005 INFO: calibration group: precursor, predicting mz
1:33:29.853133 WARNING: mz prediction was skipped as it has not been fitted yet
1:33:29.853165 INFO: calibration group: precursor, predicting rt
1:33:29.854434 INFO: calibration group: fragment, predicting mz
1:33:29.856703 INFO: Starting optimization step 0.
1:33:29.856805 PROGRESS: === Extracting elution groups 0 to 600 ===
1:33:29.856872 PROGRESS: Extracting batch of 1197 precursors
1:33:29.857796 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:33:29.857848 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:33:29.857891 INFO: FWHM in RT is 2.55 seconds, sigma is 0.33
1:33:29.857916 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:33:29.858095 INFO: Starting candidate selection
1:33:30.020481 INFO: Starting candidate scoring
1:33:30.073401 INFO: Finished candidate processing
1:33:30.073539 INFO: Collecting candidate features
1:33:30.087849 INFO: Collecting fragment features
1:33:30.093006 INFO: Finished candidate scoring
1:33:30.095930 PROGRESS: === Extracted 2394 precursors and 21270 fragments ===
1:33:30.096334 INFO: performing precursor FDR with 47 features
1:33:30.096387 INFO: Decoy channel: -1
1:33:30.096420 INFO: Competetive: True
1:33:30.099874 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:30.128667 INFO: Test AUC: 0.723
1:33:30.128806 INFO: Train AUC: 0.728
1:33:30.128842 INFO: AUC difference: 0.72%
1:33:30.312973 INFO: Resetting torch num_threads to 100
1:33:30.313846 INFO: === FDR correction performed with classifier version 7 ===
1:33:30.314619 PROGRESS: ============================= Precursor FDR =============================
1:33:30.314726 PROGRESS: Total precursors accumulated: 451
1:33:30.314788 PROGRESS: Target precursors: 438 (97.12%)
1:33:30.314841 PROGRESS: Decoy precursors: 13 (2.88%)
1:33:30.314887 PROGRESS: 
1:33:30.314931 PROGRESS: Precursor Summary:
1:33:30.315960 PROGRESS: Channel   0:	 0.05 FDR:   438; 0.01 FDR:   321; 0.001 FDR:   229
1:33:30.316054 PROGRESS: 
1:33:30.316110 PROGRESS: Protein Summary:
1:33:30.317298 PROGRESS: Channel   0:	 0.05 FDR:   422; 0.01 FDR:   309; 0.001 FDR:   221
1:33:30.317392 PROGRESS: =========================================================================
1:33:30.320633 INFO: fragments_df: keeping 3142 of 21270 [sum(precursor_idx_mask)=6329 sum(mass_error_mask)=21270 stop_rank=3142
1:33:30.326472 INFO: calibration group: precursor, fitting rt estimator 
1:33:30.439049 INFO: calibration group: fragment, fitting mz estimator 
1:33:30.793703 INFO: Using score_cutoff 39.547823181152346 (fac=0.99, q=1)
1:33:30.794198 INFO: calibration group: precursor, predicting mz
1:33:30.794288 WARNING: mz prediction was skipped as it has not been fitted yet
1:33:30.794318 INFO: calibration group: precursor, predicting rt
1:33:30.796081 INFO: calibration group: fragment, predicting mz
1:33:30.798403 INFO: === checking if optimization conditions were reached ===
1:33:30.798547 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:33:30.800069 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 270.1822.
1:33:30.800122 INFO: ==============================================
1:33:30.800225 INFO: Starting optimization step 1.
1:33:30.800296 PROGRESS: === Extracting elution groups 0 to 600 ===
1:33:30.800356 PROGRESS: Extracting batch of 1197 precursors
1:33:30.801438 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:33:30.801487 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:33:30.801517 INFO: FWHM in RT is 2.28 seconds, sigma is 0.29
1:33:30.801538 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:33:30.801719 INFO: Starting candidate selection
1:33:30.941092 INFO: Starting candidate scoring
1:33:30.991275 INFO: Finished candidate processing
1:33:30.991385 INFO: Collecting candidate features
1:33:31.003719 INFO: Collecting fragment features
1:33:31.008369 INFO: Finished candidate scoring
1:33:31.010473 PROGRESS: === Extracted 2394 precursors and 21007 fragments ===
1:33:31.010792 INFO: performing precursor FDR with 47 features
1:33:31.010828 INFO: Decoy channel: -1
1:33:31.010851 INFO: Competetive: True
1:33:31.013767 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:31.050153 INFO: Test AUC: 0.739
1:33:31.050252 INFO: Train AUC: 0.730
1:33:31.050281 INFO: AUC difference: 1.25%
1:33:31.228033 INFO: Resetting torch num_threads to 100
1:33:31.228858 INFO: === FDR correction performed with classifier version 7 ===
1:33:31.229581 PROGRESS: ============================= Precursor FDR =============================
1:33:31.229685 PROGRESS: Total precursors accumulated: 453
1:33:31.229745 PROGRESS: Target precursors: 441 (97.35%)
1:33:31.229797 PROGRESS: Decoy precursors: 12 (2.65%)
1:33:31.229843 PROGRESS: 
1:33:31.229886 PROGRESS: Precursor Summary:
1:33:31.230928 PROGRESS: Channel   0:	 0.05 FDR:   441; 0.01 FDR:   318; 0.001 FDR:   245
1:33:31.231025 PROGRESS: 
1:33:31.231083 PROGRESS: Protein Summary:
1:33:31.232268 PROGRESS: Channel   0:	 0.05 FDR:   424; 0.01 FDR:   306; 0.001 FDR:   236
1:33:31.232370 PROGRESS: =========================================================================
1:33:31.235519 INFO: fragments_df: keeping 3130 of 21007 [sum(precursor_idx_mask)=6259 sum(mass_error_mask)=21007 stop_rank=3130
1:33:31.241246 INFO: calibration group: precursor, fitting rt estimator 
1:33:31.346129 INFO: calibration group: fragment, fitting mz estimator 
1:33:31.699139 INFO: Using score_cutoff 40.20110637245178 (fac=0.99, q=1)
1:33:31.699635 INFO: calibration group: precursor, predicting mz
1:33:31.699724 WARNING: mz prediction was skipped as it has not been fitted yet
1:33:31.699754 INFO: calibration group: precursor, predicting rt
1:33:31.701550 INFO: calibration group: fragment, predicting mz
1:33:31.703889 INFO: === checking if optimization conditions were reached ===
1:33:31.704005 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:33:31.705611 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 39.3593.
1:33:31.705666 INFO: ==============================================
1:33:31.705757 INFO: Starting optimization step 2.
1:33:31.705827 PROGRESS: === Extracting elution groups 0 to 600 ===
1:33:31.705885 PROGRESS: Extracting batch of 1197 precursors
1:33:31.706950 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:33:31.706998 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:33:31.707030 INFO: FWHM in RT is 2.26 seconds, sigma is 0.29
1:33:31.707052 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:33:31.707225 INFO: Starting candidate selection
1:33:31.829382 INFO: Starting candidate scoring
1:33:31.878779 INFO: Finished candidate processing
1:33:31.878883 INFO: Collecting candidate features
1:33:31.891636 INFO: Collecting fragment features
1:33:31.895960 INFO: Finished candidate scoring
1:33:31.898290 PROGRESS: === Extracted 2380 precursors and 19177 fragments ===
1:33:31.898637 INFO: performing precursor FDR with 47 features
1:33:31.898677 INFO: Decoy channel: -1
1:33:31.898699 INFO: Competetive: True
1:33:31.901679 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:31.928336 INFO: Test AUC: 0.782
1:33:31.928415 INFO: Train AUC: 0.753
1:33:31.928444 INFO: AUC difference: 3.92%
1:33:32.105048 INFO: Resetting torch num_threads to 100
1:33:32.105872 INFO: === FDR correction performed with classifier version 7 ===
1:33:32.106614 PROGRESS: ============================= Precursor FDR =============================
1:33:32.106709 PROGRESS: Total precursors accumulated: 475
1:33:32.106770 PROGRESS: Target precursors: 462 (97.26%)
1:33:32.106821 PROGRESS: Decoy precursors: 13 (2.74%)
1:33:32.106867 PROGRESS: 
1:33:32.106910 PROGRESS: Precursor Summary:
1:33:32.107928 PROGRESS: Channel   0:	 0.05 FDR:   462; 0.01 FDR:   233; 0.001 FDR:   183
1:33:32.108021 PROGRESS: 
1:33:32.108077 PROGRESS: Protein Summary:
1:33:32.109255 PROGRESS: Channel   0:	 0.05 FDR:   443; 0.01 FDR:   225; 0.001 FDR:   176
1:33:32.109354 PROGRESS: =========================================================================
1:33:32.112276 INFO: fragments_df: keeping 2344 of 19177 [sum(precursor_idx_mask)=4562 sum(mass_error_mask)=19177 stop_rank=2344
1:33:32.118578 INFO: calibration group: precursor, fitting rt estimator 
1:33:32.213371 INFO: calibration group: fragment, fitting mz estimator 
1:33:32.480295 INFO: Using score_cutoff 41.97891851806641 (fac=0.99, q=1)
1:33:32.480780 INFO: calibration group: precursor, predicting mz
1:33:32.480869 WARNING: mz prediction was skipped as it has not been fitted yet
1:33:32.480910 INFO: calibration group: precursor, predicting rt
1:33:32.482695 INFO: calibration group: fragment, predicting mz
1:33:32.485071 INFO: === checking if optimization conditions were reached ===
1:33:32.485182 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:33:32.486300 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 270.1822 found after 3 searches.
1:33:32.486350 INFO: ==============================================
1:33:32.486446 PROGRESS: Optimization finished for rt_error.
1:33:32.491715 INFO: calibration group: precursor, predicting mz
1:33:32.491832 WARNING: mz prediction was skipped as it has not been fitted yet
1:33:32.491862 INFO: calibration group: precursor, predicting rt
1:33:32.493173 INFO: calibration group: fragment, predicting mz
1:33:32.521374 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:33:32.521545 PROGRESS: ==============================================
1:33:32.521621 PROGRESS: ms2_error      : 6.2633
1:33:32.521679 PROGRESS: rt_error       : 270.1822
1:33:32.521727 PROGRESS: ==============================================
1:33:32.522527 INFO: calibration group: precursor, predicting mz
1:33:32.522631 WARNING: mz prediction was skipped as it has not been fitted yet
1:33:32.522661 INFO: calibration group: precursor, predicting rt
1:33:32.645102 INFO: calibration group: fragment, predicting mz
1:33:33.008961 PROGRESS: Extracting batch of 220080 precursors
1:33:33.080812 INFO: Duty cycle consists of 300 frames, 1.65 seconds cycle time
1:33:33.080993 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:33:33.081029 INFO: FWHM in RT is 2.26 seconds, sigma is 0.29
1:33:33.081051 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:33:33.081347 INFO: Starting candidate selection
1:33:40.506204 INFO: Applying score cutoff of 40.20110637245178
1:33:40.514065 INFO: Removed 127794 precursors with score below cutoff
1:33:40.577784 INFO: Starting candidate scoring
1:33:42.752010 INFO: Finished candidate processing
1:33:42.752107 INFO: Collecting candidate features
1:33:43.230121 INFO: Collecting fragment features
1:33:43.441586 INFO: Finished candidate scoring
1:33:43.604082 INFO: === FDR correction performed with classifier version 9 ===
1:33:43.605211 INFO: performing precursor FDR with 47 features
1:33:43.605260 INFO: Decoy channel: -1
1:33:43.605291 INFO: Competetive: True
1:33:43.688280 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:43.720885 WARNING: FDR calculation for 182200 target and 130166 decoy PSMs
1:33:43.721017 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1:33:49.658831 INFO: Test AUC: 0.842
1:33:49.658974 INFO: Train AUC: 0.844
1:33:49.659004 INFO: AUC difference: 0.19%
1:33:49.923073 INFO: Resetting torch num_threads to 100
1:33:49.943361 INFO: Removing fragments below FDR threshold
1:33:50.011740 PROGRESS: ============================= Precursor FDR =============================
1:33:50.011996 PROGRESS: Total precursors accumulated: 99,067
1:33:50.012068 PROGRESS: Target precursors: 98,087 (99.01%)
1:33:50.012122 PROGRESS: Decoy precursors: 980 (0.99%)
1:33:50.012169 PROGRESS: 
1:33:50.012217 PROGRESS: Precursor Summary:
1:33:50.052723 PROGRESS: Channel   0:	 0.05 FDR: 98,087; 0.01 FDR: 98,087; 0.001 FDR: 89,034
1:33:50.052973 PROGRESS: 
1:33:50.053053 PROGRESS: Protein Summary:
1:33:50.114261 PROGRESS: Channel   0:	 0.05 FDR: 9,829; 0.01 FDR: 9,829; 0.001 FDR: 9,625
1:33:50.114498 PROGRESS: =========================================================================
1:33:50.835415 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:33:51.357166 PROGRESS: Processing search outputs
1:33:51.357482 PROGRESS: Performing protein grouping and FDR
1:33:51.357522 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:33:51.427577 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:33:51.499127 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:33:51.562633 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:33:51.633370 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:33:51.697158 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:33:51.768043 INFO: Building combined output
1:33:51.949003 INFO: Performing protein inference
1:33:52.543130 INFO: Inference strategy: library. Using library grouping for protein inference
1:33:52.546804 INFO: Performing protein FDR
1:33:55.913875 INFO: Normalizing q-values using 9,923 targets and 3,243 decoys
1:33:55.921741 INFO: Test AUC: 1.000
1:33:55.921805 INFO: Train AUC: 1.000
1:33:55.921840 INFO: AUC difference: 0.00%
1:33:56.654362 PROGRESS: ================ Protein FDR =================
1:33:56.654501 PROGRESS: Unique protein groups in output
1:33:56.654531 PROGRESS:   1% protein FDR: 9,922
1:33:56.654552 PROGRESS: 
1:33:56.654571 PROGRESS: Unique precursor in output
1:33:56.654589 PROGRESS:   1% protein FDR: 110,262
1:33:56.654625 PROGRESS: ================================================
1:33:56.750202 PROGRESS: Building search statistics
1:33:56.902354 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
1:33:56.902550 INFO: Initializing OptimizationManager
1:33:56.902809 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
1:33:56.902888 INFO: Initializing CalibrationManager
1:33:56.903101 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
1:33:56.903177 INFO: Initializing RawFileManager
1:33:56.945139 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
1:33:56.945331 INFO: Initializing OptimizationManager
1:33:56.945528 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
1:33:56.945604 INFO: Initializing CalibrationManager
1:33:56.945800 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
1:33:56.945880 INFO: Initializing RawFileManager
1:33:56.986353 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
1:33:56.986543 INFO: Initializing OptimizationManager
1:33:56.986757 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
1:33:56.986841 INFO: Initializing CalibrationManager
1:33:56.987059 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
1:33:56.987137 INFO: Initializing RawFileManager
1:33:57.028631 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
1:33:57.028814 INFO: Initializing OptimizationManager
1:33:57.029017 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
1:33:57.029095 INFO: Initializing CalibrationManager
1:33:57.029311 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
1:33:57.029386 INFO: Initializing RawFileManager
1:33:57.069391 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
1:33:57.069592 INFO: Initializing OptimizationManager
1:33:57.069789 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
1:33:57.069874 INFO: Initializing CalibrationManager
1:33:57.070075 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
1:33:57.070150 INFO: Initializing RawFileManager
1:33:57.111762 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
1:33:57.111949 INFO: Initializing OptimizationManager
1:33:57.112146 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
1:33:57.112222 INFO: Initializing CalibrationManager
1:33:57.112436 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
1:33:57.112510 INFO: Initializing RawFileManager
1:33:57.115628 INFO: Writing stat output to disk
1:33:57.115702 INFO: Saving run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/stat.tsv to disk
1:33:57.125903 PROGRESS: Building internal statistics
1:33:57.126226 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
1:33:57.126271 INFO: Initializing TimingManager
1:33:57.126595 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
1:33:57.126651 INFO: Initializing TimingManager
1:33:57.126830 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
1:33:57.126869 INFO: Initializing TimingManager
1:33:57.127028 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
1:33:57.127066 INFO: Initializing TimingManager
1:33:57.127221 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
1:33:57.127257 INFO: Initializing TimingManager
1:33:57.127408 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
1:33:57.127445 INFO: Initializing TimingManager
1:33:57.127851 INFO: Writing internal output to disk
1:33:57.127895 INFO: Saving run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/internal.tsv to disk
1:33:57.128391 PROGRESS: Performing label free quantification
1:33:57.234305 INFO: Accumulating fragment data
1:33:57.234457 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:33:57.362809 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:33:58.808037 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:34:00.213953 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:34:01.655524 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:34:03.089253 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:34:04.786041 PROGRESS: Performing label free quantification on the precursor level
1:34:04.786195 INFO: Filtering fragments by quality
1:34:05.134300 INFO: Performing label-free quantification using directLFQ
1:34:06.192237 INFO: 110262 lfq-groups total
1:34:45.094203 INFO: using 100 processes
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1:36:02.924082 INFO: Writing precursor output to disk
1:36:02.924527 INFO: Saving run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/precursor.matrix.tsv to disk
1:36:03.501213 PROGRESS: Performing label free quantification on the pg level
1:36:03.501392 INFO: Filtering fragments by quality
1:36:03.871500 INFO: Performing label-free quantification using directLFQ
1:36:04.243032 INFO: 9922 lfq-groups total
1:36:27.170144 INFO: using 100 processes
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1:36:31.521357 INFO: lfq-object 9900
1:36:33.534447 INFO: Writing pg output to disk
1:36:33.534707 INFO: Saving run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/pg.matrix.tsv to disk
1:36:33.900952 INFO: Writing psm output to disk
1:36:33.901138 INFO: Saving run_output_Astral/alphadia_1.10.4_noTransfer_calibrationSet/precursors.tsv to disk
1:37:02.984466 PROGRESS: Building spectral library
1:37:03.174326 INFO: Building MBR spectral library
1:37:03.174474 INFO: Running MbrLibraryBuilder
1:37:03.496480 INFO: MBR spectral library contains 110,262 precursors, 9,922 proteins
1:37:03.496628 INFO: Writing MBR spectral library to disk
1:37:04.292351 PROGRESS: =================== Search Finished ===================
1:37:04.347783 WARNING: WARNING: Temp mmap arrays were written to /tmp/temp_mmap_cmy42asb. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 620,268,470,272
