0:00:00.023358 PROGRESS:           _      _         ___ ___   _   
0:00:00.023623 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.023674 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.023716 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.023786 PROGRESS:            |_|                           
0:00:00.023821 PROGRESS: 
0:00:00.023856 PROGRESS: version: 1.10.3
0:00:00.023915 INFO: hostname: thestral
0:00:00.024018 INFO: date: 2025-04-16 17:45:58
0:00:00.024056 INFO: ================ AlphaX Environment ===============
0:00:00.024092 INFO: alphatims       : 1.0.8
0:00:00.024124 INFO: alpharaw        : 0.4.5
0:00:00.024154 INFO: alphabase       : 1.5.0
0:00:00.024184 INFO: alphapeptdeep   : 1.3.0
0:00:00.024214 INFO: directlfq       : 0.2.19
0:00:00.024241 INFO: ===================================================
0:00:00.024270 INFO: ================= Pip Environment =================
0:00:00.116037 INFO: alphatims==1.0.8 click==8.1.8 partd==1.4.2 wget==3.2 torchmetrics==1.4.0.post0 uri-template==1.3.0 directlfq==0.2.19 nvidia-nvjitlink-cu12==12.4.127 lxml==5.3.1 alphadia==1.10.3 fsspec==2025.3.0 fqdn==1.5.1 jsonref==1.1.0 simplejson==3.20.1 tornado==6.4.2 s3transfer==0.11.4 pythonnet==3.0.3 tqdm==4.67.1 psutil==7.0.0 urllib3==2.3.0 fonttools==4.56.0 arrow==1.3.0 dask==2024.11.2 numpy==1.26.4 tzdata==2025.1 gitdb==4.0.12 contextlib2==21.6.0 future==1.0.0 toolz==1.0.0 monotonic==1.6 argparse==1.4.0 nvidia-cuda-cupti-cu12==12.4.127 numba==0.59.1 importlib_resources==6.5.2 packaging==24.2 SQLAlchemy==2.0.39 typing_extensions==4.12.2 pyarrow==19.0.1 joblib==1.4.2 requests-oauthlib==2.0.0 rdkit==2024.3.3 webcolors==24.11.1 cffi==1.17.1 nvidia-cuda-nvrtc-cu12==12.4.127 protobuf==5.29.3 pyteomics==4.7.5 mpmath==1.3.0 pytz==2025.1 multiprocess==0.70.17 MarkupSafe==3.0.2 pyzstd==0.16.2 six==1.17.0 cycler==0.12.1 charset-normalizer==3.4.1 pyparsing==3.2.1 tenacity==9.0.0 llvmlite==0.42.0 attrs==25.2.0 pip==23.0.1 requests==2.32.3 triton==3.2.0 h5py==3.13.0 oauthlib==3.2.2 zstandard==0.22.0 pyahocorasick==2.1.0 swagger-spec-validator==3.0.4 blinker==1.9.0 pycparser==2.22 alpharaw==0.4.5 regex==2024.11.6 streamlit-aggrid==1.1.1 streamlit==1.43.2 tokenizers==0.19.1 websocket-client==1.8.0 certifi==2025.1.31 narwhals==1.30.0 isoduration==20.11.0 python-dateutil==2.9.0.post0 peptdeep==1.3.0 botocore==1.37.11 locket==1.0.0 referencing==0.36.2 torch==2.6.0 nvidia-cusparse-cu12==12.3.1.170 rocket-fft==0.2.5 lightning-utilities==0.14.0 neptune==1.10.4 importlib_metadata==8.6.1 cloudpickle==3.1.1 clr_loader==0.2.7.post0 setuptools==66.1.1 pandas==2.2.3 dill==0.3.9 jsonschema-specifications==2024.10.1 networkx==3.4.2 transformers==4.40.2 biopython==1.85 filelock==3.17.0 types-python-dateutil==2.9.0.20241206 seaborn==0.13.2 toml==0.10.2 zipp==3.21.0 rfc3339-validator==0.1.4 altair==5.5.0 greenlet==3.1.1 scipy==1.12.0 matplotlib==3.10.1 contourpy==1.3.1 pydeck==0.9.1 threadpoolctl==3.5.0 Jinja2==3.1.6 bravado-core==6.1.1 msgpack==1.1.0 nvidia-nvtx-cu12==12.4.127 nvidia-cusolver-cu12==11.6.1.9 xxhash==3.4.1 safetensors==0.5.3 idna==3.10 cachetools==5.5.2 huggingface-hub==0.29.3 jsonpointer==3.0.0 rpds-py==0.23.1 nvidia-cufft-cu12==11.2.1.3 jsonschema==4.23.0 watchdog==6.0.0 python-decouple==3.8 sympy==1.13.1 boto3==1.37.11 dask-expr==1.1.19 pillow==11.1.0 plotly==6.0.0 nvidia-cublas-cu12==12.4.5.8 nvidia-cudnn-cu12==9.1.0.70 smmap==5.0.2 nvidia-curand-cu12==10.3.5.147 GitPython==3.1.44 progressbar==2.5 PyJWT==2.10.1 kiwisolver==1.4.8 nvidia-cuda-runtime-cu12==12.4.127 scikit-learn==1.6.1 nvidia-nccl-cu12==2.21.5 jmespath==1.0.1 rfc3986-validator==0.1.1 bravado==11.1.0 nvidia-cusparselt-cu12==0.6.2 alphabase==1.5.0 PyYAML==6.0.2
0:00:00.116212 INFO: ===================================================
0:00:00.116268 INFO: Running step 'library'
0:00:00.116457 INFO: loading config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:00:00.134833 INFO: loading additional config provided via CLI
0:00:00.134987 INFO: loading additional config provided via CLI parameters
0:00:00.135283 INFO: Updating config with 'user defined'
0:00:00.135384 INFO: Updating config with 'user defined (cli)'
0:00:00.135413 INFO: Updating config with 'multistep search'
0:00:00.135459 INFO: ├──version: 1
0:00:00.135490 INFO: ├──workflow_name: None
0:00:00.135514 INFO: [32;20m├──output_directory: run_output_Astral/alphadia_1.10_default/library [multistep search, default: None][0m
0:00:00.135540 INFO: ├──library_path: None
0:00:00.135561 INFO: ├──raw_paths:
0:00:00.135586 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
0:00:00.135607 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
0:00:00.135629 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
0:00:00.135654 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
0:00:00.135675 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
0:00:00.135696 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
0:00:00.135718 INFO: ├──fasta_paths:
0:00:00.135760 INFO: │   [32;20m- ./ProteoBenchFASTA_DDAQuantification.fasta [user defined (cli), default: None][0m
0:00:00.135787 INFO: ├──quant_directory: None
0:00:00.135807 INFO: ├──general
0:00:00.135831 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
0:00:00.135852 INFO: │   ├──transfer_step_enabled: False
0:00:00.135872 INFO: │   ├──mbr_step_enabled: True
0:00:00.135892 INFO: │   ├──reuse_calibration: False
0:00:00.135913 INFO: │   ├──reuse_quant: False
0:00:00.135934 INFO: │   ├──astral_ms1: False
0:00:00.135955 INFO: │   ├──log_level: INFO
0:00:00.135975 INFO: │   ├──mmap_detector_events: False
0:00:00.135997 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
0:00:00.136017 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.136038 INFO: │   └──save_mbr_library: True
0:00:00.136058 INFO: ├──library_loading
0:00:00.136079 INFO: │   └──rt_heuristic: 180
0:00:00.136098 INFO: ├──library_prediction
0:00:00.136118 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.136141 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.136165 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.136186 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
0:00:00.136207 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.136226 INFO: │   ├──missed_cleavages: 1
0:00:00.136247 INFO: │   ├──precursor_len:
0:00:00.136267 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.136288 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.136309 INFO: │   ├──precursor_charge:
0:00:00.136331 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.136351 INFO: │   │   [32;20m- 4[0m
0:00:00.136371 INFO: │   ├──precursor_mz:
0:00:00.136392 INFO: │   │   [32;20m- 400[0m
0:00:00.136412 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
0:00:00.136432 INFO: │   ├──fragment_mz:
0:00:00.136452 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
0:00:00.136477 INFO: │   │   [32;20m- 2000[0m
0:00:00.136508 INFO: │   ├──nce: 25
0:00:00.136533 INFO: │   ├──fragment_types:
0:00:00.136554 INFO: │   │   [32;20m- b[0m
0:00:00.136573 INFO: │   │   [32;20m- y[0m
0:00:00.136594 INFO: │   ├──max_fragment_charge: 2
0:00:00.136613 INFO: │   [32;20m├──instrument: Astral [user defined, default: Lumos][0m
0:00:00.136644 INFO: │   ├──peptdeep_model_path: None
0:00:00.136673 INFO: │   └──peptdeep_model_type: generic
0:00:00.136702 INFO: ├──custom_modifications:
0:00:00.136724 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.136745 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.136765 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.136785 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.136804 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.136825 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.136845 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.136866 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.136886 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.136906 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.136925 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.136946 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.136967 INFO: │   ├──name: Label:13C(12)@K
0:00:00.136987 INFO: │   └──composition: C(12)
0:00:00.137007 INFO: ├──search
0:00:00.137028 INFO: │   [32;20m├──target_ms1_tolerance: 10 [user defined, default: 5][0m
0:00:00.137049 INFO: │   [32;20m├──target_ms2_tolerance: 15 [user defined, default: 10][0m
0:00:00.137069 INFO: │   ├──target_rt_tolerance: 0
0:00:00.137089 INFO: │   ├──target_mobility_tolerance: 0
0:00:00.137109 INFO: │   ├──quant_window: 3
0:00:00.137130 INFO: │   [32;20m├──target_num_candidates: 2 [user defined, default: 3][0m
0:00:00.137150 INFO: │   ├──channel_filter: 
0:00:00.137171 INFO: │   ├──exclude_shared_ions: True
0:00:00.137190 INFO: │   ├──compete_for_fragments: True
0:00:00.137210 INFO: │   ├──quant_all: True
0:00:00.137231 INFO: │   ├──top_k_fragments: 12
0:00:00.137251 INFO: │   └──experimental_xic: True
0:00:00.137270 INFO: ├──calibration
0:00:00.137291 INFO: │   ├──batch_size: 8000
0:00:00.137311 INFO: │   ├──optimization_lock_target: 200
0:00:00.137330 INFO: │   ├──max_steps: 20
0:00:00.137351 INFO: │   ├──min_steps: 2
0:00:00.137370 INFO: │   ├──max_skips: 1
0:00:00.137390 INFO: │   ├──norm_rt_mode: linear
0:00:00.137409 INFO: │   ├──max_fragments: 5000
0:00:00.137434 INFO: │   └──min_correlation: 0.7
0:00:00.137452 INFO: ├──search_initial
0:00:00.137474 INFO: │   ├──initial_num_candidates: 1
0:00:00.137493 INFO: │   ├──initial_ms1_tolerance: 30
0:00:00.137515 INFO: │   ├──initial_ms2_tolerance: 30
0:00:00.137534 INFO: │   ├──initial_mobility_tolerance: 0.1
0:00:00.137555 INFO: │   └──initial_rt_tolerance: 0.5
0:00:00.137574 INFO: ├──selection_config
0:00:00.137596 INFO: │   ├──peak_len_rt: 10.0
0:00:00.137616 INFO: │   ├──sigma_scale_rt: 0.5
0:00:00.137637 INFO: │   ├──peak_len_mobility: 0.01
0:00:00.137660 INFO: │   ├──sigma_scale_mobility: 1.0
0:00:00.137681 INFO: │   ├──top_k_precursors: 3
0:00:00.137702 INFO: │   ├──kernel_size: 30
0:00:00.137722 INFO: │   ├──f_mobility: 1.0
0:00:00.137743 INFO: │   ├──f_rt: 0.99
0:00:00.137764 INFO: │   ├──center_fraction: 0.5
0:00:00.137784 INFO: │   ├──min_size_mobility: 8
0:00:00.137805 INFO: │   ├──min_size_rt: 3
0:00:00.137826 INFO: │   ├──max_size_mobility: 20
0:00:00.137846 INFO: │   ├──max_size_rt: 15
0:00:00.137866 INFO: │   ├──group_channels: False
0:00:00.137886 INFO: │   ├──use_weighted_score: True
0:00:00.137906 INFO: │   ├──join_close_candidates: False
0:00:00.137928 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
0:00:00.137949 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
0:00:00.137969 INFO: ├──scoring_config
0:00:00.137990 INFO: │   ├──score_grouped: False
0:00:00.138010 INFO: │   ├──top_k_isotopes: 3
0:00:00.138029 INFO: │   ├──reference_channel: -1
0:00:00.138056 INFO: │   ├──precursor_mz_tolerance: 10
0:00:00.138077 INFO: │   └──fragment_mz_tolerance: 15
0:00:00.138096 INFO: ├──library_multiplexing
0:00:00.138116 INFO: │   ├──enabled: False
0:00:00.138135 INFO: │   ├──input_channel: 0
0:00:00.138155 INFO: │   └──multiplex_mapping:
0:00:00.138174 INFO: ├──multiplexing
0:00:00.138196 INFO: │   ├──enabled: False
0:00:00.138215 INFO: │   ├──target_channels: 4,8
0:00:00.138235 INFO: │   ├──decoy_channel: 12
0:00:00.138254 INFO: │   ├──reference_channel: 0
0:00:00.138274 INFO: │   └──competetive_scoring: True
0:00:00.138292 INFO: ├──fdr
0:00:00.138313 INFO: │   ├──fdr: 0.01
0:00:00.138332 INFO: │   ├──group_level: proteins
0:00:00.138352 INFO: │   ├──inference_strategy: heuristic
0:00:00.138371 INFO: │   ├──competetive_scoring: True
0:00:00.138391 INFO: │   ├──keep_decoys: False
0:00:00.138410 INFO: │   ├──channel_wise_fdr: False
0:00:00.138430 INFO: │   ├──enable_two_step_classifier: False
0:00:00.138449 INFO: │   ├──two_step_classifier_max_iterations: 5
0:00:00.138469 INFO: │   └──enable_nn_hyperparameter_tuning: False
0:00:00.138489 INFO: ├──search_output
0:00:00.138509 INFO: │   ├──file_format: tsv
0:00:00.138530 INFO: │   ├──peptide_level_lfq: False
0:00:00.138551 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
0:00:00.138572 INFO: │   ├──min_k_fragments: 12
0:00:00.138591 INFO: │   ├──min_correlation: 0.9
0:00:00.138612 INFO: │   ├──num_samples_quadratic: 50
0:00:00.138631 INFO: │   ├──min_nonnan: 3
0:00:00.138651 INFO: │   ├──normalize_lfq: True
0:00:00.138670 INFO: │   └──save_fragment_quant_matrix: False
0:00:00.138690 INFO: ├──optimization
0:00:00.138710 INFO: │   ├──order_of_optimization: None
0:00:00.138730 INFO: │   ├──ms2_error
0:00:00.138750 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.138771 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.138791 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.138812 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.138832 INFO: │   │   ├──try_narrower_values: True
0:00:00.138852 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.138873 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.138893 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.138913 INFO: │   ├──ms1_error
0:00:00.138933 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.138954 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.138973 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.138995 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.139014 INFO: │   │   ├──try_narrower_values: False
0:00:00.139035 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.139055 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.139077 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.139098 INFO: │   ├──mobility_error
0:00:00.139118 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.139139 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.139158 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.139179 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.139199 INFO: │   │   ├──try_narrower_values: False
0:00:00.139220 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.139240 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.139261 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.139279 INFO: │   └──rt_error
0:00:00.139301 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.139321 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.139342 INFO: │       ├──automatic_update_percentile_range: 0.99
0:00:00.139367 INFO: │       ├──automatic_update_factor: 1.1
0:00:00.139387 INFO: │       ├──try_narrower_values: True
0:00:00.139407 INFO: │       ├──maximal_decrease: 0.2
0:00:00.139427 INFO: │       ├──favour_narrower_optimum: True
0:00:00.139447 INFO: │       └──maximum_decrease_from_maximum: 0.1
0:00:00.139466 INFO: ├──optimization_manager
0:00:00.139487 INFO: │   ├──fwhm_rt: 5
0:00:00.139506 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.139527 INFO: │   └──score_cutoff: 0
0:00:00.139546 INFO: ├──transfer_library
0:00:00.139567 INFO: │   ├──enabled: False
0:00:00.139585 INFO: │   ├──fragment_types:
0:00:00.139606 INFO: │   │   [32;20m- b[0m
0:00:00.139624 INFO: │   │   [32;20m- y[0m
0:00:00.139645 INFO: │   ├──max_charge: 2
0:00:00.139663 INFO: │   ├──top_k_samples: 3
0:00:00.139684 INFO: │   ├──norm_delta_max: True
0:00:00.139704 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.139725 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.139761 INFO: └──transfer_learning
0:00:00.139781 INFO:     ├──enabled: False
0:00:00.139802 INFO:     ├──batch_size: 2000
0:00:00.139821 INFO:     ├──max_lr: 0.0001
0:00:00.139859 INFO:     ├──train_fraction: 0.7
0:00:00.139880 INFO:     ├──validation_fraction: 0.2
0:00:00.139899 INFO:     ├──test_fraction: 0.1
0:00:00.139920 INFO:     ├──test_interval: 1
0:00:00.139939 INFO:     ├──lr_patience: 3
0:00:00.139959 INFO:     ├──epochs: 51
0:00:00.139979 INFO:     ├──warmup_epochs: 5
0:00:00.139998 INFO:     ├──nce: 25
0:00:00.140019 INFO:     [32;20m└──instrument: Astral [user defined, default: Lumos][0m
0:00:00.147358 INFO: Registering 7 custom modifications
0:00:00.190750 PROGRESS: No library provided. Building library from fasta files.
0:00:00.190922 INFO: Running FastaDigest
0:00:01.390603 INFO: Digesting fasta file
0:00:13.392396 INFO: Adding modifications
0:02:36.823447 INFO: Removing non-canonical amino acids
0:02:46.729136 INFO: Fasta library contains 5,215,079 precursors
0:02:46.729651 PROGRESS: Predicting library properties.
0:02:46.729760 INFO: Running PeptDeepPrediction
0:02:46.729887 INFO: Device set to cpu
0:02:48.141184 INFO: Loading PeptDeep models of type generic
0:02:49.230066 INFO: Predicting RT, MS2 and mobility
0:02:49.230331 INFO: Using multiprocessing with 100 processes ...
0:02:49.873599 INFO: Predicting rt,ms2,mobility ...
0:11:41.611467 INFO: Adding fragment mz information
0:11:42.217695 INFO: Adding fragment intensity information
0:11:42.804960 INFO: Adding precursor information
0:11:43.435124 INFO: Running PrecursorInitializer
0:11:43.498382 INFO: Running AnnotateFasta
0:11:43.742407 INFO: Dropping decoys from input library before annotation
0:12:31.732793 INFO: Running IsotopeGenerator
0:13:11.840678 INFO: Running RTNormalization
0:13:11.841594 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:13:11.841774 INFO: Saving library to run_output_Astral/alphadia_1.10_default/library/speclib.hdf
0:14:12.036551 INFO: Running DecoyGenerator
0:17:02.173255 INFO: Running FlattenLibrary
0:17:52.877383 INFO: Running InitFlatColumns
0:17:53.316520 INFO: Running LogFlatLibraryStats
0:17:53.316700 INFO: ============ Library Stats ============
0:17:53.316752 INFO: Number of precursors: 10,400,392
0:17:56.228394 INFO: 	thereof targets:5,215,079
0:17:56.228594 INFO: 	thereof decoys: 5,185,313
0:17:56.384705 INFO: Number of elution groups: 5,215,079
0:17:56.384913 INFO: 	average size: 1.99
0:17:57.010077 INFO: Number of proteins: 117,993
0:17:57.043355 INFO: Number of channels: 1 ([0])
0:17:57.043623 INFO: Isotopes Distribution for 4 isotopes
0:17:57.043671 INFO: =======================================
0:17:57.055229 INFO: Searching 6 files:
0:17:57.055383 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
0:17:57.055412 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
0:17:57.055449 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
0:17:57.055469 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
0:17:57.055489 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
0:17:57.055509 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
0:17:57.055532 INFO: Using 1 fasta files:
0:17:57.055558 INFO:   ./ProteoBenchFASTA_DDAQuantification.fasta
0:17:57.055586 INFO: Using library: None
0:17:57.055608 INFO: Saving output to: run_output_Astral/alphadia_1.10_default/library
0:17:57.055640 PROGRESS: Starting Search Workflows
0:17:57.055730 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:17:57.055810 INFO: Quantification results path: run_output_Astral/alphadia_1.10_default/library/quant
0:17:57.055893 INFO: Creating parent folder for workflows at run_output_Astral/alphadia_1.10_default/library/quant
0:17:57.056039 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1 at run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:17:57.056592 INFO: Initializing RawFileManager
0:18:31.879289 INFO: Determining DIA cycle
0:18:32.614363 INFO: Found cycle with start 0.00 min and length 303.
0:18:32.949019 INFO: RT (min)            : 0.0 - 26.9
0:18:32.949155 INFO: RT duration (sec)   : 1611.2
0:18:32.949195 INFO: RT duration (min)   : 26.9
0:18:32.949230 INFO: Cycle len (scans)   : 303
0:18:32.949260 INFO: Cycle len (sec)     : 1.65
0:18:32.949288 INFO: Number of cycles    : 977
0:18:32.949317 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:18:35.281104 INFO: Initializing CalibrationManager
0:18:35.281514 INFO: Loading calibration config
0:18:35.281647 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'}]
0:18:35.281729 INFO: Calibration group :fragment, found 1 estimator(s)
0:18:35.281898 INFO: Calibration group :precursor, found 3 estimator(s)
0:18:35.281992 INFO: Disabling ion mobility calibration
0:18:35.282025 INFO: removed mobility estimator from group precursor
0:18:35.282213 INFO: Initializing OptimizationManager
0:18:35.282363 INFO: initial parameter: ms1_error = 30
0:18:35.282432 INFO: initial parameter: ms2_error = 30
0:18:35.282513 INFO: initial parameter: rt_error = 805.5992431640625
0:18:35.282575 INFO: initial parameter: mobility_error = 0.1
0:18:35.282635 INFO: initial parameter: column_type = library
0:18:35.282689 INFO: initial parameter: num_candidates = 1
0:18:35.282742 INFO: initial parameter: classifier_version = -1
0:18:35.282796 INFO: initial parameter: fwhm_rt = 5
0:18:35.282851 INFO: initial parameter: fwhm_mobility = 0.01
0:18:35.282905 INFO: initial parameter: score_cutoff = 0
0:18:35.282987 INFO: Initializing TimingManager
0:18:35.283060 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:18:35.283204 INFO: FDRManager not loaded from disk.
0:18:35.283234 INFO: Initializing FDRManager
0:18:35.283283 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:18:37.402684 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
0:18:40.727884 PROGRESS: Starting initial search for precursors.
0:18:42.273461 INFO: Starting optimization step 0.
0:18:42.273853 PROGRESS: === Extracting elution groups 0 to 8000 ===
0:18:42.273962 PROGRESS: Extracting batch of 15808 precursors
0:18:45.454041 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:18:45.454236 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:18:45.454290 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:18:45.454323 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:18:51.107596 INFO: Starting candidate selection
0:21:07.333325 INFO: Starting candidate scoring
0:34:01.778360 INFO: Finished candidate processing
0:34:01.779129 INFO: Collecting candidate features
0:34:02.947022 INFO: Collecting fragment features
0:34:06.307801 INFO: Finished candidate scoring
0:34:06.342806 PROGRESS: === Extracted 15768 precursors and 155286 fragments ===
0:34:06.343469 INFO: performing precursor FDR with 47 features
0:34:06.343521 INFO: Decoy channel: -1
0:34:06.343552 INFO: Competetive: True
0:34:06.351318 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:13.870337 INFO: Test AUC: 0.513
0:34:13.870568 INFO: Train AUC: 0.529
0:34:13.870617 INFO: AUC difference: 2.92%
0:34:14.013121 INFO: Resetting torch num_threads to 100
0:34:14.027402 INFO: === FDR correction performed with classifier version -1 ===
0:34:14.028843 PROGRESS: ============================= Precursor FDR =============================
0:34:14.028999 PROGRESS: Total precursors accumulated: 1
0:34:14.029091 PROGRESS: Target precursors: 1 (100.00%)
0:34:14.029170 PROGRESS: Decoy precursors: 0 (0.00%)
0:34:14.029242 PROGRESS: 
0:34:14.029313 PROGRESS: Precursor Summary:
0:34:14.030890 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:34:14.031021 PROGRESS: 
0:34:14.031105 PROGRESS: Protein Summary:
0:34:14.032587 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:34:14.032707 PROGRESS: =========================================================================
0:34:14.301650 INFO: Starting optimization step 1.
0:34:14.302112 PROGRESS: === Extracting elution groups 8000 to 24000 ===
0:34:14.302227 PROGRESS: Extracting batch of 31655 precursors
0:34:14.323232 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:34:14.323429 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:34:14.323489 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:34:14.323521 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:34:14.323968 INFO: Starting candidate selection
0:34:16.840006 INFO: Starting candidate scoring
0:34:17.155491 INFO: Finished candidate processing
0:34:17.158145 INFO: Collecting candidate features
0:34:17.322521 INFO: Collecting fragment features
0:34:17.360658 INFO: Finished candidate scoring
0:34:17.439280 PROGRESS: === Extracted 47346 precursors and 467323 fragments ===
0:34:17.453778 INFO: performing precursor FDR with 47 features
0:34:17.453970 INFO: Decoy channel: -1
0:34:17.454008 INFO: Competetive: True
0:34:17.510607 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:18.634726 INFO: Test AUC: 0.538
0:34:18.634935 INFO: Train AUC: 0.563
0:34:18.634979 INFO: AUC difference: 4.35%
0:34:18.780883 INFO: Resetting torch num_threads to 100
0:34:18.789784 INFO: === FDR correction performed with classifier version -1 ===
0:34:18.791436 PROGRESS: ============================= Precursor FDR =============================
0:34:18.791592 PROGRESS: Total precursors accumulated: 1
0:34:18.791681 PROGRESS: Target precursors: 1 (100.00%)
0:34:18.791780 PROGRESS: Decoy precursors: 0 (0.00%)
0:34:18.791856 PROGRESS: 
0:34:18.791921 PROGRESS: Precursor Summary:
0:34:18.793475 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:34:18.793603 PROGRESS: 
0:34:18.793686 PROGRESS: Protein Summary:
0:34:18.795347 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:34:18.795476 PROGRESS: =========================================================================
0:34:19.132494 INFO: Starting optimization step 2.
0:34:19.132873 PROGRESS: === Extracting elution groups 24000 to 56000 ===
0:34:19.132996 PROGRESS: Extracting batch of 63250 precursors
0:34:19.166562 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:34:19.166763 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:34:19.166832 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:34:19.166873 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:34:19.167593 INFO: Starting candidate selection
0:34:23.710508 INFO: Starting candidate scoring
0:34:24.244663 INFO: Finished candidate processing
0:34:24.244865 INFO: Collecting candidate features
0:34:24.534577 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 63088)
0:34:24.544413 INFO: Collecting fragment features
0:34:24.636970 INFO: Finished candidate scoring
0:34:24.864392 PROGRESS: === Extracted 110434 precursors and 1089939 fragments ===
0:34:24.890549 INFO: performing precursor FDR with 47 features
0:34:24.890784 INFO: Decoy channel: -1
0:34:24.890836 INFO: Competetive: True
0:34:25.041698 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:25.086806 WARNING: dropped 1 decoy PSMs due to missing features
0:34:28.445201 INFO: Test AUC: 0.553
0:34:28.445507 INFO: Train AUC: 0.584
0:34:28.445557 INFO: AUC difference: 5.32%
0:34:28.445591 WARNING: AUC difference > 5%. This may indicate overfitting.
0:34:28.616287 INFO: Resetting torch num_threads to 100
0:34:28.633777 INFO: === FDR correction performed with classifier version -1 ===
0:34:28.635146 PROGRESS: ============================= Precursor FDR =============================
0:34:28.635279 PROGRESS: Total precursors accumulated: 2
0:34:28.635363 PROGRESS: Target precursors: 2 (100.00%)
0:34:28.635435 PROGRESS: Decoy precursors: 0 (0.00%)
0:34:28.635498 PROGRESS: 
0:34:28.635560 PROGRESS: Precursor Summary:
0:34:28.636970 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
0:34:28.637100 PROGRESS: 
0:34:28.637179 PROGRESS: Protein Summary:
0:34:28.638719 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
0:34:28.638839 PROGRESS: =========================================================================
0:34:29.157861 INFO: Starting optimization step 3.
0:34:29.158224 PROGRESS: === Extracting elution groups 56000 to 120000 ===
0:34:29.158344 PROGRESS: Extracting batch of 126479 precursors
0:34:29.209608 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:34:29.209793 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:34:29.209851 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:34:29.209883 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:34:29.210288 INFO: Starting candidate selection
0:34:37.179070 INFO: Starting candidate scoring
0:34:38.147096 INFO: Finished candidate processing
0:34:38.147435 INFO: Collecting candidate features
0:34:38.764294 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 126196)
0:34:38.776395 INFO: Collecting fragment features
0:34:38.913148 INFO: Finished candidate scoring
0:34:39.323845 PROGRESS: === Extracted 236630 precursors and 2334015 fragments ===
0:34:39.375395 INFO: performing precursor FDR with 47 features
0:34:39.375629 INFO: Decoy channel: -1
0:34:39.375660 INFO: Competetive: True
0:34:39.559479 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:39.631143 WARNING: dropped 1 target PSMs due to missing features
0:34:39.631340 WARNING: dropped 1 decoy PSMs due to missing features
0:34:52.784776 INFO: Test AUC: 0.562
0:34:52.785314 INFO: Train AUC: 0.589
0:34:52.785444 INFO: AUC difference: 4.63%
0:34:52.950314 INFO: Resetting torch num_threads to 100
0:34:52.974943 INFO: === FDR correction performed with classifier version -1 ===
0:34:53.013155 PROGRESS: ============================= Precursor FDR =============================
0:34:53.013736 PROGRESS: Total precursors accumulated: 118,188
0:34:53.013977 PROGRESS: Target precursors: 70,747 (59.86%)
0:34:53.014173 PROGRESS: Decoy precursors: 47,441 (40.14%)
0:34:53.014353 PROGRESS: 
0:34:53.014525 PROGRESS: Precursor Summary:
0:34:53.017393 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:34:53.017782 PROGRESS: 
0:34:53.017959 PROGRESS: Protein Summary:
0:34:53.020208 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:34:53.020475 PROGRESS: =========================================================================
0:34:53.882861 INFO: Starting optimization step 4.
0:34:53.883520 PROGRESS: === Extracting elution groups 120000 to 248000 ===
0:34:53.883919 PROGRESS: Extracting batch of 252997 precursors
0:34:54.015932 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:34:54.018797 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:34:54.018974 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:34:54.019071 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:34:54.019624 INFO: Starting candidate selection
0:35:08.931315 INFO: Starting candidate scoring
0:35:10.862422 INFO: Finished candidate processing
0:35:10.862682 INFO: Collecting candidate features
0:35:12.048399 WARNING: intensity_correlation has 6 NaNs ( 0.00 % out of 252334)
0:35:12.070419 INFO: Collecting fragment features
0:35:12.396920 INFO: Finished candidate scoring
0:35:13.109413 PROGRESS: === Extracted 488964 precursors and 4821287 fragments ===
0:35:13.244978 INFO: performing precursor FDR with 47 features
0:35:13.245212 INFO: Decoy channel: -1
0:35:13.245251 INFO: Competetive: True
0:35:13.793417 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:14.035306 WARNING: dropped 3 target PSMs due to missing features
0:35:14.035525 WARNING: dropped 5 decoy PSMs due to missing features
0:35:28.421495 INFO: Test AUC: 0.572
0:35:28.421878 INFO: Train AUC: 0.590
0:35:28.421937 INFO: AUC difference: 2.90%
0:35:28.634583 INFO: Resetting torch num_threads to 100
0:35:28.752128 INFO: === FDR correction performed with classifier version -1 ===
0:35:28.753397 PROGRESS: ============================= Precursor FDR =============================
0:35:28.753534 PROGRESS: Total precursors accumulated: 17
0:35:28.753610 PROGRESS: Target precursors: 16 (94.12%)
0:35:28.753675 PROGRESS: Decoy precursors: 1 (5.88%)
0:35:28.753735 PROGRESS: 
0:35:28.753792 PROGRESS: Precursor Summary:
0:35:28.755024 PROGRESS: Channel   0:	 0.05 FDR:     7; 0.01 FDR:     7; 0.001 FDR:     7
0:35:28.755148 PROGRESS: 
0:35:28.755229 PROGRESS: Protein Summary:
0:35:28.756994 PROGRESS: Channel   0:	 0.05 FDR:     7; 0.01 FDR:     7; 0.001 FDR:     7
0:35:28.757124 PROGRESS: =========================================================================
0:35:30.306560 INFO: Starting optimization step 5.
0:35:30.306966 PROGRESS: === Extracting elution groups 248000 to 504000 ===
0:35:30.307091 PROGRESS: Extracting batch of 506030 precursors
0:35:30.607483 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:35:30.607643 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:30.607703 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:35:30.607751 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:35:30.608181 INFO: Starting candidate selection
0:35:58.460814 INFO: Starting candidate scoring
0:36:02.567793 INFO: Finished candidate processing
0:36:02.567957 INFO: Collecting candidate features
0:36:05.147048 WARNING: intensity_correlation has 7 NaNs ( 0.00 % out of 504783)
0:36:05.182829 INFO: Collecting fragment features
0:36:05.863469 INFO: Finished candidate scoring
0:36:07.401776 PROGRESS: === Extracted 993747 precursors and 9799891 fragments ===
0:36:07.639613 INFO: performing precursor FDR with 47 features
0:36:07.639818 INFO: Decoy channel: -1
0:36:07.639860 INFO: Competetive: True
0:36:08.583536 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:09.015160 WARNING: dropped 6 target PSMs due to missing features
0:36:09.015352 WARNING: dropped 9 decoy PSMs due to missing features
0:36:36.967121 INFO: Test AUC: 0.577
0:36:36.968792 INFO: Train AUC: 0.589
0:36:36.968846 INFO: AUC difference: 2.05%
0:36:37.146375 INFO: Resetting torch num_threads to 100
0:36:37.235635 INFO: === FDR correction performed with classifier version -1 ===
0:36:37.237019 PROGRESS: ============================= Precursor FDR =============================
0:36:37.237214 PROGRESS: Total precursors accumulated: 1
0:36:37.237294 PROGRESS: Target precursors: 1 (100.00%)
0:36:37.237351 PROGRESS: Decoy precursors: 0 (0.00%)
0:36:37.237401 PROGRESS: 
0:36:37.237449 PROGRESS: Precursor Summary:
0:36:37.238638 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:36:37.238765 PROGRESS: 
0:36:37.238828 PROGRESS: Protein Summary:
0:36:37.240031 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:36:37.240167 PROGRESS: =========================================================================
0:36:38.711509 INFO: Starting optimization step 6.
0:36:38.711803 PROGRESS: === Extracting elution groups 504000 to 1016000 ===
0:36:38.711898 PROGRESS: Extracting batch of 1011982 precursors
0:36:38.996151 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:36:38.996287 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:36:38.996334 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:36:38.996360 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:36:38.996689 INFO: Starting candidate selection
0:37:43.089394 INFO: Starting candidate scoring
0:37:50.774919 INFO: Finished candidate processing
0:37:50.775080 INFO: Collecting candidate features
0:37:55.014955 WARNING: intensity_correlation has 12 NaNs ( 0.00 % out of 1009488)
0:37:55.078732 INFO: Collecting fragment features
0:37:56.412393 INFO: Finished candidate scoring
0:37:59.604058 PROGRESS: === Extracted 2003235 precursors and 19755867 fragments ===
0:38:00.031683 INFO: performing precursor FDR with 47 features
0:38:00.031874 INFO: Decoy channel: -1
0:38:00.031912 INFO: Competetive: True
0:38:02.169621 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:03.028692 WARNING: dropped 9 target PSMs due to missing features
0:38:03.028950 WARNING: dropped 18 decoy PSMs due to missing features
0:38:50.872933 INFO: Test AUC: 0.582
0:38:50.873194 INFO: Train AUC: 0.588
0:38:50.873238 INFO: AUC difference: 1.02%
0:38:52.384585 INFO: Resetting torch num_threads to 100
0:38:52.904492 INFO: === FDR correction performed with classifier version -1 ===
0:38:52.908994 PROGRESS: ============================= Precursor FDR =============================
0:38:52.909242 PROGRESS: Total precursors accumulated: 46
0:38:52.909324 PROGRESS: Target precursors: 42 (91.30%)
0:38:52.909391 PROGRESS: Decoy precursors: 4 (8.70%)
0:38:52.909453 PROGRESS: 
0:38:52.909513 PROGRESS: Precursor Summary:
0:38:52.910810 PROGRESS: Channel   0:	 0.05 FDR:    12; 0.01 FDR:    12; 0.001 FDR:    12
0:38:52.910932 PROGRESS: 
0:38:52.911003 PROGRESS: Protein Summary:
0:38:52.912490 PROGRESS: Channel   0:	 0.05 FDR:    12; 0.01 FDR:    12; 0.001 FDR:    12
0:38:52.912613 PROGRESS: =========================================================================
0:38:56.859384 INFO: Starting optimization step 7.
0:38:56.860142 PROGRESS: === Extracting elution groups 1016000 to 2040000 ===
0:38:56.860291 PROGRESS: Extracting batch of 2023798 precursors
0:38:57.567406 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:38:57.567652 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:38:57.567709 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:38:57.567753 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:38:57.568341 INFO: Starting candidate selection
0:41:01.048442 INFO: Starting candidate scoring
0:41:16.707343 INFO: Finished candidate processing
0:41:16.707777 INFO: Collecting candidate features
0:41:24.593984 WARNING: intensity_correlation has 21 NaNs ( 0.00 % out of 2018640)
0:41:24.720822 INFO: Collecting fragment features
0:41:27.214859 INFO: Finished candidate scoring
0:41:32.374217 PROGRESS: === Extracted 4021875 precursors and 39655898 fragments ===
0:41:33.304902 INFO: performing precursor FDR with 47 features
0:41:33.305604 INFO: Decoy channel: -1
0:41:33.305736 INFO: Competetive: True
0:41:36.488886 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:38.022458 WARNING: dropped 15 target PSMs due to missing features
0:41:38.022666 WARNING: dropped 33 decoy PSMs due to missing features
0:43:25.027755 INFO: Test AUC: 0.587
0:43:25.028016 INFO: Train AUC: 0.590
0:43:25.028055 INFO: AUC difference: 0.54%
0:43:25.438613 INFO: Resetting torch num_threads to 100
0:43:26.396062 INFO: === FDR correction performed with classifier version -1 ===
0:43:26.397865 PROGRESS: ============================= Precursor FDR =============================
0:43:26.397980 PROGRESS: Total precursors accumulated: 2,064
0:43:26.398046 PROGRESS: Target precursors: 1,891 (91.62%)
0:43:26.398098 PROGRESS: Decoy precursors: 173 (8.38%)
0:43:26.398146 PROGRESS: 
0:43:26.398202 PROGRESS: Precursor Summary:
0:43:26.399636 PROGRESS: Channel   0:	 0.05 FDR: 1,357; 0.01 FDR:   703; 0.001 FDR:   527
0:43:26.399742 PROGRESS: 
0:43:26.399802 PROGRESS: Protein Summary:
0:43:26.401419 PROGRESS: Channel   0:	 0.05 FDR: 1,156; 0.01 FDR:   605; 0.001 FDR:   467
0:43:26.401523 PROGRESS: =========================================================================
0:43:26.919609 INFO: fragments_df_filtered: 5000
0:43:29.523504 INFO: calibration group: precursor, fitting mz estimator 
0:43:29.636973 INFO: calibration group: precursor, fitting rt estimator 
0:43:29.734046 INFO: calibration group: fragment, fitting mz estimator 
0:43:30.284005 INFO: calibration group: precursor, predicting mz
0:43:30.611957 INFO: calibration group: precursor, predicting rt
0:43:32.211331 INFO: calibration group: fragment, predicting mz
0:43:36.411658 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:43:36.412471 INFO: Starting optimization step 8.
0:43:36.412625 PROGRESS: === Extracting elution groups 0 to 1016000 ===
0:43:36.412775 PROGRESS: Extracting batch of 2008201 precursors
0:43:37.885327 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:43:37.885532 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:43:37.885598 INFO: FWHM in RT is 2.90 seconds, sigma is 0.37
0:43:37.885633 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:43:37.886170 INFO: Starting candidate selection
0:45:42.316242 INFO: Starting candidate scoring
0:46:22.633226 INFO: Finished candidate processing
0:46:22.633544 INFO: Collecting candidate features
0:46:31.816088 WARNING: intensity_correlation has 19 NaNs ( 0.00 % out of 4006211)
0:46:31.983771 INFO: Collecting fragment features
0:46:36.066128 INFO: Finished candidate scoring
0:46:40.958114 PROGRESS: === Extracted 4006211 precursors and 38965870 fragments ===
0:46:40.959318 INFO: performing precursor FDR with 47 features
0:46:40.959382 INFO: Decoy channel: -1
0:46:40.959421 INFO: Competetive: True
0:46:42.878506 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:44.151732 WARNING: dropped 4 target PSMs due to missing features
0:46:44.151947 WARNING: dropped 15 decoy PSMs due to missing features
0:48:20.497562 INFO: Test AUC: 0.586
0:48:20.497841 INFO: Train AUC: 0.590
0:48:20.497899 INFO: AUC difference: 0.64%
0:48:21.133368 INFO: Resetting torch num_threads to 100
0:48:21.297006 INFO: === FDR correction performed with classifier version 7 ===
0:48:21.299263 PROGRESS: ============================= Precursor FDR =============================
0:48:21.299577 PROGRESS: Total precursors accumulated: 1,759
0:48:21.299851 PROGRESS: Target precursors: 1,612 (91.64%)
0:48:21.300124 PROGRESS: Decoy precursors: 147 (8.36%)
0:48:21.300367 PROGRESS: 
0:48:21.300596 PROGRESS: Precursor Summary:
0:48:21.302652 PROGRESS: Channel   0:	 0.05 FDR: 1,222; 0.01 FDR:   750; 0.001 FDR:   373
0:48:21.302956 PROGRESS: 
0:48:21.303207 PROGRESS: Protein Summary:
0:48:21.305655 PROGRESS: Channel   0:	 0.05 FDR: 1,061; 0.01 FDR:   661; 0.001 FDR:   339
0:48:21.305962 PROGRESS: =========================================================================
0:48:21.658204 INFO: fragments_df_filtered: 5000
0:48:23.524489 INFO: calibration group: precursor, fitting mz estimator 
0:48:24.072356 INFO: calibration group: precursor, fitting rt estimator 
0:48:24.418333 INFO: calibration group: fragment, fitting mz estimator 
0:48:25.253943 INFO: calibration group: precursor, predicting mz
0:48:25.678840 INFO: calibration group: precursor, predicting rt
0:48:26.466312 INFO: calibration group: fragment, predicting mz
0:48:28.295246 INFO: === checking if optimization conditions were reached ===
0:48:28.298234 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
0:48:28.299658 PROGRESS: ❌ ms1_error      : 14.7448 > 10.0000 or insufficient steps taken.
0:48:28.299807 INFO: ==============================================
0:48:28.300122 INFO: Starting optimization step 9.
0:48:28.300380 PROGRESS: === Extracting elution groups 0 to 504000 ===
0:48:28.300684 PROGRESS: Extracting batch of 996219 precursors
0:48:28.707398 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:48:28.707747 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:48:28.707863 INFO: FWHM in RT is 2.98 seconds, sigma is 0.38
0:48:28.707956 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:48:28.708366 INFO: Starting candidate selection
0:49:34.913393 INFO: Starting candidate scoring
0:49:48.421900 INFO: Finished candidate processing
0:49:48.422359 INFO: Collecting candidate features
0:49:53.946811 WARNING: intensity_correlation has 32 NaNs ( 0.00 % out of 1986385)
0:49:54.064418 INFO: Collecting fragment features
0:49:56.113270 INFO: Finished candidate scoring
0:49:59.608832 PROGRESS: === Extracted 1986385 precursors and 17129301 fragments ===
0:49:59.609642 INFO: performing precursor FDR with 47 features
0:49:59.609720 INFO: Decoy channel: -1
0:49:59.609775 INFO: Competetive: True
0:50:00.506429 INFO: Setting torch num_threads to 2 for FDR classification task
0:50:01.140505 WARNING: dropped 20 target PSMs due to missing features
0:50:01.140717 WARNING: dropped 12 decoy PSMs due to missing features
0:50:48.726899 INFO: Test AUC: 0.582
0:50:48.727181 INFO: Train AUC: 0.589
0:50:48.727220 INFO: AUC difference: 1.18%
0:50:48.962107 INFO: Resetting torch num_threads to 100
0:50:49.057920 INFO: === FDR correction performed with classifier version 8 ===
0:50:49.059645 PROGRESS: ============================= Precursor FDR =============================
0:50:49.059773 PROGRESS: Total precursors accumulated: 1,567
0:50:49.059846 PROGRESS: Target precursors: 1,427 (91.07%)
0:50:49.059908 PROGRESS: Decoy precursors: 140 (8.93%)
0:50:49.059966 PROGRESS: 
0:50:49.060019 PROGRESS: Precursor Summary:
0:50:49.061638 PROGRESS: Channel   0:	 0.05 FDR: 1,096; 0.01 FDR:   754; 0.001 FDR:   375
0:50:49.061748 PROGRESS: 
0:50:49.061816 PROGRESS: Protein Summary:
0:50:49.063730 PROGRESS: Channel   0:	 0.05 FDR:   945; 0.01 FDR:   657; 0.001 FDR:   341
0:50:49.063850 PROGRESS: =========================================================================
0:50:49.207335 INFO: fragments_df_filtered: 5000
0:50:50.251104 INFO: calibration group: precursor, fitting mz estimator 
0:50:50.402769 INFO: calibration group: precursor, fitting rt estimator 
0:50:50.505074 INFO: calibration group: fragment, fitting mz estimator 
0:50:51.314935 INFO: calibration group: precursor, predicting mz
0:50:51.462339 INFO: calibration group: precursor, predicting rt
0:50:51.924634 INFO: calibration group: fragment, predicting mz
0:50:52.925905 INFO: === checking if optimization conditions were reached ===
0:50:52.929587 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
0:50:52.931359 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
0:50:52.931529 INFO: ==============================================
0:50:52.931921 PROGRESS: Optimization finished for ms2_error, ms1_error.
0:50:53.955984 INFO: calibration group: precursor, predicting mz
0:50:54.146342 INFO: calibration group: precursor, predicting rt
0:50:54.678910 INFO: calibration group: fragment, predicting mz
0:50:55.790204 INFO: Starting optimization step 0.
0:50:55.790582 PROGRESS: === Extracting elution groups 0 to 248000 ===
0:50:55.790703 PROGRESS: Extracting batch of 490189 precursors
0:50:55.980977 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:50:55.981160 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:50:55.981210 INFO: FWHM in RT is 2.71 seconds, sigma is 0.35
0:50:55.981242 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:50:55.981610 INFO: Starting candidate selection
0:51:25.464597 INFO: Starting candidate scoring
0:51:31.596025 INFO: Finished candidate processing
0:51:31.597812 INFO: Collecting candidate features
0:51:33.760504 WARNING: intensity_correlation has 11 NaNs ( 0.00 % out of 977578)
0:51:33.799817 INFO: Collecting fragment features
0:51:34.669106 INFO: Finished candidate scoring
0:51:36.243846 PROGRESS: === Extracted 977578 precursors and 8389809 fragments ===
0:51:36.244473 INFO: performing precursor FDR with 47 features
0:51:36.244526 INFO: Decoy channel: -1
0:51:36.244560 INFO: Competetive: True
0:51:36.795022 INFO: Setting torch num_threads to 2 for FDR classification task
0:51:37.025527 WARNING: dropped 6 target PSMs due to missing features
0:51:37.025708 WARNING: dropped 5 decoy PSMs due to missing features
0:51:59.217757 INFO: Test AUC: 0.581
0:51:59.217980 INFO: Train AUC: 0.595
0:51:59.218015 INFO: AUC difference: 2.23%
0:51:59.382892 INFO: Resetting torch num_threads to 100
0:51:59.412370 INFO: === FDR correction performed with classifier version 9 ===
0:51:59.413337 PROGRESS: ============================= Precursor FDR =============================
0:51:59.413435 PROGRESS: Total precursors accumulated: 837
0:51:59.413495 PROGRESS: Target precursors: 764 (91.28%)
0:51:59.413546 PROGRESS: Decoy precursors: 73 (8.72%)
0:51:59.413593 PROGRESS: 
0:51:59.413638 PROGRESS: Precursor Summary:
0:51:59.414812 PROGRESS: Channel   0:	 0.05 FDR:   608; 0.01 FDR:   440; 0.001 FDR:   377
0:51:59.414910 PROGRESS: 
0:51:59.414966 PROGRESS: Protein Summary:
0:51:59.416234 PROGRESS: Channel   0:	 0.05 FDR:   556; 0.01 FDR:   405; 0.001 FDR:   349
0:51:59.416326 PROGRESS: =========================================================================
0:51:59.450476 INFO: fragments_df_filtered: 4557
0:51:59.933994 INFO: calibration group: precursor, fitting mz estimator 
0:51:59.988876 INFO: calibration group: precursor, fitting rt estimator 
0:52:00.041554 INFO: calibration group: fragment, fitting mz estimator 
0:52:00.408408 INFO: calibration group: precursor, predicting mz
0:52:00.444599 INFO: calibration group: precursor, predicting rt
0:52:00.599292 INFO: calibration group: fragment, predicting mz
0:52:00.973444 INFO: === checking if optimization conditions were reached ===
0:52:00.973782 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:52:00.975822 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 496.2783.
0:52:00.975886 INFO: ==============================================
0:52:00.976020 INFO: Starting optimization step 1.
0:52:00.976103 PROGRESS: === Extracting elution groups 0 to 120000 ===
0:52:00.976187 PROGRESS: Extracting batch of 237192 precursors
0:52:01.108394 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:52:01.108516 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:52:01.108561 INFO: FWHM in RT is 2.65 seconds, sigma is 0.34
0:52:01.108592 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:52:01.108887 INFO: Starting candidate selection
0:52:11.685196 INFO: Starting candidate scoring
0:52:14.897084 INFO: Finished candidate processing
0:52:14.897192 INFO: Collecting candidate features
0:52:15.709917 WARNING: intensity_correlation has 12 NaNs ( 0.00 % out of 472995)
0:52:15.728318 INFO: Collecting fragment features
0:52:16.007122 INFO: Finished candidate scoring
0:52:16.262897 PROGRESS: === Extracted 472995 precursors and 4049904 fragments ===
0:52:16.263348 INFO: performing precursor FDR with 47 features
0:52:16.263405 INFO: Decoy channel: -1
0:52:16.263430 INFO: Competetive: True
0:52:16.412080 INFO: Setting torch num_threads to 2 for FDR classification task
0:52:16.503551 WARNING: dropped 7 target PSMs due to missing features
0:52:16.503709 WARNING: dropped 5 decoy PSMs due to missing features
0:52:27.178489 INFO: Test AUC: 0.584
0:52:27.178760 INFO: Train AUC: 0.597
0:52:27.178807 INFO: AUC difference: 2.17%
0:52:27.334255 INFO: Resetting torch num_threads to 100
0:52:27.362918 INFO: === FDR correction performed with classifier version 9 ===
0:52:27.364552 PROGRESS: ============================= Precursor FDR =============================
0:52:27.364876 PROGRESS: Total precursors accumulated: 520
0:52:27.365129 PROGRESS: Target precursors: 474 (91.15%)
0:52:27.365373 PROGRESS: Decoy precursors: 46 (8.85%)
0:52:27.365607 PROGRESS: 
0:52:27.365838 PROGRESS: Precursor Summary:
0:52:27.367381 PROGRESS: Channel   0:	 0.05 FDR:   321; 0.01 FDR:   169; 0.001 FDR:   161
0:52:27.367681 PROGRESS: 
0:52:27.367937 PROGRESS: Protein Summary:
0:52:27.369635 PROGRESS: Channel   0:	 0.05 FDR:   311; 0.01 FDR:   162; 0.001 FDR:   154
0:52:27.369972 PROGRESS: =========================================================================
0:52:27.966795 INFO: calibration group: precursor, predicting mz
0:52:28.077364 INFO: calibration group: precursor, predicting rt
0:52:28.332655 INFO: calibration group: fragment, predicting mz
0:52:28.914628 INFO: === skipping optimization until target number of precursors are found ===
0:52:28.915438 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
0:52:28.915613 INFO: Starting optimization step 2.
0:52:28.915908 PROGRESS: === Extracting elution groups 120000 to 248000 ===
0:52:28.916186 PROGRESS: Extracting batch of 252997 precursors
0:52:29.223176 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:52:29.223563 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:52:29.223689 INFO: FWHM in RT is 2.65 seconds, sigma is 0.34
0:52:29.223802 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:52:29.224342 INFO: Starting candidate selection
0:52:44.889891 INFO: Starting candidate scoring
0:52:49.508432 INFO: Finished candidate processing
0:52:49.509252 INFO: Collecting candidate features
0:52:51.036650 WARNING: intensity_correlation has 8 NaNs ( 0.00 % out of 504382)
0:52:51.070569 INFO: Collecting fragment features
0:52:51.548711 INFO: Finished candidate scoring
0:52:52.691990 PROGRESS: === Extracted 977377 precursors and 8366722 fragments ===
0:52:52.862508 INFO: performing precursor FDR with 47 features
0:52:52.862840 INFO: Decoy channel: -1
0:52:52.862942 INFO: Competetive: True
0:52:53.681145 INFO: Setting torch num_threads to 2 for FDR classification task
0:52:54.037088 WARNING: dropped 12 target PSMs due to missing features
0:52:54.037284 WARNING: dropped 8 decoy PSMs due to missing features
0:53:18.318946 INFO: Test AUC: 0.583
0:53:18.319226 INFO: Train AUC: 0.594
0:53:18.319273 INFO: AUC difference: 1.78%
0:53:18.551624 INFO: Resetting torch num_threads to 100
0:53:18.623602 INFO: === FDR correction performed with classifier version 9 ===
0:53:18.624705 PROGRESS: ============================= Precursor FDR =============================
0:53:18.624815 PROGRESS: Total precursors accumulated: 943
0:53:18.624879 PROGRESS: Target precursors: 859 (91.09%)
0:53:18.624934 PROGRESS: Decoy precursors: 84 (8.91%)
0:53:18.624981 PROGRESS: 
0:53:18.625042 PROGRESS: Precursor Summary:
0:53:18.626193 PROGRESS: Channel   0:	 0.05 FDR:   598; 0.01 FDR:   458; 0.001 FDR:   361
0:53:18.626291 PROGRESS: 
0:53:18.626349 PROGRESS: Protein Summary:
0:53:18.627672 PROGRESS: Channel   0:	 0.05 FDR:   549; 0.01 FDR:   422; 0.001 FDR:   335
0:53:18.627794 PROGRESS: =========================================================================
0:53:18.728529 INFO: fragments_df_filtered: 4665
0:53:19.236187 INFO: calibration group: precursor, fitting mz estimator 
0:53:19.371720 INFO: calibration group: precursor, fitting rt estimator 
0:53:20.496477 INFO: calibration group: fragment, fitting mz estimator 
0:53:21.197437 INFO: calibration group: precursor, predicting mz
0:53:21.273634 INFO: calibration group: precursor, predicting rt
0:53:21.474374 INFO: calibration group: fragment, predicting mz
0:53:22.118397 INFO: === checking if optimization conditions were reached ===
0:53:22.119354 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:53:22.121863 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 370.2787.
0:53:22.121929 INFO: ==============================================
0:53:22.122059 INFO: Starting optimization step 3.
0:53:22.122142 PROGRESS: === Extracting elution groups 0 to 120000 ===
0:53:22.122219 PROGRESS: Extracting batch of 237192 precursors
0:53:22.190390 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:53:22.190568 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:53:22.190615 INFO: FWHM in RT is 2.76 seconds, sigma is 0.36
0:53:22.190647 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:53:22.190948 INFO: Starting candidate selection
0:53:32.848710 INFO: Starting candidate scoring
0:53:35.500351 INFO: Finished candidate processing
0:53:35.500567 INFO: Collecting candidate features
0:53:36.532495 WARNING: intensity_correlation has 9 NaNs ( 0.00 % out of 472892)
0:53:36.561838 INFO: Collecting fragment features
0:53:36.977180 INFO: Finished candidate scoring
0:53:37.654681 PROGRESS: === Extracted 472892 precursors and 4047182 fragments ===
0:53:37.655524 INFO: performing precursor FDR with 47 features
0:53:37.655583 INFO: Decoy channel: -1
0:53:37.655622 INFO: Competetive: True
0:53:37.913236 INFO: Setting torch num_threads to 2 for FDR classification task
0:53:38.080547 WARNING: dropped 7 target PSMs due to missing features
0:53:38.080741 WARNING: dropped 2 decoy PSMs due to missing features
0:53:50.671885 INFO: Test AUC: 0.580
0:53:50.672164 INFO: Train AUC: 0.598
0:53:50.672213 INFO: AUC difference: 2.99%
0:53:50.862184 INFO: Resetting torch num_threads to 100
0:53:50.889396 INFO: === FDR correction performed with classifier version 9 ===
0:53:50.890707 PROGRESS: ============================= Precursor FDR =============================
0:53:50.891025 PROGRESS: Total precursors accumulated: 406
0:53:50.891109 PROGRESS: Target precursors: 369 (90.89%)
0:53:50.891178 PROGRESS: Decoy precursors: 37 (9.11%)
0:53:50.891239 PROGRESS: 
0:53:50.891300 PROGRESS: Precursor Summary:
0:53:50.892722 PROGRESS: Channel   0:	 0.05 FDR:   243; 0.01 FDR:   193; 0.001 FDR:   189
0:53:50.892840 PROGRESS: 
0:53:50.892911 PROGRESS: Protein Summary:
0:53:50.894423 PROGRESS: Channel   0:	 0.05 FDR:   233; 0.01 FDR:   185; 0.001 FDR:   181
0:53:50.894539 PROGRESS: =========================================================================
0:53:51.604021 INFO: calibration group: precursor, predicting mz
0:53:51.674211 INFO: calibration group: precursor, predicting rt
0:53:51.892408 INFO: calibration group: fragment, predicting mz
0:53:52.431600 INFO: === skipping optimization until target number of precursors are found ===
0:53:52.432026 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
0:53:52.432148 INFO: Starting optimization step 4.
0:53:52.432442 PROGRESS: === Extracting elution groups 120000 to 248000 ===
0:53:52.432702 PROGRESS: Extracting batch of 252997 precursors
0:53:52.512901 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:53:52.513054 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:53:52.513103 INFO: FWHM in RT is 2.76 seconds, sigma is 0.36
0:53:52.513135 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:53:52.513474 INFO: Starting candidate selection
0:54:04.487420 INFO: Starting candidate scoring
0:54:08.065830 INFO: Finished candidate processing
0:54:08.066040 INFO: Collecting candidate features
0:54:09.745253 WARNING: intensity_correlation has 10 NaNs ( 0.00 % out of 504241)
0:54:09.771039 INFO: Collecting fragment features
0:54:10.136291 INFO: Finished candidate scoring
0:54:10.956888 PROGRESS: === Extracted 977133 precursors and 8360537 fragments ===
0:54:11.101227 INFO: performing precursor FDR with 47 features
0:54:11.101376 INFO: Decoy channel: -1
0:54:11.101416 INFO: Competetive: True
0:54:11.652113 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:11.885553 WARNING: dropped 11 target PSMs due to missing features
0:54:11.885722 WARNING: dropped 8 decoy PSMs due to missing features
0:54:40.227872 INFO: Test AUC: 0.581
0:54:40.228306 INFO: Train AUC: 0.593
0:54:40.228438 INFO: AUC difference: 2.00%
0:54:40.478283 INFO: Resetting torch num_threads to 100
0:54:40.586369 INFO: === FDR correction performed with classifier version 9 ===
0:54:40.588147 PROGRESS: ============================= Precursor FDR =============================
0:54:40.588490 PROGRESS: Total precursors accumulated: 874
0:54:40.588757 PROGRESS: Target precursors: 799 (91.42%)
0:54:40.589007 PROGRESS: Decoy precursors: 75 (8.58%)
0:54:40.589267 PROGRESS: 
0:54:40.589510 PROGRESS: Precursor Summary:
0:54:40.591495 PROGRESS: Channel   0:	 0.05 FDR:   665; 0.01 FDR:   393; 0.001 FDR:   232
0:54:40.591826 PROGRESS: 
0:54:40.592116 PROGRESS: Protein Summary:
0:54:40.594267 PROGRESS: Channel   0:	 0.05 FDR:   615; 0.01 FDR:   363; 0.001 FDR:   217
0:54:40.594584 PROGRESS: =========================================================================
0:54:40.759009 INFO: fragments_df_filtered: 4198
0:54:41.936767 INFO: calibration group: precursor, fitting mz estimator 
0:54:42.054197 INFO: calibration group: precursor, fitting rt estimator 
0:54:42.156414 INFO: calibration group: fragment, fitting mz estimator 
0:54:42.782852 INFO: calibration group: precursor, predicting mz
0:54:42.931363 INFO: calibration group: precursor, predicting rt
0:54:43.379666 INFO: calibration group: fragment, predicting mz
0:54:44.682795 INFO: === checking if optimization conditions were reached ===
0:54:44.683559 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:54:44.687406 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 314.5682.
0:54:44.687518 INFO: ==============================================
0:54:44.687705 INFO: Starting optimization step 5.
0:54:44.687828 PROGRESS: === Extracting elution groups 0 to 248000 ===
0:54:44.687952 PROGRESS: Extracting batch of 490189 precursors
0:54:45.183021 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:54:45.183308 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:54:45.183371 INFO: FWHM in RT is 2.80 seconds, sigma is 0.36
0:54:45.183408 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:54:45.183894 INFO: Starting candidate selection
0:55:02.221888 INFO: Starting candidate scoring
0:55:07.947986 INFO: Finished candidate processing
0:55:07.949947 INFO: Collecting candidate features
0:55:10.949550 WARNING: intensity_correlation has 49 NaNs ( 0.01 % out of 975290)
0:55:11.010844 INFO: Collecting fragment features
0:55:11.959476 INFO: Finished candidate scoring
0:55:13.082764 PROGRESS: === Extracted 975290 precursors and 8240483 fragments ===
0:55:13.083454 INFO: performing precursor FDR with 47 features
0:55:13.083508 INFO: Decoy channel: -1
0:55:13.083543 INFO: Competetive: True
0:55:13.496643 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:13.735835 WARNING: dropped 26 target PSMs due to missing features
0:55:13.736108 WARNING: dropped 23 decoy PSMs due to missing features
0:55:36.045728 INFO: Test AUC: 0.580
0:55:36.046169 INFO: Train AUC: 0.592
0:55:36.046478 INFO: AUC difference: 2.05%
0:55:36.289836 INFO: Resetting torch num_threads to 100
0:55:36.348679 INFO: === FDR correction performed with classifier version 9 ===
0:55:36.350255 PROGRESS: ============================= Precursor FDR =============================
0:55:36.350415 PROGRESS: Total precursors accumulated: 978
0:55:36.350504 PROGRESS: Target precursors: 897 (91.72%)
0:55:36.350585 PROGRESS: Decoy precursors: 81 (8.28%)
0:55:36.350658 PROGRESS: 
0:55:36.350730 PROGRESS: Precursor Summary:
0:55:36.352395 PROGRESS: Channel   0:	 0.05 FDR:   739; 0.01 FDR:   372; 0.001 FDR:   285
0:55:36.352535 PROGRESS: 
0:55:36.352623 PROGRESS: Protein Summary:
0:55:36.354469 PROGRESS: Channel   0:	 0.05 FDR:   679; 0.01 FDR:   341; 0.001 FDR:   266
0:55:36.354610 PROGRESS: =========================================================================
0:55:36.440906 INFO: fragments_df_filtered: 3913
0:55:37.738990 INFO: calibration group: precursor, fitting mz estimator 
0:55:38.155950 INFO: calibration group: precursor, fitting rt estimator 
0:55:38.439339 INFO: calibration group: fragment, fitting mz estimator 
0:55:39.126883 INFO: calibration group: precursor, predicting mz
0:55:39.373070 INFO: calibration group: precursor, predicting rt
0:55:39.831422 INFO: calibration group: fragment, predicting mz
0:55:40.850673 INFO: === checking if optimization conditions were reached ===
0:55:40.851064 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:55:40.854410 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 276.9326.
0:55:40.854508 INFO: ==============================================
0:55:40.854662 INFO: Starting optimization step 6.
0:55:40.854766 PROGRESS: === Extracting elution groups 0 to 248000 ===
0:55:40.854892 PROGRESS: Extracting batch of 490189 precursors
0:55:41.200584 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:55:41.200947 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:55:41.201088 INFO: FWHM in RT is 2.80 seconds, sigma is 0.36
0:55:41.201194 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:55:41.201657 INFO: Starting candidate selection
0:56:02.710430 INFO: Starting candidate scoring
0:56:08.227580 INFO: Finished candidate processing
0:56:08.227895 INFO: Collecting candidate features
0:56:11.342616 WARNING: intensity_correlation has 75 NaNs ( 0.01 % out of 974488)
0:56:11.402639 INFO: Collecting fragment features
0:56:12.379812 INFO: Finished candidate scoring
0:56:13.722303 PROGRESS: === Extracted 974488 precursors and 8205267 fragments ===
0:56:13.723241 INFO: performing precursor FDR with 47 features
0:56:13.723365 INFO: Decoy channel: -1
0:56:13.723467 INFO: Competetive: True
0:56:14.219991 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:14.544740 WARNING: dropped 41 target PSMs due to missing features
0:56:14.545065 WARNING: dropped 34 decoy PSMs due to missing features
0:56:37.434183 INFO: Test AUC: 0.582
0:56:37.434428 INFO: Train AUC: 0.592
0:56:37.434470 INFO: AUC difference: 1.75%
0:56:37.622128 INFO: Resetting torch num_threads to 100
0:56:37.654315 INFO: === FDR correction performed with classifier version 9 ===
0:56:37.655630 PROGRESS: ============================= Precursor FDR =============================
0:56:37.655762 PROGRESS: Total precursors accumulated: 1,034
0:56:37.655851 PROGRESS: Target precursors: 948 (91.68%)
0:56:37.655921 PROGRESS: Decoy precursors: 86 (8.32%)
0:56:37.655984 PROGRESS: 
0:56:37.656046 PROGRESS: Precursor Summary:
0:56:37.657357 PROGRESS: Channel   0:	 0.05 FDR:   741; 0.01 FDR:   310; 0.001 FDR:   136
0:56:37.657469 PROGRESS: 
0:56:37.657544 PROGRESS: Protein Summary:
0:56:37.658951 PROGRESS: Channel   0:	 0.05 FDR:   684; 0.01 FDR:   287; 0.001 FDR:   132
0:56:37.659062 PROGRESS: =========================================================================
0:56:37.705677 INFO: fragments_df_filtered: 3274
0:56:38.673053 INFO: calibration group: precursor, fitting mz estimator 
0:56:38.768813 INFO: calibration group: precursor, fitting rt estimator 
0:56:38.885551 INFO: calibration group: fragment, fitting mz estimator 
0:56:39.290730 INFO: calibration group: precursor, predicting mz
0:56:39.460640 INFO: calibration group: precursor, predicting rt
0:56:39.936361 INFO: calibration group: fragment, predicting mz
0:56:40.913332 INFO: === checking if optimization conditions were reached ===
0:56:40.913713 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:56:40.916724 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 231.9724.
0:56:40.916810 INFO: ==============================================
0:56:40.916964 INFO: Starting optimization step 7.
0:56:40.917080 PROGRESS: === Extracting elution groups 0 to 248000 ===
0:56:40.917179 PROGRESS: Extracting batch of 490189 precursors
0:56:41.119988 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:56:41.120261 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:56:41.120323 INFO: FWHM in RT is 2.82 seconds, sigma is 0.36
0:56:41.120360 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:56:41.120733 INFO: Starting candidate selection
0:56:57.414405 INFO: Starting candidate scoring
0:57:03.894146 INFO: Finished candidate processing
0:57:03.894304 INFO: Collecting candidate features
0:57:06.980523 WARNING: intensity_correlation has 86 NaNs ( 0.01 % out of 973708)
0:57:07.037952 INFO: Collecting fragment features
0:57:07.974655 INFO: Finished candidate scoring
0:57:09.186908 PROGRESS: === Extracted 973708 precursors and 8140636 fragments ===
0:57:09.188102 INFO: performing precursor FDR with 47 features
0:57:09.188234 INFO: Decoy channel: -1
0:57:09.188338 INFO: Competetive: True
0:57:09.711253 INFO: Setting torch num_threads to 2 for FDR classification task
0:57:10.045177 WARNING: dropped 47 target PSMs due to missing features
0:57:10.045538 WARNING: dropped 39 decoy PSMs due to missing features
0:57:40.222620 INFO: Test AUC: 0.584
0:57:40.222895 INFO: Train AUC: 0.591
0:57:40.222954 INFO: AUC difference: 1.13%
0:57:40.465247 INFO: Resetting torch num_threads to 100
0:57:40.517559 INFO: === FDR correction performed with classifier version 9 ===
0:57:40.519016 PROGRESS: ============================= Precursor FDR =============================
0:57:40.519190 PROGRESS: Total precursors accumulated: 1,008
0:57:40.519290 PROGRESS: Target precursors: 916 (90.87%)
0:57:40.519374 PROGRESS: Decoy precursors: 92 (9.13%)
0:57:40.519454 PROGRESS: 
0:57:40.519527 PROGRESS: Precursor Summary:
0:57:40.520970 PROGRESS: Channel   0:	 0.05 FDR:   661; 0.01 FDR:   256; 0.001 FDR:   100
0:57:40.521109 PROGRESS: 
0:57:40.521194 PROGRESS: Protein Summary:
0:57:40.522832 PROGRESS: Channel   0:	 0.05 FDR:   602; 0.01 FDR:   239; 0.001 FDR:    97
0:57:40.522968 PROGRESS: =========================================================================
0:57:40.577178 INFO: fragments_df_filtered: 2862
0:57:41.718791 INFO: calibration group: precursor, fitting mz estimator 
0:57:42.070009 INFO: calibration group: precursor, fitting rt estimator 
0:57:42.275805 INFO: calibration group: fragment, fitting mz estimator 
0:57:42.725454 INFO: calibration group: precursor, predicting mz
0:57:42.996813 INFO: calibration group: precursor, predicting rt
0:57:43.503478 INFO: calibration group: fragment, predicting mz
0:57:44.594382 INFO: === checking if optimization conditions were reached ===
0:57:44.594802 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:57:44.597553 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 133.9338.
0:57:44.597648 INFO: ==============================================
0:57:44.597783 INFO: Starting optimization step 8.
0:57:44.597878 PROGRESS: === Extracting elution groups 0 to 248000 ===
0:57:44.597995 PROGRESS: Extracting batch of 490189 precursors
0:57:44.825697 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:57:44.825922 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:57:44.825987 INFO: FWHM in RT is 2.80 seconds, sigma is 0.36
0:57:44.826036 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:57:44.826415 INFO: Starting candidate selection
0:57:59.463267 INFO: Starting candidate scoring
0:58:04.916673 INFO: Finished candidate processing
0:58:04.916916 INFO: Collecting candidate features
0:58:07.198776 WARNING: intensity_correlation has 131 NaNs ( 0.01 % out of 970371)
0:58:07.239957 INFO: Collecting fragment features
0:58:08.042863 INFO: Finished candidate scoring
0:58:09.033504 PROGRESS: === Extracted 970371 precursors and 7919453 fragments ===
0:58:09.034110 INFO: performing precursor FDR with 47 features
0:58:09.034158 INFO: Decoy channel: -1
0:58:09.034197 INFO: Competetive: True
0:58:09.394154 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:09.629849 WARNING: dropped 72 target PSMs due to missing features
0:58:09.630013 WARNING: dropped 59 decoy PSMs due to missing features
0:58:33.914133 INFO: Test AUC: 0.581
0:58:33.914572 INFO: Train AUC: 0.591
0:58:33.914689 INFO: AUC difference: 1.71%
0:58:34.146696 INFO: Resetting torch num_threads to 100
0:58:34.195261 INFO: === FDR correction performed with classifier version 9 ===
0:58:34.197223 PROGRESS: ============================= Precursor FDR =============================
0:58:34.197591 PROGRESS: Total precursors accumulated: 1,297
0:58:34.197863 PROGRESS: Target precursors: 1,182 (91.13%)
0:58:34.198088 PROGRESS: Decoy precursors: 115 (8.87%)
0:58:34.198297 PROGRESS: 
0:58:34.198515 PROGRESS: Precursor Summary:
0:58:34.200239 PROGRESS: Channel   0:	 0.05 FDR:   806; 0.01 FDR:   462; 0.001 FDR:   217
0:58:34.200527 PROGRESS: 
0:58:34.200749 PROGRESS: Protein Summary:
0:58:34.202635 PROGRESS: Channel   0:	 0.05 FDR:   729; 0.01 FDR:   423; 0.001 FDR:   208
0:58:34.202908 PROGRESS: =========================================================================
0:58:34.253792 INFO: fragments_df_filtered: 4689
0:58:34.918654 INFO: calibration group: precursor, fitting mz estimator 
0:58:35.053794 INFO: calibration group: precursor, fitting rt estimator 
0:58:35.202768 INFO: calibration group: fragment, fitting mz estimator 
0:58:35.903597 INFO: calibration group: precursor, predicting mz
0:58:36.113367 INFO: calibration group: precursor, predicting rt
0:58:36.440906 INFO: calibration group: fragment, predicting mz
0:58:36.998123 INFO: === checking if optimization conditions were reached ===
0:58:36.998656 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:58:37.001658 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 109.6050.
0:58:37.001758 INFO: ==============================================
0:58:37.001903 INFO: Starting optimization step 9.
0:58:37.002003 PROGRESS: === Extracting elution groups 0 to 120000 ===
0:58:37.002113 PROGRESS: Extracting batch of 237192 precursors
0:58:37.096355 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:58:37.096578 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:58:37.096637 INFO: FWHM in RT is 2.67 seconds, sigma is 0.34
0:58:37.096678 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:58:37.097040 INFO: Starting candidate selection
0:58:45.873165 INFO: Starting candidate scoring
0:58:50.284394 INFO: Finished candidate processing
0:58:50.284607 INFO: Collecting candidate features
0:58:51.203640 WARNING: intensity_correlation has 85 NaNs ( 0.02 % out of 469053)
0:58:51.223988 INFO: Collecting fragment features
0:58:51.532264 INFO: Finished candidate scoring
0:58:52.249337 PROGRESS: === Extracted 469053 precursors and 3791983 fragments ===
0:58:52.251306 INFO: performing precursor FDR with 47 features
0:58:52.251384 INFO: Decoy channel: -1
0:58:52.251430 INFO: Competetive: True
0:58:52.500118 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:52.660350 WARNING: dropped 39 target PSMs due to missing features
0:58:52.660534 WARNING: dropped 46 decoy PSMs due to missing features
0:59:03.523825 INFO: Test AUC: 0.575
0:59:03.524087 INFO: Train AUC: 0.594
0:59:03.524133 INFO: AUC difference: 3.27%
0:59:03.751122 INFO: Resetting torch num_threads to 100
0:59:03.791855 INFO: === FDR correction performed with classifier version 9 ===
0:59:03.793758 PROGRESS: ============================= Precursor FDR =============================
0:59:03.794611 PROGRESS: Total precursors accumulated: 501
0:59:03.794981 PROGRESS: Target precursors: 455 (90.82%)
0:59:03.795321 PROGRESS: Decoy precursors: 46 (9.18%)
0:59:03.795647 PROGRESS: 
0:59:03.795983 PROGRESS: Precursor Summary:
0:59:03.797571 PROGRESS: Channel   0:	 0.05 FDR:   324; 0.01 FDR:   223; 0.001 FDR:   137
0:59:03.798652 PROGRESS: 
0:59:03.798992 PROGRESS: Protein Summary:
0:59:03.800757 PROGRESS: Channel   0:	 0.05 FDR:   310; 0.01 FDR:   212; 0.001 FDR:   133
0:59:03.801973 PROGRESS: =========================================================================
0:59:03.828788 INFO: fragments_df_filtered: 2218
0:59:04.481003 INFO: calibration group: precursor, fitting mz estimator 
0:59:05.942391 INFO: calibration group: precursor, fitting rt estimator 
0:59:06.283638 INFO: calibration group: fragment, fitting mz estimator 
0:59:06.684752 INFO: calibration group: precursor, predicting mz
0:59:06.853461 INFO: calibration group: precursor, predicting rt
0:59:07.079062 INFO: calibration group: fragment, predicting mz
0:59:07.621701 INFO: === checking if optimization conditions were reached ===
0:59:07.622098 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
0:59:07.624679 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 89.3815.
0:59:07.624749 INFO: ==============================================
0:59:07.624860 INFO: Starting optimization step 10.
0:59:07.624943 PROGRESS: === Extracting elution groups 0 to 120000 ===
0:59:07.625017 PROGRESS: Extracting batch of 237192 precursors
0:59:07.719511 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:59:07.719686 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:59:07.719734 INFO: FWHM in RT is 2.76 seconds, sigma is 0.36
0:59:07.719777 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:59:07.720105 INFO: Starting candidate selection
0:59:14.754009 INFO: Starting candidate scoring
0:59:18.508135 INFO: Finished candidate processing
0:59:18.508250 INFO: Collecting candidate features
0:59:19.572329 WARNING: intensity_correlation has 119 NaNs ( 0.03 % out of 467679)
0:59:19.594485 INFO: Collecting fragment features
0:59:20.021823 INFO: Finished candidate scoring
0:59:20.536860 PROGRESS: === Extracted 467679 precursors and 3696963 fragments ===
0:59:20.537504 INFO: performing precursor FDR with 47 features
0:59:20.537553 INFO: Decoy channel: -1
0:59:20.537589 INFO: Competetive: True
0:59:20.712012 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:20.821256 WARNING: dropped 54 target PSMs due to missing features
0:59:20.821414 WARNING: dropped 65 decoy PSMs due to missing features
0:59:31.411907 INFO: Test AUC: 0.578
0:59:31.412241 INFO: Train AUC: 0.593
0:59:31.412303 INFO: AUC difference: 2.48%
0:59:31.556035 INFO: Resetting torch num_threads to 100
0:59:31.572775 INFO: === FDR correction performed with classifier version 9 ===
0:59:31.573969 PROGRESS: ============================= Precursor FDR =============================
0:59:31.574107 PROGRESS: Total precursors accumulated: 633
0:59:31.574196 PROGRESS: Target precursors: 576 (91.00%)
0:59:31.574268 PROGRESS: Decoy precursors: 57 (9.00%)
0:59:31.574333 PROGRESS: 
0:59:31.574397 PROGRESS: Precursor Summary:
0:59:31.575721 PROGRESS: Channel   0:	 0.05 FDR:   330; 0.01 FDR:   208; 0.001 FDR:   137
0:59:31.575848 PROGRESS: 
0:59:31.575926 PROGRESS: Protein Summary:
0:59:31.577320 PROGRESS: Channel   0:	 0.05 FDR:   315; 0.01 FDR:   199; 0.001 FDR:   133
0:59:31.577441 PROGRESS: =========================================================================
0:59:31.596226 INFO: fragments_df_filtered: 2074
0:59:32.083036 INFO: calibration group: precursor, fitting mz estimator 
0:59:32.344534 INFO: calibration group: precursor, fitting rt estimator 
0:59:32.536606 INFO: calibration group: fragment, fitting mz estimator 
0:59:32.844517 INFO: calibration group: precursor, predicting mz
0:59:32.925665 INFO: calibration group: precursor, predicting rt
0:59:33.171412 INFO: calibration group: fragment, predicting mz
0:59:33.731694 INFO: === checking if optimization conditions were reached ===
0:59:33.732115 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
0:59:33.734842 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 83.9750.
0:59:33.734920 INFO: ==============================================
0:59:33.735079 INFO: Starting optimization step 11.
0:59:33.735162 PROGRESS: === Extracting elution groups 0 to 120000 ===
0:59:33.735255 PROGRESS: Extracting batch of 237192 precursors
0:59:33.828569 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:59:33.828756 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:59:33.828839 INFO: FWHM in RT is 2.79 seconds, sigma is 0.36
0:59:33.828878 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:59:33.829247 INFO: Starting candidate selection
0:59:40.840729 INFO: Starting candidate scoring
0:59:44.137004 INFO: Finished candidate processing
0:59:44.137308 INFO: Collecting candidate features
0:59:45.238408 WARNING: intensity_correlation has 106 NaNs ( 0.02 % out of 467786)
0:59:45.258920 INFO: Collecting fragment features
0:59:45.664265 INFO: Finished candidate scoring
0:59:46.304729 PROGRESS: === Extracted 467786 precursors and 3701388 fragments ===
0:59:46.305539 INFO: performing precursor FDR with 47 features
0:59:46.305607 INFO: Decoy channel: -1
0:59:46.305657 INFO: Competetive: True
0:59:46.556191 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:46.718295 WARNING: dropped 48 target PSMs due to missing features
0:59:46.718492 WARNING: dropped 58 decoy PSMs due to missing features
0:59:59.402548 INFO: Test AUC: 0.578
0:59:59.402942 INFO: Train AUC: 0.593
0:59:59.403021 INFO: AUC difference: 2.45%
0:59:59.644215 INFO: Resetting torch num_threads to 100
0:59:59.670623 INFO: === FDR correction performed with classifier version 9 ===
0:59:59.672392 PROGRESS: ============================= Precursor FDR =============================
0:59:59.672738 PROGRESS: Total precursors accumulated: 548
0:59:59.673045 PROGRESS: Target precursors: 499 (91.06%)
0:59:59.673352 PROGRESS: Decoy precursors: 49 (8.94%)
0:59:59.673639 PROGRESS: 
0:59:59.673922 PROGRESS: Precursor Summary:
0:59:59.676171 PROGRESS: Channel   0:	 0.05 FDR:   370; 0.01 FDR:   202; 0.001 FDR:   158
0:59:59.676522 PROGRESS: 
0:59:59.676836 PROGRESS: Protein Summary:
0:59:59.679363 PROGRESS: Channel   0:	 0.05 FDR:   352; 0.01 FDR:   195; 0.001 FDR:   152
0:59:59.679712 PROGRESS: =========================================================================
0:59:59.705192 INFO: fragments_df_filtered: 2097
1:00:00.374569 INFO: calibration group: precursor, fitting mz estimator 
1:00:00.855046 INFO: calibration group: precursor, fitting rt estimator 
1:00:01.318415 INFO: calibration group: fragment, fitting mz estimator 
1:00:01.972736 INFO: calibration group: precursor, predicting mz
1:00:02.167259 INFO: calibration group: precursor, predicting rt
1:00:02.489420 INFO: calibration group: fragment, predicting mz
1:00:03.100548 INFO: === checking if optimization conditions were reached ===
1:00:03.100997 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
1:00:03.103949 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 74.8916.
1:00:03.104029 INFO: ==============================================
1:00:03.104157 INFO: Starting optimization step 12.
1:00:03.104246 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:00:03.104346 PROGRESS: Extracting batch of 237192 precursors
1:00:03.202542 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:00:03.202728 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:00:03.202778 INFO: FWHM in RT is 2.76 seconds, sigma is 0.36
1:00:03.202808 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:00:03.203196 INFO: Starting candidate selection
1:00:11.881320 INFO: Starting candidate scoring
1:00:15.465492 INFO: Finished candidate processing
1:00:15.465762 INFO: Collecting candidate features
1:00:16.682961 WARNING: intensity_correlation has 141 NaNs ( 0.03 % out of 466800)
1:00:16.714264 INFO: Collecting fragment features
1:00:17.146677 INFO: Finished candidate scoring
1:00:17.724432 PROGRESS: === Extracted 466800 precursors and 3634302 fragments ===
1:00:17.725152 INFO: performing precursor FDR with 47 features
1:00:17.725226 INFO: Decoy channel: -1
1:00:17.725269 INFO: Competetive: True
1:00:17.982168 INFO: Setting torch num_threads to 2 for FDR classification task
1:00:18.149603 WARNING: dropped 70 target PSMs due to missing features
1:00:18.149809 WARNING: dropped 71 decoy PSMs due to missing features
1:00:30.233676 INFO: Test AUC: 0.573
1:00:30.234048 INFO: Train AUC: 0.592
1:00:30.234108 INFO: AUC difference: 3.19%
1:00:30.418689 INFO: Resetting torch num_threads to 100
1:00:30.445124 INFO: === FDR correction performed with classifier version 9 ===
1:00:30.447603 PROGRESS: ============================= Precursor FDR =============================
1:00:30.447783 PROGRESS: Total precursors accumulated: 529
1:00:30.447865 PROGRESS: Target precursors: 485 (91.68%)
1:00:30.447935 PROGRESS: Decoy precursors: 44 (8.32%)
1:00:30.447995 PROGRESS: 
1:00:30.448061 PROGRESS: Precursor Summary:
1:00:30.449350 PROGRESS: Channel   0:	 0.05 FDR:   341; 0.01 FDR:     1; 0.001 FDR:     1
1:00:30.449479 PROGRESS: 
1:00:30.449548 PROGRESS: Protein Summary:
1:00:30.451019 PROGRESS: Channel   0:	 0.05 FDR:   325; 0.01 FDR:     1; 0.001 FDR:     1
1:00:30.451144 PROGRESS: =========================================================================
1:00:31.176959 INFO: calibration group: precursor, predicting mz
1:00:31.532795 INFO: calibration group: precursor, predicting rt
1:00:31.864091 INFO: calibration group: fragment, predicting mz
1:00:32.827035 INFO: === skipping optimization until target number of precursors are found ===
1:00:32.827504 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1:00:32.827607 INFO: Starting optimization step 13.
1:00:32.827700 PROGRESS: === Extracting elution groups 120000 to 248000 ===
1:00:32.827837 PROGRESS: Extracting batch of 252997 precursors
1:00:32.937078 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:00:32.937279 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:00:32.937338 INFO: FWHM in RT is 2.76 seconds, sigma is 0.36
1:00:32.937378 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:00:32.937766 INFO: Starting candidate selection
1:00:41.408639 INFO: Starting candidate scoring
1:00:46.169221 INFO: Finished candidate processing
1:00:46.169375 INFO: Collecting candidate features
1:00:47.695522 WARNING: intensity_correlation has 138 NaNs ( 0.03 % out of 497625)
1:00:47.729609 INFO: Collecting fragment features
1:00:48.203577 INFO: Finished candidate scoring
1:00:49.401573 PROGRESS: === Extracted 964425 precursors and 7503630 fragments ===
1:00:49.551242 INFO: performing precursor FDR with 47 features
1:00:49.551572 INFO: Decoy channel: -1
1:00:49.551673 INFO: Competetive: True
1:00:50.316380 INFO: Setting torch num_threads to 2 for FDR classification task
1:00:50.642255 WARNING: dropped 155 target PSMs due to missing features
1:00:50.642585 WARNING: dropped 124 decoy PSMs due to missing features
1:01:17.982068 INFO: Test AUC: 0.579
1:01:17.982395 INFO: Train AUC: 0.588
1:01:17.982448 INFO: AUC difference: 1.50%
1:01:18.234087 INFO: Resetting torch num_threads to 100
1:01:18.349433 INFO: === FDR correction performed with classifier version 9 ===
1:01:18.351075 PROGRESS: ============================= Precursor FDR =============================
1:01:18.351239 PROGRESS: Total precursors accumulated: 1,272
1:01:18.351326 PROGRESS: Target precursors: 1,158 (91.04%)
1:01:18.351395 PROGRESS: Decoy precursors: 114 (8.96%)
1:01:18.351460 PROGRESS: 
1:01:18.351525 PROGRESS: Precursor Summary:
1:01:18.353348 PROGRESS: Channel   0:	 0.05 FDR:   814; 0.01 FDR:   412; 0.001 FDR:   275
1:01:18.353500 PROGRESS: 
1:01:18.353578 PROGRESS: Protein Summary:
1:01:18.355637 PROGRESS: Channel   0:	 0.05 FDR:   732; 0.01 FDR:   378; 0.001 FDR:   259
1:01:18.355794 PROGRESS: =========================================================================
1:01:18.482032 INFO: fragments_df_filtered: 4248
1:01:19.619247 INFO: calibration group: precursor, fitting mz estimator 
1:01:19.812936 INFO: calibration group: precursor, fitting rt estimator 
1:01:19.974003 INFO: calibration group: fragment, fitting mz estimator 
1:01:20.600198 INFO: calibration group: precursor, predicting mz
1:01:20.771919 INFO: calibration group: precursor, predicting rt
1:01:21.244754 INFO: calibration group: fragment, predicting mz
1:01:22.382820 INFO: === checking if optimization conditions were reached ===
1:01:22.383257 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 2 ===
1:01:22.386517 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 71.4213.
1:01:22.386607 INFO: ==============================================
1:01:22.386755 INFO: Starting optimization step 14.
1:01:22.386847 PROGRESS: === Extracting elution groups 0 to 248000 ===
1:01:22.386941 PROGRESS: Extracting batch of 490189 precursors
1:01:22.575024 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:01:22.575204 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:01:22.575254 INFO: FWHM in RT is 2.80 seconds, sigma is 0.36
1:01:22.575287 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:01:22.575638 INFO: Starting candidate selection
1:01:37.232555 INFO: Starting candidate scoring
1:01:43.138260 INFO: Finished candidate processing
1:01:43.138546 INFO: Collecting candidate features
1:01:45.231092 WARNING: intensity_correlation has 246 NaNs ( 0.03 % out of 964761)
1:01:45.267491 INFO: Collecting fragment features
1:01:45.878526 INFO: Finished candidate scoring
1:01:46.913146 PROGRESS: === Extracted 964761 precursors and 7515217 fragments ===
1:01:46.913719 INFO: performing precursor FDR with 47 features
1:01:46.913765 INFO: Decoy channel: -1
1:01:46.913789 INFO: Competetive: True
1:01:47.253857 INFO: Setting torch num_threads to 2 for FDR classification task
1:01:47.462490 WARNING: dropped 140 target PSMs due to missing features
1:01:47.462650 WARNING: dropped 106 decoy PSMs due to missing features
1:02:09.320454 INFO: Test AUC: 0.577
1:02:09.320817 INFO: Train AUC: 0.589
1:02:09.320869 INFO: AUC difference: 2.02%
1:02:09.491346 INFO: Resetting torch num_threads to 100
1:02:09.524739 INFO: === FDR correction performed with classifier version 9 ===
1:02:09.526057 PROGRESS: ============================= Precursor FDR =============================
1:02:09.526184 PROGRESS: Total precursors accumulated: 1,212
1:02:09.526274 PROGRESS: Target precursors: 1,107 (91.34%)
1:02:09.526349 PROGRESS: Decoy precursors: 105 (8.66%)
1:02:09.526418 PROGRESS: 
1:02:09.526483 PROGRESS: Precursor Summary:
1:02:09.527816 PROGRESS: Channel   0:	 0.05 FDR:   835; 0.01 FDR:   512; 0.001 FDR:   272
1:02:09.527930 PROGRESS: 
1:02:09.528008 PROGRESS: Protein Summary:
1:02:09.529466 PROGRESS: Channel   0:	 0.05 FDR:   751; 0.01 FDR:   467; 0.001 FDR:   255
1:02:09.529579 PROGRESS: =========================================================================
1:02:09.567557 INFO: fragments_df_filtered: 5000
1:02:10.054439 INFO: calibration group: precursor, fitting mz estimator 
1:02:10.211493 INFO: calibration group: precursor, fitting rt estimator 
1:02:10.371559 INFO: calibration group: fragment, fitting mz estimator 
1:02:10.996874 INFO: calibration group: precursor, predicting mz
1:02:11.053122 INFO: calibration group: precursor, predicting rt
1:02:11.271060 INFO: calibration group: fragment, predicting mz
1:02:11.831168 INFO: === checking if optimization conditions were reached ===
1:02:11.831694 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 2 ===
1:02:11.833183 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 71.4213 found after 12 searches.
1:02:11.833249 INFO: ==============================================
1:02:11.833378 PROGRESS: Optimization finished for rt_error.
1:02:12.335731 INFO: calibration group: precursor, predicting mz
1:02:12.477382 INFO: calibration group: precursor, predicting rt
1:02:12.718909 INFO: calibration group: fragment, predicting mz
1:02:13.285404 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:02:13.286021 PROGRESS: ==============================================
1:02:13.286315 PROGRESS: ms2_error      : 15.0000
1:02:13.286579 PROGRESS: ms1_error      : 10.0000
1:02:13.286835 PROGRESS: rt_error       : 71.4213
1:02:13.287070 PROGRESS: ==============================================
1:02:13.288782 INFO: calibration group: precursor, predicting mz
1:02:15.199241 INFO: calibration group: precursor, predicting rt
1:02:23.016179 INFO: calibration group: fragment, predicting mz
1:02:43.071223 PROGRESS: Extracting batch of 10183864 precursors
1:02:45.710896 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:02:45.711068 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:02:45.711114 INFO: FWHM in RT is 2.77 seconds, sigma is 0.36
1:02:45.711143 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:02:45.711565 INFO: Starting candidate selection
1:07:28.537459 INFO: Applying score cutoff of 32.591221002578735
1:07:29.400137 INFO: Removed 4370676 precursors with score below cutoff
1:07:32.800162 INFO: Starting candidate scoring
1:10:53.044916 INFO: Finished candidate processing
1:10:53.047067 INFO: Collecting candidate features
1:12:10.752133 WARNING: intensity_correlation has 459 NaNs ( 0.00 % out of 15941383)
1:12:11.372943 INFO: Collecting fragment features
1:12:23.151346 INFO: Finished candidate scoring
1:12:44.112915 INFO: === FDR correction performed with classifier version 24 ===
1:12:44.145873 INFO: performing precursor FDR with 47 features
1:12:44.146038 INFO: Decoy channel: -1
1:12:44.146086 INFO: Competetive: True
1:12:50.421429 INFO: Setting torch num_threads to 2 for FDR classification task
1:12:54.641165 WARNING: dropped 246 target PSMs due to missing features
1:12:54.641534 WARNING: dropped 213 decoy PSMs due to missing features
1:20:35.256540 INFO: Test AUC: 0.575
1:20:35.256830 INFO: Train AUC: 0.585
1:20:35.256877 INFO: AUC difference: 1.69%
1:20:36.623812 INFO: Resetting torch num_threads to 100
1:20:37.071485 INFO: Removing fragments below FDR threshold
1:20:38.604692 PROGRESS: ============================= Precursor FDR =============================
1:20:38.605169 PROGRESS: Total precursors accumulated: 11,761
1:20:38.605300 PROGRESS: Target precursors: 11,645 (99.01%)
1:20:38.605413 PROGRESS: Decoy precursors: 116 (0.99%)
1:20:38.605520 PROGRESS: 
1:20:38.605626 PROGRESS: Precursor Summary:
1:20:38.615390 PROGRESS: Channel   0:	 0.05 FDR: 11,645; 0.01 FDR: 11,645; 0.001 FDR: 7,397
1:20:38.615768 PROGRESS: 
1:20:38.616023 PROGRESS: Protein Summary:
1:20:38.629156 PROGRESS: Channel   0:	 0.05 FDR: 5,031; 0.01 FDR: 5,031; 0.001 FDR: 3,616
1:20:38.629653 PROGRESS: =========================================================================
1:20:39.359133 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:20:40.059356 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:20:40.059792 INFO: Quantification results path: run_output_Astral/alphadia_1.10_default/library/quant
1:20:40.060003 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2 at run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:20:40.061322 INFO: Initializing RawFileManager
1:21:36.405349 INFO: Determining DIA cycle
1:21:36.424623 INFO: Found cycle with start 0.00 min and length 303.
1:21:36.688931 INFO: RT (min)            : 0.0 - 26.9
1:21:36.689094 INFO: RT duration (sec)   : 1611.2
1:21:36.689139 INFO: RT duration (min)   : 26.9
1:21:36.689183 INFO: Cycle len (scans)   : 303
1:21:36.689223 INFO: Cycle len (sec)     : 1.65
1:21:36.689270 INFO: Number of cycles    : 978
1:21:36.689318 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:21:38.656410 INFO: Initializing CalibrationManager
1:21:38.656809 INFO: Loading calibration config
1:21:38.658395 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'}]
1:21:38.658546 INFO: Calibration group :fragment, found 1 estimator(s)
1:21:38.658688 INFO: Calibration group :precursor, found 3 estimator(s)
1:21:38.658813 INFO: Disabling ion mobility calibration
1:21:38.658860 INFO: removed mobility estimator from group precursor
1:21:38.659056 INFO: Initializing OptimizationManager
1:21:38.659228 INFO: initial parameter: ms1_error = 30
1:21:38.659318 INFO: initial parameter: ms2_error = 30
1:21:38.659392 INFO: initial parameter: rt_error = 805.6019897460938
1:21:38.659458 INFO: initial parameter: mobility_error = 0.1
1:21:38.659523 INFO: initial parameter: column_type = library
1:21:38.659590 INFO: initial parameter: num_candidates = 1
1:21:38.659657 INFO: initial parameter: classifier_version = -1
1:21:38.659722 INFO: initial parameter: fwhm_rt = 5
1:21:38.659799 INFO: initial parameter: fwhm_mobility = 0.01
1:21:38.659863 INFO: initial parameter: score_cutoff = 0
1:21:38.659956 INFO: Initializing TimingManager
1:21:38.660043 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:21:38.660187 INFO: FDRManager not loaded from disk.
1:21:38.660225 INFO: Initializing FDRManager
1:21:38.660279 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:21:40.261703 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
1:21:43.273121 PROGRESS: Starting initial search for precursors.
1:21:43.777548 INFO: Starting optimization step 0.
1:21:43.777896 PROGRESS: === Extracting elution groups 0 to 8000 ===
1:21:43.777997 PROGRESS: Extracting batch of 15808 precursors
1:21:43.786363 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:21:43.786613 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:21:43.786670 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:21:43.786708 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:21:43.787225 INFO: Starting candidate selection
1:21:46.073238 INFO: Starting candidate scoring
1:21:46.714071 INFO: Finished candidate processing
1:21:46.714207 INFO: Collecting candidate features
1:21:46.782180 INFO: Collecting fragment features
1:21:46.802779 INFO: Finished candidate scoring
1:21:46.815600 PROGRESS: === Extracted 15765 precursors and 154717 fragments ===
1:21:46.816151 INFO: performing precursor FDR with 47 features
1:21:46.816203 INFO: Decoy channel: -1
1:21:46.816235 INFO: Competetive: True
1:21:46.824198 INFO: Setting torch num_threads to 2 for FDR classification task
1:21:47.043760 INFO: Test AUC: 0.508
1:21:47.043928 INFO: Train AUC: 0.538
1:21:47.043973 INFO: AUC difference: 5.49%
1:21:47.044007 WARNING: AUC difference > 5%. This may indicate overfitting.
1:21:47.178212 INFO: Resetting torch num_threads to 100
1:21:47.180095 INFO: === FDR correction performed with classifier version -1 ===
1:21:47.181134 PROGRESS: ============================= Precursor FDR =============================
1:21:47.181260 PROGRESS: Total precursors accumulated: 1
1:21:47.181342 PROGRESS: Target precursors: 1 (100.00%)
1:21:47.181412 PROGRESS: Decoy precursors: 0 (0.00%)
1:21:47.181476 PROGRESS: 
1:21:47.181538 PROGRESS: Precursor Summary:
1:21:47.182929 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:21:47.183063 PROGRESS: 
1:21:47.183176 PROGRESS: Protein Summary:
1:21:47.184719 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:21:47.184859 PROGRESS: =========================================================================
1:21:47.355915 INFO: Starting optimization step 1.
1:21:47.356278 PROGRESS: === Extracting elution groups 8000 to 24000 ===
1:21:47.356374 PROGRESS: Extracting batch of 31655 precursors
1:21:47.371296 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:21:47.371482 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:21:47.371531 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:21:47.371565 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:21:47.371874 INFO: Starting candidate selection
1:21:51.224848 INFO: Starting candidate scoring
1:21:51.564476 INFO: Finished candidate processing
1:21:51.564672 INFO: Collecting candidate features
1:21:51.682304 INFO: Collecting fragment features
1:21:51.721606 INFO: Finished candidate scoring
1:21:51.773219 PROGRESS: === Extracted 47346 precursors and 466196 fragments ===
1:21:51.789894 INFO: performing precursor FDR with 47 features
1:21:51.790073 INFO: Decoy channel: -1
1:21:51.790107 INFO: Competetive: True
1:21:51.831084 INFO: Setting torch num_threads to 2 for FDR classification task
1:21:52.826452 INFO: Test AUC: 0.553
1:21:52.826692 INFO: Train AUC: 0.562
1:21:52.826749 INFO: AUC difference: 1.72%
1:21:52.960692 INFO: Resetting torch num_threads to 100
1:21:52.966328 INFO: === FDR correction performed with classifier version -1 ===
1:21:52.967559 PROGRESS: ============================= Precursor FDR =============================
1:21:52.967704 PROGRESS: Total precursors accumulated: 4
1:21:52.967813 PROGRESS: Target precursors: 4 (100.00%)
1:21:52.967898 PROGRESS: Decoy precursors: 0 (0.00%)
1:21:52.967976 PROGRESS: 
1:21:52.968048 PROGRESS: Precursor Summary:
1:21:52.969359 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
1:21:52.969497 PROGRESS: 
1:21:52.969584 PROGRESS: Protein Summary:
1:21:52.971003 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
1:21:52.971143 PROGRESS: =========================================================================
1:21:53.218680 INFO: Starting optimization step 2.
1:21:53.219079 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1:21:53.219189 PROGRESS: Extracting batch of 63250 precursors
1:21:53.245979 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:21:53.246151 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:21:53.246202 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:21:53.246235 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:21:53.246606 INFO: Starting candidate selection
1:21:57.533005 INFO: Starting candidate scoring
1:21:58.053528 INFO: Finished candidate processing
1:21:58.053762 INFO: Collecting candidate features
1:21:58.215084 INFO: Collecting fragment features
1:21:58.263459 INFO: Finished candidate scoring
1:21:58.331399 PROGRESS: === Extracted 110427 precursors and 1087786 fragments ===
1:21:58.345516 INFO: performing precursor FDR with 47 features
1:21:58.345671 INFO: Decoy channel: -1
1:21:58.345704 INFO: Competetive: True
1:21:58.399001 INFO: Setting torch num_threads to 2 for FDR classification task
1:22:00.909147 INFO: Test AUC: 0.557
1:22:00.909324 INFO: Train AUC: 0.585
1:22:00.909368 INFO: AUC difference: 4.85%
1:22:01.073378 INFO: Resetting torch num_threads to 100
1:22:01.085062 INFO: === FDR correction performed with classifier version -1 ===
1:22:01.086401 PROGRESS: ============================= Precursor FDR =============================
1:22:01.086541 PROGRESS: Total precursors accumulated: 3
1:22:01.086653 PROGRESS: Target precursors: 3 (100.00%)
1:22:01.086752 PROGRESS: Decoy precursors: 0 (0.00%)
1:22:01.086836 PROGRESS: 
1:22:01.086912 PROGRESS: Precursor Summary:
1:22:01.088524 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1:22:01.088653 PROGRESS: 
1:22:01.088738 PROGRESS: Protein Summary:
1:22:01.090504 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1:22:01.090672 PROGRESS: =========================================================================
1:22:01.456125 INFO: Starting optimization step 3.
1:22:01.456573 PROGRESS: === Extracting elution groups 56000 to 120000 ===
1:22:01.456745 PROGRESS: Extracting batch of 126479 precursors
1:22:01.507185 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:22:01.507353 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:22:01.507423 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:22:01.507465 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:22:01.507824 INFO: Starting candidate selection
1:22:11.739360 INFO: Starting candidate scoring
1:22:13.191490 INFO: Finished candidate processing
1:22:13.191830 INFO: Collecting candidate features
1:22:13.640221 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 126188)
1:22:13.655441 INFO: Collecting fragment features
1:22:13.794992 INFO: Finished candidate scoring
1:22:14.110683 PROGRESS: === Extracted 236615 precursors and 2328651 fragments ===
1:22:14.155665 INFO: performing precursor FDR with 47 features
1:22:14.156024 INFO: Decoy channel: -1
1:22:14.156127 INFO: Competetive: True
1:22:14.354331 INFO: Setting torch num_threads to 2 for FDR classification task
1:22:14.424152 WARNING: dropped 1 target PSMs due to missing features
1:22:19.991888 INFO: Test AUC: 0.564
1:22:19.992321 INFO: Train AUC: 0.591
1:22:19.992438 INFO: AUC difference: 4.47%
1:22:20.161270 INFO: Resetting torch num_threads to 100
1:22:20.191220 INFO: === FDR correction performed with classifier version -1 ===
1:22:20.192665 PROGRESS: ============================= Precursor FDR =============================
1:22:20.192996 PROGRESS: Total precursors accumulated: 12
1:22:20.193274 PROGRESS: Target precursors: 11 (91.67%)
1:22:20.193536 PROGRESS: Decoy precursors: 1 (8.33%)
1:22:20.193785 PROGRESS: 
1:22:20.194041 PROGRESS: Precursor Summary:
1:22:20.195639 PROGRESS: Channel   0:	 0.05 FDR:     6; 0.01 FDR:     6; 0.001 FDR:     6
1:22:20.195991 PROGRESS: 
1:22:20.196261 PROGRESS: Protein Summary:
1:22:20.197843 PROGRESS: Channel   0:	 0.05 FDR:     6; 0.01 FDR:     6; 0.001 FDR:     6
1:22:20.198144 PROGRESS: =========================================================================
1:22:20.902419 INFO: Starting optimization step 4.
1:22:20.903611 PROGRESS: === Extracting elution groups 120000 to 248000 ===
1:22:20.904027 PROGRESS: Extracting batch of 252997 precursors
1:22:21.009083 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:22:21.009463 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:22:21.009615 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:22:21.009727 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:22:21.010185 INFO: Starting candidate selection
1:22:36.856460 INFO: Starting candidate scoring
1:22:39.108769 INFO: Finished candidate processing
1:22:39.108998 INFO: Collecting candidate features
1:22:39.992672 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 252339)
1:22:40.012057 INFO: Collecting fragment features
1:22:40.282553 INFO: Finished candidate scoring
1:22:40.763929 PROGRESS: === Extracted 488954 precursors and 4810213 fragments ===
1:22:40.845806 INFO: performing precursor FDR with 47 features
1:22:40.846207 INFO: Decoy channel: -1
1:22:40.846305 INFO: Competetive: True
1:22:41.242202 INFO: Setting torch num_threads to 2 for FDR classification task
1:22:41.420588 WARNING: dropped 1 target PSMs due to missing features
1:22:41.420935 WARNING: dropped 2 decoy PSMs due to missing features
1:22:52.747419 INFO: Test AUC: 0.568
1:22:52.747635 INFO: Train AUC: 0.590
1:22:52.747679 INFO: AUC difference: 3.80%
1:22:52.908583 INFO: Resetting torch num_threads to 100
1:22:53.044683 INFO: === FDR correction performed with classifier version -1 ===
1:22:53.046156 PROGRESS: ============================= Precursor FDR =============================
1:22:53.046455 PROGRESS: Total precursors accumulated: 6
1:22:53.046699 PROGRESS: Target precursors: 6 (100.00%)
1:22:53.046955 PROGRESS: Decoy precursors: 0 (0.00%)
1:22:53.047184 PROGRESS: 
1:22:53.047408 PROGRESS: Precursor Summary:
1:22:53.048944 PROGRESS: Channel   0:	 0.05 FDR:     6; 0.01 FDR:     6; 0.001 FDR:     6
1:22:53.049227 PROGRESS: 
1:22:53.049476 PROGRESS: Protein Summary:
1:22:53.051165 PROGRESS: Channel   0:	 0.05 FDR:     6; 0.01 FDR:     6; 0.001 FDR:     6
1:22:53.051463 PROGRESS: =========================================================================
1:22:54.154565 INFO: Starting optimization step 5.
1:22:54.155385 PROGRESS: === Extracting elution groups 248000 to 504000 ===
1:22:54.155689 PROGRESS: Extracting batch of 506030 precursors
1:22:54.358141 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:22:54.358481 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:22:54.358700 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:22:54.358873 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:22:54.359465 INFO: Starting candidate selection
1:23:23.161980 INFO: Starting candidate scoring
1:23:26.031399 INFO: Finished candidate processing
1:23:26.031515 INFO: Collecting candidate features
1:23:27.416727 WARNING: intensity_correlation has 6 NaNs ( 0.00 % out of 504798)
1:23:27.437248 INFO: Collecting fragment features
1:23:27.823943 INFO: Finished candidate scoring
1:23:28.899592 PROGRESS: === Extracted 993752 precursors and 9778333 fragments ===
1:23:29.070474 INFO: performing precursor FDR with 47 features
1:23:29.070791 INFO: Decoy channel: -1
1:23:29.070892 INFO: Competetive: True
1:23:29.844458 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:30.205060 WARNING: dropped 3 target PSMs due to missing features
1:23:30.205382 WARNING: dropped 6 decoy PSMs due to missing features
1:23:54.577893 INFO: Test AUC: 0.573
1:23:54.578178 INFO: Train AUC: 0.587
1:23:54.578228 INFO: AUC difference: 2.48%
1:23:54.824400 INFO: Resetting torch num_threads to 100
1:23:55.029228 INFO: === FDR correction performed with classifier version -1 ===
1:23:55.031002 PROGRESS: ============================= Precursor FDR =============================
1:23:55.031319 PROGRESS: Total precursors accumulated: 33
1:23:55.031588 PROGRESS: Target precursors: 31 (93.94%)
1:23:55.031847 PROGRESS: Decoy precursors: 2 (6.06%)
1:23:55.032089 PROGRESS: 
1:23:55.032324 PROGRESS: Precursor Summary:
1:23:55.033832 PROGRESS: Channel   0:	 0.05 FDR:    31; 0.01 FDR:    10; 0.001 FDR:    10
1:23:55.034138 PROGRESS: 
1:23:55.034407 PROGRESS: Protein Summary:
1:23:55.035978 PROGRESS: Channel   0:	 0.05 FDR:    31; 0.01 FDR:    10; 0.001 FDR:    10
1:23:55.036365 PROGRESS: =========================================================================
1:23:56.693739 INFO: Starting optimization step 6.
1:23:56.694567 PROGRESS: === Extracting elution groups 504000 to 1016000 ===
1:23:56.694849 PROGRESS: Extracting batch of 1011982 precursors
1:23:57.083910 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:23:57.086600 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:23:57.086691 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:23:57.086727 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:23:57.087215 INFO: Starting candidate selection
1:24:49.857537 INFO: Starting candidate scoring
1:24:57.558588 INFO: Finished candidate processing
1:24:57.558837 INFO: Collecting candidate features
1:25:00.574961 WARNING: intensity_correlation has 9 NaNs ( 0.00 % out of 1009506)
1:25:00.614170 INFO: Collecting fragment features
1:25:01.447994 INFO: Finished candidate scoring
1:25:03.020255 PROGRESS: === Extracted 2003258 precursors and 19709295 fragments ===
1:25:03.374024 INFO: performing precursor FDR with 47 features
1:25:03.374366 INFO: Decoy channel: -1
1:25:03.374469 INFO: Competetive: True
1:25:04.998871 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:05.725325 WARNING: dropped 8 target PSMs due to missing features
1:25:05.725649 WARNING: dropped 10 decoy PSMs due to missing features
1:25:51.439898 INFO: Test AUC: 0.579
1:25:51.440538 INFO: Train AUC: 0.587
1:25:51.440692 INFO: AUC difference: 1.30%
1:25:51.838349 INFO: Resetting torch num_threads to 100
1:25:52.118485 INFO: === FDR correction performed with classifier version -1 ===
1:25:52.120224 PROGRESS: ============================= Precursor FDR =============================
1:25:52.120538 PROGRESS: Total precursors accumulated: 681
1:25:52.120767 PROGRESS: Target precursors: 627 (92.07%)
1:25:52.120985 PROGRESS: Decoy precursors: 54 (7.93%)
1:25:52.121196 PROGRESS: 
1:25:52.121404 PROGRESS: Precursor Summary:
1:25:52.122943 PROGRESS: Channel   0:	 0.05 FDR:   348; 0.01 FDR:     9; 0.001 FDR:     9
1:25:52.123214 PROGRESS: 
1:25:52.123438 PROGRESS: Protein Summary:
1:25:52.125105 PROGRESS: Channel   0:	 0.05 FDR:   319; 0.01 FDR:     9; 0.001 FDR:     9
1:25:52.125388 PROGRESS: =========================================================================
1:25:55.271047 INFO: Starting optimization step 7.
1:25:55.271705 PROGRESS: === Extracting elution groups 1016000 to 2040000 ===
1:25:55.272017 PROGRESS: Extracting batch of 2023798 precursors
1:25:56.145137 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:25:56.145495 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:25:56.145629 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:25:56.145738 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:25:56.146281 INFO: Starting candidate selection
1:27:31.887341 INFO: Starting candidate scoring
1:27:44.868865 INFO: Finished candidate processing
1:27:44.869221 INFO: Collecting candidate features
1:27:51.091908 WARNING: intensity_correlation has 20 NaNs ( 0.00 % out of 2018639)
1:27:51.204931 INFO: Collecting fragment features
1:27:53.603079 INFO: Finished candidate scoring
1:27:58.680573 PROGRESS: === Extracted 4021897 precursors and 39561291 fragments ===
1:27:59.391310 INFO: performing precursor FDR with 47 features
1:27:59.391653 INFO: Decoy channel: -1
1:27:59.391783 INFO: Competetive: True
1:28:02.578331 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:04.012362 WARNING: dropped 19 target PSMs due to missing features
1:28:04.012702 WARNING: dropped 19 decoy PSMs due to missing features
1:29:42.489973 INFO: Test AUC: 0.584
1:29:42.490264 INFO: Train AUC: 0.590
1:29:42.490326 INFO: AUC difference: 0.96%
1:29:43.055819 INFO: Resetting torch num_threads to 100
1:29:43.713783 INFO: === FDR correction performed with classifier version -1 ===
1:29:43.717757 PROGRESS: ============================= Precursor FDR =============================
1:29:43.718024 PROGRESS: Total precursors accumulated: 3,075
1:29:43.718176 PROGRESS: Target precursors: 2,831 (92.07%)
1:29:43.718293 PROGRESS: Decoy precursors: 244 (7.93%)
1:29:43.718402 PROGRESS: 
1:29:43.718507 PROGRESS: Precursor Summary:
1:29:43.722301 PROGRESS: Channel   0:	 0.05 FDR: 2,215; 0.01 FDR: 1,586; 0.001 FDR: 1,147
1:29:43.722496 PROGRESS: 
1:29:43.722596 PROGRESS: Protein Summary:
1:29:43.726223 PROGRESS: Channel   0:	 0.05 FDR: 1,728; 0.01 FDR: 1,217; 0.001 FDR:   910
1:29:43.726398 PROGRESS: =========================================================================
1:29:44.315099 INFO: fragments_df_filtered: 5000
1:29:46.259650 INFO: calibration group: precursor, fitting mz estimator 
1:29:46.571315 INFO: calibration group: precursor, fitting rt estimator 
1:29:46.809672 INFO: calibration group: fragment, fitting mz estimator 
1:29:47.613756 INFO: calibration group: precursor, predicting mz
1:29:47.948181 INFO: calibration group: precursor, predicting rt
1:29:48.802538 INFO: calibration group: fragment, predicting mz
1:29:50.758606 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:29:50.759266 INFO: Starting optimization step 8.
1:29:50.759552 PROGRESS: === Extracting elution groups 0 to 504000 ===
1:29:50.760010 PROGRESS: Extracting batch of 996219 precursors
1:29:51.155027 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:29:51.155198 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:51.155246 INFO: FWHM in RT is 2.90 seconds, sigma is 0.37
1:29:51.155300 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:29:51.155653 INFO: Starting candidate selection
1:30:51.188093 INFO: Starting candidate scoring
1:31:02.668103 INFO: Finished candidate processing
1:31:02.669103 INFO: Collecting candidate features
1:31:08.259517 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 1987498)
1:31:08.386728 INFO: Collecting fragment features
1:31:10.549309 INFO: Finished candidate scoring
1:31:13.349754 PROGRESS: === Extracted 1987498 precursors and 19291930 fragments ===
1:31:13.350961 INFO: performing precursor FDR with 47 features
1:31:13.351049 INFO: Decoy channel: -1
1:31:13.351092 INFO: Competetive: True
1:31:14.334033 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:14.891407 WARNING: dropped 2 decoy PSMs due to missing features
1:32:05.019039 INFO: Test AUC: 0.585
1:32:05.020489 INFO: Train AUC: 0.591
1:32:05.020557 INFO: AUC difference: 0.96%
1:32:05.368674 INFO: Resetting torch num_threads to 100
1:32:05.458725 INFO: === FDR correction performed with classifier version 7 ===
1:32:05.460355 PROGRESS: ============================= Precursor FDR =============================
1:32:05.460498 PROGRESS: Total precursors accumulated: 1,102
1:32:05.460585 PROGRESS: Target precursors: 1,012 (91.83%)
1:32:05.460682 PROGRESS: Decoy precursors: 90 (8.17%)
1:32:05.460815 PROGRESS: 
1:32:05.460935 PROGRESS: Precursor Summary:
1:32:05.462784 PROGRESS: Channel   0:	 0.05 FDR:   863; 0.01 FDR:   603; 0.001 FDR:   372
1:32:05.462907 PROGRESS: 
1:32:05.462993 PROGRESS: Protein Summary:
1:32:05.465129 PROGRESS: Channel   0:	 0.05 FDR:   767; 0.01 FDR:   531; 0.001 FDR:   335
1:32:05.465259 PROGRESS: =========================================================================
1:32:05.609548 INFO: fragments_df_filtered: 5000
1:32:06.803923 INFO: calibration group: precursor, fitting mz estimator 
1:32:07.030556 INFO: calibration group: precursor, fitting rt estimator 
1:32:07.241586 INFO: calibration group: fragment, fitting mz estimator 
1:32:08.064300 INFO: calibration group: precursor, predicting mz
1:32:08.248855 INFO: calibration group: precursor, predicting rt
1:32:08.738971 INFO: calibration group: fragment, predicting mz
1:32:09.796569 INFO: === checking if optimization conditions were reached ===
1:32:09.800831 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1:32:09.802480 PROGRESS: ❌ ms1_error      : 13.8233 > 10.0000 or insufficient steps taken.
1:32:09.802629 INFO: ==============================================
1:32:09.802978 INFO: Starting optimization step 9.
1:32:09.803264 PROGRESS: === Extracting elution groups 0 to 248000 ===
1:32:09.803547 PROGRESS: Extracting batch of 490189 precursors
1:32:10.244234 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:32:10.244569 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:10.244708 INFO: FWHM in RT is 2.90 seconds, sigma is 0.37
1:32:10.244810 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:10.245311 INFO: Starting candidate selection
1:32:39.707818 INFO: Starting candidate scoring
1:32:47.093049 INFO: Finished candidate processing
1:32:47.093338 INFO: Collecting candidate features
1:32:49.663879 WARNING: intensity_correlation has 8 NaNs ( 0.00 % out of 977323)
1:32:49.706195 INFO: Collecting fragment features
1:32:50.477071 INFO: Finished candidate scoring
1:32:51.574340 PROGRESS: === Extracted 977323 precursors and 8386152 fragments ===
1:32:51.575073 INFO: performing precursor FDR with 47 features
1:32:51.575151 INFO: Decoy channel: -1
1:32:51.575198 INFO: Competetive: True
1:32:52.078082 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:52.426597 WARNING: dropped 4 target PSMs due to missing features
1:32:52.426774 WARNING: dropped 4 decoy PSMs due to missing features
1:33:12.453704 INFO: Test AUC: 0.576
1:33:12.453983 INFO: Train AUC: 0.588
1:33:12.454033 INFO: AUC difference: 2.10%
1:33:12.694100 INFO: Resetting torch num_threads to 100
1:33:12.751677 INFO: === FDR correction performed with classifier version 8 ===
1:33:12.753152 PROGRESS: ============================= Precursor FDR =============================
1:33:12.753291 PROGRESS: Total precursors accumulated: 963
1:33:12.753372 PROGRESS: Target precursors: 879 (91.28%)
1:33:12.753440 PROGRESS: Decoy precursors: 84 (8.72%)
1:33:12.753499 PROGRESS: 
1:33:12.753556 PROGRESS: Precursor Summary:
1:33:12.755154 PROGRESS: Channel   0:	 0.05 FDR:   688; 0.01 FDR:   477; 0.001 FDR:   323
1:33:12.755266 PROGRESS: 
1:33:12.755339 PROGRESS: Protein Summary:
1:33:12.757162 PROGRESS: Channel   0:	 0.05 FDR:   627; 0.01 FDR:   435; 0.001 FDR:   301
1:33:12.757272 PROGRESS: =========================================================================
1:33:12.814629 INFO: fragments_df_filtered: 4699
1:33:13.546211 INFO: calibration group: precursor, fitting mz estimator 
1:33:13.638981 INFO: calibration group: precursor, fitting rt estimator 
1:33:13.771565 INFO: calibration group: fragment, fitting mz estimator 
1:33:14.404929 INFO: calibration group: precursor, predicting mz
1:33:14.479224 INFO: calibration group: precursor, predicting rt
1:33:14.708658 INFO: calibration group: fragment, predicting mz
1:33:15.167910 INFO: === checking if optimization conditions were reached ===
1:33:15.170988 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1:33:15.172440 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
1:33:15.172582 INFO: ==============================================
1:33:15.172880 PROGRESS: Optimization finished for ms2_error, ms1_error.
1:33:15.705289 INFO: calibration group: precursor, predicting mz
1:33:15.744888 INFO: calibration group: precursor, predicting rt
1:33:15.915689 INFO: calibration group: fragment, predicting mz
1:33:16.452694 INFO: Starting optimization step 0.
1:33:16.453060 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:33:16.453183 PROGRESS: Extracting batch of 237192 precursors
1:33:16.517826 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:33:16.517992 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:33:16.518048 INFO: FWHM in RT is 2.89 seconds, sigma is 0.37
1:33:16.518083 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:33:16.518461 INFO: Starting candidate selection
1:33:29.156108 INFO: Starting candidate scoring
1:33:31.708026 INFO: Finished candidate processing
1:33:31.708157 INFO: Collecting candidate features
1:33:33.645576 INFO: Collecting fragment features
1:33:33.942976 INFO: Finished candidate scoring
1:33:34.321178 PROGRESS: === Extracted 473012 precursors and 4055267 fragments ===
1:33:34.321566 INFO: performing precursor FDR with 47 features
1:33:34.321605 INFO: Decoy channel: -1
1:33:34.321629 INFO: Competetive: True
1:33:34.491824 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:44.269615 INFO: Test AUC: 0.579
1:33:44.269891 INFO: Train AUC: 0.597
1:33:44.269955 INFO: AUC difference: 3.11%
1:33:44.477407 INFO: Resetting torch num_threads to 100
1:33:44.502445 INFO: === FDR correction performed with classifier version 9 ===
1:33:44.503905 PROGRESS: ============================= Precursor FDR =============================
1:33:44.504061 PROGRESS: Total precursors accumulated: 540
1:33:44.504154 PROGRESS: Target precursors: 494 (91.48%)
1:33:44.504246 PROGRESS: Decoy precursors: 46 (8.52%)
1:33:44.504328 PROGRESS: 
1:33:44.504414 PROGRESS: Precursor Summary:
1:33:44.506174 PROGRESS: Channel   0:	 0.05 FDR:   335; 0.01 FDR:   205; 0.001 FDR:   109
1:33:44.506299 PROGRESS: 
1:33:44.506381 PROGRESS: Protein Summary:
1:33:44.508211 PROGRESS: Channel   0:	 0.05 FDR:   317; 0.01 FDR:   194; 0.001 FDR:   106
1:33:44.508344 PROGRESS: =========================================================================
1:33:44.533567 INFO: fragments_df_filtered: 2030
1:33:45.133097 INFO: calibration group: precursor, fitting mz estimator 
1:33:45.236702 INFO: calibration group: precursor, fitting rt estimator 
1:33:45.309791 INFO: calibration group: fragment, fitting mz estimator 
1:33:45.529892 INFO: calibration group: precursor, predicting mz
1:33:45.589305 INFO: calibration group: precursor, predicting rt
1:33:45.815518 INFO: calibration group: fragment, predicting mz
1:33:46.246921 INFO: === checking if optimization conditions were reached ===
1:33:46.247542 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:33:46.249820 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 380.1368.
1:33:46.249908 INFO: ==============================================
1:33:46.250063 INFO: Starting optimization step 1.
1:33:46.250161 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:33:46.250261 PROGRESS: Extracting batch of 237192 precursors
1:33:46.354808 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:33:46.354999 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:33:46.355057 INFO: FWHM in RT is 2.79 seconds, sigma is 0.36
1:33:46.355091 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:33:46.355466 INFO: Starting candidate selection
1:33:55.971289 INFO: Starting candidate scoring
1:33:59.819420 INFO: Finished candidate processing
1:33:59.819616 INFO: Collecting candidate features
1:34:01.151597 WARNING: intensity_correlation has 12 NaNs ( 0.00 % out of 472705)
1:34:01.183829 INFO: Collecting fragment features
1:34:01.592424 INFO: Finished candidate scoring
1:34:02.094751 PROGRESS: === Extracted 472705 precursors and 4021854 fragments ===
1:34:02.097801 INFO: performing precursor FDR with 47 features
1:34:02.097884 INFO: Decoy channel: -1
1:34:02.097925 INFO: Competetive: True
1:34:02.356679 INFO: Setting torch num_threads to 2 for FDR classification task
1:34:02.551757 WARNING: dropped 8 target PSMs due to missing features
1:34:02.551946 WARNING: dropped 4 decoy PSMs due to missing features
1:34:14.904555 INFO: Test AUC: 0.577
1:34:14.906073 INFO: Train AUC: 0.596
1:34:14.906142 INFO: AUC difference: 3.25%
1:34:15.089540 INFO: Resetting torch num_threads to 100
1:34:15.115430 INFO: === FDR correction performed with classifier version 9 ===
1:34:15.116858 PROGRESS: ============================= Precursor FDR =============================
1:34:15.117044 PROGRESS: Total precursors accumulated: 525
1:34:15.117124 PROGRESS: Target precursors: 477 (90.86%)
1:34:15.117191 PROGRESS: Decoy precursors: 48 (9.14%)
1:34:15.117255 PROGRESS: 
1:34:15.117317 PROGRESS: Precursor Summary:
1:34:15.118937 PROGRESS: Channel   0:	 0.05 FDR:   362; 0.01 FDR:   228; 0.001 FDR:   158
1:34:15.119063 PROGRESS: 
1:34:15.119138 PROGRESS: Protein Summary:
1:34:15.120804 PROGRESS: Channel   0:	 0.05 FDR:   341; 0.01 FDR:   217; 0.001 FDR:   152
1:34:15.120926 PROGRESS: =========================================================================
1:34:15.148651 INFO: fragments_df_filtered: 2284
1:34:15.763768 INFO: calibration group: precursor, fitting mz estimator 
1:34:15.906133 INFO: calibration group: precursor, fitting rt estimator 
1:34:16.001063 INFO: calibration group: fragment, fitting mz estimator 
1:34:16.192538 INFO: calibration group: precursor, predicting mz
1:34:16.345009 INFO: calibration group: precursor, predicting rt
1:34:16.538793 INFO: calibration group: fragment, predicting mz
1:34:17.053667 INFO: === checking if optimization conditions were reached ===
1:34:17.054011 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:34:17.056434 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 287.8724.
1:34:17.056498 INFO: ==============================================
1:34:17.056628 INFO: Starting optimization step 2.
1:34:17.056713 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:34:17.056804 PROGRESS: Extracting batch of 237192 precursors
1:34:17.194874 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:34:17.195026 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:34:17.195075 INFO: FWHM in RT is 2.75 seconds, sigma is 0.35
1:34:17.195106 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:34:17.195423 INFO: Starting candidate selection
1:34:26.684543 INFO: Starting candidate scoring
1:34:31.129923 INFO: Finished candidate processing
1:34:31.130067 INFO: Collecting candidate features
1:34:32.469068 WARNING: intensity_correlation has 26 NaNs ( 0.01 % out of 471372)
1:34:32.504738 INFO: Collecting fragment features
1:34:32.949152 INFO: Finished candidate scoring
1:34:33.640181 PROGRESS: === Extracted 471372 precursors and 3942486 fragments ===
1:34:33.640845 INFO: performing precursor FDR with 47 features
1:34:33.640904 INFO: Decoy channel: -1
1:34:33.640941 INFO: Competetive: True
1:34:33.898894 INFO: Setting torch num_threads to 2 for FDR classification task
1:34:34.076925 WARNING: dropped 17 target PSMs due to missing features
1:34:34.077142 WARNING: dropped 9 decoy PSMs due to missing features
1:34:43.489331 INFO: Test AUC: 0.578
1:34:43.491730 INFO: Train AUC: 0.595
1:34:43.491826 INFO: AUC difference: 2.83%
1:34:43.674956 INFO: Resetting torch num_threads to 100
1:34:43.700785 INFO: === FDR correction performed with classifier version 9 ===
1:34:43.702047 PROGRESS: ============================= Precursor FDR =============================
1:34:43.702171 PROGRESS: Total precursors accumulated: 520
1:34:43.702249 PROGRESS: Target precursors: 477 (91.73%)
1:34:43.702315 PROGRESS: Decoy precursors: 43 (8.27%)
1:34:43.702376 PROGRESS: 
1:34:43.702437 PROGRESS: Precursor Summary:
1:34:43.703871 PROGRESS: Channel   0:	 0.05 FDR:   348; 0.01 FDR:   218; 0.001 FDR:   202
1:34:43.703989 PROGRESS: 
1:34:43.704061 PROGRESS: Protein Summary:
1:34:43.705610 PROGRESS: Channel   0:	 0.05 FDR:   323; 0.01 FDR:   204; 0.001 FDR:   190
1:34:43.705723 PROGRESS: =========================================================================
1:34:43.733150 INFO: fragments_df_filtered: 2181
1:34:44.185828 INFO: calibration group: precursor, fitting mz estimator 
1:34:44.300074 INFO: calibration group: precursor, fitting rt estimator 
1:34:44.457411 INFO: calibration group: fragment, fitting mz estimator 
1:34:44.709181 INFO: calibration group: precursor, predicting mz
1:34:44.855469 INFO: calibration group: precursor, predicting rt
1:34:45.063192 INFO: calibration group: fragment, predicting mz
1:34:45.537389 INFO: === checking if optimization conditions were reached ===
1:34:45.537833 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:34:45.541672 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 193.8506.
1:34:45.541778 INFO: ==============================================
1:34:45.541952 INFO: Starting optimization step 3.
1:34:45.542082 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:34:45.542372 PROGRESS: Extracting batch of 237192 precursors
1:34:45.636934 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:34:45.637264 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:34:45.637380 INFO: FWHM in RT is 2.74 seconds, sigma is 0.35
1:34:45.637483 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:34:45.638014 INFO: Starting candidate selection
1:34:53.322009 INFO: Starting candidate scoring
1:34:56.586113 INFO: Finished candidate processing
1:34:56.586383 INFO: Collecting candidate features
1:34:57.847759 WARNING: intensity_correlation has 70 NaNs ( 0.01 % out of 469871)
1:34:57.868554 INFO: Collecting fragment features
1:34:58.168624 INFO: Finished candidate scoring
1:34:58.450174 PROGRESS: === Extracted 469871 precursors and 3859017 fragments ===
1:34:58.450889 INFO: performing precursor FDR with 47 features
1:34:58.450935 INFO: Decoy channel: -1
1:34:58.450966 INFO: Competetive: True
1:34:58.629465 INFO: Setting torch num_threads to 2 for FDR classification task
1:34:58.745640 WARNING: dropped 36 target PSMs due to missing features
1:34:58.745808 WARNING: dropped 34 decoy PSMs due to missing features
1:35:09.074042 INFO: Test AUC: 0.578
1:35:09.074231 INFO: Train AUC: 0.593
1:35:09.074278 INFO: AUC difference: 2.42%
1:35:09.257467 INFO: Resetting torch num_threads to 100
1:35:09.284879 INFO: === FDR correction performed with classifier version 9 ===
1:35:09.286301 PROGRESS: ============================= Precursor FDR =============================
1:35:09.286584 PROGRESS: Total precursors accumulated: 535
1:35:09.286820 PROGRESS: Target precursors: 488 (91.21%)
1:35:09.287041 PROGRESS: Decoy precursors: 47 (8.79%)
1:35:09.287256 PROGRESS: 
1:35:09.287469 PROGRESS: Precursor Summary:
1:35:09.289093 PROGRESS: Channel   0:	 0.05 FDR:   355; 0.01 FDR:   268; 0.001 FDR:   241
1:35:09.289377 PROGRESS: 
1:35:09.289599 PROGRESS: Protein Summary:
1:35:09.291392 PROGRESS: Channel   0:	 0.05 FDR:   332; 0.01 FDR:   252; 0.001 FDR:   228
1:35:09.291687 PROGRESS: =========================================================================
1:35:09.320886 INFO: fragments_df_filtered: 2565
1:35:09.932174 INFO: calibration group: precursor, fitting mz estimator 
1:35:10.204444 INFO: calibration group: precursor, fitting rt estimator 
1:35:10.390493 INFO: calibration group: fragment, fitting mz estimator 
1:35:10.759782 INFO: calibration group: precursor, predicting mz
1:35:10.874464 INFO: calibration group: precursor, predicting rt
1:35:11.204831 INFO: calibration group: fragment, predicting mz
1:35:11.784413 INFO: === checking if optimization conditions were reached ===
1:35:11.784975 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:35:11.788619 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 189.3735.
1:35:11.788698 INFO: ==============================================
1:35:11.788852 INFO: Starting optimization step 4.
1:35:11.788950 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:35:11.789055 PROGRESS: Extracting batch of 237192 precursors
1:35:12.085324 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:35:12.085510 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:35:12.085562 INFO: FWHM in RT is 2.64 seconds, sigma is 0.34
1:35:12.085591 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:35:12.086039 INFO: Starting candidate selection
1:35:21.284855 INFO: Starting candidate scoring
1:35:24.966235 INFO: Finished candidate processing
1:35:24.966356 INFO: Collecting candidate features
1:35:25.892606 WARNING: intensity_correlation has 69 NaNs ( 0.01 % out of 469981)
1:35:25.913626 INFO: Collecting fragment features
1:35:26.216209 INFO: Finished candidate scoring
1:35:26.493641 PROGRESS: === Extracted 469981 precursors and 3853925 fragments ===
1:35:26.494204 INFO: performing precursor FDR with 47 features
1:35:26.494247 INFO: Decoy channel: -1
1:35:26.494278 INFO: Competetive: True
1:35:26.669855 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:26.771667 WARNING: dropped 41 target PSMs due to missing features
1:35:26.771839 WARNING: dropped 28 decoy PSMs due to missing features
1:35:38.112679 INFO: Test AUC: 0.578
1:35:38.112947 INFO: Train AUC: 0.594
1:35:38.112998 INFO: AUC difference: 2.63%
1:35:38.295311 INFO: Resetting torch num_threads to 100
1:35:38.320768 INFO: === FDR correction performed with classifier version 9 ===
1:35:38.322018 PROGRESS: ============================= Precursor FDR =============================
1:35:38.322170 PROGRESS: Total precursors accumulated: 541
1:35:38.322262 PROGRESS: Target precursors: 493 (91.13%)
1:35:38.322338 PROGRESS: Decoy precursors: 48 (8.87%)
1:35:38.322411 PROGRESS: 
1:35:38.322525 PROGRESS: Precursor Summary:
1:35:38.323999 PROGRESS: Channel   0:	 0.05 FDR:   350; 0.01 FDR:   202; 0.001 FDR:    18
1:35:38.324401 PROGRESS: 
1:35:38.324650 PROGRESS: Protein Summary:
1:35:38.326488 PROGRESS: Channel   0:	 0.05 FDR:   328; 0.01 FDR:   193; 0.001 FDR:    18
1:35:38.326795 PROGRESS: =========================================================================
1:35:38.352494 INFO: fragments_df_filtered: 2080
1:35:38.980174 INFO: calibration group: precursor, fitting mz estimator 
1:35:39.189794 INFO: calibration group: precursor, fitting rt estimator 
1:35:39.338705 INFO: calibration group: fragment, fitting mz estimator 
1:35:39.666800 INFO: calibration group: precursor, predicting mz
1:35:39.786841 INFO: calibration group: precursor, predicting rt
1:35:40.042720 INFO: calibration group: fragment, predicting mz
1:35:40.708888 INFO: === checking if optimization conditions were reached ===
1:35:40.709318 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1:35:40.710965 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 193.8506 found after 5 searches.
1:35:40.711028 INFO: ==============================================
1:35:40.711149 PROGRESS: Optimization finished for rt_error.
1:35:41.263791 INFO: calibration group: precursor, predicting mz
1:35:41.355207 INFO: calibration group: precursor, predicting rt
1:35:41.672415 INFO: calibration group: fragment, predicting mz
1:35:42.211011 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:35:42.211451 PROGRESS: ==============================================
1:35:42.211845 PROGRESS: ms2_error      : 15.0000
1:35:42.212141 PROGRESS: ms1_error      : 10.0000
1:35:42.212444 PROGRESS: rt_error       : 193.8506
1:35:42.212723 PROGRESS: ==============================================
1:35:42.215377 INFO: calibration group: precursor, predicting mz
1:35:44.484888 INFO: calibration group: precursor, predicting rt
1:35:52.678648 INFO: calibration group: fragment, predicting mz
1:36:12.709817 PROGRESS: Extracting batch of 10183864 precursors
1:36:16.142913 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:36:16.143105 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:36:16.143172 INFO: FWHM in RT is 2.64 seconds, sigma is 0.34
1:36:16.143212 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:36:16.143755 INFO: Starting candidate selection
1:41:28.476922 INFO: Applying score cutoff of 42.02928744506836
1:41:29.347224 INFO: Removed 5259322 precursors with score below cutoff
1:41:32.997944 INFO: Starting candidate scoring
1:42:59.916570 INFO: Finished candidate processing
1:42:59.916958 INFO: Collecting candidate features
1:43:36.126971 WARNING: intensity_correlation has 78 NaNs ( 0.00 % out of 15057801)
1:43:36.841534 INFO: Collecting fragment features
1:43:51.011412 INFO: Finished candidate scoring
1:44:12.889457 INFO: === FDR correction performed with classifier version 13 ===
1:44:12.906324 INFO: performing precursor FDR with 47 features
1:44:12.906661 INFO: Decoy channel: -1
1:44:12.906772 INFO: Competetive: True
1:44:20.032274 INFO: Setting torch num_threads to 2 for FDR classification task
1:44:24.210508 WARNING: dropped 41 target PSMs due to missing features
1:44:24.210708 WARNING: dropped 37 decoy PSMs due to missing features
1:50:31.347733 INFO: Test AUC: 0.575
1:50:31.348108 INFO: Train AUC: 0.585
1:50:31.348179 INFO: AUC difference: 1.74%
1:50:32.812449 INFO: Resetting torch num_threads to 100
1:50:33.380883 INFO: Removing fragments below FDR threshold
1:50:34.615153 PROGRESS: ============================= Precursor FDR =============================
1:50:34.615612 PROGRESS: Total precursors accumulated: 13,076
1:50:34.615703 PROGRESS: Target precursors: 12,947 (99.01%)
1:50:34.615795 PROGRESS: Decoy precursors: 129 (0.99%)
1:50:34.615863 PROGRESS: 
1:50:34.615924 PROGRESS: Precursor Summary:
1:50:34.624464 PROGRESS: Channel   0:	 0.05 FDR: 12,947; 0.01 FDR: 12,947; 0.001 FDR: 6,263
1:50:34.624831 PROGRESS: 
1:50:34.624922 PROGRESS: Protein Summary:
1:50:34.637974 PROGRESS: Channel   0:	 0.05 FDR: 5,403; 0.01 FDR: 5,403; 0.001 FDR: 3,270
1:50:34.638326 PROGRESS: =========================================================================
1:50:35.332878 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:50:36.182585 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:50:36.182870 INFO: Quantification results path: run_output_Astral/alphadia_1.10_default/library/quant
1:50:36.182998 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3 at run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:50:36.183941 INFO: Initializing RawFileManager
1:51:21.378241 INFO: Determining DIA cycle
1:51:21.397331 INFO: Found cycle with start 0.00 min and length 303.
1:51:21.658219 INFO: RT (min)            : 0.0 - 26.9
1:51:21.658410 INFO: RT duration (sec)   : 1611.2
1:51:21.658519 INFO: RT duration (min)   : 26.9
1:51:21.658622 INFO: Cycle len (scans)   : 303
1:51:21.658715 INFO: Cycle len (sec)     : 1.65
1:51:21.658808 INFO: Number of cycles    : 977
1:51:21.658902 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:51:23.339130 INFO: Initializing CalibrationManager
1:51:23.339927 INFO: Loading calibration config
1:51:23.341078 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'}]
1:51:23.341405 INFO: Calibration group :fragment, found 1 estimator(s)
1:51:23.341733 INFO: Calibration group :precursor, found 3 estimator(s)
1:51:23.342059 INFO: Disabling ion mobility calibration
1:51:23.342182 INFO: removed mobility estimator from group precursor
1:51:23.342587 INFO: Initializing OptimizationManager
1:51:23.343077 INFO: initial parameter: ms1_error = 30
1:51:23.343389 INFO: initial parameter: ms2_error = 30
1:51:23.343672 INFO: initial parameter: rt_error = 805.6004638671875
1:51:23.343963 INFO: initial parameter: mobility_error = 0.1
1:51:23.344241 INFO: initial parameter: column_type = library
1:51:23.344504 INFO: initial parameter: num_candidates = 1
1:51:23.344750 INFO: initial parameter: classifier_version = -1
1:51:23.344995 INFO: initial parameter: fwhm_rt = 5
1:51:23.345240 INFO: initial parameter: fwhm_mobility = 0.01
1:51:23.345475 INFO: initial parameter: score_cutoff = 0
1:51:23.345771 INFO: Initializing TimingManager
1:51:23.346065 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:51:23.346420 INFO: FDRManager not loaded from disk.
1:51:23.346534 INFO: Initializing FDRManager
1:51:23.346671 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:51:25.398005 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
1:51:28.148800 PROGRESS: Starting initial search for precursors.
1:51:28.650568 INFO: Starting optimization step 0.
1:51:28.650887 PROGRESS: === Extracting elution groups 0 to 8000 ===
1:51:28.650988 PROGRESS: Extracting batch of 15808 precursors
1:51:28.658634 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:51:28.658768 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:51:28.658818 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:51:28.658850 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:51:28.659250 INFO: Starting candidate selection
1:51:30.378532 INFO: Starting candidate scoring
1:51:30.540460 INFO: Finished candidate processing
1:51:30.540591 INFO: Collecting candidate features
1:51:30.598002 INFO: Collecting fragment features
1:51:30.618163 INFO: Finished candidate scoring
1:51:30.629904 PROGRESS: === Extracted 15768 precursors and 155250 fragments ===
1:51:30.630424 INFO: performing precursor FDR with 47 features
1:51:30.630471 INFO: Decoy channel: -1
1:51:30.630501 INFO: Competetive: True
1:51:30.639644 INFO: Setting torch num_threads to 2 for FDR classification task
1:51:30.845948 INFO: Test AUC: 0.516
1:51:30.846112 INFO: Train AUC: 0.554
1:51:30.846151 INFO: AUC difference: 6.86%
1:51:30.846183 WARNING: AUC difference > 5%. This may indicate overfitting.
1:51:30.971342 INFO: Resetting torch num_threads to 100
1:51:30.973208 INFO: === FDR correction performed with classifier version -1 ===
1:51:30.974204 PROGRESS: ============================= Precursor FDR =============================
1:51:30.974329 PROGRESS: Total precursors accumulated: 4
1:51:30.974410 PROGRESS: Target precursors: 4 (100.00%)
1:51:30.974478 PROGRESS: Decoy precursors: 0 (0.00%)
1:51:30.974540 PROGRESS: 
1:51:30.974599 PROGRESS: Precursor Summary:
1:51:30.975906 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
1:51:30.976020 PROGRESS: 
1:51:30.976094 PROGRESS: Protein Summary:
1:51:30.977506 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
1:51:30.977623 PROGRESS: =========================================================================
1:51:31.137180 INFO: Starting optimization step 1.
1:51:31.137501 PROGRESS: === Extracting elution groups 8000 to 24000 ===
1:51:31.137599 PROGRESS: Extracting batch of 31655 precursors
1:51:31.151175 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:51:31.151330 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:51:31.151372 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:51:31.151403 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:51:31.151669 INFO: Starting candidate selection
1:51:34.159017 INFO: Starting candidate scoring
1:51:34.655539 INFO: Finished candidate processing
1:51:34.655681 INFO: Collecting candidate features
1:51:34.749127 INFO: Collecting fragment features
1:51:34.780884 INFO: Finished candidate scoring
1:51:34.815051 PROGRESS: === Extracted 47346 precursors and 466985 fragments ===
1:51:34.823231 INFO: performing precursor FDR with 47 features
1:51:34.823344 INFO: Decoy channel: -1
1:51:34.823386 INFO: Competetive: True
1:51:34.855075 INFO: Setting torch num_threads to 2 for FDR classification task
1:51:36.086308 INFO: Test AUC: 0.546
1:51:36.086480 INFO: Train AUC: 0.566
1:51:36.086520 INFO: AUC difference: 3.46%
1:51:36.217568 INFO: Resetting torch num_threads to 100
1:51:36.223658 INFO: === FDR correction performed with classifier version -1 ===
1:51:36.231663 PROGRESS: ============================= Precursor FDR =============================
1:51:36.232204 PROGRESS: Total precursors accumulated: 23,903
1:51:36.232299 PROGRESS: Target precursors: 13,908 (58.19%)
1:51:36.232373 PROGRESS: Decoy precursors: 9,995 (41.81%)
1:51:36.232440 PROGRESS: 
1:51:36.232503 PROGRESS: Precursor Summary:
1:51:36.234157 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:51:36.234290 PROGRESS: 
1:51:36.234472 PROGRESS: Protein Summary:
1:51:36.236132 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:51:36.236259 PROGRESS: =========================================================================
1:51:36.466534 INFO: Starting optimization step 2.
1:51:36.466903 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1:51:36.466997 PROGRESS: Extracting batch of 63250 precursors
1:51:36.493428 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:51:36.493713 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:51:36.493827 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:51:36.493924 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:51:36.494279 INFO: Starting candidate selection
1:51:41.751632 INFO: Starting candidate scoring
1:51:42.532470 INFO: Finished candidate processing
1:51:42.532628 INFO: Collecting candidate features
1:51:42.792053 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 63088)
1:51:42.801251 INFO: Collecting fragment features
1:51:42.872459 INFO: Finished candidate scoring
1:51:43.014776 PROGRESS: === Extracted 110434 precursors and 1089004 fragments ===
1:51:43.033928 INFO: performing precursor FDR with 47 features
1:51:43.034140 INFO: Decoy channel: -1
1:51:43.034175 INFO: Competetive: True
1:51:43.127220 INFO: Setting torch num_threads to 2 for FDR classification task
1:51:43.162294 WARNING: dropped 1 decoy PSMs due to missing features
1:51:46.642624 INFO: Test AUC: 0.556
1:51:46.642771 INFO: Train AUC: 0.578
1:51:46.642805 INFO: AUC difference: 3.91%
1:51:46.750417 INFO: Resetting torch num_threads to 100
1:51:46.760760 INFO: === FDR correction performed with classifier version -1 ===
1:51:46.773893 PROGRESS: ============================= Precursor FDR =============================
1:51:46.774229 PROGRESS: Total precursors accumulated: 55,581
1:51:46.774299 PROGRESS: Target precursors: 32,865 (59.13%)
1:51:46.774354 PROGRESS: Decoy precursors: 22,716 (40.87%)
1:51:46.774404 PROGRESS: 
1:51:46.774454 PROGRESS: Precursor Summary:
1:51:46.776009 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:51:46.776120 PROGRESS: 
1:51:46.776182 PROGRESS: Protein Summary:
1:51:46.777514 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:51:46.777615 PROGRESS: =========================================================================
1:51:47.096870 INFO: Starting optimization step 3.
1:51:47.097265 PROGRESS: === Extracting elution groups 56000 to 120000 ===
1:51:47.097356 PROGRESS: Extracting batch of 126479 precursors
1:51:47.132113 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:51:47.132266 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:51:47.132309 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:51:47.132336 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:51:47.132616 INFO: Starting candidate selection
1:51:54.208207 INFO: Starting candidate scoring
1:51:55.293471 INFO: Finished candidate processing
1:51:55.293612 INFO: Collecting candidate features
1:51:55.715072 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 126187)
1:51:55.742642 INFO: Collecting fragment features
1:51:55.889171 INFO: Finished candidate scoring
1:51:56.203905 PROGRESS: === Extracted 236621 precursors and 2331839 fragments ===
1:51:56.247046 INFO: performing precursor FDR with 47 features
1:51:56.247226 INFO: Decoy channel: -1
1:51:56.247272 INFO: Competetive: True
1:51:56.429838 INFO: Setting torch num_threads to 2 for FDR classification task
1:51:56.494970 WARNING: dropped 2 decoy PSMs due to missing features
1:52:05.755011 INFO: Test AUC: 0.563
1:52:05.755169 INFO: Train AUC: 0.587
1:52:05.755205 INFO: AUC difference: 4.06%
1:52:07.200991 INFO: Resetting torch num_threads to 100
1:52:07.306411 INFO: === FDR correction performed with classifier version -1 ===
1:52:07.353269 PROGRESS: ============================= Precursor FDR =============================
1:52:07.353684 PROGRESS: Total precursors accumulated: 118,188
1:52:07.353789 PROGRESS: Target precursors: 70,448 (59.61%)
1:52:07.353874 PROGRESS: Decoy precursors: 47,740 (40.39%)
1:52:07.353953 PROGRESS: 
1:52:07.354034 PROGRESS: Precursor Summary:
1:52:07.356739 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:52:07.356888 PROGRESS: 
1:52:07.356983 PROGRESS: Protein Summary:
1:52:07.359503 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:52:07.359643 PROGRESS: =========================================================================
1:52:08.035237 INFO: Starting optimization step 4.
1:52:08.035725 PROGRESS: === Extracting elution groups 120000 to 248000 ===
1:52:08.035963 PROGRESS: Extracting batch of 252997 precursors
1:52:08.136066 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:52:08.136334 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:52:08.136409 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:52:08.136455 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:52:08.137012 INFO: Starting candidate selection
1:52:21.185374 INFO: Starting candidate scoring
1:52:22.691869 INFO: Finished candidate processing
1:52:22.692036 INFO: Collecting candidate features
1:52:23.318830 WARNING: intensity_correlation has 5 NaNs ( 0.00 % out of 252338)
1:52:23.332242 INFO: Collecting fragment features
1:52:23.526733 INFO: Finished candidate scoring
1:52:23.928401 PROGRESS: === Extracted 488959 precursors and 4817130 fragments ===
1:52:23.992270 INFO: performing precursor FDR with 47 features
1:52:23.992411 INFO: Decoy channel: -1
1:52:23.992437 INFO: Competetive: True
1:52:24.243426 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:24.350152 WARNING: dropped 2 target PSMs due to missing features
1:52:24.350354 WARNING: dropped 5 decoy PSMs due to missing features
1:52:36.934643 INFO: Test AUC: 0.565
1:52:36.934955 INFO: Train AUC: 0.589
1:52:36.935014 INFO: AUC difference: 4.15%
1:52:37.111100 INFO: Resetting torch num_threads to 100
1:52:37.169120 INFO: === FDR correction performed with classifier version -1 ===
1:52:37.170743 PROGRESS: ============================= Precursor FDR =============================
1:52:37.171068 PROGRESS: Total precursors accumulated: 1
1:52:37.171379 PROGRESS: Target precursors: 1 (100.00%)
1:52:37.171637 PROGRESS: Decoy precursors: 0 (0.00%)
1:52:37.171900 PROGRESS: 
1:52:37.172169 PROGRESS: Precursor Summary:
1:52:37.173850 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:52:37.174169 PROGRESS: 
1:52:37.174432 PROGRESS: Protein Summary:
1:52:37.176220 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:52:37.176746 PROGRESS: =========================================================================
1:52:38.262443 INFO: Starting optimization step 5.
1:52:38.263075 PROGRESS: === Extracting elution groups 248000 to 504000 ===
1:52:38.263351 PROGRESS: Extracting batch of 506030 precursors
1:52:38.453632 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:52:38.453966 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:52:38.454081 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:52:38.454172 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:52:38.454618 INFO: Starting candidate selection
1:53:13.576387 INFO: Starting candidate scoring
1:53:16.981829 INFO: Finished candidate processing
1:53:16.981972 INFO: Collecting candidate features
1:53:19.017949 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 504790)
1:53:19.049611 INFO: Collecting fragment features
1:53:19.600452 INFO: Finished candidate scoring
1:53:20.534584 PROGRESS: === Extracted 993749 precursors and 9792451 fragments ===
1:53:20.711989 INFO: performing precursor FDR with 47 features
1:53:20.712168 INFO: Decoy channel: -1
1:53:20.712206 INFO: Competetive: True
1:53:21.353251 INFO: Setting torch num_threads to 2 for FDR classification task
1:53:21.592080 WARNING: dropped 3 target PSMs due to missing features
1:53:21.592391 WARNING: dropped 7 decoy PSMs due to missing features
1:53:44.483164 INFO: Test AUC: 0.571
1:53:44.483606 INFO: Train AUC: 0.586
1:53:44.483728 INFO: AUC difference: 2.55%
1:53:44.738704 INFO: Resetting torch num_threads to 100
1:53:44.845023 INFO: === FDR correction performed with classifier version -1 ===
1:53:44.846788 PROGRESS: ============================= Precursor FDR =============================
1:53:44.847191 PROGRESS: Total precursors accumulated: 12
1:53:44.847541 PROGRESS: Target precursors: 11 (91.67%)
1:53:44.847887 PROGRESS: Decoy precursors: 1 (8.33%)
1:53:44.848228 PROGRESS: 
1:53:44.848556 PROGRESS: Precursor Summary:
1:53:44.850263 PROGRESS: Channel   0:	 0.05 FDR:     7; 0.01 FDR:     7; 0.001 FDR:     7
1:53:44.850803 PROGRESS: 
1:53:44.851231 PROGRESS: Protein Summary:
1:53:44.853048 PROGRESS: Channel   0:	 0.05 FDR:     7; 0.01 FDR:     7; 0.001 FDR:     7
1:53:44.853489 PROGRESS: =========================================================================
1:53:46.541943 INFO: Starting optimization step 6.
1:53:46.543879 PROGRESS: === Extracting elution groups 504000 to 1016000 ===
1:53:46.544200 PROGRESS: Extracting batch of 1011982 precursors
1:53:46.934445 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:53:46.934796 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:53:46.934935 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:53:46.935030 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:53:46.935473 INFO: Starting candidate selection
1:54:46.366976 INFO: Starting candidate scoring
1:54:55.039529 INFO: Finished candidate processing
1:54:55.039976 INFO: Collecting candidate features
1:54:58.818012 WARNING: intensity_correlation has 13 NaNs ( 0.00 % out of 1009512)
1:54:58.883448 INFO: Collecting fragment features
1:55:00.003880 INFO: Finished candidate scoring
1:55:02.010153 PROGRESS: === Extracted 2003261 precursors and 19739428 fragments ===
1:55:02.362983 INFO: performing precursor FDR with 47 features
1:55:02.363328 INFO: Decoy channel: -1
1:55:02.363438 INFO: Competetive: True
1:55:03.631417 INFO: Setting torch num_threads to 2 for FDR classification task
1:55:04.330057 WARNING: dropped 8 target PSMs due to missing features
1:55:04.330380 WARNING: dropped 15 decoy PSMs due to missing features
1:58:36.309759 INFO: Test AUC: 0.576
1:58:36.310006 INFO: Train AUC: 0.586
1:58:36.310045 INFO: AUC difference: 1.63%
1:58:36.548051 INFO: Resetting torch num_threads to 100
1:58:36.706232 INFO: === FDR correction performed with classifier version -1 ===
1:58:36.928983 PROGRESS: ============================= Precursor FDR =============================
1:58:36.929377 PROGRESS: Total precursors accumulated: 931,502
1:58:36.929442 PROGRESS: Target precursors: 552,647 (59.33%)
1:58:36.929493 PROGRESS: Decoy precursors: 378,855 (40.67%)
1:58:36.929539 PROGRESS: 
1:58:36.929584 PROGRESS: Precursor Summary:
1:58:36.935071 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:58:36.935255 PROGRESS: 
1:58:36.935312 PROGRESS: Protein Summary:
1:58:36.940176 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:58:36.940320 PROGRESS: =========================================================================
1:58:39.401365 INFO: Starting optimization step 7.
1:58:39.401924 PROGRESS: === Extracting elution groups 1016000 to 2040000 ===
1:58:39.402102 PROGRESS: Extracting batch of 2023798 precursors
1:58:40.089593 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:58:40.089823 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:40.089889 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:58:40.089925 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:58:40.090435 INFO: Starting candidate selection
2:00:19.992542 INFO: Starting candidate scoring
2:00:32.840190 INFO: Finished candidate processing
2:00:32.840427 INFO: Collecting candidate features
2:00:39.656741 WARNING: intensity_correlation has 18 NaNs ( 0.00 % out of 2018585)
2:00:39.771267 INFO: Collecting fragment features
2:00:41.728166 INFO: Finished candidate scoring
2:00:46.626341 PROGRESS: === Extracted 4021846 precursors and 39625580 fragments ===
2:00:47.324226 INFO: performing precursor FDR with 47 features
2:00:47.324455 INFO: Decoy channel: -1
2:00:47.324494 INFO: Competetive: True
2:00:50.475902 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:51.702982 WARNING: dropped 17 target PSMs due to missing features
2:00:51.703460 WARNING: dropped 24 decoy PSMs due to missing features
2:02:17.268260 INFO: Test AUC: 0.586
2:02:17.268495 INFO: Train AUC: 0.589
2:02:17.268531 INFO: AUC difference: 0.55%
2:02:17.655456 INFO: Resetting torch num_threads to 100
2:02:17.895634 INFO: === FDR correction performed with classifier version -1 ===
2:02:17.896653 PROGRESS: ============================= Precursor FDR =============================
2:02:17.896795 PROGRESS: Total precursors accumulated: 12
2:02:17.896860 PROGRESS: Target precursors: 11 (91.67%)
2:02:17.896916 PROGRESS: Decoy precursors: 1 (8.33%)
2:02:17.896963 PROGRESS: 
2:02:17.897010 PROGRESS: Precursor Summary:
2:02:17.897962 PROGRESS: Channel   0:	 0.05 FDR:     9; 0.01 FDR:     9; 0.001 FDR:     9
2:02:17.898063 PROGRESS: 
2:02:17.898118 PROGRESS: Protein Summary:
2:02:17.899085 PROGRESS: Channel   0:	 0.05 FDR:     9; 0.01 FDR:     9; 0.001 FDR:     9
2:02:17.899193 PROGRESS: =========================================================================
2:02:21.329921 INFO: Starting optimization step 8.
2:02:21.330231 PROGRESS: === Extracting elution groups 2040000 to 4088000 ===
2:02:21.330322 PROGRESS: Extracting batch of 4047402 precursors
2:02:22.228590 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:02:22.228733 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:02:22.228772 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:02:22.228799 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:02:22.229110 INFO: Starting candidate selection
2:06:38.069480 INFO: Starting candidate scoring
2:07:07.449383 INFO: Finished candidate processing
2:07:07.449878 INFO: Collecting candidate features
2:07:33.977918 WARNING: intensity_correlation has 20 NaNs ( 0.00 % out of 4037144)
2:07:34.248902 INFO: Collecting fragment features
2:07:43.291832 INFO: Finished candidate scoring
2:08:13.430432 PROGRESS: === Extracted 8058990 precursors and 79408217 fragments ===
2:08:17.814884 INFO: performing precursor FDR with 47 features
2:08:17.819051 INFO: Decoy channel: -1
2:08:17.819133 INFO: Competetive: True
2:08:29.414271 INFO: Setting torch num_threads to 2 for FDR classification task
2:08:35.382639 WARNING: dropped 27 target PSMs due to missing features
2:08:35.384319 WARNING: dropped 34 decoy PSMs due to missing features
2:12:55.423071 INFO: Test AUC: 0.585
2:12:55.423362 INFO: Train AUC: 0.591
2:12:55.423405 INFO: AUC difference: 1.02%
2:12:56.063074 INFO: Resetting torch num_threads to 100
2:12:56.684897 INFO: === FDR correction performed with classifier version -1 ===
2:12:56.686077 PROGRESS: ============================= Precursor FDR =============================
2:12:56.686198 PROGRESS: Total precursors accumulated: 10
2:12:56.686260 PROGRESS: Target precursors: 10 (100.00%)
2:12:56.686311 PROGRESS: Decoy precursors: 0 (0.00%)
2:12:56.686357 PROGRESS: 
2:12:56.686401 PROGRESS: Precursor Summary:
2:12:56.687424 PROGRESS: Channel   0:	 0.05 FDR:    10; 0.01 FDR:    10; 0.001 FDR:    10
2:12:56.687515 PROGRESS: 
2:12:56.687572 PROGRESS: Protein Summary:
2:12:56.688647 PROGRESS: Channel   0:	 0.05 FDR:     9; 0.01 FDR:     9; 0.001 FDR:     9
2:12:56.688739 PROGRESS: =========================================================================
2:12:58.576612 INFO: Starting optimization step 9.
2:12:58.576901 PROGRESS: === Extracting elution groups 4088000 to 5152871 ===
2:12:58.576988 PROGRESS: Extracting batch of 2104463 precursors
2:12:59.039953 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:12:59.040094 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:12:59.040140 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:12:59.040163 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:12:59.040450 INFO: Starting candidate selection
2:15:09.541110 INFO: Starting candidate scoring
2:15:23.780161 INFO: Finished candidate processing
2:15:23.780508 INFO: Collecting candidate features
2:15:28.585772 WARNING: intensity_correlation has 16 NaNs ( 0.00 % out of 2098895)
2:15:28.657880 INFO: Collecting fragment features
2:15:30.224123 INFO: Finished candidate scoring
2:15:34.892883 PROGRESS: === Extracted 10157885 precursors and 100089667 fragments ===
2:15:36.245061 INFO: performing precursor FDR with 47 features
2:15:36.245205 INFO: Decoy channel: -1
2:15:36.245236 INFO: Competetive: True
2:15:40.884009 INFO: Setting torch num_threads to 2 for FDR classification task
2:15:43.052195 WARNING: dropped 33 target PSMs due to missing features
2:15:43.052348 WARNING: dropped 44 decoy PSMs due to missing features
2:18:49.161991 INFO: Test AUC: 0.584
2:18:49.162209 INFO: Train AUC: 0.593
2:18:49.162248 INFO: AUC difference: 1.45%
2:18:49.925228 INFO: Resetting torch num_threads to 100
2:18:50.564939 INFO: === FDR correction performed with classifier version -1 ===
2:18:50.567722 PROGRESS: ============================= Precursor FDR =============================
2:18:50.567900 PROGRESS: Total precursors accumulated: 6,089
2:18:50.567966 PROGRESS: Target precursors: 5,576 (91.57%)
2:18:50.569208 PROGRESS: Decoy precursors: 513 (8.43%)
2:18:50.569264 PROGRESS: 
2:18:50.569309 PROGRESS: Precursor Summary:
2:18:50.570304 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
2:18:50.570396 PROGRESS: 
2:18:50.570450 PROGRESS: Protein Summary:
2:18:50.571412 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
2:18:50.571509 PROGRESS: =========================================================================
2:18:50.572180 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:18:50.572269 PROGRESS: ==============================================
2:18:51.354325 INFO: fragments_df_filtered: 20
2:18:51.914048 WARNING: No more batches to process. Will proceed to extraction using best parameters available in optimization manager.
2:18:51.915626 WARNING: Using current optimal value for ms2_error: 30.00.
2:18:52.464851 WARNING: No more batches to process. Will proceed to extraction using best parameters available in optimization manager.
2:18:52.465135 WARNING: Using current optimal value for ms1_error: 30.00.
2:18:53.012649 WARNING: No more batches to process. Will proceed to extraction using best parameters available in optimization manager.
2:18:53.013687 WARNING: Using current optimal value for rt_error: 805.60.
2:18:53.021370 PROGRESS: ms2_error      : 30.0000
2:18:53.021609 PROGRESS: ms1_error      : 30.0000
2:18:53.021667 PROGRESS: rt_error       : 805.6005
2:18:53.021714 PROGRESS: ==============================================
2:18:53.022660 INFO: calibration group: precursor, predicting mz
2:18:53.022799 WARNING: mz prediction was skipped as it has not been fitted yet
2:18:53.022827 INFO: calibration group: precursor, predicting rt
2:18:53.022875 WARNING: rt prediction was skipped as it has not been fitted yet
2:18:53.022902 INFO: calibration group: fragment, predicting mz
2:18:53.022946 WARNING: mz prediction was skipped as it has not been fitted yet
2:18:53.022983 PROGRESS: Extracting batch of 10183864 precursors
2:18:55.219446 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:18:55.219586 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:18:55.219625 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:18:55.219648 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:18:55.219950 INFO: Starting candidate selection
2:29:11.312308 INFO: Applying score cutoff of 0
2:29:11.431535 INFO: Removed 0 precursors with score below cutoff
2:29:13.456812 INFO: Starting candidate scoring
2:30:24.264136 INFO: Finished candidate processing
2:30:24.265149 INFO: Collecting candidate features
2:30:42.905864 WARNING: intensity_correlation has 77 NaNs ( 0.00 % out of 10157885)
2:30:43.238097 INFO: Collecting fragment features
2:30:50.650745 INFO: Finished candidate scoring
2:31:02.999622 INFO: === FDR correction performed with classifier version 9 ===
2:31:03.019262 INFO: performing precursor FDR with 47 features
2:31:03.019348 INFO: Decoy channel: -1
2:31:03.019379 INFO: Competetive: True
2:31:06.477640 INFO: Setting torch num_threads to 2 for FDR classification task
2:31:08.198022 WARNING: dropped 33 target PSMs due to missing features
2:31:08.198256 WARNING: dropped 44 decoy PSMs due to missing features
2:34:32.158674 INFO: Test AUC: 0.587
2:34:32.158903 INFO: Train AUC: 0.593
2:34:32.158940 INFO: AUC difference: 1.05%
2:34:32.903512 INFO: Resetting torch num_threads to 100
2:34:33.240416 INFO: Removing fragments below FDR threshold
2:34:33.425713 PROGRESS: ============================= Precursor FDR =============================
2:34:33.426054 PROGRESS: Total precursors accumulated: 0
2:34:33.426129 PROGRESS: Target precursors: 0 (0.00%)
2:34:33.426182 PROGRESS: Decoy precursors: 0 (0.00%)
2:34:33.426227 PROGRESS: 
2:34:33.426273 PROGRESS: Precursor Summary:
2:34:33.426435 PROGRESS: 
2:34:33.426504 PROGRESS: Protein Summary:
2:34:33.426581 PROGRESS: =========================================================================
2:34:33.578315 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:34:34.222996 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:34:34.223170 INFO: Quantification results path: run_output_Astral/alphadia_1.10_default/library/quant
2:34:34.223270 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1 at run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:34:34.224046 INFO: Initializing RawFileManager
2:35:05.321657 INFO: Determining DIA cycle
2:35:05.337083 INFO: Found cycle with start 0.00 min and length 303.
2:35:05.521457 INFO: RT (min)            : 0.0 - 26.9
2:35:05.521548 INFO: RT duration (sec)   : 1611.2
2:35:05.521577 INFO: RT duration (min)   : 26.9
2:35:05.521599 INFO: Cycle len (scans)   : 303
2:35:05.521619 INFO: Cycle len (sec)     : 1.65
2:35:05.521638 INFO: Number of cycles    : 977
2:35:05.521658 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:35:06.639067 INFO: Initializing CalibrationManager
2:35:06.639369 INFO: Loading calibration config
2:35:06.639984 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed'], 'function': LOESSRegression()}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed'], 'function': LOESSRegression(n_kernels=2)}], 'name': 'precursor'}]
2:35:06.640090 INFO: Calibration group :fragment, found 1 estimator(s)
2:35:06.640173 INFO: Calibration group :precursor, found 3 estimator(s)
2:35:06.640244 INFO: Disabling ion mobility calibration
2:35:06.640273 INFO: removed mobility estimator from group precursor
2:35:06.640413 INFO: Initializing OptimizationManager
2:35:06.640527 INFO: initial parameter: ms1_error = 30
2:35:06.640597 INFO: initial parameter: ms2_error = 30
2:35:06.640646 INFO: initial parameter: rt_error = 805.5982666015625
2:35:06.640691 INFO: initial parameter: mobility_error = 0.1
2:35:06.640735 INFO: initial parameter: column_type = library
2:35:06.640776 INFO: initial parameter: num_candidates = 1
2:35:06.640818 INFO: initial parameter: classifier_version = -1
2:35:06.640859 INFO: initial parameter: fwhm_rt = 5
2:35:06.640903 INFO: initial parameter: fwhm_mobility = 0.01
2:35:06.640945 INFO: initial parameter: score_cutoff = 0
2:35:06.641005 INFO: Initializing TimingManager
2:35:06.641064 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:35:06.641167 INFO: FDRManager not loaded from disk.
2:35:06.641190 INFO: Initializing FDRManager
2:35:06.641223 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
2:35:08.133221 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
2:35:10.062493 PROGRESS: Starting initial search for precursors.
2:35:10.313340 INFO: Starting optimization step 0.
2:35:10.313568 PROGRESS: === Extracting elution groups 0 to 8000 ===
2:35:10.313645 PROGRESS: Extracting batch of 15808 precursors
2:35:10.317816 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:35:10.317879 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:35:10.317914 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:35:10.317935 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:35:10.318215 INFO: Starting candidate selection
2:35:11.393702 INFO: Starting candidate scoring
2:35:11.501962 INFO: Finished candidate processing
2:35:11.502070 INFO: Collecting candidate features
2:35:11.537606 INFO: Collecting fragment features
2:35:11.551904 INFO: Finished candidate scoring
2:35:11.560047 PROGRESS: === Extracted 15767 precursors and 156473 fragments ===
2:35:11.560401 INFO: performing precursor FDR with 47 features
2:35:11.560438 INFO: Decoy channel: -1
2:35:11.560460 INFO: Competetive: True
2:35:11.565432 INFO: Setting torch num_threads to 2 for FDR classification task
2:35:11.719333 INFO: Test AUC: 0.505
2:35:11.719434 INFO: Train AUC: 0.507
2:35:11.719466 INFO: AUC difference: 0.36%
2:35:11.799742 INFO: Resetting torch num_threads to 100
2:35:11.800828 INFO: === FDR correction performed with classifier version -1 ===
2:35:11.801553 PROGRESS: ============================= Precursor FDR =============================
2:35:11.801640 PROGRESS: Total precursors accumulated: 2
2:35:11.801698 PROGRESS: Target precursors: 2 (100.00%)
2:35:11.801747 PROGRESS: Decoy precursors: 0 (0.00%)
2:35:11.801790 PROGRESS: 
2:35:11.801833 PROGRESS: Precursor Summary:
2:35:11.802752 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
2:35:11.802837 PROGRESS: 
2:35:11.802892 PROGRESS: Protein Summary:
2:35:11.803924 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
2:35:11.804012 PROGRESS: =========================================================================
2:35:11.913684 INFO: Starting optimization step 1.
2:35:11.913958 PROGRESS: === Extracting elution groups 8000 to 24000 ===
2:35:11.914026 PROGRESS: Extracting batch of 31655 precursors
2:35:11.923123 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:35:11.923202 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:35:11.923234 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:35:11.923255 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:35:11.923440 INFO: Starting candidate selection
2:35:13.966748 INFO: Starting candidate scoring
2:35:14.205845 INFO: Finished candidate processing
2:35:14.206019 INFO: Collecting candidate features
2:35:14.303664 INFO: Collecting fragment features
2:35:14.338487 INFO: Finished candidate scoring
2:35:14.381934 PROGRESS: === Extracted 47342 precursors and 470310 fragments ===
2:35:14.391602 INFO: performing precursor FDR with 47 features
2:35:14.391724 INFO: Decoy channel: -1
2:35:14.391777 INFO: Competetive: True
2:35:14.427131 INFO: Setting torch num_threads to 2 for FDR classification task
2:35:15.640777 INFO: Test AUC: 0.553
2:35:15.640909 INFO: Train AUC: 0.553
2:35:15.640939 INFO: AUC difference: 0.11%
2:35:15.722143 INFO: Resetting torch num_threads to 100
2:35:15.724690 INFO: === FDR correction performed with classifier version -1 ===
2:35:15.725415 PROGRESS: ============================= Precursor FDR =============================
2:35:15.725512 PROGRESS: Total precursors accumulated: 4
2:35:15.725569 PROGRESS: Target precursors: 4 (100.00%)
2:35:15.725617 PROGRESS: Decoy precursors: 0 (0.00%)
2:35:15.725661 PROGRESS: 
2:35:15.725703 PROGRESS: Precursor Summary:
2:35:15.726611 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
2:35:15.726696 PROGRESS: 
2:35:15.726749 PROGRESS: Protein Summary:
2:35:15.727767 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
2:35:15.727854 PROGRESS: =========================================================================
2:35:15.879501 INFO: Starting optimization step 2.
2:35:15.879767 PROGRESS: === Extracting elution groups 24000 to 56000 ===
2:35:15.879838 PROGRESS: Extracting batch of 63250 precursors
2:35:15.893976 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:35:15.894096 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:35:15.894130 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:35:15.894151 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:35:15.894352 INFO: Starting candidate selection
2:35:20.017354 INFO: Starting candidate scoring
2:35:20.521487 INFO: Finished candidate processing
2:35:20.521609 INFO: Collecting candidate features
2:35:20.628970 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 63081)
2:35:20.634213 INFO: Collecting fragment features
2:35:20.679875 INFO: Finished candidate scoring
2:35:20.734721 PROGRESS: === Extracted 110423 precursors and 1097104 fragments ===
2:35:20.746473 INFO: performing precursor FDR with 47 features
2:35:20.746593 INFO: Decoy channel: -1
2:35:20.746620 INFO: Competetive: True
2:35:20.790532 INFO: Setting torch num_threads to 2 for FDR classification task
2:35:20.808471 WARNING: dropped 1 decoy PSMs due to missing features
2:35:22.515019 INFO: Test AUC: 0.552
2:35:22.515157 INFO: Train AUC: 0.577
2:35:22.515189 INFO: AUC difference: 4.36%
2:35:22.601527 INFO: Resetting torch num_threads to 100
2:35:22.607002 INFO: === FDR correction performed with classifier version -1 ===
2:35:22.607817 PROGRESS: ============================= Precursor FDR =============================
2:35:22.607920 PROGRESS: Total precursors accumulated: 1
2:35:22.607982 PROGRESS: Target precursors: 1 (100.00%)
2:35:22.608033 PROGRESS: Decoy precursors: 0 (0.00%)
2:35:22.608078 PROGRESS: 
2:35:22.608123 PROGRESS: Precursor Summary:
2:35:22.609038 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:35:22.609126 PROGRESS: 
2:35:22.609182 PROGRESS: Protein Summary:
2:35:22.610180 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:35:22.610269 PROGRESS: =========================================================================
2:35:22.847863 INFO: Starting optimization step 3.
2:35:22.848164 PROGRESS: === Extracting elution groups 56000 to 120000 ===
2:35:22.848233 PROGRESS: Extracting batch of 126479 precursors
2:35:22.879472 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:35:22.879604 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:35:22.879638 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:35:22.879660 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:35:22.879906 INFO: Starting candidate selection
2:35:30.908940 INFO: Starting candidate scoring
2:35:31.772727 INFO: Finished candidate processing
2:35:31.772839 INFO: Collecting candidate features
2:35:31.987772 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 126196)
2:35:31.995348 INFO: Collecting fragment features
2:35:32.086598 INFO: Finished candidate scoring
2:35:32.239232 PROGRESS: === Extracted 236619 precursors and 2349389 fragments ===
2:35:32.265026 INFO: performing precursor FDR with 47 features
2:35:32.265167 INFO: Decoy channel: -1
2:35:32.265196 INFO: Competetive: True
2:35:32.372196 INFO: Setting torch num_threads to 2 for FDR classification task
2:35:32.415049 WARNING: dropped 2 target PSMs due to missing features
2:35:32.415193 WARNING: dropped 2 decoy PSMs due to missing features
2:35:37.215356 INFO: Test AUC: 0.559
2:35:37.216353 INFO: Train AUC: 0.585
2:35:37.216396 INFO: AUC difference: 4.34%
2:35:37.318869 INFO: Resetting torch num_threads to 100
2:35:37.333040 INFO: === FDR correction performed with classifier version -1 ===
2:35:37.333995 PROGRESS: ============================= Precursor FDR =============================
2:35:37.334091 PROGRESS: Total precursors accumulated: 3
2:35:37.334151 PROGRESS: Target precursors: 3 (100.00%)
2:35:37.334203 PROGRESS: Decoy precursors: 0 (0.00%)
2:35:37.334247 PROGRESS: 
2:35:37.334291 PROGRESS: Precursor Summary:
2:35:37.335226 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
2:35:37.335311 PROGRESS: 
2:35:37.335366 PROGRESS: Protein Summary:
2:35:37.336374 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
2:35:37.336463 PROGRESS: =========================================================================
2:35:37.782845 INFO: Starting optimization step 4.
2:35:37.783163 PROGRESS: === Extracting elution groups 120000 to 248000 ===
2:35:37.783258 PROGRESS: Extracting batch of 252997 precursors
2:35:37.843388 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:35:37.843534 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:35:37.843591 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:35:37.843616 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:35:37.843929 INFO: Starting candidate selection
2:35:53.555586 INFO: Starting candidate scoring
2:35:55.238745 INFO: Finished candidate processing
2:35:55.238853 INFO: Collecting candidate features
2:35:55.718442 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 252330)
2:35:55.729366 INFO: Collecting fragment features
2:35:55.889266 INFO: Finished candidate scoring
2:35:56.190187 PROGRESS: === Extracted 488949 precursors and 4853892 fragments ===
2:35:56.246076 INFO: performing precursor FDR with 47 features
2:35:56.246226 INFO: Decoy channel: -1
2:35:56.246252 INFO: Competetive: True
2:35:56.478641 INFO: Setting torch num_threads to 2 for FDR classification task
2:35:56.592403 WARNING: dropped 5 target PSMs due to missing features
2:35:56.592536 WARNING: dropped 2 decoy PSMs due to missing features
2:36:05.133820 INFO: Test AUC: 0.567
2:36:05.134018 INFO: Train AUC: 0.586
2:36:05.134054 INFO: AUC difference: 3.09%
2:36:05.250497 INFO: Resetting torch num_threads to 100
2:36:05.289307 INFO: === FDR correction performed with classifier version -1 ===
2:36:05.290364 PROGRESS: ============================= Precursor FDR =============================
2:36:05.290482 PROGRESS: Total precursors accumulated: 17
2:36:05.290554 PROGRESS: Target precursors: 16 (94.12%)
2:36:05.290615 PROGRESS: Decoy precursors: 1 (5.88%)
2:36:05.290671 PROGRESS: 
2:36:05.290728 PROGRESS: Precursor Summary:
2:36:05.291794 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:36:05.291899 PROGRESS: 
2:36:05.291965 PROGRESS: Protein Summary:
2:36:05.293118 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:36:05.293221 PROGRESS: =========================================================================
2:36:06.053250 INFO: Starting optimization step 5.
2:36:06.053572 PROGRESS: === Extracting elution groups 248000 to 504000 ===
2:36:06.053659 PROGRESS: Extracting batch of 506030 precursors
2:36:06.167394 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:36:06.167533 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:36:06.167571 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:36:06.167595 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:36:06.167888 INFO: Starting candidate selection
2:36:37.627621 INFO: Starting candidate scoring
2:36:41.130301 INFO: Finished candidate processing
2:36:41.130503 INFO: Collecting candidate features
2:36:42.514057 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 504760)
2:36:42.532406 INFO: Collecting fragment features
2:36:42.901650 INFO: Finished candidate scoring
2:36:43.670545 PROGRESS: === Extracted 993709 precursors and 9865359 fragments ===
2:36:43.787269 INFO: performing precursor FDR with 47 features
2:36:43.787411 INFO: Decoy channel: -1
2:36:43.787439 INFO: Competetive: True
2:36:44.245800 INFO: Setting torch num_threads to 2 for FDR classification task
2:36:44.479402 WARNING: dropped 5 target PSMs due to missing features
2:36:44.479545 WARNING: dropped 6 decoy PSMs due to missing features
2:37:02.168488 INFO: Test AUC: 0.573
2:37:02.169374 INFO: Train AUC: 0.585
2:37:02.169416 INFO: AUC difference: 2.09%
2:37:02.329312 INFO: Resetting torch num_threads to 100
2:37:02.422542 INFO: === FDR correction performed with classifier version -1 ===
2:37:02.423568 PROGRESS: ============================= Precursor FDR =============================
2:37:02.423670 PROGRESS: Total precursors accumulated: 344
2:37:02.423733 PROGRESS: Target precursors: 314 (91.28%)
2:37:02.424675 PROGRESS: Decoy precursors: 30 (8.72%)
2:37:02.424729 PROGRESS: 
2:37:02.424781 PROGRESS: Precursor Summary:
2:37:02.425941 PROGRESS: Channel   0:	 0.05 FDR:   201; 0.01 FDR:     1; 0.001 FDR:     1
2:37:02.426053 PROGRESS: 
2:37:02.426109 PROGRESS: Protein Summary:
2:37:02.427140 PROGRESS: Channel   0:	 0.05 FDR:   191; 0.01 FDR:     1; 0.001 FDR:     1
2:37:02.427247 PROGRESS: =========================================================================
2:37:03.509310 INFO: Starting optimization step 6.
2:37:03.509672 PROGRESS: === Extracting elution groups 504000 to 1016000 ===
2:37:03.509766 PROGRESS: Extracting batch of 1011982 precursors
2:37:03.740496 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:37:03.740624 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:37:03.740665 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:37:03.740689 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:37:03.741039 INFO: Starting candidate selection
2:38:06.594667 INFO: Starting candidate scoring
2:38:14.547299 INFO: Finished candidate processing
2:38:14.547615 INFO: Collecting candidate features
2:38:17.067461 WARNING: intensity_correlation has 8 NaNs ( 0.00 % out of 1009450)
2:38:17.101451 INFO: Collecting fragment features
2:38:17.879983 INFO: Finished candidate scoring
2:38:19.568576 PROGRESS: === Extracted 2003159 precursors and 19884347 fragments ===
2:38:19.824043 INFO: performing precursor FDR with 47 features
2:38:19.824190 INFO: Decoy channel: -1
2:38:19.824219 INFO: Competetive: True
2:38:20.814817 INFO: Setting torch num_threads to 2 for FDR classification task
2:38:21.270895 WARNING: dropped 8 target PSMs due to missing features
2:38:21.271057 WARNING: dropped 11 decoy PSMs due to missing features
2:39:00.248293 INFO: Test AUC: 0.577
2:39:00.248624 INFO: Train AUC: 0.586
2:39:00.248664 INFO: AUC difference: 1.59%
2:39:00.489160 INFO: Resetting torch num_threads to 100
2:39:00.614061 INFO: === FDR correction performed with classifier version -1 ===
2:39:00.615705 PROGRESS: ============================= Precursor FDR =============================
2:39:00.615837 PROGRESS: Total precursors accumulated: 2,882
2:39:00.615899 PROGRESS: Target precursors: 2,635 (91.43%)
2:39:00.615950 PROGRESS: Decoy precursors: 247 (8.57%)
2:39:00.615995 PROGRESS: 
2:39:00.616040 PROGRESS: Precursor Summary:
2:39:00.617835 PROGRESS: Channel   0:	 0.05 FDR: 2,112; 0.01 FDR: 1,543; 0.001 FDR:   424
2:39:00.617933 PROGRESS: 
2:39:00.617988 PROGRESS: Protein Summary:
2:39:00.619843 PROGRESS: Channel   0:	 0.05 FDR: 1,569; 0.01 FDR: 1,156; 0.001 FDR:   370
2:39:00.619942 PROGRESS: =========================================================================
2:39:00.892801 INFO: fragments_df_filtered: 5000
2:39:01.746203 INFO: calibration group: precursor, fitting mz estimator 
2:39:01.842042 INFO: calibration group: precursor, fitting rt estimator 
2:39:01.939363 INFO: calibration group: fragment, fitting mz estimator 
2:39:02.357544 INFO: calibration group: precursor, predicting mz
2:39:02.437716 INFO: calibration group: precursor, predicting rt
2:39:02.779452 INFO: calibration group: fragment, predicting mz
2:39:03.517604 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:39:03.517920 INFO: Starting optimization step 7.
2:39:03.517998 PROGRESS: === Extracting elution groups 0 to 248000 ===
2:39:03.518075 PROGRESS: Extracting batch of 490189 precursors
2:39:03.632882 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:39:03.633034 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:39:03.633073 INFO: FWHM in RT is 3.04 seconds, sigma is 0.39
2:39:03.633099 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:39:03.633408 INFO: Starting candidate selection
2:39:26.689077 INFO: Starting candidate scoring
2:39:33.337790 INFO: Finished candidate processing
2:39:33.337959 INFO: Collecting candidate features
2:39:35.187067 WARNING: intensity_correlation has 5 NaNs ( 0.00 % out of 977945)
2:39:35.221506 INFO: Collecting fragment features
2:39:35.870826 INFO: Finished candidate scoring
2:39:36.773298 PROGRESS: === Extracted 977945 precursors and 9616262 fragments ===
2:39:36.773765 INFO: performing precursor FDR with 47 features
2:39:36.773806 INFO: Decoy channel: -1
2:39:36.773833 INFO: Competetive: True
2:39:37.156555 INFO: Setting torch num_threads to 2 for FDR classification task
2:39:37.359330 WARNING: dropped 4 target PSMs due to missing features
2:39:37.359910 WARNING: dropped 1 decoy PSMs due to missing features
2:39:54.106248 INFO: Test AUC: 0.578
2:39:54.106448 INFO: Train AUC: 0.589
2:39:54.106481 INFO: AUC difference: 1.88%
2:39:54.264788 INFO: Resetting torch num_threads to 100
2:39:54.394940 INFO: === FDR correction performed with classifier version 6 ===
2:39:54.396077 PROGRESS: ============================= Precursor FDR =============================
2:39:54.396230 PROGRESS: Total precursors accumulated: 1,020
2:39:54.396293 PROGRESS: Target precursors: 931 (91.27%)
2:39:54.396347 PROGRESS: Decoy precursors: 89 (8.73%)
2:39:54.396407 PROGRESS: 
2:39:54.396454 PROGRESS: Precursor Summary:
2:39:54.397657 PROGRESS: Channel   0:	 0.05 FDR:   712; 0.01 FDR:   536; 0.001 FDR:   381
2:39:54.397763 PROGRESS: 
2:39:54.397817 PROGRESS: Protein Summary:
2:39:54.399122 PROGRESS: Channel   0:	 0.05 FDR:   637; 0.01 FDR:   487; 0.001 FDR:   351
2:39:54.399215 PROGRESS: =========================================================================
2:39:54.442107 INFO: fragments_df_filtered: 5000
2:39:54.928092 INFO: calibration group: precursor, fitting mz estimator 
2:39:54.978479 INFO: calibration group: precursor, fitting rt estimator 
2:39:55.029201 INFO: calibration group: fragment, fitting mz estimator 
2:39:55.448708 INFO: calibration group: precursor, predicting mz
2:39:55.479624 INFO: calibration group: precursor, predicting rt
2:39:55.631573 INFO: calibration group: fragment, predicting mz
2:39:55.974276 INFO: === checking if optimization conditions were reached ===
2:39:55.977118 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
2:39:55.978362 PROGRESS: ❌ ms1_error      : 14.4142 > 10.0000 or insufficient steps taken.
2:39:55.978420 INFO: ==============================================
2:39:55.978532 INFO: Starting optimization step 8.
2:39:55.978619 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:39:55.978709 PROGRESS: Extracting batch of 237192 precursors
2:39:56.049510 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:39:56.049649 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:39:56.049687 INFO: FWHM in RT is 2.98 seconds, sigma is 0.38
2:39:56.049710 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:39:56.049981 INFO: Starting candidate selection
2:40:07.285534 INFO: Starting candidate scoring
2:40:11.230984 INFO: Finished candidate processing
2:40:11.231272 INFO: Collecting candidate features
2:40:12.646062 WARNING: intensity_correlation has 14 NaNs ( 0.00 % out of 473063)
2:40:12.675375 INFO: Collecting fragment features
2:40:13.014301 INFO: Finished candidate scoring
2:40:13.278141 PROGRESS: === Extracted 473063 precursors and 4116748 fragments ===
2:40:13.278677 INFO: performing precursor FDR with 47 features
2:40:13.278718 INFO: Decoy channel: -1
2:40:13.278741 INFO: Competetive: True
2:40:13.431872 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:13.530094 WARNING: dropped 6 target PSMs due to missing features
2:40:13.530238 WARNING: dropped 8 decoy PSMs due to missing features
2:40:21.718922 INFO: Test AUC: 0.570
2:40:21.719066 INFO: Train AUC: 0.590
2:40:21.719098 INFO: AUC difference: 3.45%
2:40:21.838473 INFO: Resetting torch num_threads to 100
2:40:21.851992 INFO: === FDR correction performed with classifier version 7 ===
2:40:21.852944 PROGRESS: ============================= Precursor FDR =============================
2:40:21.853063 PROGRESS: Total precursors accumulated: 821
2:40:21.853120 PROGRESS: Target precursors: 748 (91.11%)
2:40:21.853172 PROGRESS: Decoy precursors: 73 (8.89%)
2:40:21.853218 PROGRESS: 
2:40:21.853264 PROGRESS: Precursor Summary:
2:40:21.854442 PROGRESS: Channel   0:	 0.05 FDR:   596; 0.01 FDR:   403; 0.001 FDR:   304
2:40:21.854543 PROGRESS: 
2:40:21.854598 PROGRESS: Protein Summary:
2:40:21.855830 PROGRESS: Channel   0:	 0.05 FDR:   533; 0.01 FDR:   365; 0.001 FDR:   281
2:40:21.855927 PROGRESS: =========================================================================
2:40:21.873198 INFO: fragments_df_filtered: 4089
2:40:22.260262 INFO: calibration group: precursor, fitting mz estimator 
2:40:22.303577 INFO: calibration group: precursor, fitting rt estimator 
2:40:22.341965 INFO: calibration group: fragment, fitting mz estimator 
2:40:22.591252 INFO: calibration group: precursor, predicting mz
2:40:22.625696 INFO: calibration group: precursor, predicting rt
2:40:22.778647 INFO: calibration group: fragment, predicting mz
2:40:23.121959 INFO: === checking if optimization conditions were reached ===
2:40:23.124837 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
2:40:23.126050 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
2:40:23.126180 INFO: ==============================================
2:40:23.126461 PROGRESS: Optimization finished for ms2_error, ms1_error.
2:40:23.502926 INFO: calibration group: precursor, predicting mz
2:40:23.532614 INFO: calibration group: precursor, predicting rt
2:40:23.685039 INFO: calibration group: fragment, predicting mz
2:40:24.030727 INFO: Starting optimization step 0.
2:40:24.031091 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:40:24.031190 PROGRESS: Extracting batch of 237192 precursors
2:40:24.095017 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:40:24.095155 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:40:24.095193 INFO: FWHM in RT is 2.83 seconds, sigma is 0.36
2:40:24.095216 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:40:24.095485 INFO: Starting candidate selection
2:40:35.324504 INFO: Starting candidate scoring
2:40:38.444710 INFO: Finished candidate processing
2:40:38.444818 INFO: Collecting candidate features
2:40:39.274637 WARNING: intensity_correlation has 5 NaNs ( 0.00 % out of 473092)
2:40:39.292785 INFO: Collecting fragment features
2:40:39.573364 INFO: Finished candidate scoring
2:40:39.827571 PROGRESS: === Extracted 473092 precursors and 4109122 fragments ===
2:40:39.828041 INFO: performing precursor FDR with 47 features
2:40:39.828082 INFO: Decoy channel: -1
2:40:39.828107 INFO: Competetive: True
2:40:39.987681 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:40.083994 WARNING: dropped 2 target PSMs due to missing features
2:40:40.084139 WARNING: dropped 3 decoy PSMs due to missing features
2:40:48.026003 INFO: Test AUC: 0.575
2:40:48.026222 INFO: Train AUC: 0.594
2:40:48.026255 INFO: AUC difference: 3.20%
2:40:48.142699 INFO: Resetting torch num_threads to 100
2:40:48.155493 INFO: === FDR correction performed with classifier version 8 ===
2:40:48.156445 PROGRESS: ============================= Precursor FDR =============================
2:40:48.156564 PROGRESS: Total precursors accumulated: 870
2:40:48.156625 PROGRESS: Target precursors: 791 (90.92%)
2:40:48.156678 PROGRESS: Decoy precursors: 79 (9.08%)
2:40:48.156724 PROGRESS: 
2:40:48.156767 PROGRESS: Precursor Summary:
2:40:48.157756 PROGRESS: Channel   0:	 0.05 FDR:   530; 0.01 FDR:     0; 0.001 FDR:     0
2:40:48.157857 PROGRESS: 
2:40:48.157911 PROGRESS: Protein Summary:
2:40:48.158985 PROGRESS: Channel   0:	 0.05 FDR:   477; 0.01 FDR:     0; 0.001 FDR:     0
2:40:48.159076 PROGRESS: =========================================================================
2:40:48.615597 INFO: calibration group: precursor, predicting mz
2:40:48.649009 INFO: calibration group: precursor, predicting rt
2:40:48.817702 INFO: calibration group: fragment, predicting mz
2:40:49.219362 INFO: === skipping optimization until target number of precursors are found ===
2:40:49.220016 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
2:40:49.220182 INFO: Starting optimization step 1.
2:40:49.220433 PROGRESS: === Extracting elution groups 120000 to 248000 ===
2:40:49.220672 PROGRESS: Extracting batch of 252997 precursors
2:40:49.285535 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:40:49.285662 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:40:49.285702 INFO: FWHM in RT is 2.83 seconds, sigma is 0.36
2:40:49.285724 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:40:49.286042 INFO: Starting candidate selection
2:41:01.780373 INFO: Starting candidate scoring
2:41:05.416605 INFO: Finished candidate processing
2:41:05.416841 INFO: Collecting candidate features
2:41:06.630523 WARNING: intensity_correlation has 15 NaNs ( 0.00 % out of 504471)
2:41:06.650271 INFO: Collecting fragment features
2:41:06.960936 INFO: Finished candidate scoring
2:41:07.566549 PROGRESS: === Extracted 977563 precursors and 8492562 fragments ===
2:41:07.681762 INFO: performing precursor FDR with 47 features
2:41:07.681923 INFO: Decoy channel: -1
2:41:07.681951 INFO: Competetive: True
2:41:08.220334 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:08.450403 WARNING: dropped 8 target PSMs due to missing features
2:41:08.450566 WARNING: dropped 12 decoy PSMs due to missing features
2:41:27.538199 INFO: Test AUC: 0.573
2:41:27.538574 INFO: Train AUC: 0.588
2:41:27.538610 INFO: AUC difference: 2.45%
2:41:27.692850 INFO: Resetting torch num_threads to 100
2:41:27.746515 INFO: === FDR correction performed with classifier version 8 ===
2:41:27.747617 PROGRESS: ============================= Precursor FDR =============================
2:41:27.747720 PROGRESS: Total precursors accumulated: 1,530
2:41:27.747796 PROGRESS: Target precursors: 1,396 (91.24%)
2:41:27.747847 PROGRESS: Decoy precursors: 134 (8.76%)
2:41:27.747893 PROGRESS: 
2:41:27.747937 PROGRESS: Precursor Summary:
2:41:27.749223 PROGRESS: Channel   0:	 0.05 FDR: 1,155; 0.01 FDR:   782; 0.001 FDR:   625
2:41:27.749317 PROGRESS: 
2:41:27.749374 PROGRESS: Protein Summary:
2:41:27.750883 PROGRESS: Channel   0:	 0.05 FDR:   988; 0.01 FDR:   683; 0.001 FDR:   559
2:41:27.750975 PROGRESS: =========================================================================
2:41:27.872274 INFO: fragments_df_filtered: 5000
2:41:28.359033 INFO: calibration group: precursor, fitting mz estimator 
2:41:28.411652 INFO: calibration group: precursor, fitting rt estimator 
2:41:28.456802 INFO: calibration group: fragment, fitting mz estimator 
2:41:28.811217 INFO: calibration group: precursor, predicting mz
2:41:28.841921 INFO: calibration group: precursor, predicting rt
2:41:28.992886 INFO: calibration group: fragment, predicting mz
2:41:29.328707 INFO: === checking if optimization conditions were reached ===
2:41:29.329081 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2:41:29.331526 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 181.0040.
2:41:29.331605 INFO: ==============================================
2:41:29.331713 INFO: Starting optimization step 2.
2:41:29.331802 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:41:29.331881 PROGRESS: Extracting batch of 237192 precursors
2:41:29.396929 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:41:29.397068 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:41:29.397107 INFO: FWHM in RT is 2.79 seconds, sigma is 0.36
2:41:29.397131 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:41:29.397426 INFO: Starting candidate selection
2:41:38.561288 INFO: Starting candidate scoring
2:41:41.863192 INFO: Finished candidate processing
2:41:41.864870 INFO: Collecting candidate features
2:41:42.683232 WARNING: intensity_correlation has 115 NaNs ( 0.02 % out of 468911)
2:41:42.702315 INFO: Collecting fragment features
2:41:42.984964 INFO: Finished candidate scoring
2:41:43.253736 PROGRESS: === Extracted 468911 precursors and 3868125 fragments ===
2:41:43.254209 INFO: performing precursor FDR with 47 features
2:41:43.254256 INFO: Decoy channel: -1
2:41:43.254281 INFO: Competetive: True
2:41:43.401118 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:43.493318 WARNING: dropped 62 target PSMs due to missing features
2:41:43.493458 WARNING: dropped 53 decoy PSMs due to missing features
2:41:51.609550 INFO: Test AUC: 0.568
2:41:51.609754 INFO: Train AUC: 0.590
2:41:51.609788 INFO: AUC difference: 3.64%
2:41:51.725632 INFO: Resetting torch num_threads to 100
2:41:51.737981 INFO: === FDR correction performed with classifier version 8 ===
2:41:51.738934 PROGRESS: ============================= Precursor FDR =============================
2:41:51.739063 PROGRESS: Total precursors accumulated: 1,009
2:41:51.739126 PROGRESS: Target precursors: 917 (90.88%)
2:41:51.739189 PROGRESS: Decoy precursors: 92 (9.12%)
2:41:51.739238 PROGRESS: 
2:41:51.739283 PROGRESS: Precursor Summary:
2:41:51.740398 PROGRESS: Channel   0:	 0.05 FDR:   628; 0.01 FDR:   369; 0.001 FDR:   252
2:41:51.740496 PROGRESS: 
2:41:51.740553 PROGRESS: Protein Summary:
2:41:51.741805 PROGRESS: Channel   0:	 0.05 FDR:   559; 0.01 FDR:   338; 0.001 FDR:   239
2:41:51.741897 PROGRESS: =========================================================================
2:41:51.768851 INFO: fragments_df_filtered: 3893
2:41:52.191665 INFO: calibration group: precursor, fitting mz estimator 
2:41:52.245232 INFO: calibration group: precursor, fitting rt estimator 
2:41:52.293068 INFO: calibration group: fragment, fitting mz estimator 
2:41:52.518652 INFO: calibration group: precursor, predicting mz
2:41:52.558866 INFO: calibration group: precursor, predicting rt
2:41:52.713948 INFO: calibration group: fragment, predicting mz
2:41:53.052472 INFO: === checking if optimization conditions were reached ===
2:41:53.052835 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2:41:53.055149 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 117.6303.
2:41:53.055235 INFO: ==============================================
2:41:53.055343 INFO: Starting optimization step 3.
2:41:53.055420 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:41:53.055497 PROGRESS: Extracting batch of 237192 precursors
2:41:53.116231 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:41:53.116363 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:41:53.116400 INFO: FWHM in RT is 2.72 seconds, sigma is 0.35
2:41:53.116424 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:41:53.116698 INFO: Starting candidate selection
2:42:02.461386 INFO: Starting candidate scoring
2:42:05.673312 INFO: Finished candidate processing
2:42:05.673442 INFO: Collecting candidate features
2:42:06.750312 WARNING: intensity_correlation has 154 NaNs ( 0.03 % out of 467743)
2:42:06.769192 INFO: Collecting fragment features
2:42:07.115919 INFO: Finished candidate scoring
2:42:07.465438 PROGRESS: === Extracted 467743 precursors and 3763233 fragments ===
2:42:07.466123 INFO: performing precursor FDR with 47 features
2:42:07.466178 INFO: Decoy channel: -1
2:42:07.466205 INFO: Competetive: True
2:42:07.672292 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:07.793881 WARNING: dropped 78 target PSMs due to missing features
2:42:07.794045 WARNING: dropped 76 decoy PSMs due to missing features
2:42:18.112129 INFO: Test AUC: 0.571
2:42:18.112340 INFO: Train AUC: 0.587
2:42:18.112374 INFO: AUC difference: 2.72%
2:42:18.231984 INFO: Resetting torch num_threads to 100
2:42:18.244465 INFO: === FDR correction performed with classifier version 8 ===
2:42:18.245532 PROGRESS: ============================= Precursor FDR =============================
2:42:18.245660 PROGRESS: Total precursors accumulated: 1,017
2:42:18.245725 PROGRESS: Target precursors: 927 (91.15%)
2:42:18.245778 PROGRESS: Decoy precursors: 90 (8.85%)
2:42:18.245823 PROGRESS: 
2:42:18.245866 PROGRESS: Precursor Summary:
2:42:18.246975 PROGRESS: Channel   0:	 0.05 FDR:   708; 0.01 FDR:   362; 0.001 FDR:   282
2:42:18.247077 PROGRESS: 
2:42:18.247133 PROGRESS: Protein Summary:
2:42:18.248374 PROGRESS: Channel   0:	 0.05 FDR:   627; 0.01 FDR:   336; 0.001 FDR:   264
2:42:18.248470 PROGRESS: =========================================================================
2:42:18.285914 INFO: fragments_df_filtered: 3762
2:42:18.703848 INFO: calibration group: precursor, fitting mz estimator 
2:42:18.745637 INFO: calibration group: precursor, fitting rt estimator 
2:42:18.782469 INFO: calibration group: fragment, fitting mz estimator 
2:42:18.995723 INFO: calibration group: precursor, predicting mz
2:42:19.027375 INFO: calibration group: precursor, predicting rt
2:42:19.181509 INFO: calibration group: fragment, predicting mz
2:42:19.524619 INFO: === checking if optimization conditions were reached ===
2:42:19.524982 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2:42:19.527514 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 74.9442.
2:42:19.527576 INFO: ==============================================
2:42:19.527683 INFO: Starting optimization step 4.
2:42:19.527771 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:42:19.527849 PROGRESS: Extracting batch of 237192 precursors
2:42:19.593642 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:42:19.593781 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:42:19.593822 INFO: FWHM in RT is 2.72 seconds, sigma is 0.35
2:42:19.593844 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:42:19.594121 INFO: Starting candidate selection
2:42:28.685368 INFO: Starting candidate scoring
2:42:31.895130 INFO: Finished candidate processing
2:42:31.895562 INFO: Collecting candidate features
2:42:32.857847 WARNING: intensity_correlation has 186 NaNs ( 0.04 % out of 466085)
2:42:32.876407 INFO: Collecting fragment features
2:42:33.154963 INFO: Finished candidate scoring
2:42:33.557584 PROGRESS: === Extracted 466085 precursors and 3619071 fragments ===
2:42:33.558220 INFO: performing precursor FDR with 47 features
2:42:33.558268 INFO: Decoy channel: -1
2:42:33.558292 INFO: Competetive: True
2:42:33.710204 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:33.806745 WARNING: dropped 105 target PSMs due to missing features
2:42:33.806877 WARNING: dropped 81 decoy PSMs due to missing features
2:42:41.848428 INFO: Test AUC: 0.564
2:42:41.848572 INFO: Train AUC: 0.587
2:42:41.848603 INFO: AUC difference: 3.86%
2:42:41.964268 INFO: Resetting torch num_threads to 100
2:42:41.977446 INFO: === FDR correction performed with classifier version 8 ===
2:42:41.978423 PROGRESS: ============================= Precursor FDR =============================
2:42:41.978549 PROGRESS: Total precursors accumulated: 932
2:42:41.978611 PROGRESS: Target precursors: 849 (91.09%)
2:42:41.978662 PROGRESS: Decoy precursors: 83 (8.91%)
2:42:41.978708 PROGRESS: 
2:42:41.978753 PROGRESS: Precursor Summary:
2:42:41.979851 PROGRESS: Channel   0:	 0.05 FDR:   662; 0.01 FDR:   421; 0.001 FDR:   345
2:42:41.979970 PROGRESS: 
2:42:41.980026 PROGRESS: Protein Summary:
2:42:41.981256 PROGRESS: Channel   0:	 0.05 FDR:   589; 0.01 FDR:   383; 0.001 FDR:   322
2:42:41.981350 PROGRESS: =========================================================================
2:42:41.997292 INFO: fragments_df_filtered: 4151
2:42:42.389201 INFO: calibration group: precursor, fitting mz estimator 
2:42:42.449208 INFO: calibration group: precursor, fitting rt estimator 
2:42:42.496668 INFO: calibration group: fragment, fitting mz estimator 
2:42:42.816828 INFO: calibration group: precursor, predicting mz
2:42:42.851552 INFO: calibration group: precursor, predicting rt
2:42:43.003410 INFO: calibration group: fragment, predicting mz
2:42:43.350352 INFO: === checking if optimization conditions were reached ===
2:42:43.350705 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2:42:43.353205 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 66.6483.
2:42:43.353270 INFO: ==============================================
2:42:43.353379 INFO: Starting optimization step 5.
2:42:43.353456 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:42:43.353534 PROGRESS: Extracting batch of 237192 precursors
2:42:43.414448 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:42:43.414580 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:42:43.414618 INFO: FWHM in RT is 2.73 seconds, sigma is 0.35
2:42:43.414642 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:42:43.414916 INFO: Starting candidate selection
2:42:52.693889 INFO: Starting candidate scoring
2:42:55.878306 INFO: Finished candidate processing
2:42:55.878458 INFO: Collecting candidate features
2:42:56.734052 WARNING: intensity_correlation has 176 NaNs ( 0.04 % out of 466175)
2:42:56.752812 INFO: Collecting fragment features
2:42:57.048160 INFO: Finished candidate scoring
2:42:57.288282 PROGRESS: === Extracted 466175 precursors and 3620057 fragments ===
2:42:57.288802 INFO: performing precursor FDR with 47 features
2:42:57.288852 INFO: Decoy channel: -1
2:42:57.288876 INFO: Competetive: True
2:42:57.482778 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:57.605954 WARNING: dropped 97 target PSMs due to missing features
2:42:57.606098 WARNING: dropped 79 decoy PSMs due to missing features
2:43:05.867583 INFO: Test AUC: 0.570
2:43:05.867828 INFO: Train AUC: 0.586
2:43:05.867865 INFO: AUC difference: 2.77%
2:43:07.031289 INFO: Resetting torch num_threads to 100
2:43:07.043764 INFO: === FDR correction performed with classifier version 8 ===
2:43:07.044732 PROGRESS: ============================= Precursor FDR =============================
2:43:07.044856 PROGRESS: Total precursors accumulated: 1,003
2:43:07.044916 PROGRESS: Target precursors: 913 (91.03%)
2:43:07.044967 PROGRESS: Decoy precursors: 90 (8.97%)
2:43:07.045012 PROGRESS: 
2:43:07.045059 PROGRESS: Precursor Summary:
2:43:07.046307 PROGRESS: Channel   0:	 0.05 FDR:   681; 0.01 FDR:   426; 0.001 FDR:   283
2:43:07.046406 PROGRESS: 
2:43:07.046459 PROGRESS: Protein Summary:
2:43:07.047755 PROGRESS: Channel   0:	 0.05 FDR:   606; 0.01 FDR:   385; 0.001 FDR:   264
2:43:07.047850 PROGRESS: =========================================================================
2:43:07.064111 INFO: fragments_df_filtered: 4201
2:43:07.477419 INFO: calibration group: precursor, fitting mz estimator 
2:43:07.528484 INFO: calibration group: precursor, fitting rt estimator 
2:43:07.575853 INFO: calibration group: fragment, fitting mz estimator 
2:43:07.902100 INFO: calibration group: precursor, predicting mz
2:43:07.933909 INFO: calibration group: precursor, predicting rt
2:43:08.086535 INFO: calibration group: fragment, predicting mz
2:43:08.430383 INFO: === checking if optimization conditions were reached ===
2:43:08.430768 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2:43:08.433323 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 60.4844.
2:43:08.433387 INFO: ==============================================
2:43:08.433491 INFO: Starting optimization step 6.
2:43:08.433565 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:43:08.433630 PROGRESS: Extracting batch of 237192 precursors
2:43:08.497555 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:43:08.497696 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:43:08.497736 INFO: FWHM in RT is 2.74 seconds, sigma is 0.35
2:43:08.497758 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:43:08.498029 INFO: Starting candidate selection
2:43:16.077183 INFO: Starting candidate scoring
2:43:19.394971 INFO: Finished candidate processing
2:43:19.395088 INFO: Collecting candidate features
2:43:20.260072 WARNING: intensity_correlation has 210 NaNs ( 0.05 % out of 465093)
2:43:20.280105 INFO: Collecting fragment features
2:43:20.563649 INFO: Finished candidate scoring
2:43:20.959266 PROGRESS: === Extracted 465093 precursors and 3564172 fragments ===
2:43:20.959681 INFO: performing precursor FDR with 47 features
2:43:20.959727 INFO: Decoy channel: -1
2:43:20.959760 INFO: Competetive: True
2:43:21.116422 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:21.207554 WARNING: dropped 110 target PSMs due to missing features
2:43:21.207704 WARNING: dropped 100 decoy PSMs due to missing features
2:43:28.810167 INFO: Test AUC: 0.569
2:43:28.810979 INFO: Train AUC: 0.586
2:43:28.811030 INFO: AUC difference: 2.83%
2:43:28.930325 INFO: Resetting torch num_threads to 100
2:43:28.942768 INFO: === FDR correction performed with classifier version 8 ===
2:43:28.943845 PROGRESS: ============================= Precursor FDR =============================
2:43:28.943972 PROGRESS: Total precursors accumulated: 974
2:43:28.944035 PROGRESS: Target precursors: 891 (91.48%)
2:43:28.944086 PROGRESS: Decoy precursors: 83 (8.52%)
2:43:28.944131 PROGRESS: 
2:43:28.944176 PROGRESS: Precursor Summary:
2:43:28.945415 PROGRESS: Channel   0:	 0.05 FDR:   693; 0.01 FDR:   381; 0.001 FDR:   347
2:43:28.945524 PROGRESS: 
2:43:28.945581 PROGRESS: Protein Summary:
2:43:28.946899 PROGRESS: Channel   0:	 0.05 FDR:   620; 0.01 FDR:   343; 0.001 FDR:   316
2:43:28.946994 PROGRESS: =========================================================================
2:43:28.973327 INFO: fragments_df_filtered: 3836
2:43:29.361674 INFO: calibration group: precursor, fitting mz estimator 
2:43:29.411368 INFO: calibration group: precursor, fitting rt estimator 
2:43:29.460787 INFO: calibration group: fragment, fitting mz estimator 
2:43:29.749855 INFO: calibration group: precursor, predicting mz
2:43:29.781154 INFO: calibration group: precursor, predicting rt
2:43:29.936213 INFO: calibration group: fragment, predicting mz
2:43:30.278604 INFO: === checking if optimization conditions were reached ===
2:43:30.278967 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2:43:30.281499 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 57.0772.
2:43:30.281562 INFO: ==============================================
2:43:30.281676 INFO: Starting optimization step 7.
2:43:30.281750 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:43:30.281830 PROGRESS: Extracting batch of 237192 precursors
2:43:30.343656 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:43:30.343788 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:43:30.343827 INFO: FWHM in RT is 2.73 seconds, sigma is 0.35
2:43:30.343850 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:43:30.344122 INFO: Starting candidate selection
2:43:37.935229 INFO: Starting candidate scoring
2:43:41.228970 INFO: Finished candidate processing
2:43:41.229106 INFO: Collecting candidate features
2:43:42.270341 WARNING: intensity_correlation has 245 NaNs ( 0.05 % out of 465137)
2:43:42.289030 INFO: Collecting fragment features
2:43:42.568407 INFO: Finished candidate scoring
2:43:42.837792 PROGRESS: === Extracted 465137 precursors and 3561747 fragments ===
2:43:42.838343 INFO: performing precursor FDR with 47 features
2:43:42.838391 INFO: Decoy channel: -1
2:43:42.838421 INFO: Competetive: True
2:43:42.990834 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:43.080515 WARNING: dropped 120 target PSMs due to missing features
2:43:43.080660 WARNING: dropped 125 decoy PSMs due to missing features
2:43:50.837384 INFO: Test AUC: 0.568
2:43:50.837528 INFO: Train AUC: 0.587
2:43:50.837559 INFO: AUC difference: 3.22%
2:43:50.958165 INFO: Resetting torch num_threads to 100
2:43:50.971855 INFO: === FDR correction performed with classifier version 8 ===
2:43:50.972872 PROGRESS: ============================= Precursor FDR =============================
2:43:50.973009 PROGRESS: Total precursors accumulated: 1,042
2:43:50.973071 PROGRESS: Target precursors: 951 (91.27%)
2:43:50.973121 PROGRESS: Decoy precursors: 91 (8.73%)
2:43:50.973167 PROGRESS: 
2:43:50.973211 PROGRESS: Precursor Summary:
2:43:50.974414 PROGRESS: Channel   0:	 0.05 FDR:   707; 0.01 FDR:   380; 0.001 FDR:   244
2:43:50.974515 PROGRESS: 
2:43:50.974569 PROGRESS: Protein Summary:
2:43:50.975883 PROGRESS: Channel   0:	 0.05 FDR:   636; 0.01 FDR:   342; 0.001 FDR:   230
2:43:50.975981 PROGRESS: =========================================================================
2:43:51.001742 INFO: fragments_df_filtered: 3813
2:43:51.404006 INFO: calibration group: precursor, fitting mz estimator 
2:43:51.479677 INFO: calibration group: precursor, fitting rt estimator 
2:43:51.527533 INFO: calibration group: fragment, fitting mz estimator 
2:43:51.820050 INFO: calibration group: precursor, predicting mz
2:43:51.871525 INFO: calibration group: precursor, predicting rt
2:43:52.027539 INFO: calibration group: fragment, predicting mz
2:43:52.372655 INFO: === checking if optimization conditions were reached ===
2:43:52.373261 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
2:43:52.375895 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 53.0084.
2:43:52.376043 INFO: ==============================================
2:43:52.376323 INFO: Starting optimization step 8.
2:43:52.376578 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:43:52.376830 PROGRESS: Extracting batch of 237192 precursors
2:43:52.449529 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:43:52.449659 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:43:52.449699 INFO: FWHM in RT is 2.73 seconds, sigma is 0.35
2:43:52.449721 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:43:52.450010 INFO: Starting candidate selection
2:44:00.910112 INFO: Starting candidate scoring
2:44:04.672939 INFO: Finished candidate processing
2:44:04.673118 INFO: Collecting candidate features
2:44:05.623346 WARNING: intensity_correlation has 228 NaNs ( 0.05 % out of 464332)
2:44:05.641558 INFO: Collecting fragment features
2:44:05.899832 INFO: Finished candidate scoring
2:44:06.432458 PROGRESS: === Extracted 464332 precursors and 3545023 fragments ===
2:44:06.433166 INFO: performing precursor FDR with 47 features
2:44:06.433227 INFO: Decoy channel: -1
2:44:06.433252 INFO: Competetive: True
2:44:06.639663 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:06.762003 WARNING: dropped 107 target PSMs due to missing features
2:44:06.762166 WARNING: dropped 121 decoy PSMs due to missing features
2:44:16.580729 INFO: Test AUC: 0.567
2:44:16.580940 INFO: Train AUC: 0.587
2:44:16.580975 INFO: AUC difference: 3.38%
2:44:16.715159 INFO: Resetting torch num_threads to 100
2:44:16.730523 INFO: === FDR correction performed with classifier version 8 ===
2:44:16.731672 PROGRESS: ============================= Precursor FDR =============================
2:44:16.731811 PROGRESS: Total precursors accumulated: 977
2:44:16.731879 PROGRESS: Target precursors: 891 (91.20%)
2:44:16.731932 PROGRESS: Decoy precursors: 86 (8.80%)
2:44:16.731978 PROGRESS: 
2:44:16.732026 PROGRESS: Precursor Summary:
2:44:16.733276 PROGRESS: Channel   0:	 0.05 FDR:   694; 0.01 FDR:   342; 0.001 FDR:   270
2:44:16.733377 PROGRESS: 
2:44:16.733445 PROGRESS: Protein Summary:
2:44:16.735188 PROGRESS: Channel   0:	 0.05 FDR:   623; 0.01 FDR:   313; 0.001 FDR:   252
2:44:16.735336 PROGRESS: =========================================================================
2:44:16.759551 INFO: fragments_df_filtered: 3572
2:44:17.258656 INFO: calibration group: precursor, fitting mz estimator 
2:44:17.316149 INFO: calibration group: precursor, fitting rt estimator 
2:44:17.391326 INFO: calibration group: fragment, fitting mz estimator 
2:44:17.669728 INFO: calibration group: precursor, predicting mz
2:44:17.708963 INFO: calibration group: precursor, predicting rt
2:44:17.866781 INFO: calibration group: fragment, predicting mz
2:44:18.232855 INFO: === checking if optimization conditions were reached ===
2:44:18.233243 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
2:44:18.235913 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 54.3663.
2:44:18.235980 INFO: ==============================================
2:44:18.236088 INFO: Starting optimization step 9.
2:44:18.236164 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:44:18.236243 PROGRESS: Extracting batch of 237192 precursors
2:44:18.308586 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:44:18.308719 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:44:18.308757 INFO: FWHM in RT is 2.72 seconds, sigma is 0.35
2:44:18.308795 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:44:18.309078 INFO: Starting candidate selection
2:44:26.374295 INFO: Starting candidate scoring
2:44:29.740109 INFO: Finished candidate processing
2:44:29.740807 INFO: Collecting candidate features
2:44:30.767682 WARNING: intensity_correlation has 204 NaNs ( 0.04 % out of 465215)
2:44:30.789341 INFO: Collecting fragment features
2:44:31.066122 INFO: Finished candidate scoring
2:44:31.374854 PROGRESS: === Extracted 465215 precursors and 3562706 fragments ===
2:44:31.375638 INFO: performing precursor FDR with 47 features
2:44:31.375699 INFO: Decoy channel: -1
2:44:31.375724 INFO: Competetive: True
2:44:31.559276 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:31.659071 WARNING: dropped 112 target PSMs due to missing features
2:44:31.659220 WARNING: dropped 92 decoy PSMs due to missing features
2:44:40.980129 INFO: Test AUC: 0.567
2:44:40.980333 INFO: Train AUC: 0.586
2:44:40.980368 INFO: AUC difference: 3.26%
2:44:41.103291 INFO: Resetting torch num_threads to 100
2:44:41.115412 INFO: === FDR correction performed with classifier version 8 ===
2:44:41.116456 PROGRESS: ============================= Precursor FDR =============================
2:44:41.116593 PROGRESS: Total precursors accumulated: 1,003
2:44:41.116657 PROGRESS: Target precursors: 917 (91.43%)
2:44:41.116708 PROGRESS: Decoy precursors: 86 (8.57%)
2:44:41.116757 PROGRESS: 
2:44:41.116802 PROGRESS: Precursor Summary:
2:44:41.118196 PROGRESS: Channel   0:	 0.05 FDR:   751; 0.01 FDR:   421; 0.001 FDR:   316
2:44:41.118304 PROGRESS: 
2:44:41.118361 PROGRESS: Protein Summary:
2:44:41.119669 PROGRESS: Channel   0:	 0.05 FDR:   672; 0.01 FDR:   385; 0.001 FDR:   294
2:44:41.119785 PROGRESS: =========================================================================
2:44:41.135951 INFO: fragments_df_filtered: 4101
2:44:41.563878 INFO: calibration group: precursor, fitting mz estimator 
2:44:41.617113 INFO: calibration group: precursor, fitting rt estimator 
2:44:41.666298 INFO: calibration group: fragment, fitting mz estimator 
2:44:41.983445 INFO: calibration group: precursor, predicting mz
2:44:42.017778 INFO: calibration group: precursor, predicting rt
2:44:42.233804 INFO: calibration group: fragment, predicting mz
2:44:42.635412 INFO: === checking if optimization conditions were reached ===
2:44:42.635748 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
2:44:42.637029 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 54.3663 found after 9 searches.
2:44:42.637081 INFO: ==============================================
2:44:42.637180 PROGRESS: Optimization finished for rt_error.
2:44:43.001799 INFO: calibration group: precursor, predicting mz
2:44:43.033163 INFO: calibration group: precursor, predicting rt
2:44:43.187177 INFO: calibration group: fragment, predicting mz
2:44:43.554049 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:44:43.554262 PROGRESS: ==============================================
2:44:43.554329 PROGRESS: ms2_error      : 15.0000
2:44:43.554386 PROGRESS: ms1_error      : 10.0000
2:44:43.554438 PROGRESS: rt_error       : 54.3663
2:44:43.554483 PROGRESS: ==============================================
2:44:43.555981 INFO: calibration group: precursor, predicting mz
2:44:44.945808 INFO: calibration group: precursor, predicting rt
2:44:51.710608 INFO: calibration group: fragment, predicting mz
2:45:06.572161 PROGRESS: Extracting batch of 10183864 precursors
2:45:09.088605 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:45:09.088760 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:45:09.088806 INFO: FWHM in RT is 2.74 seconds, sigma is 0.35
2:45:09.088831 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:45:09.089211 INFO: Starting candidate selection
2:50:32.705025 INFO: Applying score cutoff of 31.04375328063965
2:50:33.268560 INFO: Removed 4554816 precursors with score below cutoff
2:50:35.561894 INFO: Starting candidate scoring
2:52:26.376895 INFO: Finished candidate processing
2:52:26.377254 INFO: Collecting candidate features
2:52:54.491230 WARNING: intensity_correlation has 1595 NaNs ( 0.01 % out of 15746633)
2:52:54.505247 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 15746633)
2:52:55.040659 INFO: Collecting fragment features
2:53:05.078175 INFO: Finished candidate scoring
2:53:30.047172 INFO: === FDR correction performed with classifier version 18 ===
2:53:30.107946 INFO: performing precursor FDR with 47 features
2:53:30.108059 INFO: Decoy channel: -1
2:53:30.108092 INFO: Competetive: True
2:53:34.422415 INFO: Setting torch num_threads to 2 for FDR classification task
2:53:37.082280 WARNING: dropped 899 target PSMs due to missing features
2:53:37.082437 WARNING: dropped 696 decoy PSMs due to missing features
2:59:26.936361 INFO: Test AUC: 0.580
2:59:26.936756 INFO: Train AUC: 0.586
2:59:26.936814 INFO: AUC difference: 1.14%
2:59:27.985355 INFO: Resetting torch num_threads to 100
2:59:28.394399 INFO: Removing fragments below FDR threshold
2:59:29.733755 PROGRESS: ============================= Precursor FDR =============================
2:59:29.734171 PROGRESS: Total precursors accumulated: 25,230
2:59:29.734241 PROGRESS: Target precursors: 24,981 (99.01%)
2:59:29.734295 PROGRESS: Decoy precursors: 249 (0.99%)
2:59:29.734344 PROGRESS: 
2:59:29.734394 PROGRESS: Precursor Summary:
2:59:29.743713 PROGRESS: Channel   0:	 0.05 FDR: 24,981; 0.01 FDR: 24,981; 0.001 FDR: 18,017
2:59:29.743946 PROGRESS: 
2:59:29.744006 PROGRESS: Protein Summary:
2:59:29.757374 PROGRESS: Channel   0:	 0.05 FDR: 7,287; 0.01 FDR: 7,287; 0.001 FDR: 5,809
2:59:29.757596 PROGRESS: =========================================================================
2:59:30.320852 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:59:30.903433 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:59:30.903647 INFO: Quantification results path: run_output_Astral/alphadia_1.10_default/library/quant
2:59:30.903747 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2 at run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:59:30.904550 INFO: Initializing RawFileManager
2:59:56.669476 INFO: Determining DIA cycle
2:59:56.685661 INFO: Found cycle with start 0.00 min and length 303.
2:59:56.877470 INFO: RT (min)            : 0.0 - 26.9
2:59:56.877568 INFO: RT duration (sec)   : 1611.2
2:59:56.877598 INFO: RT duration (min)   : 26.9
2:59:56.877621 INFO: Cycle len (scans)   : 303
2:59:56.877641 INFO: Cycle len (sec)     : 1.65
2:59:56.877660 INFO: Number of cycles    : 977
2:59:56.877680 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:59:58.535646 INFO: Initializing CalibrationManager
2:59:58.535980 INFO: Loading calibration config
2:59:58.537028 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed'], 'function': LOESSRegression()}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed'], 'function': LOESSRegression(n_kernels=2)}], 'name': 'precursor'}]
2:59:58.537121 INFO: Calibration group :fragment, found 1 estimator(s)
2:59:58.537259 INFO: Calibration group :precursor, found 3 estimator(s)
2:59:58.538080 INFO: Disabling ion mobility calibration
2:59:58.538113 INFO: removed mobility estimator from group precursor
2:59:58.538277 INFO: Initializing OptimizationManager
2:59:58.538402 INFO: initial parameter: ms1_error = 30
2:59:58.538462 INFO: initial parameter: ms2_error = 30
2:59:58.538510 INFO: initial parameter: rt_error = 805.6002197265625
2:59:58.538556 INFO: initial parameter: mobility_error = 0.1
2:59:58.538595 INFO: initial parameter: column_type = library
2:59:58.538636 INFO: initial parameter: num_candidates = 1
2:59:58.538675 INFO: initial parameter: classifier_version = -1
2:59:58.538717 INFO: initial parameter: fwhm_rt = 5
2:59:58.538762 INFO: initial parameter: fwhm_mobility = 0.01
2:59:58.538801 INFO: initial parameter: score_cutoff = 0
2:59:58.538870 INFO: Initializing TimingManager
2:59:58.538931 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:59:58.539037 INFO: FDRManager not loaded from disk.
2:59:58.539061 INFO: Initializing FDRManager
2:59:58.539112 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
3:00:00.126283 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
3:00:01.972819 PROGRESS: Starting initial search for precursors.
3:00:02.231144 INFO: Starting optimization step 0.
3:00:02.231401 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:00:02.231492 PROGRESS: Extracting batch of 15808 precursors
3:00:02.236910 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:00:02.236984 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:00:02.237036 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:00:02.237062 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:00:02.237478 INFO: Starting candidate selection
3:00:03.416867 INFO: Starting candidate scoring
3:00:03.548154 INFO: Finished candidate processing
3:00:03.548252 INFO: Collecting candidate features
3:00:03.593046 INFO: Collecting fragment features
3:00:03.611465 INFO: Finished candidate scoring
3:00:03.620147 PROGRESS: === Extracted 15765 precursors and 156381 fragments ===
3:00:03.620512 INFO: performing precursor FDR with 47 features
3:00:03.620552 INFO: Decoy channel: -1
3:00:03.620574 INFO: Competetive: True
3:00:03.625718 INFO: Setting torch num_threads to 2 for FDR classification task
3:00:03.780312 INFO: Test AUC: 0.534
3:00:03.780415 INFO: Train AUC: 0.552
3:00:03.780447 INFO: AUC difference: 3.20%
3:00:03.866821 INFO: Resetting torch num_threads to 100
3:00:03.868208 INFO: === FDR correction performed with classifier version -1 ===
3:00:03.868921 PROGRESS: ============================= Precursor FDR =============================
3:00:03.869010 PROGRESS: Total precursors accumulated: 4
3:00:03.869067 PROGRESS: Target precursors: 4 (100.00%)
3:00:03.869117 PROGRESS: Decoy precursors: 0 (0.00%)
3:00:03.869160 PROGRESS: 
3:00:03.869201 PROGRESS: Precursor Summary:
3:00:03.870120 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
3:00:03.870210 PROGRESS: 
3:00:03.870264 PROGRESS: Protein Summary:
3:00:03.871284 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
3:00:03.871383 PROGRESS: =========================================================================
3:00:03.983165 INFO: Starting optimization step 1.
3:00:03.983442 PROGRESS: === Extracting elution groups 8000 to 24000 ===
3:00:03.983512 PROGRESS: Extracting batch of 31655 precursors
3:00:03.991413 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:00:03.991503 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:00:03.991538 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:00:03.991560 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:00:03.991770 INFO: Starting candidate selection
3:00:05.936343 INFO: Starting candidate scoring
3:00:06.190237 INFO: Finished candidate processing
3:00:06.190344 INFO: Collecting candidate features
3:00:06.253103 INFO: Collecting fragment features
3:00:06.276885 INFO: Finished candidate scoring
3:00:06.304209 PROGRESS: === Extracted 47343 precursors and 470669 fragments ===
3:00:06.310193 INFO: performing precursor FDR with 47 features
3:00:06.310267 INFO: Decoy channel: -1
3:00:06.310293 INFO: Competetive: True
3:00:06.332479 INFO: Setting torch num_threads to 2 for FDR classification task
3:00:07.013413 INFO: Test AUC: 0.554
3:00:07.013537 INFO: Train AUC: 0.574
3:00:07.013566 INFO: AUC difference: 3.45%
3:00:07.099641 INFO: Resetting torch num_threads to 100
3:00:07.102547 INFO: === FDR correction performed with classifier version -1 ===
3:00:07.103328 PROGRESS: ============================= Precursor FDR =============================
3:00:07.103416 PROGRESS: Total precursors accumulated: 5
3:00:07.103474 PROGRESS: Target precursors: 5 (100.00%)
3:00:07.103524 PROGRESS: Decoy precursors: 0 (0.00%)
3:00:07.103568 PROGRESS: 
3:00:07.103613 PROGRESS: Precursor Summary:
3:00:07.104540 PROGRESS: Channel   0:	 0.05 FDR:     5; 0.01 FDR:     5; 0.001 FDR:     5
3:00:07.104627 PROGRESS: 
3:00:07.104681 PROGRESS: Protein Summary:
3:00:07.105686 PROGRESS: Channel   0:	 0.05 FDR:     5; 0.01 FDR:     5; 0.001 FDR:     5
3:00:07.105772 PROGRESS: =========================================================================
3:00:07.258910 INFO: Starting optimization step 2.
3:00:07.259203 PROGRESS: === Extracting elution groups 24000 to 56000 ===
3:00:07.259273 PROGRESS: Extracting batch of 63250 precursors
3:00:07.277090 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:00:07.277212 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:00:07.277245 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:00:07.277267 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:00:07.277484 INFO: Starting candidate selection
3:00:11.269983 INFO: Starting candidate scoring
3:00:11.731493 INFO: Finished candidate processing
3:00:11.731654 INFO: Collecting candidate features
3:00:11.871789 INFO: Collecting fragment features
3:00:11.918098 INFO: Finished candidate scoring
3:00:11.977083 PROGRESS: === Extracted 110427 precursors and 1097932 fragments ===
3:00:11.991595 INFO: performing precursor FDR with 47 features
3:00:11.991724 INFO: Decoy channel: -1
3:00:11.991761 INFO: Competetive: True
3:00:12.040108 INFO: Setting torch num_threads to 2 for FDR classification task
3:00:13.709477 INFO: Test AUC: 0.556
3:00:13.709597 INFO: Train AUC: 0.590
3:00:13.709626 INFO: AUC difference: 5.69%
3:00:13.709647 WARNING: AUC difference > 5%. This may indicate overfitting.
3:00:13.797892 INFO: Resetting torch num_threads to 100
3:00:13.803956 INFO: === FDR correction performed with classifier version -1 ===
3:00:13.804826 PROGRESS: ============================= Precursor FDR =============================
3:00:13.804915 PROGRESS: Total precursors accumulated: 1
3:00:13.804975 PROGRESS: Target precursors: 1 (100.00%)
3:00:13.805026 PROGRESS: Decoy precursors: 0 (0.00%)
3:00:13.805071 PROGRESS: 
3:00:13.805115 PROGRESS: Precursor Summary:
3:00:13.806041 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
3:00:13.806126 PROGRESS: 
3:00:13.806180 PROGRESS: Protein Summary:
3:00:13.807187 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
3:00:13.807271 PROGRESS: =========================================================================
3:00:14.048316 INFO: Starting optimization step 3.
3:00:14.048651 PROGRESS: === Extracting elution groups 56000 to 120000 ===
3:00:14.048722 PROGRESS: Extracting batch of 126479 precursors
3:00:14.079617 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:00:14.079754 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:00:14.079790 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:00:14.079811 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:00:14.080052 INFO: Starting candidate selection
3:00:22.062543 INFO: Starting candidate scoring
3:00:23.000096 INFO: Finished candidate processing
3:00:23.000286 INFO: Collecting candidate features
3:00:23.368692 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 126183)
3:00:23.384910 INFO: Collecting fragment features
3:00:23.478009 INFO: Finished candidate scoring
3:00:23.685230 PROGRESS: === Extracted 236610 precursors and 2351470 fragments ===
3:00:23.716795 INFO: performing precursor FDR with 47 features
3:00:23.716935 INFO: Decoy channel: -1
3:00:23.716964 INFO: Competetive: True
3:00:23.830937 INFO: Setting torch num_threads to 2 for FDR classification task
3:00:23.877890 WARNING: dropped 1 target PSMs due to missing features
3:00:23.878036 WARNING: dropped 2 decoy PSMs due to missing features
3:00:30.075703 INFO: Test AUC: 0.561
3:00:30.075838 INFO: Train AUC: 0.592
3:00:30.075869 INFO: AUC difference: 5.25%
3:00:30.075892 WARNING: AUC difference > 5%. This may indicate overfitting.
3:00:30.174779 INFO: Resetting torch num_threads to 100
3:00:30.189332 INFO: === FDR correction performed with classifier version -1 ===
3:00:30.214284 PROGRESS: ============================= Precursor FDR =============================
3:00:30.214644 PROGRESS: Total precursors accumulated: 118,479
3:00:30.214707 PROGRESS: Target precursors: 70,954 (59.89%)
3:00:30.214759 PROGRESS: Decoy precursors: 47,525 (40.11%)
3:00:30.214813 PROGRESS: 
3:00:30.214858 PROGRESS: Precursor Summary:
3:00:30.216506 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:00:30.216607 PROGRESS: 
3:00:30.216664 PROGRESS: Protein Summary:
3:00:30.218141 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:00:30.218235 PROGRESS: =========================================================================
3:00:30.652319 INFO: Starting optimization step 4.
3:00:30.652664 PROGRESS: === Extracting elution groups 120000 to 248000 ===
3:00:30.652781 PROGRESS: Extracting batch of 252997 precursors
3:00:30.712849 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:00:30.712983 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:00:30.713023 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:00:30.713046 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:00:30.713351 INFO: Starting candidate selection
3:00:46.570447 INFO: Starting candidate scoring
3:00:48.469640 INFO: Finished candidate processing
3:00:48.469741 INFO: Collecting candidate features
3:00:49.002471 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 252325)
3:00:49.013706 INFO: Collecting fragment features
3:00:49.186044 INFO: Finished candidate scoring
3:00:49.490571 PROGRESS: === Extracted 488935 precursors and 4857093 fragments ===
3:00:49.549450 INFO: performing precursor FDR with 47 features
3:00:49.549594 INFO: Decoy channel: -1
3:00:49.549621 INFO: Competetive: True
3:00:49.793126 INFO: Setting torch num_threads to 2 for FDR classification task
3:00:49.897083 WARNING: dropped 3 target PSMs due to missing features
3:00:49.897227 WARNING: dropped 4 decoy PSMs due to missing features
3:01:06.540832 INFO: Test AUC: 0.571
3:01:06.541037 INFO: Train AUC: 0.589
3:01:06.541073 INFO: AUC difference: 3.14%
3:01:06.657885 INFO: Resetting torch num_threads to 100
3:01:06.690484 INFO: === FDR correction performed with classifier version -1 ===
3:01:06.752311 PROGRESS: ============================= Precursor FDR =============================
3:01:06.752680 PROGRESS: Total precursors accumulated: 241,897
3:01:06.752745 PROGRESS: Target precursors: 144,842 (59.88%)
3:01:06.752802 PROGRESS: Decoy precursors: 97,055 (40.12%)
3:01:06.752850 PROGRESS: 
3:01:06.752893 PROGRESS: Precursor Summary:
3:01:06.755162 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:01:06.755261 PROGRESS: 
3:01:06.755317 PROGRESS: Protein Summary:
3:01:06.757282 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:01:06.757380 PROGRESS: =========================================================================
3:01:07.489385 INFO: Starting optimization step 5.
3:01:07.489765 PROGRESS: === Extracting elution groups 248000 to 504000 ===
3:01:07.489849 PROGRESS: Extracting batch of 506030 precursors
3:01:07.617702 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:01:07.617850 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:01:07.617891 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:01:07.617915 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:01:07.618248 INFO: Starting candidate selection
3:01:39.760314 INFO: Starting candidate scoring
3:01:43.693117 INFO: Finished candidate processing
3:01:43.697115 INFO: Collecting candidate features
3:01:45.197638 WARNING: intensity_correlation has 9 NaNs ( 0.00 % out of 504764)
3:01:45.216375 INFO: Collecting fragment features
3:01:45.582396 INFO: Finished candidate scoring
3:01:46.474150 PROGRESS: === Extracted 993699 precursors and 9872778 fragments ===
3:01:46.609756 INFO: performing precursor FDR with 47 features
3:01:46.609917 INFO: Decoy channel: -1
3:01:46.609946 INFO: Competetive: True
3:01:47.226898 INFO: Setting torch num_threads to 2 for FDR classification task
3:01:47.483068 WARNING: dropped 7 target PSMs due to missing features
3:01:47.483249 WARNING: dropped 9 decoy PSMs due to missing features
3:02:07.805111 INFO: Test AUC: 0.574
3:02:07.805333 INFO: Train AUC: 0.588
3:02:07.805371 INFO: AUC difference: 2.31%
3:02:07.967244 INFO: Resetting torch num_threads to 100
3:02:08.062869 INFO: === FDR correction performed with classifier version -1 ===
3:02:08.063998 PROGRESS: ============================= Precursor FDR =============================
3:02:08.064105 PROGRESS: Total precursors accumulated: 1
3:02:08.064168 PROGRESS: Target precursors: 1 (100.00%)
3:02:08.064220 PROGRESS: Decoy precursors: 0 (0.00%)
3:02:08.064268 PROGRESS: 
3:02:08.064315 PROGRESS: Precursor Summary:
3:02:08.065280 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
3:02:08.065373 PROGRESS: 
3:02:08.065431 PROGRESS: Protein Summary:
3:02:08.066476 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
3:02:08.066571 PROGRESS: =========================================================================
3:02:09.311179 INFO: Starting optimization step 6.
3:02:09.311531 PROGRESS: === Extracting elution groups 504000 to 1016000 ===
3:02:09.311622 PROGRESS: Extracting batch of 1011982 precursors
3:02:09.626563 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:02:09.626711 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:02:09.626755 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:02:09.626778 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:02:09.627141 INFO: Starting candidate selection
3:03:12.000478 INFO: Starting candidate scoring
3:03:19.552128 INFO: Finished candidate processing
3:03:19.552787 INFO: Collecting candidate features
3:03:22.015548 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 1009423)
3:03:22.049089 INFO: Collecting fragment features
3:03:22.770115 INFO: Finished candidate scoring
3:03:24.759467 PROGRESS: === Extracted 2003122 precursors and 19900775 fragments ===
3:03:25.002792 INFO: performing precursor FDR with 47 features
3:03:25.002933 INFO: Decoy channel: -1
3:03:25.002962 INFO: Competetive: True
3:03:25.949384 INFO: Setting torch num_threads to 2 for FDR classification task
3:03:26.358597 WARNING: dropped 9 target PSMs due to missing features
3:03:26.358747 WARNING: dropped 11 decoy PSMs due to missing features
3:04:04.525392 INFO: Test AUC: 0.579
3:04:04.525615 INFO: Train AUC: 0.587
3:04:04.525654 INFO: AUC difference: 1.49%
3:04:06.197302 INFO: Resetting torch num_threads to 100
3:04:06.351877 INFO: === FDR correction performed with classifier version -1 ===
3:04:06.353366 PROGRESS: ============================= Precursor FDR =============================
3:04:06.353522 PROGRESS: Total precursors accumulated: 2,095
3:04:06.353584 PROGRESS: Target precursors: 1,916 (91.46%)
3:04:06.353636 PROGRESS: Decoy precursors: 179 (8.54%)
3:04:06.353682 PROGRESS: 
3:04:06.353727 PROGRESS: Precursor Summary:
3:04:06.355425 PROGRESS: Channel   0:	 0.05 FDR: 1,493; 0.01 FDR:   961; 0.001 FDR:   492
3:04:06.355540 PROGRESS: 
3:04:06.355603 PROGRESS: Protein Summary:
3:04:06.357325 PROGRESS: Channel   0:	 0.05 FDR: 1,204; 0.01 FDR:   778; 0.001 FDR:   430
3:04:06.357438 PROGRESS: =========================================================================
3:04:06.596754 INFO: fragments_df_filtered: 5000
3:04:07.391582 INFO: calibration group: precursor, fitting mz estimator 
3:04:07.455715 INFO: calibration group: precursor, fitting rt estimator 
3:04:07.521693 INFO: calibration group: fragment, fitting mz estimator 
3:04:07.907314 INFO: calibration group: precursor, predicting mz
3:04:07.970255 INFO: calibration group: precursor, predicting rt
3:04:08.292085 INFO: calibration group: fragment, predicting mz
3:04:09.072280 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3:04:09.072604 INFO: Starting optimization step 7.
3:04:09.072706 PROGRESS: === Extracting elution groups 0 to 248000 ===
3:04:09.072776 PROGRESS: Extracting batch of 490189 precursors
3:04:09.224754 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:04:09.224891 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:04:09.224927 INFO: FWHM in RT is 2.86 seconds, sigma is 0.37
3:04:09.224950 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:04:09.225240 INFO: Starting candidate selection
3:04:32.703252 INFO: Starting candidate scoring
3:04:39.614102 INFO: Finished candidate processing
3:04:39.614265 INFO: Collecting candidate features
3:04:41.529108 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 977906)
3:04:41.563217 INFO: Collecting fragment features
3:04:42.238295 INFO: Finished candidate scoring
3:04:42.964037 PROGRESS: === Extracted 977906 precursors and 9630762 fragments ===
3:04:42.964571 INFO: performing precursor FDR with 47 features
3:04:42.964611 INFO: Decoy channel: -1
3:04:42.964636 INFO: Competetive: True
3:04:43.276737 INFO: Setting torch num_threads to 2 for FDR classification task
3:04:43.445965 WARNING: dropped 2 decoy PSMs due to missing features
3:05:01.145060 INFO: Test AUC: 0.576
3:05:01.145456 INFO: Train AUC: 0.591
3:05:01.145502 INFO: AUC difference: 2.61%
3:05:01.322282 INFO: Resetting torch num_threads to 100
3:05:01.355582 INFO: === FDR correction performed with classifier version 6 ===
3:05:01.356725 PROGRESS: ============================= Precursor FDR =============================
3:05:01.356894 PROGRESS: Total precursors accumulated: 620
3:05:01.356959 PROGRESS: Target precursors: 564 (90.97%)
3:05:01.357023 PROGRESS: Decoy precursors: 56 (9.03%)
3:05:01.357074 PROGRESS: 
3:05:01.357120 PROGRESS: Precursor Summary:
3:05:01.358432 PROGRESS: Channel   0:	 0.05 FDR:   461; 0.01 FDR:   308; 0.001 FDR:   248
3:05:01.358541 PROGRESS: 
3:05:01.358597 PROGRESS: Protein Summary:
3:05:01.359849 PROGRESS: Channel   0:	 0.05 FDR:   426; 0.01 FDR:   288; 0.001 FDR:   233
3:05:01.359950 PROGRESS: =========================================================================
3:05:01.407535 INFO: fragments_df_filtered: 3704
3:05:02.170752 INFO: calibration group: precursor, fitting mz estimator 
3:05:02.249133 INFO: calibration group: precursor, fitting rt estimator 
3:05:02.314446 INFO: calibration group: fragment, fitting mz estimator 
3:05:02.600629 INFO: calibration group: precursor, predicting mz
3:05:02.683760 INFO: calibration group: precursor, predicting rt
3:05:03.020385 INFO: calibration group: fragment, predicting mz
3:05:03.748795 INFO: === checking if optimization conditions were reached ===
3:05:03.751028 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
3:05:03.752020 PROGRESS: ❌ ms1_error      : 13.0968 > 10.0000 or insufficient steps taken.
3:05:03.752073 INFO: ==============================================
3:05:03.752167 INFO: Starting optimization step 8.
3:05:03.752232 PROGRESS: === Extracting elution groups 0 to 248000 ===
3:05:03.752298 PROGRESS: Extracting batch of 490189 precursors
3:05:03.878438 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:05:03.878581 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:05:03.878619 INFO: FWHM in RT is 2.96 seconds, sigma is 0.38
3:05:03.878641 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:05:03.878983 INFO: Starting candidate selection
3:05:27.355333 INFO: Starting candidate scoring
3:05:34.866887 INFO: Finished candidate processing
3:05:34.868689 INFO: Collecting candidate features
3:05:36.696273 WARNING: intensity_correlation has 18 NaNs ( 0.00 % out of 977626)
3:05:36.731722 INFO: Collecting fragment features
3:05:37.359172 INFO: Finished candidate scoring
3:05:38.333610 PROGRESS: === Extracted 977626 precursors and 8545015 fragments ===
3:05:38.334122 INFO: performing precursor FDR with 47 features
3:05:38.334163 INFO: Decoy channel: -1
3:05:38.334187 INFO: Competetive: True
3:05:38.647208 INFO: Setting torch num_threads to 2 for FDR classification task
3:05:38.850862 WARNING: dropped 6 target PSMs due to missing features
3:05:38.851011 WARNING: dropped 12 decoy PSMs due to missing features
3:05:56.465300 INFO: Test AUC: 0.577
3:05:56.465589 INFO: Train AUC: 0.587
3:05:56.465631 INFO: AUC difference: 1.75%
3:05:56.629244 INFO: Resetting torch num_threads to 100
3:05:56.656167 INFO: === FDR correction performed with classifier version 7 ===
3:05:56.657576 PROGRESS: ============================= Precursor FDR =============================
3:05:56.657727 PROGRESS: Total precursors accumulated: 1,334
3:05:56.657789 PROGRESS: Target precursors: 1,220 (91.45%)
3:05:56.657840 PROGRESS: Decoy precursors: 114 (8.55%)
3:05:56.657888 PROGRESS: 
3:05:56.657934 PROGRESS: Precursor Summary:
3:05:56.659397 PROGRESS: Channel   0:	 0.05 FDR:   973; 0.01 FDR:   735; 0.001 FDR:   459
3:05:56.659517 PROGRESS: 
3:05:56.659573 PROGRESS: Protein Summary:
3:05:56.661117 PROGRESS: Channel   0:	 0.05 FDR:   848; 0.01 FDR:   652; 0.001 FDR:   418
3:05:56.661216 PROGRESS: =========================================================================
3:05:56.716661 INFO: fragments_df_filtered: 5000
3:05:57.155181 INFO: calibration group: precursor, fitting mz estimator 
3:05:57.212940 INFO: calibration group: precursor, fitting rt estimator 
3:05:57.254705 INFO: calibration group: fragment, fitting mz estimator 
3:05:57.606424 INFO: calibration group: precursor, predicting mz
3:05:57.643014 INFO: calibration group: precursor, predicting rt
3:05:57.796758 INFO: calibration group: fragment, predicting mz
3:05:58.110126 INFO: === checking if optimization conditions were reached ===
3:05:58.112482 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
3:05:58.113500 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
3:05:58.113548 INFO: ==============================================
3:05:58.113664 PROGRESS: Optimization finished for ms2_error, ms1_error.
3:05:58.491149 INFO: calibration group: precursor, predicting mz
3:05:58.524624 INFO: calibration group: precursor, predicting rt
3:05:58.673054 INFO: calibration group: fragment, predicting mz
3:05:58.985032 INFO: Starting optimization step 0.
3:05:58.985370 PROGRESS: === Extracting elution groups 0 to 120000 ===
3:05:58.985470 PROGRESS: Extracting batch of 237192 precursors
3:05:59.046164 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:05:59.046301 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:05:59.046340 INFO: FWHM in RT is 2.80 seconds, sigma is 0.36
3:05:59.046365 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:05:59.046672 INFO: Starting candidate selection
3:06:10.497552 INFO: Starting candidate scoring
3:06:14.099972 INFO: Finished candidate processing
3:06:14.100080 INFO: Collecting candidate features
3:06:15.272351 WARNING: intensity_correlation has 9 NaNs ( 0.00 % out of 473145)
3:06:15.311771 INFO: Collecting fragment features
3:06:15.789550 INFO: Finished candidate scoring
3:06:16.351686 PROGRESS: === Extracted 473145 precursors and 4127559 fragments ===
3:06:16.352236 INFO: performing precursor FDR with 47 features
3:06:16.352307 INFO: Decoy channel: -1
3:06:16.352380 INFO: Competetive: True
3:06:16.588912 INFO: Setting torch num_threads to 2 for FDR classification task
3:06:16.744307 WARNING: dropped 3 target PSMs due to missing features
3:06:16.744455 WARNING: dropped 6 decoy PSMs due to missing features
3:06:26.007530 INFO: Test AUC: 0.576
3:06:26.008468 INFO: Train AUC: 0.595
3:06:26.008515 INFO: AUC difference: 3.14%
3:06:26.130195 INFO: Resetting torch num_threads to 100
3:06:26.145487 INFO: === FDR correction performed with classifier version 8 ===
3:06:26.146509 PROGRESS: ============================= Precursor FDR =============================
3:06:26.146609 PROGRESS: Total precursors accumulated: 750
3:06:26.146669 PROGRESS: Target precursors: 685 (91.33%)
3:06:26.146721 PROGRESS: Decoy precursors: 65 (8.67%)
3:06:26.146765 PROGRESS: 
3:06:26.146808 PROGRESS: Precursor Summary:
3:06:26.147941 PROGRESS: Channel   0:	 0.05 FDR:   484; 0.01 FDR:   365; 0.001 FDR:   299
3:06:26.148036 PROGRESS: 
3:06:26.148093 PROGRESS: Protein Summary:
3:06:26.149364 PROGRESS: Channel   0:	 0.05 FDR:   446; 0.01 FDR:   338; 0.001 FDR:   278
3:06:26.149457 PROGRESS: =========================================================================
3:06:26.176812 INFO: fragments_df_filtered: 3875
3:06:26.617109 INFO: calibration group: precursor, fitting mz estimator 
3:06:26.674324 INFO: calibration group: precursor, fitting rt estimator 
3:06:26.724715 INFO: calibration group: fragment, fitting mz estimator 
3:06:27.018872 INFO: calibration group: precursor, predicting mz
3:06:27.051608 INFO: calibration group: precursor, predicting rt
3:06:27.209793 INFO: calibration group: fragment, predicting mz
3:06:27.551521 INFO: === checking if optimization conditions were reached ===
3:06:27.551930 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3:06:27.555053 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 184.8633.
3:06:27.555126 INFO: ==============================================
3:06:27.555264 INFO: Starting optimization step 1.
3:06:27.557117 PROGRESS: === Extracting elution groups 0 to 120000 ===
3:06:27.557252 PROGRESS: Extracting batch of 237192 precursors
3:06:27.633653 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:06:27.633779 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:06:27.633816 INFO: FWHM in RT is 2.69 seconds, sigma is 0.35
3:06:27.633838 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:06:27.634134 INFO: Starting candidate selection
3:06:37.935169 INFO: Starting candidate scoring
3:06:41.471570 INFO: Finished candidate processing
3:06:41.471689 INFO: Collecting candidate features
3:06:42.427283 WARNING: intensity_correlation has 78 NaNs ( 0.02 % out of 469493)
3:06:42.447637 INFO: Collecting fragment features
3:06:42.739171 INFO: Finished candidate scoring
3:06:43.096415 PROGRESS: === Extracted 469493 precursors and 3889437 fragments ===
3:06:43.096973 INFO: performing precursor FDR with 47 features
3:06:43.097026 INFO: Decoy channel: -1
3:06:43.097054 INFO: Competetive: True
3:06:43.264670 INFO: Setting torch num_threads to 2 for FDR classification task
3:06:43.364391 WARNING: dropped 37 target PSMs due to missing features
3:06:43.364535 WARNING: dropped 41 decoy PSMs due to missing features
3:06:51.992538 INFO: Test AUC: 0.574
3:06:51.992752 INFO: Train AUC: 0.592
3:06:51.992787 INFO: AUC difference: 3.02%
3:06:52.129835 INFO: Resetting torch num_threads to 100
3:06:52.160428 INFO: === FDR correction performed with classifier version 8 ===
3:06:52.162386 PROGRESS: ============================= Precursor FDR =============================
3:06:52.162496 PROGRESS: Total precursors accumulated: 836
3:06:52.162558 PROGRESS: Target precursors: 762 (91.15%)
3:06:52.162608 PROGRESS: Decoy precursors: 74 (8.85%)
3:06:52.162653 PROGRESS: 
3:06:52.162695 PROGRESS: Precursor Summary:
3:06:52.163944 PROGRESS: Channel   0:	 0.05 FDR:   589; 0.01 FDR:   436; 0.001 FDR:   328
3:06:52.164041 PROGRESS: 
3:06:52.164098 PROGRESS: Protein Summary:
3:06:52.165388 PROGRESS: Channel   0:	 0.05 FDR:   535; 0.01 FDR:   402; 0.001 FDR:   302
3:06:52.165476 PROGRESS: =========================================================================
3:06:52.182808 INFO: fragments_df_filtered: 4420
3:06:52.468598 INFO: calibration group: precursor, fitting mz estimator 
3:06:52.519228 INFO: calibration group: precursor, fitting rt estimator 
3:06:52.566674 INFO: calibration group: fragment, fitting mz estimator 
3:06:52.916214 INFO: calibration group: precursor, predicting mz
3:06:52.931261 INFO: calibration group: precursor, predicting rt
3:06:53.001402 INFO: calibration group: fragment, predicting mz
3:06:53.172188 INFO: === checking if optimization conditions were reached ===
3:06:53.172547 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3:06:53.175388 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 102.0165.
3:06:53.175529 INFO: ==============================================
3:06:53.175809 INFO: Starting optimization step 2.
3:06:53.176051 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:06:53.176292 PROGRESS: Extracting batch of 110713 precursors
3:06:53.221409 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:06:53.221629 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:06:53.221729 INFO: FWHM in RT is 2.74 seconds, sigma is 0.35
3:06:53.221802 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:06:53.222174 INFO: Starting candidate selection
3:06:57.122904 INFO: Starting candidate scoring
3:06:58.620924 INFO: Finished candidate processing
3:06:58.621077 INFO: Collecting candidate features
3:06:59.211252 WARNING: intensity_correlation has 42 NaNs ( 0.02 % out of 218264)
3:06:59.222909 INFO: Collecting fragment features
3:06:59.383373 INFO: Finished candidate scoring
3:06:59.566465 PROGRESS: === Extracted 218264 precursors and 1734024 fragments ===
3:06:59.566936 INFO: performing precursor FDR with 47 features
3:06:59.566985 INFO: Decoy channel: -1
3:06:59.567012 INFO: Competetive: True
3:06:59.659575 INFO: Setting torch num_threads to 2 for FDR classification task
3:06:59.717525 WARNING: dropped 22 target PSMs due to missing features
3:06:59.717690 WARNING: dropped 20 decoy PSMs due to missing features
3:07:04.238666 INFO: Test AUC: 0.570
3:07:04.238907 INFO: Train AUC: 0.595
3:07:04.238945 INFO: AUC difference: 4.20%
3:07:04.341387 INFO: Resetting torch num_threads to 100
3:07:04.348620 INFO: === FDR correction performed with classifier version 8 ===
3:07:04.349411 PROGRESS: ============================= Precursor FDR =============================
3:07:04.349527 PROGRESS: Total precursors accumulated: 429
3:07:04.349589 PROGRESS: Target precursors: 391 (91.14%)
3:07:04.349641 PROGRESS: Decoy precursors: 38 (8.86%)
3:07:04.349687 PROGRESS: 
3:07:04.349734 PROGRESS: Precursor Summary:
3:07:04.350754 PROGRESS: Channel   0:	 0.05 FDR:   304; 0.01 FDR:   220; 0.001 FDR:   168
3:07:04.350861 PROGRESS: 
3:07:04.350919 PROGRESS: Protein Summary:
3:07:04.352039 PROGRESS: Channel   0:	 0.05 FDR:   291; 0.01 FDR:   212; 0.001 FDR:   162
3:07:04.352131 PROGRESS: =========================================================================
3:07:04.362037 INFO: fragments_df_filtered: 2092
3:07:04.656442 INFO: calibration group: precursor, fitting mz estimator 
3:07:04.698242 INFO: calibration group: precursor, fitting rt estimator 
3:07:04.734723 INFO: calibration group: fragment, fitting mz estimator 
3:07:04.832903 INFO: calibration group: precursor, predicting mz
3:07:04.847560 INFO: calibration group: precursor, predicting rt
3:07:04.920079 INFO: calibration group: fragment, predicting mz
3:07:05.096308 INFO: === checking if optimization conditions were reached ===
3:07:05.096662 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3:07:05.099120 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 87.8888.
3:07:05.099183 INFO: ==============================================
3:07:05.099306 INFO: Starting optimization step 3.
3:07:05.099383 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:07:05.099496 PROGRESS: Extracting batch of 110713 precursors
3:07:05.141211 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:07:05.141351 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:07:05.141390 INFO: FWHM in RT is 2.72 seconds, sigma is 0.35
3:07:05.141412 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:07:05.141722 INFO: Starting candidate selection
3:07:09.436663 INFO: Starting candidate scoring
3:07:10.975989 INFO: Finished candidate processing
3:07:10.976140 INFO: Collecting candidate features
3:07:11.329270 WARNING: intensity_correlation has 52 NaNs ( 0.02 % out of 218042)
3:07:11.340936 INFO: Collecting fragment features
3:07:11.471021 INFO: Finished candidate scoring
3:07:11.569973 PROGRESS: === Extracted 218042 precursors and 1732728 fragments ===
3:07:11.570360 INFO: performing precursor FDR with 47 features
3:07:11.570398 INFO: Decoy channel: -1
3:07:11.570423 INFO: Competetive: True
3:07:11.638043 INFO: Setting torch num_threads to 2 for FDR classification task
3:07:11.678760 WARNING: dropped 28 target PSMs due to missing features
3:07:11.678900 WARNING: dropped 24 decoy PSMs due to missing features
3:07:16.150586 INFO: Test AUC: 0.566
3:07:16.150718 INFO: Train AUC: 0.594
3:07:16.150750 INFO: AUC difference: 4.59%
3:07:16.259135 INFO: Resetting torch num_threads to 100
3:07:16.313339 INFO: === FDR correction performed with classifier version 8 ===
3:07:16.314259 PROGRESS: ============================= Precursor FDR =============================
3:07:16.314371 PROGRESS: Total precursors accumulated: 383
3:07:16.314435 PROGRESS: Target precursors: 349 (91.12%)
3:07:16.314490 PROGRESS: Decoy precursors: 34 (8.88%)
3:07:16.314537 PROGRESS: 
3:07:16.314581 PROGRESS: Precursor Summary:
3:07:16.315587 PROGRESS: Channel   0:	 0.05 FDR:   286; 0.01 FDR:   216; 0.001 FDR:   197
3:07:16.315680 PROGRESS: 
3:07:16.315744 PROGRESS: Protein Summary:
3:07:16.316883 PROGRESS: Channel   0:	 0.05 FDR:   274; 0.01 FDR:   207; 0.001 FDR:   189
3:07:16.316974 PROGRESS: =========================================================================
3:07:16.325783 INFO: fragments_df_filtered: 2039
3:07:16.588517 INFO: calibration group: precursor, fitting mz estimator 
3:07:16.647527 INFO: calibration group: precursor, fitting rt estimator 
3:07:16.701223 INFO: calibration group: fragment, fitting mz estimator 
3:07:16.839217 INFO: calibration group: precursor, predicting mz
3:07:16.856076 INFO: calibration group: precursor, predicting rt
3:07:16.931261 INFO: calibration group: fragment, predicting mz
3:07:17.137128 INFO: === checking if optimization conditions were reached ===
3:07:17.137437 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3:07:17.139676 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 65.5251.
3:07:17.139733 INFO: ==============================================
3:07:17.139844 INFO: Starting optimization step 4.
3:07:17.139918 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:07:17.139990 PROGRESS: Extracting batch of 110713 precursors
3:07:17.171259 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:07:17.171394 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:07:17.171434 INFO: FWHM in RT is 2.73 seconds, sigma is 0.35
3:07:17.171457 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:07:17.171779 INFO: Starting candidate selection
3:07:20.878397 INFO: Starting candidate scoring
3:07:22.421772 INFO: Finished candidate processing
3:07:22.421965 INFO: Collecting candidate features
3:07:22.900779 WARNING: intensity_correlation has 78 NaNs ( 0.04 % out of 216787)
3:07:22.911732 INFO: Collecting fragment features
3:07:23.049298 INFO: Finished candidate scoring
3:07:23.158267 PROGRESS: === Extracted 216787 precursors and 1671208 fragments ===
3:07:23.158748 INFO: performing precursor FDR with 47 features
3:07:23.158792 INFO: Decoy channel: -1
3:07:23.158816 INFO: Competetive: True
3:07:23.251888 INFO: Setting torch num_threads to 2 for FDR classification task
3:07:23.303657 WARNING: dropped 44 target PSMs due to missing features
3:07:23.303828 WARNING: dropped 34 decoy PSMs due to missing features
3:07:27.458800 INFO: Test AUC: 0.571
3:07:27.458945 INFO: Train AUC: 0.595
3:07:27.458976 INFO: AUC difference: 3.99%
3:07:27.595436 INFO: Resetting torch num_threads to 100
3:07:27.605169 INFO: === FDR correction performed with classifier version 8 ===
3:07:27.606038 PROGRESS: ============================= Precursor FDR =============================
3:07:27.606148 PROGRESS: Total precursors accumulated: 358
3:07:27.606211 PROGRESS: Target precursors: 326 (91.06%)
3:07:27.606263 PROGRESS: Decoy precursors: 32 (8.94%)
3:07:27.606310 PROGRESS: 
3:07:27.606358 PROGRESS: Precursor Summary:
3:07:27.607306 PROGRESS: Channel   0:	 0.05 FDR:   246; 0.01 FDR:    27; 0.001 FDR:    27
3:07:27.607397 PROGRESS: 
3:07:27.607453 PROGRESS: Protein Summary:
3:07:27.608498 PROGRESS: Channel   0:	 0.05 FDR:   234; 0.01 FDR:    27; 0.001 FDR:    27
3:07:27.608594 PROGRESS: =========================================================================
3:07:28.029664 INFO: calibration group: precursor, predicting mz
3:07:28.049919 INFO: calibration group: precursor, predicting rt
3:07:28.229143 INFO: calibration group: fragment, predicting mz
3:07:28.505157 INFO: === skipping optimization until target number of precursors are found ===
3:07:28.505751 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
3:07:28.505895 INFO: Starting optimization step 5.
3:07:28.506026 PROGRESS: === Extracting elution groups 56000 to 120000 ===
3:07:28.506127 PROGRESS: Extracting batch of 126479 precursors
3:07:28.580219 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:07:28.580398 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:07:28.580434 INFO: FWHM in RT is 2.73 seconds, sigma is 0.35
3:07:28.580458 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:07:28.580972 INFO: Starting candidate selection
3:07:33.173936 INFO: Starting candidate scoring
3:07:35.016909 INFO: Finished candidate processing
3:07:35.017013 INFO: Collecting candidate features
3:07:35.476459 WARNING: intensity_correlation has 114 NaNs ( 0.05 % out of 247798)
3:07:35.488022 INFO: Collecting fragment features
3:07:35.631618 INFO: Finished candidate scoring
3:07:35.926629 PROGRESS: === Extracted 464585 precursors and 3579955 fragments ===
3:07:35.976662 INFO: performing precursor FDR with 47 features
3:07:35.976806 INFO: Decoy channel: -1
3:07:35.976830 INFO: Competetive: True
3:07:36.262455 INFO: Setting torch num_threads to 2 for FDR classification task
3:07:36.378375 WARNING: dropped 97 target PSMs due to missing features
3:07:36.378531 WARNING: dropped 95 decoy PSMs due to missing features
3:07:46.401239 INFO: Test AUC: 0.572
3:07:46.401455 INFO: Train AUC: 0.590
3:07:46.401491 INFO: AUC difference: 3.06%
3:07:46.522958 INFO: Resetting torch num_threads to 100
3:07:46.548009 INFO: === FDR correction performed with classifier version 8 ===
3:07:46.548964 PROGRESS: ============================= Precursor FDR =============================
3:07:46.549062 PROGRESS: Total precursors accumulated: 928
3:07:46.549124 PROGRESS: Target precursors: 847 (91.27%)
3:07:46.549178 PROGRESS: Decoy precursors: 81 (8.73%)
3:07:46.549226 PROGRESS: 
3:07:46.549283 PROGRESS: Precursor Summary:
3:07:46.550451 PROGRESS: Channel   0:	 0.05 FDR:   649; 0.01 FDR:   460; 0.001 FDR:   410
3:07:46.550547 PROGRESS: 
3:07:46.550603 PROGRESS: Protein Summary:
3:07:46.551876 PROGRESS: Channel   0:	 0.05 FDR:   593; 0.01 FDR:   422; 0.001 FDR:   376
3:07:46.551972 PROGRESS: =========================================================================
3:07:46.601925 INFO: fragments_df_filtered: 4494
3:07:46.886341 INFO: calibration group: precursor, fitting mz estimator 
3:07:46.956892 INFO: calibration group: precursor, fitting rt estimator 
3:07:47.024831 INFO: calibration group: fragment, fitting mz estimator 
3:07:47.381754 INFO: calibration group: precursor, predicting mz
3:07:47.398894 INFO: calibration group: precursor, predicting rt
3:07:47.473141 INFO: calibration group: fragment, predicting mz
3:07:47.651138 INFO: === checking if optimization conditions were reached ===
3:07:47.651509 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3:07:47.653938 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 60.6307.
3:07:47.654005 INFO: ==============================================
3:07:47.654103 INFO: Starting optimization step 6.
3:07:47.654169 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:07:47.654241 PROGRESS: Extracting batch of 110713 precursors
3:07:47.684237 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:07:47.684362 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:07:47.684402 INFO: FWHM in RT is 2.71 seconds, sigma is 0.35
3:07:47.684428 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:07:47.684715 INFO: Starting candidate selection
3:07:51.360234 INFO: Starting candidate scoring
3:07:52.949067 INFO: Finished candidate processing
3:07:52.949173 INFO: Collecting candidate features
3:07:53.299732 WARNING: intensity_correlation has 50 NaNs ( 0.02 % out of 217151)
3:07:53.310692 INFO: Collecting fragment features
3:07:53.459148 INFO: Finished candidate scoring
3:07:53.593681 PROGRESS: === Extracted 217151 precursors and 1666396 fragments ===
3:07:53.594168 INFO: performing precursor FDR with 47 features
3:07:53.594214 INFO: Decoy channel: -1
3:07:53.594244 INFO: Competetive: True
3:07:53.706633 INFO: Setting torch num_threads to 2 for FDR classification task
3:07:53.759712 WARNING: dropped 27 target PSMs due to missing features
3:07:53.759901 WARNING: dropped 23 decoy PSMs due to missing features
3:07:58.096424 INFO: Test AUC: 0.569
3:07:58.096778 INFO: Train AUC: 0.593
3:07:58.096818 INFO: AUC difference: 3.92%
3:07:58.209435 INFO: Resetting torch num_threads to 100
3:07:58.217315 INFO: === FDR correction performed with classifier version 8 ===
3:07:58.218229 PROGRESS: ============================= Precursor FDR =============================
3:07:58.218343 PROGRESS: Total precursors accumulated: 383
3:07:58.218422 PROGRESS: Target precursors: 352 (91.91%)
3:07:58.218477 PROGRESS: Decoy precursors: 31 (8.09%)
3:07:58.218523 PROGRESS: 
3:07:58.218567 PROGRESS: Precursor Summary:
3:07:58.219582 PROGRESS: Channel   0:	 0.05 FDR:   293; 0.01 FDR:   171; 0.001 FDR:   147
3:07:58.219688 PROGRESS: 
3:07:58.220636 PROGRESS: Protein Summary:
3:07:58.221824 PROGRESS: Channel   0:	 0.05 FDR:   278; 0.01 FDR:   164; 0.001 FDR:   143
3:07:58.221929 PROGRESS: =========================================================================
3:07:58.966923 INFO: calibration group: precursor, predicting mz
3:07:58.984602 INFO: calibration group: precursor, predicting rt
3:07:59.067667 INFO: calibration group: fragment, predicting mz
3:07:59.268368 INFO: === skipping optimization until target number of precursors are found ===
3:07:59.268791 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
3:07:59.268891 INFO: Starting optimization step 7.
3:07:59.268976 PROGRESS: === Extracting elution groups 56000 to 120000 ===
3:07:59.269066 PROGRESS: Extracting batch of 126479 precursors
3:07:59.319751 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:07:59.319902 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:07:59.319959 INFO: FWHM in RT is 2.71 seconds, sigma is 0.35
3:07:59.319987 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:07:59.320353 INFO: Starting candidate selection
3:08:03.534458 INFO: Starting candidate scoring
3:08:05.262546 INFO: Finished candidate processing
3:08:05.262675 INFO: Collecting candidate features
3:08:05.744205 WARNING: intensity_correlation has 80 NaNs ( 0.03 % out of 248165)
3:08:05.756166 INFO: Collecting fragment features
3:08:05.942062 INFO: Finished candidate scoring
3:08:06.397062 PROGRESS: === Extracted 465316 precursors and 3568596 fragments ===
3:08:06.454858 INFO: performing precursor FDR with 47 features
3:08:06.455008 INFO: Decoy channel: -1
3:08:06.455036 INFO: Competetive: True
3:08:06.718820 INFO: Setting torch num_threads to 2 for FDR classification task
3:08:06.828130 WARNING: dropped 65 target PSMs due to missing features
3:08:06.828282 WARNING: dropped 65 decoy PSMs due to missing features
3:08:19.552427 INFO: Test AUC: 0.572
3:08:19.552636 INFO: Train AUC: 0.590
3:08:19.552672 INFO: AUC difference: 3.06%
3:08:19.675254 INFO: Resetting torch num_threads to 100
3:08:19.706374 INFO: === FDR correction performed with classifier version 8 ===
3:08:19.707356 PROGRESS: ============================= Precursor FDR =============================
3:08:19.707455 PROGRESS: Total precursors accumulated: 910
3:08:19.707528 PROGRESS: Target precursors: 828 (90.99%)
3:08:19.707584 PROGRESS: Decoy precursors: 82 (9.01%)
3:08:19.707629 PROGRESS: 
3:08:19.707676 PROGRESS: Precursor Summary:
3:08:19.708839 PROGRESS: Channel   0:	 0.05 FDR:   643; 0.01 FDR:   514; 0.001 FDR:   355
3:08:19.708933 PROGRESS: 
3:08:19.708989 PROGRESS: Protein Summary:
3:08:19.710260 PROGRESS: Channel   0:	 0.05 FDR:   584; 0.01 FDR:   467; 0.001 FDR:   326
3:08:19.710353 PROGRESS: =========================================================================
3:08:19.760086 INFO: fragments_df_filtered: 4866
3:08:20.095279 INFO: calibration group: precursor, fitting mz estimator 
3:08:20.139734 INFO: calibration group: precursor, fitting rt estimator 
3:08:20.178425 INFO: calibration group: fragment, fitting mz estimator 
3:08:20.534873 INFO: calibration group: precursor, predicting mz
3:08:20.553319 INFO: calibration group: precursor, predicting rt
3:08:20.626305 INFO: calibration group: fragment, predicting mz
3:08:20.807696 INFO: === checking if optimization conditions were reached ===
3:08:20.808056 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3:08:20.810780 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 60.6711.
3:08:20.810845 INFO: ==============================================
3:08:20.810961 INFO: Starting optimization step 8.
3:08:20.811038 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:08:20.811118 PROGRESS: Extracting batch of 110713 precursors
3:08:20.858276 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:08:20.858405 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:08:20.858446 INFO: FWHM in RT is 2.67 seconds, sigma is 0.34
3:08:20.858469 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:08:20.858768 INFO: Starting candidate selection
3:08:24.938742 INFO: Starting candidate scoring
3:08:26.395144 INFO: Finished candidate processing
3:08:26.395254 INFO: Collecting candidate features
3:08:26.754929 WARNING: intensity_correlation has 61 NaNs ( 0.03 % out of 217235)
3:08:26.765682 INFO: Collecting fragment features
3:08:26.910311 INFO: Finished candidate scoring
3:08:27.023269 PROGRESS: === Extracted 217235 precursors and 1652954 fragments ===
3:08:27.023952 INFO: performing precursor FDR with 47 features
3:08:27.023996 INFO: Decoy channel: -1
3:08:27.024020 INFO: Competetive: True
3:08:27.101644 INFO: Setting torch num_threads to 2 for FDR classification task
3:08:27.140041 WARNING: dropped 27 target PSMs due to missing features
3:08:27.140178 WARNING: dropped 34 decoy PSMs due to missing features
3:08:31.336763 INFO: Test AUC: 0.566
3:08:31.336898 INFO: Train AUC: 0.595
3:08:31.336929 INFO: AUC difference: 4.86%
3:08:31.435852 INFO: Resetting torch num_threads to 100
3:08:31.442020 INFO: === FDR correction performed with classifier version 8 ===
3:08:31.442737 PROGRESS: ============================= Precursor FDR =============================
3:08:31.442869 PROGRESS: Total precursors accumulated: 379
3:08:31.442930 PROGRESS: Target precursors: 348 (91.82%)
3:08:31.442980 PROGRESS: Decoy precursors: 31 (8.18%)
3:08:31.443024 PROGRESS: 
3:08:31.443069 PROGRESS: Precursor Summary:
3:08:31.444050 PROGRESS: Channel   0:	 0.05 FDR:   269; 0.01 FDR:   159; 0.001 FDR:   100
3:08:31.444142 PROGRESS: 
3:08:31.444198 PROGRESS: Protein Summary:
3:08:31.445258 PROGRESS: Channel   0:	 0.05 FDR:   259; 0.01 FDR:   154; 0.001 FDR:    98
3:08:31.445362 PROGRESS: =========================================================================
3:08:31.842895 INFO: calibration group: precursor, predicting mz
3:08:31.861656 INFO: calibration group: precursor, predicting rt
3:08:31.942188 INFO: calibration group: fragment, predicting mz
3:08:32.142665 INFO: === skipping optimization until target number of precursors are found ===
3:08:32.143062 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
3:08:32.143148 INFO: Starting optimization step 9.
3:08:32.143229 PROGRESS: === Extracting elution groups 56000 to 120000 ===
3:08:32.143327 PROGRESS: Extracting batch of 126479 precursors
3:08:32.186921 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:08:32.187060 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:08:32.187108 INFO: FWHM in RT is 2.67 seconds, sigma is 0.34
3:08:32.187132 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:08:32.187504 INFO: Starting candidate selection
3:08:38.372629 INFO: Starting candidate scoring
3:08:40.042590 INFO: Finished candidate processing
3:08:40.042698 INFO: Collecting candidate features
3:08:40.463704 WARNING: intensity_correlation has 96 NaNs ( 0.04 % out of 248204)
3:08:40.475749 INFO: Collecting fragment features
3:08:40.637924 INFO: Finished candidate scoring
3:08:40.902904 PROGRESS: === Extracted 465439 precursors and 3540072 fragments ===
3:08:40.951892 INFO: performing precursor FDR with 47 features
3:08:40.952026 INFO: Decoy channel: -1
3:08:40.952053 INFO: Competetive: True
3:08:41.165667 INFO: Setting torch num_threads to 2 for FDR classification task
3:08:41.260839 WARNING: dropped 70 target PSMs due to missing features
3:08:41.260985 WARNING: dropped 87 decoy PSMs due to missing features
3:08:50.083474 INFO: Test AUC: 0.570
3:08:50.083689 INFO: Train AUC: 0.589
3:08:50.083723 INFO: AUC difference: 3.22%
3:08:50.207429 INFO: Resetting torch num_threads to 100
3:08:50.237031 INFO: === FDR correction performed with classifier version 8 ===
3:08:50.238124 PROGRESS: ============================= Precursor FDR =============================
3:08:50.240389 PROGRESS: Total precursors accumulated: 914
3:08:50.240455 PROGRESS: Target precursors: 836 (91.47%)
3:08:50.240507 PROGRESS: Decoy precursors: 78 (8.53%)
3:08:50.240552 PROGRESS: 
3:08:50.240597 PROGRESS: Precursor Summary:
3:08:50.241879 PROGRESS: Channel   0:	 0.05 FDR:   629; 0.01 FDR:   471; 0.001 FDR:   265
3:08:50.241978 PROGRESS: 
3:08:50.242046 PROGRESS: Protein Summary:
3:08:50.243302 PROGRESS: Channel   0:	 0.05 FDR:   568; 0.01 FDR:   430; 0.001 FDR:   247
3:08:50.243404 PROGRESS: =========================================================================
3:08:50.304066 INFO: fragments_df_filtered: 4539
3:08:50.573462 INFO: calibration group: precursor, fitting mz estimator 
3:08:50.627010 INFO: calibration group: precursor, fitting rt estimator 
3:08:50.676032 INFO: calibration group: fragment, fitting mz estimator 
3:08:51.039168 INFO: calibration group: precursor, predicting mz
3:08:51.054918 INFO: calibration group: precursor, predicting rt
3:08:51.126762 INFO: calibration group: fragment, predicting mz
3:08:51.311529 INFO: === checking if optimization conditions were reached ===
3:08:51.311877 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
3:08:51.313489 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 60.6307 found after 7 searches.
3:08:51.313554 INFO: ==============================================
3:08:51.313676 PROGRESS: Optimization finished for rt_error.
3:08:51.533113 INFO: calibration group: precursor, predicting mz
3:08:51.550980 INFO: calibration group: precursor, predicting rt
3:08:51.629053 INFO: calibration group: fragment, predicting mz
3:08:51.847401 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:08:51.847632 PROGRESS: ==============================================
3:08:51.847726 PROGRESS: ms2_error      : 15.0000
3:08:51.847830 PROGRESS: ms1_error      : 10.0000
3:08:51.848023 PROGRESS: rt_error       : 60.6307
3:08:51.848110 PROGRESS: ==============================================
3:08:51.851482 INFO: calibration group: precursor, predicting mz
3:08:53.522499 INFO: calibration group: precursor, predicting rt
3:09:00.294004 INFO: calibration group: fragment, predicting mz
3:09:15.983734 PROGRESS: Extracting batch of 10183864 precursors
3:09:18.321741 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:09:18.321893 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:09:18.321938 INFO: FWHM in RT is 2.67 seconds, sigma is 0.34
3:09:18.321963 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:09:18.322360 INFO: Starting candidate selection
3:14:44.974777 INFO: Applying score cutoff of 32.933696842193605
3:14:45.506279 INFO: Removed 5672732 precursors with score below cutoff
3:14:47.721761 INFO: Starting candidate scoring
3:16:31.958708 INFO: Finished candidate processing
3:16:31.959119 INFO: Collecting candidate features
3:16:56.592602 WARNING: intensity_correlation has 502 NaNs ( 0.00 % out of 14636645)
3:16:57.098917 INFO: Collecting fragment features
3:17:08.485544 INFO: Finished candidate scoring
3:17:33.189261 INFO: === FDR correction performed with classifier version 16 ===
3:17:33.320112 INFO: performing precursor FDR with 47 features
3:17:33.320253 INFO: Decoy channel: -1
3:17:33.320292 INFO: Competetive: True
3:17:39.219978 INFO: Setting torch num_threads to 2 for FDR classification task
3:17:42.419232 WARNING: dropped 266 target PSMs due to missing features
3:17:42.419391 WARNING: dropped 236 decoy PSMs due to missing features
3:23:35.588778 INFO: Test AUC: 0.583
3:23:35.589195 INFO: Train AUC: 0.586
3:23:35.589249 INFO: AUC difference: 0.43%
3:23:36.628634 INFO: Resetting torch num_threads to 100
3:23:37.682749 INFO: Removing fragments below FDR threshold
3:23:38.799578 PROGRESS: ============================= Precursor FDR =============================
3:23:38.799976 PROGRESS: Total precursors accumulated: 24,001
3:23:38.800047 PROGRESS: Target precursors: 23,764 (99.01%)
3:23:38.800101 PROGRESS: Decoy precursors: 237 (0.99%)
3:23:38.800148 PROGRESS: 
3:23:38.800196 PROGRESS: Precursor Summary:
3:23:38.809371 PROGRESS: Channel   0:	 0.05 FDR: 23,764; 0.01 FDR: 23,764; 0.001 FDR: 15,583
3:23:38.809616 PROGRESS: 
3:23:38.809680 PROGRESS: Protein Summary:
3:23:38.823294 PROGRESS: Channel   0:	 0.05 FDR: 7,069; 0.01 FDR: 7,069; 0.001 FDR: 5,250
3:23:38.823609 PROGRESS: =========================================================================
3:23:39.312955 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:23:39.738232 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:23:39.738441 INFO: Quantification results path: run_output_Astral/alphadia_1.10_default/library/quant
3:23:39.738537 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3 at run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:23:39.739624 INFO: Initializing RawFileManager
3:24:06.720893 INFO: Determining DIA cycle
3:24:06.739150 INFO: Found cycle with start 0.00 min and length 303.
3:24:06.926132 INFO: RT (min)            : 0.0 - 26.9
3:24:06.926237 INFO: RT duration (sec)   : 1611.2
3:24:06.926267 INFO: RT duration (min)   : 26.9
3:24:06.926291 INFO: Cycle len (scans)   : 303
3:24:06.926311 INFO: Cycle len (sec)     : 1.65
3:24:06.926331 INFO: Number of cycles    : 978
3:24:06.926351 INFO: MS2 range (m/z)     : 380.4 - 980.7
3:24:08.451451 INFO: Initializing CalibrationManager
3:24:08.452093 INFO: Loading calibration config
3:24:08.453185 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'}]
3:24:08.453361 INFO: Calibration group :fragment, found 1 estimator(s)
3:24:08.453470 INFO: Calibration group :precursor, found 3 estimator(s)
3:24:08.453573 INFO: Disabling ion mobility calibration
3:24:08.453602 INFO: removed mobility estimator from group precursor
3:24:08.453783 INFO: Initializing OptimizationManager
3:24:08.453920 INFO: initial parameter: ms1_error = 30
3:24:08.453984 INFO: initial parameter: ms2_error = 30
3:24:08.454042 INFO: initial parameter: rt_error = 805.611083984375
3:24:08.454090 INFO: initial parameter: mobility_error = 0.1
3:24:08.454133 INFO: initial parameter: column_type = library
3:24:08.454173 INFO: initial parameter: num_candidates = 1
3:24:08.454211 INFO: initial parameter: classifier_version = -1
3:24:08.454250 INFO: initial parameter: fwhm_rt = 5
3:24:08.454295 INFO: initial parameter: fwhm_mobility = 0.01
3:24:08.454334 INFO: initial parameter: score_cutoff = 0
3:24:08.454402 INFO: Initializing TimingManager
3:24:08.454463 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:24:08.454630 INFO: FDRManager not loaded from disk.
3:24:08.454655 INFO: Initializing FDRManager
3:24:08.454700 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
3:24:09.772908 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
3:24:11.635071 PROGRESS: Starting initial search for precursors.
3:24:11.898108 INFO: Starting optimization step 0.
3:24:11.898375 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:24:11.898452 PROGRESS: Extracting batch of 15808 precursors
3:24:11.902525 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:24:11.902586 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:24:11.902621 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:24:11.902643 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:24:11.902936 INFO: Starting candidate selection
3:24:13.286969 INFO: Starting candidate scoring
3:24:13.410893 INFO: Finished candidate processing
3:24:13.410995 INFO: Collecting candidate features
3:24:13.449264 INFO: Collecting fragment features
3:24:13.466247 INFO: Finished candidate scoring
3:24:13.475276 PROGRESS: === Extracted 15767 precursors and 156433 fragments ===
3:24:13.475632 INFO: performing precursor FDR with 47 features
3:24:13.475670 INFO: Decoy channel: -1
3:24:13.475694 INFO: Competetive: True
3:24:13.482301 INFO: Setting torch num_threads to 2 for FDR classification task
3:24:13.658149 INFO: Test AUC: 0.510
3:24:13.658284 INFO: Train AUC: 0.510
3:24:13.658314 INFO: AUC difference: 0.10%
3:24:13.741793 INFO: Resetting torch num_threads to 100
3:24:13.743024 INFO: === FDR correction performed with classifier version -1 ===
3:24:13.745677 PROGRESS: ============================= Precursor FDR =============================
3:24:13.745825 PROGRESS: Total precursors accumulated: 7,982
3:24:13.745888 PROGRESS: Target precursors: 4,113 (51.53%)
3:24:13.745937 PROGRESS: Decoy precursors: 3,869 (48.47%)
3:24:13.745984 PROGRESS: 
3:24:13.746029 PROGRESS: Precursor Summary:
3:24:13.746966 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:24:13.747059 PROGRESS: 
3:24:13.747114 PROGRESS: Protein Summary:
3:24:13.748103 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:24:13.748195 PROGRESS: =========================================================================
3:24:13.859767 INFO: Starting optimization step 1.
3:24:13.860034 PROGRESS: === Extracting elution groups 8000 to 24000 ===
3:24:13.860106 PROGRESS: Extracting batch of 31655 precursors
3:24:13.868957 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:24:13.869031 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:24:13.869062 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:24:13.869084 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:24:13.869271 INFO: Starting candidate selection
3:24:15.952306 INFO: Starting candidate scoring
3:24:16.176337 INFO: Finished candidate processing
3:24:16.176446 INFO: Collecting candidate features
3:24:16.242105 INFO: Collecting fragment features
3:24:16.267255 INFO: Finished candidate scoring
3:24:16.298054 PROGRESS: === Extracted 47337 precursors and 470276 fragments ===
3:24:16.304401 INFO: performing precursor FDR with 47 features
3:24:16.304487 INFO: Decoy channel: -1
3:24:16.304514 INFO: Competetive: True
3:24:16.327306 INFO: Setting torch num_threads to 2 for FDR classification task
3:24:17.095088 INFO: Test AUC: 0.541
3:24:17.095215 INFO: Train AUC: 0.550
3:24:17.095245 INFO: AUC difference: 1.62%
3:24:17.181197 INFO: Resetting torch num_threads to 100
3:24:17.184287 INFO: === FDR correction performed with classifier version -1 ===
3:24:17.185068 PROGRESS: ============================= Precursor FDR =============================
3:24:17.185179 PROGRESS: Total precursors accumulated: 1
3:24:17.185243 PROGRESS: Target precursors: 1 (100.00%)
3:24:17.185297 PROGRESS: Decoy precursors: 0 (0.00%)
3:24:17.185343 PROGRESS: 
3:24:17.185391 PROGRESS: Precursor Summary:
3:24:17.186321 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
3:24:17.186409 PROGRESS: 
3:24:17.186463 PROGRESS: Protein Summary:
3:24:17.187468 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
3:24:17.187555 PROGRESS: =========================================================================
3:24:17.341375 INFO: Starting optimization step 2.
3:24:17.341661 PROGRESS: === Extracting elution groups 24000 to 56000 ===
3:24:17.341731 PROGRESS: Extracting batch of 63250 precursors
3:24:17.356395 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:24:17.356517 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:24:17.356552 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:24:17.356577 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:24:17.356786 INFO: Starting candidate selection
3:24:21.452388 INFO: Starting candidate scoring
3:24:21.881927 INFO: Finished candidate processing
3:24:21.882031 INFO: Collecting candidate features
3:24:22.015033 INFO: Collecting fragment features
3:24:22.063828 INFO: Finished candidate scoring
3:24:22.133295 PROGRESS: === Extracted 110418 precursors and 1096618 fragments ===
3:24:22.146361 INFO: performing precursor FDR with 47 features
3:24:22.146492 INFO: Decoy channel: -1
3:24:22.146519 INFO: Competetive: True
3:24:22.205523 INFO: Setting torch num_threads to 2 for FDR classification task
3:24:24.811138 INFO: Test AUC: 0.550
3:24:24.811278 INFO: Train AUC: 0.579
3:24:24.811309 INFO: AUC difference: 4.93%
3:24:24.898647 INFO: Resetting torch num_threads to 100
3:24:24.905856 INFO: === FDR correction performed with classifier version -1 ===
3:24:24.918742 PROGRESS: ============================= Precursor FDR =============================
3:24:24.919039 PROGRESS: Total precursors accumulated: 55,637
3:24:24.919113 PROGRESS: Target precursors: 33,036 (59.38%)
3:24:24.919166 PROGRESS: Decoy precursors: 22,601 (40.62%)
3:24:24.919213 PROGRESS: 
3:24:24.919259 PROGRESS: Precursor Summary:
3:24:24.920529 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:24:24.920625 PROGRESS: 
3:24:24.920680 PROGRESS: Protein Summary:
3:24:24.921895 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:24:24.921989 PROGRESS: =========================================================================
3:24:25.161157 INFO: Starting optimization step 3.
3:24:25.161503 PROGRESS: === Extracting elution groups 56000 to 120000 ===
3:24:25.161582 PROGRESS: Extracting batch of 126479 precursors
3:24:25.194322 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:24:25.194464 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:24:25.194500 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:24:25.194524 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:24:25.194765 INFO: Starting candidate selection
3:24:33.325832 INFO: Starting candidate scoring
3:24:34.240373 INFO: Finished candidate processing
3:24:34.240498 INFO: Collecting candidate features
3:24:34.560568 INFO: Collecting fragment features
3:24:34.679088 INFO: Finished candidate scoring
3:24:34.914103 PROGRESS: === Extracted 236610 precursors and 2348757 fragments ===
3:24:34.954487 INFO: performing precursor FDR with 47 features
3:24:34.954642 INFO: Decoy channel: -1
3:24:34.954671 INFO: Competetive: True
3:24:35.118555 INFO: Setting torch num_threads to 2 for FDR classification task
3:24:40.558174 INFO: Test AUC: 0.562
3:24:40.558374 INFO: Train AUC: 0.591
3:24:40.558407 INFO: AUC difference: 4.88%
3:24:40.659761 INFO: Resetting torch num_threads to 100
3:24:40.677527 INFO: === FDR correction performed with classifier version -1 ===
3:24:40.678593 PROGRESS: ============================= Precursor FDR =============================
3:24:40.678724 PROGRESS: Total precursors accumulated: 1
3:24:40.678786 PROGRESS: Target precursors: 1 (100.00%)
3:24:40.678837 PROGRESS: Decoy precursors: 0 (0.00%)
3:24:40.678887 PROGRESS: 
3:24:40.678931 PROGRESS: Precursor Summary:
3:24:40.679913 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
3:24:40.680010 PROGRESS: 
3:24:40.680068 PROGRESS: Protein Summary:
3:24:40.681099 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
3:24:40.681190 PROGRESS: =========================================================================
3:24:41.154577 INFO: Starting optimization step 4.
3:24:41.154878 PROGRESS: === Extracting elution groups 120000 to 248000 ===
3:24:41.154967 PROGRESS: Extracting batch of 252997 precursors
3:24:41.218902 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:24:41.219035 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:24:41.219074 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:24:41.219100 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:24:41.219422 INFO: Starting candidate selection
3:24:58.309188 INFO: Starting candidate scoring
3:25:00.590647 INFO: Finished candidate processing
3:25:00.591878 INFO: Collecting candidate features
3:25:01.633247 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 252328)
3:25:01.653366 INFO: Collecting fragment features
3:25:01.920359 INFO: Finished candidate scoring
3:25:02.613053 PROGRESS: === Extracted 488938 precursors and 4852274 fragments ===
3:25:02.702791 INFO: performing precursor FDR with 47 features
3:25:02.702976 INFO: Decoy channel: -1
3:25:02.703017 INFO: Competetive: True
3:25:02.994666 INFO: Setting torch num_threads to 2 for FDR classification task
3:25:03.109766 WARNING: dropped 2 target PSMs due to missing features
3:25:03.109926 WARNING: dropped 1 decoy PSMs due to missing features
3:25:13.770111 INFO: Test AUC: 0.570
3:25:13.770330 INFO: Train AUC: 0.590
3:25:13.770374 INFO: AUC difference: 3.34%
3:25:13.899591 INFO: Resetting torch num_threads to 100
3:25:13.932425 INFO: === FDR correction performed with classifier version -1 ===
3:25:13.933605 PROGRESS: ============================= Precursor FDR =============================
3:25:13.933736 PROGRESS: Total precursors accumulated: 4
3:25:13.933800 PROGRESS: Target precursors: 4 (100.00%)
3:25:13.933851 PROGRESS: Decoy precursors: 0 (0.00%)
3:25:13.933895 PROGRESS: 
3:25:13.933940 PROGRESS: Precursor Summary:
3:25:13.934918 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
3:25:13.935025 PROGRESS: 
3:25:13.935083 PROGRESS: Protein Summary:
3:25:13.936160 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
3:25:13.936263 PROGRESS: =========================================================================
3:25:14.928645 INFO: Starting optimization step 5.
3:25:14.929041 PROGRESS: === Extracting elution groups 248000 to 504000 ===
3:25:14.929144 PROGRESS: Extracting batch of 506030 precursors
3:25:15.052128 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:25:15.052263 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:25:15.052303 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:25:15.052325 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:25:15.052689 INFO: Starting candidate selection
3:25:46.753191 INFO: Starting candidate scoring
3:25:50.685963 INFO: Finished candidate processing
3:25:50.686108 INFO: Collecting candidate features
3:25:52.196867 WARNING: intensity_correlation has 5 NaNs ( 0.00 % out of 504774)
3:25:52.215769 INFO: Collecting fragment features
3:25:52.607582 INFO: Finished candidate scoring
3:25:53.400643 PROGRESS: === Extracted 993712 precursors and 9863698 fragments ===
3:25:53.567686 INFO: performing precursor FDR with 47 features
3:25:53.567869 INFO: Decoy channel: -1
3:25:53.567897 INFO: Competetive: True
3:25:54.191648 INFO: Setting torch num_threads to 2 for FDR classification task
3:25:54.452744 WARNING: dropped 3 target PSMs due to missing features
3:25:54.452917 WARNING: dropped 5 decoy PSMs due to missing features
3:26:14.599240 INFO: Test AUC: 0.572
3:26:14.599457 INFO: Train AUC: 0.585
3:26:14.599494 INFO: AUC difference: 2.24%
3:26:14.770409 INFO: Resetting torch num_threads to 100
3:26:14.839142 INFO: === FDR correction performed with classifier version -1 ===
3:26:14.840483 PROGRESS: ============================= Precursor FDR =============================
3:26:14.840642 PROGRESS: Total precursors accumulated: 919
3:26:14.840709 PROGRESS: Target precursors: 838 (91.19%)
3:26:14.840763 PROGRESS: Decoy precursors: 81 (8.81%)
3:26:14.840817 PROGRESS: 
3:26:14.840861 PROGRESS: Precursor Summary:
3:26:14.842224 PROGRESS: Channel   0:	 0.05 FDR:   676; 0.01 FDR:   429; 0.001 FDR:   272
3:26:14.842322 PROGRESS: 
3:26:14.842376 PROGRESS: Protein Summary:
3:26:14.843660 PROGRESS: Channel   0:	 0.05 FDR:   604; 0.01 FDR:   385; 0.001 FDR:   250
3:26:14.843764 PROGRESS: =========================================================================
3:26:14.965360 INFO: fragments_df_filtered: 4043
3:26:15.760401 INFO: calibration group: precursor, fitting mz estimator 
3:26:15.825953 INFO: calibration group: precursor, fitting rt estimator 
3:26:15.879199 INFO: calibration group: fragment, fitting mz estimator 
3:26:16.189517 INFO: calibration group: precursor, predicting mz
3:26:16.277253 INFO: calibration group: precursor, predicting rt
3:26:16.613539 INFO: calibration group: fragment, predicting mz
3:26:17.374476 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3:26:17.374860 INFO: Starting optimization step 6.
3:26:17.374951 PROGRESS: === Extracting elution groups 0 to 248000 ===
3:26:17.375050 PROGRESS: Extracting batch of 490189 precursors
3:26:17.681756 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:26:17.681920 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:26:17.681973 INFO: FWHM in RT is 2.71 seconds, sigma is 0.35
3:26:17.681996 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:26:17.682460 INFO: Starting candidate selection
3:26:41.384130 INFO: Starting candidate scoring
3:26:48.979383 INFO: Finished candidate processing
3:26:48.979519 INFO: Collecting candidate features
3:26:51.011688 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 977939)
3:26:51.046553 INFO: Collecting fragment features
3:26:51.749254 INFO: Finished candidate scoring
3:26:52.503614 PROGRESS: === Extracted 977939 precursors and 9610373 fragments ===
3:26:52.504250 INFO: performing precursor FDR with 47 features
3:26:52.504295 INFO: Decoy channel: -1
3:26:52.504319 INFO: Competetive: True
3:26:52.861345 INFO: Setting torch num_threads to 2 for FDR classification task
3:26:53.090169 WARNING: dropped 1 target PSMs due to missing features
3:27:14.116967 INFO: Test AUC: 0.573
3:27:14.117229 INFO: Train AUC: 0.586
3:27:14.117267 INFO: AUC difference: 2.13%
3:27:14.392540 INFO: Resetting torch num_threads to 100
3:27:14.571580 INFO: === FDR correction performed with classifier version 5 ===
3:27:14.573018 PROGRESS: ============================= Precursor FDR =============================
3:27:14.573156 PROGRESS: Total precursors accumulated: 815
3:27:14.573218 PROGRESS: Target precursors: 748 (91.78%)
3:27:14.573268 PROGRESS: Decoy precursors: 67 (8.22%)
3:27:14.573324 PROGRESS: 
3:27:14.573370 PROGRESS: Precursor Summary:
3:27:14.574640 PROGRESS: Channel   0:	 0.05 FDR:   593; 0.01 FDR:   348; 0.001 FDR:   277
3:27:14.574741 PROGRESS: 
3:27:14.574797 PROGRESS: Protein Summary:
3:27:14.576075 PROGRESS: Channel   0:	 0.05 FDR:   546; 0.01 FDR:   326; 0.001 FDR:   260
3:27:14.576171 PROGRESS: =========================================================================
3:27:14.631009 INFO: fragments_df_filtered: 4184
3:27:15.384020 INFO: calibration group: precursor, fitting mz estimator 
3:27:15.438738 INFO: calibration group: precursor, fitting rt estimator 
3:27:15.488620 INFO: calibration group: fragment, fitting mz estimator 
3:27:15.813571 INFO: calibration group: precursor, predicting mz
3:27:15.885705 INFO: calibration group: precursor, predicting rt
3:27:16.221784 INFO: calibration group: fragment, predicting mz
3:27:16.971633 INFO: === checking if optimization conditions were reached ===
3:27:16.973914 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
3:27:16.974885 PROGRESS: ❌ ms1_error      : 13.9457 > 10.0000 or insufficient steps taken.
3:27:16.974933 INFO: ==============================================
3:27:16.975026 INFO: Starting optimization step 7.
3:27:16.975092 PROGRESS: === Extracting elution groups 0 to 248000 ===
3:27:16.975161 PROGRESS: Extracting batch of 490189 precursors
3:27:17.096841 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:27:17.096974 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:27:17.097013 INFO: FWHM in RT is 2.85 seconds, sigma is 0.37
3:27:17.097036 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:27:17.097337 INFO: Starting candidate selection
3:27:40.424348 INFO: Starting candidate scoring
3:27:47.318672 INFO: Finished candidate processing
3:27:47.318780 INFO: Collecting candidate features
3:27:49.140077 WARNING: intensity_correlation has 12 NaNs ( 0.00 % out of 977620)
3:27:49.175762 INFO: Collecting fragment features
3:27:49.798004 INFO: Finished candidate scoring
3:27:50.488377 PROGRESS: === Extracted 977620 precursors and 8531379 fragments ===
3:27:50.488861 INFO: performing precursor FDR with 47 features
3:27:50.488905 INFO: Decoy channel: -1
3:27:50.488930 INFO: Competetive: True
3:27:50.798858 INFO: Setting torch num_threads to 2 for FDR classification task
3:27:50.992442 WARNING: dropped 5 target PSMs due to missing features
3:27:50.992593 WARNING: dropped 7 decoy PSMs due to missing features
3:28:10.037071 INFO: Test AUC: 0.568
3:28:10.037292 INFO: Train AUC: 0.583
3:28:10.037328 INFO: AUC difference: 2.46%
3:28:10.199238 INFO: Resetting torch num_threads to 100
3:28:10.225917 INFO: === FDR correction performed with classifier version 6 ===
3:28:10.227186 PROGRESS: ============================= Precursor FDR =============================
3:28:10.227331 PROGRESS: Total precursors accumulated: 1,464
3:28:10.227394 PROGRESS: Target precursors: 1,336 (91.26%)
3:28:10.227444 PROGRESS: Decoy precursors: 128 (8.74%)
3:28:10.227489 PROGRESS: 
3:28:10.227540 PROGRESS: Precursor Summary:
3:28:10.229023 PROGRESS: Channel   0:	 0.05 FDR: 1,027; 0.01 FDR:   741; 0.001 FDR:   427
3:28:10.229141 PROGRESS: 
3:28:10.229199 PROGRESS: Protein Summary:
3:28:10.230701 PROGRESS: Channel   0:	 0.05 FDR:   905; 0.01 FDR:   662; 0.001 FDR:   393
3:28:10.230798 PROGRESS: =========================================================================
3:28:10.286877 INFO: fragments_df_filtered: 5000
3:28:10.746946 INFO: calibration group: precursor, fitting mz estimator 
3:28:10.792139 INFO: calibration group: precursor, fitting rt estimator 
3:28:10.836669 INFO: calibration group: fragment, fitting mz estimator 
3:28:11.217995 INFO: calibration group: precursor, predicting mz
3:28:11.254392 INFO: calibration group: precursor, predicting rt
3:28:11.405237 INFO: calibration group: fragment, predicting mz
3:28:11.754852 INFO: === checking if optimization conditions were reached ===
3:28:11.757259 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
3:28:11.758290 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
3:28:11.758339 INFO: ==============================================
3:28:11.758437 PROGRESS: Optimization finished for ms2_error, ms1_error.
3:28:12.135721 INFO: calibration group: precursor, predicting mz
3:28:12.169292 INFO: calibration group: precursor, predicting rt
3:28:12.318989 INFO: calibration group: fragment, predicting mz
3:28:12.661710 INFO: Starting optimization step 0.
3:28:12.662072 PROGRESS: === Extracting elution groups 0 to 120000 ===
3:28:12.662173 PROGRESS: Extracting batch of 237192 precursors
3:28:12.734525 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:28:12.734659 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:28:12.734699 INFO: FWHM in RT is 2.74 seconds, sigma is 0.35
3:28:12.734722 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:28:12.735019 INFO: Starting candidate selection
3:28:24.011768 INFO: Starting candidate scoring
3:28:27.301178 INFO: Finished candidate processing
3:28:27.302755 INFO: Collecting candidate features
3:28:28.490543 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 473131)
3:28:28.510246 INFO: Collecting fragment features
3:28:28.810379 INFO: Finished candidate scoring
3:28:29.070467 PROGRESS: === Extracted 473131 precursors and 4120572 fragments ===
3:28:29.071595 INFO: performing precursor FDR with 47 features
3:28:29.071665 INFO: Decoy channel: -1
3:28:29.071689 INFO: Competetive: True
3:28:29.229255 INFO: Setting torch num_threads to 2 for FDR classification task
3:28:29.329874 WARNING: dropped 2 target PSMs due to missing features
3:28:29.330027 WARNING: dropped 2 decoy PSMs due to missing features
3:28:37.880909 INFO: Test AUC: 0.571
3:28:37.881141 INFO: Train AUC: 0.589
3:28:37.881175 INFO: AUC difference: 3.19%
3:28:38.004712 INFO: Resetting torch num_threads to 100
3:28:38.030013 INFO: === FDR correction performed with classifier version 7 ===
3:28:38.031264 PROGRESS: ============================= Precursor FDR =============================
3:28:38.033058 PROGRESS: Total precursors accumulated: 842
3:28:38.033166 PROGRESS: Target precursors: 766 (90.97%)
3:28:38.033225 PROGRESS: Decoy precursors: 76 (9.03%)
3:28:38.033278 PROGRESS: 
3:28:38.033329 PROGRESS: Precursor Summary:
3:28:38.034834 PROGRESS: Channel   0:	 0.05 FDR:   613; 0.01 FDR:   352; 0.001 FDR:   288
3:28:38.034944 PROGRESS: 
3:28:38.035006 PROGRESS: Protein Summary:
3:28:38.036680 PROGRESS: Channel   0:	 0.05 FDR:   558; 0.01 FDR:   324; 0.001 FDR:   265
3:28:38.036788 PROGRESS: =========================================================================
3:28:38.071825 INFO: fragments_df_filtered: 3728
3:28:38.508769 INFO: calibration group: precursor, fitting mz estimator 
3:28:38.565517 INFO: calibration group: precursor, fitting rt estimator 
3:28:38.600995 INFO: calibration group: fragment, fitting mz estimator 
3:28:38.814387 INFO: calibration group: precursor, predicting mz
3:28:38.846088 INFO: calibration group: precursor, predicting rt
3:28:39.000334 INFO: calibration group: fragment, predicting mz
3:28:39.367543 INFO: === checking if optimization conditions were reached ===
3:28:39.368193 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3:28:39.370706 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 130.5968.
3:28:39.370834 INFO: ==============================================
3:28:39.371083 INFO: Starting optimization step 1.
3:28:39.371314 PROGRESS: === Extracting elution groups 0 to 120000 ===
3:28:39.371548 PROGRESS: Extracting batch of 237192 precursors
3:28:39.437884 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:28:39.438036 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:28:39.438082 INFO: FWHM in RT is 2.81 seconds, sigma is 0.36
3:28:39.438107 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:28:39.438449 INFO: Starting candidate selection
3:28:47.755798 INFO: Starting candidate scoring
3:28:51.547709 INFO: Finished candidate processing
3:28:51.547843 INFO: Collecting candidate features
3:28:52.392877 WARNING: intensity_correlation has 76 NaNs ( 0.02 % out of 468728)
3:28:52.412140 INFO: Collecting fragment features
3:28:52.727177 INFO: Finished candidate scoring
3:28:53.069285 PROGRESS: === Extracted 468728 precursors and 3776531 fragments ===
3:28:53.070221 INFO: performing precursor FDR with 47 features
3:28:53.070294 INFO: Decoy channel: -1
3:28:53.070326 INFO: Competetive: True
3:28:53.238829 INFO: Setting torch num_threads to 2 for FDR classification task
3:28:53.377532 WARNING: dropped 40 target PSMs due to missing features
3:28:53.377686 WARNING: dropped 36 decoy PSMs due to missing features
3:29:02.345898 INFO: Test AUC: 0.564
3:29:02.346337 INFO: Train AUC: 0.585
3:29:02.346379 INFO: AUC difference: 3.58%
3:29:02.465763 INFO: Resetting torch num_threads to 100
3:29:02.480055 INFO: === FDR correction performed with classifier version 7 ===
3:29:02.481097 PROGRESS: ============================= Precursor FDR =============================
3:29:02.481237 PROGRESS: Total precursors accumulated: 926
3:29:02.481306 PROGRESS: Target precursors: 844 (91.14%)
3:29:02.481366 PROGRESS: Decoy precursors: 82 (8.86%)
3:29:02.481421 PROGRESS: 
3:29:02.481475 PROGRESS: Precursor Summary:
3:29:02.482699 PROGRESS: Channel   0:	 0.05 FDR:   719; 0.01 FDR:   443; 0.001 FDR:   369
3:29:02.482799 PROGRESS: 
3:29:02.482859 PROGRESS: Protein Summary:
3:29:02.484258 PROGRESS: Channel   0:	 0.05 FDR:   644; 0.01 FDR:   402; 0.001 FDR:   340
3:29:02.484357 PROGRESS: =========================================================================
3:29:02.502524 INFO: fragments_df_filtered: 4481
3:29:02.779023 INFO: calibration group: precursor, fitting mz estimator 
3:29:02.880159 INFO: calibration group: precursor, fitting rt estimator 
3:29:02.928471 INFO: calibration group: fragment, fitting mz estimator 
3:29:03.288579 INFO: calibration group: precursor, predicting mz
3:29:03.303484 INFO: calibration group: precursor, predicting rt
3:29:03.380085 INFO: calibration group: fragment, predicting mz
3:29:03.551129 INFO: === checking if optimization conditions were reached ===
3:29:03.551476 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3:29:03.553962 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 84.9531.
3:29:03.554024 INFO: ==============================================
3:29:03.554134 INFO: Starting optimization step 2.
3:29:03.554209 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:29:03.554287 PROGRESS: Extracting batch of 110713 precursors
3:29:03.595525 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:29:03.595677 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:29:03.595725 INFO: FWHM in RT is 2.76 seconds, sigma is 0.36
3:29:03.595764 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:29:03.596119 INFO: Starting candidate selection
3:29:07.970896 INFO: Starting candidate scoring
3:29:09.680037 INFO: Finished candidate processing
3:29:09.680160 INFO: Collecting candidate features
3:29:10.054514 WARNING: intensity_correlation has 49 NaNs ( 0.02 % out of 218142)
3:29:10.065064 INFO: Collecting fragment features
3:29:10.186003 INFO: Finished candidate scoring
3:29:10.319828 PROGRESS: === Extracted 218142 precursors and 1702757 fragments ===
3:29:10.320214 INFO: performing precursor FDR with 47 features
3:29:10.320254 INFO: Decoy channel: -1
3:29:10.320277 INFO: Competetive: True
3:29:10.403793 INFO: Setting torch num_threads to 2 for FDR classification task
3:29:10.449463 WARNING: dropped 25 target PSMs due to missing features
3:29:10.449592 WARNING: dropped 24 decoy PSMs due to missing features
3:29:14.463543 INFO: Test AUC: 0.567
3:29:14.463750 INFO: Train AUC: 0.588
3:29:14.463789 INFO: AUC difference: 3.55%
3:29:14.568849 INFO: Resetting torch num_threads to 100
3:29:14.576134 INFO: === FDR correction performed with classifier version 7 ===
3:29:14.576928 PROGRESS: ============================= Precursor FDR =============================
3:29:14.577024 PROGRESS: Total precursors accumulated: 483
3:29:14.577096 PROGRESS: Target precursors: 440 (91.10%)
3:29:14.577148 PROGRESS: Decoy precursors: 43 (8.90%)
3:29:14.577195 PROGRESS: 
3:29:14.577244 PROGRESS: Precursor Summary:
3:29:14.578278 PROGRESS: Channel   0:	 0.05 FDR:   354; 0.01 FDR:   209; 0.001 FDR:   115
3:29:14.578379 PROGRESS: 
3:29:14.578433 PROGRESS: Protein Summary:
3:29:14.579521 PROGRESS: Channel   0:	 0.05 FDR:   339; 0.01 FDR:   204; 0.001 FDR:   113
3:29:14.579610 PROGRESS: =========================================================================
3:29:14.588441 INFO: fragments_df_filtered: 1992
3:29:14.840280 INFO: calibration group: precursor, fitting mz estimator 
3:29:14.889163 INFO: calibration group: precursor, fitting rt estimator 
3:29:14.932332 INFO: calibration group: fragment, fitting mz estimator 
3:29:15.043377 INFO: calibration group: precursor, predicting mz
3:29:15.058732 INFO: calibration group: precursor, predicting rt
3:29:15.133522 INFO: calibration group: fragment, predicting mz
3:29:15.307328 INFO: === checking if optimization conditions were reached ===
3:29:15.307629 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3:29:15.309705 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 75.0917.
3:29:15.309756 INFO: ==============================================
3:29:15.309848 INFO: Starting optimization step 3.
3:29:15.309914 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:29:15.309981 PROGRESS: Extracting batch of 110713 precursors
3:29:15.348881 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:29:15.349215 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:29:15.349549 INFO: FWHM in RT is 2.82 seconds, sigma is 0.36
3:29:15.349663 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:29:15.350099 INFO: Starting candidate selection
3:29:21.524419 INFO: Starting candidate scoring
3:29:23.015239 INFO: Finished candidate processing
3:29:23.015392 INFO: Collecting candidate features
3:29:23.383261 WARNING: intensity_correlation has 51 NaNs ( 0.02 % out of 217778)
3:29:23.393857 INFO: Collecting fragment features
3:29:23.518433 INFO: Finished candidate scoring
3:29:23.668501 PROGRESS: === Extracted 217778 precursors and 1708753 fragments ===
3:29:23.668873 INFO: performing precursor FDR with 47 features
3:29:23.668911 INFO: Decoy channel: -1
3:29:23.668934 INFO: Competetive: True
3:29:23.741288 INFO: Setting torch num_threads to 2 for FDR classification task
3:29:23.782280 WARNING: dropped 24 target PSMs due to missing features
3:29:23.782419 WARNING: dropped 27 decoy PSMs due to missing features
3:29:27.363947 INFO: Test AUC: 0.563
3:29:27.364069 INFO: Train AUC: 0.590
3:29:27.364098 INFO: AUC difference: 4.63%
3:29:27.461730 INFO: Resetting torch num_threads to 100
3:29:27.468643 INFO: === FDR correction performed with classifier version 7 ===
3:29:27.469393 PROGRESS: ============================= Precursor FDR =============================
3:29:27.469487 PROGRESS: Total precursors accumulated: 517
3:29:27.469548 PROGRESS: Target precursors: 471 (91.10%)
3:29:27.469599 PROGRESS: Decoy precursors: 46 (8.90%)
3:29:27.469646 PROGRESS: 
3:29:27.469692 PROGRESS: Precursor Summary:
3:29:27.470742 PROGRESS: Channel   0:	 0.05 FDR:   357; 0.01 FDR:   266; 0.001 FDR:   179
3:29:27.470842 PROGRESS: 
3:29:27.470898 PROGRESS: Protein Summary:
3:29:27.472023 PROGRESS: Channel   0:	 0.05 FDR:   346; 0.01 FDR:   256; 0.001 FDR:   175
3:29:27.472125 PROGRESS: =========================================================================
3:29:27.481554 INFO: fragments_df_filtered: 2400
3:29:27.699002 INFO: calibration group: precursor, fitting mz estimator 
3:29:27.746679 INFO: calibration group: precursor, fitting rt estimator 
3:29:27.797428 INFO: calibration group: fragment, fitting mz estimator 
3:29:27.954714 INFO: calibration group: precursor, predicting mz
3:29:27.970800 INFO: calibration group: precursor, predicting rt
3:29:28.044210 INFO: calibration group: fragment, predicting mz
3:29:28.218465 INFO: === checking if optimization conditions were reached ===
3:29:28.218776 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3:29:28.221316 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 70.9940.
3:29:28.221381 INFO: ==============================================
3:29:28.221486 INFO: Starting optimization step 4.
3:29:28.221563 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:29:28.221630 PROGRESS: Extracting batch of 110713 precursors
3:29:28.261874 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:29:28.262027 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:29:28.262068 INFO: FWHM in RT is 2.82 seconds, sigma is 0.36
3:29:28.262097 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:29:28.262400 INFO: Starting candidate selection
3:29:32.911106 INFO: Starting candidate scoring
3:29:34.416648 INFO: Finished candidate processing
3:29:34.416785 INFO: Collecting candidate features
3:29:34.812793 WARNING: intensity_correlation has 61 NaNs ( 0.03 % out of 217664)
3:29:34.823914 INFO: Collecting fragment features
3:29:34.948014 INFO: Finished candidate scoring
3:29:35.048717 PROGRESS: === Extracted 217664 precursors and 1663781 fragments ===
3:29:35.049185 INFO: performing precursor FDR with 47 features
3:29:35.049227 INFO: Decoy channel: -1
3:29:35.049256 INFO: Competetive: True
3:29:35.123950 INFO: Setting torch num_threads to 2 for FDR classification task
3:29:35.170156 WARNING: dropped 34 target PSMs due to missing features
3:29:35.170285 WARNING: dropped 27 decoy PSMs due to missing features
3:29:38.973805 INFO: Test AUC: 0.566
3:29:38.973929 INFO: Train AUC: 0.589
3:29:38.973964 INFO: AUC difference: 4.00%
3:29:39.075347 INFO: Resetting torch num_threads to 100
3:29:39.083165 INFO: === FDR correction performed with classifier version 7 ===
3:29:39.083946 PROGRESS: ============================= Precursor FDR =============================
3:29:39.084042 PROGRESS: Total precursors accumulated: 527
3:29:39.084114 PROGRESS: Target precursors: 479 (90.89%)
3:29:39.084167 PROGRESS: Decoy precursors: 48 (9.11%)
3:29:39.084214 PROGRESS: 
3:29:39.084261 PROGRESS: Precursor Summary:
3:29:39.085375 PROGRESS: Channel   0:	 0.05 FDR:   333; 0.01 FDR:   265; 0.001 FDR:   171
3:29:39.085470 PROGRESS: 
3:29:39.085527 PROGRESS: Protein Summary:
3:29:39.086669 PROGRESS: Channel   0:	 0.05 FDR:   320; 0.01 FDR:   255; 0.001 FDR:   166
3:29:39.086762 PROGRESS: =========================================================================
3:29:39.096143 INFO: fragments_df_filtered: 2427
3:29:39.324807 INFO: calibration group: precursor, fitting mz estimator 
3:29:39.365140 INFO: calibration group: precursor, fitting rt estimator 
3:29:39.402952 INFO: calibration group: fragment, fitting mz estimator 
3:29:39.515667 INFO: calibration group: precursor, predicting mz
3:29:39.531061 INFO: calibration group: precursor, predicting rt
3:29:39.602839 INFO: calibration group: fragment, predicting mz
3:29:39.768504 INFO: === checking if optimization conditions were reached ===
3:29:39.768792 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3:29:39.770972 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 68.1720.
3:29:39.771025 INFO: ==============================================
3:29:39.771121 INFO: Starting optimization step 5.
3:29:39.771201 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:29:39.771272 PROGRESS: Extracting batch of 110713 precursors
3:29:39.813023 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:29:39.813194 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:29:39.813249 INFO: FWHM in RT is 2.85 seconds, sigma is 0.37
3:29:39.813285 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:29:39.813690 INFO: Starting candidate selection
3:29:44.103711 INFO: Starting candidate scoring
3:29:45.706015 INFO: Finished candidate processing
3:29:45.707147 INFO: Collecting candidate features
3:29:46.074388 WARNING: intensity_correlation has 55 NaNs ( 0.03 % out of 217742)
3:29:46.085405 INFO: Collecting fragment features
3:29:46.226450 INFO: Finished candidate scoring
3:29:46.340555 PROGRESS: === Extracted 217742 precursors and 1678225 fragments ===
3:29:46.341010 INFO: performing precursor FDR with 47 features
3:29:46.341050 INFO: Decoy channel: -1
3:29:46.341075 INFO: Competetive: True
3:29:46.428148 INFO: Setting torch num_threads to 2 for FDR classification task
3:29:46.486005 WARNING: dropped 32 target PSMs due to missing features
3:29:46.486162 WARNING: dropped 23 decoy PSMs due to missing features
3:29:51.515839 INFO: Test AUC: 0.563
3:29:51.516092 INFO: Train AUC: 0.590
3:29:51.516140 INFO: AUC difference: 4.64%
3:29:51.663609 INFO: Resetting torch num_threads to 100
3:29:51.678064 INFO: === FDR correction performed with classifier version 7 ===
3:29:51.679264 PROGRESS: ============================= Precursor FDR =============================
3:29:51.679394 PROGRESS: Total precursors accumulated: 508
3:29:51.679480 PROGRESS: Target precursors: 461 (90.75%)
3:29:51.679553 PROGRESS: Decoy precursors: 47 (9.25%)
3:29:51.679623 PROGRESS: 
3:29:51.679689 PROGRESS: Precursor Summary:
3:29:51.681326 PROGRESS: Channel   0:	 0.05 FDR:   340; 0.01 FDR:   236; 0.001 FDR:     0
3:29:51.681447 PROGRESS: 
3:29:51.681520 PROGRESS: Protein Summary:
3:29:51.682750 PROGRESS: Channel   0:	 0.05 FDR:   327; 0.01 FDR:   227; 0.001 FDR:     0
3:29:51.682843 PROGRESS: =========================================================================
3:29:51.700863 INFO: fragments_df_filtered: 2255
3:29:52.047750 INFO: calibration group: precursor, fitting mz estimator 
3:29:52.114300 INFO: calibration group: precursor, fitting rt estimator 
3:29:52.161777 INFO: calibration group: fragment, fitting mz estimator 
3:29:52.328840 INFO: calibration group: precursor, predicting mz
3:29:52.348689 INFO: calibration group: precursor, predicting rt
3:29:52.437937 INFO: calibration group: fragment, predicting mz
3:29:52.624641 INFO: === checking if optimization conditions were reached ===
3:29:52.625671 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3:29:52.627705 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 70.9940 found after 6 searches.
3:29:52.627933 INFO: ==============================================
3:29:52.628295 PROGRESS: Optimization finished for rt_error.
3:29:52.923636 INFO: calibration group: precursor, predicting mz
3:29:52.942542 INFO: calibration group: precursor, predicting rt
3:29:53.027981 INFO: calibration group: fragment, predicting mz
3:29:53.245265 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:29:53.245528 PROGRESS: ==============================================
3:29:53.245845 PROGRESS: ms2_error      : 15.0000
3:29:53.245973 PROGRESS: ms1_error      : 10.0000
3:29:53.246080 PROGRESS: rt_error       : 70.9940
3:29:53.246196 PROGRESS: ==============================================
3:29:53.247195 INFO: calibration group: precursor, predicting mz
3:29:54.950515 INFO: calibration group: precursor, predicting rt
3:30:01.930528 INFO: calibration group: fragment, predicting mz
3:30:17.422141 PROGRESS: Extracting batch of 10183864 precursors
3:30:20.110429 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:30:20.110890 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:30:20.111560 INFO: FWHM in RT is 2.85 seconds, sigma is 0.37
3:30:20.111593 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:30:20.113028 INFO: Starting candidate selection
3:36:44.219406 INFO: Applying score cutoff of 45.61689196777344
3:36:44.579931 INFO: Removed 10296113 precursors with score below cutoff
3:36:47.163383 INFO: Starting candidate scoring
3:38:08.787484 INFO: Finished candidate processing
3:38:08.787792 INFO: Collecting candidate features
3:38:43.918629 WARNING: intensity_correlation has 44 NaNs ( 0.00 % out of 10019320)
3:38:44.410091 INFO: Collecting fragment features
3:38:53.761257 INFO: Finished candidate scoring
3:39:09.453586 INFO: === FDR correction performed with classifier version 12 ===
3:39:09.503279 INFO: performing precursor FDR with 47 features
3:39:09.503401 INFO: Decoy channel: -1
3:39:09.503435 INFO: Competetive: True
3:39:19.088905 INFO: Setting torch num_threads to 2 for FDR classification task
3:39:21.103454 WARNING: dropped 30 target PSMs due to missing features
3:39:21.103630 WARNING: dropped 14 decoy PSMs due to missing features
3:43:39.578336 INFO: Test AUC: 0.584
3:43:39.578660 INFO: Train AUC: 0.587
3:43:39.578708 INFO: AUC difference: 0.65%
3:43:40.368556 INFO: Resetting torch num_threads to 100
3:43:40.715755 INFO: Removing fragments below FDR threshold
3:43:41.618319 PROGRESS: ============================= Precursor FDR =============================
3:43:41.618667 PROGRESS: Total precursors accumulated: 26,999
3:43:41.618733 PROGRESS: Target precursors: 26,732 (99.01%)
3:43:41.618783 PROGRESS: Decoy precursors: 267 (0.99%)
3:43:41.618833 PROGRESS: 
3:43:41.618877 PROGRESS: Precursor Summary:
3:43:41.628999 PROGRESS: Channel   0:	 0.05 FDR: 26,732; 0.01 FDR: 26,732; 0.001 FDR: 18,170
3:43:41.629247 PROGRESS: 
3:43:41.629306 PROGRESS: Protein Summary:
3:43:41.643763 PROGRESS: Channel   0:	 0.05 FDR: 7,668; 0.01 FDR: 7,668; 0.001 FDR: 5,831
3:43:41.644016 PROGRESS: =========================================================================
3:43:41.971962 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:44:08.608485 PROGRESS: Processing search outputs
3:44:08.608917 PROGRESS: Performing protein grouping and FDR
3:44:08.608976 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:44:08.664026 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:44:08.683510 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:44:08.688876 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:44:08.709538 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:44:08.724959 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:44:08.740865 INFO: Building combined output
3:44:08.980871 INFO: Performing protein inference
3:44:09.084298 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
3:44:18.354232 INFO: Performing protein FDR
3:44:20.999716 INFO: Normalizing q-values using 9,257 targets and 891 decoys
3:44:21.009783 INFO: Test AUC: 0.889
3:44:21.009848 INFO: Train AUC: 0.892
3:44:21.009885 INFO: AUC difference: 0.34%
3:44:21.218406 PROGRESS: ================ Protein FDR =================
3:44:21.218551 PROGRESS: Unique protein groups in output
3:44:21.218580 PROGRESS:   1% protein FDR: 5,891
3:44:21.218600 PROGRESS: 
3:44:21.218618 PROGRESS: Unique precursor in output
3:44:21.218636 PROGRESS:   1% protein FDR: 32,718
3:44:21.218662 PROGRESS: ================================================
3:44:21.236911 PROGRESS: Building search statistics
3:44:21.264601 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
3:44:21.264846 INFO: Initializing OptimizationManager
3:44:21.265156 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
3:44:21.265242 INFO: Initializing CalibrationManager
3:44:21.265490 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
3:44:21.265572 INFO: Initializing RawFileManager
3:44:21.273565 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
3:44:21.274125 INFO: Initializing OptimizationManager
3:44:21.274320 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
3:44:21.274389 INFO: Initializing CalibrationManager
3:44:21.274564 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
3:44:21.274644 INFO: Initializing RawFileManager
3:44:21.279439 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
3:44:21.279536 INFO: Initializing OptimizationManager
3:44:21.279695 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
3:44:21.279769 INFO: Initializing CalibrationManager
3:44:21.279931 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
3:44:21.279999 INFO: Initializing RawFileManager
3:44:21.291549 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
3:44:21.291683 INFO: Initializing OptimizationManager
3:44:21.291874 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
3:44:21.291950 INFO: Initializing CalibrationManager
3:44:21.292124 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
3:44:21.292193 INFO: Initializing RawFileManager
3:44:21.303261 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
3:44:21.303392 INFO: Initializing OptimizationManager
3:44:21.303580 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
3:44:21.303649 INFO: Initializing CalibrationManager
3:44:21.303833 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
3:44:21.303904 INFO: Initializing RawFileManager
3:44:21.314793 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
3:44:21.314948 INFO: Initializing OptimizationManager
3:44:21.315137 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
3:44:21.315204 INFO: Initializing CalibrationManager
3:44:21.315377 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
3:44:21.315448 INFO: Initializing RawFileManager
3:44:21.317242 INFO: Writing stat output to disk
3:44:21.317331 INFO: Saving run_output_Astral/alphadia_1.10_default/library/stat.tsv to disk
3:44:21.322885 PROGRESS: Building internal statistics
3:44:21.323153 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
3:44:21.323192 INFO: Initializing TimingManager
3:44:21.323428 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
3:44:21.323475 INFO: Initializing TimingManager
3:44:21.323647 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
3:44:21.323684 INFO: Initializing TimingManager
3:44:21.323851 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
3:44:21.323888 INFO: Initializing TimingManager
3:44:21.324039 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
3:44:21.324074 INFO: Initializing TimingManager
3:44:21.324221 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_default/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
3:44:21.324256 INFO: Initializing TimingManager
3:44:21.324583 INFO: Writing internal output to disk
3:44:21.324626 INFO: Saving run_output_Astral/alphadia_1.10_default/library/internal.tsv to disk
3:44:21.325010 PROGRESS: Performing label free quantification
3:44:21.340267 INFO: Accumulating fragment data
3:44:21.340429 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:44:21.591128 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:44:21.757476 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:44:21.822709 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:44:22.146962 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:44:22.492581 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:44:22.935404 PROGRESS: Performing label free quantification on the precursor level
3:44:22.935537 INFO: Filtering fragments by quality
3:44:23.021897 INFO: Performing label-free quantification using directLFQ
3:44:23.155792 INFO: to few values for normalization without missing values. Including missing values
3:44:24.139275 INFO: 32718 lfq-groups total
3:45:23.586995 INFO: using 100 processes
3:45:23.701638 INFO: lfq-object 0
3:45:23.759533 INFO: lfq-object 100
3:45:23.801656 INFO: lfq-object 200
3:45:23.838669 INFO: lfq-object 300
3:45:23.844607 INFO: lfq-object 500
3:45:23.874210 INFO: lfq-object 400
3:45:23.980526 INFO: lfq-object 600
3:45:24.075778 INFO: lfq-object 700
3:45:24.154603 INFO: lfq-object 800
3:45:24.180530 INFO: lfq-object 1000
3:45:24.204680 INFO: lfq-object 900
3:45:24.252371 INFO: lfq-object 1100
3:45:24.306682 INFO: lfq-object 1200
3:45:24.365602 INFO: lfq-object 1300
3:45:24.402625 INFO: lfq-object 1400
3:45:24.470907 INFO: lfq-object 1500
3:45:24.512611 INFO: lfq-object 1600
3:45:24.563669 INFO: lfq-object 1700
3:45:24.612684 INFO: lfq-object 1800
3:45:24.616069 INFO: lfq-object 1900
3:45:24.653352 INFO: lfq-object 2000
3:45:24.717961 INFO: lfq-object 2100
3:45:24.731370 INFO: lfq-object 2200
3:45:24.734173 INFO: lfq-object 2300
3:45:24.770888 INFO: lfq-object 2400
3:45:24.838952 INFO: lfq-object 2500
3:45:24.849550 INFO: lfq-object 2600
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3:45:24.902445 INFO: lfq-object 2800
3:45:24.944378 INFO: lfq-object 2900
3:45:25.002328 INFO: lfq-object 3000
3:45:25.020207 INFO: lfq-object 3200
3:45:25.047607 INFO: lfq-object 3100
3:45:25.070550 INFO: lfq-object 3300
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3:45:25.639567 INFO: lfq-object 5000
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3:45:38.617632 INFO: lfq-object 28400
3:45:38.662394 INFO: lfq-object 28500
3:45:38.699509 INFO: lfq-object 28700
3:45:38.723843 INFO: lfq-object 28600
3:45:38.766318 INFO: lfq-object 28800
3:45:38.818283 INFO: lfq-object 28900
3:45:38.856120 INFO: lfq-object 29000
3:45:38.892372 INFO: lfq-object 29100
3:45:38.902471 INFO: lfq-object 29200
3:45:38.949710 INFO: lfq-object 29300
3:45:39.012387 INFO: lfq-object 29400
3:45:39.077363 INFO: lfq-object 29500
3:45:39.124843 INFO: lfq-object 29600
3:45:39.166760 INFO: lfq-object 29700
3:45:39.216997 INFO: lfq-object 29800
3:45:39.270228 INFO: lfq-object 29900
3:45:39.275560 INFO: lfq-object 30100
3:45:39.317705 INFO: lfq-object 30000
3:45:39.321083 INFO: lfq-object 30200
3:45:39.366794 INFO: lfq-object 30300
3:45:39.417977 INFO: lfq-object 30400
3:45:39.429139 INFO: lfq-object 30600
3:45:39.429507 INFO: lfq-object 30500
3:45:39.480597 INFO: lfq-object 30700
3:45:39.512506 INFO: lfq-object 30800
3:45:39.550462 INFO: lfq-object 31000
3:45:39.583630 INFO: lfq-object 30900
3:45:39.590589 INFO: lfq-object 31100
3:45:39.629057 INFO: lfq-object 31200
3:45:39.697655 INFO: lfq-object 31300
3:45:39.703954 INFO: lfq-object 31500
3:45:39.711442 INFO: lfq-object 31400
3:45:41.686544 INFO: lfq-object 31600
3:45:41.729490 INFO: lfq-object 31700
3:45:41.822968 INFO: lfq-object 31800
3:45:41.827114 INFO: lfq-object 31900
3:45:41.878526 INFO: lfq-object 32000
3:45:41.952864 INFO: lfq-object 32100
3:45:41.984089 INFO: lfq-object 32200
3:45:42.047430 INFO: lfq-object 32400
3:45:42.059679 INFO: lfq-object 32300
3:45:42.119775 INFO: lfq-object 32500
3:45:42.214985 INFO: lfq-object 32600
3:45:42.257905 INFO: lfq-object 32700
3:45:46.345386 INFO: Writing precursor output to disk
3:45:46.345659 INFO: Saving run_output_Astral/alphadia_1.10_default/library/precursor.matrix.tsv to disk
3:45:46.607624 PROGRESS: Performing label free quantification on the pg level
3:45:46.607759 INFO: Filtering fragments by quality
3:45:46.736027 INFO: Performing label-free quantification using directLFQ
3:45:46.815504 INFO: to few values for normalization without missing values. Including missing values
3:45:46.884215 INFO: 5891 lfq-groups total
3:46:39.860843 INFO: using 100 processes
3:46:39.912307 INFO: lfq-object 0
3:46:39.963338 INFO: lfq-object 100
3:46:39.996214 INFO: lfq-object 200
3:46:40.017521 INFO: lfq-object 300
3:46:40.089851 INFO: lfq-object 400
3:46:40.126134 INFO: lfq-object 500
3:46:40.167086 INFO: lfq-object 600
3:46:40.226179 INFO: lfq-object 700
3:46:40.264667 INFO: lfq-object 800
3:46:40.306559 INFO: lfq-object 900
3:46:40.348768 INFO: lfq-object 1000
3:46:40.401937 INFO: lfq-object 1100
3:46:40.439348 INFO: lfq-object 1200
3:46:40.533375 INFO: lfq-object 1300
3:46:40.556157 INFO: lfq-object 1400
3:46:40.595963 INFO: lfq-object 1500
3:46:40.668070 INFO: lfq-object 1600
3:46:40.721180 INFO: lfq-object 1700
3:46:40.760981 INFO: lfq-object 1800
3:46:40.831522 INFO: lfq-object 1900
3:46:40.843777 INFO: lfq-object 2000
3:46:40.885014 INFO: lfq-object 2100
3:46:40.938582 INFO: lfq-object 2200
3:46:40.980742 INFO: lfq-object 2300
3:46:41.011882 INFO: lfq-object 2400
3:46:41.074203 INFO: lfq-object 2500
3:46:41.098532 INFO: lfq-object 2600
3:46:41.139106 INFO: lfq-object 2700
3:46:41.195069 INFO: lfq-object 2800
3:46:41.241686 INFO: lfq-object 2900
3:46:41.282763 INFO: lfq-object 3000
3:46:41.330123 INFO: lfq-object 3100
3:46:41.370422 INFO: lfq-object 3200
3:46:41.402052 INFO: lfq-object 3300
3:46:41.450398 INFO: lfq-object 3400
3:46:41.486203 INFO: lfq-object 3500
3:46:41.508744 INFO: lfq-object 3600
3:46:41.570945 INFO: lfq-object 3700
3:46:41.596329 INFO: lfq-object 3800
3:46:41.627187 INFO: lfq-object 3900
3:46:41.687752 INFO: lfq-object 4000
3:46:41.734530 INFO: lfq-object 4100
3:46:41.784289 INFO: lfq-object 4200
3:46:41.852370 INFO: lfq-object 4300
3:46:41.889388 INFO: lfq-object 4400
3:46:41.931519 INFO: lfq-object 4500
3:46:41.997030 INFO: lfq-object 4600
3:46:42.031896 INFO: lfq-object 4700
3:46:42.066715 INFO: lfq-object 4800
3:46:42.114992 INFO: lfq-object 4900
3:46:42.132691 INFO: lfq-object 5000
3:46:42.158797 INFO: lfq-object 5100
3:46:42.209438 INFO: lfq-object 5200
3:46:42.263672 INFO: lfq-object 5300
3:46:42.285195 INFO: lfq-object 5400
3:46:42.363552 INFO: lfq-object 5500
3:46:42.387851 INFO: lfq-object 5600
3:46:42.451899 INFO: lfq-object 5700
3:46:42.511752 INFO: lfq-object 5800
3:46:44.989925 INFO: Writing pg output to disk
3:46:44.990102 INFO: Saving run_output_Astral/alphadia_1.10_default/library/pg.matrix.tsv to disk
3:46:45.081847 INFO: Writing psm output to disk
3:46:45.081994 INFO: Saving run_output_Astral/alphadia_1.10_default/library/precursors.tsv to disk
3:46:50.526008 PROGRESS: Building spectral library
3:46:50.545053 INFO: Building MBR spectral library
3:46:50.545187 INFO: Running MbrLibraryBuilder
3:46:52.255341 INFO: MBR spectral library contains 32,718 precursors, 5,891 proteins
3:46:52.255479 INFO: Writing MBR spectral library to disk
3:46:53.002963 PROGRESS: =================== Search Finished ===================
3:46:53.987055 INFO: Running step 'mbr'
3:46:53.990334 INFO: Extracted extra_config from previous step: defaultdict(<class 'dict'>, {'search': {'target_ms1_tolerance': 10.0, 'target_ms2_tolerance': 15.0}})
3:46:53.990474 INFO: loading config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
3:46:54.001569 INFO: loading additional config provided via CLI
3:46:54.001637 INFO: loading additional config provided via CLI parameters
3:46:54.001884 INFO: Updating config with 'user defined'
3:46:54.001977 INFO: Updating config with 'user defined (cli)'
3:46:54.002001 INFO: Updating config with 'multistep search'
3:46:54.002043 INFO: ├──version: 1
3:46:54.002071 INFO: ├──workflow_name: None
3:46:54.002095 INFO: [32;20m├──output_directory: run_output_Astral/alphadia_1.10_default [multistep search, default: None][0m
3:46:54.002116 INFO: [32;20m├──library_path: run_output_Astral/alphadia_1.10_default/library/speclib.mbr.hdf [multistep search, default: None][0m
3:46:54.002135 INFO: ├──raw_paths:
3:46:54.002156 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
3:46:54.002175 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
3:46:54.002193 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
3:46:54.002211 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
3:46:54.002229 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
3:46:54.002247 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
3:46:54.002267 INFO: ├──fasta_paths:
3:46:54.002286 INFO: ├──quant_directory: None
3:46:54.002304 INFO: ├──general
3:46:54.002324 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
3:46:54.002345 INFO: │   ├──transfer_step_enabled: False
3:46:54.002363 INFO: │   ├──mbr_step_enabled: True
3:46:54.002383 INFO: │   ├──reuse_calibration: False
3:46:54.002402 INFO: │   ├──reuse_quant: False
3:46:54.002420 INFO: │   ├──astral_ms1: False
3:46:54.002438 INFO: │   ├──log_level: INFO
3:46:54.002456 INFO: │   ├──mmap_detector_events: False
3:46:54.002477 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
3:46:54.002495 INFO: │   ├──save_library: True
3:46:54.002523 INFO: │   └──save_mbr_library: True
3:46:54.002541 INFO: ├──library_loading
3:46:54.002665 INFO: │   └──rt_heuristic: 180
3:46:54.002687 INFO: ├──library_prediction
3:46:54.002706 INFO: │   ├──enabled: False
3:46:54.002727 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
3:46:54.002747 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
3:46:54.002765 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
3:46:54.002786 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
3:46:54.002809 INFO: │   ├──missed_cleavages: 1
3:46:54.002829 INFO: │   ├──precursor_len:
3:46:54.002847 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
3:46:54.002866 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
3:46:54.002885 INFO: │   ├──precursor_charge:
3:46:54.002903 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
3:46:54.002921 INFO: │   │   [32;20m- 4[0m
3:46:54.002938 INFO: │   ├──precursor_mz:
3:46:54.002956 INFO: │   │   [32;20m- 400[0m
3:46:54.002975 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
3:46:54.002995 INFO: │   ├──fragment_mz:
3:46:54.003014 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
3:46:54.003032 INFO: │   │   [32;20m- 2000[0m
3:46:54.003051 INFO: │   ├──nce: 25
3:46:54.003069 INFO: │   ├──fragment_types:
3:46:54.003087 INFO: │   │   [32;20m- b[0m
3:46:54.003105 INFO: │   │   [32;20m- y[0m
3:46:54.003123 INFO: │   ├──max_fragment_charge: 2
3:46:54.003141 INFO: │   [32;20m├──instrument: Astral [user defined, default: Lumos][0m
3:46:54.003160 INFO: │   ├──peptdeep_model_path: None
3:46:54.003178 INFO: │   └──peptdeep_model_type: generic
3:46:54.003196 INFO: ├──custom_modifications:
3:46:54.003217 INFO: │   ├──name: Dimethyl:d12@K
3:46:54.003235 INFO: │   └──composition: H(-2)2H(8)13C(2)
3:46:54.003253 INFO: │   ├──name: Dimethyl:d12@Any_N-term
3:46:54.003271 INFO: │   └──composition: H(-2)2H(8)13C(2)
3:46:54.003292 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
3:46:54.003311 INFO: │   └──composition: H(-2)2H(8)13C(2)
3:46:54.003329 INFO: │   ├──name: mTRAQ:d12@K
3:46:54.003347 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
3:46:54.003365 INFO: │   ├──name: mTRAQ:d12@Any_N-term
3:46:54.003382 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
3:46:54.003401 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
3:46:54.003419 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
3:46:54.003437 INFO: │   ├──name: Label:13C(12)@K
3:46:54.003455 INFO: │   └──composition: C(12)
3:46:54.003473 INFO: ├──search
3:46:54.003494 INFO: │   [32;20m├──target_ms1_tolerance: 10.0 [multistep search, default: 5][0m
3:46:54.003514 INFO: │   [32;20m├──target_ms2_tolerance: 15.0 [multistep search, default: 10][0m
3:46:54.003532 INFO: │   ├──target_rt_tolerance: 0
3:46:54.003550 INFO: │   ├──target_mobility_tolerance: 0
3:46:54.003568 INFO: │   ├──quant_window: 3
3:46:54.003588 INFO: │   [32;20m├──target_num_candidates: 2 [user defined, default: 3][0m
3:46:54.003605 INFO: │   ├──channel_filter: 
3:46:54.003623 INFO: │   ├──exclude_shared_ions: True
3:46:54.003641 INFO: │   ├──compete_for_fragments: True
3:46:54.003659 INFO: │   ├──quant_all: True
3:46:54.003678 INFO: │   ├──top_k_fragments: 12
3:46:54.003699 INFO: │   └──experimental_xic: True
3:46:54.003716 INFO: ├──calibration
3:46:54.003754 INFO: │   ├──batch_size: 8000
3:46:54.003775 INFO: │   ├──optimization_lock_target: 200
3:46:54.003793 INFO: │   ├──max_steps: 20
3:46:54.003811 INFO: │   ├──min_steps: 2
3:46:54.003830 INFO: │   ├──max_skips: 1
3:46:54.003848 INFO: │   ├──norm_rt_mode: linear
3:46:54.003870 INFO: │   ├──max_fragments: 5000
3:46:54.003894 INFO: │   └──min_correlation: 0.7
3:46:54.003911 INFO: ├──search_initial
3:46:54.003929 INFO: │   ├──initial_num_candidates: 1
3:46:54.003947 INFO: │   ├──initial_ms1_tolerance: 30
3:46:54.003966 INFO: │   ├──initial_ms2_tolerance: 30
3:46:54.003985 INFO: │   ├──initial_mobility_tolerance: 0.1
3:46:54.004005 INFO: │   └──initial_rt_tolerance: 0.5
3:46:54.004024 INFO: ├──selection_config
3:46:54.004045 INFO: │   ├──peak_len_rt: 10.0
3:46:54.004065 INFO: │   ├──sigma_scale_rt: 0.5
3:46:54.004085 INFO: │   ├──peak_len_mobility: 0.01
3:46:54.004103 INFO: │   ├──sigma_scale_mobility: 1.0
3:46:54.004123 INFO: │   ├──top_k_precursors: 3
3:46:54.004141 INFO: │   ├──kernel_size: 30
3:46:54.004159 INFO: │   ├──f_mobility: 1.0
3:46:54.004179 INFO: │   ├──f_rt: 0.99
3:46:54.004199 INFO: │   ├──center_fraction: 0.5
3:46:54.004218 INFO: │   ├──min_size_mobility: 8
3:46:54.004236 INFO: │   ├──min_size_rt: 3
3:46:54.004254 INFO: │   ├──max_size_mobility: 20
3:46:54.004272 INFO: │   ├──max_size_rt: 15
3:46:54.004291 INFO: │   ├──group_channels: False
3:46:54.004310 INFO: │   ├──use_weighted_score: True
3:46:54.004330 INFO: │   ├──join_close_candidates: False
3:46:54.004348 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
3:46:54.004368 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
3:46:54.004386 INFO: ├──scoring_config
3:46:54.004405 INFO: │   ├──score_grouped: False
3:46:54.004424 INFO: │   ├──top_k_isotopes: 3
3:46:54.004441 INFO: │   ├──reference_channel: -1
3:46:54.004459 INFO: │   ├──precursor_mz_tolerance: 10
3:46:54.004477 INFO: │   └──fragment_mz_tolerance: 15
3:46:54.004496 INFO: ├──library_multiplexing
3:46:54.004514 INFO: │   ├──enabled: False
3:46:54.004531 INFO: │   ├──input_channel: 0
3:46:54.004549 INFO: │   └──multiplex_mapping:
3:46:54.004566 INFO: ├──multiplexing
3:46:54.004584 INFO: │   ├──enabled: False
3:46:54.004602 INFO: │   ├──target_channels: 4,8
3:46:54.004619 INFO: │   ├──decoy_channel: 12
3:46:54.004637 INFO: │   ├──reference_channel: 0
3:46:54.004654 INFO: │   └──competetive_scoring: True
3:46:54.004672 INFO: ├──fdr
3:46:54.004690 INFO: │   ├──fdr: 0.01
3:46:54.004707 INFO: │   ├──group_level: proteins
3:46:54.004726 INFO: │   [32;20m├──inference_strategy: library [multistep search, default: heuristic][0m
3:46:54.004745 INFO: │   ├──competetive_scoring: True
3:46:54.004762 INFO: │   ├──keep_decoys: False
3:46:54.004781 INFO: │   ├──channel_wise_fdr: False
3:46:54.004798 INFO: │   ├──enable_two_step_classifier: False
3:46:54.004816 INFO: │   ├──two_step_classifier_max_iterations: 5
3:46:54.004835 INFO: │   └──enable_nn_hyperparameter_tuning: False
3:46:54.004852 INFO: ├──search_output
3:46:54.004870 INFO: │   ├──file_format: tsv
3:46:54.004888 INFO: │   ├──peptide_level_lfq: False
3:46:54.004907 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
3:46:54.004926 INFO: │   ├──min_k_fragments: 12
3:46:54.004943 INFO: │   ├──min_correlation: 0.9
3:46:54.004962 INFO: │   ├──num_samples_quadratic: 50
3:46:54.004979 INFO: │   ├──min_nonnan: 3
3:46:54.004997 INFO: │   ├──normalize_lfq: True
3:46:54.005016 INFO: │   └──save_fragment_quant_matrix: False
3:46:54.005033 INFO: ├──optimization
3:46:54.005051 INFO: │   ├──order_of_optimization: None
3:46:54.005068 INFO: │   ├──ms2_error
3:46:54.005087 INFO: │   │   ├──targeted_update_percentile_range: 0.95
3:46:54.005105 INFO: │   │   ├──targeted_update_factor: 1.0
3:46:54.005125 INFO: │   │   ├──automatic_update_percentile_range: 0.99
3:46:54.005148 INFO: │   │   ├──automatic_update_factor: 1.1
3:46:54.005167 INFO: │   │   ├──try_narrower_values: True
3:46:54.005187 INFO: │   │   ├──maximal_decrease: 0.5
3:46:54.005206 INFO: │   │   ├──favour_narrower_optimum: False
3:46:54.005224 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
3:46:54.005242 INFO: │   ├──ms1_error
3:46:54.005262 INFO: │   │   ├──targeted_update_percentile_range: 0.95
3:46:54.005282 INFO: │   │   ├──targeted_update_factor: 1.0
3:46:54.005301 INFO: │   │   ├──automatic_update_percentile_range: 0.99
3:46:54.005321 INFO: │   │   ├──automatic_update_factor: 1.1
3:46:54.005340 INFO: │   │   ├──try_narrower_values: False
3:46:54.005358 INFO: │   │   ├──maximal_decrease: 0.2
3:46:54.005377 INFO: │   │   ├──favour_narrower_optimum: False
3:46:54.005396 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
3:46:54.005413 INFO: │   ├──mobility_error
3:46:54.005432 INFO: │   │   ├──targeted_update_percentile_range: 0.95
3:46:54.005450 INFO: │   │   ├──targeted_update_factor: 1.0
3:46:54.005469 INFO: │   │   ├──automatic_update_percentile_range: 0.99
3:46:54.005490 INFO: │   │   ├──automatic_update_factor: 1.1
3:46:54.005509 INFO: │   │   ├──try_narrower_values: False
3:46:54.005528 INFO: │   │   ├──maximal_decrease: 0.2
3:46:54.005548 INFO: │   │   ├──favour_narrower_optimum: False
3:46:54.005567 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
3:46:54.005585 INFO: │   └──rt_error
3:46:54.005604 INFO: │       ├──targeted_update_percentile_range: 0.95
3:46:54.005623 INFO: │       ├──targeted_update_factor: 1.0
3:46:54.005643 INFO: │       ├──automatic_update_percentile_range: 0.99
3:46:54.005663 INFO: │       ├──automatic_update_factor: 1.1
3:46:54.005683 INFO: │       ├──try_narrower_values: True
3:46:54.005701 INFO: │       ├──maximal_decrease: 0.2
3:46:54.005719 INFO: │       ├──favour_narrower_optimum: True
3:46:54.005738 INFO: │       └──maximum_decrease_from_maximum: 0.1
3:46:54.005756 INFO: ├──optimization_manager
3:46:54.005774 INFO: │   ├──fwhm_rt: 5
3:46:54.005794 INFO: │   ├──fwhm_mobility: 0.01
3:46:54.005812 INFO: │   └──score_cutoff: 0
3:46:54.005830 INFO: ├──transfer_library
3:46:54.005848 INFO: │   ├──enabled: False
3:46:54.005865 INFO: │   ├──fragment_types:
3:46:54.005882 INFO: │   │   [32;20m- b[0m
3:46:54.005899 INFO: │   │   [32;20m- y[0m
3:46:54.005918 INFO: │   ├──max_charge: 2
3:46:54.005936 INFO: │   ├──top_k_samples: 3
3:46:54.005954 INFO: │   ├──norm_delta_max: True
3:46:54.005975 INFO: │   ├──precursor_correlation_cutoff: 0.5
3:46:54.005992 INFO: │   └──fragment_correlation_ratio: 0.75
3:46:54.006009 INFO: └──transfer_learning
3:46:54.006028 INFO:     ├──enabled: False
3:46:54.006046 INFO:     ├──batch_size: 2000
3:46:54.006064 INFO:     ├──max_lr: 0.0001
3:46:54.006082 INFO:     ├──train_fraction: 0.7
3:46:54.006100 INFO:     ├──validation_fraction: 0.2
3:46:54.006118 INFO:     ├──test_fraction: 0.1
3:46:54.006135 INFO:     ├──test_interval: 1
3:46:54.006153 INFO:     ├──lr_patience: 3
3:46:54.006171 INFO:     ├──epochs: 51
3:46:54.006188 INFO:     ├──warmup_epochs: 5
3:46:54.006207 INFO:     ├──nce: 25
3:46:54.006225 INFO:     [32;20m└──instrument: Astral [user defined, default: Lumos][0m
3:46:54.011602 INFO: Registering 7 custom modifications
3:46:54.029740 INFO: Running DynamicLoader
3:46:54.029836 INFO: Loading .hdf library from run_output_Astral/alphadia_1.10_default/library/speclib.mbr.hdf
3:46:54.213232 INFO: Running PrecursorInitializer
3:46:54.213382 INFO: Running AnnotateFasta
3:46:54.213634 INFO: Dropping decoys from input library before annotation
3:46:54.218745 INFO: Running IsotopeGenerator
3:46:54.218920 WARNING: Input library already contains isotope information. Skipping isotope generation. 
 Please note that isotope generation outside of alphabase is not supported.
3:46:54.218959 INFO: Running RTNormalization
3:46:54.220840 INFO: Saving library to run_output_Astral/alphadia_1.10_default/speclib.hdf
3:46:54.493242 INFO: Running DecoyGenerator
3:47:09.986000 INFO: Running FlattenLibrary
3:47:10.799548 INFO: Running InitFlatColumns
3:47:10.802987 INFO: Running LogFlatLibraryStats
3:47:10.803080 INFO: ============ Library Stats ============
3:47:10.803113 INFO: Number of precursors: 65,433
3:47:10.820034 INFO: 	thereof targets:32,718
3:47:10.820149 INFO: 	thereof decoys: 32,715
3:47:10.820720 INFO: Number of elution groups: 32,718
3:47:10.820761 INFO: 	average size: 2.00
3:47:10.823137 INFO: Number of proteins: 5,891
3:47:10.823552 INFO: Number of channels: 1 ([0])
3:47:10.823628 INFO: Isotopes Distribution for 4 isotopes
3:47:10.823652 INFO: =======================================
3:47:10.823810 INFO: Searching 6 files:
3:47:10.823838 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
3:47:10.823858 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
3:47:10.823878 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
3:47:10.823895 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
3:47:10.823912 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
3:47:10.823929 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
3:47:10.823948 INFO: Using 0 fasta files:
3:47:10.823966 INFO: Using library: run_output_Astral/alphadia_1.10_default/library/speclib.mbr.hdf
3:47:10.823983 INFO: Saving output to: run_output_Astral/alphadia_1.10_default
3:47:10.824013 PROGRESS: Starting Search Workflows
3:47:10.824057 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:47:10.824109 INFO: Quantification results path: run_output_Astral/alphadia_1.10_default/quant
3:47:10.824157 INFO: Creating parent folder for workflows at run_output_Astral/alphadia_1.10_default/quant
3:47:10.824264 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1 at run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:47:10.824646 INFO: Initializing RawFileManager
3:47:38.098556 INFO: Determining DIA cycle
3:47:38.114918 INFO: Found cycle with start 0.00 min and length 303.
3:47:38.286099 INFO: RT (min)            : 0.0 - 26.9
3:47:38.286201 INFO: RT duration (sec)   : 1611.2
3:47:38.286229 INFO: RT duration (min)   : 26.9
3:47:38.286253 INFO: Cycle len (scans)   : 303
3:47:38.286272 INFO: Cycle len (sec)     : 1.65
3:47:38.286291 INFO: Number of cycles    : 977
3:47:38.286309 INFO: MS2 range (m/z)     : 380.4 - 980.7
3:47:38.305157 INFO: Initializing CalibrationManager
3:47:38.305494 INFO: Loading calibration config
3:47:38.306247 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'}]
3:47:38.306338 INFO: Calibration group :fragment, found 1 estimator(s)
3:47:38.306442 INFO: Calibration group :precursor, found 3 estimator(s)
3:47:38.306584 INFO: Disabling ion mobility calibration
3:47:38.306614 INFO: removed mobility estimator from group precursor
3:47:38.306771 INFO: Initializing OptimizationManager
3:47:38.306915 INFO: initial parameter: ms1_error = 30
3:47:38.306973 INFO: initial parameter: ms2_error = 30
3:47:38.307020 INFO: initial parameter: rt_error = 805.5992431640625
3:47:38.307064 INFO: initial parameter: mobility_error = 0.1
3:47:38.307106 INFO: initial parameter: column_type = library
3:47:38.307148 INFO: initial parameter: num_candidates = 1
3:47:38.307188 INFO: initial parameter: classifier_version = -1
3:47:38.307227 INFO: initial parameter: fwhm_rt = 5
3:47:38.307267 INFO: initial parameter: fwhm_mobility = 0.01
3:47:38.307306 INFO: initial parameter: score_cutoff = 0
3:47:38.307372 INFO: Initializing TimingManager
3:47:38.307441 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:47:38.307596 INFO: FDRManager not loaded from disk.
3:47:38.307621 INFO: Initializing FDRManager
3:47:38.307666 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
3:47:38.322027 PROGRESS: 32,718 target precursors potentially observable (0 removed)
3:47:38.337759 PROGRESS: Starting initial search for precursors.
3:47:38.354542 INFO: Starting optimization step 0.
3:47:38.354780 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:47:38.354859 PROGRESS: Extracting batch of 15933 precursors
3:47:38.358444 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:47:38.358496 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:47:38.358539 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:47:38.358561 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:47:38.358894 INFO: Starting candidate selection
3:47:39.459898 INFO: Starting candidate scoring
3:47:39.569515 INFO: Finished candidate processing
3:47:39.569624 INFO: Collecting candidate features
3:47:39.605893 INFO: Collecting fragment features
3:47:39.621325 INFO: Finished candidate scoring
3:47:39.630256 PROGRESS: === Extracted 15933 precursors and 171799 fragments ===
3:47:39.630638 INFO: performing precursor FDR with 47 features
3:47:39.630677 INFO: Decoy channel: -1
3:47:39.630701 INFO: Competetive: True
3:47:39.638285 INFO: Setting torch num_threads to 2 for FDR classification task
3:47:39.820927 INFO: Test AUC: 0.588
3:47:39.821037 INFO: Train AUC: 0.605
3:47:39.821068 INFO: AUC difference: 2.81%
3:47:39.921313 INFO: Resetting torch num_threads to 100
3:47:39.922772 INFO: === FDR correction performed with classifier version -1 ===
3:47:39.924068 PROGRESS: ============================= Precursor FDR =============================
3:47:39.924344 PROGRESS: Total precursors accumulated: 1,431
3:47:39.924574 PROGRESS: Target precursors: 1,329 (92.87%)
3:47:39.924798 PROGRESS: Decoy precursors: 102 (7.13%)
3:47:39.925020 PROGRESS: 
3:47:39.925231 PROGRESS: Precursor Summary:
3:47:39.927036 PROGRESS: Channel   0:	 0.05 FDR: 1,182; 0.01 FDR:   839; 0.001 FDR:   508
3:47:39.927323 PROGRESS: 
3:47:39.927548 PROGRESS: Protein Summary:
3:47:39.929704 PROGRESS: Channel   0:	 0.05 FDR:   920; 0.01 FDR:   679; 0.001 FDR:   429
3:47:39.930005 PROGRESS: =========================================================================
3:47:39.935532 INFO: fragments_df_filtered: 5000
3:47:39.949327 INFO: calibration group: precursor, fitting mz estimator 
3:47:40.015308 INFO: calibration group: precursor, fitting rt estimator 
3:47:40.075695 INFO: calibration group: fragment, fitting mz estimator 
3:47:40.494128 INFO: calibration group: precursor, predicting mz
3:47:40.497364 INFO: calibration group: precursor, predicting rt
3:47:40.507140 INFO: calibration group: fragment, predicting mz
3:47:40.530014 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3:47:40.530277 INFO: Starting optimization step 1.
3:47:40.530366 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:47:40.530445 PROGRESS: Extracting batch of 15933 precursors
3:47:40.544083 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:47:40.544179 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:47:40.544220 INFO: FWHM in RT is 2.93 seconds, sigma is 0.38
3:47:40.544250 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:47:40.544493 INFO: Starting candidate selection
3:47:41.429872 INFO: Starting candidate scoring
3:47:41.621220 INFO: Finished candidate processing
3:47:41.621323 INFO: Collecting candidate features
3:47:41.673767 INFO: Collecting fragment features
3:47:41.692818 INFO: Finished candidate scoring
3:47:41.708261 PROGRESS: === Extracted 31866 precursors and 340624 fragments ===
3:47:41.708639 INFO: performing precursor FDR with 47 features
3:47:41.708678 INFO: Decoy channel: -1
3:47:41.708702 INFO: Competetive: True
3:47:41.716562 INFO: Setting torch num_threads to 2 for FDR classification task
3:47:42.095667 INFO: Test AUC: 0.582
3:47:42.096017 INFO: Train AUC: 0.591
3:47:42.096050 INFO: AUC difference: 1.58%
3:47:42.180107 INFO: Resetting torch num_threads to 100
3:47:42.181355 INFO: === FDR correction performed with classifier version 0 ===
3:47:42.182301 PROGRESS: ============================= Precursor FDR =============================
3:47:42.182403 PROGRESS: Total precursors accumulated: 2,615
3:47:42.182462 PROGRESS: Target precursors: 2,446 (93.54%)
3:47:42.182512 PROGRESS: Decoy precursors: 169 (6.46%)
3:47:42.182558 PROGRESS: 
3:47:42.182600 PROGRESS: Precursor Summary:
3:47:42.184116 PROGRESS: Channel   0:	 0.05 FDR: 2,325; 0.01 FDR: 1,739; 0.001 FDR: 1,051
3:47:42.184222 PROGRESS: 
3:47:42.184278 PROGRESS: Protein Summary:
3:47:42.186216 PROGRESS: Channel   0:	 0.05 FDR: 1,637; 0.01 FDR: 1,299; 0.001 FDR:   842
3:47:42.186314 PROGRESS: =========================================================================
3:47:42.194689 INFO: fragments_df_filtered: 5000
3:47:42.205546 INFO: calibration group: precursor, fitting mz estimator 
3:47:42.352338 INFO: calibration group: precursor, fitting rt estimator 
3:47:42.465726 INFO: calibration group: fragment, fitting mz estimator 
3:47:42.884201 INFO: calibration group: precursor, predicting mz
3:47:42.887193 INFO: calibration group: precursor, predicting rt
3:47:42.897184 INFO: calibration group: fragment, predicting mz
3:47:42.918506 INFO: === checking if optimization conditions were reached ===
3:47:42.920690 PROGRESS: ❌ ms2_error      : 15.9839 > 15.0000 or insufficient steps taken.
3:47:42.922066 PROGRESS: ❌ ms1_error      : 13.6056 > 10.0000 or insufficient steps taken.
3:47:42.922123 INFO: ==============================================
3:47:42.922224 INFO: Starting optimization step 2.
3:47:42.922300 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:47:42.922366 PROGRESS: Extracting batch of 15933 precursors
3:47:42.929621 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:47:42.929701 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:47:42.929739 INFO: FWHM in RT is 2.88 seconds, sigma is 0.37
3:47:42.929768 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:47:42.929983 INFO: Starting candidate selection
3:47:43.845064 INFO: Starting candidate scoring
3:47:44.042647 INFO: Finished candidate processing
3:47:44.042750 INFO: Collecting candidate features
3:47:44.090761 INFO: Collecting fragment features
3:47:44.112133 INFO: Finished candidate scoring
3:47:44.126950 PROGRESS: === Extracted 31864 precursors and 316599 fragments ===
3:47:44.127353 INFO: performing precursor FDR with 47 features
3:47:44.127391 INFO: Decoy channel: -1
3:47:44.127416 INFO: Competetive: True
3:47:44.135425 INFO: Setting torch num_threads to 2 for FDR classification task
3:47:44.619761 INFO: Test AUC: 0.617
3:47:44.619882 INFO: Train AUC: 0.617
3:47:44.619912 INFO: AUC difference: 0.02%
3:47:44.703951 INFO: Resetting torch num_threads to 100
3:47:44.705193 INFO: === FDR correction performed with classifier version 1 ===
3:47:44.706857 PROGRESS: ============================= Precursor FDR =============================
3:47:44.706963 PROGRESS: Total precursors accumulated: 7,994
3:47:44.707044 PROGRESS: Target precursors: 7,445 (93.13%)
3:47:44.707095 PROGRESS: Decoy precursors: 549 (6.87%)
3:47:44.707140 PROGRESS: 
3:47:44.707185 PROGRESS: Precursor Summary:
3:47:44.709126 PROGRESS: Channel   0:	 0.05 FDR: 3,449; 0.01 FDR: 2,959; 0.001 FDR: 1,610
3:47:44.709232 PROGRESS: 
3:47:44.709287 PROGRESS: Protein Summary:
3:47:44.711671 PROGRESS: Channel   0:	 0.05 FDR: 2,236; 0.01 FDR: 1,980; 0.001 FDR: 1,227
3:47:44.711784 PROGRESS: =========================================================================
3:47:44.725727 INFO: fragments_df_filtered: 5000
3:47:44.736574 INFO: calibration group: precursor, fitting mz estimator 
3:47:44.988224 INFO: calibration group: precursor, fitting rt estimator 
3:47:45.218365 INFO: calibration group: fragment, fitting mz estimator 
3:47:45.633741 INFO: calibration group: precursor, predicting mz
3:47:45.636751 INFO: calibration group: precursor, predicting rt
3:47:45.646349 INFO: calibration group: fragment, predicting mz
3:47:45.675231 INFO: === checking if optimization conditions were reached ===
3:47:45.677438 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
3:47:45.679066 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
3:47:45.679126 INFO: ==============================================
3:47:45.679248 PROGRESS: Optimization finished for ms2_error, ms1_error.
3:47:45.693693 INFO: calibration group: precursor, predicting mz
3:47:45.696935 INFO: calibration group: precursor, predicting rt
3:47:45.707336 INFO: calibration group: fragment, predicting mz
3:47:45.731302 INFO: Starting optimization step 0.
3:47:45.731497 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:47:45.731576 PROGRESS: Extracting batch of 15933 precursors
3:47:45.737566 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:47:45.737638 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:47:45.737717 INFO: FWHM in RT is 2.65 seconds, sigma is 0.34
3:47:45.737748 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:47:45.737987 INFO: Starting candidate selection
3:47:46.643350 INFO: Starting candidate scoring
3:47:46.824458 INFO: Finished candidate processing
3:47:46.824563 INFO: Collecting candidate features
3:47:46.873466 INFO: Collecting fragment features
3:47:46.896630 INFO: Finished candidate scoring
3:47:46.910728 PROGRESS: === Extracted 31864 precursors and 316014 fragments ===
3:47:46.911109 INFO: performing precursor FDR with 47 features
3:47:46.911148 INFO: Decoy channel: -1
3:47:46.911173 INFO: Competetive: True
3:47:46.919199 INFO: Setting torch num_threads to 2 for FDR classification task
3:47:47.406968 INFO: Test AUC: 0.615
3:47:47.407093 INFO: Train AUC: 0.621
3:47:47.407123 INFO: AUC difference: 1.01%
3:47:47.491202 INFO: Resetting torch num_threads to 100
3:47:47.492458 INFO: === FDR correction performed with classifier version 2 ===
3:47:47.493926 PROGRESS: ============================= Precursor FDR =============================
3:47:47.494029 PROGRESS: Total precursors accumulated: 7,986
3:47:47.494089 PROGRESS: Target precursors: 7,456 (93.36%)
3:47:47.494142 PROGRESS: Decoy precursors: 530 (6.64%)
3:47:47.494190 PROGRESS: 
3:47:47.494237 PROGRESS: Precursor Summary:
3:47:47.496314 PROGRESS: Channel   0:	 0.05 FDR: 3,684; 0.01 FDR: 3,181; 0.001 FDR: 2,155
3:47:47.496428 PROGRESS: 
3:47:47.496485 PROGRESS: Protein Summary:
3:47:47.499044 PROGRESS: Channel   0:	 0.05 FDR: 2,346; 0.01 FDR: 2,088; 0.001 FDR: 1,552
3:47:47.499143 PROGRESS: =========================================================================
3:47:47.511656 INFO: fragments_df_filtered: 5000
3:47:47.522420 INFO: calibration group: precursor, fitting mz estimator 
3:47:47.789612 INFO: calibration group: precursor, fitting rt estimator 
3:47:48.057924 INFO: calibration group: fragment, fitting mz estimator 
3:47:48.478495 INFO: calibration group: precursor, predicting mz
3:47:48.481472 INFO: calibration group: precursor, predicting rt
3:47:48.491316 INFO: calibration group: fragment, predicting mz
3:47:48.512217 INFO: === checking if optimization conditions were reached ===
3:47:48.512411 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3:47:48.515909 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 107.7061.
3:47:48.515972 INFO: ==============================================
3:47:48.516076 INFO: Starting optimization step 1.
3:47:48.516151 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:47:48.516217 PROGRESS: Extracting batch of 15933 precursors
3:47:48.524039 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:47:48.524109 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:47:48.524146 INFO: FWHM in RT is 2.62 seconds, sigma is 0.34
3:47:48.524175 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:47:48.524386 INFO: Starting candidate selection
3:47:50.428425 INFO: Starting candidate scoring
3:47:50.633443 INFO: Finished candidate processing
3:47:50.633547 INFO: Collecting candidate features
3:47:50.677166 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 31817)
3:47:50.681377 INFO: Collecting fragment features
3:47:50.700718 INFO: Finished candidate scoring
3:47:50.715370 PROGRESS: === Extracted 31817 precursors and 301496 fragments ===
3:47:50.715775 INFO: performing precursor FDR with 47 features
3:47:50.715818 INFO: Decoy channel: -1
3:47:50.715844 INFO: Competetive: True
3:47:50.723732 INFO: Setting torch num_threads to 2 for FDR classification task
3:47:50.727972 WARNING: dropped 3 decoy PSMs due to missing features
3:47:51.212463 INFO: Test AUC: 0.654
3:47:51.212594 INFO: Train AUC: 0.655
3:47:51.212631 INFO: AUC difference: 0.22%
3:47:51.295249 INFO: Resetting torch num_threads to 100
3:47:51.296580 INFO: === FDR correction performed with classifier version 2 ===
3:47:51.298133 PROGRESS: ============================= Precursor FDR =============================
3:47:51.298241 PROGRESS: Total precursors accumulated: 7,853
3:47:51.298320 PROGRESS: Target precursors: 7,413 (94.40%)
3:47:51.298389 PROGRESS: Decoy precursors: 440 (5.60%)
3:47:51.298450 PROGRESS: 
3:47:51.298512 PROGRESS: Precursor Summary:
3:47:51.300761 PROGRESS: Channel   0:	 0.05 FDR: 4,516; 0.01 FDR: 3,895; 0.001 FDR: 2,651
3:47:51.300890 PROGRESS: 
3:47:51.300963 PROGRESS: Protein Summary:
3:47:51.303890 PROGRESS: Channel   0:	 0.05 FDR: 2,696; 0.01 FDR: 2,426; 0.001 FDR: 1,833
3:47:51.304012 PROGRESS: =========================================================================
3:47:51.318866 INFO: fragments_df_filtered: 5000
3:47:51.330851 INFO: calibration group: precursor, fitting mz estimator 
3:47:51.631818 INFO: calibration group: precursor, fitting rt estimator 
3:47:51.930860 INFO: calibration group: fragment, fitting mz estimator 
3:47:52.345717 INFO: calibration group: precursor, predicting mz
3:47:52.348826 INFO: calibration group: precursor, predicting rt
3:47:52.358445 INFO: calibration group: fragment, predicting mz
3:47:52.379307 INFO: === checking if optimization conditions were reached ===
3:47:52.379493 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3:47:52.383601 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 60.4030.
3:47:52.383672 INFO: ==============================================
3:47:52.383795 INFO: Starting optimization step 2.
3:47:52.383875 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:47:52.383942 PROGRESS: Extracting batch of 15933 precursors
3:47:52.390274 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:47:52.390354 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:47:52.390393 INFO: FWHM in RT is 2.62 seconds, sigma is 0.34
3:47:52.390425 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:47:52.390643 INFO: Starting candidate selection
3:47:52.985789 INFO: Starting candidate scoring
3:47:53.180706 INFO: Finished candidate processing
3:47:53.180809 INFO: Collecting candidate features
3:47:53.226054 WARNING: intensity_correlation has 2 NaNs ( 0.01 % out of 31768)
3:47:53.230283 INFO: Collecting fragment features
3:47:53.254339 INFO: Finished candidate scoring
3:47:53.268227 PROGRESS: === Extracted 31768 precursors and 293326 fragments ===
3:47:53.268610 INFO: performing precursor FDR with 47 features
3:47:53.268650 INFO: Decoy channel: -1
3:47:53.268677 INFO: Competetive: True
3:47:53.279240 INFO: Setting torch num_threads to 2 for FDR classification task
3:47:53.284037 WARNING: dropped 2 decoy PSMs due to missing features
3:47:53.772267 INFO: Test AUC: 0.666
3:47:53.772399 INFO: Train AUC: 0.662
3:47:53.772432 INFO: AUC difference: 0.62%
3:47:53.855545 INFO: Resetting torch num_threads to 100
3:47:53.856838 INFO: === FDR correction performed with classifier version 2 ===
3:47:53.858328 PROGRESS: ============================= Precursor FDR =============================
3:47:53.858443 PROGRESS: Total precursors accumulated: 7,892
3:47:53.858510 PROGRESS: Target precursors: 7,482 (94.80%)
3:47:53.858568 PROGRESS: Decoy precursors: 410 (5.20%)
3:47:53.858625 PROGRESS: 
3:47:53.858676 PROGRESS: Precursor Summary:
3:47:53.861847 PROGRESS: Channel   0:	 0.05 FDR: 4,701; 0.01 FDR: 4,014; 0.001 FDR: 3,309
3:47:53.861980 PROGRESS: 
3:47:53.862043 PROGRESS: Protein Summary:
3:47:53.865067 PROGRESS: Channel   0:	 0.05 FDR: 2,776; 0.01 FDR: 2,483; 0.001 FDR: 2,157
3:47:53.865176 PROGRESS: =========================================================================
3:47:53.879367 INFO: fragments_df_filtered: 5000
3:47:53.892658 INFO: calibration group: precursor, fitting mz estimator 
3:47:54.200287 INFO: calibration group: precursor, fitting rt estimator 
3:47:54.527400 INFO: calibration group: fragment, fitting mz estimator 
3:47:54.936709 INFO: calibration group: precursor, predicting mz
3:47:54.939792 INFO: calibration group: precursor, predicting rt
3:47:54.949740 INFO: calibration group: fragment, predicting mz
3:47:54.971326 INFO: === checking if optimization conditions were reached ===
3:47:54.971552 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3:47:54.975882 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 44.9748.
3:47:54.975953 INFO: ==============================================
3:47:54.976066 INFO: Starting optimization step 3.
3:47:54.976155 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:47:54.976239 PROGRESS: Extracting batch of 15933 precursors
3:47:54.983283 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:47:54.983356 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:47:54.983399 INFO: FWHM in RT is 2.63 seconds, sigma is 0.34
3:47:54.983428 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:47:54.983655 INFO: Starting candidate selection
3:47:55.658875 INFO: Starting candidate scoring
3:47:55.858474 INFO: Finished candidate processing
3:47:55.858667 INFO: Collecting candidate features
3:47:55.935809 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 31753)
3:47:55.940956 INFO: Collecting fragment features
3:47:55.976748 INFO: Finished candidate scoring
3:47:56.001130 PROGRESS: === Extracted 31753 precursors and 290761 fragments ===
3:47:56.001942 INFO: performing precursor FDR with 47 features
3:47:56.001986 INFO: Decoy channel: -1
3:47:56.002016 INFO: Competetive: True
3:47:56.022751 INFO: Setting torch num_threads to 2 for FDR classification task
3:47:56.028711 WARNING: dropped 1 decoy PSMs due to missing features
3:47:56.590633 INFO: Test AUC: 0.679
3:47:56.590763 INFO: Train AUC: 0.664
3:47:56.590792 INFO: AUC difference: 2.18%
3:47:56.674051 INFO: Resetting torch num_threads to 100
3:47:56.675338 INFO: === FDR correction performed with classifier version 2 ===
3:47:56.676961 PROGRESS: ============================= Precursor FDR =============================
3:47:56.677074 PROGRESS: Total precursors accumulated: 7,827
3:47:56.677134 PROGRESS: Target precursors: 7,389 (94.40%)
3:47:56.677184 PROGRESS: Decoy precursors: 438 (5.60%)
3:47:56.677228 PROGRESS: 
3:47:56.677272 PROGRESS: Precursor Summary:
3:47:56.679684 PROGRESS: Channel   0:	 0.05 FDR: 4,750; 0.01 FDR: 4,029; 0.001 FDR: 3,226
3:47:56.679825 PROGRESS: 
3:47:56.679884 PROGRESS: Protein Summary:
3:47:56.682865 PROGRESS: Channel   0:	 0.05 FDR: 2,807; 0.01 FDR: 2,495; 0.001 FDR: 2,128
3:47:56.682965 PROGRESS: =========================================================================
3:47:56.698212 INFO: fragments_df_filtered: 5000
3:47:56.710586 INFO: calibration group: precursor, fitting mz estimator 
3:47:57.000921 INFO: calibration group: precursor, fitting rt estimator 
3:47:57.322279 INFO: calibration group: fragment, fitting mz estimator 
3:47:57.744709 INFO: calibration group: precursor, predicting mz
3:47:57.747759 INFO: calibration group: precursor, predicting rt
3:47:57.757272 INFO: calibration group: fragment, predicting mz
3:47:57.786808 INFO: === checking if optimization conditions were reached ===
3:47:57.787016 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3:47:57.791194 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 36.7035.
3:47:57.791262 INFO: ==============================================
3:47:57.791364 INFO: Starting optimization step 4.
3:47:57.791437 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:47:57.791503 PROGRESS: Extracting batch of 15933 precursors
3:47:57.806418 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:47:57.806500 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:47:57.806543 INFO: FWHM in RT is 2.62 seconds, sigma is 0.34
3:47:57.806571 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:47:57.806838 INFO: Starting candidate selection
3:47:58.476851 INFO: Starting candidate scoring
3:47:58.688735 INFO: Finished candidate processing
3:47:58.688852 INFO: Collecting candidate features
3:47:58.734282 WARNING: intensity_correlation has 8 NaNs ( 0.03 % out of 31646)
3:47:58.738573 INFO: Collecting fragment features
3:47:58.765960 INFO: Finished candidate scoring
3:47:58.778939 PROGRESS: === Extracted 31646 precursors and 285055 fragments ===
3:47:58.779325 INFO: performing precursor FDR with 47 features
3:47:58.779363 INFO: Decoy channel: -1
3:47:58.779388 INFO: Competetive: True
3:47:58.788137 INFO: Setting torch num_threads to 2 for FDR classification task
3:47:58.793697 WARNING: dropped 3 target PSMs due to missing features
3:47:58.793811 WARNING: dropped 5 decoy PSMs due to missing features
3:47:59.290360 INFO: Test AUC: 0.675
3:47:59.290494 INFO: Train AUC: 0.676
3:47:59.290523 INFO: AUC difference: 0.05%
3:47:59.373164 INFO: Resetting torch num_threads to 100
3:47:59.374363 INFO: === FDR correction performed with classifier version 2 ===
3:47:59.375881 PROGRESS: ============================= Precursor FDR =============================
3:47:59.375990 PROGRESS: Total precursors accumulated: 7,685
3:47:59.376050 PROGRESS: Target precursors: 7,253 (94.38%)
3:47:59.376107 PROGRESS: Decoy precursors: 432 (5.62%)
3:47:59.376167 PROGRESS: 
3:47:59.376213 PROGRESS: Precursor Summary:
3:47:59.378730 PROGRESS: Channel   0:	 0.05 FDR: 4,794; 0.01 FDR: 4,027; 0.001 FDR: 3,085
3:47:59.378857 PROGRESS: 
3:47:59.378914 PROGRESS: Protein Summary:
3:47:59.381866 PROGRESS: Channel   0:	 0.05 FDR: 2,811; 0.01 FDR: 2,495; 0.001 FDR: 2,057
3:47:59.381980 PROGRESS: =========================================================================
3:47:59.396588 INFO: fragments_df_filtered: 5000
3:47:59.407678 INFO: calibration group: precursor, fitting mz estimator 
3:47:59.684895 INFO: calibration group: precursor, fitting rt estimator 
3:48:00.031631 INFO: calibration group: fragment, fitting mz estimator 
3:48:00.488082 INFO: calibration group: precursor, predicting mz
3:48:00.491017 INFO: calibration group: precursor, predicting rt
3:48:00.500465 INFO: calibration group: fragment, predicting mz
3:48:00.521607 INFO: === checking if optimization conditions were reached ===
3:48:00.521789 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3:48:00.526184 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 32.0295.
3:48:00.526263 INFO: ==============================================
3:48:00.526369 INFO: Starting optimization step 5.
3:48:00.526446 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:48:00.526512 PROGRESS: Extracting batch of 15933 precursors
3:48:00.532164 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:48:00.532244 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:48:00.532282 INFO: FWHM in RT is 2.61 seconds, sigma is 0.34
3:48:00.532310 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:48:00.532520 INFO: Starting candidate selection
3:48:01.163294 INFO: Starting candidate scoring
3:48:01.365644 INFO: Finished candidate processing
3:48:01.365821 INFO: Collecting candidate features
3:48:01.433331 WARNING: intensity_correlation has 7 NaNs ( 0.02 % out of 31659)
3:48:01.437824 INFO: Collecting fragment features
3:48:01.460881 INFO: Finished candidate scoring
3:48:01.478705 PROGRESS: === Extracted 31659 precursors and 286091 fragments ===
3:48:01.479097 INFO: performing precursor FDR with 47 features
3:48:01.479137 INFO: Decoy channel: -1
3:48:01.479162 INFO: Competetive: True
3:48:01.488913 INFO: Setting torch num_threads to 2 for FDR classification task
3:48:01.494898 WARNING: dropped 2 target PSMs due to missing features
3:48:01.495015 WARNING: dropped 5 decoy PSMs due to missing features
3:48:02.091869 INFO: Test AUC: 0.682
3:48:02.092014 INFO: Train AUC: 0.676
3:48:02.092045 INFO: AUC difference: 0.91%
3:48:02.180290 INFO: Resetting torch num_threads to 100
3:48:02.181852 INFO: === FDR correction performed with classifier version 2 ===
3:48:02.183113 PROGRESS: ============================= Precursor FDR =============================
3:48:02.183216 PROGRESS: Total precursors accumulated: 4,831
3:48:02.183279 PROGRESS: Target precursors: 4,627 (95.78%)
3:48:02.183332 PROGRESS: Decoy precursors: 204 (4.22%)
3:48:02.183381 PROGRESS: 
3:48:02.183427 PROGRESS: Precursor Summary:
3:48:02.186051 PROGRESS: Channel   0:	 0.05 FDR: 4,627; 0.01 FDR: 3,988; 0.001 FDR: 3,188
3:48:02.186175 PROGRESS: 
3:48:02.186235 PROGRESS: Protein Summary:
3:48:02.189188 PROGRESS: Channel   0:	 0.05 FDR: 2,737; 0.01 FDR: 2,468; 0.001 FDR: 2,091
3:48:02.189291 PROGRESS: =========================================================================
3:48:02.204021 INFO: fragments_df_filtered: 5000
3:48:02.216787 INFO: calibration group: precursor, fitting mz estimator 
3:48:02.458716 INFO: calibration group: precursor, fitting rt estimator 
3:48:02.706111 INFO: calibration group: fragment, fitting mz estimator 
3:48:03.063815 INFO: calibration group: precursor, predicting mz
3:48:03.067054 INFO: calibration group: precursor, predicting rt
3:48:03.077415 INFO: calibration group: fragment, predicting mz
3:48:03.098811 INFO: === checking if optimization conditions were reached ===
3:48:03.099019 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3:48:03.102921 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 27.2835.
3:48:03.102984 INFO: ==============================================
3:48:03.103094 INFO: Starting optimization step 6.
3:48:03.103167 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:48:03.103230 PROGRESS: Extracting batch of 15933 precursors
3:48:03.109836 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:48:03.109899 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:48:03.109933 INFO: FWHM in RT is 2.61 seconds, sigma is 0.34
3:48:03.109956 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:48:03.110161 INFO: Starting candidate selection
3:48:03.777414 INFO: Starting candidate scoring
3:48:04.000828 INFO: Finished candidate processing
3:48:04.000941 INFO: Collecting candidate features
3:48:04.046819 WARNING: intensity_correlation has 4 NaNs ( 0.01 % out of 31677)
3:48:04.051078 INFO: Collecting fragment features
3:48:04.070301 INFO: Finished candidate scoring
3:48:04.083914 PROGRESS: === Extracted 31677 precursors and 287036 fragments ===
3:48:04.085551 INFO: performing precursor FDR with 47 features
3:48:04.085593 INFO: Decoy channel: -1
3:48:04.085618 INFO: Competetive: True
3:48:04.093856 INFO: Setting torch num_threads to 2 for FDR classification task
3:48:04.099316 WARNING: dropped 1 target PSMs due to missing features
3:48:04.099436 WARNING: dropped 3 decoy PSMs due to missing features
3:48:04.595299 INFO: Test AUC: 0.673
3:48:04.595435 INFO: Train AUC: 0.681
3:48:04.595466 INFO: AUC difference: 1.26%
3:48:04.678695 INFO: Resetting torch num_threads to 100
3:48:04.679993 INFO: === FDR correction performed with classifier version 2 ===
3:48:04.681194 PROGRESS: ============================= Precursor FDR =============================
3:48:04.681290 PROGRESS: Total precursors accumulated: 4,847
3:48:04.681351 PROGRESS: Target precursors: 4,636 (95.65%)
3:48:04.681401 PROGRESS: Decoy precursors: 211 (4.35%)
3:48:04.681446 PROGRESS: 
3:48:04.681490 PROGRESS: Precursor Summary:
3:48:04.683676 PROGRESS: Channel   0:	 0.05 FDR: 4,636; 0.01 FDR: 3,868; 0.001 FDR: 3,172
3:48:04.683805 PROGRESS: 
3:48:04.683876 PROGRESS: Protein Summary:
3:48:04.686729 PROGRESS: Channel   0:	 0.05 FDR: 2,726; 0.01 FDR: 2,392; 0.001 FDR: 2,083
3:48:04.686829 PROGRESS: =========================================================================
3:48:04.701522 INFO: fragments_df_filtered: 5000
3:48:04.712450 INFO: calibration group: precursor, fitting mz estimator 
3:48:05.004569 INFO: calibration group: precursor, fitting rt estimator 
3:48:05.299957 INFO: calibration group: fragment, fitting mz estimator 
3:48:05.715585 INFO: calibration group: precursor, predicting mz
3:48:05.718560 INFO: calibration group: precursor, predicting rt
3:48:05.728041 INFO: calibration group: fragment, predicting mz
3:48:05.748985 INFO: === checking if optimization conditions were reached ===
3:48:05.749174 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
3:48:05.753198 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 24.1895.
3:48:05.753266 INFO: ==============================================
3:48:05.753371 INFO: Starting optimization step 7.
3:48:05.753447 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:48:05.753514 PROGRESS: Extracting batch of 15933 precursors
3:48:05.759454 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:48:05.759526 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:48:05.759565 INFO: FWHM in RT is 2.62 seconds, sigma is 0.34
3:48:05.759593 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:48:05.759817 INFO: Starting candidate selection
3:48:06.357192 INFO: Starting candidate scoring
3:48:06.567293 INFO: Finished candidate processing
3:48:06.567410 INFO: Collecting candidate features
3:48:06.614421 WARNING: intensity_correlation has 10 NaNs ( 0.03 % out of 30813)
3:48:06.618684 INFO: Collecting fragment features
3:48:06.637966 INFO: Finished candidate scoring
3:48:06.651270 PROGRESS: === Extracted 30813 precursors and 271898 fragments ===
3:48:06.651651 INFO: performing precursor FDR with 47 features
3:48:06.651689 INFO: Decoy channel: -1
3:48:06.651713 INFO: Competetive: True
3:48:06.660077 INFO: Setting torch num_threads to 2 for FDR classification task
3:48:06.665328 WARNING: dropped 2 target PSMs due to missing features
3:48:06.665426 WARNING: dropped 8 decoy PSMs due to missing features
3:48:07.091433 INFO: Test AUC: 0.666
3:48:07.091564 INFO: Train AUC: 0.681
3:48:07.091596 INFO: AUC difference: 2.20%
3:48:07.176552 INFO: Resetting torch num_threads to 100
3:48:07.177839 INFO: === FDR correction performed with classifier version 2 ===
3:48:07.179366 PROGRESS: ============================= Precursor FDR =============================
3:48:07.179462 PROGRESS: Total precursors accumulated: 7,755
3:48:07.179521 PROGRESS: Target precursors: 7,348 (94.75%)
3:48:07.179571 PROGRESS: Decoy precursors: 407 (5.25%)
3:48:07.179617 PROGRESS: 
3:48:07.179662 PROGRESS: Precursor Summary:
3:48:07.181813 PROGRESS: Channel   0:	 0.05 FDR: 4,788; 0.01 FDR: 3,979; 0.001 FDR: 3,177
3:48:07.181944 PROGRESS: 
3:48:07.182002 PROGRESS: Protein Summary:
3:48:07.184963 PROGRESS: Channel   0:	 0.05 FDR: 2,813; 0.01 FDR: 2,457; 0.001 FDR: 2,089
3:48:07.185065 PROGRESS: =========================================================================
3:48:07.198846 INFO: fragments_df_filtered: 5000
3:48:07.210068 INFO: calibration group: precursor, fitting mz estimator 
3:48:07.514719 INFO: calibration group: precursor, fitting rt estimator 
3:48:07.820640 INFO: calibration group: fragment, fitting mz estimator 
3:48:08.235896 INFO: calibration group: precursor, predicting mz
3:48:08.238913 INFO: calibration group: precursor, predicting rt
3:48:08.248914 INFO: calibration group: fragment, predicting mz
3:48:08.269268 INFO: === checking if optimization conditions were reached ===
3:48:08.269460 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
3:48:08.273525 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 19.9375.
3:48:08.273592 INFO: ==============================================
3:48:08.273696 INFO: Starting optimization step 8.
3:48:08.273770 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:48:08.273837 PROGRESS: Extracting batch of 15933 precursors
3:48:08.279073 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:48:08.279152 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:48:08.279189 INFO: FWHM in RT is 2.61 seconds, sigma is 0.34
3:48:08.279217 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:48:08.279425 INFO: Starting candidate selection
3:48:08.869381 INFO: Starting candidate scoring
3:48:09.089197 INFO: Finished candidate processing
3:48:09.089319 INFO: Collecting candidate features
3:48:09.145447 WARNING: intensity_correlation has 11 NaNs ( 0.04 % out of 30836)
3:48:09.149960 INFO: Collecting fragment features
3:48:09.178769 INFO: Finished candidate scoring
3:48:09.195301 PROGRESS: === Extracted 30836 precursors and 273477 fragments ===
3:48:09.195713 INFO: performing precursor FDR with 47 features
3:48:09.195761 INFO: Decoy channel: -1
3:48:09.195787 INFO: Competetive: True
3:48:09.208689 INFO: Setting torch num_threads to 2 for FDR classification task
3:48:09.214049 WARNING: dropped 3 target PSMs due to missing features
3:48:09.214150 WARNING: dropped 8 decoy PSMs due to missing features
3:48:09.741577 INFO: Test AUC: 0.671
3:48:09.741708 INFO: Train AUC: 0.671
3:48:09.741738 INFO: AUC difference: 0.03%
3:48:09.844669 INFO: Resetting torch num_threads to 100
3:48:09.849925 INFO: === FDR correction performed with classifier version 2 ===
3:48:09.851816 PROGRESS: ============================= Precursor FDR =============================
3:48:09.851944 PROGRESS: Total precursors accumulated: 7,876
3:48:09.852011 PROGRESS: Target precursors: 7,505 (95.29%)
3:48:09.852065 PROGRESS: Decoy precursors: 371 (4.71%)
3:48:09.852110 PROGRESS: 
3:48:09.852156 PROGRESS: Precursor Summary:
3:48:09.854599 PROGRESS: Channel   0:	 0.05 FDR: 7,505; 0.01 FDR: 3,966; 0.001 FDR: 3,169
3:48:09.854713 PROGRESS: 
3:48:09.854771 PROGRESS: Protein Summary:
3:48:09.858165 PROGRESS: Channel   0:	 0.05 FDR: 3,618; 0.01 FDR: 2,446; 0.001 FDR: 2,076
3:48:09.858275 PROGRESS: =========================================================================
3:48:09.880159 INFO: fragments_df_filtered: 5000
3:48:09.909307 INFO: calibration group: precursor, fitting mz estimator 
3:48:10.158415 INFO: calibration group: precursor, fitting rt estimator 
3:48:10.452712 INFO: calibration group: fragment, fitting mz estimator 
3:48:10.809068 INFO: calibration group: precursor, predicting mz
3:48:10.812919 INFO: calibration group: precursor, predicting rt
3:48:10.823579 INFO: calibration group: fragment, predicting mz
3:48:10.848663 INFO: === checking if optimization conditions were reached ===
3:48:10.848897 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
3:48:10.853533 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 17.6800.
3:48:10.853609 INFO: ==============================================
3:48:10.853728 INFO: Starting optimization step 9.
3:48:10.853801 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:48:10.853889 PROGRESS: Extracting batch of 15933 precursors
3:48:10.860984 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:48:10.861054 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:48:10.861108 INFO: FWHM in RT is 2.60 seconds, sigma is 0.33
3:48:10.861132 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:48:10.861544 INFO: Starting candidate selection
3:48:11.532918 INFO: Starting candidate scoring
3:48:11.753839 INFO: Finished candidate processing
3:48:11.753962 INFO: Collecting candidate features
3:48:11.810664 WARNING: intensity_correlation has 11 NaNs ( 0.04 % out of 30851)
3:48:11.815109 INFO: Collecting fragment features
3:48:11.837909 INFO: Finished candidate scoring
3:48:11.855057 PROGRESS: === Extracted 30851 precursors and 274291 fragments ===
3:48:11.855522 INFO: performing precursor FDR with 47 features
3:48:11.855563 INFO: Decoy channel: -1
3:48:11.855586 INFO: Competetive: True
3:48:11.869104 INFO: Setting torch num_threads to 2 for FDR classification task
3:48:11.874969 WARNING: dropped 1 target PSMs due to missing features
3:48:11.875073 WARNING: dropped 10 decoy PSMs due to missing features
3:48:12.328709 INFO: Test AUC: 0.675
3:48:12.328851 INFO: Train AUC: 0.676
3:48:12.328882 INFO: AUC difference: 0.14%
3:48:12.412484 INFO: Resetting torch num_threads to 100
3:48:12.413995 INFO: === FDR correction performed with classifier version 2 ===
3:48:12.415806 PROGRESS: ============================= Precursor FDR =============================
3:48:12.415905 PROGRESS: Total precursors accumulated: 7,768
3:48:12.415964 PROGRESS: Target precursors: 7,375 (94.94%)
3:48:12.416016 PROGRESS: Decoy precursors: 393 (5.06%)
3:48:12.416066 PROGRESS: 
3:48:12.416110 PROGRESS: Precursor Summary:
3:48:12.418341 PROGRESS: Channel   0:	 0.05 FDR: 4,731; 0.01 FDR: 3,967; 0.001 FDR: 2,696
3:48:12.418459 PROGRESS: 
3:48:12.418516 PROGRESS: Protein Summary:
3:48:12.421518 PROGRESS: Channel   0:	 0.05 FDR: 2,790; 0.01 FDR: 2,447; 0.001 FDR: 1,848
3:48:12.421622 PROGRESS: =========================================================================
3:48:12.435985 INFO: fragments_df_filtered: 5000
3:48:12.449790 INFO: calibration group: precursor, fitting mz estimator 
3:48:12.809878 INFO: calibration group: precursor, fitting rt estimator 
3:48:13.116286 INFO: calibration group: fragment, fitting mz estimator 
3:48:13.532767 INFO: calibration group: precursor, predicting mz
3:48:13.535862 INFO: calibration group: precursor, predicting rt
3:48:13.545166 INFO: calibration group: fragment, predicting mz
3:48:13.565972 INFO: === checking if optimization conditions were reached ===
3:48:13.566192 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
3:48:13.570388 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 16.7932.
3:48:13.570464 INFO: ==============================================
3:48:13.570578 INFO: Starting optimization step 10.
3:48:13.570656 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:48:13.570725 PROGRESS: Extracting batch of 15933 precursors
3:48:13.577470 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:48:13.577549 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:48:13.577589 INFO: FWHM in RT is 2.60 seconds, sigma is 0.34
3:48:13.577617 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:48:13.577856 INFO: Starting candidate selection
3:48:14.171424 INFO: Starting candidate scoring
3:48:14.409647 INFO: Finished candidate processing
3:48:14.409777 INFO: Collecting candidate features
3:48:14.474060 WARNING: intensity_correlation has 10 NaNs ( 0.03 % out of 30865)
3:48:14.478559 INFO: Collecting fragment features
3:48:14.498363 INFO: Finished candidate scoring
3:48:14.513560 PROGRESS: === Extracted 30865 precursors and 274533 fragments ===
3:48:14.513978 INFO: performing precursor FDR with 47 features
3:48:14.514021 INFO: Decoy channel: -1
3:48:14.514045 INFO: Competetive: True
3:48:14.523486 INFO: Setting torch num_threads to 2 for FDR classification task
3:48:14.529768 WARNING: dropped 1 target PSMs due to missing features
3:48:14.529893 WARNING: dropped 9 decoy PSMs due to missing features
3:48:14.961764 INFO: Test AUC: 0.682
3:48:14.961908 INFO: Train AUC: 0.677
3:48:14.961946 INFO: AUC difference: 0.78%
3:48:15.044874 INFO: Resetting torch num_threads to 100
3:48:15.046436 INFO: === FDR correction performed with classifier version 2 ===
3:48:15.048091 PROGRESS: ============================= Precursor FDR =============================
3:48:15.048206 PROGRESS: Total precursors accumulated: 7,676
3:48:15.048293 PROGRESS: Target precursors: 7,239 (94.31%)
3:48:15.048356 PROGRESS: Decoy precursors: 437 (5.69%)
3:48:15.048422 PROGRESS: 
3:48:15.048484 PROGRESS: Precursor Summary:
3:48:15.051021 PROGRESS: Channel   0:	 0.05 FDR: 4,705; 0.01 FDR: 3,837; 0.001 FDR: 3,109
3:48:15.051151 PROGRESS: 
3:48:15.051229 PROGRESS: Protein Summary:
3:48:15.054376 PROGRESS: Channel   0:	 0.05 FDR: 2,773; 0.01 FDR: 2,387; 0.001 FDR: 2,058
3:48:15.054503 PROGRESS: =========================================================================
3:48:15.068528 INFO: fragments_df_filtered: 5000
3:48:15.081297 INFO: calibration group: precursor, fitting mz estimator 
3:48:15.413342 INFO: calibration group: precursor, fitting rt estimator 
3:48:15.709051 INFO: calibration group: fragment, fitting mz estimator 
3:48:16.128044 INFO: calibration group: precursor, predicting mz
3:48:16.131205 INFO: calibration group: precursor, predicting rt
3:48:16.140400 INFO: calibration group: fragment, predicting mz
3:48:16.161179 INFO: === checking if optimization conditions were reached ===
3:48:16.161364 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 2 ===
3:48:16.165487 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 16.2711.
3:48:16.165562 INFO: ==============================================
3:48:16.165674 INFO: Starting optimization step 11.
3:48:16.165750 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:48:16.165819 PROGRESS: Extracting batch of 15933 precursors
3:48:16.172359 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:48:16.172447 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:48:16.172487 INFO: FWHM in RT is 2.61 seconds, sigma is 0.34
3:48:16.172516 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:48:16.172751 INFO: Starting candidate selection
3:48:16.786618 INFO: Starting candidate scoring
3:48:17.017211 INFO: Finished candidate processing
3:48:17.017331 INFO: Collecting candidate features
3:48:17.065634 WARNING: intensity_correlation has 11 NaNs ( 0.04 % out of 30880)
3:48:17.069919 INFO: Collecting fragment features
3:48:17.089499 INFO: Finished candidate scoring
3:48:17.104519 PROGRESS: === Extracted 30880 precursors and 274906 fragments ===
3:48:17.104923 INFO: performing precursor FDR with 47 features
3:48:17.104961 INFO: Decoy channel: -1
3:48:17.104984 INFO: Competetive: True
3:48:17.114079 INFO: Setting torch num_threads to 2 for FDR classification task
3:48:17.119504 WARNING: dropped 2 target PSMs due to missing features
3:48:17.119606 WARNING: dropped 9 decoy PSMs due to missing features
3:48:17.564246 INFO: Test AUC: 0.684
3:48:17.564385 INFO: Train AUC: 0.676
3:48:17.564416 INFO: AUC difference: 1.09%
3:48:17.648982 INFO: Resetting torch num_threads to 100
3:48:17.650478 INFO: === FDR correction performed with classifier version 2 ===
3:48:17.652090 PROGRESS: ============================= Precursor FDR =============================
3:48:17.652199 PROGRESS: Total precursors accumulated: 7,638
3:48:17.652256 PROGRESS: Target precursors: 7,193 (94.17%)
3:48:17.652307 PROGRESS: Decoy precursors: 445 (5.83%)
3:48:17.652355 PROGRESS: 
3:48:17.652398 PROGRESS: Precursor Summary:
3:48:17.654645 PROGRESS: Channel   0:	 0.05 FDR: 4,674; 0.01 FDR: 3,874; 0.001 FDR: 2,936
3:48:17.654757 PROGRESS: 
3:48:17.654812 PROGRESS: Protein Summary:
3:48:17.658721 PROGRESS: Channel   0:	 0.05 FDR: 2,747; 0.01 FDR: 2,406; 0.001 FDR: 1,977
3:48:17.658822 PROGRESS: =========================================================================
3:48:17.672535 INFO: fragments_df_filtered: 5000
3:48:17.685407 INFO: calibration group: precursor, fitting mz estimator 
3:48:17.979620 INFO: calibration group: precursor, fitting rt estimator 
3:48:18.277965 INFO: calibration group: fragment, fitting mz estimator 
3:48:18.695045 INFO: calibration group: precursor, predicting mz
3:48:18.698144 INFO: calibration group: precursor, predicting rt
3:48:18.708318 INFO: calibration group: fragment, predicting mz
3:48:18.729450 INFO: === checking if optimization conditions were reached ===
3:48:18.729855 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 2 ===
3:48:18.731393 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 16.2711 found after 12 searches.
3:48:18.731518 INFO: ==============================================
3:48:18.731793 PROGRESS: Optimization finished for rt_error.
3:48:18.749081 INFO: calibration group: precursor, predicting mz
3:48:18.752702 INFO: calibration group: precursor, predicting rt
3:48:18.762579 INFO: calibration group: fragment, predicting mz
3:48:18.821131 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:48:18.821572 PROGRESS: ==============================================
3:48:18.821825 PROGRESS: ms2_error      : 15.0000
3:48:18.822059 PROGRESS: ms1_error      : 10.0000
3:48:18.822281 PROGRESS: rt_error       : 16.2711
3:48:18.822500 PROGRESS: ==============================================
3:48:18.824434 INFO: calibration group: precursor, predicting mz
3:48:18.834302 INFO: calibration group: precursor, predicting rt
3:48:18.871394 INFO: calibration group: fragment, predicting mz
3:48:18.977754 PROGRESS: Extracting batch of 65173 precursors
3:48:19.007253 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:48:19.007566 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:48:19.007676 INFO: FWHM in RT is 2.62 seconds, sigma is 0.34
3:48:19.007776 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:48:19.008176 INFO: Starting candidate selection
3:48:21.343796 INFO: Applying score cutoff of 18.267935708999634
3:48:21.347541 INFO: Removed 5489 precursors with score below cutoff
3:48:21.379027 INFO: Starting candidate scoring
3:48:22.306945 INFO: Finished candidate processing
3:48:22.307066 INFO: Collecting candidate features
3:48:22.488394 WARNING: intensity_correlation has 16 NaNs ( 0.01 % out of 121636)
3:48:22.503748 INFO: Collecting fragment features
3:48:22.583684 INFO: Finished candidate scoring
3:48:22.641517 INFO: === FDR correction performed with classifier version 14 ===
3:48:22.642396 INFO: performing precursor FDR with 47 features
3:48:22.642430 INFO: Decoy channel: -1
3:48:22.642454 INFO: Competetive: True
3:48:22.691994 INFO: Setting torch num_threads to 2 for FDR classification task
3:48:22.714869 WARNING: dropped 5 target PSMs due to missing features
3:48:22.715022 WARNING: dropped 11 decoy PSMs due to missing features
3:48:24.523539 INFO: Test AUC: 0.758
3:48:24.523785 INFO: Train AUC: 0.764
3:48:24.523824 INFO: AUC difference: 0.82%
3:48:24.623102 INFO: Resetting torch num_threads to 100
3:48:24.631113 INFO: Removing fragments below FDR threshold
3:48:24.658678 PROGRESS: ============================= Precursor FDR =============================
3:48:24.659050 PROGRESS: Total precursors accumulated: 17,320
3:48:24.659119 PROGRESS: Target precursors: 17,149 (99.01%)
3:48:24.659176 PROGRESS: Decoy precursors: 171 (0.99%)
3:48:24.659226 PROGRESS: 
3:48:24.659273 PROGRESS: Precursor Summary:
3:48:24.665734 PROGRESS: Channel   0:	 0.05 FDR: 17,149; 0.01 FDR: 17,149; 0.001 FDR: 14,323
3:48:24.665901 PROGRESS: 
3:48:24.665960 PROGRESS: Protein Summary:
3:48:24.675179 PROGRESS: Channel   0:	 0.05 FDR: 5,117; 0.01 FDR: 5,117; 0.001 FDR: 4,793
3:48:24.675365 PROGRESS: =========================================================================
3:48:24.890709 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:48:24.909262 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:48:24.909456 INFO: Quantification results path: run_output_Astral/alphadia_1.10_default/quant
3:48:24.909542 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2 at run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:48:24.910282 INFO: Initializing RawFileManager
3:48:52.875689 INFO: Determining DIA cycle
3:48:52.891956 INFO: Found cycle with start 0.00 min and length 303.
3:48:53.064775 INFO: RT (min)            : 0.0 - 26.9
3:48:53.064897 INFO: RT duration (sec)   : 1611.2
3:48:53.064927 INFO: RT duration (min)   : 26.9
3:48:53.064951 INFO: Cycle len (scans)   : 303
3:48:53.064970 INFO: Cycle len (sec)     : 1.65
3:48:53.064988 INFO: Number of cycles    : 978
3:48:53.065007 INFO: MS2 range (m/z)     : 380.4 - 980.7
3:48:53.081516 INFO: Initializing CalibrationManager
3:48:53.081832 INFO: Loading calibration config
3:48:53.082419 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'}]
3:48:53.082508 INFO: Calibration group :fragment, found 1 estimator(s)
3:48:53.082603 INFO: Calibration group :precursor, found 3 estimator(s)
3:48:53.082695 INFO: Disabling ion mobility calibration
3:48:53.082725 INFO: removed mobility estimator from group precursor
3:48:53.082869 INFO: Initializing OptimizationManager
3:48:53.082986 INFO: initial parameter: ms1_error = 30
3:48:53.083061 INFO: initial parameter: ms2_error = 30
3:48:53.083114 INFO: initial parameter: rt_error = 805.6019897460938
3:48:53.083160 INFO: initial parameter: mobility_error = 0.1
3:48:53.083204 INFO: initial parameter: column_type = library
3:48:53.083246 INFO: initial parameter: num_candidates = 1
3:48:53.083287 INFO: initial parameter: classifier_version = -1
3:48:53.083326 INFO: initial parameter: fwhm_rt = 5
3:48:53.083366 INFO: initial parameter: fwhm_mobility = 0.01
3:48:53.083404 INFO: initial parameter: score_cutoff = 0
3:48:53.083463 INFO: Initializing TimingManager
3:48:53.083538 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:48:53.083635 INFO: FDRManager not loaded from disk.
3:48:53.083660 INFO: Initializing FDRManager
3:48:53.083694 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
3:48:53.102803 PROGRESS: 32,718 target precursors potentially observable (0 removed)
3:48:53.126294 PROGRESS: Starting initial search for precursors.
3:48:53.141499 INFO: Starting optimization step 0.
3:48:53.141778 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:48:53.141863 PROGRESS: Extracting batch of 15933 precursors
3:48:53.146317 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:48:53.146390 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:48:53.146435 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:48:53.146459 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:48:53.146752 INFO: Starting candidate selection
3:48:54.158696 INFO: Starting candidate scoring
3:48:54.279429 INFO: Finished candidate processing
3:48:54.279558 INFO: Collecting candidate features
3:48:54.330071 INFO: Collecting fragment features
3:48:54.344936 INFO: Finished candidate scoring
3:48:54.354164 PROGRESS: === Extracted 15933 precursors and 171506 fragments ===
3:48:54.354527 INFO: performing precursor FDR with 47 features
3:48:54.354565 INFO: Decoy channel: -1
3:48:54.354588 INFO: Competetive: True
3:48:54.359237 INFO: Setting torch num_threads to 2 for FDR classification task
3:48:54.543135 INFO: Test AUC: 0.585
3:48:54.543262 INFO: Train AUC: 0.593
3:48:54.543293 INFO: AUC difference: 1.34%
3:48:54.624876 INFO: Resetting torch num_threads to 100
3:48:54.626030 INFO: === FDR correction performed with classifier version -1 ===
3:48:54.626878 PROGRESS: ============================= Precursor FDR =============================
3:48:54.626971 PROGRESS: Total precursors accumulated: 6
3:48:54.627031 PROGRESS: Target precursors: 6 (100.00%)
3:48:54.627082 PROGRESS: Decoy precursors: 0 (0.00%)
3:48:54.627132 PROGRESS: 
3:48:54.627177 PROGRESS: Precursor Summary:
3:48:54.628534 PROGRESS: Channel   0:	 0.05 FDR:     6; 0.01 FDR:     6; 0.001 FDR:     6
3:48:54.628629 PROGRESS: 
3:48:54.628685 PROGRESS: Protein Summary:
3:48:54.629716 PROGRESS: Channel   0:	 0.05 FDR:     6; 0.01 FDR:     6; 0.001 FDR:     6
3:48:54.629804 PROGRESS: =========================================================================
3:48:54.656204 INFO: Starting optimization step 1.
3:48:54.656532 PROGRESS: === Extracting elution groups 8000 to 24000 ===
3:48:54.656606 PROGRESS: Extracting batch of 31879 precursors
3:48:54.665027 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:48:54.665133 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:48:54.665168 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:48:54.665191 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:48:54.665444 INFO: Starting candidate selection
3:48:58.719776 INFO: Starting candidate scoring
3:48:59.090754 INFO: Finished candidate processing
3:48:59.090880 INFO: Collecting candidate features
3:48:59.160319 INFO: Collecting fragment features
3:48:59.208236 INFO: Finished candidate scoring
3:48:59.245894 PROGRESS: === Extracted 47812 precursors and 514457 fragments ===
3:48:59.252539 INFO: performing precursor FDR with 47 features
3:48:59.252671 INFO: Decoy channel: -1
3:48:59.252701 INFO: Competetive: True
3:48:59.274674 INFO: Setting torch num_threads to 2 for FDR classification task
3:49:00.052922 INFO: Test AUC: 0.645
3:49:00.053256 INFO: Train AUC: 0.648
3:49:00.053305 INFO: AUC difference: 0.54%
3:49:00.148453 INFO: Resetting torch num_threads to 100
3:49:00.152214 INFO: === FDR correction performed with classifier version -1 ===
3:49:00.154254 PROGRESS: ============================= Precursor FDR =============================
3:49:00.154392 PROGRESS: Total precursors accumulated: 4,873
3:49:00.154473 PROGRESS: Target precursors: 4,526 (92.88%)
3:49:00.154543 PROGRESS: Decoy precursors: 347 (7.12%)
3:49:00.154604 PROGRESS: 
3:49:00.154664 PROGRESS: Precursor Summary:
3:49:00.156900 PROGRESS: Channel   0:	 0.05 FDR: 4,230; 0.01 FDR: 3,427; 0.001 FDR: 2,437
3:49:00.157032 PROGRESS: 
3:49:00.157109 PROGRESS: Protein Summary:
3:49:00.159895 PROGRESS: Channel   0:	 0.05 FDR: 2,371; 0.01 FDR: 2,014; 0.001 FDR: 1,541
3:49:00.160013 PROGRESS: =========================================================================
3:49:00.176854 INFO: fragments_df_filtered: 5000
3:49:00.200759 INFO: calibration group: precursor, fitting mz estimator 
3:49:00.598284 INFO: calibration group: precursor, fitting rt estimator 
3:49:00.897772 INFO: calibration group: fragment, fitting mz estimator 
3:49:01.337755 INFO: calibration group: precursor, predicting mz
3:49:01.341032 INFO: calibration group: precursor, predicting rt
3:49:01.351958 INFO: calibration group: fragment, predicting mz
3:49:01.410278 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3:49:01.410635 INFO: Starting optimization step 2.
3:49:01.410717 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:49:01.410799 PROGRESS: Extracting batch of 15933 precursors
3:49:01.418789 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:49:01.418875 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:49:01.418919 INFO: FWHM in RT is 2.99 seconds, sigma is 0.39
3:49:01.418948 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:49:01.419275 INFO: Starting candidate selection
3:49:02.339856 INFO: Starting candidate scoring
3:49:02.572449 INFO: Finished candidate processing
3:49:02.572604 INFO: Collecting candidate features
3:49:02.640887 INFO: Collecting fragment features
3:49:02.666554 INFO: Finished candidate scoring
3:49:02.687831 PROGRESS: === Extracted 31866 precursors and 339742 fragments ===
3:49:02.688285 INFO: performing precursor FDR with 47 features
3:49:02.688326 INFO: Decoy channel: -1
3:49:02.688350 INFO: Competetive: True
3:49:02.707058 INFO: Setting torch num_threads to 2 for FDR classification task
3:49:03.322806 INFO: Test AUC: 0.629
3:49:03.322954 INFO: Train AUC: 0.641
3:49:03.322986 INFO: AUC difference: 1.82%
3:49:03.411883 INFO: Resetting torch num_threads to 100
3:49:03.413913 INFO: === FDR correction performed with classifier version 1 ===
3:49:03.415487 PROGRESS: ============================= Precursor FDR =============================
3:49:03.415679 PROGRESS: Total precursors accumulated: 2,588
3:49:03.415753 PROGRESS: Target precursors: 2,408 (93.04%)
3:49:03.415823 PROGRESS: Decoy precursors: 180 (6.96%)
3:49:03.415890 PROGRESS: 
3:49:03.415959 PROGRESS: Precursor Summary:
3:49:03.418010 PROGRESS: Channel   0:	 0.05 FDR: 2,267; 0.01 FDR: 1,719; 0.001 FDR: 1,252
3:49:03.418151 PROGRESS: 
3:49:03.418223 PROGRESS: Protein Summary:
3:49:03.420406 PROGRESS: Channel   0:	 0.05 FDR: 1,598; 0.01 FDR: 1,267; 0.001 FDR:   975
3:49:03.420509 PROGRESS: =========================================================================
3:49:03.431102 INFO: fragments_df_filtered: 5000
3:49:03.445588 INFO: calibration group: precursor, fitting mz estimator 
3:49:03.554423 INFO: calibration group: precursor, fitting rt estimator 
3:49:03.669952 INFO: calibration group: fragment, fitting mz estimator 
3:49:04.089153 INFO: calibration group: precursor, predicting mz
3:49:04.092086 INFO: calibration group: precursor, predicting rt
3:49:04.101431 INFO: calibration group: fragment, predicting mz
3:49:04.166005 INFO: === checking if optimization conditions were reached ===
3:49:04.177208 PROGRESS: ❌ ms2_error      : 16.7186 > 15.0000 or insufficient steps taken.
3:49:04.179095 PROGRESS: ❌ ms1_error      : 14.4202 > 10.0000 or insufficient steps taken.
3:49:04.179159 INFO: ==============================================
3:49:04.179328 INFO: Starting optimization step 3.
3:49:04.179403 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:49:04.179473 PROGRESS: Extracting batch of 15933 precursors
3:49:04.185057 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:49:04.185119 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:49:04.185157 INFO: FWHM in RT is 2.91 seconds, sigma is 0.37
3:49:04.185184 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:49:04.185394 INFO: Starting candidate selection
3:49:05.064114 INFO: Starting candidate scoring
3:49:05.289997 INFO: Finished candidate processing
3:49:05.290120 INFO: Collecting candidate features
3:49:05.348799 INFO: Collecting fragment features
3:49:05.369114 INFO: Finished candidate scoring
3:49:05.385212 PROGRESS: === Extracted 31863 precursors and 318125 fragments ===
3:49:05.385589 INFO: performing precursor FDR with 47 features
3:49:05.385628 INFO: Decoy channel: -1
3:49:05.385651 INFO: Competetive: True
3:49:05.394478 INFO: Setting torch num_threads to 2 for FDR classification task
3:49:05.871464 INFO: Test AUC: 0.647
3:49:05.871583 INFO: Train AUC: 0.670
3:49:05.871625 INFO: AUC difference: 3.39%
3:49:05.956594 INFO: Resetting torch num_threads to 100
3:49:05.957836 INFO: === FDR correction performed with classifier version 2 ===
3:49:05.958910 PROGRESS: ============================= Precursor FDR =============================
3:49:05.959010 PROGRESS: Total precursors accumulated: 3,668
3:49:05.959070 PROGRESS: Target precursors: 3,435 (93.65%)
3:49:05.959120 PROGRESS: Decoy precursors: 233 (6.35%)
3:49:05.959165 PROGRESS: 
3:49:05.959211 PROGRESS: Precursor Summary:
3:49:05.961844 PROGRESS: Channel   0:	 0.05 FDR: 3,268; 0.01 FDR: 2,817; 0.001 FDR: 2,061
3:49:05.961958 PROGRESS: 
3:49:05.962016 PROGRESS: Protein Summary:
3:49:05.964452 PROGRESS: Channel   0:	 0.05 FDR: 2,126; 0.01 FDR: 1,890; 0.001 FDR: 1,478
3:49:05.964556 PROGRESS: =========================================================================
3:49:05.977208 INFO: fragments_df_filtered: 5000
3:49:05.988390 INFO: calibration group: precursor, fitting mz estimator 
3:49:06.124628 INFO: calibration group: precursor, fitting rt estimator 
3:49:06.268344 INFO: calibration group: fragment, fitting mz estimator 
3:49:06.616853 INFO: calibration group: precursor, predicting mz
3:49:06.619817 INFO: calibration group: precursor, predicting rt
3:49:06.629080 INFO: calibration group: fragment, predicting mz
3:49:06.648620 INFO: === checking if optimization conditions were reached ===
3:49:06.650409 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
3:49:06.651719 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
3:49:06.651787 INFO: ==============================================
3:49:06.651895 PROGRESS: Optimization finished for ms2_error, ms1_error.
3:49:06.663595 INFO: calibration group: precursor, predicting mz
3:49:06.666385 INFO: calibration group: precursor, predicting rt
3:49:06.675512 INFO: calibration group: fragment, predicting mz
3:49:06.696289 INFO: Starting optimization step 0.
3:49:06.696438 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:49:06.696515 PROGRESS: Extracting batch of 15933 precursors
3:49:06.700821 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:49:06.700886 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:49:06.700927 INFO: FWHM in RT is 2.69 seconds, sigma is 0.35
3:49:06.700955 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:49:06.701148 INFO: Starting candidate selection
3:49:07.618775 INFO: Starting candidate scoring
3:49:07.848552 INFO: Finished candidate processing
3:49:07.848686 INFO: Collecting candidate features
3:49:07.902066 INFO: Collecting fragment features
3:49:07.924461 INFO: Finished candidate scoring
3:49:07.941829 PROGRESS: === Extracted 31863 precursors and 314887 fragments ===
3:49:07.942255 INFO: performing precursor FDR with 47 features
3:49:07.942296 INFO: Decoy channel: -1
3:49:07.942320 INFO: Competetive: True
3:49:07.952008 INFO: Setting torch num_threads to 2 for FDR classification task
3:49:08.579685 INFO: Test AUC: 0.666
3:49:08.579842 INFO: Train AUC: 0.687
3:49:08.579874 INFO: AUC difference: 3.13%
3:49:08.670944 INFO: Resetting torch num_threads to 100
3:49:08.672705 INFO: === FDR correction performed with classifier version 3 ===
3:49:08.674216 PROGRESS: ============================= Precursor FDR =============================
3:49:08.674335 PROGRESS: Total precursors accumulated: 3,954
3:49:08.674400 PROGRESS: Target precursors: 3,709 (93.80%)
3:49:08.674449 PROGRESS: Decoy precursors: 245 (6.20%)
3:49:08.674496 PROGRESS: 
3:49:08.674550 PROGRESS: Precursor Summary:
3:49:08.676858 PROGRESS: Channel   0:	 0.05 FDR: 3,575; 0.01 FDR: 3,053; 0.001 FDR: 2,278
3:49:08.676975 PROGRESS: 
3:49:08.677032 PROGRESS: Protein Summary:
3:49:08.679784 PROGRESS: Channel   0:	 0.05 FDR: 2,261; 0.01 FDR: 1,998; 0.001 FDR: 1,610
3:49:08.679898 PROGRESS: =========================================================================
3:49:08.694987 INFO: fragments_df_filtered: 5000
3:49:08.708591 INFO: calibration group: precursor, fitting mz estimator 
3:49:08.932584 INFO: calibration group: precursor, fitting rt estimator 
3:49:09.162751 INFO: calibration group: fragment, fitting mz estimator 
3:49:09.577897 INFO: calibration group: precursor, predicting mz
3:49:09.580907 INFO: calibration group: precursor, predicting rt
3:49:09.590342 INFO: calibration group: fragment, predicting mz
3:49:09.611314 INFO: === checking if optimization conditions were reached ===
3:49:09.611516 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3:49:09.614539 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 144.4724.
3:49:09.614596 INFO: ==============================================
3:49:09.614687 INFO: Starting optimization step 1.
3:49:09.614753 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:49:09.614808 PROGRESS: Extracting batch of 15933 precursors
3:49:09.618857 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:49:09.618915 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:49:09.618948 INFO: FWHM in RT is 2.63 seconds, sigma is 0.34
3:49:09.618970 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:49:09.619157 INFO: Starting candidate selection
3:49:10.275778 INFO: Starting candidate scoring
3:49:10.499472 INFO: Finished candidate processing
3:49:10.499601 INFO: Collecting candidate features
3:49:10.550647 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 31822)
3:49:10.559942 INFO: Collecting fragment features
3:49:10.582801 INFO: Finished candidate scoring
3:49:10.600796 PROGRESS: === Extracted 31822 precursors and 302466 fragments ===
3:49:10.601233 INFO: performing precursor FDR with 47 features
3:49:10.601274 INFO: Decoy channel: -1
3:49:10.601299 INFO: Competetive: True
3:49:10.610737 INFO: Setting torch num_threads to 2 for FDR classification task
3:49:10.616636 WARNING: dropped 1 decoy PSMs due to missing features
3:49:11.226076 INFO: Test AUC: 0.702
3:49:11.226227 INFO: Train AUC: 0.723
3:49:11.226259 INFO: AUC difference: 2.94%
3:49:11.311231 INFO: Resetting torch num_threads to 100
3:49:11.312799 INFO: === FDR correction performed with classifier version 3 ===
3:49:11.314141 PROGRESS: ============================= Precursor FDR =============================
3:49:11.314241 PROGRESS: Total precursors accumulated: 4,671
3:49:11.314304 PROGRESS: Target precursors: 4,439 (95.03%)
3:49:11.314355 PROGRESS: Decoy precursors: 232 (4.97%)
3:49:11.314401 PROGRESS: 
3:49:11.314447 PROGRESS: Precursor Summary:
3:49:11.316992 PROGRESS: Channel   0:	 0.05 FDR: 4,403; 0.01 FDR: 3,751; 0.001 FDR: 2,826
3:49:11.317123 PROGRESS: 
3:49:11.317182 PROGRESS: Protein Summary:
3:49:11.320220 PROGRESS: Channel   0:	 0.05 FDR: 2,629; 0.01 FDR: 2,339; 0.001 FDR: 1,911
3:49:11.320335 PROGRESS: =========================================================================
3:49:11.336644 INFO: fragments_df_filtered: 5000
3:49:11.350014 INFO: calibration group: precursor, fitting mz estimator 
3:49:11.634332 INFO: calibration group: precursor, fitting rt estimator 
3:49:11.925200 INFO: calibration group: fragment, fitting mz estimator 
3:49:12.309351 INFO: calibration group: precursor, predicting mz
3:49:12.312545 INFO: calibration group: precursor, predicting rt
3:49:12.322037 INFO: calibration group: fragment, predicting mz
3:49:12.342654 INFO: === checking if optimization conditions were reached ===
3:49:12.342839 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3:49:12.346535 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 74.0593.
3:49:12.346598 INFO: ==============================================
3:49:12.346697 INFO: Starting optimization step 2.
3:49:12.346766 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:49:12.346825 PROGRESS: Extracting batch of 15933 precursors
3:49:12.351946 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:49:12.352006 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:49:12.352039 INFO: FWHM in RT is 2.63 seconds, sigma is 0.34
3:49:12.352063 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:49:12.352259 INFO: Starting candidate selection
3:49:12.975667 INFO: Starting candidate scoring
3:49:13.207712 INFO: Finished candidate processing
3:49:13.207884 INFO: Collecting candidate features
3:49:13.280077 INFO: Collecting fragment features
3:49:13.305445 INFO: Finished candidate scoring
3:49:13.320679 PROGRESS: === Extracted 31775 precursors and 295346 fragments ===
3:49:13.321055 INFO: performing precursor FDR with 47 features
3:49:13.321093 INFO: Decoy channel: -1
3:49:13.321117 INFO: Competetive: True
3:49:13.334324 INFO: Setting torch num_threads to 2 for FDR classification task
3:49:13.810340 INFO: Test AUC: 0.721
3:49:13.810491 INFO: Train AUC: 0.733
3:49:13.810522 INFO: AUC difference: 1.55%
3:49:13.898068 INFO: Resetting torch num_threads to 100
3:49:13.899868 INFO: === FDR correction performed with classifier version 3 ===
3:49:13.901259 PROGRESS: ============================= Precursor FDR =============================
3:49:13.901364 PROGRESS: Total precursors accumulated: 4,871
3:49:13.901424 PROGRESS: Target precursors: 4,633 (95.11%)
3:49:13.901474 PROGRESS: Decoy precursors: 238 (4.89%)
3:49:13.901523 PROGRESS: 
3:49:13.901567 PROGRESS: Precursor Summary:
3:49:13.904707 PROGRESS: Channel   0:	 0.05 FDR: 4,615; 0.01 FDR: 4,032; 0.001 FDR: 3,311
3:49:13.904835 PROGRESS: 
3:49:13.904894 PROGRESS: Protein Summary:
3:49:13.907860 PROGRESS: Channel   0:	 0.05 FDR: 2,723; 0.01 FDR: 2,480; 0.001 FDR: 2,140
3:49:13.907958 PROGRESS: =========================================================================
3:49:13.924240 INFO: fragments_df_filtered: 5000
3:49:13.940844 INFO: calibration group: precursor, fitting mz estimator 
3:49:14.251142 INFO: calibration group: precursor, fitting rt estimator 
3:49:14.563502 INFO: calibration group: fragment, fitting mz estimator 
3:49:14.979635 INFO: calibration group: precursor, predicting mz
3:49:14.982828 INFO: calibration group: precursor, predicting rt
3:49:14.992410 INFO: calibration group: fragment, predicting mz
3:49:15.016212 INFO: === checking if optimization conditions were reached ===
3:49:15.016563 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3:49:15.021714 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 42.5141.
3:49:15.021777 INFO: ==============================================
3:49:15.021897 INFO: Starting optimization step 3.
3:49:15.021971 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:49:15.022045 PROGRESS: Extracting batch of 15933 precursors
3:49:15.031843 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:49:15.032008 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:49:15.032076 INFO: FWHM in RT is 2.64 seconds, sigma is 0.34
3:49:15.032109 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:49:15.032648 INFO: Starting candidate selection
3:49:15.710309 INFO: Starting candidate scoring
3:49:15.934806 INFO: Finished candidate processing
3:49:15.934951 INFO: Collecting candidate features
3:49:15.984123 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 31751)
3:49:15.989490 INFO: Collecting fragment features
3:49:16.012920 INFO: Finished candidate scoring
3:49:16.026772 PROGRESS: === Extracted 31751 precursors and 291720 fragments ===
3:49:16.028100 INFO: performing precursor FDR with 47 features
3:49:16.028144 INFO: Decoy channel: -1
3:49:16.028167 INFO: Competetive: True
3:49:16.038179 INFO: Setting torch num_threads to 2 for FDR classification task
3:49:16.044394 WARNING: dropped 1 target PSMs due to missing features
3:49:16.044495 WARNING: dropped 2 decoy PSMs due to missing features
3:49:16.527158 INFO: Test AUC: 0.742
3:49:16.527276 INFO: Train AUC: 0.741
3:49:16.527305 INFO: AUC difference: 0.10%
3:49:16.612978 INFO: Resetting torch num_threads to 100
3:49:16.614312 INFO: === FDR correction performed with classifier version 3 ===
3:49:16.615890 PROGRESS: ============================= Precursor FDR =============================
3:49:16.615999 PROGRESS: Total precursors accumulated: 4,998
3:49:16.616068 PROGRESS: Target precursors: 4,756 (95.16%)
3:49:16.616119 PROGRESS: Decoy precursors: 242 (4.84%)
3:49:16.616164 PROGRESS: 
3:49:16.616208 PROGRESS: Precursor Summary:
3:49:16.618527 PROGRESS: Channel   0:	 0.05 FDR: 4,750; 0.01 FDR: 4,151; 0.001 FDR: 3,268
3:49:16.618644 PROGRESS: 
3:49:16.618701 PROGRESS: Protein Summary:
3:49:16.621725 PROGRESS: Channel   0:	 0.05 FDR: 2,774; 0.01 FDR: 2,539; 0.001 FDR: 2,122
3:49:16.621830 PROGRESS: =========================================================================
3:49:16.636853 INFO: fragments_df_filtered: 5000
3:49:16.649787 INFO: calibration group: precursor, fitting mz estimator 
3:49:16.971705 INFO: calibration group: precursor, fitting rt estimator 
3:49:17.299166 INFO: calibration group: fragment, fitting mz estimator 
3:49:17.714022 INFO: calibration group: precursor, predicting mz
3:49:17.716997 INFO: calibration group: precursor, predicting rt
3:49:17.726381 INFO: calibration group: fragment, predicting mz
3:49:17.747199 INFO: === checking if optimization conditions were reached ===
3:49:17.747382 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3:49:17.751080 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 29.6682.
3:49:17.751138 INFO: ==============================================
3:49:17.751243 INFO: Starting optimization step 4.
3:49:17.751324 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:49:17.751399 PROGRESS: Extracting batch of 15933 precursors
3:49:17.755590 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:49:17.755650 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:49:17.755697 INFO: FWHM in RT is 2.64 seconds, sigma is 0.34
3:49:17.755726 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:49:17.755935 INFO: Starting candidate selection
3:49:18.426095 INFO: Starting candidate scoring
3:49:18.650877 INFO: Finished candidate processing
3:49:18.651006 INFO: Collecting candidate features
3:49:18.700919 WARNING: intensity_correlation has 11 NaNs ( 0.03 % out of 31702)
3:49:18.708766 INFO: Collecting fragment features
3:49:18.734853 INFO: Finished candidate scoring
3:49:18.751658 PROGRESS: === Extracted 31702 precursors and 288465 fragments ===
3:49:18.752097 INFO: performing precursor FDR with 47 features
3:49:18.752136 INFO: Decoy channel: -1
3:49:18.752160 INFO: Competetive: True
3:49:18.764165 INFO: Setting torch num_threads to 2 for FDR classification task
3:49:18.771935 WARNING: dropped 3 target PSMs due to missing features
3:49:18.772103 WARNING: dropped 8 decoy PSMs due to missing features
3:49:19.403692 INFO: Test AUC: 0.739
3:49:19.403844 INFO: Train AUC: 0.749
3:49:19.403877 INFO: AUC difference: 1.33%
3:49:19.492440 INFO: Resetting torch num_threads to 100
3:49:19.493985 INFO: === FDR correction performed with classifier version 3 ===
3:49:19.495403 PROGRESS: ============================= Precursor FDR =============================
3:49:19.495510 PROGRESS: Total precursors accumulated: 5,042
3:49:19.495571 PROGRESS: Target precursors: 4,808 (95.36%)
3:49:19.495620 PROGRESS: Decoy precursors: 234 (4.64%)
3:49:19.495665 PROGRESS: 
3:49:19.495711 PROGRESS: Precursor Summary:
3:49:19.498169 PROGRESS: Channel   0:	 0.05 FDR: 4,808; 0.01 FDR: 4,152; 0.001 FDR: 3,070
3:49:19.498308 PROGRESS: 
3:49:19.498368 PROGRESS: Protein Summary:
3:49:19.501480 PROGRESS: Channel   0:	 0.05 FDR: 2,798; 0.01 FDR: 2,538; 0.001 FDR: 2,024
3:49:19.501597 PROGRESS: =========================================================================
3:49:19.518500 INFO: fragments_df_filtered: 5000
3:49:19.531388 INFO: calibration group: precursor, fitting mz estimator 
3:49:19.799093 INFO: calibration group: precursor, fitting rt estimator 
3:49:20.091617 INFO: calibration group: fragment, fitting mz estimator 
3:49:20.529996 INFO: calibration group: precursor, predicting mz
3:49:20.533168 INFO: calibration group: precursor, predicting rt
3:49:20.542533 INFO: calibration group: fragment, predicting mz
3:49:20.564121 INFO: === checking if optimization conditions were reached ===
3:49:20.564319 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3:49:20.568713 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 22.0292.
3:49:20.568777 INFO: ==============================================
3:49:20.568890 INFO: Starting optimization step 5.
3:49:20.568969 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:49:20.569037 PROGRESS: Extracting batch of 15933 precursors
3:49:20.576992 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:49:20.577067 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:49:20.577106 INFO: FWHM in RT is 2.64 seconds, sigma is 0.34
3:49:20.577135 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:49:20.577353 INFO: Starting candidate selection
3:49:21.234923 INFO: Starting candidate scoring
3:49:21.451466 INFO: Finished candidate processing
3:49:21.451599 INFO: Collecting candidate features
3:49:21.513674 WARNING: intensity_correlation has 18 NaNs ( 0.06 % out of 30895)
3:49:21.518245 INFO: Collecting fragment features
3:49:21.540550 INFO: Finished candidate scoring
3:49:21.555789 PROGRESS: === Extracted 30895 precursors and 275631 fragments ===
3:49:21.556242 INFO: performing precursor FDR with 47 features
3:49:21.556283 INFO: Decoy channel: -1
3:49:21.556307 INFO: Competetive: True
3:49:21.573424 INFO: Setting torch num_threads to 2 for FDR classification task
3:49:21.580318 WARNING: dropped 6 target PSMs due to missing features
3:49:21.580449 WARNING: dropped 12 decoy PSMs due to missing features
3:49:22.117657 INFO: Test AUC: 0.763
3:49:22.117801 INFO: Train AUC: 0.759
3:49:22.117832 INFO: AUC difference: 0.51%
3:49:22.208741 INFO: Resetting torch num_threads to 100
3:49:22.210279 INFO: === FDR correction performed with classifier version 3 ===
3:49:22.211788 PROGRESS: ============================= Precursor FDR =============================
3:49:22.211919 PROGRESS: Total precursors accumulated: 5,157
3:49:22.211983 PROGRESS: Target precursors: 4,927 (95.54%)
3:49:22.212035 PROGRESS: Decoy precursors: 230 (4.46%)
3:49:22.212083 PROGRESS: 
3:49:22.212126 PROGRESS: Precursor Summary:
3:49:22.214670 PROGRESS: Channel   0:	 0.05 FDR: 4,927; 0.01 FDR: 4,336; 0.001 FDR: 3,398
3:49:22.214787 PROGRESS: 
3:49:22.214844 PROGRESS: Protein Summary:
3:49:22.218010 PROGRESS: Channel   0:	 0.05 FDR: 2,848; 0.01 FDR: 2,622; 0.001 FDR: 2,197
3:49:22.218114 PROGRESS: =========================================================================
3:49:22.234107 INFO: fragments_df_filtered: 5000
3:49:22.247564 INFO: calibration group: precursor, fitting mz estimator 
3:49:22.579856 INFO: calibration group: precursor, fitting rt estimator 
3:49:22.861939 INFO: calibration group: fragment, fitting mz estimator 
3:49:23.213897 INFO: calibration group: precursor, predicting mz
3:49:23.217024 INFO: calibration group: precursor, predicting rt
3:49:23.226612 INFO: calibration group: fragment, predicting mz
3:49:23.247387 INFO: === checking if optimization conditions were reached ===
3:49:23.247581 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3:49:23.251537 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 17.9679.
3:49:23.251601 INFO: ==============================================
3:49:23.251699 INFO: Starting optimization step 6.
3:49:23.251784 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:49:23.251845 PROGRESS: Extracting batch of 15933 precursors
3:49:23.256746 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:49:23.256808 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:49:23.256840 INFO: FWHM in RT is 2.61 seconds, sigma is 0.34
3:49:23.256862 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:49:23.257053 INFO: Starting candidate selection
3:49:23.913183 INFO: Starting candidate scoring
3:49:24.140249 INFO: Finished candidate processing
3:49:24.140393 INFO: Collecting candidate features
3:49:24.190896 WARNING: intensity_correlation has 14 NaNs ( 0.05 % out of 30929)
3:49:24.200842 INFO: Collecting fragment features
3:49:24.222092 INFO: Finished candidate scoring
3:49:24.236703 PROGRESS: === Extracted 30929 precursors and 276896 fragments ===
3:49:24.237127 INFO: performing precursor FDR with 47 features
3:49:24.237167 INFO: Decoy channel: -1
3:49:24.237192 INFO: Competetive: True
3:49:24.246216 INFO: Setting torch num_threads to 2 for FDR classification task
3:49:24.251611 WARNING: dropped 5 target PSMs due to missing features
3:49:24.251721 WARNING: dropped 9 decoy PSMs due to missing features
3:49:24.731174 INFO: Test AUC: 0.758
3:49:24.731310 INFO: Train AUC: 0.763
3:49:24.731342 INFO: AUC difference: 0.66%
3:49:24.823671 INFO: Resetting torch num_threads to 100
3:49:24.825204 INFO: === FDR correction performed with classifier version 3 ===
3:49:24.826580 PROGRESS: ============================= Precursor FDR =============================
3:49:24.826681 PROGRESS: Total precursors accumulated: 5,159
3:49:24.826741 PROGRESS: Target precursors: 4,932 (95.60%)
3:49:24.826791 PROGRESS: Decoy precursors: 227 (4.40%)
3:49:24.826838 PROGRESS: 
3:49:24.826882 PROGRESS: Precursor Summary:
3:49:24.829190 PROGRESS: Channel   0:	 0.05 FDR: 4,932; 0.01 FDR: 4,308; 0.001 FDR: 3,277
3:49:24.829318 PROGRESS: 
3:49:24.829375 PROGRESS: Protein Summary:
3:49:24.832502 PROGRESS: Channel   0:	 0.05 FDR: 2,848; 0.01 FDR: 2,605; 0.001 FDR: 2,139
3:49:24.832604 PROGRESS: =========================================================================
3:49:24.848429 INFO: fragments_df_filtered: 5000
3:49:24.862803 INFO: calibration group: precursor, fitting mz estimator 
3:49:25.137925 INFO: calibration group: precursor, fitting rt estimator 
3:49:25.452096 INFO: calibration group: fragment, fitting mz estimator 
3:49:25.835228 INFO: calibration group: precursor, predicting mz
3:49:25.838324 INFO: calibration group: precursor, predicting rt
3:49:25.847688 INFO: calibration group: fragment, predicting mz
3:49:25.868576 INFO: === checking if optimization conditions were reached ===
3:49:25.868748 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
3:49:25.872572 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 17.4789.
3:49:25.872634 INFO: ==============================================
3:49:25.872729 INFO: Starting optimization step 7.
3:49:25.872796 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:49:25.872855 PROGRESS: Extracting batch of 15933 precursors
3:49:25.878462 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:49:25.878532 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:49:25.878565 INFO: FWHM in RT is 2.61 seconds, sigma is 0.34
3:49:25.878587 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:49:25.878786 INFO: Starting candidate selection
3:49:26.509977 INFO: Starting candidate scoring
3:49:26.720387 INFO: Finished candidate processing
3:49:26.720491 INFO: Collecting candidate features
3:49:26.766489 WARNING: intensity_correlation has 13 NaNs ( 0.04 % out of 30932)
3:49:26.770725 INFO: Collecting fragment features
3:49:26.791071 INFO: Finished candidate scoring
3:49:26.804420 PROGRESS: === Extracted 30932 precursors and 277074 fragments ===
3:49:26.804791 INFO: performing precursor FDR with 47 features
3:49:26.804830 INFO: Decoy channel: -1
3:49:26.804857 INFO: Competetive: True
3:49:26.812915 INFO: Setting torch num_threads to 2 for FDR classification task
3:49:26.818374 WARNING: dropped 4 target PSMs due to missing features
3:49:26.818485 WARNING: dropped 9 decoy PSMs due to missing features
3:49:27.223854 INFO: Test AUC: 0.762
3:49:27.223976 INFO: Train AUC: 0.763
3:49:27.224005 INFO: AUC difference: 0.24%
3:49:27.309004 INFO: Resetting torch num_threads to 100
3:49:27.310199 INFO: === FDR correction performed with classifier version 3 ===
3:49:27.311378 PROGRESS: ============================= Precursor FDR =============================
3:49:27.311492 PROGRESS: Total precursors accumulated: 5,172
3:49:27.311553 PROGRESS: Target precursors: 4,943 (95.57%)
3:49:27.311603 PROGRESS: Decoy precursors: 229 (4.43%)
3:49:27.311647 PROGRESS: 
3:49:27.311690 PROGRESS: Precursor Summary:
3:49:27.313815 PROGRESS: Channel   0:	 0.05 FDR: 4,943; 0.01 FDR: 4,312; 0.001 FDR: 3,563
3:49:27.313928 PROGRESS: 
3:49:27.313985 PROGRESS: Protein Summary:
3:49:27.317011 PROGRESS: Channel   0:	 0.05 FDR: 2,851; 0.01 FDR: 2,599; 0.001 FDR: 2,267
3:49:27.317113 PROGRESS: =========================================================================
3:49:27.333538 INFO: fragments_df_filtered: 5000
3:49:27.346773 INFO: calibration group: precursor, fitting mz estimator 
3:49:27.636867 INFO: calibration group: precursor, fitting rt estimator 
3:49:27.912701 INFO: calibration group: fragment, fitting mz estimator 
3:49:28.263526 INFO: calibration group: precursor, predicting mz
3:49:28.266517 INFO: calibration group: precursor, predicting rt
3:49:28.276438 INFO: calibration group: fragment, predicting mz
3:49:28.298249 INFO: === checking if optimization conditions were reached ===
3:49:28.298407 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
3:49:28.299486 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 17.4789 found after 8 searches.
3:49:28.299538 INFO: ==============================================
3:49:28.299630 PROGRESS: Optimization finished for rt_error.
3:49:28.311413 INFO: calibration group: precursor, predicting mz
3:49:28.314253 INFO: calibration group: precursor, predicting rt
3:49:28.323431 INFO: calibration group: fragment, predicting mz
3:49:28.371979 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:49:28.372178 PROGRESS: ==============================================
3:49:28.372266 PROGRESS: ms2_error      : 15.0000
3:49:28.372339 PROGRESS: ms1_error      : 10.0000
3:49:28.372400 PROGRESS: rt_error       : 17.4789
3:49:28.372457 PROGRESS: ==============================================
3:49:28.374321 INFO: calibration group: precursor, predicting mz
3:49:28.383113 INFO: calibration group: precursor, predicting rt
3:49:28.419127 INFO: calibration group: fragment, predicting mz
3:49:28.514119 PROGRESS: Extracting batch of 65173 precursors
3:49:28.532348 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:49:28.532476 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:49:28.532517 INFO: FWHM in RT is 2.62 seconds, sigma is 0.34
3:49:28.532546 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:49:28.532794 INFO: Starting candidate selection
3:49:30.941778 INFO: Applying score cutoff of 17.40812623977661
3:49:30.946962 INFO: Removed 4226 precursors with score below cutoff
3:49:30.987613 INFO: Starting candidate scoring
3:49:31.904463 INFO: Finished candidate processing
3:49:31.904611 INFO: Collecting candidate features
3:49:32.077176 WARNING: intensity_correlation has 16 NaNs ( 0.01 % out of 122874)
3:49:32.084688 INFO: Collecting fragment features
3:49:32.159619 INFO: Finished candidate scoring
3:49:32.218369 INFO: === FDR correction performed with classifier version 11 ===
3:49:32.219185 INFO: performing precursor FDR with 47 features
3:49:32.219221 INFO: Decoy channel: -1
3:49:32.219247 INFO: Competetive: True
3:49:32.258220 INFO: Setting torch num_threads to 2 for FDR classification task
3:49:32.277218 WARNING: dropped 6 target PSMs due to missing features
3:49:32.277354 WARNING: dropped 10 decoy PSMs due to missing features
3:49:35.437999 INFO: Test AUC: 0.781
3:49:35.438135 INFO: Train AUC: 0.787
3:49:35.438167 INFO: AUC difference: 0.70%
3:49:35.564489 INFO: Resetting torch num_threads to 100
3:49:35.578576 INFO: Removing fragments below FDR threshold
3:49:35.612530 PROGRESS: ============================= Precursor FDR =============================
3:49:35.612898 PROGRESS: Total precursors accumulated: 18,522
3:49:35.612983 PROGRESS: Target precursors: 18,339 (99.01%)
3:49:35.613052 PROGRESS: Decoy precursors: 183 (0.99%)
3:49:35.613113 PROGRESS: 
3:49:35.613192 PROGRESS: Precursor Summary:
3:49:35.625666 PROGRESS: Channel   0:	 0.05 FDR: 18,339; 0.01 FDR: 18,339; 0.001 FDR: 15,425
3:49:35.625965 PROGRESS: 
3:49:35.626043 PROGRESS: Protein Summary:
3:49:35.643435 PROGRESS: Channel   0:	 0.05 FDR: 5,239; 0.01 FDR: 5,239; 0.001 FDR: 4,902
3:49:35.643986 PROGRESS: =========================================================================
3:49:36.026570 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:49:36.049609 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:49:36.049751 INFO: Quantification results path: run_output_Astral/alphadia_1.10_default/quant
3:49:36.049903 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3 at run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:49:36.050768 INFO: Initializing RawFileManager
3:50:02.324034 INFO: Determining DIA cycle
3:50:02.340896 INFO: Found cycle with start 0.00 min and length 303.
3:50:02.506508 INFO: RT (min)            : 0.0 - 26.9
3:50:02.506606 INFO: RT duration (sec)   : 1611.2
3:50:02.506635 INFO: RT duration (min)   : 26.9
3:50:02.506660 INFO: Cycle len (scans)   : 303
3:50:02.506681 INFO: Cycle len (sec)     : 1.65
3:50:02.506700 INFO: Number of cycles    : 977
3:50:02.506719 INFO: MS2 range (m/z)     : 380.4 - 980.7
3:50:02.523147 INFO: Initializing CalibrationManager
3:50:02.523397 INFO: Loading calibration config
3:50:02.524359 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'}]
3:50:02.524452 INFO: Calibration group :fragment, found 1 estimator(s)
3:50:02.524538 INFO: Calibration group :precursor, found 3 estimator(s)
3:50:02.524639 INFO: Disabling ion mobility calibration
3:50:02.524666 INFO: removed mobility estimator from group precursor
3:50:02.524786 INFO: Initializing OptimizationManager
3:50:02.524893 INFO: initial parameter: ms1_error = 30
3:50:02.524953 INFO: initial parameter: ms2_error = 30
3:50:02.525001 INFO: initial parameter: rt_error = 805.6004638671875
3:50:02.525048 INFO: initial parameter: mobility_error = 0.1
3:50:02.525090 INFO: initial parameter: column_type = library
3:50:02.525129 INFO: initial parameter: num_candidates = 1
3:50:02.525168 INFO: initial parameter: classifier_version = -1
3:50:02.525207 INFO: initial parameter: fwhm_rt = 5
3:50:02.525248 INFO: initial parameter: fwhm_mobility = 0.01
3:50:02.525288 INFO: initial parameter: score_cutoff = 0
3:50:02.525342 INFO: Initializing TimingManager
3:50:02.525399 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:50:02.525470 INFO: FDRManager not loaded from disk.
3:50:02.525492 INFO: Initializing FDRManager
3:50:02.525522 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
3:50:02.540617 PROGRESS: 32,718 target precursors potentially observable (0 removed)
3:50:02.557882 PROGRESS: Starting initial search for precursors.
3:50:02.571535 INFO: Starting optimization step 0.
3:50:02.571778 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:50:02.571879 PROGRESS: Extracting batch of 15933 precursors
3:50:02.575392 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:50:02.575448 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:50:02.575485 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:50:02.575511 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:50:02.575774 INFO: Starting candidate selection
3:50:03.582498 INFO: Starting candidate scoring
3:50:03.714588 INFO: Finished candidate processing
3:50:03.714698 INFO: Collecting candidate features
3:50:03.759299 INFO: Collecting fragment features
3:50:03.781115 INFO: Finished candidate scoring
3:50:03.789572 PROGRESS: === Extracted 15933 precursors and 171580 fragments ===
3:50:03.790121 INFO: performing precursor FDR with 47 features
3:50:03.790162 INFO: Decoy channel: -1
3:50:03.790187 INFO: Competetive: True
3:50:03.796214 INFO: Setting torch num_threads to 2 for FDR classification task
3:50:03.993192 INFO: Test AUC: 0.601
3:50:03.993299 INFO: Train AUC: 0.628
3:50:03.993329 INFO: AUC difference: 4.35%
3:50:04.083652 INFO: Resetting torch num_threads to 100
3:50:04.084841 INFO: === FDR correction performed with classifier version -1 ===
3:50:04.085646 PROGRESS: ============================= Precursor FDR =============================
3:50:04.085739 PROGRESS: Total precursors accumulated: 1,093
3:50:04.085799 PROGRESS: Target precursors: 1,009 (92.31%)
3:50:04.085848 PROGRESS: Decoy precursors: 84 (7.69%)
3:50:04.085892 PROGRESS: 
3:50:04.085935 PROGRESS: Precursor Summary:
3:50:04.086913 PROGRESS: Channel   0:	 0.05 FDR:   584; 0.01 FDR:     0; 0.001 FDR:     0
3:50:04.087008 PROGRESS: 
3:50:04.087062 PROGRESS: Protein Summary:
3:50:04.088177 PROGRESS: Channel   0:	 0.05 FDR:   484; 0.01 FDR:     0; 0.001 FDR:     0
3:50:04.088287 PROGRESS: =========================================================================
3:50:04.119624 INFO: Starting optimization step 1.
3:50:04.119918 PROGRESS: === Extracting elution groups 8000 to 24000 ===
3:50:04.120001 PROGRESS: Extracting batch of 31879 precursors
3:50:04.128364 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:50:04.128458 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:50:04.128497 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:50:04.128520 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:50:04.128784 INFO: Starting candidate selection
3:50:06.015586 INFO: Starting candidate scoring
3:50:06.265182 INFO: Finished candidate processing
3:50:06.265330 INFO: Collecting candidate features
3:50:06.349951 INFO: Collecting fragment features
3:50:06.383152 INFO: Finished candidate scoring
3:50:06.424866 PROGRESS: === Extracted 47812 precursors and 514262 fragments ===
3:50:06.433226 INFO: performing precursor FDR with 47 features
3:50:06.433354 INFO: Decoy channel: -1
3:50:06.433383 INFO: Competetive: True
3:50:06.457669 INFO: Setting torch num_threads to 2 for FDR classification task
3:50:07.276006 INFO: Test AUC: 0.639
3:50:07.276158 INFO: Train AUC: 0.648
3:50:07.276191 INFO: AUC difference: 1.37%
3:50:07.362063 INFO: Resetting torch num_threads to 100
3:50:07.364966 INFO: === FDR correction performed with classifier version -1 ===
3:50:07.366319 PROGRESS: ============================= Precursor FDR =============================
3:50:07.366434 PROGRESS: Total precursors accumulated: 4,878
3:50:07.366497 PROGRESS: Target precursors: 4,526 (92.78%)
3:50:07.366550 PROGRESS: Decoy precursors: 352 (7.22%)
3:50:07.366597 PROGRESS: 
3:50:07.366642 PROGRESS: Precursor Summary:
3:50:07.368752 PROGRESS: Channel   0:	 0.05 FDR: 4,252; 0.01 FDR: 3,591; 0.001 FDR: 2,976
3:50:07.368876 PROGRESS: 
3:50:07.368935 PROGRESS: Protein Summary:
3:50:07.371770 PROGRESS: Channel   0:	 0.05 FDR: 2,389; 0.01 FDR: 2,091; 0.001 FDR: 1,785
3:50:07.371876 PROGRESS: =========================================================================
3:50:07.386031 INFO: fragments_df_filtered: 5000
3:50:07.400725 INFO: calibration group: precursor, fitting mz estimator 
3:50:07.690062 INFO: calibration group: precursor, fitting rt estimator 
3:50:07.986512 INFO: calibration group: fragment, fitting mz estimator 
3:50:08.422866 INFO: calibration group: precursor, predicting mz
3:50:08.425985 INFO: calibration group: precursor, predicting rt
3:50:08.435779 INFO: calibration group: fragment, predicting mz
3:50:08.533148 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3:50:08.533759 INFO: Starting optimization step 2.
3:50:08.533851 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:50:08.533944 PROGRESS: Extracting batch of 15933 precursors
3:50:08.539700 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:50:08.539828 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:50:08.539872 INFO: FWHM in RT is 2.95 seconds, sigma is 0.38
3:50:08.539901 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:50:08.540163 INFO: Starting candidate selection
3:50:11.859149 INFO: Starting candidate scoring
3:50:12.095246 INFO: Finished candidate processing
3:50:12.095398 INFO: Collecting candidate features
3:50:12.156736 INFO: Collecting fragment features
3:50:12.177477 INFO: Finished candidate scoring
3:50:12.197850 PROGRESS: === Extracted 31865 precursors and 340110 fragments ===
3:50:12.198281 INFO: performing precursor FDR with 47 features
3:50:12.198320 INFO: Decoy channel: -1
3:50:12.198344 INFO: Competetive: True
3:50:12.208210 INFO: Setting torch num_threads to 2 for FDR classification task
3:50:12.788480 INFO: Test AUC: 0.629
3:50:12.788619 INFO: Train AUC: 0.639
3:50:12.788649 INFO: AUC difference: 1.63%
3:50:12.884749 INFO: Resetting torch num_threads to 100
3:50:12.886315 INFO: === FDR correction performed with classifier version 1 ===
3:50:12.887471 PROGRESS: ============================= Precursor FDR =============================
3:50:12.887574 PROGRESS: Total precursors accumulated: 2,587
3:50:12.887635 PROGRESS: Target precursors: 2,410 (93.16%)
3:50:12.887685 PROGRESS: Decoy precursors: 177 (6.84%)
3:50:12.887731 PROGRESS: 
3:50:12.887790 PROGRESS: Precursor Summary:
3:50:12.889605 PROGRESS: Channel   0:	 0.05 FDR: 2,285; 0.01 FDR: 1,815; 0.001 FDR: 1,614
3:50:12.889706 PROGRESS: 
3:50:12.889773 PROGRESS: Protein Summary:
3:50:12.891807 PROGRESS: Channel   0:	 0.05 FDR: 1,611; 0.01 FDR: 1,340; 0.001 FDR: 1,212
3:50:12.891911 PROGRESS: =========================================================================
3:50:12.901350 INFO: fragments_df_filtered: 5000
3:50:12.914406 INFO: calibration group: precursor, fitting mz estimator 
3:50:13.077360 INFO: calibration group: precursor, fitting rt estimator 
3:50:13.198536 INFO: calibration group: fragment, fitting mz estimator 
3:50:13.618366 INFO: calibration group: precursor, predicting mz
3:50:13.621537 INFO: calibration group: precursor, predicting rt
3:50:13.631245 INFO: calibration group: fragment, predicting mz
3:50:13.693647 INFO: === checking if optimization conditions were reached ===
3:50:13.696990 PROGRESS: ❌ ms2_error      : 15.7284 > 15.0000 or insufficient steps taken.
3:50:13.698830 PROGRESS: ❌ ms1_error      : 13.2759 > 10.0000 or insufficient steps taken.
3:50:13.699054 INFO: ==============================================
3:50:13.699390 INFO: Starting optimization step 3.
3:50:13.699656 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:50:13.699924 PROGRESS: Extracting batch of 15933 precursors
3:50:13.708597 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:50:13.708820 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:50:13.708925 INFO: FWHM in RT is 2.95 seconds, sigma is 0.38
3:50:13.709014 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:50:13.709383 INFO: Starting candidate selection
3:50:14.596025 INFO: Starting candidate scoring
3:50:14.810145 INFO: Finished candidate processing
3:50:14.810282 INFO: Collecting candidate features
3:50:14.875577 INFO: Collecting fragment features
3:50:14.900386 INFO: Finished candidate scoring
3:50:14.919431 PROGRESS: === Extracted 31863 precursors and 315492 fragments ===
3:50:14.919863 INFO: performing precursor FDR with 47 features
3:50:14.919919 INFO: Decoy channel: -1
3:50:14.919946 INFO: Competetive: True
3:50:14.929078 INFO: Setting torch num_threads to 2 for FDR classification task
3:50:15.377728 INFO: Test AUC: 0.667
3:50:15.377882 INFO: Train AUC: 0.667
3:50:15.377913 INFO: AUC difference: 0.02%
3:50:15.463700 INFO: Resetting torch num_threads to 100
3:50:15.465280 INFO: === FDR correction performed with classifier version 2 ===
3:50:15.466940 PROGRESS: ============================= Precursor FDR =============================
3:50:15.467049 PROGRESS: Total precursors accumulated: 3,665
3:50:15.467108 PROGRESS: Target precursors: 3,434 (93.70%)
3:50:15.467158 PROGRESS: Decoy precursors: 231 (6.30%)
3:50:15.467203 PROGRESS: 
3:50:15.467245 PROGRESS: Precursor Summary:
3:50:15.469159 PROGRESS: Channel   0:	 0.05 FDR: 3,313; 0.01 FDR: 2,841; 0.001 FDR: 2,301
3:50:15.469261 PROGRESS: 
3:50:15.469316 PROGRESS: Protein Summary:
3:50:15.471796 PROGRESS: Channel   0:	 0.05 FDR: 2,139; 0.01 FDR: 1,915; 0.001 FDR: 1,627
3:50:15.471899 PROGRESS: =========================================================================
3:50:15.486058 INFO: fragments_df_filtered: 5000
3:50:15.499770 INFO: calibration group: precursor, fitting mz estimator 
3:50:15.712063 INFO: calibration group: precursor, fitting rt estimator 
3:50:15.927993 INFO: calibration group: fragment, fitting mz estimator 
3:50:16.378952 INFO: calibration group: precursor, predicting mz
3:50:16.382325 INFO: calibration group: precursor, predicting rt
3:50:16.392462 INFO: calibration group: fragment, predicting mz
3:50:16.418866 INFO: === checking if optimization conditions were reached ===
3:50:16.422278 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
3:50:16.423946 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
3:50:16.424004 INFO: ==============================================
3:50:16.424125 PROGRESS: Optimization finished for ms2_error, ms1_error.
3:50:16.442957 INFO: calibration group: precursor, predicting mz
3:50:16.446556 INFO: calibration group: precursor, predicting rt
3:50:16.457572 INFO: calibration group: fragment, predicting mz
3:50:16.483883 INFO: Starting optimization step 0.
3:50:16.484155 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:50:16.484240 PROGRESS: Extracting batch of 15933 precursors
3:50:16.491815 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:50:16.491916 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:50:16.491954 INFO: FWHM in RT is 2.70 seconds, sigma is 0.35
3:50:16.491981 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:50:16.492241 INFO: Starting candidate selection
3:50:17.427315 INFO: Starting candidate scoring
3:50:17.623930 INFO: Finished candidate processing
3:50:17.624055 INFO: Collecting candidate features
3:50:17.684310 INFO: Collecting fragment features
3:50:17.710199 INFO: Finished candidate scoring
3:50:17.727564 PROGRESS: === Extracted 31862 precursors and 315018 fragments ===
3:50:17.728112 INFO: performing precursor FDR with 47 features
3:50:17.728153 INFO: Decoy channel: -1
3:50:17.728180 INFO: Competetive: True
3:50:17.739640 INFO: Setting torch num_threads to 2 for FDR classification task
3:50:18.319196 INFO: Test AUC: 0.665
3:50:18.319360 INFO: Train AUC: 0.678
3:50:18.319396 INFO: AUC difference: 1.86%
3:50:18.432035 INFO: Resetting torch num_threads to 100
3:50:18.434330 INFO: === FDR correction performed with classifier version 3 ===
3:50:18.436154 PROGRESS: ============================= Precursor FDR =============================
3:50:18.436279 PROGRESS: Total precursors accumulated: 3,868
3:50:18.436351 PROGRESS: Target precursors: 3,634 (93.95%)
3:50:18.436409 PROGRESS: Decoy precursors: 234 (6.05%)
3:50:18.436462 PROGRESS: 
3:50:18.436523 PROGRESS: Precursor Summary:
3:50:18.439316 PROGRESS: Channel   0:	 0.05 FDR: 3,524; 0.01 FDR: 3,012; 0.001 FDR: 2,473
3:50:18.439450 PROGRESS: 
3:50:18.439514 PROGRESS: Protein Summary:
3:50:18.443015 PROGRESS: Channel   0:	 0.05 FDR: 2,244; 0.01 FDR: 2,006; 0.001 FDR: 1,735
3:50:18.443138 PROGRESS: =========================================================================
3:50:18.460732 INFO: fragments_df_filtered: 5000
3:50:18.485770 INFO: calibration group: precursor, fitting mz estimator 
3:50:18.836938 INFO: calibration group: precursor, fitting rt estimator 
3:50:19.146905 INFO: calibration group: fragment, fitting mz estimator 
3:50:19.640726 INFO: calibration group: precursor, predicting mz
3:50:19.643951 INFO: calibration group: precursor, predicting rt
3:50:19.653695 INFO: calibration group: fragment, predicting mz
3:50:19.755098 INFO: === checking if optimization conditions were reached ===
3:50:19.755506 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3:50:19.760077 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 85.2814.
3:50:19.760734 INFO: ==============================================
3:50:19.761236 INFO: Starting optimization step 1.
3:50:19.761574 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:50:19.762119 PROGRESS: Extracting batch of 15933 precursors
3:50:19.770046 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:50:19.770268 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:50:19.770429 INFO: FWHM in RT is 2.64 seconds, sigma is 0.34
3:50:19.770562 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:50:19.770991 INFO: Starting candidate selection
3:50:20.426673 INFO: Starting candidate scoring
3:50:20.626900 INFO: Finished candidate processing
3:50:20.627071 INFO: Collecting candidate features
3:50:20.695616 WARNING: intensity_correlation has 2 NaNs ( 0.01 % out of 31791)
3:50:20.700107 INFO: Collecting fragment features
3:50:20.734874 INFO: Finished candidate scoring
3:50:20.751377 PROGRESS: === Extracted 31791 precursors and 297116 fragments ===
3:50:20.751794 INFO: performing precursor FDR with 47 features
3:50:20.751846 INFO: Decoy channel: -1
3:50:20.751868 INFO: Competetive: True
3:50:20.761132 INFO: Setting torch num_threads to 2 for FDR classification task
3:50:20.767548 WARNING: dropped 1 target PSMs due to missing features
3:50:20.767653 WARNING: dropped 1 decoy PSMs due to missing features
3:50:21.380984 INFO: Test AUC: 0.708
3:50:21.381117 INFO: Train AUC: 0.725
3:50:21.381148 INFO: AUC difference: 2.42%
3:50:21.466326 INFO: Resetting torch num_threads to 100
3:50:21.467616 INFO: === FDR correction performed with classifier version 3 ===
3:50:21.468881 PROGRESS: ============================= Precursor FDR =============================
3:50:21.468982 PROGRESS: Total precursors accumulated: 4,769
3:50:21.469044 PROGRESS: Target precursors: 4,528 (94.95%)
3:50:21.469097 PROGRESS: Decoy precursors: 241 (5.05%)
3:50:21.469144 PROGRESS: 
3:50:21.469187 PROGRESS: Precursor Summary:
3:50:21.472042 PROGRESS: Channel   0:	 0.05 FDR: 4,490; 0.01 FDR: 3,813; 0.001 FDR: 3,044
3:50:21.472167 PROGRESS: 
3:50:21.472225 PROGRESS: Protein Summary:
3:50:21.475121 PROGRESS: Channel   0:	 0.05 FDR: 2,659; 0.01 FDR: 2,391; 0.001 FDR: 2,023
3:50:21.475223 PROGRESS: =========================================================================
3:50:21.489531 INFO: fragments_df_filtered: 5000
3:50:21.501914 INFO: calibration group: precursor, fitting mz estimator 
3:50:21.757319 INFO: calibration group: precursor, fitting rt estimator 
3:50:21.994530 INFO: calibration group: fragment, fitting mz estimator 
3:50:22.423447 INFO: calibration group: precursor, predicting mz
3:50:22.426519 INFO: calibration group: precursor, predicting rt
3:50:22.436434 INFO: calibration group: fragment, predicting mz
3:50:22.459751 INFO: === checking if optimization conditions were reached ===
3:50:22.459957 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3:50:22.463984 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 51.2168.
3:50:22.464052 INFO: ==============================================
3:50:22.464159 INFO: Starting optimization step 2.
3:50:22.464235 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:50:22.464320 PROGRESS: Extracting batch of 15933 precursors
3:50:22.470519 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:50:22.470593 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:50:22.470631 INFO: FWHM in RT is 2.63 seconds, sigma is 0.34
3:50:22.470659 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:50:22.470874 INFO: Starting candidate selection
3:50:23.173472 INFO: Starting candidate scoring
3:50:23.411931 INFO: Finished candidate processing
3:50:23.412075 INFO: Collecting candidate features
3:50:23.468374 WARNING: intensity_correlation has 7 NaNs ( 0.02 % out of 31746)
3:50:23.477834 INFO: Collecting fragment features
3:50:23.502204 INFO: Finished candidate scoring
3:50:23.519243 PROGRESS: === Extracted 31746 precursors and 290416 fragments ===
3:50:23.519656 INFO: performing precursor FDR with 47 features
3:50:23.519696 INFO: Decoy channel: -1
3:50:23.519720 INFO: Competetive: True
3:50:23.529720 INFO: Setting torch num_threads to 2 for FDR classification task
3:50:23.535478 WARNING: dropped 3 target PSMs due to missing features
3:50:23.535601 WARNING: dropped 4 decoy PSMs due to missing features
3:50:24.099511 INFO: Test AUC: 0.729
3:50:24.099660 INFO: Train AUC: 0.737
3:50:24.099689 INFO: AUC difference: 1.06%
3:50:24.190715 INFO: Resetting torch num_threads to 100
3:50:24.192375 INFO: === FDR correction performed with classifier version 3 ===
3:50:24.193827 PROGRESS: ============================= Precursor FDR =============================
3:50:24.193942 PROGRESS: Total precursors accumulated: 4,886
3:50:24.194007 PROGRESS: Target precursors: 4,677 (95.72%)
3:50:24.194060 PROGRESS: Decoy precursors: 209 (4.28%)
3:50:24.194106 PROGRESS: 
3:50:24.194151 PROGRESS: Precursor Summary:
3:50:24.196438 PROGRESS: Channel   0:	 0.05 FDR: 4,677; 0.01 FDR: 4,054; 0.001 FDR: 3,319
3:50:24.196590 PROGRESS: 
3:50:24.196666 PROGRESS: Protein Summary:
3:50:24.199799 PROGRESS: Channel   0:	 0.05 FDR: 2,733; 0.01 FDR: 2,484; 0.001 FDR: 2,162
3:50:24.199913 PROGRESS: =========================================================================
3:50:24.216454 INFO: fragments_df_filtered: 5000
3:50:24.229654 INFO: calibration group: precursor, fitting mz estimator 
3:50:24.545501 INFO: calibration group: precursor, fitting rt estimator 
3:50:24.930504 INFO: calibration group: fragment, fitting mz estimator 
3:50:25.428660 INFO: calibration group: precursor, predicting mz
3:50:25.432049 INFO: calibration group: precursor, predicting rt
3:50:25.442285 INFO: calibration group: fragment, predicting mz
3:50:25.464641 INFO: === checking if optimization conditions were reached ===
3:50:25.464978 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3:50:25.470081 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 29.5473.
3:50:25.470170 INFO: ==============================================
3:50:25.470303 INFO: Starting optimization step 3.
3:50:25.470379 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:50:25.470451 PROGRESS: Extracting batch of 15933 precursors
3:50:25.476611 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:50:25.476705 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:50:25.476745 INFO: FWHM in RT is 2.62 seconds, sigma is 0.34
3:50:25.476774 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:50:25.477025 INFO: Starting candidate selection
3:50:26.150484 INFO: Starting candidate scoring
3:50:26.391105 INFO: Finished candidate processing
3:50:26.391249 INFO: Collecting candidate features
3:50:26.446596 WARNING: intensity_correlation has 7 NaNs ( 0.02 % out of 31686)
3:50:26.454165 INFO: Collecting fragment features
3:50:26.476638 INFO: Finished candidate scoring
3:50:26.493225 PROGRESS: === Extracted 31686 precursors and 288192 fragments ===
3:50:26.493700 INFO: performing precursor FDR with 47 features
3:50:26.493743 INFO: Decoy channel: -1
3:50:26.493774 INFO: Competetive: True
3:50:26.503047 INFO: Setting torch num_threads to 2 for FDR classification task
3:50:26.509029 WARNING: dropped 3 target PSMs due to missing features
3:50:26.509159 WARNING: dropped 4 decoy PSMs due to missing features
3:50:27.059131 INFO: Test AUC: 0.737
3:50:27.059281 INFO: Train AUC: 0.742
3:50:27.059312 INFO: AUC difference: 0.74%
3:50:27.149001 INFO: Resetting torch num_threads to 100
3:50:27.150674 INFO: === FDR correction performed with classifier version 3 ===
3:50:27.152195 PROGRESS: ============================= Precursor FDR =============================
3:50:27.152314 PROGRESS: Total precursors accumulated: 4,986
3:50:27.152375 PROGRESS: Target precursors: 4,766 (95.59%)
3:50:27.152427 PROGRESS: Decoy precursors: 220 (4.41%)
3:50:27.152476 PROGRESS: 
3:50:27.152520 PROGRESS: Precursor Summary:
3:50:27.154938 PROGRESS: Channel   0:	 0.05 FDR: 4,766; 0.01 FDR: 4,124; 0.001 FDR: 3,437
3:50:27.155054 PROGRESS: 
3:50:27.155110 PROGRESS: Protein Summary:
3:50:27.158217 PROGRESS: Channel   0:	 0.05 FDR: 2,776; 0.01 FDR: 2,516; 0.001 FDR: 2,223
3:50:27.158334 PROGRESS: =========================================================================
3:50:27.175076 INFO: fragments_df_filtered: 5000
3:50:27.188320 INFO: calibration group: precursor, fitting mz estimator 
3:50:27.576005 INFO: calibration group: precursor, fitting rt estimator 
3:50:27.934990 INFO: calibration group: fragment, fitting mz estimator 
3:50:28.355306 INFO: calibration group: precursor, predicting mz
3:50:28.358650 INFO: calibration group: precursor, predicting rt
3:50:28.369686 INFO: calibration group: fragment, predicting mz
3:50:28.414289 INFO: === checking if optimization conditions were reached ===
3:50:28.414700 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3:50:28.419823 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 23.5560.
3:50:28.419903 INFO: ==============================================
3:50:28.420032 INFO: Starting optimization step 4.
3:50:28.420111 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:50:28.420182 PROGRESS: Extracting batch of 15933 precursors
3:50:28.427227 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:50:28.427308 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:50:28.427348 INFO: FWHM in RT is 2.61 seconds, sigma is 0.34
3:50:28.427377 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:50:28.427614 INFO: Starting candidate selection
3:50:29.038783 INFO: Starting candidate scoring
3:50:29.238540 INFO: Finished candidate processing
3:50:29.238687 INFO: Collecting candidate features
3:50:29.306245 WARNING: intensity_correlation has 17 NaNs ( 0.06 % out of 30881)
3:50:29.311370 INFO: Collecting fragment features
3:50:29.336446 INFO: Finished candidate scoring
3:50:29.359689 PROGRESS: === Extracted 30881 precursors and 274922 fragments ===
3:50:29.360395 INFO: performing precursor FDR with 47 features
3:50:29.360463 INFO: Decoy channel: -1
3:50:29.360489 INFO: Competetive: True
3:50:29.374632 INFO: Setting torch num_threads to 2 for FDR classification task
3:50:29.380393 WARNING: dropped 4 target PSMs due to missing features
3:50:29.380517 WARNING: dropped 13 decoy PSMs due to missing features
3:50:29.857335 INFO: Test AUC: 0.743
3:50:29.857618 INFO: Train AUC: 0.750
3:50:29.857657 INFO: AUC difference: 0.91%
3:50:29.954264 INFO: Resetting torch num_threads to 100
3:50:29.955962 INFO: === FDR correction performed with classifier version 3 ===
3:50:29.957952 PROGRESS: ============================= Precursor FDR =============================
3:50:29.958056 PROGRESS: Total precursors accumulated: 5,176
3:50:29.958119 PROGRESS: Target precursors: 4,923 (95.11%)
3:50:29.958170 PROGRESS: Decoy precursors: 253 (4.89%)
3:50:29.958216 PROGRESS: 
3:50:29.958260 PROGRESS: Precursor Summary:
3:50:29.961943 PROGRESS: Channel   0:	 0.05 FDR: 4,896; 0.01 FDR: 4,156; 0.001 FDR: 3,422
3:50:29.962078 PROGRESS: 
3:50:29.962137 PROGRESS: Protein Summary:
3:50:29.965206 PROGRESS: Channel   0:	 0.05 FDR: 2,824; 0.01 FDR: 2,530; 0.001 FDR: 2,207
3:50:29.965318 PROGRESS: =========================================================================
3:50:29.983722 INFO: fragments_df_filtered: 5000
3:50:30.008783 INFO: calibration group: precursor, fitting mz estimator 
3:50:30.362604 INFO: calibration group: precursor, fitting rt estimator 
3:50:30.689826 INFO: calibration group: fragment, fitting mz estimator 
3:50:31.153203 INFO: calibration group: precursor, predicting mz
3:50:31.156588 INFO: calibration group: precursor, predicting rt
3:50:31.166641 INFO: calibration group: fragment, predicting mz
3:50:31.247185 INFO: === checking if optimization conditions were reached ===
3:50:31.247708 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3:50:31.253153 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 17.2769.
3:50:31.253224 INFO: ==============================================
3:50:31.253340 INFO: Starting optimization step 5.
3:50:31.253416 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:50:31.253510 PROGRESS: Extracting batch of 15933 precursors
3:50:31.260435 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:50:31.260508 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:50:31.260554 INFO: FWHM in RT is 2.60 seconds, sigma is 0.33
3:50:31.260582 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:50:31.260921 INFO: Starting candidate selection
3:50:31.854838 INFO: Starting candidate scoring
3:50:32.044685 INFO: Finished candidate processing
3:50:32.044789 INFO: Collecting candidate features
3:50:32.099597 WARNING: intensity_correlation has 10 NaNs ( 0.03 % out of 30924)
3:50:32.104330 INFO: Collecting fragment features
3:50:32.125559 INFO: Finished candidate scoring
3:50:32.139023 PROGRESS: === Extracted 30924 precursors and 276974 fragments ===
3:50:32.139413 INFO: performing precursor FDR with 47 features
3:50:32.139452 INFO: Decoy channel: -1
3:50:32.139476 INFO: Competetive: True
3:50:32.148726 INFO: Setting torch num_threads to 2 for FDR classification task
3:50:32.154348 WARNING: dropped 4 target PSMs due to missing features
3:50:32.154452 WARNING: dropped 6 decoy PSMs due to missing features
3:50:32.574908 INFO: Test AUC: 0.752
3:50:32.575037 INFO: Train AUC: 0.753
3:50:32.575067 INFO: AUC difference: 0.13%
3:50:32.662198 INFO: Resetting torch num_threads to 100
3:50:32.663610 INFO: === FDR correction performed with classifier version 3 ===
3:50:32.664862 PROGRESS: ============================= Precursor FDR =============================
3:50:32.664964 PROGRESS: Total precursors accumulated: 5,131
3:50:32.665023 PROGRESS: Target precursors: 4,902 (95.54%)
3:50:32.665072 PROGRESS: Decoy precursors: 229 (4.46%)
3:50:32.665118 PROGRESS: 
3:50:32.665162 PROGRESS: Precursor Summary:
3:50:32.667287 PROGRESS: Channel   0:	 0.05 FDR: 4,902; 0.01 FDR: 4,148; 0.001 FDR: 3,443
3:50:32.667401 PROGRESS: 
3:50:32.667455 PROGRESS: Protein Summary:
3:50:32.670451 PROGRESS: Channel   0:	 0.05 FDR: 2,819; 0.01 FDR: 2,527; 0.001 FDR: 2,218
3:50:32.670550 PROGRESS: =========================================================================
3:50:32.685011 INFO: fragments_df_filtered: 5000
3:50:32.696735 INFO: calibration group: precursor, fitting mz estimator 
3:50:33.091483 INFO: calibration group: precursor, fitting rt estimator 
3:50:33.450941 INFO: calibration group: fragment, fitting mz estimator 
3:50:33.901337 INFO: calibration group: precursor, predicting mz
3:50:33.904412 INFO: calibration group: precursor, predicting rt
3:50:33.914011 INFO: calibration group: fragment, predicting mz
3:50:33.968819 INFO: === checking if optimization conditions were reached ===
3:50:33.969131 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3:50:33.973829 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 17.6377.
3:50:33.973902 INFO: ==============================================
3:50:33.974015 INFO: Starting optimization step 6.
3:50:33.974093 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:50:33.974180 PROGRESS: Extracting batch of 15933 precursors
3:50:33.991356 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:50:33.991456 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:50:33.991495 INFO: FWHM in RT is 2.60 seconds, sigma is 0.34
3:50:33.991525 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:50:33.991779 INFO: Starting candidate selection
3:50:34.630593 INFO: Starting candidate scoring
3:50:34.881234 INFO: Finished candidate processing
3:50:34.881382 INFO: Collecting candidate features
3:50:34.977261 WARNING: intensity_correlation has 9 NaNs ( 0.03 % out of 30945)
3:50:34.984637 INFO: Collecting fragment features
3:50:35.015038 INFO: Finished candidate scoring
3:50:35.039172 PROGRESS: === Extracted 30945 precursors and 277082 fragments ===
3:50:35.039682 INFO: performing precursor FDR with 47 features
3:50:35.039732 INFO: Decoy channel: -1
3:50:35.039782 INFO: Competetive: True
3:50:35.054498 INFO: Setting torch num_threads to 2 for FDR classification task
3:50:35.067776 WARNING: dropped 4 target PSMs due to missing features
3:50:35.067944 WARNING: dropped 5 decoy PSMs due to missing features
3:50:35.696926 INFO: Test AUC: 0.748
3:50:35.697091 INFO: Train AUC: 0.755
3:50:35.697149 INFO: AUC difference: 0.90%
3:50:35.808416 INFO: Resetting torch num_threads to 100
3:50:35.809965 INFO: === FDR correction performed with classifier version 3 ===
3:50:35.811471 PROGRESS: ============================= Precursor FDR =============================
3:50:35.811596 PROGRESS: Total precursors accumulated: 5,132
3:50:35.811658 PROGRESS: Target precursors: 4,903 (95.54%)
3:50:35.811710 PROGRESS: Decoy precursors: 229 (4.46%)
3:50:35.811773 PROGRESS: 
3:50:35.811821 PROGRESS: Precursor Summary:
3:50:35.814332 PROGRESS: Channel   0:	 0.05 FDR: 4,903; 0.01 FDR: 4,172; 0.001 FDR: 3,512
3:50:35.814493 PROGRESS: 
3:50:35.814554 PROGRESS: Protein Summary:
3:50:35.817791 PROGRESS: Channel   0:	 0.05 FDR: 2,825; 0.01 FDR: 2,543; 0.001 FDR: 2,249
3:50:35.817930 PROGRESS: =========================================================================
3:50:35.833488 INFO: fragments_df_filtered: 5000
3:50:35.848111 INFO: calibration group: precursor, fitting mz estimator 
3:50:36.281317 INFO: calibration group: precursor, fitting rt estimator 
3:50:36.610124 INFO: calibration group: fragment, fitting mz estimator 
3:50:37.052779 INFO: calibration group: precursor, predicting mz
3:50:37.055826 INFO: calibration group: precursor, predicting rt
3:50:37.065283 INFO: calibration group: fragment, predicting mz
3:50:37.105744 INFO: === checking if optimization conditions were reached ===
3:50:37.106062 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
3:50:37.107520 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 17.2769 found after 7 searches.
3:50:37.107579 INFO: ==============================================
3:50:37.107681 PROGRESS: Optimization finished for rt_error.
3:50:37.121980 INFO: calibration group: precursor, predicting mz
3:50:37.125214 INFO: calibration group: precursor, predicting rt
3:50:37.135629 INFO: calibration group: fragment, predicting mz
3:50:37.192995 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:50:37.193207 PROGRESS: ==============================================
3:50:37.193293 PROGRESS: ms2_error      : 15.0000
3:50:37.193363 PROGRESS: ms1_error      : 10.0000
3:50:37.195103 PROGRESS: rt_error       : 17.2769
3:50:37.195179 PROGRESS: ==============================================
3:50:37.196289 INFO: calibration group: precursor, predicting mz
3:50:37.205665 INFO: calibration group: precursor, predicting rt
3:50:37.242599 INFO: calibration group: fragment, predicting mz
3:50:37.344600 PROGRESS: Extracting batch of 65173 precursors
3:50:37.365246 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:50:37.365394 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:50:37.365434 INFO: FWHM in RT is 2.60 seconds, sigma is 0.34
3:50:37.365477 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:50:37.365756 INFO: Starting candidate selection
3:50:39.486209 INFO: Applying score cutoff of 17.24431997680664
3:50:39.490198 INFO: Removed 4080 precursors with score below cutoff
3:50:39.523185 INFO: Starting candidate scoring
3:50:40.424423 INFO: Finished candidate processing
3:50:40.424613 INFO: Collecting candidate features
3:50:40.612290 WARNING: intensity_correlation has 21 NaNs ( 0.02 % out of 123085)
3:50:40.627531 INFO: Collecting fragment features
3:50:40.708328 INFO: Finished candidate scoring
3:50:40.765396 INFO: === FDR correction performed with classifier version 9 ===
3:50:40.766237 INFO: performing precursor FDR with 47 features
3:50:40.766272 INFO: Decoy channel: -1
3:50:40.766303 INFO: Competetive: True
3:50:40.812400 INFO: Setting torch num_threads to 2 for FDR classification task
3:50:40.831995 WARNING: dropped 2 target PSMs due to missing features
3:50:40.832128 WARNING: dropped 19 decoy PSMs due to missing features
3:50:43.294963 INFO: Test AUC: 0.777
3:50:43.295126 INFO: Train AUC: 0.783
3:50:43.295158 INFO: AUC difference: 0.78%
3:50:43.396642 INFO: Resetting torch num_threads to 100
3:50:43.404297 INFO: Removing fragments below FDR threshold
3:50:43.434425 PROGRESS: ============================= Precursor FDR =============================
3:50:43.434776 PROGRESS: Total precursors accumulated: 18,220
3:50:43.434847 PROGRESS: Target precursors: 18,040 (99.01%)
3:50:43.434900 PROGRESS: Decoy precursors: 180 (0.99%)
3:50:43.434948 PROGRESS: 
3:50:43.434994 PROGRESS: Precursor Summary:
3:50:43.442651 PROGRESS: Channel   0:	 0.05 FDR: 18,040; 0.01 FDR: 18,040; 0.001 FDR: 16,157
3:50:43.442858 PROGRESS: 
3:50:43.442920 PROGRESS: Protein Summary:
3:50:43.452719 PROGRESS: Channel   0:	 0.05 FDR: 5,188; 0.01 FDR: 5,188; 0.001 FDR: 4,981
3:50:43.452917 PROGRESS: =========================================================================
3:50:43.677629 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:50:43.701339 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:50:43.701541 INFO: Quantification results path: run_output_Astral/alphadia_1.10_default/quant
3:50:43.701628 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1 at run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:50:43.702454 INFO: Initializing RawFileManager
3:51:14.020953 INFO: Determining DIA cycle
3:51:14.040388 INFO: Found cycle with start 0.00 min and length 303.
3:51:14.225608 INFO: RT (min)            : 0.0 - 26.9
3:51:14.225725 INFO: RT duration (sec)   : 1611.2
3:51:14.225757 INFO: RT duration (min)   : 26.9
3:51:14.225782 INFO: Cycle len (scans)   : 303
3:51:14.225806 INFO: Cycle len (sec)     : 1.65
3:51:14.225830 INFO: Number of cycles    : 977
3:51:14.225852 INFO: MS2 range (m/z)     : 380.4 - 980.7
3:51:14.269343 INFO: Initializing CalibrationManager
3:51:14.269806 INFO: Loading calibration config
3:51:14.270638 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'}]
3:51:14.270746 INFO: Calibration group :fragment, found 1 estimator(s)
3:51:14.270837 INFO: Calibration group :precursor, found 3 estimator(s)
3:51:14.270954 INFO: Disabling ion mobility calibration
3:51:14.270984 INFO: removed mobility estimator from group precursor
3:51:14.271210 INFO: Initializing OptimizationManager
3:51:14.271336 INFO: initial parameter: ms1_error = 30
3:51:14.271397 INFO: initial parameter: ms2_error = 30
3:51:14.271452 INFO: initial parameter: rt_error = 805.5982666015625
3:51:14.271499 INFO: initial parameter: mobility_error = 0.1
3:51:14.271544 INFO: initial parameter: column_type = library
3:51:14.271584 INFO: initial parameter: num_candidates = 1
3:51:14.271625 INFO: initial parameter: classifier_version = -1
3:51:14.271664 INFO: initial parameter: fwhm_rt = 5
3:51:14.271703 INFO: initial parameter: fwhm_mobility = 0.01
3:51:14.271756 INFO: initial parameter: score_cutoff = 0
3:51:14.271823 INFO: Initializing TimingManager
3:51:14.271882 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:51:14.271985 INFO: FDRManager not loaded from disk.
3:51:14.272006 INFO: Initializing FDRManager
3:51:14.272044 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
3:51:14.297977 PROGRESS: 32,718 target precursors potentially observable (0 removed)
3:51:14.319860 PROGRESS: Starting initial search for precursors.
3:51:14.336154 INFO: Starting optimization step 0.
3:51:14.336389 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:51:14.336478 PROGRESS: Extracting batch of 15933 precursors
3:51:14.340847 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:51:14.340915 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:51:14.340956 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:51:14.340979 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:51:14.341297 INFO: Starting candidate selection
3:51:15.377687 INFO: Starting candidate scoring
3:51:15.485072 INFO: Finished candidate processing
3:51:15.485178 INFO: Collecting candidate features
3:51:15.524780 INFO: Collecting fragment features
3:51:15.539962 INFO: Finished candidate scoring
3:51:15.548061 PROGRESS: === Extracted 15933 precursors and 173214 fragments ===
3:51:15.548435 INFO: performing precursor FDR with 47 features
3:51:15.548473 INFO: Decoy channel: -1
3:51:15.548496 INFO: Competetive: True
3:51:15.552908 INFO: Setting torch num_threads to 2 for FDR classification task
3:51:15.733219 INFO: Test AUC: 0.726
3:51:15.733332 INFO: Train AUC: 0.736
3:51:15.733360 INFO: AUC difference: 1.32%
3:51:15.828866 INFO: Resetting torch num_threads to 100
3:51:15.830112 INFO: === FDR correction performed with classifier version -1 ===
3:51:15.831210 PROGRESS: ============================= Precursor FDR =============================
3:51:15.831313 PROGRESS: Total precursors accumulated: 3,397
3:51:15.831387 PROGRESS: Target precursors: 3,208 (94.44%)
3:51:15.831454 PROGRESS: Decoy precursors: 189 (5.56%)
3:51:15.831511 PROGRESS: 
3:51:15.831566 PROGRESS: Precursor Summary:
3:51:15.833372 PROGRESS: Channel   0:	 0.05 FDR: 3,122; 0.01 FDR: 2,301; 0.001 FDR: 1,136
3:51:15.833477 PROGRESS: 
3:51:15.833549 PROGRESS: Protein Summary:
3:51:15.835753 PROGRESS: Channel   0:	 0.05 FDR: 1,984; 0.01 FDR: 1,570; 0.001 FDR:   883
3:51:15.835863 PROGRESS: =========================================================================
3:51:15.842143 INFO: fragments_df_filtered: 5000
3:51:15.853321 INFO: calibration group: precursor, fitting mz estimator 
3:51:16.007858 INFO: calibration group: precursor, fitting rt estimator 
3:51:16.141187 INFO: calibration group: fragment, fitting mz estimator 
3:51:16.557768 INFO: calibration group: precursor, predicting mz
3:51:16.560525 INFO: calibration group: precursor, predicting rt
3:51:16.569014 INFO: calibration group: fragment, predicting mz
3:51:16.591606 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3:51:16.591851 INFO: Starting optimization step 1.
3:51:16.591943 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:51:16.592010 PROGRESS: Extracting batch of 15933 precursors
3:51:16.598279 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:51:16.598343 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:51:16.598381 INFO: FWHM in RT is 2.92 seconds, sigma is 0.38
3:51:16.598407 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:51:16.598623 INFO: Starting candidate selection
3:51:17.500975 INFO: Starting candidate scoring
3:51:17.761334 INFO: Finished candidate processing
3:51:17.761468 INFO: Collecting candidate features
3:51:17.829751 INFO: Collecting fragment features
3:51:17.862298 INFO: Finished candidate scoring
3:51:17.877775 PROGRESS: === Extracted 31866 precursors and 342862 fragments ===
3:51:17.878215 INFO: performing precursor FDR with 47 features
3:51:17.878256 INFO: Decoy channel: -1
3:51:17.878284 INFO: Competetive: True
3:51:17.888171 INFO: Setting torch num_threads to 2 for FDR classification task
3:51:18.512796 INFO: Test AUC: 0.709
3:51:18.512958 INFO: Train AUC: 0.712
3:51:18.512990 INFO: AUC difference: 0.35%
3:51:18.599916 INFO: Resetting torch num_threads to 100
3:51:18.601243 INFO: === FDR correction performed with classifier version 0 ===
3:51:18.602513 PROGRESS: ============================= Precursor FDR =============================
3:51:18.602607 PROGRESS: Total precursors accumulated: 5,027
3:51:18.602667 PROGRESS: Target precursors: 4,794 (95.37%)
3:51:18.602720 PROGRESS: Decoy precursors: 233 (4.63%)
3:51:18.602767 PROGRESS: 
3:51:18.602811 PROGRESS: Precursor Summary:
3:51:18.605350 PROGRESS: Channel   0:	 0.05 FDR: 4,794; 0.01 FDR: 3,971; 0.001 FDR: 3,093
3:51:18.605470 PROGRESS: 
3:51:18.605528 PROGRESS: Protein Summary:
3:51:18.608424 PROGRESS: Channel   0:	 0.05 FDR: 2,691; 0.01 FDR: 2,350; 0.001 FDR: 1,929
3:51:18.608536 PROGRESS: =========================================================================
3:51:18.623935 INFO: fragments_df_filtered: 5000
3:51:18.636153 INFO: calibration group: precursor, fitting mz estimator 
3:51:18.937399 INFO: calibration group: precursor, fitting rt estimator 
3:51:19.266292 INFO: calibration group: fragment, fitting mz estimator 
3:51:19.848028 INFO: calibration group: precursor, predicting mz
3:51:19.851724 INFO: calibration group: precursor, predicting rt
3:51:19.862786 INFO: calibration group: fragment, predicting mz
3:51:19.894555 INFO: === checking if optimization conditions were reached ===
3:51:19.897401 PROGRESS: ❌ ms2_error      : 19.0749 > 15.0000 or insufficient steps taken.
3:51:19.899119 PROGRESS: ❌ ms1_error      : 13.7609 > 10.0000 or insufficient steps taken.
3:51:19.899184 INFO: ==============================================
3:51:19.899463 INFO: Starting optimization step 2.
3:51:19.899633 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:51:19.899814 PROGRESS: Extracting batch of 15933 precursors
3:51:19.906314 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:51:19.906631 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:51:19.906791 INFO: FWHM in RT is 2.96 seconds, sigma is 0.38
3:51:19.906949 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:51:19.907305 INFO: Starting candidate selection
3:51:20.954556 INFO: Starting candidate scoring
3:51:21.232105 INFO: Finished candidate processing
3:51:21.232231 INFO: Collecting candidate features
3:51:21.308301 INFO: Collecting fragment features
3:51:21.341320 INFO: Finished candidate scoring
3:51:21.367287 PROGRESS: === Extracted 31863 precursors and 330216 fragments ===
3:51:21.367798 INFO: performing precursor FDR with 47 features
3:51:21.367849 INFO: Decoy channel: -1
3:51:21.367881 INFO: Competetive: True
3:51:21.383112 INFO: Setting torch num_threads to 2 for FDR classification task
3:51:22.234593 INFO: Test AUC: 0.741
3:51:22.234741 INFO: Train AUC: 0.747
3:51:22.234783 INFO: AUC difference: 0.79%
3:51:22.348535 INFO: Resetting torch num_threads to 100
3:51:22.350109 INFO: === FDR correction performed with classifier version 1 ===
3:51:22.351582 PROGRESS: ============================= Precursor FDR =============================
3:51:22.351685 PROGRESS: Total precursors accumulated: 6,044
3:51:22.351753 PROGRESS: Target precursors: 5,840 (96.62%)
3:51:22.351809 PROGRESS: Decoy precursors: 204 (3.38%)
3:51:22.351857 PROGRESS: 
3:51:22.351901 PROGRESS: Precursor Summary:
3:51:22.354551 PROGRESS: Channel   0:	 0.05 FDR: 5,840; 0.01 FDR: 5,415; 0.001 FDR: 4,032
3:51:22.354664 PROGRESS: 
3:51:22.354720 PROGRESS: Protein Summary:
3:51:22.358124 PROGRESS: Channel   0:	 0.05 FDR: 3,081; 0.01 FDR: 2,923; 0.001 FDR: 2,383
3:51:22.358228 PROGRESS: =========================================================================
3:51:22.378169 INFO: fragments_df_filtered: 5000
3:51:22.390829 INFO: calibration group: precursor, fitting mz estimator 
3:51:22.867924 INFO: calibration group: precursor, fitting rt estimator 
3:51:23.299800 INFO: calibration group: fragment, fitting mz estimator 
3:51:23.654918 INFO: calibration group: precursor, predicting mz
3:51:23.658152 INFO: calibration group: precursor, predicting rt
3:51:23.667104 INFO: calibration group: fragment, predicting mz
3:51:23.688392 INFO: === checking if optimization conditions were reached ===
3:51:23.690109 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
3:51:23.691681 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
3:51:23.691730 INFO: ==============================================
3:51:23.691859 PROGRESS: Optimization finished for ms2_error, ms1_error.
3:51:23.703859 INFO: calibration group: precursor, predicting mz
3:51:23.706530 INFO: calibration group: precursor, predicting rt
3:51:23.715153 INFO: calibration group: fragment, predicting mz
3:51:23.736988 INFO: Starting optimization step 0.
3:51:23.737139 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:51:23.737210 PROGRESS: Extracting batch of 15933 precursors
3:51:23.741466 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:51:23.741529 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:51:23.741562 INFO: FWHM in RT is 2.81 seconds, sigma is 0.36
3:51:23.741584 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:51:23.741776 INFO: Starting candidate selection
3:51:24.620602 INFO: Starting candidate scoring
3:51:24.832263 INFO: Finished candidate processing
3:51:24.832370 INFO: Collecting candidate features
3:51:24.886623 INFO: Collecting fragment features
3:51:24.909787 INFO: Finished candidate scoring
3:51:24.923932 PROGRESS: === Extracted 31861 precursors and 320824 fragments ===
3:51:24.924308 INFO: performing precursor FDR with 47 features
3:51:24.924346 INFO: Decoy channel: -1
3:51:24.924369 INFO: Competetive: True
3:51:24.935194 INFO: Setting torch num_threads to 2 for FDR classification task
3:51:25.446589 INFO: Test AUC: 0.755
3:51:25.446712 INFO: Train AUC: 0.766
3:51:25.446742 INFO: AUC difference: 1.40%
3:51:25.541915 INFO: Resetting torch num_threads to 100
3:51:25.544401 INFO: === FDR correction performed with classifier version 2 ===
3:51:25.545793 PROGRESS: ============================= Precursor FDR =============================
3:51:25.545885 PROGRESS: Total precursors accumulated: 6,523
3:51:25.545943 PROGRESS: Target precursors: 6,363 (97.55%)
3:51:25.546000 PROGRESS: Decoy precursors: 160 (2.45%)
3:51:25.546045 PROGRESS: 
3:51:25.546088 PROGRESS: Precursor Summary:
3:51:25.548789 PROGRESS: Channel   0:	 0.05 FDR: 6,363; 0.01 FDR: 6,067; 0.001 FDR: 5,140
3:51:25.548902 PROGRESS: 
3:51:25.548964 PROGRESS: Protein Summary:
3:51:25.552727 PROGRESS: Channel   0:	 0.05 FDR: 3,244; 0.01 FDR: 3,146; 0.001 FDR: 2,834
3:51:25.552841 PROGRESS: =========================================================================
3:51:25.574546 INFO: fragments_df_filtered: 5000
3:51:25.589379 INFO: calibration group: precursor, fitting mz estimator 
3:51:26.166185 INFO: calibration group: precursor, fitting rt estimator 
3:51:26.754172 INFO: calibration group: fragment, fitting mz estimator 
3:51:27.171595 INFO: calibration group: precursor, predicting mz
3:51:27.175121 INFO: calibration group: precursor, predicting rt
3:51:27.184281 INFO: calibration group: fragment, predicting mz
3:51:27.205959 INFO: === checking if optimization conditions were reached ===
3:51:27.206148 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3:51:27.211017 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 105.3828.
3:51:27.211076 INFO: ==============================================
3:51:27.211196 INFO: Starting optimization step 1.
3:51:27.211285 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:51:27.211366 PROGRESS: Extracting batch of 15933 precursors
3:51:27.221475 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:51:27.221541 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:51:27.221584 INFO: FWHM in RT is 2.72 seconds, sigma is 0.35
3:51:27.221609 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:51:27.221890 INFO: Starting candidate selection
3:51:27.879210 INFO: Starting candidate scoring
3:51:28.094352 INFO: Finished candidate processing
3:51:28.094455 INFO: Collecting candidate features
3:51:28.145323 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 31812)
3:51:28.149611 INFO: Collecting fragment features
3:51:28.172827 INFO: Finished candidate scoring
3:51:28.186601 PROGRESS: === Extracted 31812 precursors and 307010 fragments ===
3:51:28.187012 INFO: performing precursor FDR with 47 features
3:51:28.187051 INFO: Decoy channel: -1
3:51:28.187075 INFO: Competetive: True
3:51:28.197108 INFO: Setting torch num_threads to 2 for FDR classification task
3:51:28.202907 WARNING: dropped 2 target PSMs due to missing features
3:51:28.202995 WARNING: dropped 1 decoy PSMs due to missing features
3:51:28.734710 INFO: Test AUC: 0.811
3:51:28.734834 INFO: Train AUC: 0.808
3:51:28.734864 INFO: AUC difference: 0.44%
3:51:28.821114 INFO: Resetting torch num_threads to 100
3:51:28.822555 INFO: === FDR correction performed with classifier version 2 ===
3:51:28.824063 PROGRESS: ============================= Precursor FDR =============================
3:51:28.824158 PROGRESS: Total precursors accumulated: 7,390
3:51:28.824218 PROGRESS: Target precursors: 7,290 (98.65%)
3:51:28.824267 PROGRESS: Decoy precursors: 100 (1.35%)
3:51:28.824313 PROGRESS: 
3:51:28.824356 PROGRESS: Precursor Summary:
3:51:28.827235 PROGRESS: Channel   0:	 0.05 FDR: 7,290; 0.01 FDR: 7,178; 0.001 FDR: 5,689
3:51:28.827346 PROGRESS: 
3:51:28.827403 PROGRESS: Protein Summary:
3:51:28.831519 PROGRESS: Channel   0:	 0.05 FDR: 3,532; 0.01 FDR: 3,506; 0.001 FDR: 3,029
3:51:28.831625 PROGRESS: =========================================================================
3:51:28.856457 INFO: fragments_df_filtered: 5000
3:51:28.869667 INFO: calibration group: precursor, fitting mz estimator 
3:51:29.613427 INFO: calibration group: precursor, fitting rt estimator 
3:51:30.390695 INFO: calibration group: fragment, fitting mz estimator 
3:51:33.322632 INFO: calibration group: precursor, predicting mz
3:51:33.325713 INFO: calibration group: precursor, predicting rt
3:51:33.334929 INFO: calibration group: fragment, predicting mz
3:51:33.355770 INFO: === checking if optimization conditions were reached ===
3:51:33.355965 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3:51:33.362386 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 35.3703.
3:51:33.362454 INFO: ==============================================
3:51:33.362564 INFO: Starting optimization step 2.
3:51:33.362638 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:51:33.362704 PROGRESS: Extracting batch of 15933 precursors
3:51:33.369086 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:51:33.369154 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:51:33.369192 INFO: FWHM in RT is 2.69 seconds, sigma is 0.35
3:51:33.369218 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:51:33.369428 INFO: Starting candidate selection
3:51:33.942061 INFO: Starting candidate scoring
3:51:34.127311 INFO: Finished candidate processing
3:51:34.127409 INFO: Collecting candidate features
3:51:34.172311 WARNING: intensity_correlation has 12 NaNs ( 0.04 % out of 31662)
3:51:34.176611 INFO: Collecting fragment features
3:51:34.203022 INFO: Finished candidate scoring
3:51:34.219920 PROGRESS: === Extracted 31662 precursors and 295332 fragments ===
3:51:34.220293 INFO: performing precursor FDR with 47 features
3:51:34.220331 INFO: Decoy channel: -1
3:51:34.220356 INFO: Competetive: True
3:51:34.229058 INFO: Setting torch num_threads to 2 for FDR classification task
3:51:34.234956 WARNING: dropped 3 target PSMs due to missing features
3:51:34.235061 WARNING: dropped 9 decoy PSMs due to missing features
3:51:34.619574 INFO: Test AUC: 0.842
3:51:34.619704 INFO: Train AUC: 0.848
3:51:34.619751 INFO: AUC difference: 0.72%
3:51:34.702876 INFO: Resetting torch num_threads to 100
3:51:34.704293 INFO: === FDR correction performed with classifier version 2 ===
3:51:34.705863 PROGRESS: ============================= Precursor FDR =============================
3:51:34.705963 PROGRESS: Total precursors accumulated: 7,591
3:51:34.706032 PROGRESS: Target precursors: 7,522 (99.09%)
3:51:34.706090 PROGRESS: Decoy precursors: 69 (0.91%)
3:51:34.706145 PROGRESS: 
3:51:34.706195 PROGRESS: Precursor Summary:
3:51:34.709274 PROGRESS: Channel   0:	 0.05 FDR: 7,522; 0.01 FDR: 7,522; 0.001 FDR: 6,634
3:51:34.709413 PROGRESS: 
3:51:34.709480 PROGRESS: Protein Summary:
3:51:34.713894 PROGRESS: Channel   0:	 0.05 FDR: 3,590; 0.01 FDR: 3,590; 0.001 FDR: 3,331
3:51:34.714001 PROGRESS: =========================================================================
3:51:34.742522 INFO: fragments_df_filtered: 5000
3:51:34.755410 INFO: calibration group: precursor, fitting mz estimator 
3:51:35.564496 INFO: calibration group: precursor, fitting rt estimator 
3:51:36.406305 INFO: calibration group: fragment, fitting mz estimator 
3:51:36.825387 INFO: calibration group: precursor, predicting mz
3:51:36.828953 INFO: calibration group: precursor, predicting rt
3:51:36.838463 INFO: calibration group: fragment, predicting mz
3:51:36.860058 INFO: === checking if optimization conditions were reached ===
3:51:36.860235 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3:51:36.866903 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 22.2715.
3:51:36.866969 INFO: ==============================================
3:51:36.867075 INFO: Starting optimization step 3.
3:51:36.867150 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:51:36.867216 PROGRESS: Extracting batch of 15933 precursors
3:51:36.875299 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:51:36.875376 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:51:36.875414 INFO: FWHM in RT is 2.69 seconds, sigma is 0.35
3:51:36.875441 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:51:36.875669 INFO: Starting candidate selection
3:51:37.421138 INFO: Starting candidate scoring
3:51:37.605971 INFO: Finished candidate processing
3:51:37.606071 INFO: Collecting candidate features
3:51:37.664586 WARNING: intensity_correlation has 14 NaNs ( 0.05 % out of 30831)
3:51:37.669014 INFO: Collecting fragment features
3:51:37.691814 INFO: Finished candidate scoring
3:51:37.708431 PROGRESS: === Extracted 30831 precursors and 283341 fragments ===
3:51:37.708814 INFO: performing precursor FDR with 47 features
3:51:37.708853 INFO: Decoy channel: -1
3:51:37.708876 INFO: Competetive: True
3:51:37.718915 INFO: Setting torch num_threads to 2 for FDR classification task
3:51:37.723829 WARNING: dropped 6 target PSMs due to missing features
3:51:37.723913 WARNING: dropped 8 decoy PSMs due to missing features
3:51:38.156107 INFO: Test AUC: 0.859
3:51:38.156263 INFO: Train AUC: 0.859
3:51:38.156295 INFO: AUC difference: 0.03%
3:51:38.255008 INFO: Resetting torch num_threads to 100
3:51:38.256919 INFO: === FDR correction performed with classifier version 2 ===
3:51:38.258637 PROGRESS: ============================= Precursor FDR =============================
3:51:38.258766 PROGRESS: Total precursors accumulated: 7,634
3:51:38.258825 PROGRESS: Target precursors: 7,573 (99.20%)
3:51:38.258874 PROGRESS: Decoy precursors: 61 (0.80%)
3:51:38.258919 PROGRESS: 
3:51:38.258963 PROGRESS: Precursor Summary:
3:51:38.262126 PROGRESS: Channel   0:	 0.05 FDR: 7,573; 0.01 FDR: 7,573; 0.001 FDR: 6,843
3:51:38.262253 PROGRESS: 
3:51:38.262310 PROGRESS: Protein Summary:
3:51:38.266668 PROGRESS: Channel   0:	 0.05 FDR: 3,604; 0.01 FDR: 3,604; 0.001 FDR: 3,399
3:51:38.266767 PROGRESS: =========================================================================
3:51:38.293452 INFO: fragments_df_filtered: 5000
3:51:38.314006 INFO: calibration group: precursor, fitting mz estimator 
3:51:39.110571 INFO: calibration group: precursor, fitting rt estimator 
3:51:39.948720 INFO: calibration group: fragment, fitting mz estimator 
3:51:40.364193 INFO: calibration group: precursor, predicting mz
3:51:40.367627 INFO: calibration group: precursor, predicting rt
3:51:40.376980 INFO: calibration group: fragment, predicting mz
3:51:40.399271 INFO: === checking if optimization conditions were reached ===
3:51:40.399591 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3:51:40.406661 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 16.4254.
3:51:40.406733 INFO: ==============================================
3:51:40.406865 INFO: Starting optimization step 4.
3:51:40.406946 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:51:40.407036 PROGRESS: Extracting batch of 15933 precursors
3:51:40.413870 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:51:40.413937 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:51:40.413981 INFO: FWHM in RT is 2.68 seconds, sigma is 0.35
3:51:40.414009 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:51:40.414326 INFO: Starting candidate selection
3:51:40.952712 INFO: Starting candidate scoring
3:51:41.189037 INFO: Finished candidate processing
3:51:41.189135 INFO: Collecting candidate features
3:51:41.237275 WARNING: intensity_correlation has 13 NaNs ( 0.04 % out of 30881)
3:51:41.241800 INFO: Collecting fragment features
3:51:41.268326 INFO: Finished candidate scoring
3:51:41.283559 PROGRESS: === Extracted 30881 precursors and 285431 fragments ===
3:51:41.283971 INFO: performing precursor FDR with 47 features
3:51:41.284011 INFO: Decoy channel: -1
3:51:41.284035 INFO: Competetive: True
3:51:41.294523 INFO: Setting torch num_threads to 2 for FDR classification task
3:51:41.299907 WARNING: dropped 4 target PSMs due to missing features
3:51:41.300009 WARNING: dropped 9 decoy PSMs due to missing features
3:51:41.706318 INFO: Test AUC: 0.874
3:51:41.706436 INFO: Train AUC: 0.874
3:51:41.706466 INFO: AUC difference: 0.01%
3:51:41.791752 INFO: Resetting torch num_threads to 100
3:51:41.792948 INFO: === FDR correction performed with classifier version 2 ===
3:51:41.794507 PROGRESS: ============================= Precursor FDR =============================
3:51:41.794607 PROGRESS: Total precursors accumulated: 7,586
3:51:41.794667 PROGRESS: Target precursors: 7,521 (99.14%)
3:51:41.794717 PROGRESS: Decoy precursors: 65 (0.86%)
3:51:41.794762 PROGRESS: 
3:51:41.794808 PROGRESS: Precursor Summary:
3:51:41.797791 PROGRESS: Channel   0:	 0.05 FDR: 7,521; 0.01 FDR: 7,521; 0.001 FDR: 6,726
3:51:41.797920 PROGRESS: 
3:51:41.797979 PROGRESS: Protein Summary:
3:51:41.802329 PROGRESS: Channel   0:	 0.05 FDR: 3,591; 0.01 FDR: 3,591; 0.001 FDR: 3,359
3:51:41.802431 PROGRESS: =========================================================================
3:51:41.827759 INFO: fragments_df_filtered: 5000
3:51:41.839946 INFO: calibration group: precursor, fitting mz estimator 
3:51:42.667891 INFO: calibration group: precursor, fitting rt estimator 
3:51:43.559879 INFO: calibration group: fragment, fitting mz estimator 
3:51:43.978799 INFO: calibration group: precursor, predicting mz
3:51:43.981832 INFO: calibration group: precursor, predicting rt
3:51:43.991902 INFO: calibration group: fragment, predicting mz
3:51:44.012636 INFO: === checking if optimization conditions were reached ===
3:51:44.012815 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3:51:44.018433 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 17.3406.
3:51:44.018501 INFO: ==============================================
3:51:44.018599 INFO: Starting optimization step 5.
3:51:44.018672 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:51:44.018737 PROGRESS: Extracting batch of 15933 precursors
3:51:44.022708 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:51:44.022775 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:51:44.022813 INFO: FWHM in RT is 2.68 seconds, sigma is 0.35
3:51:44.022840 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:51:44.023029 INFO: Starting candidate selection
3:51:44.567950 INFO: Starting candidate scoring
3:51:44.760858 INFO: Finished candidate processing
3:51:44.760965 INFO: Collecting candidate features
3:51:44.804801 WARNING: intensity_correlation has 7 NaNs ( 0.02 % out of 30891)
3:51:44.809084 INFO: Collecting fragment features
3:51:44.827663 INFO: Finished candidate scoring
3:51:44.842182 PROGRESS: === Extracted 30891 precursors and 285205 fragments ===
3:51:44.842559 INFO: performing precursor FDR with 47 features
3:51:44.842597 INFO: Decoy channel: -1
3:51:44.842621 INFO: Competetive: True
3:51:44.850871 INFO: Setting torch num_threads to 2 for FDR classification task
3:51:44.855779 WARNING: dropped 4 target PSMs due to missing features
3:51:44.855876 WARNING: dropped 3 decoy PSMs due to missing features
3:51:45.241508 INFO: Test AUC: 0.870
3:51:45.241631 INFO: Train AUC: 0.872
3:51:45.241661 INFO: AUC difference: 0.18%
3:51:45.328146 INFO: Resetting torch num_threads to 100
3:51:45.329358 INFO: === FDR correction performed with classifier version 2 ===
3:51:45.330781 PROGRESS: ============================= Precursor FDR =============================
3:51:45.330877 PROGRESS: Total precursors accumulated: 7,594
3:51:45.330935 PROGRESS: Target precursors: 7,527 (99.12%)
3:51:45.330986 PROGRESS: Decoy precursors: 67 (0.88%)
3:51:45.331031 PROGRESS: 
3:51:45.331074 PROGRESS: Precursor Summary:
3:51:45.334279 PROGRESS: Channel   0:	 0.05 FDR: 7,527; 0.01 FDR: 7,527; 0.001 FDR: 6,814
3:51:45.334401 PROGRESS: 
3:51:45.334458 PROGRESS: Protein Summary:
3:51:45.338704 PROGRESS: Channel   0:	 0.05 FDR: 3,594; 0.01 FDR: 3,594; 0.001 FDR: 3,385
3:51:45.338809 PROGRESS: =========================================================================
3:51:45.362200 INFO: fragments_df_filtered: 5000
3:51:45.374383 INFO: calibration group: precursor, fitting mz estimator 
3:51:46.184044 INFO: calibration group: precursor, fitting rt estimator 
3:51:47.095150 INFO: calibration group: fragment, fitting mz estimator 
3:51:47.516821 INFO: calibration group: precursor, predicting mz
3:51:47.520235 INFO: calibration group: precursor, predicting rt
3:51:47.530426 INFO: calibration group: fragment, predicting mz
3:51:47.551162 INFO: === checking if optimization conditions were reached ===
3:51:47.551353 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3:51:47.557613 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 17.3735.
3:51:47.557681 INFO: ==============================================
3:51:47.557788 INFO: Starting optimization step 6.
3:51:47.557865 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:51:47.557933 PROGRESS: Extracting batch of 15933 precursors
3:51:47.563885 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:51:47.563959 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:51:47.563997 INFO: FWHM in RT is 2.68 seconds, sigma is 0.35
3:51:47.564024 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:51:47.564239 INFO: Starting candidate selection
3:51:48.102853 INFO: Starting candidate scoring
3:51:48.280365 INFO: Finished candidate processing
3:51:48.280469 INFO: Collecting candidate features
3:51:48.325580 WARNING: intensity_correlation has 7 NaNs ( 0.02 % out of 30872)
3:51:48.329854 INFO: Collecting fragment features
3:51:48.349833 INFO: Finished candidate scoring
3:51:48.363775 PROGRESS: === Extracted 30872 precursors and 285130 fragments ===
3:51:48.364620 INFO: performing precursor FDR with 47 features
3:51:48.364660 INFO: Decoy channel: -1
3:51:48.364684 INFO: Competetive: True
3:51:48.372464 INFO: Setting torch num_threads to 2 for FDR classification task
3:51:48.377488 WARNING: dropped 5 target PSMs due to missing features
3:51:48.377589 WARNING: dropped 2 decoy PSMs due to missing features
3:51:48.774737 INFO: Test AUC: 0.867
3:51:48.774858 INFO: Train AUC: 0.873
3:51:48.774887 INFO: AUC difference: 0.68%
3:51:48.862300 INFO: Resetting torch num_threads to 100
3:51:48.863538 INFO: === FDR correction performed with classifier version 2 ===
3:51:48.865061 PROGRESS: ============================= Precursor FDR =============================
3:51:48.865164 PROGRESS: Total precursors accumulated: 7,603
3:51:48.865223 PROGRESS: Target precursors: 7,530 (99.04%)
3:51:48.865280 PROGRESS: Decoy precursors: 73 (0.96%)
3:51:48.865326 PROGRESS: 
3:51:48.865372 PROGRESS: Precursor Summary:
3:51:48.868376 PROGRESS: Channel   0:	 0.05 FDR: 7,530; 0.01 FDR: 7,530; 0.001 FDR: 6,629
3:51:48.868499 PROGRESS: 
3:51:48.868567 PROGRESS: Protein Summary:
3:51:48.872873 PROGRESS: Channel   0:	 0.05 FDR: 3,593; 0.01 FDR: 3,593; 0.001 FDR: 3,332
3:51:48.872981 PROGRESS: =========================================================================
3:51:48.897542 INFO: fragments_df_filtered: 5000
3:51:48.909786 INFO: calibration group: precursor, fitting mz estimator 
3:51:49.725761 INFO: calibration group: precursor, fitting rt estimator 
3:51:50.571774 INFO: calibration group: fragment, fitting mz estimator 
3:51:50.985367 INFO: calibration group: precursor, predicting mz
3:51:50.988332 INFO: calibration group: precursor, predicting rt
3:51:50.997761 INFO: calibration group: fragment, predicting mz
3:51:51.018762 INFO: === checking if optimization conditions were reached ===
3:51:51.018960 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
3:51:51.020515 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 16.4254 found after 7 searches.
3:51:51.020574 INFO: ==============================================
3:51:51.020683 PROGRESS: Optimization finished for rt_error.
3:51:51.040601 INFO: calibration group: precursor, predicting mz
3:51:51.043778 INFO: calibration group: precursor, predicting rt
3:51:51.053582 INFO: calibration group: fragment, predicting mz
3:51:51.110471 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:51:51.110666 PROGRESS: ==============================================
3:51:51.110760 PROGRESS: ms2_error      : 15.0000
3:51:51.110834 PROGRESS: ms1_error      : 10.0000
3:51:51.110897 PROGRESS: rt_error       : 16.4254
3:51:51.110965 PROGRESS: ==============================================
3:51:51.113661 INFO: calibration group: precursor, predicting mz
3:51:51.123301 INFO: calibration group: precursor, predicting rt
3:51:51.158994 INFO: calibration group: fragment, predicting mz
3:51:51.259613 PROGRESS: Extracting batch of 65173 precursors
3:51:51.279041 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:51:51.279176 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:51:51.279230 INFO: FWHM in RT is 2.68 seconds, sigma is 0.35
3:51:51.279254 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:51:51.279504 INFO: Starting candidate selection
3:51:53.236177 INFO: Applying score cutoff of 27.08817855834961
3:51:53.240094 INFO: Removed 10879 precursors with score below cutoff
3:51:53.279129 INFO: Starting candidate scoring
3:51:54.283459 INFO: Finished candidate processing
3:51:54.283583 INFO: Collecting candidate features
3:51:54.517444 WARNING: intensity_correlation has 10 NaNs ( 0.01 % out of 116096)
3:51:54.528066 INFO: Collecting fragment features
3:51:54.640571 INFO: Finished candidate scoring
3:51:54.755079 INFO: === FDR correction performed with classifier version 7 ===
3:51:54.756271 INFO: performing precursor FDR with 47 features
3:51:54.756309 INFO: Decoy channel: -1
3:51:54.756332 INFO: Competetive: True
3:51:54.815942 INFO: Setting torch num_threads to 2 for FDR classification task
3:51:54.845640 WARNING: dropped 4 target PSMs due to missing features
3:51:54.845778 WARNING: dropped 6 decoy PSMs due to missing features
3:51:54.845837 WARNING: FDR calculation for 61180 target and 54906 decoy PSMs
3:51:54.845867 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
3:51:58.161990 INFO: Test AUC: 0.897
3:51:58.162145 INFO: Train AUC: 0.901
3:51:58.162190 INFO: AUC difference: 0.44%
3:51:58.290963 INFO: Resetting torch num_threads to 100
3:51:58.300880 INFO: Removing fragments below FDR threshold
3:51:58.334093 PROGRESS: ============================= Precursor FDR =============================
3:51:58.334387 PROGRESS: Total precursors accumulated: 31,261
3:51:58.334459 PROGRESS: Target precursors: 31,042 (99.30%)
3:51:58.334523 PROGRESS: Decoy precursors: 219 (0.70%)
3:51:58.334579 PROGRESS: 
3:51:58.334626 PROGRESS: Precursor Summary:
3:51:58.352411 PROGRESS: Channel   0:	 0.05 FDR: 31,042; 0.01 FDR: 31,042; 0.001 FDR: 28,672
3:51:58.352739 PROGRESS: 
3:51:58.352803 PROGRESS: Protein Summary:
3:51:58.377749 PROGRESS: Channel   0:	 0.05 FDR: 5,884; 0.01 FDR: 5,884; 0.001 FDR: 5,847
3:51:58.378110 PROGRESS: =========================================================================
3:51:58.768928 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:51:58.785097 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:51:58.785302 INFO: Quantification results path: run_output_Astral/alphadia_1.10_default/quant
3:51:58.785385 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2 at run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:51:58.786205 INFO: Initializing RawFileManager
3:52:26.170660 INFO: Determining DIA cycle
3:52:26.187901 INFO: Found cycle with start 0.00 min and length 303.
3:52:26.372654 INFO: RT (min)            : 0.0 - 26.9
3:52:26.372759 INFO: RT duration (sec)   : 1611.2
3:52:26.372788 INFO: RT duration (min)   : 26.9
3:52:26.372812 INFO: Cycle len (scans)   : 303
3:52:26.372833 INFO: Cycle len (sec)     : 1.65
3:52:26.372853 INFO: Number of cycles    : 977
3:52:26.372875 INFO: MS2 range (m/z)     : 380.4 - 980.7
3:52:26.395180 INFO: Initializing CalibrationManager
3:52:26.395438 INFO: Loading calibration config
3:52:26.396138 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'}]
3:52:26.396226 INFO: Calibration group :fragment, found 1 estimator(s)
3:52:26.396333 INFO: Calibration group :precursor, found 3 estimator(s)
3:52:26.396444 INFO: Disabling ion mobility calibration
3:52:26.396473 INFO: removed mobility estimator from group precursor
3:52:26.396615 INFO: Initializing OptimizationManager
3:52:26.396725 INFO: initial parameter: ms1_error = 30
3:52:26.396782 INFO: initial parameter: ms2_error = 30
3:52:26.396829 INFO: initial parameter: rt_error = 805.6002197265625
3:52:26.396875 INFO: initial parameter: mobility_error = 0.1
3:52:26.396917 INFO: initial parameter: column_type = library
3:52:26.396955 INFO: initial parameter: num_candidates = 1
3:52:26.396994 INFO: initial parameter: classifier_version = -1
3:52:26.397032 INFO: initial parameter: fwhm_rt = 5
3:52:26.397073 INFO: initial parameter: fwhm_mobility = 0.01
3:52:26.397113 INFO: initial parameter: score_cutoff = 0
3:52:26.397176 INFO: Initializing TimingManager
3:52:26.397232 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:52:26.397341 INFO: FDRManager not loaded from disk.
3:52:26.397363 INFO: Initializing FDRManager
3:52:26.397399 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
3:52:26.413329 PROGRESS: 32,718 target precursors potentially observable (0 removed)
3:52:26.430789 PROGRESS: Starting initial search for precursors.
3:52:26.446260 INFO: Starting optimization step 0.
3:52:26.446501 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:52:26.446582 PROGRESS: Extracting batch of 15933 precursors
3:52:26.450161 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:52:26.450215 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:52:26.450255 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:52:26.450277 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:52:26.450601 INFO: Starting candidate selection
3:52:27.481288 INFO: Starting candidate scoring
3:52:27.592725 INFO: Finished candidate processing
3:52:27.592829 INFO: Collecting candidate features
3:52:27.631253 INFO: Collecting fragment features
3:52:27.645047 INFO: Finished candidate scoring
3:52:27.653883 PROGRESS: === Extracted 15933 precursors and 173283 fragments ===
3:52:27.654245 INFO: performing precursor FDR with 47 features
3:52:27.654283 INFO: Decoy channel: -1
3:52:27.654307 INFO: Competetive: True
3:52:27.659059 INFO: Setting torch num_threads to 2 for FDR classification task
3:52:27.837331 INFO: Test AUC: 0.704
3:52:27.837459 INFO: Train AUC: 0.698
3:52:27.837491 INFO: AUC difference: 0.98%
3:52:27.923908 INFO: Resetting torch num_threads to 100
3:52:27.924946 INFO: === FDR correction performed with classifier version -1 ===
3:52:27.926588 PROGRESS: ============================= Precursor FDR =============================
3:52:27.926693 PROGRESS: Total precursors accumulated: 7,983
3:52:27.926752 PROGRESS: Target precursors: 5,605 (70.21%)
3:52:27.926801 PROGRESS: Decoy precursors: 2,378 (29.79%)
3:52:27.926846 PROGRESS: 
3:52:27.926889 PROGRESS: Precursor Summary:
3:52:27.927842 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:52:27.927934 PROGRESS: 
3:52:27.927989 PROGRESS: Protein Summary:
3:52:27.928973 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:52:27.929061 PROGRESS: =========================================================================
3:52:27.949626 INFO: Starting optimization step 1.
3:52:27.949908 PROGRESS: === Extracting elution groups 8000 to 24000 ===
3:52:27.949979 PROGRESS: Extracting batch of 31879 precursors
3:52:27.957517 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:52:27.957609 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:52:27.957644 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:52:27.957667 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:52:27.957886 INFO: Starting candidate selection
3:52:29.882930 INFO: Starting candidate scoring
3:52:30.105457 INFO: Finished candidate processing
3:52:30.105568 INFO: Collecting candidate features
3:52:30.167666 INFO: Collecting fragment features
3:52:30.189948 INFO: Finished candidate scoring
3:52:30.214896 PROGRESS: === Extracted 47811 precursors and 519535 fragments ===
3:52:30.220513 INFO: performing precursor FDR with 47 features
3:52:30.220592 INFO: Decoy channel: -1
3:52:30.220617 INFO: Competetive: True
3:52:30.238897 INFO: Setting torch num_threads to 2 for FDR classification task
3:52:30.982223 INFO: Test AUC: 0.746
3:52:30.982353 INFO: Train AUC: 0.752
3:52:30.982384 INFO: AUC difference: 0.81%
3:52:31.072555 INFO: Resetting torch num_threads to 100
3:52:31.075524 INFO: === FDR correction performed with classifier version -1 ===
3:52:31.077669 PROGRESS: ============================= Precursor FDR =============================
3:52:31.077815 PROGRESS: Total precursors accumulated: 10,237
3:52:31.077877 PROGRESS: Target precursors: 9,667 (94.43%)
3:52:31.077929 PROGRESS: Decoy precursors: 570 (5.57%)
3:52:31.077981 PROGRESS: 
3:52:31.078032 PROGRESS: Precursor Summary:
3:52:31.081267 PROGRESS: Channel   0:	 0.05 FDR: 9,493; 0.01 FDR: 8,190; 0.001 FDR: 4,839
3:52:31.081413 PROGRESS: 
3:52:31.081471 PROGRESS: Protein Summary:
3:52:31.085995 PROGRESS: Channel   0:	 0.05 FDR: 3,789; 0.01 FDR: 3,412; 0.001 FDR: 2,369
3:52:31.086114 PROGRESS: =========================================================================
3:52:31.108747 INFO: fragments_df_filtered: 5000
3:52:31.122285 INFO: calibration group: precursor, fitting mz estimator 
3:52:32.047524 INFO: calibration group: precursor, fitting rt estimator 
3:52:33.016589 INFO: calibration group: fragment, fitting mz estimator 
3:52:33.435219 INFO: calibration group: precursor, predicting mz
3:52:33.438096 INFO: calibration group: precursor, predicting rt
3:52:33.446814 INFO: calibration group: fragment, predicting mz
3:52:33.469317 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3:52:33.469527 INFO: Starting optimization step 2.
3:52:33.469605 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:52:33.469673 PROGRESS: Extracting batch of 15933 precursors
3:52:33.475827 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:52:33.475898 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:52:33.475934 INFO: FWHM in RT is 2.96 seconds, sigma is 0.38
3:52:33.475961 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:52:33.476186 INFO: Starting candidate selection
3:52:34.360729 INFO: Starting candidate scoring
3:52:34.612582 INFO: Finished candidate processing
3:52:34.612727 INFO: Collecting candidate features
3:52:34.674664 INFO: Collecting fragment features
3:52:34.697015 INFO: Finished candidate scoring
3:52:34.713931 PROGRESS: === Extracted 31866 precursors and 343574 fragments ===
3:52:34.714370 INFO: performing precursor FDR with 47 features
3:52:34.714409 INFO: Decoy channel: -1
3:52:34.714432 INFO: Competetive: True
3:52:34.724126 INFO: Setting torch num_threads to 2 for FDR classification task
3:52:35.358511 INFO: Test AUC: 0.714
3:52:35.358666 INFO: Train AUC: 0.718
3:52:35.358695 INFO: AUC difference: 0.55%
3:52:35.445979 INFO: Resetting torch num_threads to 100
3:52:35.447384 INFO: === FDR correction performed with classifier version 1 ===
3:52:35.448727 PROGRESS: ============================= Precursor FDR =============================
3:52:35.448825 PROGRESS: Total precursors accumulated: 5,124
3:52:35.448884 PROGRESS: Target precursors: 4,920 (96.02%)
3:52:35.448934 PROGRESS: Decoy precursors: 204 (3.98%)
3:52:35.448979 PROGRESS: 
3:52:35.449022 PROGRESS: Precursor Summary:
3:52:35.451313 PROGRESS: Channel   0:	 0.05 FDR: 4,920; 0.01 FDR: 4,344; 0.001 FDR: 3,254
3:52:35.451445 PROGRESS: 
3:52:35.451533 PROGRESS: Protein Summary:
3:52:35.454649 PROGRESS: Channel   0:	 0.05 FDR: 2,755; 0.01 FDR: 2,541; 0.001 FDR: 2,046
3:52:35.454756 PROGRESS: =========================================================================
3:52:35.472900 INFO: fragments_df_filtered: 5000
3:52:35.487038 INFO: calibration group: precursor, fitting mz estimator 
3:52:35.763330 INFO: calibration group: precursor, fitting rt estimator 
3:52:36.119978 INFO: calibration group: fragment, fitting mz estimator 
3:52:36.535562 INFO: calibration group: precursor, predicting mz
3:52:36.539029 INFO: calibration group: precursor, predicting rt
3:52:36.549038 INFO: calibration group: fragment, predicting mz
3:52:36.570388 INFO: === checking if optimization conditions were reached ===
3:52:36.572489 PROGRESS: ❌ ms2_error      : 19.9486 > 15.0000 or insufficient steps taken.
3:52:36.574113 PROGRESS: ❌ ms1_error      : 13.4714 > 10.0000 or insufficient steps taken.
3:52:36.574168 INFO: ==============================================
3:52:36.574282 INFO: Starting optimization step 3.
3:52:36.574370 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:52:36.574451 PROGRESS: Extracting batch of 15933 precursors
3:52:36.580755 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:52:36.580827 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:52:36.580866 INFO: FWHM in RT is 2.96 seconds, sigma is 0.38
3:52:36.580894 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:52:36.581116 INFO: Starting candidate selection
3:52:37.492745 INFO: Starting candidate scoring
3:52:37.723050 INFO: Finished candidate processing
3:52:37.723218 INFO: Collecting candidate features
3:52:37.779150 INFO: Collecting fragment features
3:52:37.809955 INFO: Finished candidate scoring
3:52:37.827622 PROGRESS: === Extracted 31866 precursors and 331079 fragments ===
3:52:37.828076 INFO: performing precursor FDR with 47 features
3:52:37.828119 INFO: Decoy channel: -1
3:52:37.828144 INFO: Competetive: True
3:52:37.844316 INFO: Setting torch num_threads to 2 for FDR classification task
3:52:38.262994 INFO: Test AUC: 0.737
3:52:38.263151 INFO: Train AUC: 0.745
3:52:38.263183 INFO: AUC difference: 1.13%
3:52:38.351873 INFO: Resetting torch num_threads to 100
3:52:38.353805 INFO: === FDR correction performed with classifier version 2 ===
3:52:38.355548 PROGRESS: ============================= Precursor FDR =============================
3:52:38.355648 PROGRESS: Total precursors accumulated: 5,975
3:52:38.355707 PROGRESS: Target precursors: 5,789 (96.89%)
3:52:38.355766 PROGRESS: Decoy precursors: 186 (3.11%)
3:52:38.355814 PROGRESS: 
3:52:38.355864 PROGRESS: Precursor Summary:
3:52:38.358325 PROGRESS: Channel   0:	 0.05 FDR: 5,789; 0.01 FDR: 5,463; 0.001 FDR: 4,488
3:52:38.358436 PROGRESS: 
3:52:38.358492 PROGRESS: Protein Summary:
3:52:38.361917 PROGRESS: Channel   0:	 0.05 FDR: 3,072; 0.01 FDR: 2,955; 0.001 FDR: 2,593
3:52:38.362019 PROGRESS: =========================================================================
3:52:38.382232 INFO: fragments_df_filtered: 5000
3:52:38.398486 INFO: calibration group: precursor, fitting mz estimator 
3:52:38.893279 INFO: calibration group: precursor, fitting rt estimator 
3:52:39.383709 INFO: calibration group: fragment, fitting mz estimator 
3:52:39.803812 INFO: calibration group: precursor, predicting mz
3:52:39.807601 INFO: calibration group: precursor, predicting rt
3:52:39.818429 INFO: calibration group: fragment, predicting mz
3:52:39.854755 INFO: === checking if optimization conditions were reached ===
3:52:39.857941 PROGRESS: ❌ ms2_error      : 15.3498 > 15.0000 or insufficient steps taken.
3:52:39.870405 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
3:52:39.870567 INFO: ==============================================
3:52:39.870819 INFO: Starting optimization step 4.
3:52:39.870911 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:52:39.871018 PROGRESS: Extracting batch of 15933 precursors
3:52:39.892663 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:52:39.892849 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:52:39.892911 INFO: FWHM in RT is 2.79 seconds, sigma is 0.36
3:52:39.892943 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:52:39.893456 INFO: Starting candidate selection
3:52:40.879188 INFO: Starting candidate scoring
3:52:41.109120 INFO: Finished candidate processing
3:52:41.109276 INFO: Collecting candidate features
3:52:41.166648 INFO: Collecting fragment features
3:52:41.195064 INFO: Finished candidate scoring
3:52:41.216844 PROGRESS: === Extracted 31865 precursors and 322252 fragments ===
3:52:41.217288 INFO: performing precursor FDR with 47 features
3:52:41.217341 INFO: Decoy channel: -1
3:52:41.217366 INFO: Competetive: True
3:52:41.227874 INFO: Setting torch num_threads to 2 for FDR classification task
3:52:41.829965 INFO: Test AUC: 0.756
3:52:41.830107 INFO: Train AUC: 0.762
3:52:41.830138 INFO: AUC difference: 0.70%
3:52:41.917495 INFO: Resetting torch num_threads to 100
3:52:41.919000 INFO: === FDR correction performed with classifier version 3 ===
3:52:41.920672 PROGRESS: ============================= Precursor FDR =============================
3:52:41.920778 PROGRESS: Total precursors accumulated: 6,456
3:52:41.920838 PROGRESS: Target precursors: 6,290 (97.43%)
3:52:41.920891 PROGRESS: Decoy precursors: 166 (2.57%)
3:52:41.920940 PROGRESS: 
3:52:41.920984 PROGRESS: Precursor Summary:
3:52:41.923773 PROGRESS: Channel   0:	 0.05 FDR: 6,290; 0.01 FDR: 6,062; 0.001 FDR: 5,288
3:52:41.923894 PROGRESS: 
3:52:41.923953 PROGRESS: Protein Summary:
3:52:41.927834 PROGRESS: Channel   0:	 0.05 FDR: 3,252; 0.01 FDR: 3,171; 0.001 FDR: 2,907
3:52:41.927951 PROGRESS: =========================================================================
3:52:41.951143 INFO: fragments_df_filtered: 5000
3:52:41.964952 INFO: calibration group: precursor, fitting mz estimator 
3:52:42.461908 INFO: calibration group: precursor, fitting rt estimator 
3:52:42.983217 INFO: calibration group: fragment, fitting mz estimator 
3:52:43.369351 INFO: calibration group: precursor, predicting mz
3:52:43.372366 INFO: calibration group: precursor, predicting rt
3:52:43.381050 INFO: calibration group: fragment, predicting mz
3:52:43.400562 INFO: === checking if optimization conditions were reached ===
3:52:43.402406 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
3:52:43.402468 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
3:52:43.402497 INFO: ==============================================
3:52:43.402593 PROGRESS: Optimization finished for ms2_error, ms1_error.
3:52:43.415908 INFO: calibration group: precursor, predicting mz
3:52:43.418738 INFO: calibration group: precursor, predicting rt
3:52:43.427440 INFO: calibration group: fragment, predicting mz
3:52:43.449329 INFO: Starting optimization step 0.
3:52:43.449527 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:52:43.449599 PROGRESS: Extracting batch of 15933 precursors
3:52:43.454264 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:52:43.454333 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:52:43.454366 INFO: FWHM in RT is 2.68 seconds, sigma is 0.35
3:52:43.454392 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:52:43.454596 INFO: Starting candidate selection
3:52:44.347272 INFO: Starting candidate scoring
3:52:44.570905 INFO: Finished candidate processing
3:52:44.571024 INFO: Collecting candidate features
3:52:44.626561 INFO: Collecting fragment features
3:52:44.648201 INFO: Finished candidate scoring
3:52:44.661350 PROGRESS: === Extracted 31865 precursors and 321866 fragments ===
3:52:44.661721 INFO: performing precursor FDR with 47 features
3:52:44.661760 INFO: Decoy channel: -1
3:52:44.661783 INFO: Competetive: True
3:52:44.670094 INFO: Setting torch num_threads to 2 for FDR classification task
3:52:45.172966 INFO: Test AUC: 0.754
3:52:45.173092 INFO: Train AUC: 0.770
3:52:45.173124 INFO: AUC difference: 2.08%
3:52:45.256535 INFO: Resetting torch num_threads to 100
3:52:45.257800 INFO: === FDR correction performed with classifier version 4 ===
3:52:45.259281 PROGRESS: ============================= Precursor FDR =============================
3:52:45.259377 PROGRESS: Total precursors accumulated: 6,535
3:52:45.259441 PROGRESS: Target precursors: 6,354 (97.23%)
3:52:45.259493 PROGRESS: Decoy precursors: 181 (2.77%)
3:52:45.259540 PROGRESS: 
3:52:45.259583 PROGRESS: Precursor Summary:
3:52:45.262254 PROGRESS: Channel   0:	 0.05 FDR: 6,354; 0.01 FDR: 6,135; 0.001 FDR: 5,408
3:52:45.262372 PROGRESS: 
3:52:45.262428 PROGRESS: Protein Summary:
3:52:45.266160 PROGRESS: Channel   0:	 0.05 FDR: 3,268; 0.01 FDR: 3,196; 0.001 FDR: 2,945
3:52:45.266266 PROGRESS: =========================================================================
3:52:45.286479 INFO: fragments_df_filtered: 5000
3:52:45.297760 INFO: calibration group: precursor, fitting mz estimator 
3:52:45.839850 INFO: calibration group: precursor, fitting rt estimator 
3:52:46.367867 INFO: calibration group: fragment, fitting mz estimator 
3:52:46.763093 INFO: calibration group: precursor, predicting mz
3:52:46.766644 INFO: calibration group: precursor, predicting rt
3:52:46.777303 INFO: calibration group: fragment, predicting mz
3:52:46.854174 INFO: === checking if optimization conditions were reached ===
3:52:46.854546 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3:52:46.872460 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 146.1587.
3:52:46.872552 INFO: ==============================================
3:52:46.872689 INFO: Starting optimization step 1.
3:52:46.872768 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:52:46.872842 PROGRESS: Extracting batch of 15933 precursors
3:52:46.878397 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:52:46.878469 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:52:46.878507 INFO: FWHM in RT is 2.67 seconds, sigma is 0.34
3:52:46.878536 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:52:46.878757 INFO: Starting candidate selection
3:52:47.576297 INFO: Starting candidate scoring
3:52:47.818958 INFO: Finished candidate processing
3:52:47.819079 INFO: Collecting candidate features
3:52:47.870169 WARNING: intensity_correlation has 6 NaNs ( 0.02 % out of 31828)
3:52:47.874516 INFO: Collecting fragment features
3:52:47.901355 INFO: Finished candidate scoring
3:52:47.917080 PROGRESS: === Extracted 31828 precursors and 310966 fragments ===
3:52:47.917543 INFO: performing precursor FDR with 47 features
3:52:47.917584 INFO: Decoy channel: -1
3:52:47.917610 INFO: Competetive: True
3:52:47.927031 INFO: Setting torch num_threads to 2 for FDR classification task
3:52:47.932422 WARNING: dropped 6 decoy PSMs due to missing features
3:52:48.384687 INFO: Test AUC: 0.784
3:52:48.384813 INFO: Train AUC: 0.801
3:52:48.384843 INFO: AUC difference: 2.13%
3:52:48.470445 INFO: Resetting torch num_threads to 100
3:52:48.471642 INFO: === FDR correction performed with classifier version 4 ===
3:52:48.473038 PROGRESS: ============================= Precursor FDR =============================
3:52:48.473137 PROGRESS: Total precursors accumulated: 7,137
3:52:48.473196 PROGRESS: Target precursors: 7,011 (98.23%)
3:52:48.473246 PROGRESS: Decoy precursors: 126 (1.77%)
3:52:48.473290 PROGRESS: 
3:52:48.473343 PROGRESS: Precursor Summary:
3:52:48.476068 PROGRESS: Channel   0:	 0.05 FDR: 7,011; 0.01 FDR: 6,889; 0.001 FDR: 5,863
3:52:48.476198 PROGRESS: 
3:52:48.476257 PROGRESS: Protein Summary:
3:52:48.480189 PROGRESS: Channel   0:	 0.05 FDR: 3,465; 0.01 FDR: 3,433; 0.001 FDR: 3,114
3:52:48.480288 PROGRESS: =========================================================================
3:52:48.504084 INFO: fragments_df_filtered: 5000
3:52:48.515351 INFO: calibration group: precursor, fitting mz estimator 
3:52:49.177986 INFO: calibration group: precursor, fitting rt estimator 
3:52:49.879551 INFO: calibration group: fragment, fitting mz estimator 
3:52:50.235687 INFO: calibration group: precursor, predicting mz
3:52:50.239123 INFO: calibration group: precursor, predicting rt
3:52:50.248787 INFO: calibration group: fragment, predicting mz
3:52:50.271648 INFO: === checking if optimization conditions were reached ===
3:52:50.271986 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3:52:50.278442 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 65.2057.
3:52:50.278510 INFO: ==============================================
3:52:50.278625 INFO: Starting optimization step 2.
3:52:50.278703 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:52:50.278775 PROGRESS: Extracting batch of 15933 precursors
3:52:50.285732 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:52:50.285802 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:52:50.285841 INFO: FWHM in RT is 2.67 seconds, sigma is 0.34
3:52:50.285873 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:52:50.286096 INFO: Starting candidate selection
3:52:50.874557 INFO: Starting candidate scoring
3:52:51.111820 INFO: Finished candidate processing
3:52:51.111962 INFO: Collecting candidate features
3:52:51.160476 WARNING: intensity_correlation has 5 NaNs ( 0.02 % out of 31760)
3:52:51.164874 INFO: Collecting fragment features
3:52:51.189855 INFO: Finished candidate scoring
3:52:51.203676 PROGRESS: === Extracted 31760 precursors and 299268 fragments ===
3:52:51.204639 INFO: performing precursor FDR with 47 features
3:52:51.204679 INFO: Decoy channel: -1
3:52:51.204704 INFO: Competetive: True
3:52:51.215860 INFO: Setting torch num_threads to 2 for FDR classification task
3:52:51.220593 WARNING: dropped 5 decoy PSMs due to missing features
3:52:51.859422 INFO: Test AUC: 0.820
3:52:51.860525 INFO: Train AUC: 0.826
3:52:51.860569 INFO: AUC difference: 0.71%
3:52:51.950847 INFO: Resetting torch num_threads to 100
3:52:51.952481 INFO: === FDR correction performed with classifier version 4 ===
3:52:51.954092 PROGRESS: ============================= Precursor FDR =============================
3:52:51.954188 PROGRESS: Total precursors accumulated: 7,371
3:52:51.954246 PROGRESS: Target precursors: 7,287 (98.86%)
3:52:51.954296 PROGRESS: Decoy precursors: 84 (1.14%)
3:52:51.954341 PROGRESS: 
3:52:51.954388 PROGRESS: Precursor Summary:
3:52:51.957798 PROGRESS: Channel   0:	 0.05 FDR: 7,287; 0.01 FDR: 7,268; 0.001 FDR: 6,462
3:52:51.957919 PROGRESS: 
3:52:51.957975 PROGRESS: Protein Summary:
3:52:51.962247 PROGRESS: Channel   0:	 0.05 FDR: 3,538; 0.01 FDR: 3,535; 0.001 FDR: 3,295
3:52:51.962366 PROGRESS: =========================================================================
3:52:51.988892 INFO: fragments_df_filtered: 5000
3:52:52.011060 INFO: calibration group: precursor, fitting mz estimator 
3:52:52.775595 INFO: calibration group: precursor, fitting rt estimator 
3:52:53.620644 INFO: calibration group: fragment, fitting mz estimator 
3:52:54.036907 INFO: calibration group: precursor, predicting mz
3:52:54.040031 INFO: calibration group: precursor, predicting rt
3:52:54.049052 INFO: calibration group: fragment, predicting mz
3:52:54.075426 INFO: === checking if optimization conditions were reached ===
3:52:54.075799 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3:52:54.082727 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 26.0091.
3:52:54.082797 INFO: ==============================================
3:52:54.082925 INFO: Starting optimization step 3.
3:52:54.083005 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:52:54.083092 PROGRESS: Extracting batch of 15933 precursors
3:52:54.091226 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:52:54.091307 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:52:54.091359 INFO: FWHM in RT is 2.67 seconds, sigma is 0.34
3:52:54.091388 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:52:54.091688 INFO: Starting candidate selection
3:52:54.649342 INFO: Starting candidate scoring
3:52:54.886722 INFO: Finished candidate processing
3:52:54.886882 INFO: Collecting candidate features
3:52:54.949708 WARNING: intensity_correlation has 11 NaNs ( 0.04 % out of 30862)
3:52:54.960078 INFO: Collecting fragment features
3:52:54.983565 INFO: Finished candidate scoring
3:52:54.997335 PROGRESS: === Extracted 30862 precursors and 280705 fragments ===
3:52:54.997748 INFO: performing precursor FDR with 47 features
3:52:54.997787 INFO: Decoy channel: -1
3:52:54.997814 INFO: Competetive: True
3:52:55.009133 INFO: Setting torch num_threads to 2 for FDR classification task
3:52:55.014608 WARNING: dropped 3 target PSMs due to missing features
3:52:55.014715 WARNING: dropped 8 decoy PSMs due to missing features
3:52:55.520149 INFO: Test AUC: 0.836
3:52:55.520298 INFO: Train AUC: 0.838
3:52:55.520328 INFO: AUC difference: 0.25%
3:52:55.606508 INFO: Resetting torch num_threads to 100
3:52:55.608003 INFO: === FDR correction performed with classifier version 4 ===
3:52:55.609715 PROGRESS: ============================= Precursor FDR =============================
3:52:55.609809 PROGRESS: Total precursors accumulated: 7,506
3:52:55.609866 PROGRESS: Target precursors: 7,428 (98.96%)
3:52:55.609915 PROGRESS: Decoy precursors: 78 (1.04%)
3:52:55.609960 PROGRESS: 
3:52:55.610002 PROGRESS: Precursor Summary:
3:52:55.612939 PROGRESS: Channel   0:	 0.05 FDR: 7,428; 0.01 FDR: 7,394; 0.001 FDR: 6,601
3:52:55.613049 PROGRESS: 
3:52:55.613105 PROGRESS: Protein Summary:
3:52:55.617353 PROGRESS: Channel   0:	 0.05 FDR: 3,574; 0.01 FDR: 3,565; 0.001 FDR: 3,342
3:52:55.617454 PROGRESS: =========================================================================
3:52:55.644013 INFO: fragments_df_filtered: 5000
3:52:55.657336 INFO: calibration group: precursor, fitting mz estimator 
3:52:56.441788 INFO: calibration group: precursor, fitting rt estimator 
3:52:57.248380 INFO: calibration group: fragment, fitting mz estimator 
3:52:57.698064 INFO: calibration group: precursor, predicting mz
3:52:57.701244 INFO: calibration group: precursor, predicting rt
3:52:57.710167 INFO: calibration group: fragment, predicting mz
3:52:57.729580 INFO: === checking if optimization conditions were reached ===
3:52:57.729777 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3:52:57.736323 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 14.3104.
3:52:57.736395 INFO: ==============================================
3:52:57.736511 INFO: Starting optimization step 4.
3:52:57.736590 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:52:57.736659 PROGRESS: Extracting batch of 15933 precursors
3:52:57.742960 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:52:57.743025 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:52:57.743062 INFO: FWHM in RT is 2.65 seconds, sigma is 0.34
3:52:57.743091 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:52:57.743328 INFO: Starting candidate selection
3:52:58.301834 INFO: Starting candidate scoring
3:52:58.552280 INFO: Finished candidate processing
3:52:58.552389 INFO: Collecting candidate features
3:52:58.600672 WARNING: intensity_correlation has 12 NaNs ( 0.04 % out of 30984)
3:52:58.608152 INFO: Collecting fragment features
3:52:58.630836 INFO: Finished candidate scoring
3:52:58.646067 PROGRESS: === Extracted 30984 precursors and 285117 fragments ===
3:52:58.646439 INFO: performing precursor FDR with 47 features
3:52:58.646477 INFO: Decoy channel: -1
3:52:58.646505 INFO: Competetive: True
3:52:58.654392 INFO: Setting torch num_threads to 2 for FDR classification task
3:52:58.658305 WARNING: dropped 12 decoy PSMs due to missing features
3:52:59.070048 INFO: Test AUC: 0.859
3:52:59.070179 INFO: Train AUC: 0.865
3:52:59.070209 INFO: AUC difference: 0.75%
3:52:59.156501 INFO: Resetting torch num_threads to 100
3:52:59.157770 INFO: === FDR correction performed with classifier version 4 ===
3:52:59.159132 PROGRESS: ============================= Precursor FDR =============================
3:52:59.159227 PROGRESS: Total precursors accumulated: 7,426
3:52:59.159287 PROGRESS: Target precursors: 7,350 (98.98%)
3:52:59.159339 PROGRESS: Decoy precursors: 76 (1.02%)
3:52:59.159386 PROGRESS: 
3:52:59.159431 PROGRESS: Precursor Summary:
3:52:59.162212 PROGRESS: Channel   0:	 0.05 FDR: 7,350; 0.01 FDR: 7,348; 0.001 FDR: 6,405
3:52:59.162334 PROGRESS: 
3:52:59.162394 PROGRESS: Protein Summary:
3:52:59.166540 PROGRESS: Channel   0:	 0.05 FDR: 3,559; 0.01 FDR: 3,558; 0.001 FDR: 3,296
3:52:59.166645 PROGRESS: =========================================================================
3:52:59.192863 INFO: fragments_df_filtered: 5000
3:52:59.206144 INFO: calibration group: precursor, fitting mz estimator 
3:52:59.917578 INFO: calibration group: precursor, fitting rt estimator 
3:53:00.661912 INFO: calibration group: fragment, fitting mz estimator 
3:53:03.478375 INFO: calibration group: precursor, predicting mz
3:53:03.482088 INFO: calibration group: precursor, predicting rt
3:53:03.493207 INFO: calibration group: fragment, predicting mz
3:53:03.539210 INFO: === checking if optimization conditions were reached ===
3:53:03.539524 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3:53:03.569803 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 17.2254.
3:53:03.569901 INFO: ==============================================
3:53:03.570033 INFO: Starting optimization step 5.
3:53:03.570109 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:53:03.570179 PROGRESS: Extracting batch of 15933 precursors
3:53:03.579098 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:53:03.579173 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:53:03.579216 INFO: FWHM in RT is 2.66 seconds, sigma is 0.34
3:53:03.579244 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:53:03.579534 INFO: Starting candidate selection
3:53:04.175025 INFO: Starting candidate scoring
3:53:04.426944 INFO: Finished candidate processing
3:53:04.427077 INFO: Collecting candidate features
3:53:04.494108 WARNING: intensity_correlation has 12 NaNs ( 0.04 % out of 30976)
3:53:04.498788 INFO: Collecting fragment features
3:53:04.527459 INFO: Finished candidate scoring
3:53:04.548480 PROGRESS: === Extracted 30976 precursors and 284395 fragments ===
3:53:04.548913 INFO: performing precursor FDR with 47 features
3:53:04.548956 INFO: Decoy channel: -1
3:53:04.548980 INFO: Competetive: True
3:53:04.564278 INFO: Setting torch num_threads to 2 for FDR classification task
3:53:04.572219 WARNING: dropped 3 target PSMs due to missing features
3:53:04.572362 WARNING: dropped 9 decoy PSMs due to missing features
3:53:05.070196 INFO: Test AUC: 0.858
3:53:05.070350 INFO: Train AUC: 0.864
3:53:05.070387 INFO: AUC difference: 0.74%
3:53:05.156464 INFO: Resetting torch num_threads to 100
3:53:05.158479 INFO: === FDR correction performed with classifier version 4 ===
3:53:05.161320 PROGRESS: ============================= Precursor FDR =============================
3:53:05.161539 PROGRESS: Total precursors accumulated: 7,451
3:53:05.161603 PROGRESS: Target precursors: 7,380 (99.05%)
3:53:05.161653 PROGRESS: Decoy precursors: 71 (0.95%)
3:53:05.161701 PROGRESS: 
3:53:05.161746 PROGRESS: Precursor Summary:
3:53:05.166199 PROGRESS: Channel   0:	 0.05 FDR: 7,380; 0.01 FDR: 7,380; 0.001 FDR: 6,467
3:53:05.166546 PROGRESS: 
3:53:05.166609 PROGRESS: Protein Summary:
3:53:05.172536 PROGRESS: Channel   0:	 0.05 FDR: 3,561; 0.01 FDR: 3,561; 0.001 FDR: 3,314
3:53:05.172814 PROGRESS: =========================================================================
3:53:05.209518 INFO: fragments_df_filtered: 5000
3:53:05.243088 INFO: calibration group: precursor, fitting mz estimator 
3:53:06.037220 INFO: calibration group: precursor, fitting rt estimator 
3:53:06.839328 INFO: calibration group: fragment, fitting mz estimator 
3:53:07.257685 INFO: calibration group: precursor, predicting mz
3:53:07.260870 INFO: calibration group: precursor, predicting rt
3:53:07.269827 INFO: calibration group: fragment, predicting mz
3:53:07.290268 INFO: === checking if optimization conditions were reached ===
3:53:07.290476 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3:53:07.296801 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 17.3743.
3:53:07.296870 INFO: ==============================================
3:53:07.296987 INFO: Starting optimization step 6.
3:53:07.297061 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:53:07.297129 PROGRESS: Extracting batch of 15933 precursors
3:53:07.303538 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:53:07.303605 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:53:07.303651 INFO: FWHM in RT is 2.66 seconds, sigma is 0.34
3:53:07.303679 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:53:07.303908 INFO: Starting candidate selection
3:53:07.859615 INFO: Starting candidate scoring
3:53:08.046826 INFO: Finished candidate processing
3:53:08.046998 INFO: Collecting candidate features
3:53:08.089112 WARNING: intensity_correlation has 13 NaNs ( 0.04 % out of 30946)
3:53:08.093534 INFO: Collecting fragment features
3:53:08.112068 INFO: Finished candidate scoring
3:53:08.127252 PROGRESS: === Extracted 30946 precursors and 284129 fragments ===
3:53:08.127641 INFO: performing precursor FDR with 47 features
3:53:08.127681 INFO: Decoy channel: -1
3:53:08.127704 INFO: Competetive: True
3:53:08.135578 INFO: Setting torch num_threads to 2 for FDR classification task
3:53:08.140711 WARNING: dropped 5 target PSMs due to missing features
3:53:08.140794 WARNING: dropped 8 decoy PSMs due to missing features
3:53:08.558807 INFO: Test AUC: 0.861
3:53:08.558936 INFO: Train AUC: 0.864
3:53:08.558965 INFO: AUC difference: 0.33%
3:53:08.641435 INFO: Resetting torch num_threads to 100
3:53:08.642707 INFO: === FDR correction performed with classifier version 4 ===
3:53:08.644138 PROGRESS: ============================= Precursor FDR =============================
3:53:08.644239 PROGRESS: Total precursors accumulated: 7,460
3:53:08.644299 PROGRESS: Target precursors: 7,384 (98.98%)
3:53:08.644351 PROGRESS: Decoy precursors: 76 (1.02%)
3:53:08.644397 PROGRESS: 
3:53:08.644440 PROGRESS: Precursor Summary:
3:53:08.647414 PROGRESS: Channel   0:	 0.05 FDR: 7,384; 0.01 FDR: 7,384; 0.001 FDR: 6,451
3:53:08.647536 PROGRESS: 
3:53:08.647593 PROGRESS: Protein Summary:
3:53:08.652169 PROGRESS: Channel   0:	 0.05 FDR: 3,561; 0.01 FDR: 3,561; 0.001 FDR: 3,312
3:53:08.652285 PROGRESS: =========================================================================
3:53:08.676310 INFO: fragments_df_filtered: 5000
3:53:08.688025 INFO: calibration group: precursor, fitting mz estimator 
3:53:09.471767 INFO: calibration group: precursor, fitting rt estimator 
3:53:10.279701 INFO: calibration group: fragment, fitting mz estimator 
3:53:10.703255 INFO: calibration group: precursor, predicting mz
3:53:10.706219 INFO: calibration group: precursor, predicting rt
3:53:10.715184 INFO: calibration group: fragment, predicting mz
3:53:10.735135 INFO: === checking if optimization conditions were reached ===
3:53:10.735305 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
3:53:10.736367 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 14.3104 found after 7 searches.
3:53:10.736420 INFO: ==============================================
3:53:10.736509 PROGRESS: Optimization finished for rt_error.
3:53:10.748588 INFO: calibration group: precursor, predicting mz
3:53:10.751346 INFO: calibration group: precursor, predicting rt
3:53:10.760054 INFO: calibration group: fragment, predicting mz
3:53:10.807203 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:53:10.807376 PROGRESS: ==============================================
3:53:10.807445 PROGRESS: ms2_error      : 15.0000
3:53:10.807501 PROGRESS: ms1_error      : 10.0000
3:53:10.807550 PROGRESS: rt_error       : 14.3104
3:53:10.807593 PROGRESS: ==============================================
3:53:10.808625 INFO: calibration group: precursor, predicting mz
3:53:10.816864 INFO: calibration group: precursor, predicting rt
3:53:10.850079 INFO: calibration group: fragment, predicting mz
3:53:10.941721 PROGRESS: Extracting batch of 65173 precursors
3:53:10.956428 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:53:10.956563 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:53:10.956599 INFO: FWHM in RT is 2.66 seconds, sigma is 0.34
3:53:10.956623 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:53:10.956868 INFO: Starting candidate selection
3:53:12.912607 INFO: Applying score cutoff of 26.421156621932983
3:53:12.915965 INFO: Removed 10926 precursors with score below cutoff
3:53:12.947667 INFO: Starting candidate scoring
3:53:13.781632 INFO: Finished candidate processing
3:53:13.781773 INFO: Collecting candidate features
3:53:13.964002 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 116431)
3:53:13.980808 INFO: Collecting fragment features
3:53:14.071421 INFO: Finished candidate scoring
3:53:14.139579 INFO: === FDR correction performed with classifier version 9 ===
3:53:14.140849 INFO: performing precursor FDR with 47 features
3:53:14.140893 INFO: Decoy channel: -1
3:53:14.140921 INFO: Competetive: True
3:53:14.198096 INFO: Setting torch num_threads to 2 for FDR classification task
3:53:14.228306 WARNING: dropped 4 decoy PSMs due to missing features
3:53:14.228500 WARNING: FDR calculation for 61450 target and 54977 decoy PSMs
3:53:14.228533 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
3:53:16.865516 INFO: Test AUC: 0.891
3:53:16.865897 INFO: Train AUC: 0.894
3:53:16.865937 INFO: AUC difference: 0.37%
3:53:16.968117 INFO: Resetting torch num_threads to 100
3:53:16.974157 INFO: Removing fragments below FDR threshold
3:53:17.006513 PROGRESS: ============================= Precursor FDR =============================
3:53:17.006999 PROGRESS: Total precursors accumulated: 30,707
3:53:17.007071 PROGRESS: Target precursors: 30,433 (99.11%)
3:53:17.007126 PROGRESS: Decoy precursors: 274 (0.89%)
3:53:17.007174 PROGRESS: 
3:53:17.007218 PROGRESS: Precursor Summary:
3:53:17.019865 PROGRESS: Channel   0:	 0.05 FDR: 30,433; 0.01 FDR: 30,433; 0.001 FDR: 28,442
3:53:17.020166 PROGRESS: 
3:53:17.020228 PROGRESS: Protein Summary:
3:53:17.037184 PROGRESS: Channel   0:	 0.05 FDR: 5,884; 0.01 FDR: 5,884; 0.001 FDR: 5,869
3:53:17.037482 PROGRESS: =========================================================================
3:53:17.374619 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:53:17.398262 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:53:17.398432 INFO: Quantification results path: run_output_Astral/alphadia_1.10_default/quant
3:53:17.398516 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3 at run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:53:17.399701 INFO: Initializing RawFileManager
3:53:46.938763 INFO: Determining DIA cycle
3:53:46.955153 INFO: Found cycle with start 0.00 min and length 303.
3:53:47.129013 INFO: RT (min)            : 0.0 - 26.9
3:53:47.129131 INFO: RT duration (sec)   : 1611.2
3:53:47.129163 INFO: RT duration (min)   : 26.9
3:53:47.129187 INFO: Cycle len (scans)   : 303
3:53:47.129206 INFO: Cycle len (sec)     : 1.65
3:53:47.129225 INFO: Number of cycles    : 978
3:53:47.129242 INFO: MS2 range (m/z)     : 380.4 - 980.7
3:53:47.148379 INFO: Initializing CalibrationManager
3:53:47.148662 INFO: Loading calibration config
3:53:47.149203 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'}]
3:53:47.149300 INFO: Calibration group :fragment, found 1 estimator(s)
3:53:47.149408 INFO: Calibration group :precursor, found 3 estimator(s)
3:53:47.149506 INFO: Disabling ion mobility calibration
3:53:47.149534 INFO: removed mobility estimator from group precursor
3:53:47.149663 INFO: Initializing OptimizationManager
3:53:47.149773 INFO: initial parameter: ms1_error = 30
3:53:47.149831 INFO: initial parameter: ms2_error = 30
3:53:47.149877 INFO: initial parameter: rt_error = 805.611083984375
3:53:47.149920 INFO: initial parameter: mobility_error = 0.1
3:53:47.149965 INFO: initial parameter: column_type = library
3:53:47.150003 INFO: initial parameter: num_candidates = 1
3:53:47.150044 INFO: initial parameter: classifier_version = -1
3:53:47.150082 INFO: initial parameter: fwhm_rt = 5
3:53:47.150122 INFO: initial parameter: fwhm_mobility = 0.01
3:53:47.150162 INFO: initial parameter: score_cutoff = 0
3:53:47.150221 INFO: Initializing TimingManager
3:53:47.150271 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:53:47.150347 INFO: FDRManager not loaded from disk.
3:53:47.150369 INFO: Initializing FDRManager
3:53:47.150407 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
3:53:47.166783 PROGRESS: 32,718 target precursors potentially observable (0 removed)
3:53:47.183327 PROGRESS: Starting initial search for precursors.
3:53:47.200033 INFO: Starting optimization step 0.
3:53:47.200314 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:53:47.200406 PROGRESS: Extracting batch of 15933 precursors
3:53:47.204398 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:53:47.204454 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:53:47.204506 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:53:47.204533 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:53:47.204942 INFO: Starting candidate selection
3:53:48.178113 INFO: Starting candidate scoring
3:53:48.290739 INFO: Finished candidate processing
3:53:48.290859 INFO: Collecting candidate features
3:53:48.323484 INFO: Collecting fragment features
3:53:48.339251 INFO: Finished candidate scoring
3:53:48.349501 PROGRESS: === Extracted 15933 precursors and 173278 fragments ===
3:53:48.349904 INFO: performing precursor FDR with 47 features
3:53:48.349943 INFO: Decoy channel: -1
3:53:48.349967 INFO: Competetive: True
3:53:48.355175 INFO: Setting torch num_threads to 2 for FDR classification task
3:53:48.549098 INFO: Test AUC: 0.738
3:53:48.549229 INFO: Train AUC: 0.738
3:53:48.549260 INFO: AUC difference: 0.07%
3:53:48.636144 INFO: Resetting torch num_threads to 100
3:53:48.637302 INFO: === FDR correction performed with classifier version -1 ===
3:53:48.638449 PROGRESS: ============================= Precursor FDR =============================
3:53:48.638546 PROGRESS: Total precursors accumulated: 3,390
3:53:48.638605 PROGRESS: Target precursors: 3,195 (94.25%)
3:53:48.638657 PROGRESS: Decoy precursors: 195 (5.75%)
3:53:48.638705 PROGRESS: 
3:53:48.638752 PROGRESS: Precursor Summary:
3:53:48.640592 PROGRESS: Channel   0:	 0.05 FDR: 3,080; 0.01 FDR: 2,405; 0.001 FDR: 1,469
3:53:48.640699 PROGRESS: 
3:53:48.640755 PROGRESS: Protein Summary:
3:53:48.642998 PROGRESS: Channel   0:	 0.05 FDR: 1,969; 0.01 FDR: 1,614; 0.001 FDR: 1,082
3:53:48.643100 PROGRESS: =========================================================================
3:53:48.649899 INFO: fragments_df_filtered: 5000
3:53:48.664257 INFO: calibration group: precursor, fitting mz estimator 
3:53:48.829790 INFO: calibration group: precursor, fitting rt estimator 
3:53:48.999335 INFO: calibration group: fragment, fitting mz estimator 
3:53:49.414752 INFO: calibration group: precursor, predicting mz
3:53:49.417844 INFO: calibration group: precursor, predicting rt
3:53:49.426885 INFO: calibration group: fragment, predicting mz
3:53:49.451516 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3:53:49.451867 INFO: Starting optimization step 1.
3:53:49.451945 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:53:49.452833 PROGRESS: Extracting batch of 15933 precursors
3:53:49.458411 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:53:49.458469 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:53:49.458501 INFO: FWHM in RT is 2.94 seconds, sigma is 0.38
3:53:49.458523 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:53:49.458726 INFO: Starting candidate selection
3:53:50.380572 INFO: Starting candidate scoring
3:53:50.568960 INFO: Finished candidate processing
3:53:50.569086 INFO: Collecting candidate features
3:53:50.626120 INFO: Collecting fragment features
3:53:50.653008 INFO: Finished candidate scoring
3:53:50.668420 PROGRESS: === Extracted 31866 precursors and 343674 fragments ===
3:53:50.668880 INFO: performing precursor FDR with 47 features
3:53:50.668919 INFO: Decoy channel: -1
3:53:50.668944 INFO: Competetive: True
3:53:50.682262 INFO: Setting torch num_threads to 2 for FDR classification task
3:53:51.203503 INFO: Test AUC: 0.707
3:53:51.203670 INFO: Train AUC: 0.717
3:53:51.203702 INFO: AUC difference: 1.42%
3:53:51.297683 INFO: Resetting torch num_threads to 100
3:53:51.299824 INFO: === FDR correction performed with classifier version 0 ===
3:53:51.301390 PROGRESS: ============================= Precursor FDR =============================
3:53:51.301497 PROGRESS: Total precursors accumulated: 5,103
3:53:51.301556 PROGRESS: Target precursors: 4,867 (95.38%)
3:53:51.301606 PROGRESS: Decoy precursors: 236 (4.62%)
3:53:51.301653 PROGRESS: 
3:53:51.301697 PROGRESS: Precursor Summary:
3:53:51.304003 PROGRESS: Channel   0:	 0.05 FDR: 4,867; 0.01 FDR: 4,019; 0.001 FDR: 1,084
3:53:51.304111 PROGRESS: 
3:53:51.304167 PROGRESS: Protein Summary:
3:53:51.306847 PROGRESS: Channel   0:	 0.05 FDR: 2,720; 0.01 FDR: 2,370; 0.001 FDR:   781
3:53:51.306954 PROGRESS: =========================================================================
3:53:51.323216 INFO: fragments_df_filtered: 5000
3:53:51.340300 INFO: calibration group: precursor, fitting mz estimator 
3:53:51.647056 INFO: calibration group: precursor, fitting rt estimator 
3:53:51.966053 INFO: calibration group: fragment, fitting mz estimator 
3:53:52.347143 INFO: calibration group: precursor, predicting mz
3:53:52.350289 INFO: calibration group: precursor, predicting rt
3:53:52.359059 INFO: calibration group: fragment, predicting mz
3:53:52.385578 INFO: === checking if optimization conditions were reached ===
3:53:52.388592 PROGRESS: ❌ ms2_error      : 19.7514 > 15.0000 or insufficient steps taken.
3:53:52.390385 PROGRESS: ❌ ms1_error      : 13.9059 > 10.0000 or insufficient steps taken.
3:53:52.390443 INFO: ==============================================
3:53:52.390567 INFO: Starting optimization step 2.
3:53:52.390645 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:53:52.390728 PROGRESS: Extracting batch of 15933 precursors
3:53:52.397364 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:53:52.397431 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:53:52.397475 INFO: FWHM in RT is 2.94 seconds, sigma is 0.38
3:53:52.397503 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:53:52.397802 INFO: Starting candidate selection
3:53:53.365145 INFO: Starting candidate scoring
3:53:53.549817 INFO: Finished candidate processing
3:53:53.549936 INFO: Collecting candidate features
3:53:53.600374 INFO: Collecting fragment features
3:53:53.625814 INFO: Finished candidate scoring
3:53:53.639935 PROGRESS: === Extracted 31866 precursors and 331239 fragments ===
3:53:53.640348 INFO: performing precursor FDR with 47 features
3:53:53.640388 INFO: Decoy channel: -1
3:53:53.640413 INFO: Competetive: True
3:53:53.649690 INFO: Setting torch num_threads to 2 for FDR classification task
3:53:54.143803 INFO: Test AUC: 0.736
3:53:54.143941 INFO: Train AUC: 0.749
3:53:54.143971 INFO: AUC difference: 1.73%
3:53:54.231783 INFO: Resetting torch num_threads to 100
3:53:54.233198 INFO: === FDR correction performed with classifier version 1 ===
3:53:54.234642 PROGRESS: ============================= Precursor FDR =============================
3:53:54.234749 PROGRESS: Total precursors accumulated: 6,165
3:53:54.234809 PROGRESS: Target precursors: 5,973 (96.89%)
3:53:54.234860 PROGRESS: Decoy precursors: 192 (3.11%)
3:53:54.234907 PROGRESS: 
3:53:54.234950 PROGRESS: Precursor Summary:
3:53:54.237645 PROGRESS: Channel   0:	 0.05 FDR: 5,973; 0.01 FDR: 5,532; 0.001 FDR: 4,438
3:53:54.237773 PROGRESS: 
3:53:54.237830 PROGRESS: Protein Summary:
3:53:54.241340 PROGRESS: Channel   0:	 0.05 FDR: 3,118; 0.01 FDR: 2,947; 0.001 FDR: 2,529
3:53:54.241447 PROGRESS: =========================================================================
3:53:54.260939 INFO: fragments_df_filtered: 5000
3:53:54.272819 INFO: calibration group: precursor, fitting mz estimator 
3:53:54.724090 INFO: calibration group: precursor, fitting rt estimator 
3:53:55.227372 INFO: calibration group: fragment, fitting mz estimator 
3:53:55.650574 INFO: calibration group: precursor, predicting mz
3:53:55.653561 INFO: calibration group: precursor, predicting rt
3:53:55.662267 INFO: calibration group: fragment, predicting mz
3:53:55.683120 INFO: === checking if optimization conditions were reached ===
3:53:55.684968 PROGRESS: ❌ ms2_error      : 15.5132 > 15.0000 or insufficient steps taken.
3:53:55.686619 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
3:53:55.686670 INFO: ==============================================
3:53:55.686780 INFO: Starting optimization step 3.
3:53:55.686848 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:53:55.686907 PROGRESS: Extracting batch of 15933 precursors
3:53:55.690981 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:53:55.691039 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:53:55.691074 INFO: FWHM in RT is 2.80 seconds, sigma is 0.36
3:53:55.691096 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:53:55.691282 INFO: Starting candidate selection
3:53:56.608439 INFO: Starting candidate scoring
3:53:56.844734 INFO: Finished candidate processing
3:53:56.844876 INFO: Collecting candidate features
3:53:56.902817 INFO: Collecting fragment features
3:53:56.928801 INFO: Finished candidate scoring
3:53:56.943637 PROGRESS: === Extracted 31866 precursors and 322287 fragments ===
3:53:56.944046 INFO: performing precursor FDR with 47 features
3:53:56.944087 INFO: Decoy channel: -1
3:53:56.944115 INFO: Competetive: True
3:53:56.952288 INFO: Setting torch num_threads to 2 for FDR classification task
3:53:57.456355 INFO: Test AUC: 0.758
3:53:57.456493 INFO: Train AUC: 0.769
3:53:57.456844 INFO: AUC difference: 1.54%
3:53:57.541919 INFO: Resetting torch num_threads to 100
3:53:57.543282 INFO: === FDR correction performed with classifier version 2 ===
3:53:57.544689 PROGRESS: ============================= Precursor FDR =============================
3:53:57.544789 PROGRESS: Total precursors accumulated: 6,646
3:53:57.544846 PROGRESS: Target precursors: 6,461 (97.22%)
3:53:57.544898 PROGRESS: Decoy precursors: 185 (2.78%)
3:53:57.544946 PROGRESS: 
3:53:57.544990 PROGRESS: Precursor Summary:
3:53:57.547625 PROGRESS: Channel   0:	 0.05 FDR: 6,461; 0.01 FDR: 6,158; 0.001 FDR: 5,374
3:53:57.547750 PROGRESS: 
3:53:57.547810 PROGRESS: Protein Summary:
3:53:57.551587 PROGRESS: Channel   0:	 0.05 FDR: 3,274; 0.01 FDR: 3,169; 0.001 FDR: 2,896
3:53:57.551708 PROGRESS: =========================================================================
3:53:57.573351 INFO: fragments_df_filtered: 5000
3:53:57.585229 INFO: calibration group: precursor, fitting mz estimator 
3:53:58.166319 INFO: calibration group: precursor, fitting rt estimator 
3:53:58.749656 INFO: calibration group: fragment, fitting mz estimator 
3:53:59.101725 INFO: calibration group: precursor, predicting mz
3:53:59.104715 INFO: calibration group: precursor, predicting rt
3:53:59.113539 INFO: calibration group: fragment, predicting mz
3:53:59.135579 INFO: === checking if optimization conditions were reached ===
3:53:59.137418 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
3:53:59.137477 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
3:53:59.137504 INFO: ==============================================
3:53:59.137606 PROGRESS: Optimization finished for ms2_error, ms1_error.
3:53:59.149323 INFO: calibration group: precursor, predicting mz
3:53:59.152178 INFO: calibration group: precursor, predicting rt
3:53:59.161238 INFO: calibration group: fragment, predicting mz
3:53:59.182348 INFO: Starting optimization step 0.
3:53:59.182506 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:53:59.182575 PROGRESS: Extracting batch of 15933 precursors
3:53:59.186625 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:53:59.186696 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:53:59.186729 INFO: FWHM in RT is 2.71 seconds, sigma is 0.35
3:53:59.186752 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:53:59.186966 INFO: Starting candidate selection
3:54:00.106266 INFO: Starting candidate scoring
3:54:00.343652 INFO: Finished candidate processing
3:54:00.343772 INFO: Collecting candidate features
3:54:00.393194 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 31866)
3:54:00.398430 INFO: Collecting fragment features
3:54:00.421866 INFO: Finished candidate scoring
3:54:00.440384 PROGRESS: === Extracted 31866 precursors and 322290 fragments ===
3:54:00.440781 INFO: performing precursor FDR with 47 features
3:54:00.440821 INFO: Decoy channel: -1
3:54:00.440844 INFO: Competetive: True
3:54:00.450167 INFO: Setting torch num_threads to 2 for FDR classification task
3:54:00.454942 WARNING: dropped 1 decoy PSMs due to missing features
3:54:01.127725 INFO: Test AUC: 0.766
3:54:01.127903 INFO: Train AUC: 0.777
3:54:01.127947 INFO: AUC difference: 1.46%
3:54:01.220388 INFO: Resetting torch num_threads to 100
3:54:01.221842 INFO: === FDR correction performed with classifier version 3 ===
3:54:01.223221 PROGRESS: ============================= Precursor FDR =============================
3:54:01.223325 PROGRESS: Total precursors accumulated: 6,734
3:54:01.223385 PROGRESS: Target precursors: 6,558 (97.39%)
3:54:01.223435 PROGRESS: Decoy precursors: 176 (2.61%)
3:54:01.223480 PROGRESS: 
3:54:01.223523 PROGRESS: Precursor Summary:
3:54:01.226228 PROGRESS: Channel   0:	 0.05 FDR: 6,558; 0.01 FDR: 6,255; 0.001 FDR: 5,411
3:54:01.226345 PROGRESS: 
3:54:01.226403 PROGRESS: Protein Summary:
3:54:01.230216 PROGRESS: Channel   0:	 0.05 FDR: 3,308; 0.01 FDR: 3,211; 0.001 FDR: 2,912
3:54:01.230326 PROGRESS: =========================================================================
3:54:01.253236 INFO: fragments_df_filtered: 5000
3:54:01.265083 INFO: calibration group: precursor, fitting mz estimator 
3:54:01.799238 INFO: calibration group: precursor, fitting rt estimator 
3:54:02.351916 INFO: calibration group: fragment, fitting mz estimator 
3:54:02.703366 INFO: calibration group: precursor, predicting mz
3:54:02.707452 INFO: calibration group: precursor, predicting rt
3:54:02.717918 INFO: calibration group: fragment, predicting mz
3:54:02.740935 INFO: === checking if optimization conditions were reached ===
3:54:02.741163 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3:54:02.746876 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 50.3361.
3:54:02.746944 INFO: ==============================================
3:54:02.747059 INFO: Starting optimization step 1.
3:54:02.747135 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:54:02.747205 PROGRESS: Extracting batch of 15933 precursors
3:54:02.753467 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:54:02.753540 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:54:02.753579 INFO: FWHM in RT is 2.70 seconds, sigma is 0.35
3:54:02.753607 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:54:02.753832 INFO: Starting candidate selection
3:54:03.383142 INFO: Starting candidate scoring
3:54:03.636003 INFO: Finished candidate processing
3:54:03.636119 INFO: Collecting candidate features
3:54:03.696387 WARNING: intensity_correlation has 10 NaNs ( 0.03 % out of 31730)
3:54:03.701170 INFO: Collecting fragment features
3:54:03.736997 INFO: Finished candidate scoring
3:54:03.753054 PROGRESS: === Extracted 31730 precursors and 297665 fragments ===
3:54:03.753590 INFO: performing precursor FDR with 47 features
3:54:03.753632 INFO: Decoy channel: -1
3:54:03.753656 INFO: Competetive: True
3:54:03.771573 INFO: Setting torch num_threads to 2 for FDR classification task
3:54:03.781168 WARNING: dropped 2 target PSMs due to missing features
3:54:03.781261 WARNING: dropped 8 decoy PSMs due to missing features
3:54:04.337384 INFO: Test AUC: 0.844
3:54:04.337521 INFO: Train AUC: 0.841
3:54:04.337551 INFO: AUC difference: 0.45%
3:54:04.431546 INFO: Resetting torch num_threads to 100
3:54:04.433227 INFO: === FDR correction performed with classifier version 3 ===
3:54:04.434950 PROGRESS: ============================= Precursor FDR =============================
3:54:04.435050 PROGRESS: Total precursors accumulated: 7,632
3:54:04.435108 PROGRESS: Target precursors: 7,554 (98.98%)
3:54:04.435164 PROGRESS: Decoy precursors: 78 (1.02%)
3:54:04.435210 PROGRESS: 
3:54:04.435253 PROGRESS: Precursor Summary:
3:54:04.438222 PROGRESS: Channel   0:	 0.05 FDR: 7,554; 0.01 FDR: 7,544; 0.001 FDR: 6,522
3:54:04.438350 PROGRESS: 
3:54:04.438407 PROGRESS: Protein Summary:
3:54:04.442891 PROGRESS: Channel   0:	 0.05 FDR: 3,613; 0.01 FDR: 3,610; 0.001 FDR: 3,294
3:54:04.443001 PROGRESS: =========================================================================
3:54:04.469492 INFO: fragments_df_filtered: 5000
3:54:04.488005 INFO: calibration group: precursor, fitting mz estimator 
3:54:05.300392 INFO: calibration group: precursor, fitting rt estimator 
3:54:06.144287 INFO: calibration group: fragment, fitting mz estimator 
3:54:06.559518 INFO: calibration group: precursor, predicting mz
3:54:06.562519 INFO: calibration group: precursor, predicting rt
3:54:06.571669 INFO: calibration group: fragment, predicting mz
3:54:06.592613 INFO: === checking if optimization conditions were reached ===
3:54:06.592837 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3:54:06.599079 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 20.1706.
3:54:06.599146 INFO: ==============================================
3:54:06.599257 INFO: Starting optimization step 2.
3:54:06.599336 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:54:06.599426 PROGRESS: Extracting batch of 15933 precursors
3:54:06.606481 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:54:06.606555 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:54:06.606598 INFO: FWHM in RT is 2.68 seconds, sigma is 0.35
3:54:06.606626 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:54:06.606902 INFO: Starting candidate selection
3:54:07.246290 INFO: Starting candidate scoring
3:54:07.450173 INFO: Finished candidate processing
3:54:07.450282 INFO: Collecting candidate features
3:54:07.506161 WARNING: intensity_correlation has 10 NaNs ( 0.03 % out of 30893)
3:54:07.510419 INFO: Collecting fragment features
3:54:07.531597 INFO: Finished candidate scoring
3:54:07.544944 PROGRESS: === Extracted 30893 precursors and 283306 fragments ===
3:54:07.545323 INFO: performing precursor FDR with 47 features
3:54:07.545362 INFO: Decoy channel: -1
3:54:07.545385 INFO: Competetive: True
3:54:07.554923 INFO: Setting torch num_threads to 2 for FDR classification task
3:54:07.561559 WARNING: dropped 4 target PSMs due to missing features
3:54:07.561669 WARNING: dropped 6 decoy PSMs due to missing features
3:54:08.012637 INFO: Test AUC: 0.874
3:54:08.012774 INFO: Train AUC: 0.873
3:54:08.012803 INFO: AUC difference: 0.07%
3:54:08.096915 INFO: Resetting torch num_threads to 100
3:54:08.098416 INFO: === FDR correction performed with classifier version 3 ===
3:54:08.099912 PROGRESS: ============================= Precursor FDR =============================
3:54:08.100009 PROGRESS: Total precursors accumulated: 7,679
3:54:08.100069 PROGRESS: Target precursors: 7,623 (99.27%)
3:54:08.100118 PROGRESS: Decoy precursors: 56 (0.73%)
3:54:08.100176 PROGRESS: 
3:54:08.100220 PROGRESS: Precursor Summary:
3:54:08.103200 PROGRESS: Channel   0:	 0.05 FDR: 7,623; 0.01 FDR: 7,623; 0.001 FDR: 6,542
3:54:08.103311 PROGRESS: 
3:54:08.103365 PROGRESS: Protein Summary:
3:54:08.107668 PROGRESS: Channel   0:	 0.05 FDR: 3,632; 0.01 FDR: 3,632; 0.001 FDR: 3,303
3:54:08.107984 PROGRESS: =========================================================================
3:54:08.131650 INFO: fragments_df_filtered: 5000
3:54:08.143855 INFO: calibration group: precursor, fitting mz estimator 
3:54:08.972999 INFO: calibration group: precursor, fitting rt estimator 
3:54:09.919599 INFO: calibration group: fragment, fitting mz estimator 
3:54:10.491522 INFO: calibration group: precursor, predicting mz
3:54:10.495123 INFO: calibration group: precursor, predicting rt
3:54:10.507851 INFO: calibration group: fragment, predicting mz
3:54:10.536054 INFO: === checking if optimization conditions were reached ===
3:54:10.536853 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3:54:10.544618 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 16.4168.
3:54:10.544886 INFO: ==============================================
3:54:10.545222 INFO: Starting optimization step 3.
3:54:10.545520 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:54:10.545796 PROGRESS: Extracting batch of 15933 precursors
3:54:10.557440 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:54:10.557696 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:54:10.557843 INFO: FWHM in RT is 2.68 seconds, sigma is 0.35
3:54:10.557967 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:54:10.558317 INFO: Starting candidate selection
3:54:11.244696 INFO: Starting candidate scoring
3:54:11.457827 INFO: Finished candidate processing
3:54:11.457938 INFO: Collecting candidate features
3:54:11.506375 WARNING: intensity_correlation has 9 NaNs ( 0.03 % out of 30950)
3:54:11.510559 INFO: Collecting fragment features
3:54:11.533127 INFO: Finished candidate scoring
3:54:11.546849 PROGRESS: === Extracted 30950 precursors and 284934 fragments ===
3:54:11.547229 INFO: performing precursor FDR with 47 features
3:54:11.547266 INFO: Decoy channel: -1
3:54:11.547289 INFO: Competetive: True
3:54:11.555594 INFO: Setting torch num_threads to 2 for FDR classification task
3:54:11.560832 WARNING: dropped 2 target PSMs due to missing features
3:54:11.560923 WARNING: dropped 7 decoy PSMs due to missing features
3:54:11.880018 INFO: Test AUC: 0.883
3:54:11.880149 INFO: Train AUC: 0.882
3:54:11.880179 INFO: AUC difference: 0.10%
3:54:11.964810 INFO: Resetting torch num_threads to 100
3:54:11.966310 INFO: === FDR correction performed with classifier version 3 ===
3:54:11.967896 PROGRESS: ============================= Precursor FDR =============================
3:54:11.967994 PROGRESS: Total precursors accumulated: 7,660
3:54:11.968055 PROGRESS: Target precursors: 7,601 (99.23%)
3:54:11.968107 PROGRESS: Decoy precursors: 59 (0.77%)
3:54:11.968157 PROGRESS: 
3:54:11.968201 PROGRESS: Precursor Summary:
3:54:11.971192 PROGRESS: Channel   0:	 0.05 FDR: 7,601; 0.01 FDR: 7,601; 0.001 FDR: 6,827
3:54:11.971320 PROGRESS: 
3:54:11.971378 PROGRESS: Protein Summary:
3:54:11.975706 PROGRESS: Channel   0:	 0.05 FDR: 3,626; 0.01 FDR: 3,626; 0.001 FDR: 3,399
3:54:11.975826 PROGRESS: =========================================================================
3:54:11.999588 INFO: fragments_df_filtered: 5000
3:54:12.011914 INFO: calibration group: precursor, fitting mz estimator 
3:54:12.839209 INFO: calibration group: precursor, fitting rt estimator 
3:54:13.716897 INFO: calibration group: fragment, fitting mz estimator 
3:54:14.105315 INFO: calibration group: precursor, predicting mz
3:54:14.108262 INFO: calibration group: precursor, predicting rt
3:54:14.117352 INFO: calibration group: fragment, predicting mz
3:54:14.160240 INFO: === checking if optimization conditions were reached ===
3:54:14.160469 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3:54:14.167261 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 17.7409.
3:54:14.167332 INFO: ==============================================
3:54:14.167453 INFO: Starting optimization step 4.
3:54:14.167536 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:54:14.167607 PROGRESS: Extracting batch of 15933 precursors
3:54:14.173487 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:54:14.173557 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:54:14.173597 INFO: FWHM in RT is 2.68 seconds, sigma is 0.34
3:54:14.173625 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:54:14.173840 INFO: Starting candidate selection
3:54:14.832181 INFO: Starting candidate scoring
3:54:15.050172 INFO: Finished candidate processing
3:54:15.050283 INFO: Collecting candidate features
3:54:15.101676 WARNING: intensity_correlation has 13 NaNs ( 0.04 % out of 30894)
3:54:15.108961 INFO: Collecting fragment features
3:54:15.135295 INFO: Finished candidate scoring
3:54:15.148825 PROGRESS: === Extracted 30894 precursors and 284178 fragments ===
3:54:15.149225 INFO: performing precursor FDR with 47 features
3:54:15.149263 INFO: Decoy channel: -1
3:54:15.149285 INFO: Competetive: True
3:54:15.157936 INFO: Setting torch num_threads to 2 for FDR classification task
3:54:15.163160 WARNING: dropped 4 target PSMs due to missing features
3:54:15.163251 WARNING: dropped 9 decoy PSMs due to missing features
3:54:15.632407 INFO: Test AUC: 0.880
3:54:15.632529 INFO: Train AUC: 0.880
3:54:15.632560 INFO: AUC difference: 0.01%
3:54:15.740664 INFO: Resetting torch num_threads to 100
3:54:15.743977 INFO: === FDR correction performed with classifier version 3 ===
3:54:15.747039 PROGRESS: ============================= Precursor FDR =============================
3:54:15.747219 PROGRESS: Total precursors accumulated: 7,667
3:54:15.747297 PROGRESS: Target precursors: 7,603 (99.17%)
3:54:15.747363 PROGRESS: Decoy precursors: 64 (0.83%)
3:54:15.747424 PROGRESS: 
3:54:15.747481 PROGRESS: Precursor Summary:
3:54:15.752042 PROGRESS: Channel   0:	 0.05 FDR: 7,603; 0.01 FDR: 7,603; 0.001 FDR: 6,513
3:54:15.752237 PROGRESS: 
3:54:15.752314 PROGRESS: Protein Summary:
3:54:15.758932 PROGRESS: Channel   0:	 0.05 FDR: 3,625; 0.01 FDR: 3,625; 0.001 FDR: 3,297
3:54:15.759132 PROGRESS: =========================================================================
3:54:15.789321 INFO: fragments_df_filtered: 5000
3:54:15.810428 INFO: calibration group: precursor, fitting mz estimator 
3:54:16.660073 INFO: calibration group: precursor, fitting rt estimator 
3:54:17.486688 INFO: calibration group: fragment, fitting mz estimator 
3:54:17.836758 INFO: calibration group: precursor, predicting mz
3:54:17.839844 INFO: calibration group: precursor, predicting rt
3:54:17.849324 INFO: calibration group: fragment, predicting mz
3:54:17.871012 INFO: === checking if optimization conditions were reached ===
3:54:17.871230 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3:54:17.877955 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 17.3079.
3:54:17.878026 INFO: ==============================================
3:54:17.878147 INFO: Starting optimization step 5.
3:54:17.878238 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:54:17.878326 PROGRESS: Extracting batch of 15933 precursors
3:54:17.892959 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:54:17.893045 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:54:17.893085 INFO: FWHM in RT is 2.68 seconds, sigma is 0.35
3:54:17.893108 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:54:17.893390 INFO: Starting candidate selection
3:54:18.540380 INFO: Starting candidate scoring
3:54:18.725707 INFO: Finished candidate processing
3:54:18.725810 INFO: Collecting candidate features
3:54:18.778201 WARNING: intensity_correlation has 10 NaNs ( 0.03 % out of 30888)
3:54:18.783409 INFO: Collecting fragment features
3:54:18.804726 INFO: Finished candidate scoring
3:54:18.817879 PROGRESS: === Extracted 30888 precursors and 284358 fragments ===
3:54:18.818299 INFO: performing precursor FDR with 47 features
3:54:18.818336 INFO: Decoy channel: -1
3:54:18.818362 INFO: Competetive: True
3:54:18.830181 INFO: Setting torch num_threads to 2 for FDR classification task
3:54:18.835454 WARNING: dropped 3 target PSMs due to missing features
3:54:18.835546 WARNING: dropped 7 decoy PSMs due to missing features
3:54:19.169844 INFO: Test AUC: 0.877
3:54:19.169967 INFO: Train AUC: 0.882
3:54:19.169999 INFO: AUC difference: 0.53%
3:54:19.254777 INFO: Resetting torch num_threads to 100
3:54:19.256106 INFO: === FDR correction performed with classifier version 3 ===
3:54:19.257747 PROGRESS: ============================= Precursor FDR =============================
3:54:19.257839 PROGRESS: Total precursors accumulated: 7,655
3:54:19.257898 PROGRESS: Target precursors: 7,601 (99.29%)
3:54:19.257949 PROGRESS: Decoy precursors: 54 (0.71%)
3:54:19.257995 PROGRESS: 
3:54:19.258040 PROGRESS: Precursor Summary:
3:54:19.260982 PROGRESS: Channel   0:	 0.05 FDR: 7,601; 0.01 FDR: 7,601; 0.001 FDR: 6,833
3:54:19.261098 PROGRESS: 
3:54:19.261167 PROGRESS: Protein Summary:
3:54:19.265399 PROGRESS: Channel   0:	 0.05 FDR: 3,619; 0.01 FDR: 3,619; 0.001 FDR: 3,390
3:54:19.265501 PROGRESS: =========================================================================
3:54:19.290828 INFO: fragments_df_filtered: 5000
3:54:19.303807 INFO: calibration group: precursor, fitting mz estimator 
3:54:20.120794 INFO: calibration group: precursor, fitting rt estimator 
3:54:20.973447 INFO: calibration group: fragment, fitting mz estimator 
3:54:21.388226 INFO: calibration group: precursor, predicting mz
3:54:21.391039 INFO: calibration group: precursor, predicting rt
3:54:21.399883 INFO: calibration group: fragment, predicting mz
3:54:21.419976 INFO: === checking if optimization conditions were reached ===
3:54:21.420150 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3:54:21.421441 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 16.4168 found after 6 searches.
3:54:21.421498 INFO: ==============================================
3:54:21.421603 PROGRESS: Optimization finished for rt_error.
3:54:21.445517 INFO: calibration group: precursor, predicting mz
3:54:21.450085 INFO: calibration group: precursor, predicting rt
3:54:21.464415 INFO: calibration group: fragment, predicting mz
3:54:21.522845 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:54:21.523272 PROGRESS: ==============================================
3:54:21.523535 PROGRESS: ms2_error      : 15.0000
3:54:21.523785 PROGRESS: ms1_error      : 10.0000
3:54:21.524012 PROGRESS: rt_error       : 16.4168
3:54:21.524236 PROGRESS: ==============================================
3:54:21.526199 INFO: calibration group: precursor, predicting mz
3:54:21.535695 INFO: calibration group: precursor, predicting rt
3:54:21.572293 INFO: calibration group: fragment, predicting mz
3:54:21.673115 PROGRESS: Extracting batch of 65173 precursors
3:54:21.699262 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:54:21.699414 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:54:21.699454 INFO: FWHM in RT is 2.68 seconds, sigma is 0.34
3:54:21.699482 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:54:21.699794 INFO: Starting candidate selection
3:54:24.099324 INFO: Applying score cutoff of 27.039879989624023
3:54:24.102054 INFO: Removed 11845 precursors with score below cutoff
3:54:24.131873 INFO: Starting candidate scoring
3:54:24.920943 INFO: Finished candidate processing
3:54:24.921690 INFO: Collecting candidate features
3:54:25.097704 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 115372)
3:54:25.109736 INFO: Collecting fragment features
3:54:25.191067 INFO: Finished candidate scoring
3:54:25.240780 INFO: === FDR correction performed with classifier version 7 ===
3:54:25.241465 INFO: performing precursor FDR with 47 features
3:54:25.241501 INFO: Decoy channel: -1
3:54:25.241524 INFO: Competetive: True
3:54:25.285903 INFO: Setting torch num_threads to 2 for FDR classification task
3:54:25.303074 WARNING: dropped 4 decoy PSMs due to missing features
3:54:25.303230 WARNING: FDR calculation for 61119 target and 54249 decoy PSMs
3:54:25.303259 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
3:54:27.431378 INFO: Test AUC: 0.903
3:54:27.431501 INFO: Train AUC: 0.903
3:54:27.431530 INFO: AUC difference: 0.09%
3:54:27.519830 INFO: Resetting torch num_threads to 100
3:54:27.527872 INFO: Removing fragments below FDR threshold
3:54:27.551106 PROGRESS: ============================= Precursor FDR =============================
3:54:27.551343 PROGRESS: Total precursors accumulated: 31,501
3:54:27.551409 PROGRESS: Target precursors: 31,294 (99.34%)
3:54:27.551462 PROGRESS: Decoy precursors: 207 (0.66%)
3:54:27.551510 PROGRESS: 
3:54:27.551555 PROGRESS: Precursor Summary:
3:54:27.565182 PROGRESS: Channel   0:	 0.05 FDR: 31,294; 0.01 FDR: 31,294; 0.001 FDR: 29,312
3:54:27.565482 PROGRESS: 
3:54:27.565543 PROGRESS: Protein Summary:
3:54:27.589628 PROGRESS: Channel   0:	 0.05 FDR: 5,882; 0.01 FDR: 5,882; 0.001 FDR: 5,852
3:54:27.589905 PROGRESS: =========================================================================
3:54:27.932783 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:54:28.123360 PROGRESS: Processing search outputs
3:54:28.123498 PROGRESS: Performing protein grouping and FDR
3:54:28.123535 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:54:28.147558 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:54:28.171745 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:54:28.193866 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:54:28.225070 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:54:28.256284 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:54:28.289495 INFO: Building combined output
3:54:28.358026 INFO: Performing protein inference
3:54:28.508134 INFO: Inference strategy: library. Using library grouping for protein inference
3:54:28.509624 INFO: Performing protein FDR
3:54:30.290416 INFO: Normalizing q-values using 5,891 targets and 946 decoys
3:54:30.296483 INFO: Test AUC: 1.000
3:54:30.296539 INFO: Train AUC: 1.000
3:54:30.296568 INFO: AUC difference: 0.01%
3:54:30.542969 PROGRESS: ================ Protein FDR =================
3:54:30.543103 PROGRESS: Unique protein groups in output
3:54:30.543135 PROGRESS:   1% protein FDR: 5,890
3:54:30.543156 PROGRESS: 
3:54:30.543175 PROGRESS: Unique precursor in output
3:54:30.543193 PROGRESS:   1% protein FDR: 32,677
3:54:30.543216 PROGRESS: ================================================
3:54:30.571563 PROGRESS: Building search statistics
3:54:30.615619 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
3:54:30.615834 INFO: Initializing OptimizationManager
3:54:30.616108 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
3:54:30.616186 INFO: Initializing CalibrationManager
3:54:30.616426 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
3:54:30.616503 INFO: Initializing RawFileManager
3:54:30.627247 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
3:54:30.627376 INFO: Initializing OptimizationManager
3:54:30.627569 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
3:54:30.627648 INFO: Initializing CalibrationManager
3:54:30.627852 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
3:54:30.627937 INFO: Initializing RawFileManager
3:54:30.638621 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
3:54:30.638744 INFO: Initializing OptimizationManager
3:54:30.638934 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
3:54:30.639008 INFO: Initializing CalibrationManager
3:54:30.639190 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
3:54:30.639263 INFO: Initializing RawFileManager
3:54:30.653677 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
3:54:30.653857 INFO: Initializing OptimizationManager
3:54:30.654061 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
3:54:30.654134 INFO: Initializing CalibrationManager
3:54:30.654339 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
3:54:30.654413 INFO: Initializing RawFileManager
3:54:30.669552 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
3:54:30.669724 INFO: Initializing OptimizationManager
3:54:30.669944 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
3:54:30.670016 INFO: Initializing CalibrationManager
3:54:30.670211 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
3:54:30.670282 INFO: Initializing RawFileManager
3:54:30.684791 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
3:54:30.684973 INFO: Initializing OptimizationManager
3:54:30.685180 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
3:54:30.685252 INFO: Initializing CalibrationManager
3:54:30.685450 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
3:54:30.685525 INFO: Initializing RawFileManager
3:54:30.687293 INFO: Writing stat output to disk
3:54:30.687356 INFO: Saving run_output_Astral/alphadia_1.10_default/stat.tsv to disk
3:54:30.690895 PROGRESS: Building internal statistics
3:54:30.691103 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
3:54:30.691142 INFO: Initializing TimingManager
3:54:30.691370 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
3:54:30.691409 INFO: Initializing TimingManager
3:54:30.691576 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
3:54:30.691615 INFO: Initializing TimingManager
3:54:30.691782 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
3:54:30.691823 INFO: Initializing TimingManager
3:54:30.691983 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
3:54:30.692018 INFO: Initializing TimingManager
3:54:30.692172 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_default/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
3:54:30.692213 INFO: Initializing TimingManager
3:54:30.692572 INFO: Writing internal output to disk
3:54:30.692616 INFO: Saving run_output_Astral/alphadia_1.10_default/internal.tsv to disk
3:54:30.693053 PROGRESS: Performing label free quantification
3:54:30.731051 INFO: Accumulating fragment data
3:54:30.731212 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:54:30.750697 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:54:31.012226 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:54:31.252608 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:54:31.652360 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:54:32.050750 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:54:32.507482 PROGRESS: Performing label free quantification on the precursor level
3:54:32.507672 INFO: Filtering fragments by quality
3:54:32.595059 INFO: Performing label-free quantification using directLFQ
3:54:32.853243 INFO: 32677 lfq-groups total
3:55:26.686954 INFO: using 100 processes
3:55:26.796620 INFO: lfq-object 0
3:55:26.838212 INFO: lfq-object 100
3:55:26.878009 INFO: lfq-object 200
3:55:26.922078 INFO: lfq-object 300
3:55:26.938090 INFO: lfq-object 500
3:55:26.967251 INFO: lfq-object 400
3:55:26.975979 INFO: lfq-object 600
3:55:27.048591 INFO: lfq-object 700
3:55:27.104306 INFO: lfq-object 800
3:55:27.150249 INFO: lfq-object 1000
3:55:27.181076 INFO: lfq-object 900
3:55:27.215495 INFO: lfq-object 1100
3:55:27.273953 INFO: lfq-object 1200
3:55:27.285745 INFO: lfq-object 1400
3:55:27.314944 INFO: lfq-object 1300
3:55:27.350549 INFO: lfq-object 1500
3:55:27.403989 INFO: lfq-object 1600
3:55:27.457362 INFO: lfq-object 1700
3:55:27.509442 INFO: lfq-object 1800
3:55:27.549705 INFO: lfq-object 1900
3:55:27.592802 INFO: lfq-object 2000
3:55:27.675787 INFO: lfq-object 2300
3:55:27.689174 INFO: lfq-object 2100
3:55:27.737354 INFO: lfq-object 2400
3:55:27.746684 INFO: lfq-object 2200
3:55:27.757092 INFO: lfq-object 2500
3:55:27.804284 INFO: lfq-object 2600
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3:55:27.898466 INFO: lfq-object 2900
3:55:27.945355 INFO: lfq-object 3000
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3:55:28.696966 INFO: lfq-object 5000
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3:55:29.467462 INFO: lfq-object 7000
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3:55:29.575600 INFO: lfq-object 7300
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3:55:41.930938 INFO: lfq-object 27000
3:55:41.987842 INFO: lfq-object 27100
3:55:42.051482 INFO: lfq-object 27200
3:55:42.093760 INFO: lfq-object 27400
3:55:42.106039 INFO: lfq-object 27300
3:55:42.151718 INFO: lfq-object 27500
3:55:42.192993 INFO: lfq-object 27600
3:55:42.237782 INFO: lfq-object 27800
3:55:42.270680 INFO: lfq-object 27700
3:55:42.308809 INFO: lfq-object 27900
3:55:42.378552 INFO: lfq-object 28000
3:55:42.411800 INFO: lfq-object 28300
3:55:42.427646 INFO: lfq-object 28100
3:55:42.433730 INFO: lfq-object 28200
3:55:42.454094 INFO: lfq-object 28400
3:55:42.544963 INFO: lfq-object 28500
3:55:42.563359 INFO: lfq-object 28700
3:55:42.592740 INFO: lfq-object 28600
3:55:42.632325 INFO: lfq-object 28800
3:55:42.714892 INFO: lfq-object 28900
3:55:42.781475 INFO: lfq-object 29000
3:55:42.817927 INFO: lfq-object 29200
3:55:42.824879 INFO: lfq-object 29100
3:55:42.899840 INFO: lfq-object 29300
3:55:42.950204 INFO: lfq-object 29400
3:55:43.015480 INFO: lfq-object 29500
3:55:43.070548 INFO: lfq-object 29600
3:55:43.074564 INFO: lfq-object 29700
3:55:43.143132 INFO: lfq-object 29800
3:55:43.197817 INFO: lfq-object 29900
3:55:43.203809 INFO: lfq-object 30100
3:55:43.244472 INFO: lfq-object 30000
3:55:43.287250 INFO: lfq-object 30200
3:55:43.356125 INFO: lfq-object 30300
3:55:43.370533 INFO: lfq-object 30400
3:55:43.408722 INFO: lfq-object 30600
3:55:43.419718 INFO: lfq-object 30500
3:55:43.496343 INFO: lfq-object 30700
3:55:43.580139 INFO: lfq-object 31000
3:55:43.584204 INFO: lfq-object 30800
3:55:43.631083 INFO: lfq-object 30900
3:55:43.641472 INFO: lfq-object 31100
3:55:43.710949 INFO: lfq-object 31200
3:55:43.715214 INFO: lfq-object 31300
3:55:43.766331 INFO: lfq-object 31500
3:55:43.807843 INFO: lfq-object 31400
3:55:43.864190 INFO: lfq-object 31600
3:55:43.878350 INFO: lfq-object 31700
3:55:43.908947 INFO: lfq-object 31900
3:55:43.917984 INFO: lfq-object 31800
3:55:43.949998 INFO: lfq-object 32000
3:55:44.011163 INFO: lfq-object 32100
3:55:44.047513 INFO: lfq-object 32200
3:55:44.067256 INFO: lfq-object 32400
3:55:44.113173 INFO: lfq-object 32300
3:55:44.143893 INFO: lfq-object 32500
3:55:44.236927 INFO: lfq-object 32600
3:55:47.504306 INFO: Writing precursor output to disk
3:55:47.504491 INFO: Saving run_output_Astral/alphadia_1.10_default/precursor.matrix.tsv to disk
3:55:47.681469 PROGRESS: Performing label free quantification on the pg level
3:55:47.681570 INFO: Filtering fragments by quality
3:55:47.780504 INFO: Performing label-free quantification using directLFQ
3:55:47.899655 INFO: 5890 lfq-groups total
3:56:37.790024 INFO: using 100 processes
3:56:37.812850 INFO: lfq-object 0
3:56:37.922830 INFO: lfq-object 200
3:56:37.922975 INFO: lfq-object 300
3:56:37.925379 INFO: lfq-object 100
3:56:38.023099 INFO: lfq-object 400
3:56:38.060161 INFO: lfq-object 500
3:56:38.077784 INFO: lfq-object 600
3:56:38.192599 INFO: lfq-object 900
3:56:38.205572 INFO: lfq-object 800
3:56:38.303815 INFO: lfq-object 1000
3:56:38.308931 INFO: lfq-object 1200
3:56:38.310174 INFO: lfq-object 1100
3:56:38.368002 INFO: lfq-object 700
3:56:38.417355 INFO: lfq-object 1300
3:56:38.465659 INFO: lfq-object 1400
3:56:38.477139 INFO: lfq-object 1500
3:56:38.547758 INFO: lfq-object 1600
3:56:38.587020 INFO: lfq-object 1700
3:56:38.622408 INFO: lfq-object 1800
3:56:38.711954 INFO: lfq-object 1900
3:56:38.722943 INFO: lfq-object 2000
3:56:38.751986 INFO: lfq-object 2100
3:56:38.846874 INFO: lfq-object 2300
3:56:38.895407 INFO: lfq-object 2400
3:56:38.964256 INFO: lfq-object 2500
3:56:38.970871 INFO: lfq-object 2200
3:56:39.004116 INFO: lfq-object 2600
3:56:39.045462 INFO: lfq-object 2700
3:56:39.120768 INFO: lfq-object 2900
3:56:39.141952 INFO: lfq-object 2800
3:56:39.165190 INFO: lfq-object 3000
3:56:39.261551 INFO: lfq-object 3200
3:56:39.297360 INFO: lfq-object 3300
3:56:39.364526 INFO: lfq-object 3400
3:56:39.398845 INFO: lfq-object 3100
3:56:39.414366 INFO: lfq-object 3500
3:56:39.462692 INFO: lfq-object 3600
3:56:39.523590 INFO: lfq-object 3700
3:56:39.606757 INFO: lfq-object 3900
3:56:39.650099 INFO: lfq-object 4000
3:56:39.698163 INFO: lfq-object 4100
3:56:39.719252 INFO: lfq-object 3800
3:56:39.727291 INFO: lfq-object 4200
3:56:39.784643 INFO: lfq-object 4300
3:56:39.807892 INFO: lfq-object 4400
3:56:39.841916 INFO: lfq-object 4500
3:56:39.919351 INFO: lfq-object 4600
3:56:39.951927 INFO: lfq-object 4700
3:56:39.963077 INFO: lfq-object 4800
3:56:40.025859 INFO: lfq-object 4900
3:56:40.061011 INFO: lfq-object 5000
3:56:40.096967 INFO: lfq-object 5100
3:56:40.170162 INFO: lfq-object 5200
3:56:40.194451 INFO: lfq-object 5300
3:56:40.244872 INFO: lfq-object 5400
3:56:40.305961 INFO: lfq-object 5500
3:56:40.349076 INFO: lfq-object 5600
3:56:40.391178 INFO: lfq-object 5700
3:56:40.440736 INFO: lfq-object 5800
3:56:44.672373 INFO: Writing pg output to disk
3:56:44.672543 INFO: Saving run_output_Astral/alphadia_1.10_default/pg.matrix.tsv to disk
3:56:44.792752 INFO: Writing psm output to disk
3:56:44.792900 INFO: Saving run_output_Astral/alphadia_1.10_default/precursors.tsv to disk
3:56:53.122497 PROGRESS: Building spectral library
3:56:53.164091 INFO: Building MBR spectral library
3:56:53.164229 INFO: Running MbrLibraryBuilder
3:56:53.249503 INFO: MBR spectral library contains 32,677 precursors, 5,890 proteins
3:56:53.249646 INFO: Writing MBR spectral library to disk
3:56:53.526583 PROGRESS: =================== Search Finished ===================
3:56:53.538180 WARNING: WARNING: Temp mmap arrays were written to /tmp/temp_mmap_tdngo30u. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 702,937,538,560
