0:00:00.013381 PROGRESS:           _      _         ___ ___   _   
0:00:00.013496 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.013527 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.013554 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.013582 PROGRESS:            |_|                           
0:00:00.013604 PROGRESS: 
0:00:00.013626 PROGRESS: version: 1.10.3
0:00:00.013660 INFO: hostname: thestral
0:00:00.013713 INFO: date: 2025-05-03 18:51:01
0:00:00.013736 INFO: ================ AlphaX Environment ===============
0:00:00.013758 INFO: alphatims       : 1.0.8
0:00:00.013776 INFO: alpharaw        : 0.4.5
0:00:00.013795 INFO: alphabase       : 1.5.0
0:00:00.013812 INFO: alphapeptdeep   : 1.3.0
0:00:00.013830 INFO: directlfq       : 0.2.19
0:00:00.013847 INFO: ===================================================
0:00:00.013864 INFO: ================= Pip Environment =================
0:00:00.070277 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
0:00:00.070360 INFO: ===================================================
0:00:00.070389 INFO: Running step 'library'
0:00:00.070492 INFO: loading config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:00:00.080989 INFO: loading additional config provided via CLI
0:00:00.081050 INFO: loading additional config provided via CLI parameters
0:00:00.081295 INFO: Updating config with 'user defined'
0:00:00.081374 INFO: Updating config with 'user defined (cli)'
0:00:00.081398 INFO: Updating config with 'multistep search'
0:00:00.081431 INFO: ├──version: 1
0:00:00.081457 INFO: ├──workflow_name: None
0:00:00.081478 INFO: [32;20m├──output_directory: run_output_Astral/alphadia_1.10_MBRSetValues/library [multistep search, default: None][0m
0:00:00.081499 INFO: ├──library_path: None
0:00:00.081519 INFO: ├──raw_paths:
0:00:00.081539 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
0:00:00.081559 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
0:00:00.081580 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
0:00:00.081604 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
0:00:00.081622 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
0:00:00.081640 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
0:00:00.081661 INFO: ├──fasta_paths:
0:00:00.081680 INFO: │   [32;20m- ./ProteoBenchFASTA_DDAQuantification.fasta [user defined (cli), default: None][0m
0:00:00.081699 INFO: ├──quant_directory: None
0:00:00.081718 INFO: ├──general
0:00:00.081738 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
0:00:00.081757 INFO: │   ├──transfer_step_enabled: False
0:00:00.081774 INFO: │   ├──mbr_step_enabled: True
0:00:00.081794 INFO: │   ├──reuse_calibration: False
0:00:00.081811 INFO: │   ├──reuse_quant: False
0:00:00.081829 INFO: │   ├──astral_ms1: False
0:00:00.081848 INFO: │   ├──log_level: INFO
0:00:00.081866 INFO: │   ├──mmap_detector_events: False
0:00:00.081885 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
0:00:00.081903 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.081922 INFO: │   └──save_mbr_library: True
0:00:00.081940 INFO: ├──library_loading
0:00:00.081958 INFO: │   └──rt_heuristic: 180
0:00:00.081976 INFO: ├──library_prediction
0:00:00.081995 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.082014 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.082035 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.082054 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
0:00:00.082072 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.082089 INFO: │   ├──missed_cleavages: 1
0:00:00.082108 INFO: │   ├──precursor_len:
0:00:00.082127 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.082144 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.082162 INFO: │   ├──precursor_charge:
0:00:00.082182 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.082199 INFO: │   │   [32;20m- 4[0m
0:00:00.082217 INFO: │   ├──precursor_mz:
0:00:00.082235 INFO: │   │   [32;20m- 400[0m
0:00:00.082253 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
0:00:00.082270 INFO: │   ├──fragment_mz:
0:00:00.082288 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
0:00:00.082308 INFO: │   │   [32;20m- 2000[0m
0:00:00.082328 INFO: │   ├──nce: 25
0:00:00.082346 INFO: │   ├──fragment_types:
0:00:00.082363 INFO: │   │   [32;20m- b[0m
0:00:00.082382 INFO: │   │   [32;20m- y[0m
0:00:00.082402 INFO: │   ├──max_fragment_charge: 2
0:00:00.082419 INFO: │   [32;20m├──instrument: Astral [user defined, default: Lumos][0m
0:00:00.082444 INFO: │   ├──peptdeep_model_path: None
0:00:00.082461 INFO: │   └──peptdeep_model_type: generic
0:00:00.082479 INFO: ├──custom_modifications:
0:00:00.082500 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.082518 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.082536 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.082553 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.082573 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.082590 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.082608 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.082627 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.082644 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.082662 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.082680 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.082699 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.082716 INFO: │   ├──name: Label:13C(12)@K
0:00:00.082733 INFO: │   └──composition: C(12)
0:00:00.082750 INFO: ├──search
0:00:00.082770 INFO: │   [32;20m├──target_ms1_tolerance: 3 [user defined, default: 5][0m
0:00:00.082788 INFO: │   [32;20m├──target_ms2_tolerance: 8 [user defined, default: 10][0m
0:00:00.082806 INFO: │   ├──target_rt_tolerance: 0
0:00:00.082825 INFO: │   ├──target_mobility_tolerance: 0
0:00:00.082843 INFO: │   ├──quant_window: 3
0:00:00.082862 INFO: │   [32;20m├──target_num_candidates: 2 [user defined, default: 3][0m
0:00:00.082880 INFO: │   ├──channel_filter: 
0:00:00.082900 INFO: │   ├──exclude_shared_ions: True
0:00:00.082918 INFO: │   ├──compete_for_fragments: True
0:00:00.082937 INFO: │   ├──quant_all: True
0:00:00.082957 INFO: │   ├──top_k_fragments: 12
0:00:00.082974 INFO: │   └──experimental_xic: True
0:00:00.082992 INFO: ├──calibration
0:00:00.083013 INFO: │   ├──batch_size: 8000
0:00:00.083032 INFO: │   ├──optimization_lock_target: 200
0:00:00.083050 INFO: │   ├──max_steps: 20
0:00:00.083069 INFO: │   ├──min_steps: 2
0:00:00.083089 INFO: │   ├──max_skips: 1
0:00:00.083107 INFO: │   ├──norm_rt_mode: linear
0:00:00.083124 INFO: │   ├──max_fragments: 5000
0:00:00.083148 INFO: │   └──min_correlation: 0.7
0:00:00.083165 INFO: ├──search_initial
0:00:00.083184 INFO: │   ├──initial_num_candidates: 1
0:00:00.083204 INFO: │   ├──initial_ms1_tolerance: 30
0:00:00.083222 INFO: │   ├──initial_ms2_tolerance: 30
0:00:00.083240 INFO: │   ├──initial_mobility_tolerance: 0.1
0:00:00.083258 INFO: │   └──initial_rt_tolerance: 0.5
0:00:00.083277 INFO: ├──selection_config
0:00:00.083295 INFO: │   ├──peak_len_rt: 10.0
0:00:00.083315 INFO: │   ├──sigma_scale_rt: 0.5
0:00:00.083335 INFO: │   ├──peak_len_mobility: 0.01
0:00:00.083355 INFO: │   ├──sigma_scale_mobility: 1.0
0:00:00.083375 INFO: │   ├──top_k_precursors: 3
0:00:00.083393 INFO: │   ├──kernel_size: 30
0:00:00.083413 INFO: │   ├──f_mobility: 1.0
0:00:00.083432 INFO: │   ├──f_rt: 0.99
0:00:00.083450 INFO: │   ├──center_fraction: 0.5
0:00:00.083470 INFO: │   ├──min_size_mobility: 8
0:00:00.083488 INFO: │   ├──min_size_rt: 3
0:00:00.083506 INFO: │   ├──max_size_mobility: 20
0:00:00.083524 INFO: │   ├──max_size_rt: 15
0:00:00.083544 INFO: │   ├──group_channels: False
0:00:00.083562 INFO: │   ├──use_weighted_score: True
0:00:00.083580 INFO: │   ├──join_close_candidates: False
0:00:00.083601 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
0:00:00.083619 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
0:00:00.083637 INFO: ├──scoring_config
0:00:00.083655 INFO: │   ├──score_grouped: False
0:00:00.083674 INFO: │   ├──top_k_isotopes: 3
0:00:00.083692 INFO: │   ├──reference_channel: -1
0:00:00.083714 INFO: │   ├──precursor_mz_tolerance: 10
0:00:00.083734 INFO: │   └──fragment_mz_tolerance: 15
0:00:00.083751 INFO: ├──library_multiplexing
0:00:00.083769 INFO: │   ├──enabled: False
0:00:00.083789 INFO: │   ├──input_channel: 0
0:00:00.083806 INFO: │   └──multiplex_mapping:
0:00:00.083823 INFO: ├──multiplexing
0:00:00.083841 INFO: │   ├──enabled: False
0:00:00.083860 INFO: │   ├──target_channels: 4,8
0:00:00.083878 INFO: │   ├──decoy_channel: 12
0:00:00.083896 INFO: │   ├──reference_channel: 0
0:00:00.083913 INFO: │   └──competetive_scoring: True
0:00:00.083932 INFO: ├──fdr
0:00:00.083952 INFO: │   ├──fdr: 0.01
0:00:00.083970 INFO: │   ├──group_level: proteins
0:00:00.083990 INFO: │   ├──inference_strategy: heuristic
0:00:00.084009 INFO: │   ├──competetive_scoring: True
0:00:00.084027 INFO: │   ├──keep_decoys: False
0:00:00.084045 INFO: │   ├──channel_wise_fdr: False
0:00:00.084063 INFO: │   ├──enable_two_step_classifier: False
0:00:00.084081 INFO: │   ├──two_step_classifier_max_iterations: 5
0:00:00.084099 INFO: │   └──enable_nn_hyperparameter_tuning: False
0:00:00.084117 INFO: ├──search_output
0:00:00.084135 INFO: │   ├──file_format: tsv
0:00:00.084152 INFO: │   ├──peptide_level_lfq: False
0:00:00.084171 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
0:00:00.084191 INFO: │   ├──min_k_fragments: 12
0:00:00.084209 INFO: │   ├──min_correlation: 0.9
0:00:00.084227 INFO: │   ├──num_samples_quadratic: 50
0:00:00.084246 INFO: │   ├──min_nonnan: 3
0:00:00.084263 INFO: │   ├──normalize_lfq: True
0:00:00.084281 INFO: │   └──save_fragment_quant_matrix: False
0:00:00.084298 INFO: ├──optimization
0:00:00.084319 INFO: │   ├──order_of_optimization: None
0:00:00.084336 INFO: │   ├──ms2_error
0:00:00.084354 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.084373 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.084392 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.084409 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.084427 INFO: │   │   ├──try_narrower_values: True
0:00:00.084446 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.084463 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.084481 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.084499 INFO: │   ├──ms1_error
0:00:00.084518 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.084535 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.084553 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.084573 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.084592 INFO: │   │   ├──try_narrower_values: False
0:00:00.084609 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.084628 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.084647 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.084665 INFO: │   ├──mobility_error
0:00:00.084683 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.084708 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.084728 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.084747 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.084764 INFO: │   │   ├──try_narrower_values: False
0:00:00.084785 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.084803 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.084821 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.084840 INFO: │   └──rt_error
0:00:00.084860 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.084878 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.085557 INFO: │       ├──automatic_update_percentile_range: 0.99
0:00:00.085582 INFO: │       ├──automatic_update_factor: 1.1
0:00:00.085600 INFO: │       ├──try_narrower_values: True
0:00:00.085619 INFO: │       ├──maximal_decrease: 0.2
0:00:00.085637 INFO: │       ├──favour_narrower_optimum: True
0:00:00.085655 INFO: │       └──maximum_decrease_from_maximum: 0.1
0:00:00.085673 INFO: ├──optimization_manager
0:00:00.085692 INFO: │   ├──fwhm_rt: 5
0:00:00.085710 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.085727 INFO: │   └──score_cutoff: 0
0:00:00.085744 INFO: ├──transfer_library
0:00:00.085764 INFO: │   ├──enabled: False
0:00:00.085781 INFO: │   ├──fragment_types:
0:00:00.085797 INFO: │   │   [32;20m- b[0m
0:00:00.085816 INFO: │   │   [32;20m- y[0m
0:00:00.085833 INFO: │   ├──max_charge: 2
0:00:00.085850 INFO: │   ├──top_k_samples: 3
0:00:00.085867 INFO: │   ├──norm_delta_max: True
0:00:00.085889 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.085906 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.085924 INFO: └──transfer_learning
0:00:00.085941 INFO:     ├──enabled: False
0:00:00.085960 INFO:     ├──batch_size: 2000
0:00:00.085977 INFO:     ├──max_lr: 0.0001
0:00:00.085995 INFO:     ├──train_fraction: 0.7
0:00:00.086014 INFO:     ├──validation_fraction: 0.2
0:00:00.086031 INFO:     ├──test_fraction: 0.1
0:00:00.086048 INFO:     ├──test_interval: 1
0:00:00.086066 INFO:     ├──lr_patience: 3
0:00:00.086085 INFO:     ├──epochs: 51
0:00:00.086102 INFO:     ├──warmup_epochs: 5
0:00:00.086119 INFO:     ├──nce: 25
0:00:00.086137 INFO:     [32;20m└──instrument: Astral [user defined, default: Lumos][0m
0:00:00.090760 INFO: Registering 7 custom modifications
0:00:00.117479 PROGRESS: No library provided. Building library from fasta files.
0:00:00.117558 INFO: Running FastaDigest
0:00:00.965083 INFO: Digesting fasta file
0:00:07.498471 INFO: Adding modifications
0:01:33.967992 INFO: Removing non-canonical amino acids
0:01:40.031736 INFO: Fasta library contains 5,215,079 precursors
0:01:40.032010 PROGRESS: Predicting library properties.
0:01:40.032094 INFO: Running PeptDeepPrediction
0:01:40.032180 INFO: Device set to cpu
0:01:40.945987 INFO: Loading PeptDeep models of type generic
0:01:41.721635 INFO: Predicting RT, MS2 and mobility
0:01:41.721806 INFO: Using multiprocessing with 100 processes ...
0:01:42.132784 INFO: Predicting rt,ms2,mobility ...
0:09:05.560838 INFO: Adding fragment mz information
0:09:05.862255 INFO: Adding fragment intensity information
0:09:06.161215 INFO: Adding precursor information
0:09:06.616060 INFO: Running PrecursorInitializer
0:09:06.682803 INFO: Running AnnotateFasta
0:09:06.860228 INFO: Dropping decoys from input library before annotation
0:09:36.403568 INFO: Running IsotopeGenerator
0:10:03.573065 INFO: Running RTNormalization
0:10:03.573721 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:10:03.573825 INFO: Saving library to run_output_Astral/alphadia_1.10_MBRSetValues/library/speclib.hdf
0:10:36.311669 INFO: Running DecoyGenerator
0:12:58.524220 INFO: Running FlattenLibrary
0:13:36.896387 INFO: Running InitFlatColumns
0:13:37.206770 INFO: Running LogFlatLibraryStats
0:13:37.206936 INFO: ============ Library Stats ============
0:13:37.206980 INFO: Number of precursors: 10,400,392
0:13:39.420583 INFO: 	thereof targets:5,215,079
0:13:39.420882 INFO: 	thereof decoys: 5,185,313
0:13:39.496776 INFO: Number of elution groups: 5,215,079
0:13:39.496948 INFO: 	average size: 1.99
0:13:39.946091 INFO: Number of proteins: 117,993
0:13:39.971653 INFO: Number of channels: 1 ([0])
0:13:39.971901 INFO: Isotopes Distribution for 4 isotopes
0:13:39.971935 INFO: =======================================
0:13:39.983090 INFO: Searching 6 files:
0:13:39.983241 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
0:13:39.983263 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
0:13:39.983297 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
0:13:39.983316 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
0:13:39.983334 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
0:13:39.983351 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
0:13:39.983375 INFO: Using 1 fasta files:
0:13:39.983395 INFO:   ./ProteoBenchFASTA_DDAQuantification.fasta
0:13:39.983420 INFO: Using library: None
0:13:39.983444 INFO: Saving output to: run_output_Astral/alphadia_1.10_MBRSetValues/library
0:13:39.983480 PROGRESS: Starting Search Workflows
0:13:39.983595 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:13:39.983676 INFO: Quantification results path: run_output_Astral/alphadia_1.10_MBRSetValues/library/quant
0:13:39.983768 INFO: Creating parent folder for workflows at run_output_Astral/alphadia_1.10_MBRSetValues/library/quant
0:13:39.983922 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1 at run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:13:39.984533 INFO: Initializing RawFileManager
0:14:11.037169 INFO: Determining DIA cycle
0:14:11.488066 INFO: Found cycle with start 0.00 min and length 303.
0:14:11.800477 INFO: RT (min)            : 0.0 - 26.9
0:14:11.800579 INFO: RT duration (sec)   : 1611.2
0:14:11.800607 INFO: RT duration (min)   : 26.9
0:14:11.800632 INFO: Cycle len (scans)   : 303
0:14:11.800656 INFO: Cycle len (sec)     : 1.65
0:14:11.800675 INFO: Number of cycles    : 977
0:14:11.800695 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:14:13.914493 INFO: Initializing CalibrationManager
0:14:13.915091 INFO: Loading calibration config
0:14:13.915246 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'}]
0:14:13.915336 INFO: Calibration group :fragment, found 1 estimator(s)
0:14:13.915480 INFO: Calibration group :precursor, found 3 estimator(s)
0:14:13.915580 INFO: Disabling ion mobility calibration
0:14:13.915610 INFO: removed mobility estimator from group precursor
0:14:13.916118 INFO: Initializing OptimizationManager
0:14:13.916268 INFO: initial parameter: ms1_error = 30
0:14:13.916328 INFO: initial parameter: ms2_error = 30
0:14:13.916399 INFO: initial parameter: rt_error = 805.5992431640625
0:14:13.916447 INFO: initial parameter: mobility_error = 0.1
0:14:13.916495 INFO: initial parameter: column_type = library
0:14:13.916540 INFO: initial parameter: num_candidates = 1
0:14:13.916582 INFO: initial parameter: classifier_version = -1
0:14:13.916625 INFO: initial parameter: fwhm_rt = 5
0:14:13.916667 INFO: initial parameter: fwhm_mobility = 0.01
0:14:13.916721 INFO: initial parameter: score_cutoff = 0
0:14:13.916803 INFO: Initializing TimingManager
0:14:13.916873 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:14:13.917039 INFO: FDRManager not loaded from disk.
0:14:13.917065 INFO: Initializing FDRManager
0:14:13.917118 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:14:15.824731 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
0:14:18.608413 PROGRESS: Starting initial search for precursors.
0:14:19.595778 INFO: Starting optimization step 0.
0:14:19.596116 PROGRESS: === Extracting elution groups 0 to 8000 ===
0:14:19.596198 PROGRESS: Extracting batch of 15815 precursors
0:14:21.340632 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:14:21.340883 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:14:21.340931 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:14:21.340955 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:14:25.707217 INFO: Starting candidate selection
0:15:54.604986 INFO: Starting candidate scoring
0:23:58.899931 INFO: Finished candidate processing
0:23:58.900240 INFO: Collecting candidate features
0:23:59.523210 INFO: Collecting fragment features
0:24:01.339864 INFO: Finished candidate scoring
0:24:01.354681 PROGRESS: === Extracted 15769 precursors and 155129 fragments ===
0:24:01.355157 INFO: performing precursor FDR with 47 features
0:24:01.355199 INFO: Decoy channel: -1
0:24:01.355222 INFO: Competetive: True
0:24:01.359808 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:05.626348 INFO: Test AUC: 0.498
0:24:05.626513 INFO: Train AUC: 0.510
0:24:05.626565 INFO: AUC difference: 2.36%
0:24:05.716972 INFO: Resetting torch num_threads to 100
0:24:05.718119 INFO: === FDR correction performed with classifier version -1 ===
0:24:05.719605 PROGRESS: ============================= Precursor FDR =============================
0:24:05.719703 PROGRESS: Total precursors accumulated: 7,977
0:24:05.719761 PROGRESS: Target precursors: 4,068 (51.00%)
0:24:05.719813 PROGRESS: Decoy precursors: 3,909 (49.00%)
0:24:05.719858 PROGRESS: 
0:24:05.719901 PROGRESS: Precursor Summary:
0:24:05.720840 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:24:05.720935 PROGRESS: 
0:24:05.720992 PROGRESS: Protein Summary:
0:24:05.721973 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:24:05.722067 PROGRESS: =========================================================================
0:24:05.869013 INFO: Starting optimization step 1.
0:24:05.869284 PROGRESS: === Extracting elution groups 8000 to 24000 ===
0:24:05.869355 PROGRESS: Extracting batch of 31636 precursors
0:24:05.876882 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:24:05.876970 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:05.877009 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:24:05.877032 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:24:05.877273 INFO: Starting candidate selection
0:24:07.899854 INFO: Starting candidate scoring
0:24:08.097356 INFO: Finished candidate processing
0:24:08.097462 INFO: Collecting candidate features
0:24:08.155703 INFO: Collecting fragment features
0:24:08.176969 INFO: Finished candidate scoring
0:24:08.201714 PROGRESS: === Extracted 47338 precursors and 466616 fragments ===
0:24:08.206930 INFO: performing precursor FDR with 47 features
0:24:08.207005 INFO: Decoy channel: -1
0:24:08.207031 INFO: Competetive: True
0:24:08.226007 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:08.960397 INFO: Test AUC: 0.535
0:24:08.960534 INFO: Train AUC: 0.550
0:24:08.960565 INFO: AUC difference: 2.70%
0:24:09.043290 INFO: Resetting torch num_threads to 100
0:24:09.045974 INFO: === FDR correction performed with classifier version -1 ===
0:24:09.049756 PROGRESS: ============================= Precursor FDR =============================
0:24:09.049915 PROGRESS: Total precursors accumulated: 23,901
0:24:09.049980 PROGRESS: Target precursors: 13,471 (56.36%)
0:24:09.050035 PROGRESS: Decoy precursors: 10,430 (43.64%)
0:24:09.050082 PROGRESS: 
0:24:09.050129 PROGRESS: Precursor Summary:
0:24:09.051130 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:24:09.051221 PROGRESS: 
0:24:09.051280 PROGRESS: Protein Summary:
0:24:09.052328 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:24:09.052419 PROGRESS: =========================================================================
0:24:09.243584 INFO: Starting optimization step 2.
0:24:09.243881 PROGRESS: === Extracting elution groups 24000 to 56000 ===
0:24:09.243953 PROGRESS: Extracting batch of 63234 precursors
0:24:09.258123 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:24:09.258255 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:09.258290 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:24:09.258314 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:24:09.258535 INFO: Starting candidate selection
0:24:13.291910 INFO: Starting candidate scoring
0:24:13.688552 INFO: Finished candidate processing
0:24:13.688659 INFO: Collecting candidate features
0:24:13.803325 INFO: Collecting fragment features
0:24:13.848390 INFO: Finished candidate scoring
0:24:13.934741 PROGRESS: === Extracted 110407 precursors and 1090454 fragments ===
0:24:13.946684 INFO: performing precursor FDR with 47 features
0:24:13.946817 INFO: Decoy channel: -1
0:24:13.946844 INFO: Competetive: True
0:24:13.990111 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:15.662004 INFO: Test AUC: 0.549
0:24:15.662138 INFO: Train AUC: 0.563
0:24:15.662171 INFO: AUC difference: 2.35%
0:24:15.754912 INFO: Resetting torch num_threads to 100
0:24:15.760470 INFO: === FDR correction performed with classifier version -1 ===
0:24:15.761162 PROGRESS: ============================= Precursor FDR =============================
0:24:15.761256 PROGRESS: Total precursors accumulated: 24
0:24:15.761315 PROGRESS: Target precursors: 22 (91.67%)
0:24:15.761366 PROGRESS: Decoy precursors: 2 (8.33%)
0:24:15.761411 PROGRESS: 
0:24:15.761453 PROGRESS: Precursor Summary:
0:24:15.762314 PROGRESS: Channel   0:	 0.05 FDR:     5; 0.01 FDR:     5; 0.001 FDR:     5
0:24:15.762407 PROGRESS: 
0:24:15.762465 PROGRESS: Protein Summary:
0:24:15.763407 PROGRESS: Channel   0:	 0.05 FDR:     5; 0.01 FDR:     5; 0.001 FDR:     5
0:24:15.763496 PROGRESS: =========================================================================
0:24:16.037568 INFO: Starting optimization step 3.
0:24:16.037851 PROGRESS: === Extracting elution groups 56000 to 120000 ===
0:24:16.037939 PROGRESS: Extracting batch of 126528 precursors
0:24:16.066843 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:24:16.066969 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:16.067011 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:24:16.067034 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:24:16.067297 INFO: Starting candidate selection
0:24:24.092134 INFO: Starting candidate scoring
0:24:24.970273 INFO: Finished candidate processing
0:24:24.970434 INFO: Collecting candidate features
0:24:25.470998 INFO: Collecting fragment features
0:24:25.576588 INFO: Finished candidate scoring
0:24:25.904662 PROGRESS: === Extracted 236578 precursors and 2335347 fragments ===
0:24:25.964696 INFO: performing precursor FDR with 47 features
0:24:25.964954 INFO: Decoy channel: -1
0:24:25.964987 INFO: Competetive: True
0:24:26.119389 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:32.204178 INFO: Test AUC: 0.555
0:24:32.204411 INFO: Train AUC: 0.570
0:24:32.204443 INFO: AUC difference: 2.50%
0:24:32.316762 INFO: Resetting torch num_threads to 100
0:24:32.340271 INFO: === FDR correction performed with classifier version -1 ===
0:24:32.341536 PROGRESS: ============================= Precursor FDR =============================
0:24:32.341700 PROGRESS: Total precursors accumulated: 2
0:24:32.341770 PROGRESS: Target precursors: 2 (100.00%)
0:24:32.341822 PROGRESS: Decoy precursors: 0 (0.00%)
0:24:32.341871 PROGRESS: 
0:24:32.341915 PROGRESS: Precursor Summary:
0:24:32.343013 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
0:24:32.343125 PROGRESS: 
0:24:32.343182 PROGRESS: Protein Summary:
0:24:32.344282 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
0:24:32.344391 PROGRESS: =========================================================================
0:24:32.912906 INFO: Starting optimization step 4.
0:24:32.913263 PROGRESS: === Extracting elution groups 120000 to 248000 ===
0:24:32.913392 PROGRESS: Extracting batch of 253020 precursors
0:24:32.995123 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:24:32.995293 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:32.995335 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:24:32.995357 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:24:32.995715 INFO: Starting candidate selection
0:24:48.845265 INFO: Starting candidate scoring
0:24:50.541267 INFO: Finished candidate processing
0:24:50.541406 INFO: Collecting candidate features
0:24:51.488288 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 252394)
0:24:51.500505 INFO: Collecting fragment features
0:24:51.735952 INFO: Finished candidate scoring
0:24:52.301005 PROGRESS: === Extracted 488972 precursors and 4824409 fragments ===
0:24:52.401796 INFO: performing precursor FDR with 47 features
0:24:52.401984 INFO: Decoy channel: -1
0:24:52.402013 INFO: Competetive: True
0:24:52.820808 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:52.990488 WARNING: dropped 1 target PSMs due to missing features
0:24:52.990672 WARNING: dropped 2 decoy PSMs due to missing features
0:25:02.828401 INFO: Test AUC: 0.562
0:25:02.828631 INFO: Train AUC: 0.573
0:25:02.828667 INFO: AUC difference: 1.99%
0:25:02.963800 INFO: Resetting torch num_threads to 100
0:25:03.005886 INFO: === FDR correction performed with classifier version -1 ===
0:25:03.006888 PROGRESS: ============================= Precursor FDR =============================
0:25:03.006988 PROGRESS: Total precursors accumulated: 3
0:25:03.007049 PROGRESS: Target precursors: 3 (100.00%)
0:25:03.007102 PROGRESS: Decoy precursors: 0 (0.00%)
0:25:03.007149 PROGRESS: 
0:25:03.007195 PROGRESS: Precursor Summary:
0:25:03.008185 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
0:25:03.008276 PROGRESS: 
0:25:03.008332 PROGRESS: Protein Summary:
0:25:03.009401 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
0:25:03.009495 PROGRESS: =========================================================================
0:25:03.953511 INFO: Starting optimization step 5.
0:25:03.954008 PROGRESS: === Extracting elution groups 248000 to 504000 ===
0:25:03.954103 PROGRESS: Extracting batch of 505949 precursors
0:25:04.102005 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:25:04.102245 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:25:04.102301 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:25:04.102325 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:25:04.102723 INFO: Starting candidate selection
0:25:36.036844 INFO: Starting candidate scoring
0:25:39.644374 INFO: Finished candidate processing
0:25:39.644692 INFO: Collecting candidate features
0:25:41.546686 WARNING: intensity_correlation has 7 NaNs ( 0.00 % out of 504790)
0:25:41.566822 INFO: Collecting fragment features
0:25:42.109611 INFO: Finished candidate scoring
0:25:43.212488 PROGRESS: === Extracted 993762 precursors and 9806270 fragments ===
0:25:43.411634 INFO: performing precursor FDR with 47 features
0:25:43.411793 INFO: Decoy channel: -1
0:25:43.411820 INFO: Competetive: True
0:25:44.085736 INFO: Setting torch num_threads to 2 for FDR classification task
0:25:44.396337 WARNING: dropped 2 target PSMs due to missing features
0:25:44.396597 WARNING: dropped 8 decoy PSMs due to missing features
0:26:05.544355 INFO: Test AUC: 0.567
0:26:05.544580 INFO: Train AUC: 0.578
0:26:05.544620 INFO: AUC difference: 1.80%
0:26:05.713575 INFO: Resetting torch num_threads to 100
0:26:05.799415 INFO: === FDR correction performed with classifier version -1 ===
0:26:05.800395 PROGRESS: ============================= Precursor FDR =============================
0:26:05.800498 PROGRESS: Total precursors accumulated: 149
0:26:05.800561 PROGRESS: Target precursors: 136 (91.28%)
0:26:05.800616 PROGRESS: Decoy precursors: 13 (8.72%)
0:26:05.800667 PROGRESS: 
0:26:05.800738 PROGRESS: Precursor Summary:
0:26:05.801708 PROGRESS: Channel   0:	 0.05 FDR:    71; 0.01 FDR:    32; 0.001 FDR:    32
0:26:05.802757 PROGRESS: 
0:26:05.802818 PROGRESS: Protein Summary:
0:26:05.803850 PROGRESS: Channel   0:	 0.05 FDR:    70; 0.01 FDR:    32; 0.001 FDR:    32
0:26:05.803939 PROGRESS: =========================================================================
0:26:07.231350 INFO: Starting optimization step 6.
0:26:07.231704 PROGRESS: === Extracting elution groups 504000 to 1016000 ===
0:26:07.231798 PROGRESS: Extracting batch of 1011924 precursors
0:26:07.522293 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:26:07.522449 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:26:07.522497 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:26:07.522520 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:26:07.522885 INFO: Starting candidate selection
0:27:12.151320 INFO: Starting candidate scoring
0:27:18.699342 INFO: Finished candidate processing
0:27:18.699726 INFO: Collecting candidate features
0:27:21.766134 WARNING: intensity_correlation has 5 NaNs ( 0.00 % out of 1009388)
0:27:21.803101 INFO: Collecting fragment features
0:27:22.788806 INFO: Finished candidate scoring
0:27:24.639848 PROGRESS: === Extracted 2003150 precursors and 19769679 fragments ===
0:27:24.996479 INFO: performing precursor FDR with 47 features
0:27:24.996681 INFO: Decoy channel: -1
0:27:24.996736 INFO: Competetive: True
0:27:26.297523 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:26.860616 WARNING: dropped 3 target PSMs due to missing features
0:27:26.860788 WARNING: dropped 12 decoy PSMs due to missing features
0:28:07.853516 INFO: Test AUC: 0.573
0:28:07.853763 INFO: Train AUC: 0.579
0:28:07.853799 INFO: AUC difference: 0.95%
0:28:08.100910 INFO: Resetting torch num_threads to 100
0:28:08.236685 INFO: === FDR correction performed with classifier version -1 ===
0:28:08.237842 PROGRESS: ============================= Precursor FDR =============================
0:28:08.237946 PROGRESS: Total precursors accumulated: 893
0:28:08.238009 PROGRESS: Target precursors: 818 (91.60%)
0:28:08.238061 PROGRESS: Decoy precursors: 75 (8.40%)
0:28:08.238110 PROGRESS: 
0:28:08.238155 PROGRESS: Precursor Summary:
0:28:08.239313 PROGRESS: Channel   0:	 0.05 FDR:   570; 0.01 FDR:   361; 0.001 FDR:   176
0:28:08.239411 PROGRESS: 
0:28:08.239467 PROGRESS: Protein Summary:
0:28:08.240732 PROGRESS: Channel   0:	 0.05 FDR:   521; 0.01 FDR:   332; 0.001 FDR:   167
0:28:08.240830 PROGRESS: =========================================================================
0:28:08.545498 INFO: fragments_df_filtered: 3347
0:28:10.993586 INFO: calibration group: precursor, fitting mz estimator 
0:28:11.092048 INFO: calibration group: precursor, fitting rt estimator 
0:28:11.281852 INFO: calibration group: fragment, fitting mz estimator 
0:28:11.542458 INFO: calibration group: precursor, predicting mz
0:28:11.841416 INFO: calibration group: precursor, predicting rt
0:28:13.362248 INFO: calibration group: fragment, predicting mz
0:28:16.793465 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:28:16.794171 INFO: Starting optimization step 7.
0:28:16.794304 PROGRESS: === Extracting elution groups 0 to 1016000 ===
0:28:16.794478 PROGRESS: Extracting batch of 2008106 precursors
0:28:17.616501 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:28:17.616642 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:28:17.616693 INFO: FWHM in RT is 2.71 seconds, sigma is 0.35
0:28:17.616726 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:28:17.617186 INFO: Starting candidate selection
0:29:50.737870 INFO: Starting candidate scoring
0:30:18.821940 INFO: Finished candidate processing
0:30:18.822463 INFO: Collecting candidate features
0:30:26.464127 WARNING: intensity_correlation has 10 NaNs ( 0.00 % out of 4006376)
0:30:26.600987 INFO: Collecting fragment features
0:30:29.445935 INFO: Finished candidate scoring
0:30:33.343830 PROGRESS: === Extracted 4006376 precursors and 38962881 fragments ===
0:30:33.344408 INFO: performing precursor FDR with 47 features
0:30:33.344464 INFO: Decoy channel: -1
0:30:33.344495 INFO: Competetive: True
0:30:34.480314 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:35.191367 WARNING: dropped 4 target PSMs due to missing features
0:30:35.191515 WARNING: dropped 6 decoy PSMs due to missing features
0:31:44.899128 INFO: Test AUC: 0.578
0:31:44.899389 INFO: Train AUC: 0.582
0:31:44.899427 INFO: AUC difference: 0.63%
0:31:45.281874 INFO: Resetting torch num_threads to 100
0:31:45.452743 INFO: === FDR correction performed with classifier version 6 ===
0:31:45.454232 PROGRESS: ============================= Precursor FDR =============================
0:31:45.454377 PROGRESS: Total precursors accumulated: 1,898
0:31:45.454439 PROGRESS: Target precursors: 1,728 (91.04%)
0:31:45.454492 PROGRESS: Decoy precursors: 170 (8.96%)
0:31:45.454540 PROGRESS: 
0:31:45.454600 PROGRESS: Precursor Summary:
0:31:45.456092 PROGRESS: Channel   0:	 0.05 FDR: 1,362; 0.01 FDR:   926; 0.001 FDR:   569
0:31:45.456193 PROGRESS: 
0:31:45.456252 PROGRESS: Protein Summary:
0:31:45.457838 PROGRESS: Channel   0:	 0.05 FDR: 1,131; 0.01 FDR:   765; 0.001 FDR:   501
0:31:45.457933 PROGRESS: =========================================================================
0:31:45.607476 INFO: fragments_df_filtered: 5000
0:31:46.337267 INFO: calibration group: precursor, fitting mz estimator 
0:31:46.386519 INFO: calibration group: precursor, fitting rt estimator 
0:31:46.436218 INFO: calibration group: fragment, fitting mz estimator 
0:31:46.788891 INFO: calibration group: precursor, predicting mz
0:31:46.856064 INFO: calibration group: precursor, predicting rt
0:31:47.182897 INFO: calibration group: fragment, predicting mz
0:31:47.945442 INFO: === checking if optimization conditions were reached ===
0:31:47.947620 PROGRESS: ❌ ms2_error      : 14.1126 > 8.0000 or insufficient steps taken.
0:31:47.948652 PROGRESS: ❌ ms1_error      : 15.5144 > 3.0000 or insufficient steps taken.
0:31:47.948719 INFO: ==============================================
0:31:47.948819 INFO: Starting optimization step 8.
0:31:47.948885 PROGRESS: === Extracting elution groups 0 to 248000 ===
0:31:47.948951 PROGRESS: Extracting batch of 490233 precursors
0:31:48.062684 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:31:48.062820 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:31:48.062859 INFO: FWHM in RT is 2.89 seconds, sigma is 0.37
0:31:48.062882 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:31:48.063167 INFO: Starting candidate selection
0:32:11.417590 INFO: Starting candidate scoring
0:32:18.682391 INFO: Finished candidate processing
0:32:18.682582 INFO: Collecting candidate features
0:32:20.773007 WARNING: intensity_correlation has 19 NaNs ( 0.00 % out of 977358)
0:32:20.812017 INFO: Collecting fragment features
0:32:21.552982 INFO: Finished candidate scoring
0:32:23.039130 PROGRESS: === Extracted 977358 precursors and 8297505 fragments ===
0:32:23.039629 INFO: performing precursor FDR with 47 features
0:32:23.039669 INFO: Decoy channel: -1
0:32:23.039694 INFO: Competetive: True
0:32:23.492276 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:23.808078 WARNING: dropped 8 target PSMs due to missing features
0:32:23.808247 WARNING: dropped 11 decoy PSMs due to missing features
0:32:42.381827 INFO: Test AUC: 0.574
0:32:42.382051 INFO: Train AUC: 0.585
0:32:42.382086 INFO: AUC difference: 1.92%
0:32:42.555137 INFO: Resetting torch num_threads to 100
0:32:42.670566 INFO: === FDR correction performed with classifier version 7 ===
0:32:42.671659 PROGRESS: ============================= Precursor FDR =============================
0:32:42.671760 PROGRESS: Total precursors accumulated: 860
0:32:42.671822 PROGRESS: Target precursors: 784 (91.16%)
0:32:42.671875 PROGRESS: Decoy precursors: 76 (8.84%)
0:32:42.671922 PROGRESS: 
0:32:42.671966 PROGRESS: Precursor Summary:
0:32:42.673039 PROGRESS: Channel   0:	 0.05 FDR:   542; 0.01 FDR:   370; 0.001 FDR:   283
0:32:42.673135 PROGRESS: 
0:32:42.673193 PROGRESS: Protein Summary:
0:32:42.674432 PROGRESS: Channel   0:	 0.05 FDR:   511; 0.01 FDR:   356; 0.001 FDR:   273
0:32:42.674523 PROGRESS: =========================================================================
0:32:42.730533 INFO: fragments_df_filtered: 3985
0:32:43.678021 INFO: calibration group: precursor, fitting mz estimator 
0:32:43.825077 INFO: calibration group: precursor, fitting rt estimator 
0:32:43.918701 INFO: calibration group: fragment, fitting mz estimator 
0:32:44.226815 INFO: calibration group: precursor, predicting mz
0:32:44.295959 INFO: calibration group: precursor, predicting rt
0:32:44.647292 INFO: calibration group: fragment, predicting mz
0:32:45.505845 INFO: === checking if optimization conditions were reached ===
0:32:45.508242 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
0:32:45.509243 PROGRESS: ❌ ms1_error      : 7.0439 > 3.0000 or insufficient steps taken.
0:32:45.509294 INFO: ==============================================
0:32:45.509397 INFO: Starting optimization step 9.
0:32:45.509473 PROGRESS: === Extracting elution groups 0 to 248000 ===
0:32:45.509544 PROGRESS: Extracting batch of 490233 precursors
0:32:45.651434 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:32:45.651602 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:32:45.651643 INFO: FWHM in RT is 2.60 seconds, sigma is 0.33
0:32:45.651667 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:32:45.652023 INFO: Starting candidate selection
0:33:08.755789 INFO: Starting candidate scoring
0:33:16.044967 INFO: Finished candidate processing
0:33:16.045151 INFO: Collecting candidate features
0:33:18.289625 WARNING: intensity_correlation has 45 NaNs ( 0.00 % out of 976065)
0:33:18.325878 INFO: Collecting fragment features
0:33:18.963169 INFO: Finished candidate scoring
0:33:20.044368 PROGRESS: === Extracted 976065 precursors and 7164237 fragments ===
0:33:20.044895 INFO: performing precursor FDR with 47 features
0:33:20.044939 INFO: Decoy channel: -1
0:33:20.044965 INFO: Competetive: True
0:33:20.383636 INFO: Setting torch num_threads to 2 for FDR classification task
0:33:20.642607 WARNING: dropped 23 target PSMs due to missing features
0:33:20.642783 WARNING: dropped 22 decoy PSMs due to missing features
0:33:38.230694 INFO: Test AUC: 0.575
0:33:38.230948 INFO: Train AUC: 0.586
0:33:38.230982 INFO: AUC difference: 1.90%
0:33:38.395134 INFO: Resetting torch num_threads to 100
0:33:38.430241 INFO: === FDR correction performed with classifier version 8 ===
0:33:38.431285 PROGRESS: ============================= Precursor FDR =============================
0:33:38.431384 PROGRESS: Total precursors accumulated: 1,105
0:33:38.431446 PROGRESS: Target precursors: 1,012 (91.58%)
0:33:38.431498 PROGRESS: Decoy precursors: 93 (8.42%)
0:33:38.431544 PROGRESS: 
0:33:38.431603 PROGRESS: Precursor Summary:
0:33:38.432738 PROGRESS: Channel   0:	 0.05 FDR:   820; 0.01 FDR:   583; 0.001 FDR:   362
0:33:38.432834 PROGRESS: 
0:33:38.432889 PROGRESS: Protein Summary:
0:33:38.434213 PROGRESS: Channel   0:	 0.05 FDR:   762; 0.01 FDR:   547; 0.001 FDR:   346
0:33:38.434307 PROGRESS: =========================================================================
0:33:38.471010 INFO: fragments_df_filtered: 5000
0:33:38.995508 INFO: calibration group: precursor, fitting mz estimator 
0:33:39.129799 INFO: calibration group: precursor, fitting rt estimator 
0:33:39.189195 INFO: calibration group: fragment, fitting mz estimator 
0:33:39.626416 INFO: calibration group: precursor, predicting mz
0:33:39.663311 INFO: calibration group: precursor, predicting rt
0:33:39.821658 INFO: calibration group: fragment, predicting mz
0:33:40.213051 INFO: === checking if optimization conditions were reached ===
0:33:40.213425 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
0:33:40.215069 PROGRESS: ❌ ms1_error      : 3.4846 > 3.0000 or insufficient steps taken.
0:33:40.215128 INFO: ==============================================
0:33:40.215237 INFO: Starting optimization step 10.
0:33:40.215314 PROGRESS: === Extracting elution groups 0 to 120000 ===
0:33:40.215418 PROGRESS: Extracting batch of 237213 precursors
0:33:40.297916 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:33:40.298066 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:33:40.298105 INFO: FWHM in RT is 2.42 seconds, sigma is 0.31
0:33:40.298128 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:33:40.298441 INFO: Starting candidate selection
0:33:52.039127 INFO: Starting candidate scoring
0:33:55.476830 INFO: Finished candidate processing
0:33:55.477027 INFO: Collecting candidate features
0:33:57.462206 WARNING: intensity_correlation has 17 NaNs ( 0.00 % out of 472331)
0:33:57.481611 INFO: Collecting fragment features
0:33:57.793619 INFO: Finished candidate scoring
0:33:58.138250 PROGRESS: === Extracted 472331 precursors and 3463575 fragments ===
0:33:58.138846 INFO: performing precursor FDR with 47 features
0:33:58.138888 INFO: Decoy channel: -1
0:33:58.138915 INFO: Competetive: True
0:33:58.375637 INFO: Setting torch num_threads to 2 for FDR classification task
0:33:58.519597 WARNING: dropped 12 target PSMs due to missing features
0:33:58.519778 WARNING: dropped 5 decoy PSMs due to missing features
0:34:07.600222 INFO: Test AUC: 0.573
0:34:07.601038 INFO: Train AUC: 0.591
0:34:07.601085 INFO: AUC difference: 3.04%
0:34:07.728117 INFO: Resetting torch num_threads to 100
0:34:07.792258 INFO: === FDR correction performed with classifier version 9 ===
0:34:07.793294 PROGRESS: ============================= Precursor FDR =============================
0:34:07.793395 PROGRESS: Total precursors accumulated: 653
0:34:07.793456 PROGRESS: Target precursors: 596 (91.27%)
0:34:07.793509 PROGRESS: Decoy precursors: 57 (8.73%)
0:34:07.793556 PROGRESS: 
0:34:07.793602 PROGRESS: Precursor Summary:
0:34:07.794538 PROGRESS: Channel   0:	 0.05 FDR:   385; 0.01 FDR:   215; 0.001 FDR:   162
0:34:07.794629 PROGRESS: 
0:34:07.794683 PROGRESS: Protein Summary:
0:34:07.795777 PROGRESS: Channel   0:	 0.05 FDR:   378; 0.01 FDR:   213; 0.001 FDR:   161
0:34:07.795866 PROGRESS: =========================================================================
0:34:07.810807 INFO: fragments_df_filtered: 2083
0:34:08.420491 INFO: calibration group: precursor, fitting mz estimator 
0:34:08.488961 INFO: calibration group: precursor, fitting rt estimator 
0:34:08.576881 INFO: calibration group: fragment, fitting mz estimator 
0:34:08.720374 INFO: calibration group: precursor, predicting mz
0:34:08.758096 INFO: calibration group: precursor, predicting rt
0:34:08.934849 INFO: calibration group: fragment, predicting mz
0:34:09.334091 INFO: === checking if optimization conditions were reached ===
0:34:09.334557 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
0:34:09.336631 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
0:34:09.336688 INFO: ==============================================
0:34:09.336819 PROGRESS: Optimization finished for ms2_error, ms1_error.
0:34:09.848362 INFO: calibration group: precursor, predicting mz
0:34:09.885021 INFO: calibration group: precursor, predicting rt
0:34:10.056010 INFO: calibration group: fragment, predicting mz
0:34:10.456468 INFO: Starting optimization step 0.
0:34:10.456830 PROGRESS: === Extracting elution groups 0 to 120000 ===
0:34:10.456941 PROGRESS: Extracting batch of 237213 precursors
0:34:10.549701 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:34:10.549857 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:34:10.549899 INFO: FWHM in RT is 2.35 seconds, sigma is 0.30
0:34:10.549923 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:34:10.550292 INFO: Starting candidate selection
0:34:22.467182 INFO: Starting candidate scoring
0:34:25.884457 INFO: Finished candidate processing
0:34:25.884608 INFO: Collecting candidate features
0:34:26.926410 WARNING: intensity_correlation has 15 NaNs ( 0.00 % out of 472375)
0:34:26.944972 INFO: Collecting fragment features
0:34:27.209185 INFO: Finished candidate scoring
0:34:27.728288 PROGRESS: === Extracted 472375 precursors and 3462924 fragments ===
0:34:27.728847 INFO: performing precursor FDR with 47 features
0:34:27.728904 INFO: Decoy channel: -1
0:34:27.728931 INFO: Competetive: True
0:34:27.905776 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:28.006348 WARNING: dropped 10 target PSMs due to missing features
0:34:28.006510 WARNING: dropped 5 decoy PSMs due to missing features
0:34:36.860609 INFO: Test AUC: 0.576
0:34:36.860857 INFO: Train AUC: 0.596
0:34:36.860894 INFO: AUC difference: 3.32%
0:34:36.990334 INFO: Resetting torch num_threads to 100
0:34:37.006031 INFO: === FDR correction performed with classifier version 10 ===
0:34:37.006976 PROGRESS: ============================= Precursor FDR =============================
0:34:37.007094 PROGRESS: Total precursors accumulated: 763
0:34:37.007159 PROGRESS: Target precursors: 694 (90.96%)
0:34:37.007211 PROGRESS: Decoy precursors: 69 (9.04%)
0:34:37.007260 PROGRESS: 
0:34:37.007306 PROGRESS: Precursor Summary:
0:34:37.008280 PROGRESS: Channel   0:	 0.05 FDR:   355; 0.01 FDR:   202; 0.001 FDR:   165
0:34:37.008372 PROGRESS: 
0:34:37.008429 PROGRESS: Protein Summary:
0:34:37.009551 PROGRESS: Channel   0:	 0.05 FDR:   351; 0.01 FDR:   201; 0.001 FDR:   164
0:34:37.009644 PROGRESS: =========================================================================
0:34:37.024095 INFO: fragments_df_filtered: 1921
0:34:37.522137 INFO: calibration group: precursor, fitting mz estimator 
0:34:37.584186 INFO: calibration group: precursor, fitting rt estimator 
0:34:37.632402 INFO: calibration group: fragment, fitting mz estimator 
0:34:37.762643 INFO: calibration group: precursor, predicting mz
0:34:37.799250 INFO: calibration group: precursor, predicting rt
0:34:37.969587 INFO: calibration group: fragment, predicting mz
0:34:38.344922 INFO: === checking if optimization conditions were reached ===
0:34:38.345308 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:34:38.347531 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 254.0595.
0:34:38.347591 INFO: ==============================================
0:34:38.347737 INFO: Starting optimization step 1.
0:34:38.347825 PROGRESS: === Extracting elution groups 0 to 120000 ===
0:34:38.347936 PROGRESS: Extracting batch of 237213 precursors
0:34:38.421720 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:34:38.421868 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:34:38.421909 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
0:34:38.421931 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:34:38.422220 INFO: Starting candidate selection
0:34:49.082592 INFO: Starting candidate scoring
0:34:52.385381 INFO: Finished candidate processing
0:34:52.385503 INFO: Collecting candidate features
0:34:53.255225 WARNING: intensity_correlation has 45 NaNs ( 0.01 % out of 470255)
0:34:53.275514 INFO: Collecting fragment features
0:34:53.575885 INFO: Finished candidate scoring
0:34:53.942680 PROGRESS: === Extracted 470255 precursors and 3354029 fragments ===
0:34:53.943193 INFO: performing precursor FDR with 47 features
0:34:53.943233 INFO: Decoy channel: -1
0:34:53.943258 INFO: Competetive: True
0:34:54.154626 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:54.264801 WARNING: dropped 14 target PSMs due to missing features
0:34:54.264948 WARNING: dropped 31 decoy PSMs due to missing features
0:35:00.559976 INFO: Test AUC: 0.572
0:35:00.560128 INFO: Train AUC: 0.591
0:35:00.560160 INFO: AUC difference: 3.16%
0:35:00.682660 INFO: Resetting torch num_threads to 100
0:35:00.738446 INFO: === FDR correction performed with classifier version 10 ===
0:35:00.739492 PROGRESS: ============================= Precursor FDR =============================
0:35:00.739586 PROGRESS: Total precursors accumulated: 748
0:35:00.739646 PROGRESS: Target precursors: 681 (91.04%)
0:35:00.739695 PROGRESS: Decoy precursors: 67 (8.96%)
0:35:00.739740 PROGRESS: 
0:35:00.739783 PROGRESS: Precursor Summary:
0:35:00.740820 PROGRESS: Channel   0:	 0.05 FDR:   449; 0.01 FDR:   255; 0.001 FDR:   137
0:35:00.740911 PROGRESS: 
0:35:00.740982 PROGRESS: Protein Summary:
0:35:00.742141 PROGRESS: Channel   0:	 0.05 FDR:   435; 0.01 FDR:   251; 0.001 FDR:   137
0:35:00.742231 PROGRESS: =========================================================================
0:35:00.758312 INFO: fragments_df_filtered: 2381
0:35:01.233615 INFO: calibration group: precursor, fitting mz estimator 
0:35:01.286001 INFO: calibration group: precursor, fitting rt estimator 
0:35:01.337320 INFO: calibration group: fragment, fitting mz estimator 
0:35:01.509043 INFO: calibration group: precursor, predicting mz
0:35:01.544131 INFO: calibration group: precursor, predicting rt
0:35:01.706089 INFO: calibration group: fragment, predicting mz
0:35:02.102003 INFO: === checking if optimization conditions were reached ===
0:35:02.102415 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:35:02.104964 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 158.3915.
0:35:02.105053 INFO: ==============================================
0:35:02.105189 INFO: Starting optimization step 2.
0:35:02.105287 PROGRESS: === Extracting elution groups 0 to 120000 ===
0:35:02.105388 PROGRESS: Extracting batch of 237213 precursors
0:35:02.202688 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:35:02.202854 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:02.202894 INFO: FWHM in RT is 2.42 seconds, sigma is 0.31
0:35:02.202918 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:35:02.203205 INFO: Starting candidate selection
0:35:12.313443 INFO: Starting candidate scoring
0:35:15.709896 INFO: Finished candidate processing
0:35:15.710155 INFO: Collecting candidate features
0:35:16.836615 WARNING: intensity_correlation has 66 NaNs ( 0.01 % out of 467443)
0:35:16.856557 INFO: Collecting fragment features
0:35:17.204009 INFO: Finished candidate scoring
0:35:17.845093 PROGRESS: === Extracted 467443 precursors and 3205455 fragments ===
0:35:17.845670 INFO: performing precursor FDR with 47 features
0:35:17.845711 INFO: Decoy channel: -1
0:35:17.845737 INFO: Competetive: True
0:35:18.050124 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:18.180081 WARNING: dropped 36 target PSMs due to missing features
0:35:18.180280 WARNING: dropped 30 decoy PSMs due to missing features
0:35:26.958968 INFO: Test AUC: 0.571
0:35:26.959173 INFO: Train AUC: 0.589
0:35:26.959207 INFO: AUC difference: 3.00%
0:35:27.087252 INFO: Resetting torch num_threads to 100
0:35:27.104268 INFO: === FDR correction performed with classifier version 10 ===
0:35:27.106072 PROGRESS: ============================= Precursor FDR =============================
0:35:27.106320 PROGRESS: Total precursors accumulated: 773
0:35:27.106444 PROGRESS: Target precursors: 703 (90.94%)
0:35:27.106528 PROGRESS: Decoy precursors: 70 (9.06%)
0:35:27.106584 PROGRESS: 
0:35:27.106634 PROGRESS: Precursor Summary:
0:35:27.108304 PROGRESS: Channel   0:	 0.05 FDR:   503; 0.01 FDR:   309; 0.001 FDR:   151
0:35:27.108454 PROGRESS: 
0:35:27.108522 PROGRESS: Protein Summary:
0:35:27.110029 PROGRESS: Channel   0:	 0.05 FDR:   490; 0.01 FDR:   304; 0.001 FDR:   150
0:35:27.110152 PROGRESS: =========================================================================
0:35:27.129052 INFO: fragments_df_filtered: 2774
0:35:27.683360 INFO: calibration group: precursor, fitting mz estimator 
0:35:27.750422 INFO: calibration group: precursor, fitting rt estimator 
0:35:27.801571 INFO: calibration group: fragment, fitting mz estimator 
0:35:28.011343 INFO: calibration group: precursor, predicting mz
0:35:28.051235 INFO: calibration group: precursor, predicting rt
0:35:28.227841 INFO: calibration group: fragment, predicting mz
0:35:28.797852 INFO: === checking if optimization conditions were reached ===
0:35:28.798201 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:35:28.800755 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 153.6449.
0:35:28.800838 INFO: ==============================================
0:35:28.800948 INFO: Starting optimization step 3.
0:35:28.801024 PROGRESS: === Extracting elution groups 0 to 120000 ===
0:35:28.801107 PROGRESS: Extracting batch of 237213 precursors
0:35:28.903047 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:35:28.903201 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:28.903249 INFO: FWHM in RT is 2.42 seconds, sigma is 0.31
0:35:28.903276 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:35:28.903609 INFO: Starting candidate selection
0:35:38.779880 INFO: Starting candidate scoring
0:35:42.227178 INFO: Finished candidate processing
0:35:42.227350 INFO: Collecting candidate features
0:35:43.421445 WARNING: intensity_correlation has 66 NaNs ( 0.01 % out of 466558)
0:35:43.441460 INFO: Collecting fragment features
0:35:43.768193 INFO: Finished candidate scoring
0:35:44.158621 PROGRESS: === Extracted 466558 precursors and 3146623 fragments ===
0:35:44.159179 INFO: performing precursor FDR with 47 features
0:35:44.159220 INFO: Decoy channel: -1
0:35:44.159245 INFO: Competetive: True
0:35:44.375017 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:44.501675 WARNING: dropped 33 target PSMs due to missing features
0:35:44.501837 WARNING: dropped 33 decoy PSMs due to missing features
0:35:53.079883 INFO: Test AUC: 0.570
0:35:53.080097 INFO: Train AUC: 0.588
0:35:53.080135 INFO: AUC difference: 2.98%
0:35:53.209672 INFO: Resetting torch num_threads to 100
0:35:53.226482 INFO: === FDR correction performed with classifier version 10 ===
0:35:53.227571 PROGRESS: ============================= Precursor FDR =============================
0:35:53.227673 PROGRESS: Total precursors accumulated: 788
0:35:53.227748 PROGRESS: Target precursors: 715 (90.74%)
0:35:53.227812 PROGRESS: Decoy precursors: 73 (9.26%)
0:35:53.227865 PROGRESS: 
0:35:53.227916 PROGRESS: Precursor Summary:
0:35:53.229069 PROGRESS: Channel   0:	 0.05 FDR:   519; 0.01 FDR:   319; 0.001 FDR:   252
0:35:53.229172 PROGRESS: 
0:35:53.229237 PROGRESS: Protein Summary:
0:35:53.230510 PROGRESS: Channel   0:	 0.05 FDR:   504; 0.01 FDR:   315; 0.001 FDR:   249
0:35:53.230608 PROGRESS: =========================================================================
0:35:53.249812 INFO: fragments_df_filtered: 2823
0:35:53.762626 INFO: calibration group: precursor, fitting mz estimator 
0:35:53.819704 INFO: calibration group: precursor, fitting rt estimator 
0:35:53.866998 INFO: calibration group: fragment, fitting mz estimator 
0:35:54.068892 INFO: calibration group: precursor, predicting mz
0:35:54.106349 INFO: calibration group: precursor, predicting rt
0:35:54.264160 INFO: calibration group: fragment, predicting mz
0:35:54.663475 INFO: === checking if optimization conditions were reached ===
0:35:54.663887 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:35:54.665506 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 153.6449 found after 4 searches.
0:35:54.665588 INFO: ==============================================
0:35:54.665715 PROGRESS: Optimization finished for rt_error.
0:35:55.115812 INFO: calibration group: precursor, predicting mz
0:35:55.175236 INFO: calibration group: precursor, predicting rt
0:35:55.353752 INFO: calibration group: fragment, predicting mz
0:35:55.782575 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:35:55.782839 PROGRESS: ==============================================
0:35:55.782932 PROGRESS: ms2_error      : 8.0000
0:35:55.783012 PROGRESS: ms1_error      : 3.0000
0:35:55.783087 PROGRESS: rt_error       : 153.6449
0:35:55.783157 PROGRESS: ==============================================
0:35:55.783997 INFO: calibration group: precursor, predicting mz
0:35:57.433842 INFO: calibration group: precursor, predicting rt
0:36:04.711166 INFO: calibration group: fragment, predicting mz
0:36:21.801216 PROGRESS: Extracting batch of 10183864 precursors
0:36:24.063061 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:36:24.063229 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:36:24.063276 INFO: FWHM in RT is 2.42 seconds, sigma is 0.31
0:36:24.063304 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:36:24.063707 INFO: Starting candidate selection
0:43:07.636860 INFO: Applying score cutoff of 40.921551628112795
0:43:08.068860 INFO: Removed 10648349 precursors with score below cutoff
0:43:10.784248 INFO: Starting candidate scoring
0:44:21.658478 INFO: Finished candidate processing
0:44:21.658981 INFO: Collecting candidate features
0:44:39.816741 WARNING: intensity_correlation has 95 NaNs ( 0.00 % out of 9669226)
0:44:40.141951 INFO: Collecting fragment features
0:44:46.565273 INFO: Finished candidate scoring
0:44:55.573605 INFO: === FDR correction performed with classifier version 14 ===
0:44:55.587046 INFO: performing precursor FDR with 47 features
0:44:55.587131 INFO: Decoy channel: -1
0:44:55.587158 INFO: Competetive: True
0:44:58.473964 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:00.282324 WARNING: dropped 51 target PSMs due to missing features
0:45:00.282477 WARNING: dropped 44 decoy PSMs due to missing features
0:48:05.354651 INFO: Test AUC: 0.576
0:48:05.354927 INFO: Train AUC: 0.585
0:48:05.354968 INFO: AUC difference: 1.54%
0:48:06.126585 INFO: Resetting torch num_threads to 100
0:48:06.518359 INFO: Removing fragments below FDR threshold
0:48:07.138934 PROGRESS: ============================= Precursor FDR =============================
0:48:07.139312 PROGRESS: Total precursors accumulated: 15,554
0:48:07.139380 PROGRESS: Target precursors: 15,400 (99.01%)
0:48:07.139432 PROGRESS: Decoy precursors: 154 (0.99%)
0:48:07.139479 PROGRESS: 
0:48:07.139523 PROGRESS: Precursor Summary:
0:48:07.147295 PROGRESS: Channel   0:	 0.05 FDR: 15,400; 0.01 FDR: 15,396; 0.001 FDR: 10,067
0:48:07.147780 PROGRESS: 
0:48:07.147841 PROGRESS: Protein Summary:
0:48:07.162561 PROGRESS: Channel   0:	 0.05 FDR: 6,135; 0.01 FDR: 6,134; 0.001 FDR: 4,514
0:48:07.162857 PROGRESS: =========================================================================
0:48:07.436110 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:48:07.994730 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:48:07.994982 INFO: Quantification results path: run_output_Astral/alphadia_1.10_MBRSetValues/library/quant
0:48:07.995086 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2 at run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:48:07.995963 INFO: Initializing RawFileManager
0:48:39.455812 INFO: Determining DIA cycle
0:48:39.472242 INFO: Found cycle with start 0.00 min and length 303.
0:48:39.740588 INFO: RT (min)            : 0.0 - 26.9
0:48:39.740710 INFO: RT duration (sec)   : 1611.2
0:48:39.740749 INFO: RT duration (min)   : 26.9
0:48:39.740779 INFO: Cycle len (scans)   : 303
0:48:39.740803 INFO: Cycle len (sec)     : 1.65
0:48:39.740827 INFO: Number of cycles    : 978
0:48:39.740850 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:48:41.582119 INFO: Initializing CalibrationManager
0:48:41.582439 INFO: Loading calibration config
0:48:41.583613 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed'], 'function': LOESSRegression()}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed'], 'function': LOESSRegression(n_kernels=2)}], 'name': 'precursor'}]
0:48:41.583726 INFO: Calibration group :fragment, found 1 estimator(s)
0:48:41.583826 INFO: Calibration group :precursor, found 3 estimator(s)
0:48:41.583914 INFO: Disabling ion mobility calibration
0:48:41.583944 INFO: removed mobility estimator from group precursor
0:48:41.584097 INFO: Initializing OptimizationManager
0:48:41.584214 INFO: initial parameter: ms1_error = 30
0:48:41.584276 INFO: initial parameter: ms2_error = 30
0:48:41.584330 INFO: initial parameter: rt_error = 805.6019897460938
0:48:41.584376 INFO: initial parameter: mobility_error = 0.1
0:48:41.584420 INFO: initial parameter: column_type = library
0:48:41.584464 INFO: initial parameter: num_candidates = 1
0:48:41.584504 INFO: initial parameter: classifier_version = -1
0:48:41.584544 INFO: initial parameter: fwhm_rt = 5
0:48:41.584587 INFO: initial parameter: fwhm_mobility = 0.01
0:48:41.584628 INFO: initial parameter: score_cutoff = 0
0:48:41.584690 INFO: Initializing TimingManager
0:48:41.584777 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:48:41.584897 INFO: FDRManager not loaded from disk.
0:48:41.584922 INFO: Initializing FDRManager
0:48:41.584955 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:48:43.148061 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
0:48:45.443756 PROGRESS: Starting initial search for precursors.
0:48:45.697326 INFO: Starting optimization step 0.
0:48:45.697623 PROGRESS: === Extracting elution groups 0 to 8000 ===
0:48:45.697704 PROGRESS: Extracting batch of 15815 precursors
0:48:45.702529 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:48:45.702598 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:48:45.702635 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:48:45.702658 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:48:45.702961 INFO: Starting candidate selection
0:48:47.046587 INFO: Starting candidate scoring
0:48:47.202414 INFO: Finished candidate processing
0:48:47.202584 INFO: Collecting candidate features
0:48:47.249356 INFO: Collecting fragment features
0:48:47.268434 INFO: Finished candidate scoring
0:48:47.279797 PROGRESS: === Extracted 15768 precursors and 154571 fragments ===
0:48:47.280233 INFO: performing precursor FDR with 47 features
0:48:47.280272 INFO: Decoy channel: -1
0:48:47.280298 INFO: Competetive: True
0:48:47.285761 INFO: Setting torch num_threads to 2 for FDR classification task
0:48:47.525569 INFO: Test AUC: 0.532
0:48:47.525722 INFO: Train AUC: 0.527
0:48:47.525755 INFO: AUC difference: 0.86%
0:48:47.625068 INFO: Resetting torch num_threads to 100
0:48:47.626772 INFO: === FDR correction performed with classifier version -1 ===
0:48:47.629183 PROGRESS: ============================= Precursor FDR =============================
0:48:47.629336 PROGRESS: Total precursors accumulated: 7,980
0:48:47.629400 PROGRESS: Target precursors: 4,265 (53.45%)
0:48:47.629450 PROGRESS: Decoy precursors: 3,715 (46.55%)
0:48:47.629497 PROGRESS: 
0:48:47.629540 PROGRESS: Precursor Summary:
0:48:47.630479 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:48:47.630571 PROGRESS: 
0:48:47.630627 PROGRESS: Protein Summary:
0:48:47.631601 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:48:47.631697 PROGRESS: =========================================================================
0:48:47.754751 INFO: Starting optimization step 1.
0:48:47.755065 PROGRESS: === Extracting elution groups 8000 to 24000 ===
0:48:47.755138 PROGRESS: Extracting batch of 31636 precursors
0:48:47.763950 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:48:47.764086 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:48:47.764121 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:48:47.764160 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:48:47.764383 INFO: Starting candidate selection
0:48:50.145942 INFO: Starting candidate scoring
0:48:50.421421 INFO: Finished candidate processing
0:48:50.421586 INFO: Collecting candidate features
0:48:50.495652 INFO: Collecting fragment features
0:48:50.519629 INFO: Finished candidate scoring
0:48:50.570117 PROGRESS: === Extracted 47335 precursors and 465306 fragments ===
0:48:50.577771 INFO: performing precursor FDR with 47 features
0:48:50.577915 INFO: Decoy channel: -1
0:48:50.577942 INFO: Competetive: True
0:48:50.605349 INFO: Setting torch num_threads to 2 for FDR classification task
0:48:51.474948 INFO: Test AUC: 0.539
0:48:51.475116 INFO: Train AUC: 0.568
0:48:51.475147 INFO: AUC difference: 5.21%
0:48:51.475173 WARNING: AUC difference > 5%. This may indicate overfitting.
0:48:51.561969 INFO: Resetting torch num_threads to 100
0:48:51.564846 INFO: === FDR correction performed with classifier version -1 ===
0:48:51.569490 PROGRESS: ============================= Precursor FDR =============================
0:48:51.569671 PROGRESS: Total precursors accumulated: 23,909
0:48:51.569734 PROGRESS: Target precursors: 13,971 (58.43%)
0:48:51.569785 PROGRESS: Decoy precursors: 9,938 (41.57%)
0:48:51.569830 PROGRESS: 
0:48:51.569874 PROGRESS: Precursor Summary:
0:48:51.570878 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:48:51.570964 PROGRESS: 
0:48:51.571019 PROGRESS: Protein Summary:
0:48:51.572033 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:48:51.572120 PROGRESS: =========================================================================
0:48:51.778779 INFO: Starting optimization step 2.
0:48:51.779099 PROGRESS: === Extracting elution groups 24000 to 56000 ===
0:48:51.779182 PROGRESS: Extracting batch of 63234 precursors
0:48:51.796207 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:48:51.796376 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:48:51.796423 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:48:51.796449 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:48:51.796802 INFO: Starting candidate selection
0:48:55.978948 INFO: Starting candidate scoring
0:48:56.474749 INFO: Finished candidate processing
0:48:56.474952 INFO: Collecting candidate features
0:48:56.651986 INFO: Collecting fragment features
0:48:56.698853 INFO: Finished candidate scoring
0:48:56.759332 PROGRESS: === Extracted 110401 precursors and 1087467 fragments ===
0:48:56.773425 INFO: performing precursor FDR with 47 features
0:48:56.773627 INFO: Decoy channel: -1
0:48:56.773660 INFO: Competetive: True
0:48:56.828135 INFO: Setting torch num_threads to 2 for FDR classification task
0:48:58.715423 INFO: Test AUC: 0.558
0:48:58.715578 INFO: Train AUC: 0.580
0:48:58.715611 INFO: AUC difference: 3.89%
0:48:58.808061 INFO: Resetting torch num_threads to 100
0:48:58.814186 INFO: === FDR correction performed with classifier version -1 ===
0:48:58.815270 PROGRESS: ============================= Precursor FDR =============================
0:48:58.815372 PROGRESS: Total precursors accumulated: 1
0:48:58.815431 PROGRESS: Target precursors: 1 (100.00%)
0:48:58.815480 PROGRESS: Decoy precursors: 0 (0.00%)
0:48:58.815527 PROGRESS: 
0:48:58.815571 PROGRESS: Precursor Summary:
0:48:58.816493 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:48:58.816581 PROGRESS: 
0:48:58.816637 PROGRESS: Protein Summary:
0:48:58.817666 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:48:58.817755 PROGRESS: =========================================================================
0:48:59.121847 INFO: Starting optimization step 3.
0:48:59.122172 PROGRESS: === Extracting elution groups 56000 to 120000 ===
0:48:59.122244 PROGRESS: Extracting batch of 126528 precursors
0:48:59.152820 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:48:59.152954 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:48:59.152990 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:48:59.153028 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:48:59.153265 INFO: Starting candidate selection
0:49:08.492631 INFO: Starting candidate scoring
0:49:09.544938 INFO: Finished candidate processing
0:49:09.545049 INFO: Collecting candidate features
0:49:09.821844 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 126166)
0:49:09.830171 INFO: Collecting fragment features
0:49:09.948288 INFO: Finished candidate scoring
0:49:10.139738 PROGRESS: === Extracted 236567 precursors and 2328945 fragments ===
0:49:10.163834 INFO: performing precursor FDR with 47 features
0:49:10.163970 INFO: Decoy channel: -1
0:49:10.163996 INFO: Competetive: True
0:49:10.287669 INFO: Setting torch num_threads to 2 for FDR classification task
0:49:10.347209 WARNING: dropped 1 decoy PSMs due to missing features
0:49:14.332166 INFO: Test AUC: 0.561
0:49:14.332314 INFO: Train AUC: 0.585
0:49:14.332345 INFO: AUC difference: 3.99%
0:49:14.432668 INFO: Resetting torch num_threads to 100
0:49:14.447740 INFO: === FDR correction performed with classifier version -1 ===
0:49:14.448986 PROGRESS: ============================= Precursor FDR =============================
0:49:14.449081 PROGRESS: Total precursors accumulated: 1
0:49:14.449142 PROGRESS: Target precursors: 1 (100.00%)
0:49:14.449194 PROGRESS: Decoy precursors: 0 (0.00%)
0:49:14.449238 PROGRESS: 
0:49:14.449285 PROGRESS: Precursor Summary:
0:49:14.450226 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:49:14.450313 PROGRESS: 
0:49:14.450366 PROGRESS: Protein Summary:
0:49:14.451359 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:49:14.451446 PROGRESS: =========================================================================
0:49:14.904621 INFO: Starting optimization step 4.
0:49:14.904995 PROGRESS: === Extracting elution groups 120000 to 248000 ===
0:49:14.905088 PROGRESS: Extracting batch of 253020 precursors
0:49:14.974688 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:49:14.974843 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:49:14.974882 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:49:14.974905 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:49:14.975183 INFO: Starting candidate selection
0:49:31.142419 INFO: Starting candidate scoring
0:49:33.031182 INFO: Finished candidate processing
0:49:33.031365 INFO: Collecting candidate features
0:49:33.657156 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 252398)
0:49:33.668983 INFO: Collecting fragment features
0:49:33.848650 INFO: Finished candidate scoring
0:49:34.176063 PROGRESS: === Extracted 488965 precursors and 4813056 fragments ===
0:49:34.243249 INFO: performing precursor FDR with 47 features
0:49:34.243398 INFO: Decoy channel: -1
0:49:34.243427 INFO: Competetive: True
0:49:34.540104 INFO: Setting torch num_threads to 2 for FDR classification task
0:49:34.658369 WARNING: dropped 1 target PSMs due to missing features
0:49:34.658535 WARNING: dropped 2 decoy PSMs due to missing features
0:49:43.578241 INFO: Test AUC: 0.563
0:49:43.578397 INFO: Train AUC: 0.583
0:49:43.578429 INFO: AUC difference: 3.39%
0:49:43.703790 INFO: Resetting torch num_threads to 100
0:49:43.741334 INFO: === FDR correction performed with classifier version -1 ===
0:49:43.742383 PROGRESS: ============================= Precursor FDR =============================
0:49:43.742480 PROGRESS: Total precursors accumulated: 1
0:49:43.742540 PROGRESS: Target precursors: 1 (100.00%)
0:49:43.742590 PROGRESS: Decoy precursors: 0 (0.00%)
0:49:43.742635 PROGRESS: 
0:49:43.742678 PROGRESS: Precursor Summary:
0:49:43.743628 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:49:43.743712 PROGRESS: 
0:49:43.743767 PROGRESS: Protein Summary:
0:49:43.744783 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:49:43.744871 PROGRESS: =========================================================================
0:49:44.566519 INFO: Starting optimization step 5.
0:49:44.566887 PROGRESS: === Extracting elution groups 248000 to 504000 ===
0:49:44.566986 PROGRESS: Extracting batch of 505949 precursors
0:49:44.707837 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:49:44.708000 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:49:44.708043 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:49:44.708067 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:49:44.708377 INFO: Starting candidate selection
0:50:16.693221 INFO: Starting candidate scoring
0:50:20.412716 INFO: Finished candidate processing
0:50:20.412817 INFO: Collecting candidate features
0:50:21.568902 WARNING: intensity_correlation has 6 NaNs ( 0.00 % out of 504780)
0:50:21.588603 INFO: Collecting fragment features
0:50:21.970513 INFO: Finished candidate scoring
0:50:22.669874 PROGRESS: === Extracted 993745 precursors and 9781468 fragments ===
0:50:22.824530 INFO: performing precursor FDR with 47 features
0:50:22.824663 INFO: Decoy channel: -1
0:50:22.824690 INFO: Competetive: True
0:50:23.385248 INFO: Setting torch num_threads to 2 for FDR classification task
0:50:23.635947 WARNING: dropped 5 target PSMs due to missing features
0:50:23.636102 WARNING: dropped 4 decoy PSMs due to missing features
0:50:42.179887 INFO: Test AUC: 0.568
0:50:42.180111 INFO: Train AUC: 0.581
0:50:42.180148 INFO: AUC difference: 2.26%
0:50:42.340259 INFO: Resetting torch num_threads to 100
0:50:42.405478 INFO: === FDR correction performed with classifier version -1 ===
0:50:42.406621 PROGRESS: ============================= Precursor FDR =============================
0:50:42.406723 PROGRESS: Total precursors accumulated: 1
0:50:42.406782 PROGRESS: Target precursors: 1 (100.00%)
0:50:42.406832 PROGRESS: Decoy precursors: 0 (0.00%)
0:50:42.406877 PROGRESS: 
0:50:42.406921 PROGRESS: Precursor Summary:
0:50:42.407868 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:50:42.407955 PROGRESS: 
0:50:42.408009 PROGRESS: Protein Summary:
0:50:42.409048 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:50:42.409137 PROGRESS: =========================================================================
0:50:43.702601 INFO: Starting optimization step 6.
0:50:43.702921 PROGRESS: === Extracting elution groups 504000 to 1016000 ===
0:50:43.703005 PROGRESS: Extracting batch of 1011924 precursors
0:50:43.977140 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:50:43.977273 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:50:43.977316 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:50:43.977342 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:50:43.977681 INFO: Starting candidate selection
0:51:47.017936 INFO: Starting candidate scoring
0:51:54.037359 INFO: Finished candidate processing
0:51:54.037625 INFO: Collecting candidate features
0:51:56.451134 WARNING: intensity_correlation has 13 NaNs ( 0.00 % out of 1009372)
0:51:56.484905 INFO: Collecting fragment features
0:51:57.202356 INFO: Finished candidate scoring
0:51:58.663140 PROGRESS: === Extracted 2003117 precursors and 19718485 fragments ===
0:51:58.890971 INFO: performing precursor FDR with 47 features
0:51:58.891114 INFO: Decoy channel: -1
0:51:58.891143 INFO: Competetive: True
0:51:59.802453 INFO: Setting torch num_threads to 2 for FDR classification task
0:52:00.208011 WARNING: dropped 9 target PSMs due to missing features
0:52:00.208153 WARNING: dropped 13 decoy PSMs due to missing features
0:52:34.393434 INFO: Test AUC: 0.572
0:52:34.393652 INFO: Train AUC: 0.580
0:52:34.393686 INFO: AUC difference: 1.50%
0:52:34.626658 INFO: Resetting torch num_threads to 100
0:52:34.734015 INFO: === FDR correction performed with classifier version -1 ===
0:52:34.734957 PROGRESS: ============================= Precursor FDR =============================
0:52:34.735055 PROGRESS: Total precursors accumulated: 1
0:52:34.735117 PROGRESS: Target precursors: 1 (100.00%)
0:52:34.735168 PROGRESS: Decoy precursors: 0 (0.00%)
0:52:34.735214 PROGRESS: 
0:52:34.735260 PROGRESS: Precursor Summary:
0:52:34.736197 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:52:34.736300 PROGRESS: 
0:52:34.736356 PROGRESS: Protein Summary:
0:52:34.737363 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:52:34.737451 PROGRESS: =========================================================================
0:52:36.516388 INFO: Starting optimization step 7.
0:52:36.516690 PROGRESS: === Extracting elution groups 1016000 to 2040000 ===
0:52:36.516818 PROGRESS: Extracting batch of 2023834 precursors
0:52:36.964425 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:52:36.964567 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:52:36.964607 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:52:36.964629 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:52:36.964953 INFO: Starting candidate selection
0:54:42.674690 INFO: Starting candidate scoring
0:54:57.969706 INFO: Finished candidate processing
0:54:57.970010 INFO: Collecting candidate features
0:55:02.863585 WARNING: intensity_correlation has 17 NaNs ( 0.00 % out of 2018685)
0:55:02.930433 INFO: Collecting fragment features
0:55:04.651109 INFO: Finished candidate scoring
0:55:08.598383 PROGRESS: === Extracted 4021802 precursors and 39591870 fragments ===
0:55:09.269039 INFO: performing precursor FDR with 47 features
0:55:09.269191 INFO: Decoy channel: -1
0:55:09.269221 INFO: Competetive: True
0:55:11.757748 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:12.865936 WARNING: dropped 16 target PSMs due to missing features
0:55:12.866189 WARNING: dropped 23 decoy PSMs due to missing features
0:56:29.745170 INFO: Test AUC: 0.581
0:56:29.746307 INFO: Train AUC: 0.585
0:56:29.746382 INFO: AUC difference: 0.60%
0:56:30.135305 INFO: Resetting torch num_threads to 100
0:56:30.449486 INFO: === FDR correction performed with classifier version -1 ===
0:56:30.450528 PROGRESS: ============================= Precursor FDR =============================
0:56:30.450681 PROGRESS: Total precursors accumulated: 55
0:56:30.450745 PROGRESS: Target precursors: 50 (90.91%)
0:56:30.450795 PROGRESS: Decoy precursors: 5 (9.09%)
0:56:30.450840 PROGRESS: 
0:56:30.450883 PROGRESS: Precursor Summary:
0:56:30.451819 PROGRESS: Channel   0:	 0.05 FDR:    10; 0.01 FDR:    10; 0.001 FDR:    10
0:56:30.451929 PROGRESS: 
0:56:30.451985 PROGRESS: Protein Summary:
0:56:30.452951 PROGRESS: Channel   0:	 0.05 FDR:    10; 0.01 FDR:    10; 0.001 FDR:    10
0:56:30.453050 PROGRESS: =========================================================================
0:56:34.855668 INFO: Starting optimization step 8.
0:56:34.856100 PROGRESS: === Extracting elution groups 2040000 to 4088000 ===
0:56:34.856218 PROGRESS: Extracting batch of 4047565 precursors
0:56:35.967709 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:56:35.967921 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:56:35.967972 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:56:35.968001 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:56:35.968476 INFO: Starting candidate selection
1:00:42.655078 INFO: Starting candidate scoring
1:01:11.238840 INFO: Finished candidate processing
1:01:11.239128 INFO: Collecting candidate features
1:01:19.767859 WARNING: intensity_correlation has 46 NaNs ( 0.00 % out of 4037178)
1:01:19.901680 INFO: Collecting fragment features
1:01:22.990049 INFO: Finished candidate scoring
1:01:30.817764 PROGRESS: === Extracted 8058980 precursors and 79325127 fragments ===
1:01:31.822726 INFO: performing precursor FDR with 47 features
1:01:31.822902 INFO: Decoy channel: -1
1:01:31.822933 INFO: Competetive: True
1:01:35.283882 INFO: Setting torch num_threads to 2 for FDR classification task
1:01:36.833874 WARNING: dropped 36 target PSMs due to missing features
1:01:36.834028 WARNING: dropped 49 decoy PSMs due to missing features
1:04:04.909113 INFO: Test AUC: 0.581
1:04:04.909390 INFO: Train AUC: 0.586
1:04:04.909434 INFO: AUC difference: 0.95%
1:04:05.620107 INFO: Resetting torch num_threads to 100
1:04:06.228509 INFO: === FDR correction performed with classifier version -1 ===
1:04:06.231476 PROGRESS: ============================= Precursor FDR =============================
1:04:06.231681 PROGRESS: Total precursors accumulated: 6,267
1:04:06.231748 PROGRESS: Target precursors: 5,790 (92.39%)
1:04:06.231800 PROGRESS: Decoy precursors: 477 (7.61%)
1:04:06.231846 PROGRESS: 
1:04:06.231891 PROGRESS: Precursor Summary:
1:04:06.235151 PROGRESS: Channel   0:	 0.05 FDR: 4,762; 0.01 FDR: 3,410; 0.001 FDR: 2,610
1:04:06.235298 PROGRESS: 
1:04:06.235357 PROGRESS: Protein Summary:
1:04:06.239020 PROGRESS: Channel   0:	 0.05 FDR: 3,203; 0.01 FDR: 2,152; 0.001 FDR: 1,709
1:04:06.239130 PROGRESS: =========================================================================
1:04:07.335577 INFO: fragments_df_filtered: 5000
1:04:08.558689 INFO: calibration group: precursor, fitting mz estimator 
1:04:08.829652 INFO: calibration group: precursor, fitting rt estimator 
1:04:09.087557 INFO: calibration group: fragment, fitting mz estimator 
1:04:09.505935 INFO: calibration group: precursor, predicting mz
1:04:09.577733 INFO: calibration group: precursor, predicting rt
1:04:09.910192 INFO: calibration group: fragment, predicting mz
1:04:10.710011 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:04:10.710353 INFO: Starting optimization step 9.
1:04:10.710423 PROGRESS: === Extracting elution groups 0 to 248000 ===
1:04:10.710496 PROGRESS: Extracting batch of 490233 precursors
1:04:10.844506 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:04:10.844672 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:04:10.844721 INFO: FWHM in RT is 2.91 seconds, sigma is 0.38
1:04:10.844743 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:04:10.845081 INFO: Starting candidate selection
1:04:34.599127 INFO: Starting candidate scoring
1:04:41.855385 INFO: Finished candidate processing
1:04:41.855613 INFO: Collecting candidate features
1:04:43.948034 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 977933)
1:04:43.983198 INFO: Collecting fragment features
1:04:44.689087 INFO: Finished candidate scoring
1:04:45.817555 PROGRESS: === Extracted 977933 precursors and 9500317 fragments ===
1:04:45.818099 INFO: performing precursor FDR with 47 features
1:04:45.818139 INFO: Decoy channel: -1
1:04:45.818164 INFO: Competetive: True
1:04:46.158909 INFO: Setting torch num_threads to 2 for FDR classification task
1:04:46.343653 WARNING: dropped 1 decoy PSMs due to missing features
1:05:04.058132 INFO: Test AUC: 0.580
1:05:04.058347 INFO: Train AUC: 0.592
1:05:04.058385 INFO: AUC difference: 1.99%
1:05:04.214926 INFO: Resetting torch num_threads to 100
1:05:04.244668 INFO: === FDR correction performed with classifier version 8 ===
1:05:04.245639 PROGRESS: ============================= Precursor FDR =============================
1:05:04.245740 PROGRESS: Total precursors accumulated: 722
1:05:04.245823 PROGRESS: Target precursors: 661 (91.55%)
1:05:04.245881 PROGRESS: Decoy precursors: 61 (8.45%)
1:05:04.245932 PROGRESS: 
1:05:04.245986 PROGRESS: Precursor Summary:
1:05:04.247062 PROGRESS: Channel   0:	 0.05 FDR:   527; 0.01 FDR:   324; 0.001 FDR:   289
1:05:04.247160 PROGRESS: 
1:05:04.247223 PROGRESS: Protein Summary:
1:05:04.248446 PROGRESS: Channel   0:	 0.05 FDR:   501; 0.01 FDR:   307; 0.001 FDR:   275
1:05:04.248542 PROGRESS: =========================================================================
1:05:04.297599 INFO: fragments_df_filtered: 3493
1:05:05.109578 INFO: calibration group: precursor, fitting mz estimator 
1:05:05.165673 INFO: calibration group: precursor, fitting rt estimator 
1:05:05.217394 INFO: calibration group: fragment, fitting mz estimator 
1:05:05.473129 INFO: calibration group: precursor, predicting mz
1:05:05.549204 INFO: calibration group: precursor, predicting rt
1:05:05.893570 INFO: calibration group: fragment, predicting mz
1:05:06.724336 INFO: === checking if optimization conditions were reached ===
1:05:06.726530 PROGRESS: ❌ ms2_error      : 14.8116 > 8.0000 or insufficient steps taken.
1:05:06.727541 PROGRESS: ❌ ms1_error      : 14.5669 > 3.0000 or insufficient steps taken.
1:05:06.727594 INFO: ==============================================
1:05:06.727713 INFO: Starting optimization step 10.
1:05:06.727781 PROGRESS: === Extracting elution groups 0 to 248000 ===
1:05:06.727852 PROGRESS: Extracting batch of 490233 precursors
1:05:06.869832 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:05:06.870001 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:05:06.870042 INFO: FWHM in RT is 2.97 seconds, sigma is 0.38
1:05:06.870064 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:05:06.870382 INFO: Starting candidate selection
1:05:34.216708 INFO: Starting candidate scoring
1:05:41.203151 INFO: Finished candidate processing
1:05:41.203269 INFO: Collecting candidate features
1:05:43.198178 WARNING: intensity_correlation has 29 NaNs ( 0.00 % out of 977381)
1:05:43.235907 INFO: Collecting fragment features
1:05:43.866669 INFO: Finished candidate scoring
1:05:44.722395 PROGRESS: === Extracted 977381 precursors and 8267992 fragments ===
1:05:44.722979 INFO: performing precursor FDR with 47 features
1:05:44.723016 INFO: Decoy channel: -1
1:05:44.723042 INFO: Competetive: True
1:05:45.078564 INFO: Setting torch num_threads to 2 for FDR classification task
1:05:45.298542 WARNING: dropped 17 target PSMs due to missing features
1:05:45.298685 WARNING: dropped 12 decoy PSMs due to missing features
1:06:02.949120 INFO: Test AUC: 0.577
1:06:02.949341 INFO: Train AUC: 0.589
1:06:02.949375 INFO: AUC difference: 2.14%
1:06:03.106492 INFO: Resetting torch num_threads to 100
1:06:03.140823 INFO: === FDR correction performed with classifier version 9 ===
1:06:03.141955 PROGRESS: ============================= Precursor FDR =============================
1:06:03.142056 PROGRESS: Total precursors accumulated: 1,103
1:06:03.142118 PROGRESS: Target precursors: 1,005 (91.12%)
1:06:03.142169 PROGRESS: Decoy precursors: 98 (8.88%)
1:06:03.142216 PROGRESS: 
1:06:03.142260 PROGRESS: Precursor Summary:
1:06:03.143383 PROGRESS: Channel   0:	 0.05 FDR:   684; 0.01 FDR:   516; 0.001 FDR:   352
1:06:03.143475 PROGRESS: 
1:06:03.143531 PROGRESS: Protein Summary:
1:06:03.144829 PROGRESS: Channel   0:	 0.05 FDR:   636; 0.01 FDR:   482; 0.001 FDR:   335
1:06:03.144921 PROGRESS: =========================================================================
1:06:03.181869 INFO: fragments_df_filtered: 5000
1:06:03.684287 INFO: calibration group: precursor, fitting mz estimator 
1:06:03.801298 INFO: calibration group: precursor, fitting rt estimator 
1:06:03.846577 INFO: calibration group: fragment, fitting mz estimator 
1:06:04.308132 INFO: calibration group: precursor, predicting mz
1:06:04.342610 INFO: calibration group: precursor, predicting rt
1:06:04.502566 INFO: calibration group: fragment, predicting mz
1:06:04.876806 INFO: === checking if optimization conditions were reached ===
1:06:04.879077 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
1:06:04.880099 PROGRESS: ❌ ms1_error      : 7.2088 > 3.0000 or insufficient steps taken.
1:06:04.880159 INFO: ==============================================
1:06:04.880282 INFO: Starting optimization step 11.
1:06:04.880365 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:06:04.880456 PROGRESS: Extracting batch of 237213 precursors
1:06:04.943400 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:06:04.943552 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:06:04.943602 INFO: FWHM in RT is 2.70 seconds, sigma is 0.35
1:06:04.943632 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:06:04.943969 INFO: Starting candidate selection
1:06:16.460875 INFO: Starting candidate scoring
1:06:19.837747 INFO: Finished candidate processing
1:06:19.837873 INFO: Collecting candidate features
1:06:20.679684 WARNING: intensity_correlation has 35 NaNs ( 0.01 % out of 472147)
1:06:20.698079 INFO: Collecting fragment features
1:06:20.970349 INFO: Finished candidate scoring
1:06:21.285182 PROGRESS: === Extracted 472147 precursors and 3455927 fragments ===
1:06:21.285685 INFO: performing precursor FDR with 47 features
1:06:21.285726 INFO: Decoy channel: -1
1:06:21.285751 INFO: Competetive: True
1:06:21.443559 INFO: Setting torch num_threads to 2 for FDR classification task
1:06:21.539247 WARNING: dropped 17 target PSMs due to missing features
1:06:21.539407 WARNING: dropped 18 decoy PSMs due to missing features
1:06:29.929297 INFO: Test AUC: 0.573
1:06:29.929492 INFO: Train AUC: 0.593
1:06:29.929526 INFO: AUC difference: 3.29%
1:06:30.827508 INFO: Resetting torch num_threads to 100
1:06:30.840932 INFO: === FDR correction performed with classifier version 10 ===
1:06:30.841804 PROGRESS: ============================= Precursor FDR =============================
1:06:30.841901 PROGRESS: Total precursors accumulated: 684
1:06:30.841972 PROGRESS: Target precursors: 623 (91.08%)
1:06:30.842028 PROGRESS: Decoy precursors: 61 (8.92%)
1:06:30.842073 PROGRESS: 
1:06:30.842117 PROGRESS: Precursor Summary:
1:06:30.843135 PROGRESS: Channel   0:	 0.05 FDR:   445; 0.01 FDR:   302; 0.001 FDR:   193
1:06:30.843229 PROGRESS: 
1:06:30.843283 PROGRESS: Protein Summary:
1:06:30.844422 PROGRESS: Channel   0:	 0.05 FDR:   425; 0.01 FDR:   291; 0.001 FDR:   189
1:06:30.844512 PROGRESS: =========================================================================
1:06:30.862894 INFO: fragments_df_filtered: 2741
1:06:31.274957 INFO: calibration group: precursor, fitting mz estimator 
1:06:31.322260 INFO: calibration group: precursor, fitting rt estimator 
1:06:31.358626 INFO: calibration group: fragment, fitting mz estimator 
1:06:31.502728 INFO: calibration group: precursor, predicting mz
1:06:31.569012 INFO: calibration group: precursor, predicting rt
1:06:31.772743 INFO: calibration group: fragment, predicting mz
1:06:32.177554 INFO: === checking if optimization conditions were reached ===
1:06:32.177968 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
1:06:32.179652 PROGRESS: ❌ ms1_error      : 3.5517 > 3.0000 or insufficient steps taken.
1:06:32.179706 INFO: ==============================================
1:06:32.179821 INFO: Starting optimization step 12.
1:06:32.179903 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:06:32.179979 PROGRESS: Extracting batch of 237213 precursors
1:06:32.264435 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:06:32.264595 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:06:32.264648 INFO: FWHM in RT is 2.50 seconds, sigma is 0.32
1:06:32.264683 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:06:32.265135 INFO: Starting candidate selection
1:06:44.241987 INFO: Starting candidate scoring
1:06:47.664359 INFO: Finished candidate processing
1:06:47.664471 INFO: Collecting candidate features
1:06:48.651581 WARNING: intensity_correlation has 20 NaNs ( 0.00 % out of 472346)
1:06:48.670497 INFO: Collecting fragment features
1:06:48.964340 INFO: Finished candidate scoring
1:06:49.351172 PROGRESS: === Extracted 472346 precursors and 3457088 fragments ===
1:06:49.351831 INFO: performing precursor FDR with 47 features
1:06:49.351885 INFO: Decoy channel: -1
1:06:49.351911 INFO: Competetive: True
1:06:49.526054 INFO: Setting torch num_threads to 2 for FDR classification task
1:06:49.632176 WARNING: dropped 7 target PSMs due to missing features
1:06:49.632326 WARNING: dropped 13 decoy PSMs due to missing features
1:06:58.413848 INFO: Test AUC: 0.577
1:06:58.414075 INFO: Train AUC: 0.597
1:06:58.414109 INFO: AUC difference: 3.23%
1:06:58.535401 INFO: Resetting torch num_threads to 100
1:06:58.552581 INFO: === FDR correction performed with classifier version 11 ===
1:06:58.553673 PROGRESS: ============================= Precursor FDR =============================
1:06:58.553816 PROGRESS: Total precursors accumulated: 717
1:06:58.553877 PROGRESS: Target precursors: 657 (91.63%)
1:06:58.553932 PROGRESS: Decoy precursors: 60 (8.37%)
1:06:58.553983 PROGRESS: 
1:06:58.554029 PROGRESS: Precursor Summary:
1:06:58.555171 PROGRESS: Channel   0:	 0.05 FDR:   471; 0.01 FDR:   249; 0.001 FDR:   151
1:06:58.555276 PROGRESS: 
1:06:58.555331 PROGRESS: Protein Summary:
1:06:58.556539 PROGRESS: Channel   0:	 0.05 FDR:   453; 0.01 FDR:   242; 0.001 FDR:   149
1:06:58.556635 PROGRESS: =========================================================================
1:06:58.573428 INFO: fragments_df_filtered: 2428
1:06:59.009176 INFO: calibration group: precursor, fitting mz estimator 
1:06:59.053450 INFO: calibration group: precursor, fitting rt estimator 
1:06:59.099341 INFO: calibration group: fragment, fitting mz estimator 
1:06:59.270670 INFO: calibration group: precursor, predicting mz
1:06:59.303566 INFO: calibration group: precursor, predicting rt
1:06:59.460651 INFO: calibration group: fragment, predicting mz
1:06:59.850975 INFO: === checking if optimization conditions were reached ===
1:06:59.851317 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
1:06:59.852773 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
1:06:59.852826 INFO: ==============================================
1:06:59.852932 PROGRESS: Optimization finished for ms2_error, ms1_error.
1:07:00.237361 INFO: calibration group: precursor, predicting mz
1:07:00.271368 INFO: calibration group: precursor, predicting rt
1:07:00.431236 INFO: calibration group: fragment, predicting mz
1:07:00.819732 INFO: Starting optimization step 0.
1:07:00.820056 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:07:00.820143 PROGRESS: Extracting batch of 237213 precursors
1:07:00.883680 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:07:00.883829 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:07:00.883873 INFO: FWHM in RT is 2.36 seconds, sigma is 0.30
1:07:00.883898 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:07:00.884208 INFO: Starting candidate selection
1:07:12.316945 INFO: Starting candidate scoring
1:07:16.020977 INFO: Finished candidate processing
1:07:16.021920 INFO: Collecting candidate features
1:07:17.276873 WARNING: intensity_correlation has 16 NaNs ( 0.00 % out of 472370)
1:07:17.296472 INFO: Collecting fragment features
1:07:17.637789 INFO: Finished candidate scoring
1:07:18.269215 PROGRESS: === Extracted 472370 precursors and 3452017 fragments ===
1:07:18.269903 INFO: performing precursor FDR with 47 features
1:07:18.269946 INFO: Decoy channel: -1
1:07:18.269972 INFO: Competetive: True
1:07:18.464243 INFO: Setting torch num_threads to 2 for FDR classification task
1:07:18.576425 WARNING: dropped 7 target PSMs due to missing features
1:07:18.576588 WARNING: dropped 9 decoy PSMs due to missing features
1:07:28.057618 INFO: Test AUC: 0.584
1:07:28.057828 INFO: Train AUC: 0.599
1:07:28.057863 INFO: AUC difference: 2.58%
1:07:28.186645 INFO: Resetting torch num_threads to 100
1:07:28.200190 INFO: === FDR correction performed with classifier version 12 ===
1:07:28.201429 PROGRESS: ============================= Precursor FDR =============================
1:07:28.201576 PROGRESS: Total precursors accumulated: 813
1:07:28.201639 PROGRESS: Target precursors: 739 (90.90%)
1:07:28.201693 PROGRESS: Decoy precursors: 74 (9.10%)
1:07:28.201739 PROGRESS: 
1:07:28.201785 PROGRESS: Precursor Summary:
1:07:28.202954 PROGRESS: Channel   0:	 0.05 FDR:   504; 0.01 FDR:   255; 0.001 FDR:   148
1:07:28.203058 PROGRESS: 
1:07:28.203116 PROGRESS: Protein Summary:
1:07:28.204294 PROGRESS: Channel   0:	 0.05 FDR:   486; 0.01 FDR:   248; 0.001 FDR:   146
1:07:28.204386 PROGRESS: =========================================================================
1:07:28.221765 INFO: fragments_df_filtered: 2464
1:07:28.719780 INFO: calibration group: precursor, fitting mz estimator 
1:07:28.768606 INFO: calibration group: precursor, fitting rt estimator 
1:07:28.816267 INFO: calibration group: fragment, fitting mz estimator 
1:07:28.990320 INFO: calibration group: precursor, predicting mz
1:07:29.023791 INFO: calibration group: precursor, predicting rt
1:07:29.185114 INFO: calibration group: fragment, predicting mz
1:07:29.561428 INFO: === checking if optimization conditions were reached ===
1:07:29.561840 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:07:29.564244 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 236.8065.
1:07:29.564304 INFO: ==============================================
1:07:29.564423 INFO: Starting optimization step 1.
1:07:29.564500 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:07:29.564590 PROGRESS: Extracting batch of 237213 precursors
1:07:29.633438 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:07:29.633574 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:07:29.633622 INFO: FWHM in RT is 2.28 seconds, sigma is 0.29
1:07:29.633647 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:07:29.634009 INFO: Starting candidate selection
1:07:40.022920 INFO: Starting candidate scoring
1:07:43.427878 INFO: Finished candidate processing
1:07:43.428031 INFO: Collecting candidate features
1:07:44.594306 WARNING: intensity_correlation has 58 NaNs ( 0.01 % out of 469159)
1:07:44.595068 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 469159)
1:07:44.614877 INFO: Collecting fragment features
1:07:44.932668 INFO: Finished candidate scoring
1:07:45.287920 PROGRESS: === Extracted 469159 precursors and 3293842 fragments ===
1:07:45.288552 INFO: performing precursor FDR with 47 features
1:07:45.288595 INFO: Decoy channel: -1
1:07:45.288625 INFO: Competetive: True
1:07:45.468473 INFO: Setting torch num_threads to 2 for FDR classification task
1:07:45.576836 WARNING: dropped 27 target PSMs due to missing features
1:07:45.576981 WARNING: dropped 31 decoy PSMs due to missing features
1:07:54.397877 INFO: Test AUC: 0.574
1:07:54.398029 INFO: Train AUC: 0.593
1:07:54.398061 INFO: AUC difference: 3.16%
1:07:54.518377 INFO: Resetting torch num_threads to 100
1:07:54.534785 INFO: === FDR correction performed with classifier version 12 ===
1:07:54.535812 PROGRESS: ============================= Precursor FDR =============================
1:07:54.535944 PROGRESS: Total precursors accumulated: 842
1:07:54.536006 PROGRESS: Target precursors: 769 (91.33%)
1:07:54.536057 PROGRESS: Decoy precursors: 73 (8.67%)
1:07:54.536104 PROGRESS: 
1:07:54.536148 PROGRESS: Precursor Summary:
1:07:54.537331 PROGRESS: Channel   0:	 0.05 FDR:   522; 0.01 FDR:   334; 0.001 FDR:   179
1:07:54.537434 PROGRESS: 
1:07:54.537488 PROGRESS: Protein Summary:
1:07:54.538681 PROGRESS: Channel   0:	 0.05 FDR:   498; 0.01 FDR:   325; 0.001 FDR:   175
1:07:54.538786 PROGRESS: =========================================================================
1:07:54.559289 INFO: fragments_df_filtered: 2990
1:07:54.980402 INFO: calibration group: precursor, fitting mz estimator 
1:07:55.021139 INFO: calibration group: precursor, fitting rt estimator 
1:07:55.057069 INFO: calibration group: fragment, fitting mz estimator 
1:07:55.210392 INFO: calibration group: precursor, predicting mz
1:07:55.242678 INFO: calibration group: precursor, predicting rt
1:07:55.397712 INFO: calibration group: fragment, predicting mz
1:07:55.781631 INFO: === checking if optimization conditions were reached ===
1:07:55.782004 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:07:55.784570 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 129.1818.
1:07:55.784728 INFO: ==============================================
1:07:55.785039 INFO: Starting optimization step 2.
1:07:55.785120 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:07:55.785200 PROGRESS: Extracting batch of 237213 precursors
1:07:55.848145 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:07:55.848287 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:07:55.848332 INFO: FWHM in RT is 2.31 seconds, sigma is 0.30
1:07:55.848354 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:07:55.848629 INFO: Starting candidate selection
1:08:05.475632 INFO: Starting candidate scoring
1:08:08.847893 INFO: Finished candidate processing
1:08:08.848020 INFO: Collecting candidate features
1:08:10.155858 WARNING: intensity_correlation has 76 NaNs ( 0.02 % out of 465840)
1:08:10.156606 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 465840)
1:08:10.174701 INFO: Collecting fragment features
1:08:10.465255 INFO: Finished candidate scoring
1:08:10.866091 PROGRESS: === Extracted 465840 precursors and 3100433 fragments ===
1:08:10.866791 INFO: performing precursor FDR with 47 features
1:08:10.866834 INFO: Decoy channel: -1
1:08:10.866860 INFO: Competetive: True
1:08:11.055647 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:11.162399 WARNING: dropped 41 target PSMs due to missing features
1:08:11.162564 WARNING: dropped 35 decoy PSMs due to missing features
1:08:20.331118 INFO: Test AUC: 0.569
1:08:20.331340 INFO: Train AUC: 0.591
1:08:20.331375 INFO: AUC difference: 3.74%
1:08:20.455866 INFO: Resetting torch num_threads to 100
1:08:20.473166 INFO: === FDR correction performed with classifier version 12 ===
1:08:20.474304 PROGRESS: ============================= Precursor FDR =============================
1:08:20.474446 PROGRESS: Total precursors accumulated: 869
1:08:20.474508 PROGRESS: Target precursors: 794 (91.37%)
1:08:20.474560 PROGRESS: Decoy precursors: 75 (8.63%)
1:08:20.474605 PROGRESS: 
1:08:20.474648 PROGRESS: Precursor Summary:
1:08:20.475822 PROGRESS: Channel   0:	 0.05 FDR:   547; 0.01 FDR:   365; 0.001 FDR:   241
1:08:20.475925 PROGRESS: 
1:08:20.475981 PROGRESS: Protein Summary:
1:08:20.477273 PROGRESS: Channel   0:	 0.05 FDR:   526; 0.01 FDR:   352; 0.001 FDR:   235
1:08:20.477375 PROGRESS: =========================================================================
1:08:20.509789 INFO: fragments_df_filtered: 3189
1:08:21.331644 INFO: calibration group: precursor, fitting mz estimator 
1:08:21.381773 INFO: calibration group: precursor, fitting rt estimator 
1:08:21.427501 INFO: calibration group: fragment, fitting mz estimator 
1:08:21.639341 INFO: calibration group: precursor, predicting mz
1:08:21.674035 INFO: calibration group: precursor, predicting rt
1:08:21.842491 INFO: calibration group: fragment, predicting mz
1:08:22.210506 INFO: === checking if optimization conditions were reached ===
1:08:22.210868 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:08:22.213263 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 88.4895.
1:08:22.213334 INFO: ==============================================
1:08:22.213482 INFO: Starting optimization step 3.
1:08:22.213556 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:08:22.213650 PROGRESS: Extracting batch of 237213 precursors
1:08:22.285095 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:08:22.285234 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:08:22.285294 INFO: FWHM in RT is 2.30 seconds, sigma is 0.30
1:08:22.285318 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:08:22.285717 INFO: Starting candidate selection
1:08:32.066830 INFO: Starting candidate scoring
1:08:35.365352 INFO: Finished candidate processing
1:08:35.365462 INFO: Collecting candidate features
1:08:36.289098 WARNING: intensity_correlation has 103 NaNs ( 0.02 % out of 463733)
1:08:36.289730 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 463733)
1:08:36.307645 INFO: Collecting fragment features
1:08:36.561063 INFO: Finished candidate scoring
1:08:37.158266 PROGRESS: === Extracted 463733 precursors and 3008184 fragments ===
1:08:37.158962 INFO: performing precursor FDR with 47 features
1:08:37.159018 INFO: Decoy channel: -1
1:08:37.159044 INFO: Competetive: True
1:08:37.310132 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:37.419339 WARNING: dropped 55 target PSMs due to missing features
1:08:37.419530 WARNING: dropped 48 decoy PSMs due to missing features
1:08:45.971827 INFO: Test AUC: 0.569
1:08:45.972014 INFO: Train AUC: 0.589
1:08:45.972049 INFO: AUC difference: 3.35%
1:08:46.094537 INFO: Resetting torch num_threads to 100
1:08:46.107599 INFO: === FDR correction performed with classifier version 12 ===
1:08:46.108621 PROGRESS: ============================= Precursor FDR =============================
1:08:46.108772 PROGRESS: Total precursors accumulated: 786
1:08:46.108850 PROGRESS: Target precursors: 720 (91.60%)
1:08:46.108903 PROGRESS: Decoy precursors: 66 (8.40%)
1:08:46.108953 PROGRESS: 
1:08:46.109002 PROGRESS: Precursor Summary:
1:08:46.110193 PROGRESS: Channel   0:	 0.05 FDR:   547; 0.01 FDR:   378; 0.001 FDR:   289
1:08:46.110300 PROGRESS: 
1:08:46.110360 PROGRESS: Protein Summary:
1:08:46.111594 PROGRESS: Channel   0:	 0.05 FDR:   526; 0.01 FDR:   361; 0.001 FDR:   282
1:08:46.111699 PROGRESS: =========================================================================
1:08:46.134161 INFO: fragments_df_filtered: 3235
1:08:46.560487 INFO: calibration group: precursor, fitting mz estimator 
1:08:46.602712 INFO: calibration group: precursor, fitting rt estimator 
1:08:46.640277 INFO: calibration group: fragment, fitting mz estimator 
1:08:46.812868 INFO: calibration group: precursor, predicting mz
1:08:46.849419 INFO: calibration group: precursor, predicting rt
1:08:47.000045 INFO: calibration group: fragment, predicting mz
1:08:47.369070 INFO: === checking if optimization conditions were reached ===
1:08:47.369412 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:08:47.371688 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 78.5619.
1:08:47.371752 INFO: ==============================================
1:08:47.371871 INFO: Starting optimization step 4.
1:08:47.371943 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:08:47.372017 PROGRESS: Extracting batch of 237213 precursors
1:08:47.431187 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:08:47.431315 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:08:47.431368 INFO: FWHM in RT is 2.29 seconds, sigma is 0.29
1:08:47.431393 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:08:47.431774 INFO: Starting candidate selection
1:08:56.736930 INFO: Starting candidate scoring
1:09:00.173850 INFO: Finished candidate processing
1:09:00.173951 INFO: Collecting candidate features
1:09:01.013330 WARNING: intensity_correlation has 141 NaNs ( 0.03 % out of 462100)
1:09:01.031319 INFO: Collecting fragment features
1:09:01.295914 INFO: Finished candidate scoring
1:09:01.722108 PROGRESS: === Extracted 462100 precursors and 2932923 fragments ===
1:09:01.722670 INFO: performing precursor FDR with 47 features
1:09:01.722718 INFO: Decoy channel: -1
1:09:01.722743 INFO: Competetive: True
1:09:01.874149 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:01.963740 WARNING: dropped 77 target PSMs due to missing features
1:09:01.963888 WARNING: dropped 64 decoy PSMs due to missing features
1:09:10.992608 INFO: Test AUC: 0.570
1:09:10.992783 INFO: Train AUC: 0.585
1:09:10.992817 INFO: AUC difference: 2.58%
1:09:11.125280 INFO: Resetting torch num_threads to 100
1:09:11.154188 INFO: === FDR correction performed with classifier version 12 ===
1:09:11.155633 PROGRESS: ============================= Precursor FDR =============================
1:09:11.155812 PROGRESS: Total precursors accumulated: 899
1:09:11.155881 PROGRESS: Target precursors: 822 (91.43%)
1:09:11.155935 PROGRESS: Decoy precursors: 77 (8.57%)
1:09:11.155981 PROGRESS: 
1:09:11.156026 PROGRESS: Precursor Summary:
1:09:11.157420 PROGRESS: Channel   0:	 0.05 FDR:   570; 0.01 FDR:   375; 0.001 FDR:   235
1:09:11.157561 PROGRESS: 
1:09:11.157620 PROGRESS: Protein Summary:
1:09:11.159042 PROGRESS: Channel   0:	 0.05 FDR:   549; 0.01 FDR:   361; 0.001 FDR:   231
1:09:11.159170 PROGRESS: =========================================================================
1:09:11.181835 INFO: fragments_df_filtered: 3221
1:09:11.718696 INFO: calibration group: precursor, fitting mz estimator 
1:09:11.768121 INFO: calibration group: precursor, fitting rt estimator 
1:09:11.815051 INFO: calibration group: fragment, fitting mz estimator 
1:09:12.044144 INFO: calibration group: precursor, predicting mz
1:09:12.090246 INFO: calibration group: precursor, predicting rt
1:09:12.252824 INFO: calibration group: fragment, predicting mz
1:09:12.644600 INFO: === checking if optimization conditions were reached ===
1:09:12.645025 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1:09:12.647751 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 65.8746.
1:09:12.647814 INFO: ==============================================
1:09:12.647927 INFO: Starting optimization step 5.
1:09:12.648022 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:09:12.648109 PROGRESS: Extracting batch of 237213 precursors
1:09:12.733078 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:09:12.733244 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:09:12.733289 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
1:09:12.733312 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:09:12.733647 INFO: Starting candidate selection
1:09:22.070761 INFO: Starting candidate scoring
1:09:25.875233 INFO: Finished candidate processing
1:09:25.875395 INFO: Collecting candidate features
1:09:27.243976 WARNING: intensity_correlation has 143 NaNs ( 0.03 % out of 460546)
1:09:27.267350 INFO: Collecting fragment features
1:09:27.583475 INFO: Finished candidate scoring
1:09:28.579867 PROGRESS: === Extracted 460546 precursors and 2885513 fragments ===
1:09:28.580438 INFO: performing precursor FDR with 47 features
1:09:28.580479 INFO: Decoy channel: -1
1:09:28.580503 INFO: Competetive: True
1:09:28.848814 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:29.035769 WARNING: dropped 79 target PSMs due to missing features
1:09:29.035957 WARNING: dropped 64 decoy PSMs due to missing features
1:09:37.839962 INFO: Test AUC: 0.569
1:09:37.840180 INFO: Train AUC: 0.586
1:09:37.840215 INFO: AUC difference: 2.82%
1:09:37.970582 INFO: Resetting torch num_threads to 100
1:09:37.990155 INFO: === FDR correction performed with classifier version 12 ===
1:09:37.991708 PROGRESS: ============================= Precursor FDR =============================
1:09:37.991904 PROGRESS: Total precursors accumulated: 826
1:09:37.991975 PROGRESS: Target precursors: 753 (91.16%)
1:09:37.992029 PROGRESS: Decoy precursors: 73 (8.84%)
1:09:37.992075 PROGRESS: 
1:09:37.992122 PROGRESS: Precursor Summary:
1:09:37.993534 PROGRESS: Channel   0:	 0.05 FDR:   542; 0.01 FDR:   309; 0.001 FDR:   203
1:09:37.993672 PROGRESS: 
1:09:37.993731 PROGRESS: Protein Summary:
1:09:37.995121 PROGRESS: Channel   0:	 0.05 FDR:   521; 0.01 FDR:   302; 0.001 FDR:   200
1:09:37.995244 PROGRESS: =========================================================================
1:09:38.015111 INFO: fragments_df_filtered: 2726
1:09:38.567009 INFO: calibration group: precursor, fitting mz estimator 
1:09:38.636029 INFO: calibration group: precursor, fitting rt estimator 
1:09:40.179794 INFO: calibration group: fragment, fitting mz estimator 
1:09:40.333185 INFO: calibration group: precursor, predicting mz
1:09:40.381602 INFO: calibration group: precursor, predicting rt
1:09:40.554140 INFO: calibration group: fragment, predicting mz
1:09:40.938876 INFO: === checking if optimization conditions were reached ===
1:09:40.939517 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1:09:40.942240 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 62.5842.
1:09:40.942386 INFO: ==============================================
1:09:40.942666 INFO: Starting optimization step 6.
1:09:40.942915 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:09:40.943156 PROGRESS: Extracting batch of 237213 precursors
1:09:41.059508 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:09:41.059686 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:09:41.059740 INFO: FWHM in RT is 2.32 seconds, sigma is 0.30
1:09:41.059770 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:09:41.060162 INFO: Starting candidate selection
1:09:49.342547 INFO: Starting candidate scoring
1:09:53.234744 INFO: Finished candidate processing
1:09:53.235016 INFO: Collecting candidate features
1:09:54.797185 WARNING: intensity_correlation has 143 NaNs ( 0.03 % out of 460629)
1:09:54.826306 INFO: Collecting fragment features
1:09:55.191024 INFO: Finished candidate scoring
1:09:56.054636 PROGRESS: === Extracted 460629 precursors and 2912149 fragments ===
1:09:56.055343 INFO: performing precursor FDR with 47 features
1:09:56.055387 INFO: Decoy channel: -1
1:09:56.055421 INFO: Competetive: True
1:09:56.273207 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:56.413902 WARNING: dropped 73 target PSMs due to missing features
1:09:56.414070 WARNING: dropped 70 decoy PSMs due to missing features
1:10:05.267048 INFO: Test AUC: 0.572
1:10:05.267359 INFO: Train AUC: 0.586
1:10:05.267400 INFO: AUC difference: 2.33%
1:10:05.391427 INFO: Resetting torch num_threads to 100
1:10:05.408026 INFO: === FDR correction performed with classifier version 12 ===
1:10:05.409459 PROGRESS: ============================= Precursor FDR =============================
1:10:05.409628 PROGRESS: Total precursors accumulated: 813
1:10:05.409692 PROGRESS: Target precursors: 738 (90.77%)
1:10:05.409742 PROGRESS: Decoy precursors: 75 (9.23%)
1:10:05.409788 PROGRESS: 
1:10:05.409830 PROGRESS: Precursor Summary:
1:10:05.411233 PROGRESS: Channel   0:	 0.05 FDR:   509; 0.01 FDR:   368; 0.001 FDR:   214
1:10:05.411370 PROGRESS: 
1:10:05.411426 PROGRESS: Protein Summary:
1:10:05.413345 PROGRESS: Channel   0:	 0.05 FDR:   491; 0.01 FDR:   359; 0.001 FDR:   209
1:10:05.413466 PROGRESS: =========================================================================
1:10:05.436254 INFO: fragments_df_filtered: 3128
1:10:05.965161 INFO: calibration group: precursor, fitting mz estimator 
1:10:06.057732 INFO: calibration group: precursor, fitting rt estimator 
1:10:06.098890 INFO: calibration group: fragment, fitting mz estimator 
1:10:06.266675 INFO: calibration group: precursor, predicting mz
1:10:06.304760 INFO: calibration group: precursor, predicting rt
1:10:06.464784 INFO: calibration group: fragment, predicting mz
1:10:06.841382 INFO: === checking if optimization conditions were reached ===
1:10:06.841822 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1:10:06.843447 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 62.5842 found after 7 searches.
1:10:06.843508 INFO: ==============================================
1:10:06.843621 PROGRESS: Optimization finished for rt_error.
1:10:07.320403 INFO: calibration group: precursor, predicting mz
1:10:07.356567 INFO: calibration group: precursor, predicting rt
1:10:07.513682 INFO: calibration group: fragment, predicting mz
1:10:07.912699 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:10:07.913123 PROGRESS: ==============================================
1:10:07.913311 PROGRESS: ms2_error      : 8.0000
1:10:07.913477 PROGRESS: ms1_error      : 3.0000
1:10:07.913635 PROGRESS: rt_error       : 62.5842
1:10:07.913787 PROGRESS: ==============================================
1:10:07.915060 INFO: calibration group: precursor, predicting mz
1:10:09.567752 INFO: calibration group: precursor, predicting rt
1:10:16.950876 INFO: calibration group: fragment, predicting mz
1:10:34.947340 PROGRESS: Extracting batch of 10183864 precursors
1:10:38.198179 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:10:38.198339 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:10:38.198379 INFO: FWHM in RT is 2.28 seconds, sigma is 0.29
1:10:38.198402 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:10:38.198838 INFO: Starting candidate selection
1:16:11.482112 INFO: Applying score cutoff of 21.303189664840698
1:16:12.063865 INFO: Removed 4530293 precursors with score below cutoff
1:16:14.701511 INFO: Starting candidate scoring
1:18:08.301359 INFO: Finished candidate processing
1:18:08.301727 INFO: Collecting candidate features
1:19:33.694283 WARNING: intensity_correlation has 1250 NaNs ( 0.01 % out of 15762000)
1:19:34.418341 INFO: Collecting fragment features
1:20:24.375751 INFO: Finished candidate scoring
1:20:45.297644 INFO: === FDR correction performed with classifier version 19 ===
1:20:45.335511 INFO: performing precursor FDR with 47 features
1:20:45.335736 INFO: Decoy channel: -1
1:20:45.335781 INFO: Competetive: True
1:20:53.215115 INFO: Setting torch num_threads to 2 for FDR classification task
1:20:57.138408 WARNING: dropped 652 target PSMs due to missing features
1:20:57.138615 WARNING: dropped 598 decoy PSMs due to missing features
1:26:24.769423 INFO: Test AUC: 0.578
1:26:24.769803 INFO: Train AUC: 0.581
1:26:24.769850 INFO: AUC difference: 0.44%
1:26:25.792390 INFO: Resetting torch num_threads to 100
1:26:26.192821 INFO: Removing fragments below FDR threshold
1:26:26.918069 PROGRESS: ============================= Precursor FDR =============================
1:26:26.918441 PROGRESS: Total precursors accumulated: 15,691
1:26:26.918518 PROGRESS: Target precursors: 15,536 (99.01%)
1:26:26.918573 PROGRESS: Decoy precursors: 155 (0.99%)
1:26:26.918622 PROGRESS: 
1:26:26.918670 PROGRESS: Precursor Summary:
1:26:26.924379 PROGRESS: Channel   0:	 0.05 FDR: 15,536; 0.01 FDR: 15,536; 0.001 FDR: 10,550
1:26:26.924518 PROGRESS: 
1:26:26.924577 PROGRESS: Protein Summary:
1:26:26.933028 PROGRESS: Channel   0:	 0.05 FDR: 6,110; 0.01 FDR: 6,110; 0.001 FDR: 4,616
1:26:26.933165 PROGRESS: =========================================================================
1:26:27.983754 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:26:28.433302 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:26:28.433477 INFO: Quantification results path: run_output_Astral/alphadia_1.10_MBRSetValues/library/quant
1:26:28.433573 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3 at run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:26:28.434329 INFO: Initializing RawFileManager
1:26:53.701961 INFO: Determining DIA cycle
1:26:53.717495 INFO: Found cycle with start 0.00 min and length 303.
1:26:53.886835 INFO: RT (min)            : 0.0 - 26.9
1:26:53.886949 INFO: RT duration (sec)   : 1611.2
1:26:53.886980 INFO: RT duration (min)   : 26.9
1:26:53.887008 INFO: Cycle len (scans)   : 303
1:26:53.887029 INFO: Cycle len (sec)     : 1.65
1:26:53.887048 INFO: Number of cycles    : 977
1:26:53.887068 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:26:55.226025 INFO: Initializing CalibrationManager
1:26:55.226553 INFO: Loading calibration config
1:26:55.227608 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'}]
1:26:55.227734 INFO: Calibration group :fragment, found 1 estimator(s)
1:26:55.227864 INFO: Calibration group :precursor, found 3 estimator(s)
1:26:55.227961 INFO: Disabling ion mobility calibration
1:26:55.227993 INFO: removed mobility estimator from group precursor
1:26:55.228150 INFO: Initializing OptimizationManager
1:26:55.228293 INFO: initial parameter: ms1_error = 30
1:26:55.228371 INFO: initial parameter: ms2_error = 30
1:26:55.228434 INFO: initial parameter: rt_error = 805.6004638671875
1:26:55.228501 INFO: initial parameter: mobility_error = 0.1
1:26:55.228548 INFO: initial parameter: column_type = library
1:26:55.228593 INFO: initial parameter: num_candidates = 1
1:26:55.228635 INFO: initial parameter: classifier_version = -1
1:26:55.228690 INFO: initial parameter: fwhm_rt = 5
1:26:55.228751 INFO: initial parameter: fwhm_mobility = 0.01
1:26:55.228806 INFO: initial parameter: score_cutoff = 0
1:26:55.228905 INFO: Initializing TimingManager
1:26:55.228979 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:26:55.229172 INFO: FDRManager not loaded from disk.
1:26:55.229207 INFO: Initializing FDRManager
1:26:55.229244 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:26:56.620328 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
1:26:58.488824 PROGRESS: Starting initial search for precursors.
1:26:58.747194 INFO: Starting optimization step 0.
1:26:58.747452 PROGRESS: === Extracting elution groups 0 to 8000 ===
1:26:58.747546 PROGRESS: Extracting batch of 15815 precursors
1:26:58.751946 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:26:58.752006 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:26:58.752043 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:26:58.752066 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:26:58.752426 INFO: Starting candidate selection
1:26:59.978136 INFO: Starting candidate scoring
1:27:00.124182 INFO: Finished candidate processing
1:27:00.124303 INFO: Collecting candidate features
1:27:00.173902 INFO: Collecting fragment features
1:27:00.191546 INFO: Finished candidate scoring
1:27:00.201273 PROGRESS: === Extracted 15772 precursors and 155030 fragments ===
1:27:00.201661 INFO: performing precursor FDR with 47 features
1:27:00.201701 INFO: Decoy channel: -1
1:27:00.201726 INFO: Competetive: True
1:27:00.207165 INFO: Setting torch num_threads to 2 for FDR classification task
1:27:00.365999 INFO: Test AUC: 0.505
1:27:00.366109 INFO: Train AUC: 0.504
1:27:00.366139 INFO: AUC difference: 0.16%
1:27:00.451819 INFO: Resetting torch num_threads to 100
1:27:00.452908 INFO: === FDR correction performed with classifier version -1 ===
1:27:00.453610 PROGRESS: ============================= Precursor FDR =============================
1:27:00.453710 PROGRESS: Total precursors accumulated: 1
1:27:00.453770 PROGRESS: Target precursors: 1 (100.00%)
1:27:00.453824 PROGRESS: Decoy precursors: 0 (0.00%)
1:27:00.453869 PROGRESS: 
1:27:00.453914 PROGRESS: Precursor Summary:
1:27:00.454833 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:27:00.454919 PROGRESS: 
1:27:00.454974 PROGRESS: Protein Summary:
1:27:00.455978 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:27:00.456068 PROGRESS: =========================================================================
1:27:00.565138 INFO: Starting optimization step 1.
1:27:00.565418 PROGRESS: === Extracting elution groups 8000 to 24000 ===
1:27:00.565491 PROGRESS: Extracting batch of 31636 precursors
1:27:00.573126 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:27:00.573203 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:27:00.573237 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:27:00.573261 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:27:00.573462 INFO: Starting candidate selection
1:27:02.262851 INFO: Starting candidate scoring
1:27:02.503114 INFO: Finished candidate processing
1:27:02.503214 INFO: Collecting candidate features
1:27:02.564511 INFO: Collecting fragment features
1:27:02.588675 INFO: Finished candidate scoring
1:27:02.616427 PROGRESS: === Extracted 47340 precursors and 466082 fragments ===
1:27:02.622501 INFO: performing precursor FDR with 47 features
1:27:02.622574 INFO: Decoy channel: -1
1:27:02.622601 INFO: Competetive: True
1:27:02.651325 INFO: Setting torch num_threads to 2 for FDR classification task
1:27:03.361150 INFO: Test AUC: 0.530
1:27:03.361272 INFO: Train AUC: 0.545
1:27:03.361302 INFO: AUC difference: 2.79%
1:27:03.446083 INFO: Resetting torch num_threads to 100
1:27:03.448771 INFO: === FDR correction performed with classifier version -1 ===
1:27:03.449496 PROGRESS: ============================= Precursor FDR =============================
1:27:03.449585 PROGRESS: Total precursors accumulated: 1
1:27:03.449646 PROGRESS: Target precursors: 1 (100.00%)
1:27:03.449695 PROGRESS: Decoy precursors: 0 (0.00%)
1:27:03.449739 PROGRESS: 
1:27:03.449782 PROGRESS: Precursor Summary:
1:27:03.450705 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:27:03.450788 PROGRESS: 
1:27:03.450841 PROGRESS: Protein Summary:
1:27:03.451835 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:27:03.451918 PROGRESS: =========================================================================
1:27:03.603935 INFO: Starting optimization step 2.
1:27:03.604209 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1:27:03.604278 PROGRESS: Extracting batch of 63234 precursors
1:27:03.618785 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:27:03.618912 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:27:03.618946 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:27:03.618967 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:27:03.619187 INFO: Starting candidate selection
1:27:07.642240 INFO: Starting candidate scoring
1:27:08.110774 INFO: Finished candidate processing
1:27:08.110878 INFO: Collecting candidate features
1:27:08.217733 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 63069)
1:27:08.223115 INFO: Collecting fragment features
1:27:08.269953 INFO: Finished candidate scoring
1:27:08.334478 PROGRESS: === Extracted 110409 precursors and 1089002 fragments ===
1:27:08.348145 INFO: performing precursor FDR with 47 features
1:27:08.348293 INFO: Decoy channel: -1
1:27:08.348321 INFO: Competetive: True
1:27:08.392973 INFO: Setting torch num_threads to 2 for FDR classification task
1:27:08.412162 WARNING: dropped 1 decoy PSMs due to missing features
1:27:10.190517 INFO: Test AUC: 0.551
1:27:10.190648 INFO: Train AUC: 0.556
1:27:10.190678 INFO: AUC difference: 0.99%
1:27:10.278537 INFO: Resetting torch num_threads to 100
1:27:10.284256 INFO: === FDR correction performed with classifier version -1 ===
1:27:10.285057 PROGRESS: ============================= Precursor FDR =============================
1:27:10.285150 PROGRESS: Total precursors accumulated: 4
1:27:10.285208 PROGRESS: Target precursors: 4 (100.00%)
1:27:10.285259 PROGRESS: Decoy precursors: 0 (0.00%)
1:27:10.285305 PROGRESS: 
1:27:10.285348 PROGRESS: Precursor Summary:
1:27:10.286266 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
1:27:10.286350 PROGRESS: 
1:27:10.286403 PROGRESS: Protein Summary:
1:27:10.287399 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
1:27:10.287487 PROGRESS: =========================================================================
1:27:10.520260 INFO: Starting optimization step 3.
1:27:10.520566 PROGRESS: === Extracting elution groups 56000 to 120000 ===
1:27:10.520641 PROGRESS: Extracting batch of 126528 precursors
1:27:10.548874 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:27:10.549013 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:27:10.549049 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:27:10.549074 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:27:10.549294 INFO: Starting candidate selection
1:27:18.521616 INFO: Starting candidate scoring
1:27:19.448105 INFO: Finished candidate processing
1:27:19.448207 INFO: Collecting candidate features
1:27:19.689080 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 126164)
1:27:19.696465 INFO: Collecting fragment features
1:27:19.789292 INFO: Finished candidate scoring
1:27:19.958544 PROGRESS: === Extracted 236573 precursors and 2333072 fragments ===
1:27:19.984478 INFO: performing precursor FDR with 47 features
1:27:19.984615 INFO: Decoy channel: -1
1:27:19.984643 INFO: Competetive: True
1:27:20.095156 INFO: Setting torch num_threads to 2 for FDR classification task
1:27:20.132518 WARNING: dropped 2 decoy PSMs due to missing features
1:27:24.152866 INFO: Test AUC: 0.557
1:27:24.153057 INFO: Train AUC: 0.568
1:27:24.153090 INFO: AUC difference: 1.92%
1:27:24.254749 INFO: Resetting torch num_threads to 100
1:27:24.268825 INFO: === FDR correction performed with classifier version -1 ===
1:27:24.269804 PROGRESS: ============================= Precursor FDR =============================
1:27:24.269925 PROGRESS: Total precursors accumulated: 3
1:27:24.269987 PROGRESS: Target precursors: 3 (100.00%)
1:27:24.270040 PROGRESS: Decoy precursors: 0 (0.00%)
1:27:24.270086 PROGRESS: 
1:27:24.270130 PROGRESS: Precursor Summary:
1:27:24.271093 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1:27:24.271186 PROGRESS: 
1:27:24.271242 PROGRESS: Protein Summary:
1:27:24.272254 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1:27:24.272344 PROGRESS: =========================================================================
1:27:24.721345 INFO: Starting optimization step 4.
1:27:24.721609 PROGRESS: === Extracting elution groups 120000 to 248000 ===
1:27:24.721725 PROGRESS: Extracting batch of 253020 precursors
1:27:24.782797 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:27:24.782921 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:27:24.782982 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:27:24.783009 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:27:24.783439 INFO: Starting candidate selection
1:27:40.469635 INFO: Starting candidate scoring
1:27:42.316736 INFO: Finished candidate processing
1:27:42.316839 INFO: Collecting candidate features
1:27:42.856124 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 252391)
1:27:42.867075 INFO: Collecting fragment features
1:27:43.058282 INFO: Finished candidate scoring
1:27:43.376863 PROGRESS: === Extracted 488964 precursors and 4820780 fragments ===
1:27:43.431351 INFO: performing precursor FDR with 47 features
1:27:43.431494 INFO: Decoy channel: -1
1:27:43.431521 INFO: Competetive: True
1:27:43.656616 INFO: Setting torch num_threads to 2 for FDR classification task
1:27:43.737034 WARNING: dropped 3 decoy PSMs due to missing features
1:27:52.385884 INFO: Test AUC: 0.565
1:27:52.386097 INFO: Train AUC: 0.576
1:27:52.386131 INFO: AUC difference: 1.93%
1:27:52.503506 INFO: Resetting torch num_threads to 100
1:27:52.532292 INFO: === FDR correction performed with classifier version -1 ===
1:27:52.533321 PROGRESS: ============================= Precursor FDR =============================
1:27:52.533451 PROGRESS: Total precursors accumulated: 2
1:27:52.533517 PROGRESS: Target precursors: 2 (100.00%)
1:27:52.533571 PROGRESS: Decoy precursors: 0 (0.00%)
1:27:52.533624 PROGRESS: 
1:27:52.533671 PROGRESS: Precursor Summary:
1:27:52.534659 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:27:52.534754 PROGRESS: 
1:27:52.534814 PROGRESS: Protein Summary:
1:27:52.535828 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:27:52.535919 PROGRESS: =========================================================================
1:27:53.238033 INFO: Starting optimization step 5.
1:27:53.238360 PROGRESS: === Extracting elution groups 248000 to 504000 ===
1:27:53.238444 PROGRESS: Extracting batch of 505949 precursors
1:27:53.357657 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:27:53.357790 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:27:53.357830 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:27:53.357853 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:27:53.358142 INFO: Starting candidate selection
1:28:24.817212 INFO: Starting candidate scoring
1:28:28.567707 INFO: Finished candidate processing
1:28:28.567826 INFO: Collecting candidate features
1:28:29.685816 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 504787)
1:28:29.704893 INFO: Collecting fragment features
1:28:30.088720 INFO: Finished candidate scoring
1:28:31.023849 PROGRESS: === Extracted 993751 precursors and 9797241 fragments ===
1:28:31.163994 INFO: performing precursor FDR with 47 features
1:28:31.164149 INFO: Decoy channel: -1
1:28:31.164183 INFO: Competetive: True
1:28:31.694002 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:31.924714 WARNING: dropped 3 target PSMs due to missing features
1:28:31.924884 WARNING: dropped 4 decoy PSMs due to missing features
1:28:45.153971 INFO: Test AUC: 0.567
1:28:45.154099 INFO: Train AUC: 0.576
1:28:45.154133 INFO: AUC difference: 1.67%
1:28:45.318260 INFO: Resetting torch num_threads to 100
1:28:45.401765 INFO: === FDR correction performed with classifier version -1 ===
1:28:45.402802 PROGRESS: ============================= Precursor FDR =============================
1:28:45.402920 PROGRESS: Total precursors accumulated: 2
1:28:45.402983 PROGRESS: Target precursors: 2 (100.00%)
1:28:45.403034 PROGRESS: Decoy precursors: 0 (0.00%)
1:28:45.403080 PROGRESS: 
1:28:45.403124 PROGRESS: Precursor Summary:
1:28:45.404105 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:28:45.404197 PROGRESS: 
1:28:45.404254 PROGRESS: Protein Summary:
1:28:45.405325 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:28:45.405416 PROGRESS: =========================================================================
1:28:46.842280 INFO: Starting optimization step 6.
1:28:46.842612 PROGRESS: === Extracting elution groups 504000 to 1016000 ===
1:28:46.842709 PROGRESS: Extracting batch of 1011924 precursors
1:28:47.178084 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:28:47.178263 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:28:47.178307 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:28:47.178330 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:28:47.178699 INFO: Starting candidate selection
1:29:50.171932 INFO: Starting candidate scoring
1:29:57.979722 INFO: Finished candidate processing
1:29:57.980073 INFO: Collecting candidate features
1:30:00.459376 WARNING: intensity_correlation has 9 NaNs ( 0.00 % out of 1009359)
1:30:00.493132 INFO: Collecting fragment features
1:30:01.270376 INFO: Finished candidate scoring
1:30:03.099977 PROGRESS: === Extracted 2003110 precursors and 19751603 fragments ===
1:30:03.419612 INFO: performing precursor FDR with 47 features
1:30:03.419758 INFO: Decoy channel: -1
1:30:03.419792 INFO: Competetive: True
1:30:04.538152 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:05.069442 WARNING: dropped 10 target PSMs due to missing features
1:30:05.069624 WARNING: dropped 6 decoy PSMs due to missing features
1:30:40.622033 INFO: Test AUC: 0.571
1:30:40.622279 INFO: Train AUC: 0.577
1:30:40.622313 INFO: AUC difference: 0.98%
1:30:40.850953 INFO: Resetting torch num_threads to 100
1:30:40.989122 INFO: === FDR correction performed with classifier version -1 ===
1:30:40.990125 PROGRESS: ============================= Precursor FDR =============================
1:30:40.990227 PROGRESS: Total precursors accumulated: 1
1:30:40.990291 PROGRESS: Target precursors: 1 (100.00%)
1:30:40.990344 PROGRESS: Decoy precursors: 0 (0.00%)
1:30:40.990395 PROGRESS: 
1:30:40.990442 PROGRESS: Precursor Summary:
1:30:40.991396 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:30:40.991486 PROGRESS: 
1:30:40.991544 PROGRESS: Protein Summary:
1:30:40.992561 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:30:40.992652 PROGRESS: =========================================================================
1:30:42.965615 INFO: Starting optimization step 7.
1:30:42.965985 PROGRESS: === Extracting elution groups 1016000 to 2040000 ===
1:30:42.966087 PROGRESS: Extracting batch of 2023834 precursors
1:30:43.467269 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:30:43.467417 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:43.467471 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:30:43.467497 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:30:43.467813 INFO: Starting candidate selection
1:32:45.345503 INFO: Starting candidate scoring
1:33:01.898659 INFO: Finished candidate processing
1:33:01.899017 INFO: Collecting candidate features
1:33:06.630163 WARNING: intensity_correlation has 16 NaNs ( 0.00 % out of 2018677)
1:33:06.695081 INFO: Collecting fragment features
1:33:08.421864 INFO: Finished candidate scoring
1:33:13.147572 PROGRESS: === Extracted 4021787 precursors and 39659389 fragments ===
1:33:13.906052 INFO: performing precursor FDR with 47 features
1:33:13.906324 INFO: Decoy channel: -1
1:33:13.906360 INFO: Competetive: True
1:33:16.323906 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:17.399393 WARNING: dropped 17 target PSMs due to missing features
1:33:17.399571 WARNING: dropped 15 decoy PSMs due to missing features
1:34:31.653095 INFO: Test AUC: 0.576
1:34:31.654336 INFO: Train AUC: 0.579
1:34:31.654377 INFO: AUC difference: 0.54%
1:34:32.050098 INFO: Resetting torch num_threads to 100
1:34:32.456394 INFO: === FDR correction performed with classifier version -1 ===
1:34:32.458127 PROGRESS: ============================= Precursor FDR =============================
1:34:32.458289 PROGRESS: Total precursors accumulated: 2,160
1:34:32.458362 PROGRESS: Target precursors: 1,979 (91.62%)
1:34:32.458416 PROGRESS: Decoy precursors: 181 (8.38%)
1:34:32.458464 PROGRESS: 
1:34:32.458511 PROGRESS: Precursor Summary:
1:34:32.460193 PROGRESS: Channel   0:	 0.05 FDR: 1,646; 0.01 FDR: 1,205; 0.001 FDR: 1,047
1:34:32.460312 PROGRESS: 
1:34:32.460371 PROGRESS: Protein Summary:
1:34:32.462222 PROGRESS: Channel   0:	 0.05 FDR: 1,286; 0.01 FDR:   950; 0.001 FDR:   834
1:34:32.462324 PROGRESS: =========================================================================
1:34:32.909066 INFO: fragments_df_filtered: 5000
1:34:34.136933 INFO: calibration group: precursor, fitting mz estimator 
1:34:34.213976 INFO: calibration group: precursor, fitting rt estimator 
1:34:34.291160 INFO: calibration group: fragment, fitting mz estimator 
1:34:35.732700 INFO: calibration group: precursor, predicting mz
1:34:35.876623 INFO: calibration group: precursor, predicting rt
1:34:36.561444 INFO: calibration group: fragment, predicting mz
1:34:38.069685 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:34:38.069966 INFO: Starting optimization step 8.
1:34:38.070037 PROGRESS: === Extracting elution groups 0 to 504000 ===
1:34:38.070099 PROGRESS: Extracting batch of 996182 precursors
1:34:38.312256 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:34:38.312390 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:34:38.312427 INFO: FWHM in RT is 2.96 seconds, sigma is 0.38
1:34:38.312451 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:34:38.312719 INFO: Starting candidate selection
1:35:24.921982 INFO: Starting candidate scoring
1:35:39.305376 INFO: Finished candidate processing
1:35:39.305538 INFO: Collecting candidate features
1:35:43.491434 WARNING: intensity_correlation has 6 NaNs ( 0.00 % out of 1987505)
1:35:43.567871 INFO: Collecting fragment features
1:35:44.892016 INFO: Finished candidate scoring
1:35:47.783104 PROGRESS: === Extracted 1987505 precursors and 19328561 fragments ===
1:35:47.785177 INFO: performing precursor FDR with 47 features
1:35:47.785225 INFO: Decoy channel: -1
1:35:47.785256 INFO: Competetive: True
1:35:48.422552 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:48.808024 WARNING: dropped 1 target PSMs due to missing features
1:35:48.808174 WARNING: dropped 5 decoy PSMs due to missing features
1:36:22.944668 INFO: Test AUC: 0.577
1:36:22.944910 INFO: Train AUC: 0.584
1:36:22.944944 INFO: AUC difference: 1.20%
1:36:23.199720 INFO: Resetting torch num_threads to 100
1:36:23.258835 INFO: === FDR correction performed with classifier version 7 ===
1:36:23.260247 PROGRESS: ============================= Precursor FDR =============================
1:36:23.260443 PROGRESS: Total precursors accumulated: 973
1:36:23.260517 PROGRESS: Target precursors: 886 (91.06%)
1:36:23.260568 PROGRESS: Decoy precursors: 87 (8.94%)
1:36:23.260615 PROGRESS: 
1:36:23.260661 PROGRESS: Precursor Summary:
1:36:23.262471 PROGRESS: Channel   0:	 0.05 FDR:   664; 0.01 FDR:   464; 0.001 FDR:   384
1:36:23.262618 PROGRESS: 
1:36:23.262674 PROGRESS: Protein Summary:
1:36:23.264195 PROGRESS: Channel   0:	 0.05 FDR:   610; 0.01 FDR:   421; 0.001 FDR:   352
1:36:23.264313 PROGRESS: =========================================================================
1:36:23.338570 INFO: fragments_df_filtered: 5000
1:36:24.212917 INFO: calibration group: precursor, fitting mz estimator 
1:36:24.267702 INFO: calibration group: precursor, fitting rt estimator 
1:36:24.320302 INFO: calibration group: fragment, fitting mz estimator 
1:36:24.756720 INFO: calibration group: precursor, predicting mz
1:36:24.915111 INFO: calibration group: precursor, predicting rt
1:36:25.257626 INFO: calibration group: fragment, predicting mz
1:36:26.073520 INFO: === checking if optimization conditions were reached ===
1:36:26.076156 PROGRESS: ❌ ms2_error      : 14.2078 > 8.0000 or insufficient steps taken.
1:36:26.077148 PROGRESS: ❌ ms1_error      : 13.7558 > 3.0000 or insufficient steps taken.
1:36:26.077201 INFO: ==============================================
1:36:26.077297 INFO: Starting optimization step 9.
1:36:26.077363 PROGRESS: === Extracting elution groups 0 to 248000 ===
1:36:26.077432 PROGRESS: Extracting batch of 490233 precursors
1:36:26.220552 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:36:26.220696 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:36:26.220754 INFO: FWHM in RT is 2.96 seconds, sigma is 0.38
1:36:26.220777 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:36:26.221071 INFO: Starting candidate selection
1:36:51.103106 INFO: Starting candidate scoring
1:36:58.485233 INFO: Finished candidate processing
1:36:58.485341 INFO: Collecting candidate features
1:37:00.595548 WARNING: intensity_correlation has 31 NaNs ( 0.00 % out of 977183)
1:37:00.634782 INFO: Collecting fragment features
1:37:01.398106 INFO: Finished candidate scoring
1:37:02.718901 PROGRESS: === Extracted 977183 precursors and 8281095 fragments ===
1:37:02.720003 INFO: performing precursor FDR with 47 features
1:37:02.720046 INFO: Decoy channel: -1
1:37:02.720072 INFO: Competetive: True
1:37:03.122578 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:03.354927 WARNING: dropped 20 target PSMs due to missing features
1:37:03.355077 WARNING: dropped 11 decoy PSMs due to missing features
1:37:21.530852 INFO: Test AUC: 0.573
1:37:21.531077 INFO: Train AUC: 0.584
1:37:21.531115 INFO: AUC difference: 1.84%
1:37:21.699653 INFO: Resetting torch num_threads to 100
1:37:21.735177 INFO: === FDR correction performed with classifier version 8 ===
1:37:21.736766 PROGRESS: ============================= Precursor FDR =============================
1:37:21.736953 PROGRESS: Total precursors accumulated: 842
1:37:21.737021 PROGRESS: Target precursors: 770 (91.45%)
1:37:21.737075 PROGRESS: Decoy precursors: 72 (8.55%)
1:37:21.737123 PROGRESS: 
1:37:21.737171 PROGRESS: Precursor Summary:
1:37:21.738484 PROGRESS: Channel   0:	 0.05 FDR:   636; 0.01 FDR:   428; 0.001 FDR:   258
1:37:21.738619 PROGRESS: 
1:37:21.738679 PROGRESS: Protein Summary:
1:37:21.740030 PROGRESS: Channel   0:	 0.05 FDR:   594; 0.01 FDR:   406; 0.001 FDR:   248
1:37:21.740133 PROGRESS: =========================================================================
1:37:21.774134 INFO: fragments_df_filtered: 4349
1:37:22.301978 INFO: calibration group: precursor, fitting mz estimator 
1:37:22.361999 INFO: calibration group: precursor, fitting rt estimator 
1:37:22.413913 INFO: calibration group: fragment, fitting mz estimator 
1:37:22.762670 INFO: calibration group: precursor, predicting mz
1:37:22.800594 INFO: calibration group: precursor, predicting rt
1:37:22.958677 INFO: calibration group: fragment, predicting mz
1:37:23.337440 INFO: === checking if optimization conditions were reached ===
1:37:23.340539 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
1:37:23.341845 PROGRESS: ❌ ms1_error      : 6.1604 > 3.0000 or insufficient steps taken.
1:37:23.342179 INFO: ==============================================
1:37:23.342507 INFO: Starting optimization step 10.
1:37:23.342806 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:37:23.343179 PROGRESS: Extracting batch of 237213 precursors
1:37:23.419198 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:37:23.419353 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:37:23.419396 INFO: FWHM in RT is 2.62 seconds, sigma is 0.34
1:37:23.419420 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:37:23.419727 INFO: Starting candidate selection
1:37:35.533507 INFO: Starting candidate scoring
1:37:39.152766 INFO: Finished candidate processing
1:37:39.152994 INFO: Collecting candidate features
1:37:40.159616 WARNING: intensity_correlation has 23 NaNs ( 0.00 % out of 471998)
1:37:40.178249 INFO: Collecting fragment features
1:37:40.449964 INFO: Finished candidate scoring
1:37:41.045087 PROGRESS: === Extracted 471998 precursors and 3462746 fragments ===
1:37:41.045637 INFO: performing precursor FDR with 47 features
1:37:41.045685 INFO: Decoy channel: -1
1:37:41.045712 INFO: Competetive: True
1:37:41.220061 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:41.330134 WARNING: dropped 14 target PSMs due to missing features
1:37:41.330284 WARNING: dropped 9 decoy PSMs due to missing features
1:37:48.807981 INFO: Test AUC: 0.571
1:37:48.808210 INFO: Train AUC: 0.588
1:37:48.808244 INFO: AUC difference: 2.84%
1:37:48.942182 INFO: Resetting torch num_threads to 100
1:37:48.959999 INFO: === FDR correction performed with classifier version 9 ===
1:37:48.961355 PROGRESS: ============================= Precursor FDR =============================
1:37:48.961661 PROGRESS: Total precursors accumulated: 620
1:37:48.961748 PROGRESS: Target precursors: 567 (91.45%)
1:37:48.961850 PROGRESS: Decoy precursors: 53 (8.55%)
1:37:48.961916 PROGRESS: 
1:37:48.961980 PROGRESS: Precursor Summary:
1:37:48.963254 PROGRESS: Channel   0:	 0.05 FDR:   394; 0.01 FDR:   260; 0.001 FDR:   233
1:37:48.963376 PROGRESS: 
1:37:48.963448 PROGRESS: Protein Summary:
1:37:48.964723 PROGRESS: Channel   0:	 0.05 FDR:   378; 0.01 FDR:   252; 0.001 FDR:   226
1:37:48.964831 PROGRESS: =========================================================================
1:37:48.983178 INFO: fragments_df_filtered: 2468
1:37:49.497287 INFO: calibration group: precursor, fitting mz estimator 
1:37:49.544480 INFO: calibration group: precursor, fitting rt estimator 
1:37:49.583734 INFO: calibration group: fragment, fitting mz estimator 
1:37:49.701258 INFO: calibration group: precursor, predicting mz
1:37:49.747294 INFO: calibration group: precursor, predicting rt
1:37:49.909324 INFO: calibration group: fragment, predicting mz
1:37:50.282309 INFO: === checking if optimization conditions were reached ===
1:37:50.282664 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
1:37:50.284044 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
1:37:50.284100 INFO: ==============================================
1:37:50.284230 PROGRESS: Optimization finished for ms2_error, ms1_error.
1:37:50.716438 INFO: calibration group: precursor, predicting mz
1:37:50.750790 INFO: calibration group: precursor, predicting rt
1:37:50.910494 INFO: calibration group: fragment, predicting mz
1:37:51.280376 INFO: Starting optimization step 0.
1:37:51.280757 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:37:51.280862 PROGRESS: Extracting batch of 237213 precursors
1:37:51.351144 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:37:51.351300 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:37:51.351340 INFO: FWHM in RT is 2.63 seconds, sigma is 0.34
1:37:51.351365 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:37:51.351657 INFO: Starting candidate selection
1:38:03.228171 INFO: Starting candidate scoring
1:38:06.950307 INFO: Finished candidate processing
1:38:06.950531 INFO: Collecting candidate features
1:38:07.911545 WARNING: intensity_correlation has 15 NaNs ( 0.00 % out of 472383)
1:38:07.930406 INFO: Collecting fragment features
1:38:08.193067 INFO: Finished candidate scoring
1:38:08.583643 PROGRESS: === Extracted 472383 precursors and 3477744 fragments ===
1:38:08.584183 INFO: performing precursor FDR with 47 features
1:38:08.584224 INFO: Decoy channel: -1
1:38:08.584246 INFO: Competetive: True
1:38:08.733470 INFO: Setting torch num_threads to 2 for FDR classification task
1:38:08.831473 WARNING: dropped 7 target PSMs due to missing features
1:38:08.831631 WARNING: dropped 8 decoy PSMs due to missing features
1:38:17.064825 INFO: Test AUC: 0.578
1:38:17.065004 INFO: Train AUC: 0.590
1:38:17.065038 INFO: AUC difference: 2.01%
1:38:17.186903 INFO: Resetting torch num_threads to 100
1:38:17.202771 INFO: === FDR correction performed with classifier version 10 ===
1:38:17.203691 PROGRESS: ============================= Precursor FDR =============================
1:38:17.203785 PROGRESS: Total precursors accumulated: 626
1:38:17.203845 PROGRESS: Target precursors: 578 (92.33%)
1:38:17.203895 PROGRESS: Decoy precursors: 48 (7.67%)
1:38:17.203941 PROGRESS: 
1:38:17.203984 PROGRESS: Precursor Summary:
1:38:17.204952 PROGRESS: Channel   0:	 0.05 FDR:   383; 0.01 FDR:   219; 0.001 FDR:   180
1:38:17.205047 PROGRESS: 
1:38:17.205102 PROGRESS: Protein Summary:
1:38:17.206204 PROGRESS: Channel   0:	 0.05 FDR:   370; 0.01 FDR:   214; 0.001 FDR:   176
1:38:17.206317 PROGRESS: =========================================================================
1:38:17.222346 INFO: fragments_df_filtered: 2145
1:38:17.665664 INFO: calibration group: precursor, fitting mz estimator 
1:38:17.715033 INFO: calibration group: precursor, fitting rt estimator 
1:38:17.765767 INFO: calibration group: fragment, fitting mz estimator 
1:38:17.912024 INFO: calibration group: precursor, predicting mz
1:38:17.955195 INFO: calibration group: precursor, predicting rt
1:38:18.124085 INFO: calibration group: fragment, predicting mz
1:38:18.489109 INFO: === checking if optimization conditions were reached ===
1:38:18.489555 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:38:18.491773 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 319.5887.
1:38:18.491834 INFO: ==============================================
1:38:18.491938 INFO: Starting optimization step 1.
1:38:18.492013 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:38:18.492096 PROGRESS: Extracting batch of 237213 precursors
1:38:18.557873 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:38:18.558038 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:38:18.558079 INFO: FWHM in RT is 2.53 seconds, sigma is 0.33
1:38:18.558102 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:38:18.558385 INFO: Starting candidate selection
1:38:28.840434 INFO: Starting candidate scoring
1:38:32.533415 INFO: Finished candidate processing
1:38:32.533796 INFO: Collecting candidate features
1:38:33.537076 WARNING: intensity_correlation has 43 NaNs ( 0.01 % out of 470093)
1:38:33.555815 INFO: Collecting fragment features
1:38:33.813743 INFO: Finished candidate scoring
1:38:34.240071 PROGRESS: === Extracted 470093 precursors and 3376094 fragments ===
1:38:34.240667 INFO: performing precursor FDR with 47 features
1:38:34.240721 INFO: Decoy channel: -1
1:38:34.240754 INFO: Competetive: True
1:38:34.424132 INFO: Setting torch num_threads to 2 for FDR classification task
1:38:34.524989 WARNING: dropped 26 target PSMs due to missing features
1:38:34.525140 WARNING: dropped 17 decoy PSMs due to missing features
1:38:42.893321 INFO: Test AUC: 0.573
1:38:42.893552 INFO: Train AUC: 0.587
1:38:42.893592 INFO: AUC difference: 2.49%
1:38:43.019073 INFO: Resetting torch num_threads to 100
1:38:43.035013 INFO: === FDR correction performed with classifier version 10 ===
1:38:43.035971 PROGRESS: ============================= Precursor FDR =============================
1:38:43.036066 PROGRESS: Total precursors accumulated: 629
1:38:43.036127 PROGRESS: Target precursors: 572 (90.94%)
1:38:43.036178 PROGRESS: Decoy precursors: 57 (9.06%)
1:38:43.036223 PROGRESS: 
1:38:43.036265 PROGRESS: Precursor Summary:
1:38:43.037273 PROGRESS: Channel   0:	 0.05 FDR:   390; 0.01 FDR:   320; 0.001 FDR:   172
1:38:43.037365 PROGRESS: 
1:38:43.037420 PROGRESS: Protein Summary:
1:38:43.038535 PROGRESS: Channel   0:	 0.05 FDR:   378; 0.01 FDR:   309; 0.001 FDR:   170
1:38:43.038623 PROGRESS: =========================================================================
1:38:43.058482 INFO: fragments_df_filtered: 2947
1:38:43.519505 INFO: calibration group: precursor, fitting mz estimator 
1:38:43.584929 INFO: calibration group: precursor, fitting rt estimator 
1:38:43.633092 INFO: calibration group: fragment, fitting mz estimator 
1:38:43.851308 INFO: calibration group: precursor, predicting mz
1:38:43.890000 INFO: calibration group: precursor, predicting rt
1:38:44.040982 INFO: calibration group: fragment, predicting mz
1:38:44.407225 INFO: === checking if optimization conditions were reached ===
1:38:44.407876 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:38:44.410356 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 256.4107.
1:38:44.410484 INFO: ==============================================
1:38:44.410754 INFO: Starting optimization step 2.
1:38:44.411012 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:38:44.411258 PROGRESS: Extracting batch of 237213 precursors
1:38:44.484282 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:38:44.484425 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:38:44.484466 INFO: FWHM in RT is 2.41 seconds, sigma is 0.31
1:38:44.484489 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:38:44.484818 INFO: Starting candidate selection
1:38:54.459117 INFO: Starting candidate scoring
1:38:58.272596 INFO: Finished candidate processing
1:38:58.272728 INFO: Collecting candidate features
1:38:59.289529 WARNING: intensity_correlation has 37 NaNs ( 0.01 % out of 469441)
1:38:59.308236 INFO: Collecting fragment features
1:38:59.611127 INFO: Finished candidate scoring
1:38:59.936217 PROGRESS: === Extracted 469441 precursors and 3335197 fragments ===
1:38:59.936688 INFO: performing precursor FDR with 47 features
1:38:59.936737 INFO: Decoy channel: -1
1:38:59.936762 INFO: Competetive: True
1:39:00.093493 INFO: Setting torch num_threads to 2 for FDR classification task
1:39:00.189574 WARNING: dropped 25 target PSMs due to missing features
1:39:00.189737 WARNING: dropped 12 decoy PSMs due to missing features
1:39:06.466909 INFO: Test AUC: 0.574
1:39:06.467126 INFO: Train AUC: 0.588
1:39:06.467160 INFO: AUC difference: 2.37%
1:39:06.590786 INFO: Resetting torch num_threads to 100
1:39:06.606202 INFO: === FDR correction performed with classifier version 10 ===
1:39:06.607185 PROGRESS: ============================= Precursor FDR =============================
1:39:06.607283 PROGRESS: Total precursors accumulated: 684
1:39:06.607341 PROGRESS: Target precursors: 626 (91.52%)
1:39:06.607390 PROGRESS: Decoy precursors: 58 (8.48%)
1:39:06.607434 PROGRESS: 
1:39:06.607478 PROGRESS: Precursor Summary:
1:39:06.608444 PROGRESS: Channel   0:	 0.05 FDR:   422; 0.01 FDR:   258; 0.001 FDR:   198
1:39:06.608533 PROGRESS: 
1:39:06.608586 PROGRESS: Protein Summary:
1:39:06.609685 PROGRESS: Channel   0:	 0.05 FDR:   410; 0.01 FDR:   251; 0.001 FDR:   195
1:39:06.609774 PROGRESS: =========================================================================
1:39:06.625875 INFO: fragments_df_filtered: 2473
1:39:07.095480 INFO: calibration group: precursor, fitting mz estimator 
1:39:07.150644 INFO: calibration group: precursor, fitting rt estimator 
1:39:07.205404 INFO: calibration group: fragment, fitting mz estimator 
1:39:07.375936 INFO: calibration group: precursor, predicting mz
1:39:07.430295 INFO: calibration group: precursor, predicting rt
1:39:07.581843 INFO: calibration group: fragment, predicting mz
1:39:07.947080 INFO: === checking if optimization conditions were reached ===
1:39:07.947455 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:39:07.952429 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 157.0008.
1:39:07.952501 INFO: ==============================================
1:39:07.952611 INFO: Starting optimization step 3.
1:39:07.952684 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:39:07.952779 PROGRESS: Extracting batch of 237213 precursors
1:39:08.018075 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:39:08.018210 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:39:08.018249 INFO: FWHM in RT is 2.40 seconds, sigma is 0.31
1:39:08.018272 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:39:08.018547 INFO: Starting candidate selection
1:39:17.761879 INFO: Starting candidate scoring
1:39:21.572603 INFO: Finished candidate processing
1:39:21.572737 INFO: Collecting candidate features
1:39:22.408913 WARNING: intensity_correlation has 56 NaNs ( 0.01 % out of 467329)
1:39:22.427203 INFO: Collecting fragment features
1:39:22.683975 INFO: Finished candidate scoring
1:39:23.045775 PROGRESS: === Extracted 467329 precursors and 3221060 fragments ===
1:39:23.046301 INFO: performing precursor FDR with 47 features
1:39:23.046338 INFO: Decoy channel: -1
1:39:23.046360 INFO: Competetive: True
1:39:23.227902 INFO: Setting torch num_threads to 2 for FDR classification task
1:39:23.327061 WARNING: dropped 28 target PSMs due to missing features
1:39:23.327260 WARNING: dropped 28 decoy PSMs due to missing features
1:39:31.402051 INFO: Test AUC: 0.570
1:39:31.402227 INFO: Train AUC: 0.584
1:39:31.402259 INFO: AUC difference: 2.44%
1:39:31.526839 INFO: Resetting torch num_threads to 100
1:39:31.544013 INFO: === FDR correction performed with classifier version 10 ===
1:39:31.545088 PROGRESS: ============================= Precursor FDR =============================
1:39:31.545207 PROGRESS: Total precursors accumulated: 650
1:39:31.545268 PROGRESS: Target precursors: 591 (90.92%)
1:39:31.545319 PROGRESS: Decoy precursors: 59 (9.08%)
1:39:31.545362 PROGRESS: 
1:39:31.545406 PROGRESS: Precursor Summary:
1:39:31.546457 PROGRESS: Channel   0:	 0.05 FDR:   491; 0.01 FDR:   307; 0.001 FDR:   278
1:39:31.546548 PROGRESS: 
1:39:31.546602 PROGRESS: Protein Summary:
1:39:31.547779 PROGRESS: Channel   0:	 0.05 FDR:   475; 0.01 FDR:   298; 0.001 FDR:   269
1:39:31.547874 PROGRESS: =========================================================================
1:39:31.565958 INFO: fragments_df_filtered: 2803
1:39:32.039002 INFO: calibration group: precursor, fitting mz estimator 
1:39:32.085583 INFO: calibration group: precursor, fitting rt estimator 
1:39:32.121647 INFO: calibration group: fragment, fitting mz estimator 
1:39:32.270097 INFO: calibration group: precursor, predicting mz
1:39:32.312023 INFO: calibration group: precursor, predicting rt
1:39:32.478282 INFO: calibration group: fragment, predicting mz
1:39:32.868066 INFO: === checking if optimization conditions were reached ===
1:39:32.868550 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:39:32.871324 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 120.9425.
1:39:32.871425 INFO: ==============================================
1:39:32.871581 INFO: Starting optimization step 4.
1:39:32.871661 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:39:32.871762 PROGRESS: Extracting batch of 237213 precursors
1:39:32.943140 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:39:32.943295 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:39:32.943338 INFO: FWHM in RT is 2.41 seconds, sigma is 0.31
1:39:32.943360 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:39:32.943679 INFO: Starting candidate selection
1:39:42.781463 INFO: Starting candidate scoring
1:39:46.542008 INFO: Finished candidate processing
1:39:46.542141 INFO: Collecting candidate features
1:39:47.469667 WARNING: intensity_correlation has 79 NaNs ( 0.02 % out of 466181)
1:39:47.493943 INFO: Collecting fragment features
1:39:47.752898 INFO: Finished candidate scoring
1:39:48.142691 PROGRESS: === Extracted 466181 precursors and 3134561 fragments ===
1:39:48.143284 INFO: performing precursor FDR with 47 features
1:39:48.143322 INFO: Decoy channel: -1
1:39:48.143345 INFO: Competetive: True
1:39:48.299449 INFO: Setting torch num_threads to 2 for FDR classification task
1:39:48.390193 WARNING: dropped 39 target PSMs due to missing features
1:39:48.390355 WARNING: dropped 40 decoy PSMs due to missing features
1:39:56.496882 INFO: Test AUC: 0.565
1:39:56.498435 INFO: Train AUC: 0.584
1:39:56.498525 INFO: AUC difference: 3.21%
1:39:56.624565 INFO: Resetting torch num_threads to 100
1:39:56.639252 INFO: === FDR correction performed with classifier version 10 ===
1:39:56.640300 PROGRESS: ============================= Precursor FDR =============================
1:39:56.640393 PROGRESS: Total precursors accumulated: 746
1:39:56.640454 PROGRESS: Target precursors: 683 (91.55%)
1:39:56.640506 PROGRESS: Decoy precursors: 63 (8.45%)
1:39:56.640553 PROGRESS: 
1:39:56.640597 PROGRESS: Precursor Summary:
1:39:56.641623 PROGRESS: Channel   0:	 0.05 FDR:   466; 0.01 FDR:   323; 0.001 FDR:   277
1:39:56.641717 PROGRESS: 
1:39:56.641771 PROGRESS: Protein Summary:
1:39:56.642929 PROGRESS: Channel   0:	 0.05 FDR:   451; 0.01 FDR:   315; 0.001 FDR:   269
1:39:56.643016 PROGRESS: =========================================================================
1:39:56.662212 INFO: fragments_df_filtered: 2916
1:39:57.109144 INFO: calibration group: precursor, fitting mz estimator 
1:39:57.189996 INFO: calibration group: precursor, fitting rt estimator 
1:39:57.234722 INFO: calibration group: fragment, fitting mz estimator 
1:39:57.451087 INFO: calibration group: precursor, predicting mz
1:39:57.491038 INFO: calibration group: precursor, predicting rt
1:39:57.647947 INFO: calibration group: fragment, predicting mz
1:39:58.012510 INFO: === checking if optimization conditions were reached ===
1:39:58.012950 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1:39:58.015533 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 115.3629.
1:39:58.015597 INFO: ==============================================
1:39:58.015740 INFO: Starting optimization step 5.
1:39:58.015829 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:39:58.015923 PROGRESS: Extracting batch of 237213 precursors
1:39:58.084012 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:39:58.084179 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:39:58.084226 INFO: FWHM in RT is 2.41 seconds, sigma is 0.31
1:39:58.084255 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:39:58.084565 INFO: Starting candidate selection
1:40:08.482292 INFO: Starting candidate scoring
1:40:12.103219 INFO: Finished candidate processing
1:40:12.103428 INFO: Collecting candidate features
1:40:13.088938 WARNING: intensity_correlation has 89 NaNs ( 0.02 % out of 465439)
1:40:13.107262 INFO: Collecting fragment features
1:40:13.349652 INFO: Finished candidate scoring
1:40:13.772950 PROGRESS: === Extracted 465439 precursors and 3100290 fragments ===
1:40:13.773525 INFO: performing precursor FDR with 47 features
1:40:13.773565 INFO: Decoy channel: -1
1:40:13.773591 INFO: Competetive: True
1:40:13.917710 INFO: Setting torch num_threads to 2 for FDR classification task
1:40:14.005899 WARNING: dropped 46 target PSMs due to missing features
1:40:14.006057 WARNING: dropped 43 decoy PSMs due to missing features
1:40:22.399684 INFO: Test AUC: 0.567
1:40:22.399831 INFO: Train AUC: 0.584
1:40:22.399864 INFO: AUC difference: 2.95%
1:40:22.535415 INFO: Resetting torch num_threads to 100
1:40:22.568701 INFO: === FDR correction performed with classifier version 10 ===
1:40:22.570048 PROGRESS: ============================= Precursor FDR =============================
1:40:22.570163 PROGRESS: Total precursors accumulated: 635
1:40:22.570238 PROGRESS: Target precursors: 576 (90.71%)
1:40:22.570297 PROGRESS: Decoy precursors: 59 (9.29%)
1:40:22.570349 PROGRESS: 
1:40:22.570400 PROGRESS: Precursor Summary:
1:40:22.571628 PROGRESS: Channel   0:	 0.05 FDR:   437; 0.01 FDR:   303; 0.001 FDR:   252
1:40:22.571725 PROGRESS: 
1:40:22.571787 PROGRESS: Protein Summary:
1:40:22.573258 PROGRESS: Channel   0:	 0.05 FDR:   420; 0.01 FDR:   292; 0.001 FDR:   245
1:40:22.573363 PROGRESS: =========================================================================
1:40:22.592165 INFO: fragments_df_filtered: 2720
1:40:23.169424 INFO: calibration group: precursor, fitting mz estimator 
1:40:23.229519 INFO: calibration group: precursor, fitting rt estimator 
1:40:23.276656 INFO: calibration group: fragment, fitting mz estimator 
1:40:23.476833 INFO: calibration group: precursor, predicting mz
1:40:23.520543 INFO: calibration group: precursor, predicting rt
1:40:23.747360 INFO: calibration group: fragment, predicting mz
1:40:24.147260 INFO: === checking if optimization conditions were reached ===
1:40:24.147738 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1:40:24.149577 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 115.3629 found after 6 searches.
1:40:24.149685 INFO: ==============================================
1:40:24.149885 PROGRESS: Optimization finished for rt_error.
1:40:24.647391 INFO: calibration group: precursor, predicting mz
1:40:24.685060 INFO: calibration group: precursor, predicting rt
1:40:24.840628 INFO: calibration group: fragment, predicting mz
1:40:25.256600 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:40:25.256858 PROGRESS: ==============================================
1:40:25.256938 PROGRESS: ms2_error      : 8.0000
1:40:25.256999 PROGRESS: ms1_error      : 3.0000
1:40:25.257049 PROGRESS: rt_error       : 115.3629
1:40:25.257093 PROGRESS: ==============================================
1:40:25.257767 INFO: calibration group: precursor, predicting mz
1:40:26.945642 INFO: calibration group: precursor, predicting rt
1:40:34.317520 INFO: calibration group: fragment, predicting mz
1:40:51.493426 PROGRESS: Extracting batch of 10183864 precursors
1:40:53.747646 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:40:53.747785 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:40:53.747826 INFO: FWHM in RT is 2.46 seconds, sigma is 0.32
1:40:53.747857 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:40:53.748243 INFO: Starting candidate selection
1:46:58.178933 INFO: Applying score cutoff of 30.42850703430176
1:46:58.858157 INFO: Removed 6465218 precursors with score below cutoff
1:47:01.832124 INFO: Starting candidate scoring
1:48:50.063500 INFO: Finished candidate processing
1:48:50.064087 INFO: Collecting candidate features
1:49:13.683387 WARNING: intensity_correlation has 310 NaNs ( 0.00 % out of 13847957)
1:49:14.143187 INFO: Collecting fragment features
1:49:22.702136 INFO: Finished candidate scoring
1:49:36.672732 INFO: === FDR correction performed with classifier version 16 ===
1:49:36.678478 INFO: performing precursor FDR with 47 features
1:49:36.678551 INFO: Decoy channel: -1
1:49:36.678576 INFO: Competetive: True
1:49:40.330415 INFO: Setting torch num_threads to 2 for FDR classification task
1:49:42.787826 WARNING: dropped 177 target PSMs due to missing features
1:49:42.788069 WARNING: dropped 133 decoy PSMs due to missing features
1:54:18.519678 INFO: Test AUC: 0.578
1:54:18.519984 INFO: Train AUC: 0.582
1:54:18.520030 INFO: AUC difference: 0.58%
1:54:19.526823 INFO: Resetting torch num_threads to 100
1:54:19.998242 INFO: Removing fragments below FDR threshold
1:54:20.846257 PROGRESS: ============================= Precursor FDR =============================
1:54:20.846665 PROGRESS: Total precursors accumulated: 14,977
1:54:20.846740 PROGRESS: Target precursors: 14,829 (99.01%)
1:54:20.846793 PROGRESS: Decoy precursors: 148 (0.99%)
1:54:20.846842 PROGRESS: 
1:54:20.846886 PROGRESS: Precursor Summary:
1:54:20.853134 PROGRESS: Channel   0:	 0.05 FDR: 14,829; 0.01 FDR: 14,829; 0.001 FDR: 8,625
1:54:20.853354 PROGRESS: 
1:54:20.853414 PROGRESS: Protein Summary:
1:54:20.861866 PROGRESS: Channel   0:	 0.05 FDR: 5,944; 0.01 FDR: 5,944; 0.001 FDR: 4,143
1:54:20.862109 PROGRESS: =========================================================================
1:54:21.111069 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:54:21.649568 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:54:21.649873 INFO: Quantification results path: run_output_Astral/alphadia_1.10_MBRSetValues/library/quant
1:54:21.649993 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1 at run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:54:21.651144 INFO: Initializing RawFileManager
1:54:53.295197 INFO: Determining DIA cycle
1:54:53.310693 INFO: Found cycle with start 0.00 min and length 303.
1:54:53.629660 INFO: RT (min)            : 0.0 - 26.9
1:54:53.629789 INFO: RT duration (sec)   : 1611.2
1:54:53.629818 INFO: RT duration (min)   : 26.9
1:54:53.629844 INFO: Cycle len (scans)   : 303
1:54:53.629864 INFO: Cycle len (sec)     : 1.65
1:54:53.629886 INFO: Number of cycles    : 977
1:54:53.629906 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:54:55.606122 INFO: Initializing CalibrationManager
1:54:55.606419 INFO: Loading calibration config
1:54:55.607029 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'}]
1:54:55.607145 INFO: Calibration group :fragment, found 1 estimator(s)
1:54:55.607234 INFO: Calibration group :precursor, found 3 estimator(s)
1:54:55.607307 INFO: Disabling ion mobility calibration
1:54:55.607335 INFO: removed mobility estimator from group precursor
1:54:55.607476 INFO: Initializing OptimizationManager
1:54:55.607586 INFO: initial parameter: ms1_error = 30
1:54:55.607653 INFO: initial parameter: ms2_error = 30
1:54:55.607702 INFO: initial parameter: rt_error = 805.5982666015625
1:54:55.607746 INFO: initial parameter: mobility_error = 0.1
1:54:55.607789 INFO: initial parameter: column_type = library
1:54:55.607829 INFO: initial parameter: num_candidates = 1
1:54:55.607869 INFO: initial parameter: classifier_version = -1
1:54:55.607908 INFO: initial parameter: fwhm_rt = 5
1:54:55.607952 INFO: initial parameter: fwhm_mobility = 0.01
1:54:55.607994 INFO: initial parameter: score_cutoff = 0
1:54:55.608058 INFO: Initializing TimingManager
1:54:55.608114 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:54:55.608222 INFO: FDRManager not loaded from disk.
1:54:55.608245 INFO: Initializing FDRManager
1:54:55.608281 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:54:56.898616 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
1:54:58.739664 PROGRESS: Starting initial search for precursors.
1:54:58.986458 INFO: Starting optimization step 0.
1:54:58.986716 PROGRESS: === Extracting elution groups 0 to 8000 ===
1:54:58.986791 PROGRESS: Extracting batch of 15815 precursors
1:54:58.990853 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:54:58.990907 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:54:58.990942 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:54:58.990964 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:54:58.991261 INFO: Starting candidate selection
1:55:00.162075 INFO: Starting candidate scoring
1:55:00.270205 INFO: Finished candidate processing
1:55:00.270308 INFO: Collecting candidate features
1:55:00.301574 WARNING: intensity_correlation has 1 NaNs ( 0.01 % out of 15768)
1:55:00.305032 INFO: Collecting fragment features
1:55:00.319469 INFO: Finished candidate scoring
1:55:00.327571 PROGRESS: === Extracted 15768 precursors and 156188 fragments ===
1:55:00.327914 INFO: performing precursor FDR with 47 features
1:55:00.327950 INFO: Decoy channel: -1
1:55:00.327974 INFO: Competetive: True
1:55:00.332278 INFO: Setting torch num_threads to 2 for FDR classification task
1:55:00.335037 WARNING: dropped 1 decoy PSMs due to missing features
1:55:00.480200 INFO: Test AUC: 0.468
1:55:00.480305 INFO: Train AUC: 0.502
1:55:00.480336 INFO: AUC difference: 6.82%
1:55:00.480360 WARNING: AUC difference > 5%. This may indicate overfitting.
1:55:00.560525 INFO: Resetting torch num_threads to 100
1:55:00.561601 INFO: === FDR correction performed with classifier version -1 ===
1:55:00.562300 PROGRESS: ============================= Precursor FDR =============================
1:55:00.562391 PROGRESS: Total precursors accumulated: 1
1:55:00.562448 PROGRESS: Target precursors: 1 (100.00%)
1:55:00.562498 PROGRESS: Decoy precursors: 0 (0.00%)
1:55:00.562542 PROGRESS: 
1:55:00.562585 PROGRESS: Precursor Summary:
1:55:00.563494 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:55:00.563585 PROGRESS: 
1:55:00.563639 PROGRESS: Protein Summary:
1:55:00.564627 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:55:00.564719 PROGRESS: =========================================================================
1:55:00.674239 INFO: Starting optimization step 1.
1:55:00.674509 PROGRESS: === Extracting elution groups 8000 to 24000 ===
1:55:00.674576 PROGRESS: Extracting batch of 31636 precursors
1:55:00.682287 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:55:00.682367 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:55:00.682400 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:55:00.682421 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:55:00.682608 INFO: Starting candidate selection
1:55:02.700930 INFO: Starting candidate scoring
1:55:02.946566 INFO: Finished candidate processing
1:55:02.946666 INFO: Collecting candidate features
1:55:03.005223 INFO: Collecting fragment features
1:55:03.027182 INFO: Finished candidate scoring
1:55:03.051931 PROGRESS: === Extracted 47336 precursors and 469668 fragments ===
1:55:03.057455 INFO: performing precursor FDR with 47 features
1:55:03.057523 INFO: Decoy channel: -1
1:55:03.057549 INFO: Competetive: True
1:55:03.077852 INFO: Setting torch num_threads to 2 for FDR classification task
1:55:03.085243 WARNING: dropped 1 decoy PSMs due to missing features
1:55:03.758494 INFO: Test AUC: 0.554
1:55:03.758608 INFO: Train AUC: 0.560
1:55:03.758637 INFO: AUC difference: 1.03%
1:55:03.841530 INFO: Resetting torch num_threads to 100
1:55:03.844068 INFO: === FDR correction performed with classifier version -1 ===
1:55:03.844814 PROGRESS: ============================= Precursor FDR =============================
1:55:03.844911 PROGRESS: Total precursors accumulated: 2
1:55:03.844969 PROGRESS: Target precursors: 2 (100.00%)
1:55:03.845019 PROGRESS: Decoy precursors: 0 (0.00%)
1:55:03.845063 PROGRESS: 
1:55:03.845107 PROGRESS: Precursor Summary:
1:55:03.846033 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:55:03.846118 PROGRESS: 
1:55:03.846173 PROGRESS: Protein Summary:
1:55:03.847167 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:55:03.847255 PROGRESS: =========================================================================
1:55:03.998332 INFO: Starting optimization step 2.
1:55:03.998612 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1:55:03.998682 PROGRESS: Extracting batch of 63234 precursors
1:55:04.013444 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:55:04.013566 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:55:04.013598 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:55:04.013619 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:55:04.013852 INFO: Starting candidate selection
1:55:08.015473 INFO: Starting candidate scoring
1:55:08.425937 INFO: Finished candidate processing
1:55:08.426044 INFO: Collecting candidate features
1:55:08.533272 INFO: Collecting fragment features
1:55:08.576042 INFO: Finished candidate scoring
1:55:08.627037 PROGRESS: === Extracted 110402 precursors and 1097388 fragments ===
1:55:08.638921 INFO: performing precursor FDR with 47 features
1:55:08.639052 INFO: Decoy channel: -1
1:55:08.639079 INFO: Competetive: True
1:55:08.682540 INFO: Setting torch num_threads to 2 for FDR classification task
1:55:08.701725 WARNING: dropped 1 decoy PSMs due to missing features
1:55:10.352847 INFO: Test AUC: 0.547
1:55:10.352977 INFO: Train AUC: 0.578
1:55:10.353008 INFO: AUC difference: 5.25%
1:55:10.353031 WARNING: AUC difference > 5%. This may indicate overfitting.
1:55:10.438329 INFO: Resetting torch num_threads to 100
1:55:10.443984 INFO: === FDR correction performed with classifier version -1 ===
1:55:10.444797 PROGRESS: ============================= Precursor FDR =============================
1:55:10.444890 PROGRESS: Total precursors accumulated: 1
1:55:10.444949 PROGRESS: Target precursors: 1 (100.00%)
1:55:10.444999 PROGRESS: Decoy precursors: 0 (0.00%)
1:55:10.445043 PROGRESS: 
1:55:10.445091 PROGRESS: Precursor Summary:
1:55:10.446007 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:55:10.446095 PROGRESS: 
1:55:10.446149 PROGRESS: Protein Summary:
1:55:10.447141 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:55:10.447226 PROGRESS: =========================================================================
1:55:10.680138 INFO: Starting optimization step 3.
1:55:10.680459 PROGRESS: === Extracting elution groups 56000 to 120000 ===
1:55:10.680537 PROGRESS: Extracting batch of 126528 precursors
1:55:10.709064 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:55:10.709198 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:55:10.709233 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:55:10.709256 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:55:10.709474 INFO: Starting candidate selection
1:55:18.814849 INFO: Starting candidate scoring
1:55:19.751252 INFO: Finished candidate processing
1:55:19.751360 INFO: Collecting candidate features
1:55:20.007286 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 126160)
1:55:20.017139 INFO: Collecting fragment features
1:55:20.102222 INFO: Finished candidate scoring
1:55:20.256362 PROGRESS: === Extracted 236562 precursors and 2350642 fragments ===
1:55:20.284004 INFO: performing precursor FDR with 47 features
1:55:20.284148 INFO: Decoy channel: -1
1:55:20.284175 INFO: Competetive: True
1:55:20.389219 INFO: Setting torch num_threads to 2 for FDR classification task
1:55:20.434817 WARNING: dropped 1 target PSMs due to missing features
1:55:20.434961 WARNING: dropped 1 decoy PSMs due to missing features
1:55:24.443911 INFO: Test AUC: 0.559
1:55:24.444104 INFO: Train AUC: 0.589
1:55:24.444136 INFO: AUC difference: 5.20%
1:55:24.444159 WARNING: AUC difference > 5%. This may indicate overfitting.
1:55:24.545366 INFO: Resetting torch num_threads to 100
1:55:24.560945 INFO: === FDR correction performed with classifier version -1 ===
1:55:24.562016 PROGRESS: ============================= Precursor FDR =============================
1:55:24.562140 PROGRESS: Total precursors accumulated: 6
1:55:24.562204 PROGRESS: Target precursors: 6 (100.00%)
1:55:24.562254 PROGRESS: Decoy precursors: 0 (0.00%)
1:55:24.562300 PROGRESS: 
1:55:24.562344 PROGRESS: Precursor Summary:
1:55:24.563321 PROGRESS: Channel   0:	 0.05 FDR:     6; 0.01 FDR:     6; 0.001 FDR:     6
1:55:24.563411 PROGRESS: 
1:55:24.563466 PROGRESS: Protein Summary:
1:55:24.564490 PROGRESS: Channel   0:	 0.05 FDR:     6; 0.01 FDR:     6; 0.001 FDR:     6
1:55:24.564583 PROGRESS: =========================================================================
1:55:25.013511 INFO: Starting optimization step 4.
1:55:25.013831 PROGRESS: === Extracting elution groups 120000 to 248000 ===
1:55:25.013922 PROGRESS: Extracting batch of 253020 precursors
1:55:25.072615 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:55:25.072757 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:55:25.072797 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:55:25.072819 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:55:25.073120 INFO: Starting candidate selection
1:55:41.130557 INFO: Starting candidate scoring
1:55:43.039276 INFO: Finished candidate processing
1:55:43.039400 INFO: Collecting candidate features
1:55:43.703438 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 252385)
1:55:43.714870 INFO: Collecting fragment features
1:55:43.894391 INFO: Finished candidate scoring
1:55:44.468584 PROGRESS: === Extracted 488947 precursors and 4855993 fragments ===
1:55:44.535269 INFO: performing precursor FDR with 47 features
1:55:44.535470 INFO: Decoy channel: -1
1:55:44.535506 INFO: Competetive: True
1:55:44.832129 INFO: Setting torch num_threads to 2 for FDR classification task
1:55:44.958188 WARNING: dropped 2 target PSMs due to missing features
1:55:44.958416 WARNING: dropped 1 decoy PSMs due to missing features
1:55:54.230616 INFO: Test AUC: 0.563
1:55:54.230779 INFO: Train AUC: 0.587
1:55:54.230811 INFO: AUC difference: 4.05%
1:55:54.352494 INFO: Resetting torch num_threads to 100
1:55:54.392426 INFO: === FDR correction performed with classifier version -1 ===
1:55:54.393562 PROGRESS: ============================= Precursor FDR =============================
1:55:54.393701 PROGRESS: Total precursors accumulated: 168
1:55:54.393766 PROGRESS: Target precursors: 153 (91.07%)
1:55:54.393816 PROGRESS: Decoy precursors: 15 (8.93%)
1:55:54.393863 PROGRESS: 
1:55:54.393908 PROGRESS: Precursor Summary:
1:55:54.394839 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1:55:54.394933 PROGRESS: 
1:55:54.394990 PROGRESS: Protein Summary:
1:55:54.395941 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1:55:54.396033 PROGRESS: =========================================================================
1:55:55.144783 INFO: Starting optimization step 5.
1:55:55.145153 PROGRESS: === Extracting elution groups 248000 to 504000 ===
1:55:55.145245 PROGRESS: Extracting batch of 505949 precursors
1:55:55.282112 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:55:55.282272 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:55:55.282314 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:55:55.282337 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:55:55.282684 INFO: Starting candidate selection
1:56:26.973711 INFO: Starting candidate scoring
1:56:30.396773 INFO: Finished candidate processing
1:56:30.396919 INFO: Collecting candidate features
1:56:31.501693 WARNING: intensity_correlation has 8 NaNs ( 0.00 % out of 504767)
1:56:31.520397 INFO: Collecting fragment features
1:56:31.849225 INFO: Finished candidate scoring
1:56:32.471986 PROGRESS: === Extracted 993714 precursors and 9870130 fragments ===
1:56:32.586906 INFO: performing precursor FDR with 47 features
1:56:32.587048 INFO: Decoy channel: -1
1:56:32.587076 INFO: Competetive: True
1:56:33.024797 INFO: Setting torch num_threads to 2 for FDR classification task
1:56:33.226293 WARNING: dropped 5 target PSMs due to missing features
1:56:33.226442 WARNING: dropped 6 decoy PSMs due to missing features
1:56:50.469517 INFO: Test AUC: 0.567
1:56:50.469734 INFO: Train AUC: 0.584
1:56:50.469768 INFO: AUC difference: 2.80%
1:56:50.626298 INFO: Resetting torch num_threads to 100
1:56:50.681760 INFO: === FDR correction performed with classifier version -1 ===
1:56:50.682852 PROGRESS: ============================= Precursor FDR =============================
1:56:50.682997 PROGRESS: Total precursors accumulated: 817
1:56:50.683059 PROGRESS: Target precursors: 746 (91.31%)
1:56:50.683109 PROGRESS: Decoy precursors: 71 (8.69%)
1:56:50.683155 PROGRESS: 
1:56:50.683197 PROGRESS: Precursor Summary:
1:56:50.684337 PROGRESS: Channel   0:	 0.05 FDR:   596; 0.01 FDR:   276; 0.001 FDR:    18
1:56:50.684435 PROGRESS: 
1:56:50.684490 PROGRESS: Protein Summary:
1:56:50.685715 PROGRESS: Channel   0:	 0.05 FDR:   547; 0.01 FDR:   260; 0.001 FDR:    18
1:56:50.685809 PROGRESS: =========================================================================
1:56:50.796050 INFO: fragments_df_filtered: 2662
1:56:51.848293 INFO: calibration group: precursor, fitting mz estimator 
1:56:51.887712 INFO: calibration group: precursor, fitting rt estimator 
1:56:51.926151 INFO: calibration group: fragment, fitting mz estimator 
1:56:52.052084 INFO: calibration group: precursor, predicting mz
1:56:52.201541 INFO: calibration group: precursor, predicting rt
1:56:52.883407 INFO: calibration group: fragment, predicting mz
1:56:54.421578 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:56:54.421873 INFO: Starting optimization step 6.
1:56:54.421957 PROGRESS: === Extracting elution groups 0 to 504000 ===
1:56:54.422037 PROGRESS: Extracting batch of 996182 precursors
1:56:54.658308 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:56:54.658451 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:56:54.658496 INFO: FWHM in RT is 3.05 seconds, sigma is 0.39
1:56:54.658523 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:56:54.658804 INFO: Starting candidate selection
1:57:42.295701 INFO: Starting candidate scoring
1:57:56.562053 INFO: Finished candidate processing
1:57:56.562348 INFO: Collecting candidate features
1:58:00.517893 WARNING: intensity_correlation has 5 NaNs ( 0.00 % out of 1987545)
1:58:00.585325 INFO: Collecting fragment features
1:58:02.277624 INFO: Finished candidate scoring
1:58:04.514858 PROGRESS: === Extracted 1987545 precursors and 19558839 fragments ===
1:58:04.515471 INFO: performing precursor FDR with 47 features
1:58:04.515512 INFO: Decoy channel: -1
1:58:04.515537 INFO: Competetive: True
1:58:05.388745 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:05.920536 WARNING: dropped 4 target PSMs due to missing features
1:58:05.920760 WARNING: dropped 1 decoy PSMs due to missing features
1:58:42.536089 INFO: Test AUC: 0.574
1:58:42.536323 INFO: Train AUC: 0.581
1:58:42.536359 INFO: AUC difference: 1.27%
1:58:42.781457 INFO: Resetting torch num_threads to 100
1:58:42.842594 INFO: === FDR correction performed with classifier version 5 ===
1:58:42.843877 PROGRESS: ============================= Precursor FDR =============================
1:58:42.843978 PROGRESS: Total precursors accumulated: 1,845
1:58:42.844039 PROGRESS: Target precursors: 1,685 (91.33%)
1:58:42.844089 PROGRESS: Decoy precursors: 160 (8.67%)
1:58:42.844135 PROGRESS: 
1:58:42.844193 PROGRESS: Precursor Summary:
1:58:42.845555 PROGRESS: Channel   0:	 0.05 FDR: 1,326; 0.01 FDR:   965; 0.001 FDR:   376
1:58:42.845650 PROGRESS: 
1:58:42.845731 PROGRESS: Protein Summary:
1:58:42.847260 PROGRESS: Channel   0:	 0.05 FDR: 1,154; 0.01 FDR:   847; 0.001 FDR:   347
1:58:42.847351 PROGRESS: =========================================================================
1:58:42.928049 INFO: fragments_df_filtered: 5000
1:58:43.490634 INFO: calibration group: precursor, fitting mz estimator 
1:58:43.546961 INFO: calibration group: precursor, fitting rt estimator 
1:58:43.599247 INFO: calibration group: fragment, fitting mz estimator 
1:58:43.950685 INFO: calibration group: precursor, predicting mz
1:58:44.009308 INFO: calibration group: precursor, predicting rt
1:58:44.169553 INFO: calibration group: fragment, predicting mz
1:58:44.536462 INFO: === checking if optimization conditions were reached ===
1:58:44.539257 PROGRESS: ❌ ms2_error      : 13.4361 > 8.0000 or insufficient steps taken.
1:58:44.540630 PROGRESS: ❌ ms1_error      : 13.5697 > 3.0000 or insufficient steps taken.
1:58:44.540721 INFO: ==============================================
1:58:44.540870 INFO: Starting optimization step 7.
1:58:44.540960 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:58:44.541053 PROGRESS: Extracting batch of 237213 precursors
1:58:44.612485 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:58:44.612635 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:44.612677 INFO: FWHM in RT is 2.99 seconds, sigma is 0.39
1:58:44.612700 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:58:44.613033 INFO: Starting candidate selection
1:58:56.183430 INFO: Starting candidate scoring
1:58:59.547588 INFO: Finished candidate processing
1:58:59.547751 INFO: Collecting candidate features
1:59:00.491084 WARNING: intensity_correlation has 22 NaNs ( 0.00 % out of 472826)
1:59:00.510300 INFO: Collecting fragment features
1:59:00.797511 INFO: Finished candidate scoring
1:59:01.206962 PROGRESS: === Extracted 472826 precursors and 3985573 fragments ===
1:59:01.207449 INFO: performing precursor FDR with 47 features
1:59:01.207489 INFO: Decoy channel: -1
1:59:01.207512 INFO: Competetive: True
1:59:01.368824 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:01.467364 WARNING: dropped 10 target PSMs due to missing features
1:59:01.467527 WARNING: dropped 12 decoy PSMs due to missing features
1:59:10.273405 INFO: Test AUC: 0.564
1:59:10.273621 INFO: Train AUC: 0.587
1:59:10.273656 INFO: AUC difference: 3.98%
1:59:10.397795 INFO: Resetting torch num_threads to 100
1:59:10.418862 INFO: === FDR correction performed with classifier version 6 ===
1:59:10.419997 PROGRESS: ============================= Precursor FDR =============================
1:59:10.420165 PROGRESS: Total precursors accumulated: 722
1:59:10.420228 PROGRESS: Target precursors: 656 (90.86%)
1:59:10.420283 PROGRESS: Decoy precursors: 66 (9.14%)
1:59:10.420328 PROGRESS: 
1:59:10.420377 PROGRESS: Precursor Summary:
1:59:10.421589 PROGRESS: Channel   0:	 0.05 FDR:   505; 0.01 FDR:   327; 0.001 FDR:   202
1:59:10.421697 PROGRESS: 
1:59:10.421753 PROGRESS: Protein Summary:
1:59:10.422943 PROGRESS: Channel   0:	 0.05 FDR:   478; 0.01 FDR:   315; 0.001 FDR:   200
1:59:10.423037 PROGRESS: =========================================================================
1:59:10.446836 INFO: fragments_df_filtered: 3494
1:59:10.942390 INFO: calibration group: precursor, fitting mz estimator 
1:59:11.110037 INFO: calibration group: precursor, fitting rt estimator 
1:59:11.173284 INFO: calibration group: fragment, fitting mz estimator 
1:59:11.444678 INFO: calibration group: precursor, predicting mz
1:59:11.487751 INFO: calibration group: precursor, predicting rt
1:59:11.643194 INFO: calibration group: fragment, predicting mz
1:59:11.998174 INFO: === checking if optimization conditions were reached ===
1:59:12.000541 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
1:59:12.001671 PROGRESS: ❌ ms1_error      : 6.4516 > 3.0000 or insufficient steps taken.
1:59:12.001729 INFO: ==============================================
1:59:12.001839 INFO: Starting optimization step 8.
1:59:12.001914 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:59:12.001994 PROGRESS: Extracting batch of 237213 precursors
1:59:12.068096 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:59:12.068235 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:12.068279 INFO: FWHM in RT is 2.78 seconds, sigma is 0.36
1:59:12.068303 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:59:12.068580 INFO: Starting candidate selection
1:59:23.760145 INFO: Starting candidate scoring
1:59:27.067631 INFO: Finished candidate processing
1:59:27.067843 INFO: Collecting candidate features
1:59:28.119122 WARNING: intensity_correlation has 39 NaNs ( 0.01 % out of 472206)
1:59:28.137640 INFO: Collecting fragment features
1:59:28.404999 INFO: Finished candidate scoring
1:59:28.697966 PROGRESS: === Extracted 472206 precursors and 3502797 fragments ===
1:59:28.698507 INFO: performing precursor FDR with 47 features
1:59:28.698548 INFO: Decoy channel: -1
1:59:28.698572 INFO: Competetive: True
1:59:28.858304 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:28.950441 WARNING: dropped 26 target PSMs due to missing features
1:59:28.950607 WARNING: dropped 13 decoy PSMs due to missing features
1:59:37.220834 INFO: Test AUC: 0.565
1:59:37.220994 INFO: Train AUC: 0.589
1:59:37.221026 INFO: AUC difference: 4.06%
1:59:38.789801 INFO: Resetting torch num_threads to 100
1:59:38.804537 INFO: === FDR correction performed with classifier version 7 ===
1:59:38.805557 PROGRESS: ============================= Precursor FDR =============================
1:59:38.805651 PROGRESS: Total precursors accumulated: 1,029
1:59:38.805712 PROGRESS: Target precursors: 943 (91.64%)
1:59:38.805762 PROGRESS: Decoy precursors: 86 (8.36%)
1:59:38.805809 PROGRESS: 
1:59:38.805868 PROGRESS: Precursor Summary:
1:59:38.806945 PROGRESS: Channel   0:	 0.05 FDR:   687; 0.01 FDR:   342; 0.001 FDR:   141
1:59:38.807034 PROGRESS: 
1:59:38.807089 PROGRESS: Protein Summary:
1:59:38.808311 PROGRESS: Channel   0:	 0.05 FDR:   645; 0.01 FDR:   333; 0.001 FDR:   139
1:59:38.808401 PROGRESS: =========================================================================
1:59:38.830290 INFO: fragments_df_filtered: 3607
1:59:39.270447 INFO: calibration group: precursor, fitting mz estimator 
1:59:39.321965 INFO: calibration group: precursor, fitting rt estimator 
1:59:39.373190 INFO: calibration group: fragment, fitting mz estimator 
1:59:39.627879 INFO: calibration group: precursor, predicting mz
1:59:39.663185 INFO: calibration group: precursor, predicting rt
1:59:39.822080 INFO: calibration group: fragment, predicting mz
1:59:40.172813 INFO: === checking if optimization conditions were reached ===
1:59:40.173441 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
1:59:40.175083 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
1:59:40.175202 INFO: ==============================================
1:59:40.175462 PROGRESS: Optimization finished for ms2_error, ms1_error.
1:59:40.601362 INFO: calibration group: precursor, predicting mz
1:59:40.633321 INFO: calibration group: precursor, predicting rt
1:59:40.788067 INFO: calibration group: fragment, predicting mz
1:59:41.138057 INFO: Starting optimization step 0.
1:59:41.138442 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:59:41.138544 PROGRESS: Extracting batch of 237213 precursors
1:59:41.283802 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:59:41.283939 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:41.283976 INFO: FWHM in RT is 2.61 seconds, sigma is 0.34
1:59:41.284001 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:59:41.284276 INFO: Starting candidate selection
1:59:53.714888 INFO: Starting candidate scoring
1:59:57.128390 INFO: Finished candidate processing
1:59:57.128551 INFO: Collecting candidate features
1:59:58.389015 WARNING: intensity_correlation has 22 NaNs ( 0.00 % out of 472455)
1:59:58.412118 INFO: Collecting fragment features
1:59:58.695880 INFO: Finished candidate scoring
1:59:59.199922 PROGRESS: === Extracted 472455 precursors and 3516472 fragments ===
1:59:59.200467 INFO: performing precursor FDR with 47 features
1:59:59.200506 INFO: Decoy channel: -1
1:59:59.200531 INFO: Competetive: True
1:59:59.379644 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:59.479944 WARNING: dropped 17 target PSMs due to missing features
1:59:59.480095 WARNING: dropped 5 decoy PSMs due to missing features
2:00:08.198434 INFO: Test AUC: 0.570
2:00:08.198663 INFO: Train AUC: 0.590
2:00:08.198702 INFO: AUC difference: 3.42%
2:00:08.326066 INFO: Resetting torch num_threads to 100
2:00:08.340946 INFO: === FDR correction performed with classifier version 8 ===
2:00:08.342101 PROGRESS: ============================= Precursor FDR =============================
2:00:08.342207 PROGRESS: Total precursors accumulated: 1,023
2:00:08.342267 PROGRESS: Target precursors: 933 (91.20%)
2:00:08.342317 PROGRESS: Decoy precursors: 90 (8.80%)
2:00:08.342363 PROGRESS: 
2:00:08.342405 PROGRESS: Precursor Summary:
2:00:08.343592 PROGRESS: Channel   0:	 0.05 FDR:   739; 0.01 FDR:   509; 0.001 FDR:   442
2:00:08.343690 PROGRESS: 
2:00:08.343746 PROGRESS: Protein Summary:
2:00:08.345095 PROGRESS: Channel   0:	 0.05 FDR:   687; 0.01 FDR:   480; 0.001 FDR:   420
2:00:08.345192 PROGRESS: =========================================================================
2:00:08.364147 INFO: fragments_df_filtered: 5000
2:00:08.650075 INFO: calibration group: precursor, fitting mz estimator 
2:00:08.709458 INFO: calibration group: precursor, fitting rt estimator 
2:00:08.763611 INFO: calibration group: fragment, fitting mz estimator 
2:00:09.174925 INFO: calibration group: precursor, predicting mz
2:00:09.189500 INFO: calibration group: precursor, predicting rt
2:00:09.262351 INFO: calibration group: fragment, predicting mz
2:00:09.424261 INFO: === checking if optimization conditions were reached ===
2:00:09.424701 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2:00:09.427315 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 143.4132.
2:00:09.427400 INFO: ==============================================
2:00:09.427546 INFO: Starting optimization step 1.
2:00:09.427622 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:00:09.427702 PROGRESS: Extracting batch of 110685 precursors
2:00:09.472443 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:00:09.472616 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:09.472664 INFO: FWHM in RT is 2.43 seconds, sigma is 0.31
2:00:09.472696 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:09.473047 INFO: Starting candidate selection
2:00:14.151347 INFO: Starting candidate scoring
2:00:16.006317 INFO: Finished candidate processing
2:00:16.006514 INFO: Collecting candidate features
2:00:16.490031 WARNING: intensity_correlation has 57 NaNs ( 0.03 % out of 217448)
2:00:16.500928 INFO: Collecting fragment features
2:00:16.614594 INFO: Finished candidate scoring
2:00:16.757095 PROGRESS: === Extracted 217448 precursors and 1480672 fragments ===
2:00:16.757610 INFO: performing precursor FDR with 47 features
2:00:16.757651 INFO: Decoy channel: -1
2:00:16.757675 INFO: Competetive: True
2:00:16.829418 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:16.869459 WARNING: dropped 37 target PSMs due to missing features
2:00:16.869587 WARNING: dropped 20 decoy PSMs due to missing features
2:00:19.992074 INFO: Test AUC: 0.557
2:00:19.992266 INFO: Train AUC: 0.589
2:00:19.992299 INFO: AUC difference: 5.42%
2:00:19.992325 WARNING: AUC difference > 5%. This may indicate overfitting.
2:00:20.094478 INFO: Resetting torch num_threads to 100
2:00:20.101128 INFO: === FDR correction performed with classifier version 8 ===
2:00:20.102180 PROGRESS: ============================= Precursor FDR =============================
2:00:20.102281 PROGRESS: Total precursors accumulated: 471
2:00:20.102359 PROGRESS: Target precursors: 430 (91.30%)
2:00:20.102412 PROGRESS: Decoy precursors: 41 (8.70%)
2:00:20.102458 PROGRESS: 
2:00:20.102503 PROGRESS: Precursor Summary:
2:00:20.103449 PROGRESS: Channel   0:	 0.05 FDR:   309; 0.01 FDR:   221; 0.001 FDR:     0
2:00:20.103544 PROGRESS: 
2:00:20.103601 PROGRESS: Protein Summary:
2:00:20.104646 PROGRESS: Channel   0:	 0.05 FDR:   298; 0.01 FDR:   216; 0.001 FDR:     0
2:00:20.104741 PROGRESS: =========================================================================
2:00:20.112794 INFO: fragments_df_filtered: 2140
2:00:20.347819 INFO: calibration group: precursor, fitting mz estimator 
2:00:20.401021 INFO: calibration group: precursor, fitting rt estimator 
2:00:20.446792 INFO: calibration group: fragment, fitting mz estimator 
2:00:20.593495 INFO: calibration group: precursor, predicting mz
2:00:20.609741 INFO: calibration group: precursor, predicting rt
2:00:20.685127 INFO: calibration group: fragment, predicting mz
2:00:20.856102 INFO: === checking if optimization conditions were reached ===
2:00:20.856493 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2:00:20.858525 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 96.5337.
2:00:20.858589 INFO: ==============================================
2:00:20.858708 INFO: Starting optimization step 2.
2:00:20.858797 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:00:20.858885 PROGRESS: Extracting batch of 110685 precursors
2:00:20.888343 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:00:20.888501 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:20.888558 INFO: FWHM in RT is 2.41 seconds, sigma is 0.31
2:00:20.888590 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:20.888931 INFO: Starting candidate selection
2:00:24.849158 INFO: Starting candidate scoring
2:00:26.369569 INFO: Finished candidate processing
2:00:26.369680 INFO: Collecting candidate features
2:00:26.768431 WARNING: intensity_correlation has 70 NaNs ( 0.03 % out of 216556)
2:00:26.779304 INFO: Collecting fragment features
2:00:26.900685 INFO: Finished candidate scoring
2:00:27.025742 PROGRESS: === Extracted 216556 precursors and 1422984 fragments ===
2:00:27.026166 INFO: performing precursor FDR with 47 features
2:00:27.026203 INFO: Decoy channel: -1
2:00:27.026232 INFO: Competetive: True
2:00:27.105034 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:27.148217 WARNING: dropped 44 target PSMs due to missing features
2:00:27.148370 WARNING: dropped 26 decoy PSMs due to missing features
2:00:31.153308 INFO: Test AUC: 0.555
2:00:31.153512 INFO: Train AUC: 0.587
2:00:31.153543 INFO: AUC difference: 5.58%
2:00:31.153566 WARNING: AUC difference > 5%. This may indicate overfitting.
2:00:31.256562 INFO: Resetting torch num_threads to 100
2:00:31.263505 INFO: === FDR correction performed with classifier version 8 ===
2:00:31.265118 PROGRESS: ============================= Precursor FDR =============================
2:00:31.265221 PROGRESS: Total precursors accumulated: 528
2:00:31.265283 PROGRESS: Target precursors: 480 (90.91%)
2:00:31.265335 PROGRESS: Decoy precursors: 48 (9.09%)
2:00:31.265381 PROGRESS: 
2:00:31.265427 PROGRESS: Precursor Summary:
2:00:31.266483 PROGRESS: Channel   0:	 0.05 FDR:   365; 0.01 FDR:   245; 0.001 FDR:   232
2:00:31.266574 PROGRESS: 
2:00:31.266627 PROGRESS: Protein Summary:
2:00:31.267740 PROGRESS: Channel   0:	 0.05 FDR:   352; 0.01 FDR:   236; 0.001 FDR:   225
2:00:31.267826 PROGRESS: =========================================================================
2:00:31.276274 INFO: fragments_df_filtered: 2348
2:00:31.538836 INFO: calibration group: precursor, fitting mz estimator 
2:00:31.591797 INFO: calibration group: precursor, fitting rt estimator 
2:00:31.640504 INFO: calibration group: fragment, fitting mz estimator 
2:00:31.805615 INFO: calibration group: precursor, predicting mz
2:00:31.822952 INFO: calibration group: precursor, predicting rt
2:00:31.896116 INFO: calibration group: fragment, predicting mz
2:00:32.066921 INFO: === checking if optimization conditions were reached ===
2:00:32.067306 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2:00:32.069776 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 68.3180.
2:00:32.069843 INFO: ==============================================
2:00:32.069963 INFO: Starting optimization step 3.
2:00:32.070039 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:00:32.070117 PROGRESS: Extracting batch of 110685 precursors
2:00:32.114660 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:00:32.114835 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:32.114884 INFO: FWHM in RT is 2.38 seconds, sigma is 0.31
2:00:32.114913 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:32.115291 INFO: Starting candidate selection
2:00:36.355504 INFO: Starting candidate scoring
2:00:37.862127 INFO: Finished candidate processing
2:00:37.862239 INFO: Collecting candidate features
2:00:38.211374 WARNING: intensity_correlation has 75 NaNs ( 0.03 % out of 215629)
2:00:38.222213 INFO: Collecting fragment features
2:00:38.334819 INFO: Finished candidate scoring
2:00:38.436460 PROGRESS: === Extracted 215629 precursors and 1387311 fragments ===
2:00:38.436899 INFO: performing precursor FDR with 47 features
2:00:38.436939 INFO: Decoy channel: -1
2:00:38.436964 INFO: Competetive: True
2:00:38.501069 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:38.540270 WARNING: dropped 48 target PSMs due to missing features
2:00:38.540421 WARNING: dropped 27 decoy PSMs due to missing features
2:00:42.292676 INFO: Test AUC: 0.551
2:00:42.292876 INFO: Train AUC: 0.585
2:00:42.292908 INFO: AUC difference: 5.82%
2:00:42.292931 WARNING: AUC difference > 5%. This may indicate overfitting.
2:00:42.402335 INFO: Resetting torch num_threads to 100
2:00:42.409404 INFO: === FDR correction performed with classifier version 8 ===
2:00:42.410242 PROGRESS: ============================= Precursor FDR =============================
2:00:42.410348 PROGRESS: Total precursors accumulated: 504
2:00:42.410428 PROGRESS: Target precursors: 462 (91.67%)
2:00:42.410479 PROGRESS: Decoy precursors: 42 (8.33%)
2:00:42.410524 PROGRESS: 
2:00:42.410567 PROGRESS: Precursor Summary:
2:00:42.411539 PROGRESS: Channel   0:	 0.05 FDR:   377; 0.01 FDR:   256; 0.001 FDR:    26
2:00:42.411627 PROGRESS: 
2:00:42.411682 PROGRESS: Protein Summary:
2:00:42.412779 PROGRESS: Channel   0:	 0.05 FDR:   362; 0.01 FDR:   250; 0.001 FDR:    26
2:00:42.412869 PROGRESS: =========================================================================
2:00:42.421424 INFO: fragments_df_filtered: 2425
2:00:42.679332 INFO: calibration group: precursor, fitting mz estimator 
2:00:42.767007 INFO: calibration group: precursor, fitting rt estimator 
2:00:42.817433 INFO: calibration group: fragment, fitting mz estimator 
2:00:42.990043 INFO: calibration group: precursor, predicting mz
2:00:43.007272 INFO: calibration group: precursor, predicting rt
2:00:43.080216 INFO: calibration group: fragment, predicting mz
2:00:43.248067 INFO: === checking if optimization conditions were reached ===
2:00:43.248608 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2:00:43.251189 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 65.9249.
2:00:43.251333 INFO: ==============================================
2:00:43.251610 INFO: Starting optimization step 4.
2:00:43.251842 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:00:43.252074 PROGRESS: Extracting batch of 110685 precursors
2:00:43.294837 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:00:43.295140 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:43.295254 INFO: FWHM in RT is 2.38 seconds, sigma is 0.31
2:00:43.295339 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:00:43.295753 INFO: Starting candidate selection
2:00:47.209923 INFO: Starting candidate scoring
2:00:48.743251 INFO: Finished candidate processing
2:00:48.743452 INFO: Collecting candidate features
2:00:49.408423 WARNING: intensity_correlation has 91 NaNs ( 0.04 % out of 215074)
2:00:49.423125 INFO: Collecting fragment features
2:00:49.603884 INFO: Finished candidate scoring
2:00:50.018795 PROGRESS: === Extracted 215074 precursors and 1380737 fragments ===
2:00:50.019415 INFO: performing precursor FDR with 47 features
2:00:50.019459 INFO: Decoy channel: -1
2:00:50.019491 INFO: Competetive: True
2:00:50.162875 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:50.242690 WARNING: dropped 58 target PSMs due to missing features
2:00:50.242958 WARNING: dropped 33 decoy PSMs due to missing features
2:00:55.672123 INFO: Test AUC: 0.553
2:00:55.672342 INFO: Train AUC: 0.586
2:00:55.672374 INFO: AUC difference: 5.74%
2:00:55.672398 WARNING: AUC difference > 5%. This may indicate overfitting.
2:00:55.776130 INFO: Resetting torch num_threads to 100
2:00:55.784945 INFO: === FDR correction performed with classifier version 8 ===
2:00:55.785818 PROGRESS: ============================= Precursor FDR =============================
2:00:55.785916 PROGRESS: Total precursors accumulated: 511
2:00:55.785977 PROGRESS: Target precursors: 468 (91.59%)
2:00:55.786029 PROGRESS: Decoy precursors: 43 (8.41%)
2:00:55.786076 PROGRESS: 
2:00:55.786122 PROGRESS: Precursor Summary:
2:00:55.787082 PROGRESS: Channel   0:	 0.05 FDR:   368; 0.01 FDR:   240; 0.001 FDR:     0
2:00:55.787176 PROGRESS: 
2:00:55.787233 PROGRESS: Protein Summary:
2:00:55.788302 PROGRESS: Channel   0:	 0.05 FDR:   353; 0.01 FDR:   234; 0.001 FDR:     0
2:00:55.788394 PROGRESS: =========================================================================
2:00:55.800663 INFO: fragments_df_filtered: 2298
2:00:56.071098 INFO: calibration group: precursor, fitting mz estimator 
2:00:56.217736 INFO: calibration group: precursor, fitting rt estimator 
2:00:56.257773 INFO: calibration group: fragment, fitting mz estimator 
2:00:56.410163 INFO: calibration group: precursor, predicting mz
2:00:56.430577 INFO: calibration group: precursor, predicting rt
2:00:56.524144 INFO: calibration group: fragment, predicting mz
2:00:56.746785 INFO: === checking if optimization conditions were reached ===
2:00:56.747486 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2:00:56.749281 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 65.9249 found after 5 searches.
2:00:56.749451 INFO: ==============================================
2:00:56.749780 PROGRESS: Optimization finished for rt_error.
2:00:56.994603 INFO: calibration group: precursor, predicting mz
2:00:57.011349 INFO: calibration group: precursor, predicting rt
2:00:57.083421 INFO: calibration group: fragment, predicting mz
2:00:57.293975 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:00:57.294377 PROGRESS: ==============================================
2:00:57.294623 PROGRESS: ms2_error      : 8.0000
2:00:57.294844 PROGRESS: ms1_error      : 3.0000
2:00:57.295058 PROGRESS: rt_error       : 65.9249
2:00:57.295266 PROGRESS: ==============================================
2:00:57.296717 INFO: calibration group: precursor, predicting mz
2:00:58.951717 INFO: calibration group: precursor, predicting rt
2:01:05.960788 INFO: calibration group: fragment, predicting mz
2:01:23.129248 PROGRESS: Extracting batch of 10183864 precursors
2:01:26.109130 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:01:26.109286 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:26.109330 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
2:01:26.109356 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:01:26.109799 INFO: Starting candidate selection
2:07:11.453635 INFO: Applying score cutoff of 29.148203004837036
2:07:11.978173 INFO: Removed 7997227 precursors with score below cutoff
2:07:14.670861 INFO: Starting candidate scoring
2:08:42.774797 INFO: Finished candidate processing
2:08:42.775150 INFO: Collecting candidate features
2:09:06.860851 WARNING: intensity_correlation has 865 NaNs ( 0.01 % out of 12296213)
2:09:07.328753 INFO: Collecting fragment features
2:09:16.957101 INFO: Finished candidate scoring
2:09:34.275181 INFO: === FDR correction performed with classifier version 13 ===
2:09:34.286835 INFO: performing precursor FDR with 47 features
2:09:34.286927 INFO: Decoy channel: -1
2:09:34.286955 INFO: Competetive: True
2:09:38.548038 INFO: Setting torch num_threads to 2 for FDR classification task
2:09:41.309508 WARNING: dropped 506 target PSMs due to missing features
2:09:41.309798 WARNING: dropped 359 decoy PSMs due to missing features
2:14:09.570837 INFO: Test AUC: 0.577
2:14:09.571078 INFO: Train AUC: 0.582
2:14:09.571115 INFO: AUC difference: 0.77%
2:14:10.445629 INFO: Resetting torch num_threads to 100
2:14:10.729512 INFO: Removing fragments below FDR threshold
2:14:11.455322 PROGRESS: ============================= Precursor FDR =============================
2:14:11.455679 PROGRESS: Total precursors accumulated: 29,464
2:14:11.455746 PROGRESS: Target precursors: 29,173 (99.01%)
2:14:11.455798 PROGRESS: Decoy precursors: 291 (0.99%)
2:14:11.455844 PROGRESS: 
2:14:11.455888 PROGRESS: Precursor Summary:
2:14:11.466924 PROGRESS: Channel   0:	 0.05 FDR: 29,173; 0.01 FDR: 29,173; 0.001 FDR: 19,603
2:14:11.467216 PROGRESS: 
2:14:11.467274 PROGRESS: Protein Summary:
2:14:11.483198 PROGRESS: Channel   0:	 0.05 FDR: 8,024; 0.01 FDR: 8,024; 0.001 FDR: 5,997
2:14:11.483485 PROGRESS: =========================================================================
2:14:12.058110 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:14:12.549350 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:14:12.549544 INFO: Quantification results path: run_output_Astral/alphadia_1.10_MBRSetValues/library/quant
2:14:12.549639 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2 at run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:14:12.550523 INFO: Initializing RawFileManager
2:14:43.457387 INFO: Determining DIA cycle
2:14:43.472412 INFO: Found cycle with start 0.00 min and length 303.
2:14:43.771015 INFO: RT (min)            : 0.0 - 26.9
2:14:43.771120 INFO: RT duration (sec)   : 1611.2
2:14:43.771148 INFO: RT duration (min)   : 26.9
2:14:43.771172 INFO: Cycle len (scans)   : 303
2:14:43.771191 INFO: Cycle len (sec)     : 1.65
2:14:43.771211 INFO: Number of cycles    : 977
2:14:43.771232 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:14:45.661693 INFO: Initializing CalibrationManager
2:14:45.662207 INFO: Loading calibration config
2:14:45.662886 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'}]
2:14:45.662977 INFO: Calibration group :fragment, found 1 estimator(s)
2:14:45.663068 INFO: Calibration group :precursor, found 3 estimator(s)
2:14:45.663163 INFO: Disabling ion mobility calibration
2:14:45.663191 INFO: removed mobility estimator from group precursor
2:14:45.663355 INFO: Initializing OptimizationManager
2:14:45.663483 INFO: initial parameter: ms1_error = 30
2:14:45.663551 INFO: initial parameter: ms2_error = 30
2:14:45.663604 INFO: initial parameter: rt_error = 805.6002197265625
2:14:45.663647 INFO: initial parameter: mobility_error = 0.1
2:14:45.663687 INFO: initial parameter: column_type = library
2:14:45.663728 INFO: initial parameter: num_candidates = 1
2:14:45.663768 INFO: initial parameter: classifier_version = -1
2:14:45.663807 INFO: initial parameter: fwhm_rt = 5
2:14:45.663851 INFO: initial parameter: fwhm_mobility = 0.01
2:14:45.663899 INFO: initial parameter: score_cutoff = 0
2:14:45.663964 INFO: Initializing TimingManager
2:14:45.664021 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:14:45.664140 INFO: FDRManager not loaded from disk.
2:14:45.664165 INFO: Initializing FDRManager
2:14:45.664203 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
2:14:47.279670 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
2:14:49.844935 PROGRESS: Starting initial search for precursors.
2:14:50.140479 INFO: Starting optimization step 0.
2:14:50.140807 PROGRESS: === Extracting elution groups 0 to 8000 ===
2:14:50.140893 PROGRESS: Extracting batch of 15815 precursors
2:14:50.146777 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:14:50.146855 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:14:50.146893 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:14:50.146915 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:14:50.147235 INFO: Starting candidate selection
2:14:51.582422 INFO: Starting candidate scoring
2:14:51.705232 INFO: Finished candidate processing
2:14:51.705342 INFO: Collecting candidate features
2:14:51.748692 INFO: Collecting fragment features
2:14:51.763346 INFO: Finished candidate scoring
2:14:51.772024 PROGRESS: === Extracted 15770 precursors and 156436 fragments ===
2:14:51.772474 INFO: performing precursor FDR with 47 features
2:14:51.772511 INFO: Decoy channel: -1
2:14:51.772535 INFO: Competetive: True
2:14:51.777696 INFO: Setting torch num_threads to 2 for FDR classification task
2:14:51.947619 INFO: Test AUC: 0.518
2:14:51.947738 INFO: Train AUC: 0.532
2:14:51.947770 INFO: AUC difference: 2.62%
2:14:52.032348 INFO: Resetting torch num_threads to 100
2:14:52.033587 INFO: === FDR correction performed with classifier version -1 ===
2:14:52.034291 PROGRESS: ============================= Precursor FDR =============================
2:14:52.034381 PROGRESS: Total precursors accumulated: 3
2:14:52.034442 PROGRESS: Target precursors: 3 (100.00%)
2:14:52.034494 PROGRESS: Decoy precursors: 0 (0.00%)
2:14:52.034539 PROGRESS: 
2:14:52.034587 PROGRESS: Precursor Summary:
2:14:52.035499 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
2:14:52.035585 PROGRESS: 
2:14:52.035639 PROGRESS: Protein Summary:
2:14:52.036641 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
2:14:52.036735 PROGRESS: =========================================================================
2:14:52.148356 INFO: Starting optimization step 1.
2:14:52.148668 PROGRESS: === Extracting elution groups 8000 to 24000 ===
2:14:52.148752 PROGRESS: Extracting batch of 31636 precursors
2:14:52.156373 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:14:52.156462 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:14:52.156496 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:14:52.156519 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:14:52.156731 INFO: Starting candidate selection
2:14:54.461225 INFO: Starting candidate scoring
2:14:54.756419 INFO: Finished candidate processing
2:14:54.756605 INFO: Collecting candidate features
2:14:54.904349 INFO: Collecting fragment features
2:14:54.936871 INFO: Finished candidate scoring
2:14:54.988767 PROGRESS: === Extracted 47333 precursors and 470325 fragments ===
2:14:55.000130 INFO: performing precursor FDR with 47 features
2:14:55.000309 INFO: Decoy channel: -1
2:14:55.000338 INFO: Competetive: True
2:14:55.057758 INFO: Setting torch num_threads to 2 for FDR classification task
2:14:55.864246 INFO: Test AUC: 0.542
2:14:55.864400 INFO: Train AUC: 0.562
2:14:55.864429 INFO: AUC difference: 3.56%
2:14:55.954012 INFO: Resetting torch num_threads to 100
2:14:55.957045 INFO: === FDR correction performed with classifier version -1 ===
2:14:55.957840 PROGRESS: ============================= Precursor FDR =============================
2:14:55.957934 PROGRESS: Total precursors accumulated: 12
2:14:55.958020 PROGRESS: Target precursors: 11 (91.67%)
2:14:55.958075 PROGRESS: Decoy precursors: 1 (8.33%)
2:14:55.958128 PROGRESS: 
2:14:55.958176 PROGRESS: Precursor Summary:
2:14:55.959051 PROGRESS: Channel   0:	 0.05 FDR:     8; 0.01 FDR:     8; 0.001 FDR:     8
2:14:55.959145 PROGRESS: 
2:14:55.959205 PROGRESS: Protein Summary:
2:14:55.960146 PROGRESS: Channel   0:	 0.05 FDR:     8; 0.01 FDR:     8; 0.001 FDR:     8
2:14:55.960238 PROGRESS: =========================================================================
2:14:56.130589 INFO: Starting optimization step 2.
2:14:56.130933 PROGRESS: === Extracting elution groups 24000 to 56000 ===
2:14:56.131008 PROGRESS: Extracting batch of 63234 precursors
2:14:56.148526 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:14:56.148672 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:14:56.148717 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:14:56.148742 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:14:56.148977 INFO: Starting candidate selection
2:15:00.283626 INFO: Starting candidate scoring
2:15:00.819577 INFO: Finished candidate processing
2:15:00.819696 INFO: Collecting candidate features
2:15:01.024424 INFO: Collecting fragment features
2:15:01.076179 INFO: Finished candidate scoring
2:15:01.220826 PROGRESS: === Extracted 110391 precursors and 1098720 fragments ===
2:15:01.237513 INFO: performing precursor FDR with 47 features
2:15:01.237667 INFO: Decoy channel: -1
2:15:01.237696 INFO: Competetive: True
2:15:01.294360 INFO: Setting torch num_threads to 2 for FDR classification task
2:15:03.240544 INFO: Test AUC: 0.549
2:15:03.240741 INFO: Train AUC: 0.580
2:15:03.240779 INFO: AUC difference: 5.42%
2:15:03.240804 WARNING: AUC difference > 5%. This may indicate overfitting.
2:15:03.332469 INFO: Resetting torch num_threads to 100
2:15:03.342589 INFO: === FDR correction performed with classifier version -1 ===
2:15:03.343602 PROGRESS: ============================= Precursor FDR =============================
2:15:03.343702 PROGRESS: Total precursors accumulated: 6
2:15:03.343764 PROGRESS: Target precursors: 6 (100.00%)
2:15:03.343816 PROGRESS: Decoy precursors: 0 (0.00%)
2:15:03.343862 PROGRESS: 
2:15:03.343907 PROGRESS: Precursor Summary:
2:15:03.344871 PROGRESS: Channel   0:	 0.05 FDR:     6; 0.01 FDR:     6; 0.001 FDR:     6
2:15:03.344959 PROGRESS: 
2:15:03.345015 PROGRESS: Protein Summary:
2:15:03.346063 PROGRESS: Channel   0:	 0.05 FDR:     6; 0.01 FDR:     6; 0.001 FDR:     6
2:15:03.346153 PROGRESS: =========================================================================
2:15:03.661882 INFO: Starting optimization step 3.
2:15:03.662231 PROGRESS: === Extracting elution groups 56000 to 120000 ===
2:15:03.662316 PROGRESS: Extracting batch of 126528 precursors
2:15:03.696429 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:15:03.696573 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:15:03.696616 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:15:03.696641 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:15:03.696955 INFO: Starting candidate selection
2:15:11.738162 INFO: Starting candidate scoring
2:15:12.627356 INFO: Finished candidate processing
2:15:12.627467 INFO: Collecting candidate features
2:15:12.851949 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 126164)
2:15:12.861854 INFO: Collecting fragment features
2:15:12.951020 INFO: Finished candidate scoring
2:15:13.095543 PROGRESS: === Extracted 236555 precursors and 2353058 fragments ===
2:15:13.131594 INFO: performing precursor FDR with 47 features
2:15:13.131756 INFO: Decoy channel: -1
2:15:13.131783 INFO: Competetive: True
2:15:13.245908 INFO: Setting torch num_threads to 2 for FDR classification task
2:15:13.295964 WARNING: dropped 1 target PSMs due to missing features
2:15:13.296111 WARNING: dropped 1 decoy PSMs due to missing features
2:15:20.087571 INFO: Test AUC: 0.562
2:15:20.087794 INFO: Train AUC: 0.584
2:15:20.087831 INFO: AUC difference: 3.73%
2:15:20.190971 INFO: Resetting torch num_threads to 100
2:15:20.210823 INFO: === FDR correction performed with classifier version -1 ===
2:15:20.237520 PROGRESS: ============================= Precursor FDR =============================
2:15:20.237898 PROGRESS: Total precursors accumulated: 118,422
2:15:20.237966 PROGRESS: Target precursors: 70,651 (59.66%)
2:15:20.238020 PROGRESS: Decoy precursors: 47,771 (40.34%)
2:15:20.238069 PROGRESS: 
2:15:20.238114 PROGRESS: Precursor Summary:
2:15:20.239816 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:15:20.239919 PROGRESS: 
2:15:20.239978 PROGRESS: Protein Summary:
2:15:20.241469 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:15:20.241565 PROGRESS: =========================================================================
2:15:20.757730 INFO: Starting optimization step 4.
2:15:20.758013 PROGRESS: === Extracting elution groups 120000 to 248000 ===
2:15:20.758102 PROGRESS: Extracting batch of 253020 precursors
2:15:20.827313 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:15:20.827444 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:15:20.827484 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:15:20.827508 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:15:20.827838 INFO: Starting candidate selection
2:15:36.609686 INFO: Starting candidate scoring
2:15:38.443616 INFO: Finished candidate processing
2:15:38.443785 INFO: Collecting candidate features
2:15:39.258551 INFO: Collecting fragment features
2:15:39.448588 INFO: Finished candidate scoring
2:15:39.906653 PROGRESS: === Extracted 488936 precursors and 4861385 fragments ===
2:15:39.976234 INFO: performing precursor FDR with 47 features
2:15:39.976398 INFO: Decoy channel: -1
2:15:39.976425 INFO: Competetive: True
2:15:40.266739 INFO: Setting torch num_threads to 2 for FDR classification task
2:15:40.386579 WARNING: dropped 1 target PSMs due to missing features
2:15:40.386751 WARNING: dropped 1 decoy PSMs due to missing features
2:15:49.633341 INFO: Test AUC: 0.565
2:15:49.634169 INFO: Train AUC: 0.583
2:15:49.634207 INFO: AUC difference: 3.14%
2:15:51.157592 INFO: Resetting torch num_threads to 100
2:15:51.192164 INFO: === FDR correction performed with classifier version -1 ===
2:15:51.193280 PROGRESS: ============================= Precursor FDR =============================
2:15:51.193414 PROGRESS: Total precursors accumulated: 100
2:15:51.193478 PROGRESS: Target precursors: 91 (91.00%)
2:15:51.193530 PROGRESS: Decoy precursors: 9 (9.00%)
2:15:51.193575 PROGRESS: 
2:15:51.193620 PROGRESS: Precursor Summary:
2:15:51.194497 PROGRESS: Channel   0:	 0.05 FDR:    10; 0.01 FDR:    10; 0.001 FDR:    10
2:15:51.194593 PROGRESS: 
2:15:51.194649 PROGRESS: Protein Summary:
2:15:51.195585 PROGRESS: Channel   0:	 0.05 FDR:    10; 0.01 FDR:    10; 0.001 FDR:    10
2:15:51.195673 PROGRESS: =========================================================================
2:15:52.006647 INFO: Starting optimization step 5.
2:15:52.007050 PROGRESS: === Extracting elution groups 248000 to 504000 ===
2:15:52.007128 PROGRESS: Extracting batch of 505949 precursors
2:15:52.139547 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:15:52.139703 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:15:52.139741 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:15:52.139763 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:15:52.140067 INFO: Starting candidate selection
2:16:24.558430 INFO: Starting candidate scoring
2:16:28.131704 INFO: Finished candidate processing
2:16:28.131915 INFO: Collecting candidate features
2:16:29.396945 WARNING: intensity_correlation has 8 NaNs ( 0.00 % out of 504789)
2:16:29.416403 INFO: Collecting fragment features
2:16:29.794629 INFO: Finished candidate scoring
2:16:30.552710 PROGRESS: === Extracted 993725 precursors and 9879901 fragments ===
2:16:30.704243 INFO: performing precursor FDR with 47 features
2:16:30.704416 INFO: Decoy channel: -1
2:16:30.704445 INFO: Competetive: True
2:16:31.254680 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:31.508740 WARNING: dropped 4 target PSMs due to missing features
2:16:31.508918 WARNING: dropped 6 decoy PSMs due to missing features
2:16:50.629177 INFO: Test AUC: 0.568
2:16:50.629400 INFO: Train AUC: 0.581
2:16:50.629434 INFO: AUC difference: 2.30%
2:16:50.796415 INFO: Resetting torch num_threads to 100
2:16:50.875398 INFO: === FDR correction performed with classifier version -1 ===
2:16:50.876891 PROGRESS: ============================= Precursor FDR =============================
2:16:50.877062 PROGRESS: Total precursors accumulated: 1,065
2:16:50.877130 PROGRESS: Target precursors: 970 (91.08%)
2:16:50.877193 PROGRESS: Decoy precursors: 95 (8.92%)
2:16:50.877243 PROGRESS: 
2:16:50.877290 PROGRESS: Precursor Summary:
2:16:50.878799 PROGRESS: Channel   0:	 0.05 FDR:   730; 0.01 FDR:   541; 0.001 FDR:   426
2:16:50.878931 PROGRESS: 
2:16:50.878989 PROGRESS: Protein Summary:
2:16:50.880450 PROGRESS: Channel   0:	 0.05 FDR:   652; 0.01 FDR:   486; 0.001 FDR:   388
2:16:50.880564 PROGRESS: =========================================================================
2:16:51.026504 INFO: fragments_df_filtered: 4870
2:16:51.915441 INFO: calibration group: precursor, fitting mz estimator 
2:16:51.973067 INFO: calibration group: precursor, fitting rt estimator 
2:16:52.030615 INFO: calibration group: fragment, fitting mz estimator 
2:16:52.433851 INFO: calibration group: precursor, predicting mz
2:16:52.512587 INFO: calibration group: precursor, predicting rt
2:16:52.849724 INFO: calibration group: fragment, predicting mz
2:16:53.625079 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:16:53.625468 INFO: Starting optimization step 6.
2:16:53.625541 PROGRESS: === Extracting elution groups 0 to 248000 ===
2:16:53.625612 PROGRESS: Extracting batch of 490233 precursors
2:16:53.764329 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:16:53.764483 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:16:53.764526 INFO: FWHM in RT is 3.05 seconds, sigma is 0.39
2:16:53.764551 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:16:53.764878 INFO: Starting candidate selection
2:17:17.067199 INFO: Starting candidate scoring
2:17:24.462694 INFO: Finished candidate processing
2:17:24.462896 INFO: Collecting candidate features
2:17:26.724317 WARNING: intensity_correlation has 8 NaNs ( 0.00 % out of 977923)
2:17:26.758713 INFO: Collecting fragment features
2:17:27.432792 INFO: Finished candidate scoring
2:17:28.525722 PROGRESS: === Extracted 977923 precursors and 9648815 fragments ===
2:17:28.526254 INFO: performing precursor FDR with 47 features
2:17:28.526300 INFO: Decoy channel: -1
2:17:28.526324 INFO: Competetive: True
2:17:28.871391 INFO: Setting torch num_threads to 2 for FDR classification task
2:17:29.093310 WARNING: dropped 3 target PSMs due to missing features
2:17:29.093463 WARNING: dropped 5 decoy PSMs due to missing features
2:17:47.463838 INFO: Test AUC: 0.569
2:17:47.464063 INFO: Train AUC: 0.585
2:17:47.464103 INFO: AUC difference: 2.68%
2:17:47.624963 INFO: Resetting torch num_threads to 100
2:17:47.648914 INFO: === FDR correction performed with classifier version 5 ===
2:17:47.650014 PROGRESS: ============================= Precursor FDR =============================
2:17:47.650170 PROGRESS: Total precursors accumulated: 811
2:17:47.650236 PROGRESS: Target precursors: 738 (91.00%)
2:17:47.650289 PROGRESS: Decoy precursors: 73 (9.00%)
2:17:47.650337 PROGRESS: 
2:17:47.650397 PROGRESS: Precursor Summary:
2:17:47.651669 PROGRESS: Channel   0:	 0.05 FDR:   561; 0.01 FDR:   416; 0.001 FDR:   381
2:17:47.651778 PROGRESS: 
2:17:47.651835 PROGRESS: Protein Summary:
2:17:47.653147 PROGRESS: Channel   0:	 0.05 FDR:   522; 0.01 FDR:   391; 0.001 FDR:   361
2:17:47.653247 PROGRESS: =========================================================================
2:17:47.690019 INFO: fragments_df_filtered: 4922
2:17:48.165661 INFO: calibration group: precursor, fitting mz estimator 
2:17:48.207524 INFO: calibration group: precursor, fitting rt estimator 
2:17:48.246896 INFO: calibration group: fragment, fitting mz estimator 
2:17:48.586045 INFO: calibration group: precursor, predicting mz
2:17:48.621175 INFO: calibration group: precursor, predicting rt
2:17:48.780797 INFO: calibration group: fragment, predicting mz
2:17:49.127925 INFO: === checking if optimization conditions were reached ===
2:17:49.130317 PROGRESS: ❌ ms2_error      : 14.2029 > 8.0000 or insufficient steps taken.
2:17:49.131395 PROGRESS: ❌ ms1_error      : 12.7890 > 3.0000 or insufficient steps taken.
2:17:49.131454 INFO: ==============================================
2:17:49.131572 INFO: Starting optimization step 7.
2:17:49.131644 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:17:49.131711 PROGRESS: Extracting batch of 237213 precursors
2:17:49.189233 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:17:49.189368 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:17:49.189409 INFO: FWHM in RT is 2.99 seconds, sigma is 0.38
2:17:49.189433 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:17:49.189745 INFO: Starting candidate selection
2:18:00.250795 INFO: Starting candidate scoring
2:18:03.692792 INFO: Finished candidate processing
2:18:03.692929 INFO: Collecting candidate features
2:18:04.541230 WARNING: intensity_correlation has 8 NaNs ( 0.00 % out of 472979)
2:18:04.561793 INFO: Collecting fragment features
2:18:04.862896 INFO: Finished candidate scoring
2:18:05.109307 PROGRESS: === Extracted 472979 precursors and 4077979 fragments ===
2:18:05.109711 INFO: performing precursor FDR with 47 features
2:18:05.109749 INFO: Decoy channel: -1
2:18:05.109773 INFO: Competetive: True
2:18:05.256715 INFO: Setting torch num_threads to 2 for FDR classification task
2:18:05.343348 WARNING: dropped 2 target PSMs due to missing features
2:18:05.343487 WARNING: dropped 6 decoy PSMs due to missing features
2:18:13.869313 INFO: Test AUC: 0.562
2:18:13.869513 INFO: Train AUC: 0.584
2:18:13.869547 INFO: AUC difference: 3.84%
2:18:13.990679 INFO: Resetting torch num_threads to 100
2:18:14.003678 INFO: === FDR correction performed with classifier version 6 ===
2:18:14.004616 PROGRESS: ============================= Precursor FDR =============================
2:18:14.004729 PROGRESS: Total precursors accumulated: 669
2:18:14.004795 PROGRESS: Target precursors: 609 (91.03%)
2:18:14.004847 PROGRESS: Decoy precursors: 60 (8.97%)
2:18:14.004893 PROGRESS: 
2:18:14.004936 PROGRESS: Precursor Summary:
2:18:14.006106 PROGRESS: Channel   0:	 0.05 FDR:   491; 0.01 FDR:   344; 0.001 FDR:   312
2:18:14.006198 PROGRESS: 
2:18:14.006253 PROGRESS: Protein Summary:
2:18:14.007429 PROGRESS: Channel   0:	 0.05 FDR:   477; 0.01 FDR:   337; 0.001 FDR:   305
2:18:14.007519 PROGRESS: =========================================================================
2:18:14.033523 INFO: fragments_df_filtered: 3698
2:18:14.454295 INFO: calibration group: precursor, fitting mz estimator 
2:18:14.497827 INFO: calibration group: precursor, fitting rt estimator 
2:18:14.535725 INFO: calibration group: fragment, fitting mz estimator 
2:18:14.777864 INFO: calibration group: precursor, predicting mz
2:18:14.811711 INFO: calibration group: precursor, predicting rt
2:18:14.964027 INFO: calibration group: fragment, predicting mz
2:18:15.302377 INFO: === checking if optimization conditions were reached ===
2:18:15.304916 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
2:18:15.306056 PROGRESS: ❌ ms1_error      : 5.1648 > 3.0000 or insufficient steps taken.
2:18:15.306113 INFO: ==============================================
2:18:15.306227 INFO: Starting optimization step 8.
2:18:15.306302 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:18:15.306379 PROGRESS: Extracting batch of 237213 precursors
2:18:15.367287 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:18:15.367417 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:18:15.367457 INFO: FWHM in RT is 2.68 seconds, sigma is 0.35
2:18:15.367481 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:18:15.367765 INFO: Starting candidate selection
2:18:26.805938 INFO: Starting candidate scoring
2:18:30.116046 INFO: Finished candidate processing
2:18:30.116149 INFO: Collecting candidate features
2:18:30.944031 WARNING: intensity_correlation has 20 NaNs ( 0.00 % out of 472494)
2:18:30.962305 INFO: Collecting fragment features
2:18:31.230466 INFO: Finished candidate scoring
2:18:31.679352 PROGRESS: === Extracted 472494 precursors and 3524970 fragments ===
2:18:31.679802 INFO: performing precursor FDR with 47 features
2:18:31.679840 INFO: Decoy channel: -1
2:18:31.679863 INFO: Competetive: True
2:18:31.823246 INFO: Setting torch num_threads to 2 for FDR classification task
2:18:31.909747 WARNING: dropped 10 target PSMs due to missing features
2:18:31.909888 WARNING: dropped 10 decoy PSMs due to missing features
2:18:40.198445 INFO: Test AUC: 0.568
2:18:40.198645 INFO: Train AUC: 0.585
2:18:40.198678 INFO: AUC difference: 2.97%
2:18:40.320763 INFO: Resetting torch num_threads to 100
2:18:40.333686 INFO: === FDR correction performed with classifier version 7 ===
2:18:40.334658 PROGRESS: ============================= Precursor FDR =============================
2:18:40.334758 PROGRESS: Total precursors accumulated: 958
2:18:40.334817 PROGRESS: Target precursors: 871 (90.92%)
2:18:40.334869 PROGRESS: Decoy precursors: 87 (9.08%)
2:18:40.334914 PROGRESS: 
2:18:40.334970 PROGRESS: Precursor Summary:
2:18:40.336097 PROGRESS: Channel   0:	 0.05 FDR:   633; 0.01 FDR:   376; 0.001 FDR:   292
2:18:40.336189 PROGRESS: 
2:18:40.336243 PROGRESS: Protein Summary:
2:18:40.337488 PROGRESS: Channel   0:	 0.05 FDR:   595; 0.01 FDR:   361; 0.001 FDR:   282
2:18:40.337581 PROGRESS: =========================================================================
2:18:40.363028 INFO: fragments_df_filtered: 3948
2:18:40.782810 INFO: calibration group: precursor, fitting mz estimator 
2:18:40.831090 INFO: calibration group: precursor, fitting rt estimator 
2:18:40.880715 INFO: calibration group: fragment, fitting mz estimator 
2:18:41.184080 INFO: calibration group: precursor, predicting mz
2:18:41.215576 INFO: calibration group: precursor, predicting rt
2:18:41.370962 INFO: calibration group: fragment, predicting mz
2:18:41.703713 INFO: === checking if optimization conditions were reached ===
2:18:41.704046 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
2:18:41.705565 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
2:18:41.705626 INFO: ==============================================
2:18:41.705740 PROGRESS: Optimization finished for ms2_error, ms1_error.
2:18:42.079290 INFO: calibration group: precursor, predicting mz
2:18:42.111706 INFO: calibration group: precursor, predicting rt
2:18:42.261002 INFO: calibration group: fragment, predicting mz
2:18:42.603131 INFO: Starting optimization step 0.
2:18:42.603450 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:18:42.603561 PROGRESS: Extracting batch of 237213 precursors
2:18:42.667016 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:18:42.667142 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:18:42.667181 INFO: FWHM in RT is 2.58 seconds, sigma is 0.33
2:18:42.667205 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:18:42.667485 INFO: Starting candidate selection
2:18:54.491842 INFO: Starting candidate scoring
2:18:58.131051 INFO: Finished candidate processing
2:18:58.131172 INFO: Collecting candidate features
2:18:59.028235 WARNING: intensity_correlation has 16 NaNs ( 0.00 % out of 472638)
2:18:59.046626 INFO: Collecting fragment features
2:18:59.302227 INFO: Finished candidate scoring
2:18:59.588446 PROGRESS: === Extracted 472638 precursors and 3531086 fragments ===
2:18:59.588920 INFO: performing precursor FDR with 47 features
2:18:59.588961 INFO: Decoy channel: -1
2:18:59.588984 INFO: Competetive: True
2:18:59.743629 INFO: Setting torch num_threads to 2 for FDR classification task
2:18:59.850961 WARNING: dropped 7 target PSMs due to missing features
2:18:59.851115 WARNING: dropped 9 decoy PSMs due to missing features
2:19:08.531367 INFO: Test AUC: 0.570
2:19:08.531583 INFO: Train AUC: 0.589
2:19:08.531633 INFO: AUC difference: 3.24%
2:19:08.659594 INFO: Resetting torch num_threads to 100
2:19:08.676324 INFO: === FDR correction performed with classifier version 8 ===
2:19:08.677342 PROGRESS: ============================= Precursor FDR =============================
2:19:08.677444 PROGRESS: Total precursors accumulated: 1,027
2:19:08.677506 PROGRESS: Target precursors: 935 (91.04%)
2:19:08.677559 PROGRESS: Decoy precursors: 92 (8.96%)
2:19:08.677604 PROGRESS: 
2:19:08.677648 PROGRESS: Precursor Summary:
2:19:08.678858 PROGRESS: Channel   0:	 0.05 FDR:   733; 0.01 FDR:   409; 0.001 FDR:   169
2:19:08.678951 PROGRESS: 
2:19:08.679023 PROGRESS: Protein Summary:
2:19:08.680267 PROGRESS: Channel   0:	 0.05 FDR:   685; 0.01 FDR:   389; 0.001 FDR:   167
2:19:08.680358 PROGRESS: =========================================================================
2:19:08.696620 INFO: fragments_df_filtered: 4301
2:19:09.138726 INFO: calibration group: precursor, fitting mz estimator 
2:19:09.187958 INFO: calibration group: precursor, fitting rt estimator 
2:19:09.236953 INFO: calibration group: fragment, fitting mz estimator 
2:19:09.575880 INFO: calibration group: precursor, predicting mz
2:19:09.606866 INFO: calibration group: precursor, predicting rt
2:19:09.757200 INFO: calibration group: fragment, predicting mz
2:19:10.097721 INFO: === checking if optimization conditions were reached ===
2:19:10.098104 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2:19:10.100353 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 183.5348.
2:19:10.100417 INFO: ==============================================
2:19:10.100521 INFO: Starting optimization step 1.
2:19:10.100594 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:19:10.100670 PROGRESS: Extracting batch of 237213 precursors
2:19:10.168083 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:19:10.168230 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:19:10.168269 INFO: FWHM in RT is 2.50 seconds, sigma is 0.32
2:19:10.168294 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:19:10.168603 INFO: Starting candidate selection
2:19:20.420154 INFO: Starting candidate scoring
2:19:23.740381 INFO: Finished candidate processing
2:19:23.740540 INFO: Collecting candidate features
2:19:24.626826 WARNING: intensity_correlation has 81 NaNs ( 0.02 % out of 467517)
2:19:24.645626 INFO: Collecting fragment features
2:19:24.885084 INFO: Finished candidate scoring
2:19:25.172323 PROGRESS: === Extracted 467517 precursors and 3249837 fragments ===
2:19:25.172810 INFO: performing precursor FDR with 47 features
2:19:25.172851 INFO: Decoy channel: -1
2:19:25.172874 INFO: Competetive: True
2:19:25.319230 INFO: Setting torch num_threads to 2 for FDR classification task
2:19:25.404061 WARNING: dropped 34 target PSMs due to missing features
2:19:25.404202 WARNING: dropped 47 decoy PSMs due to missing features
2:19:32.475550 INFO: Test AUC: 0.561
2:19:32.475748 INFO: Train AUC: 0.584
2:19:32.475780 INFO: AUC difference: 3.89%
2:19:32.595226 INFO: Resetting torch num_threads to 100
2:19:32.608019 INFO: === FDR correction performed with classifier version 8 ===
2:19:32.609012 PROGRESS: ============================= Precursor FDR =============================
2:19:32.609112 PROGRESS: Total precursors accumulated: 1,042
2:19:32.609186 PROGRESS: Target precursors: 951 (91.27%)
2:19:32.609238 PROGRESS: Decoy precursors: 91 (8.73%)
2:19:32.609287 PROGRESS: 
2:19:32.609331 PROGRESS: Precursor Summary:
2:19:32.610547 PROGRESS: Channel   0:	 0.05 FDR:   757; 0.01 FDR:   570; 0.001 FDR:   479
2:19:32.610644 PROGRESS: 
2:19:32.610702 PROGRESS: Protein Summary:
2:19:32.612030 PROGRESS: Channel   0:	 0.05 FDR:   707; 0.01 FDR:   537; 0.001 FDR:   457
2:19:32.612122 PROGRESS: =========================================================================
2:19:32.630507 INFO: fragments_df_filtered: 5000
2:19:32.890091 INFO: calibration group: precursor, fitting mz estimator 
2:19:32.941230 INFO: calibration group: precursor, fitting rt estimator 
2:19:32.991905 INFO: calibration group: fragment, fitting mz estimator 
2:19:33.418672 INFO: calibration group: precursor, predicting mz
2:19:33.434350 INFO: calibration group: precursor, predicting rt
2:19:33.509162 INFO: calibration group: fragment, predicting mz
2:19:33.680767 INFO: === checking if optimization conditions were reached ===
2:19:33.681092 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2:19:33.683588 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 123.1487.
2:19:33.683650 INFO: ==============================================
2:19:33.683757 INFO: Starting optimization step 2.
2:19:33.683831 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:19:33.683907 PROGRESS: Extracting batch of 110685 precursors
2:19:33.724120 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:19:33.724275 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:19:33.724323 INFO: FWHM in RT is 2.46 seconds, sigma is 0.32
2:19:33.724352 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:19:33.724676 INFO: Starting candidate selection
2:19:37.812571 INFO: Starting candidate scoring
2:19:39.304924 INFO: Finished candidate processing
2:19:39.305045 INFO: Collecting candidate features
2:19:39.647890 WARNING: intensity_correlation has 41 NaNs ( 0.02 % out of 217493)
2:19:39.658403 INFO: Collecting fragment features
2:19:39.764774 INFO: Finished candidate scoring
2:19:39.857873 PROGRESS: === Extracted 217493 precursors and 1452477 fragments ===
2:19:39.858275 INFO: performing precursor FDR with 47 features
2:19:39.858316 INFO: Decoy channel: -1
2:19:39.858341 INFO: Competetive: True
2:19:39.921977 INFO: Setting torch num_threads to 2 for FDR classification task
2:19:39.959515 WARNING: dropped 13 target PSMs due to missing features
2:19:39.959652 WARNING: dropped 28 decoy PSMs due to missing features
2:19:43.555540 INFO: Test AUC: 0.555
2:19:43.555722 INFO: Train AUC: 0.587
2:19:43.555753 INFO: AUC difference: 5.53%
2:19:43.555778 WARNING: AUC difference > 5%. This may indicate overfitting.
2:19:43.657011 INFO: Resetting torch num_threads to 100
2:19:43.664563 INFO: === FDR correction performed with classifier version 8 ===
2:19:43.665337 PROGRESS: ============================= Precursor FDR =============================
2:19:43.665437 PROGRESS: Total precursors accumulated: 486
2:19:43.665495 PROGRESS: Target precursors: 447 (91.98%)
2:19:43.665547 PROGRESS: Decoy precursors: 39 (8.02%)
2:19:43.665592 PROGRESS: 
2:19:43.665637 PROGRESS: Precursor Summary:
2:19:43.666613 PROGRESS: Channel   0:	 0.05 FDR:   373; 0.01 FDR:   274; 0.001 FDR:   246
2:19:43.666705 PROGRESS: 
2:19:43.666760 PROGRESS: Protein Summary:
2:19:43.667877 PROGRESS: Channel   0:	 0.05 FDR:   358; 0.01 FDR:   265; 0.001 FDR:   240
2:19:43.667967 PROGRESS: =========================================================================
2:19:43.677194 INFO: fragments_df_filtered: 2506
2:19:43.914239 INFO: calibration group: precursor, fitting mz estimator 
2:19:43.953331 INFO: calibration group: precursor, fitting rt estimator 
2:19:43.987426 INFO: calibration group: fragment, fitting mz estimator 
2:19:44.105603 INFO: calibration group: precursor, predicting mz
2:19:44.120184 INFO: calibration group: precursor, predicting rt
2:19:44.189425 INFO: calibration group: fragment, predicting mz
2:19:44.356135 INFO: === checking if optimization conditions were reached ===
2:19:44.356451 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2:19:44.358824 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 95.7775.
2:19:44.358888 INFO: ==============================================
2:19:44.358997 INFO: Starting optimization step 3.
2:19:44.359069 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:19:44.359144 PROGRESS: Extracting batch of 110685 precursors
2:19:44.396875 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:19:44.397054 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:19:44.397101 INFO: FWHM in RT is 2.45 seconds, sigma is 0.32
2:19:44.397129 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:19:44.397453 INFO: Starting candidate selection
2:19:48.429203 INFO: Starting candidate scoring
2:19:49.952059 INFO: Finished candidate processing
2:19:49.952170 INFO: Collecting candidate features
2:19:50.330015 WARNING: intensity_correlation has 40 NaNs ( 0.02 % out of 216948)
2:19:50.340651 INFO: Collecting fragment features
2:19:50.456719 INFO: Finished candidate scoring
2:19:50.560000 PROGRESS: === Extracted 216948 precursors and 1443222 fragments ===
2:19:50.560465 INFO: performing precursor FDR with 47 features
2:19:50.560503 INFO: Decoy channel: -1
2:19:50.560527 INFO: Competetive: True
2:19:50.625196 INFO: Setting torch num_threads to 2 for FDR classification task
2:19:50.664843 WARNING: dropped 13 target PSMs due to missing features
2:19:50.664990 WARNING: dropped 27 decoy PSMs due to missing features
2:19:54.191746 INFO: Test AUC: 0.559
2:19:54.191890 INFO: Train AUC: 0.586
2:19:54.191922 INFO: AUC difference: 4.64%
2:19:54.288808 INFO: Resetting torch num_threads to 100
2:19:54.295465 INFO: === FDR correction performed with classifier version 8 ===
2:19:54.296285 PROGRESS: ============================= Precursor FDR =============================
2:19:54.296382 PROGRESS: Total precursors accumulated: 527
2:19:54.296459 PROGRESS: Target precursors: 483 (91.65%)
2:19:54.296513 PROGRESS: Decoy precursors: 44 (8.35%)
2:19:54.296557 PROGRESS: 
2:19:54.296599 PROGRESS: Precursor Summary:
2:19:54.297587 PROGRESS: Channel   0:	 0.05 FDR:   402; 0.01 FDR:   252; 0.001 FDR:   170
2:19:54.297678 PROGRESS: 
2:19:54.297733 PROGRESS: Protein Summary:
2:19:54.298852 PROGRESS: Channel   0:	 0.05 FDR:   385; 0.01 FDR:   245; 0.001 FDR:   166
2:19:54.298959 PROGRESS: =========================================================================
2:19:54.307118 INFO: fragments_df_filtered: 2333
2:19:54.534548 INFO: calibration group: precursor, fitting mz estimator 
2:19:54.586891 INFO: calibration group: precursor, fitting rt estimator 
2:19:54.641694 INFO: calibration group: fragment, fitting mz estimator 
2:19:54.796102 INFO: calibration group: precursor, predicting mz
2:19:54.812595 INFO: calibration group: precursor, predicting rt
2:19:54.970543 INFO: calibration group: fragment, predicting mz
2:19:55.146407 INFO: === checking if optimization conditions were reached ===
2:19:55.146765 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2:19:55.149166 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 76.4932.
2:19:55.149231 INFO: ==============================================
2:19:55.149335 INFO: Starting optimization step 4.
2:19:55.149412 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:19:55.149484 PROGRESS: Extracting batch of 110685 precursors
2:19:55.193765 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:19:55.193944 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:19:55.194021 INFO: FWHM in RT is 2.51 seconds, sigma is 0.32
2:19:55.194262 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:19:55.194589 INFO: Starting candidate selection
2:19:59.705494 INFO: Starting candidate scoring
2:20:01.215889 INFO: Finished candidate processing
2:20:01.216009 INFO: Collecting candidate features
2:20:01.558707 WARNING: intensity_correlation has 77 NaNs ( 0.04 % out of 215586)
2:20:01.569424 INFO: Collecting fragment features
2:20:01.681477 INFO: Finished candidate scoring
2:20:01.794130 PROGRESS: === Extracted 215586 precursors and 1368520 fragments ===
2:20:01.794605 INFO: performing precursor FDR with 47 features
2:20:01.794643 INFO: Decoy channel: -1
2:20:01.794667 INFO: Competetive: True
2:20:01.866504 INFO: Setting torch num_threads to 2 for FDR classification task
2:20:01.906179 WARNING: dropped 39 target PSMs due to missing features
2:20:01.906338 WARNING: dropped 38 decoy PSMs due to missing features
2:20:04.605398 INFO: Test AUC: 0.553
2:20:04.605530 INFO: Train AUC: 0.585
2:20:04.605561 INFO: AUC difference: 5.48%
2:20:04.605587 WARNING: AUC difference > 5%. This may indicate overfitting.
2:20:04.705392 INFO: Resetting torch num_threads to 100
2:20:04.712307 INFO: === FDR correction performed with classifier version 8 ===
2:20:04.713082 PROGRESS: ============================= Precursor FDR =============================
2:20:04.713178 PROGRESS: Total precursors accumulated: 532
2:20:04.713239 PROGRESS: Target precursors: 485 (91.17%)
2:20:04.713291 PROGRESS: Decoy precursors: 47 (8.83%)
2:20:04.713339 PROGRESS: 
2:20:04.713384 PROGRESS: Precursor Summary:
2:20:04.714371 PROGRESS: Channel   0:	 0.05 FDR:   401; 0.01 FDR:   311; 0.001 FDR:   278
2:20:04.714464 PROGRESS: 
2:20:04.714521 PROGRESS: Protein Summary:
2:20:04.715669 PROGRESS: Channel   0:	 0.05 FDR:   387; 0.01 FDR:   300; 0.001 FDR:   268
2:20:04.715756 PROGRESS: =========================================================================
2:20:04.725088 INFO: fragments_df_filtered: 2707
2:20:04.954601 INFO: calibration group: precursor, fitting mz estimator 
2:20:05.019958 INFO: calibration group: precursor, fitting rt estimator 
2:20:05.086583 INFO: calibration group: fragment, fitting mz estimator 
2:20:05.305790 INFO: calibration group: precursor, predicting mz
2:20:05.321502 INFO: calibration group: precursor, predicting rt
2:20:05.417181 INFO: calibration group: fragment, predicting mz
2:20:05.621301 INFO: === checking if optimization conditions were reached ===
2:20:05.621620 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2:20:05.624022 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 74.7676.
2:20:05.624086 INFO: ==============================================
2:20:05.624198 INFO: Starting optimization step 5.
2:20:05.624271 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:20:05.624347 PROGRESS: Extracting batch of 110685 precursors
2:20:05.663222 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:20:05.663381 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:20:05.663453 INFO: FWHM in RT is 2.47 seconds, sigma is 0.32
2:20:05.663492 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:20:05.663822 INFO: Starting candidate selection
2:20:10.172254 INFO: Starting candidate scoring
2:20:11.665497 INFO: Finished candidate processing
2:20:11.665609 INFO: Collecting candidate features
2:20:12.010710 WARNING: intensity_correlation has 84 NaNs ( 0.04 % out of 215679)
2:20:12.021326 INFO: Collecting fragment features
2:20:12.128980 INFO: Finished candidate scoring
2:20:12.227867 PROGRESS: === Extracted 215679 precursors and 1373949 fragments ===
2:20:12.228823 INFO: performing precursor FDR with 47 features
2:20:12.228862 INFO: Decoy channel: -1
2:20:12.228886 INFO: Competetive: True
2:20:12.293419 INFO: Setting torch num_threads to 2 for FDR classification task
2:20:12.331910 WARNING: dropped 43 target PSMs due to missing features
2:20:12.332067 WARNING: dropped 41 decoy PSMs due to missing features
2:20:16.116755 INFO: Test AUC: 0.561
2:20:16.116968 INFO: Train AUC: 0.584
2:20:16.117000 INFO: AUC difference: 4.01%
2:20:16.218088 INFO: Resetting torch num_threads to 100
2:20:16.224918 INFO: === FDR correction performed with classifier version 8 ===
2:20:16.225703 PROGRESS: ============================= Precursor FDR =============================
2:20:16.225810 PROGRESS: Total precursors accumulated: 519
2:20:16.225875 PROGRESS: Target precursors: 474 (91.33%)
2:20:16.225949 PROGRESS: Decoy precursors: 45 (8.67%)
2:20:16.226000 PROGRESS: 
2:20:16.226050 PROGRESS: Precursor Summary:
2:20:16.227042 PROGRESS: Channel   0:	 0.05 FDR:   356; 0.01 FDR:   248; 0.001 FDR:   171
2:20:16.227137 PROGRESS: 
2:20:16.227196 PROGRESS: Protein Summary:
2:20:16.228329 PROGRESS: Channel   0:	 0.05 FDR:   344; 0.01 FDR:   241; 0.001 FDR:   167
2:20:16.228418 PROGRESS: =========================================================================
2:20:16.237045 INFO: fragments_df_filtered: 2301
2:20:16.490009 INFO: calibration group: precursor, fitting mz estimator 
2:20:16.562646 INFO: calibration group: precursor, fitting rt estimator 
2:20:16.612988 INFO: calibration group: fragment, fitting mz estimator 
2:20:16.776012 INFO: calibration group: precursor, predicting mz
2:20:16.794885 INFO: calibration group: precursor, predicting rt
2:20:16.878267 INFO: calibration group: fragment, predicting mz
2:20:17.104284 INFO: === checking if optimization conditions were reached ===
2:20:17.113719 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2:20:17.115834 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 76.4932 found after 6 searches.
2:20:17.117910 INFO: ==============================================
2:20:17.118341 PROGRESS: Optimization finished for rt_error.
2:20:17.367523 INFO: calibration group: precursor, predicting mz
2:20:17.387546 INFO: calibration group: precursor, predicting rt
2:20:17.465092 INFO: calibration group: fragment, predicting mz
2:20:17.661423 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:20:17.661662 PROGRESS: ==============================================
2:20:17.661741 PROGRESS: ms2_error      : 8.0000
2:20:17.661805 PROGRESS: ms1_error      : 3.0000
2:20:17.661862 PROGRESS: rt_error       : 76.4932
2:20:17.661915 PROGRESS: ==============================================
2:20:17.663033 INFO: calibration group: precursor, predicting mz
2:20:19.226871 INFO: calibration group: precursor, predicting rt
2:20:26.347409 INFO: calibration group: fragment, predicting mz
2:20:43.385723 PROGRESS: Extracting batch of 10183864 precursors
2:20:46.103179 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:20:46.103332 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:20:46.103375 INFO: FWHM in RT is 2.47 seconds, sigma is 0.32
2:20:46.103399 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:20:46.103807 INFO: Starting candidate selection
2:27:03.160487 INFO: Applying score cutoff of 34.30271545410156
2:27:03.517963 INFO: Removed 11117226 precursors with score below cutoff
2:27:05.769695 INFO: Starting candidate scoring
2:28:11.511823 INFO: Finished candidate processing
2:28:11.512312 INFO: Collecting candidate features
2:28:28.976676 WARNING: intensity_correlation has 184 NaNs ( 0.00 % out of 9190168)
2:28:29.290796 INFO: Collecting fragment features
2:28:35.313327 INFO: Finished candidate scoring
2:28:45.684781 INFO: === FDR correction performed with classifier version 13 ===
2:28:45.721807 INFO: performing precursor FDR with 47 features
2:28:45.721899 INFO: Decoy channel: -1
2:28:45.721931 INFO: Competetive: True
2:28:48.226066 INFO: Setting torch num_threads to 2 for FDR classification task
2:28:49.818531 WARNING: dropped 93 target PSMs due to missing features
2:28:49.818679 WARNING: dropped 91 decoy PSMs due to missing features
2:31:55.936062 INFO: Test AUC: 0.582
2:31:55.936318 INFO: Train AUC: 0.587
2:31:55.936355 INFO: AUC difference: 0.98%
2:31:56.714956 INFO: Resetting torch num_threads to 100
2:31:56.944735 INFO: Removing fragments below FDR threshold
2:31:57.527330 PROGRESS: ============================= Precursor FDR =============================
2:31:57.527725 PROGRESS: Total precursors accumulated: 28,715
2:31:57.527805 PROGRESS: Target precursors: 28,431 (99.01%)
2:31:57.527858 PROGRESS: Decoy precursors: 284 (0.99%)
2:31:57.527908 PROGRESS: 
2:31:57.527954 PROGRESS: Precursor Summary:
2:31:57.540626 PROGRESS: Channel   0:	 0.05 FDR: 28,431; 0.01 FDR: 28,431; 0.001 FDR: 19,416
2:31:57.540947 PROGRESS: 
2:31:57.541009 PROGRESS: Protein Summary:
2:31:57.559912 PROGRESS: Channel   0:	 0.05 FDR: 7,932; 0.01 FDR: 7,932; 0.001 FDR: 6,089
2:31:57.560219 PROGRESS: =========================================================================
2:31:58.099067 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:31:58.614912 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:31:58.615132 INFO: Quantification results path: run_output_Astral/alphadia_1.10_MBRSetValues/library/quant
2:31:58.615238 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3 at run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:31:58.616216 INFO: Initializing RawFileManager
2:32:30.061874 INFO: Determining DIA cycle
2:32:30.078240 INFO: Found cycle with start 0.00 min and length 303.
2:32:30.378344 INFO: RT (min)            : 0.0 - 26.9
2:32:30.378465 INFO: RT duration (sec)   : 1611.2
2:32:30.378495 INFO: RT duration (min)   : 26.9
2:32:30.378518 INFO: Cycle len (scans)   : 303
2:32:30.378538 INFO: Cycle len (sec)     : 1.65
2:32:30.378556 INFO: Number of cycles    : 978
2:32:30.378574 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:32:32.455511 INFO: Initializing CalibrationManager
2:32:32.455909 INFO: Loading calibration config
2:32:32.456650 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'}]
2:32:32.456779 INFO: Calibration group :fragment, found 1 estimator(s)
2:32:32.456872 INFO: Calibration group :precursor, found 3 estimator(s)
2:32:32.456955 INFO: Disabling ion mobility calibration
2:32:32.456984 INFO: removed mobility estimator from group precursor
2:32:32.457197 INFO: Initializing OptimizationManager
2:32:32.457338 INFO: initial parameter: ms1_error = 30
2:32:32.457409 INFO: initial parameter: ms2_error = 30
2:32:32.457458 INFO: initial parameter: rt_error = 805.611083984375
2:32:32.457501 INFO: initial parameter: mobility_error = 0.1
2:32:32.457543 INFO: initial parameter: column_type = library
2:32:32.457584 INFO: initial parameter: num_candidates = 1
2:32:32.457625 INFO: initial parameter: classifier_version = -1
2:32:32.457665 INFO: initial parameter: fwhm_rt = 5
2:32:32.457705 INFO: initial parameter: fwhm_mobility = 0.01
2:32:32.457744 INFO: initial parameter: score_cutoff = 0
2:32:32.457810 INFO: Initializing TimingManager
2:32:32.457867 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:32:32.457999 INFO: FDRManager not loaded from disk.
2:32:32.458023 INFO: Initializing FDRManager
2:32:32.458062 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
2:32:34.094468 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
2:32:36.753563 PROGRESS: Starting initial search for precursors.
2:32:37.010294 INFO: Starting optimization step 0.
2:32:37.010592 PROGRESS: === Extracting elution groups 0 to 8000 ===
2:32:37.010671 PROGRESS: Extracting batch of 15815 precursors
2:32:37.015342 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:32:37.015404 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:32:37.015442 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:32:37.015464 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:32:37.015787 INFO: Starting candidate selection
2:32:38.379879 INFO: Starting candidate scoring
2:32:38.483771 INFO: Finished candidate processing
2:32:38.483897 INFO: Collecting candidate features
2:32:38.541521 INFO: Collecting fragment features
2:32:38.557281 INFO: Finished candidate scoring
2:32:38.572117 PROGRESS: === Extracted 15769 precursors and 155891 fragments ===
2:32:38.572576 INFO: performing precursor FDR with 47 features
2:32:38.572612 INFO: Decoy channel: -1
2:32:38.572643 INFO: Competetive: True
2:32:38.580172 INFO: Setting torch num_threads to 2 for FDR classification task
2:32:38.748827 INFO: Test AUC: 0.500
2:32:38.748960 INFO: Train AUC: 0.520
2:32:38.748991 INFO: AUC difference: 3.91%
2:32:38.839050 INFO: Resetting torch num_threads to 100
2:32:38.840428 INFO: === FDR correction performed with classifier version -1 ===
2:32:38.841319 PROGRESS: ============================= Precursor FDR =============================
2:32:38.841414 PROGRESS: Total precursors accumulated: 1
2:32:38.841475 PROGRESS: Target precursors: 1 (100.00%)
2:32:38.841524 PROGRESS: Decoy precursors: 0 (0.00%)
2:32:38.841569 PROGRESS: 
2:32:38.841613 PROGRESS: Precursor Summary:
2:32:38.842532 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:32:38.842614 PROGRESS: 
2:32:38.842669 PROGRESS: Protein Summary:
2:32:38.843668 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:32:38.843754 PROGRESS: =========================================================================
2:32:38.964441 INFO: Starting optimization step 1.
2:32:38.964769 PROGRESS: === Extracting elution groups 8000 to 24000 ===
2:32:38.964851 PROGRESS: Extracting batch of 31636 precursors
2:32:38.975167 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:32:38.975293 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:32:38.975326 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:32:38.975347 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:32:38.975565 INFO: Starting candidate selection
2:32:41.220643 INFO: Starting candidate scoring
2:32:41.482575 INFO: Finished candidate processing
2:32:41.482691 INFO: Collecting candidate features
2:32:41.544760 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 31566)
2:32:41.549078 INFO: Collecting fragment features
2:32:41.573809 INFO: Finished candidate scoring
2:32:41.609567 PROGRESS: === Extracted 47335 precursors and 468863 fragments ===
2:32:41.617077 INFO: performing precursor FDR with 47 features
2:32:41.617219 INFO: Decoy channel: -1
2:32:41.617249 INFO: Competetive: True
2:32:41.646051 INFO: Setting torch num_threads to 2 for FDR classification task
2:32:41.655387 WARNING: dropped 1 target PSMs due to missing features
2:32:42.455137 INFO: Test AUC: 0.545
2:32:42.455379 INFO: Train AUC: 0.565
2:32:42.455416 INFO: AUC difference: 3.50%
2:32:42.542676 INFO: Resetting torch num_threads to 100
2:32:42.546270 INFO: === FDR correction performed with classifier version -1 ===
2:32:42.554978 PROGRESS: ============================= Precursor FDR =============================
2:32:42.555686 PROGRESS: Total precursors accumulated: 23,910
2:32:42.555760 PROGRESS: Target precursors: 13,888 (58.08%)
2:32:42.555813 PROGRESS: Decoy precursors: 10,022 (41.92%)
2:32:42.555861 PROGRESS: 
2:32:42.555907 PROGRESS: Precursor Summary:
2:32:42.557868 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:32:42.558073 PROGRESS: 
2:32:42.558134 PROGRESS: Protein Summary:
2:32:42.559293 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
2:32:42.559417 PROGRESS: =========================================================================
2:32:42.737221 INFO: Starting optimization step 2.
2:32:42.737573 PROGRESS: === Extracting elution groups 24000 to 56000 ===
2:32:42.737648 PROGRESS: Extracting batch of 63234 precursors
2:32:42.755640 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:32:42.755785 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:32:42.755821 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:32:42.755847 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:32:42.756080 INFO: Starting candidate selection
2:32:46.993811 INFO: Starting candidate scoring
2:32:47.469928 INFO: Finished candidate processing
2:32:47.470087 INFO: Collecting candidate features
2:32:47.601351 INFO: Collecting fragment features
2:32:47.652491 INFO: Finished candidate scoring
2:32:47.755692 PROGRESS: === Extracted 110399 precursors and 1096363 fragments ===
2:32:47.769860 INFO: performing precursor FDR with 47 features
2:32:47.769954 INFO: Decoy channel: -1
2:32:47.769983 INFO: Competetive: True
2:32:47.827969 INFO: Setting torch num_threads to 2 for FDR classification task
2:32:47.851198 WARNING: dropped 1 target PSMs due to missing features
2:32:49.220428 INFO: Test AUC: 0.553
2:32:49.220565 INFO: Train AUC: 0.583
2:32:49.220597 INFO: AUC difference: 5.28%
2:32:49.220622 WARNING: AUC difference > 5%. This may indicate overfitting.
2:32:49.313776 INFO: Resetting torch num_threads to 100
2:32:49.320168 INFO: === FDR correction performed with classifier version -1 ===
2:32:49.321130 PROGRESS: ============================= Precursor FDR =============================
2:32:49.321228 PROGRESS: Total precursors accumulated: 1
2:32:49.321286 PROGRESS: Target precursors: 1 (100.00%)
2:32:49.321337 PROGRESS: Decoy precursors: 0 (0.00%)
2:32:49.321383 PROGRESS: 
2:32:49.321427 PROGRESS: Precursor Summary:
2:32:49.322371 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:32:49.322468 PROGRESS: 
2:32:49.322521 PROGRESS: Protein Summary:
2:32:49.323536 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:32:49.323624 PROGRESS: =========================================================================
2:32:49.632159 INFO: Starting optimization step 3.
2:32:49.632513 PROGRESS: === Extracting elution groups 56000 to 120000 ===
2:32:49.632596 PROGRESS: Extracting batch of 126528 precursors
2:32:49.669078 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:32:49.669241 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:32:49.669285 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:32:49.669308 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:32:49.669657 INFO: Starting candidate selection
2:32:57.769479 INFO: Starting candidate scoring
2:32:58.722786 INFO: Finished candidate processing
2:32:58.722901 INFO: Collecting candidate features
2:32:59.051008 INFO: Collecting fragment features
2:32:59.140766 INFO: Finished candidate scoring
2:32:59.303619 PROGRESS: === Extracted 236565 precursors and 2349494 fragments ===
2:32:59.339863 INFO: performing precursor FDR with 47 features
2:32:59.340083 INFO: Decoy channel: -1
2:32:59.340114 INFO: Competetive: True
2:32:59.471634 INFO: Setting torch num_threads to 2 for FDR classification task
2:32:59.516901 WARNING: dropped 1 target PSMs due to missing features
2:33:04.034814 INFO: Test AUC: 0.554
2:33:04.035021 INFO: Train AUC: 0.591
2:33:04.035054 INFO: AUC difference: 6.27%
2:33:04.035077 WARNING: AUC difference > 5%. This may indicate overfitting.
2:33:04.143655 INFO: Resetting torch num_threads to 100
2:33:04.164129 INFO: === FDR correction performed with classifier version -1 ===
2:33:04.165111 PROGRESS: ============================= Precursor FDR =============================
2:33:04.165212 PROGRESS: Total precursors accumulated: 15
2:33:04.165272 PROGRESS: Target precursors: 14 (93.33%)
2:33:04.165321 PROGRESS: Decoy precursors: 1 (6.67%)
2:33:04.165370 PROGRESS: 
2:33:04.165415 PROGRESS: Precursor Summary:
2:33:04.166285 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
2:33:04.166376 PROGRESS: 
2:33:04.166431 PROGRESS: Protein Summary:
2:33:04.167403 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
2:33:04.167490 PROGRESS: =========================================================================
2:33:04.692479 INFO: Starting optimization step 4.
2:33:04.692887 PROGRESS: === Extracting elution groups 120000 to 248000 ===
2:33:04.692979 PROGRESS: Extracting batch of 253020 precursors
2:33:04.765722 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:33:04.765891 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:33:04.765952 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:33:04.765980 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:33:04.766336 INFO: Starting candidate selection
2:33:20.961726 INFO: Starting candidate scoring
2:33:22.917292 INFO: Finished candidate processing
2:33:22.917494 INFO: Collecting candidate features
2:33:23.713728 WARNING: intensity_correlation has 8 NaNs ( 0.00 % out of 252390)
2:33:23.725457 INFO: Collecting fragment features
2:33:23.956203 INFO: Finished candidate scoring
2:33:24.474478 PROGRESS: === Extracted 488955 precursors and 4854344 fragments ===
2:33:24.547341 INFO: performing precursor FDR with 47 features
2:33:24.547507 INFO: Decoy channel: -1
2:33:24.547539 INFO: Competetive: True
2:33:24.865189 INFO: Setting torch num_threads to 2 for FDR classification task
2:33:24.999869 WARNING: dropped 5 target PSMs due to missing features
2:33:25.000043 WARNING: dropped 4 decoy PSMs due to missing features
2:33:34.911933 INFO: Test AUC: 0.561
2:33:34.912103 INFO: Train AUC: 0.589
2:33:34.912136 INFO: AUC difference: 4.75%
2:33:35.037784 INFO: Resetting torch num_threads to 100
2:33:35.068985 INFO: === FDR correction performed with classifier version -1 ===
2:33:35.070056 PROGRESS: ============================= Precursor FDR =============================
2:33:35.070187 PROGRESS: Total precursors accumulated: 683
2:33:35.070249 PROGRESS: Target precursors: 624 (91.36%)
2:33:35.070300 PROGRESS: Decoy precursors: 59 (8.64%)
2:33:35.070345 PROGRESS: 
2:33:35.070390 PROGRESS: Precursor Summary:
2:33:35.071639 PROGRESS: Channel   0:	 0.05 FDR:   521; 0.01 FDR:   396; 0.001 FDR:   241
2:33:35.071745 PROGRESS: 
2:33:35.071800 PROGRESS: Protein Summary:
2:33:35.073076 PROGRESS: Channel   0:	 0.05 FDR:   481; 0.01 FDR:   366; 0.001 FDR:   229
2:33:35.073176 PROGRESS: =========================================================================
2:33:35.139305 INFO: fragments_df_filtered: 3565
2:33:35.841912 INFO: calibration group: precursor, fitting mz estimator 
2:33:35.883177 INFO: calibration group: precursor, fitting rt estimator 
2:33:35.919193 INFO: calibration group: fragment, fitting mz estimator 
2:33:36.113722 INFO: calibration group: precursor, predicting mz
2:33:36.171979 INFO: calibration group: precursor, predicting rt
2:33:36.481126 INFO: calibration group: fragment, predicting mz
2:33:37.147231 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:33:37.147542 INFO: Starting optimization step 5.
2:33:37.147615 PROGRESS: === Extracting elution groups 0 to 248000 ===
2:33:37.147685 PROGRESS: Extracting batch of 490233 precursors
2:33:37.266844 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:33:37.266977 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:33:37.267018 INFO: FWHM in RT is 2.89 seconds, sigma is 0.37
2:33:37.267041 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:33:37.267315 INFO: Starting candidate selection
2:34:01.448435 INFO: Starting candidate scoring
2:34:08.874467 INFO: Finished candidate processing
2:34:08.875577 INFO: Collecting candidate features
2:34:11.166845 WARNING: intensity_correlation has 6 NaNs ( 0.00 % out of 977969)
2:34:11.202207 INFO: Collecting fragment features
2:34:11.887926 INFO: Finished candidate scoring
2:34:13.138818 PROGRESS: === Extracted 977969 precursors and 9623862 fragments ===
2:34:13.139781 INFO: performing precursor FDR with 47 features
2:34:13.139828 INFO: Decoy channel: -1
2:34:13.139853 INFO: Competetive: True
2:34:13.475932 INFO: Setting torch num_threads to 2 for FDR classification task
2:34:13.675383 WARNING: dropped 2 target PSMs due to missing features
2:34:13.675526 WARNING: dropped 4 decoy PSMs due to missing features
2:34:31.523573 INFO: Test AUC: 0.565
2:34:31.523774 INFO: Train AUC: 0.584
2:34:31.523809 INFO: AUC difference: 3.24%
2:34:31.693757 INFO: Resetting torch num_threads to 100
2:34:31.721499 INFO: === FDR correction performed with classifier version 4 ===
2:34:31.722702 PROGRESS: ============================= Precursor FDR =============================
2:34:31.722867 PROGRESS: Total precursors accumulated: 1,042
2:34:31.722934 PROGRESS: Target precursors: 949 (91.07%)
2:34:31.722986 PROGRESS: Decoy precursors: 93 (8.93%)
2:34:31.723032 PROGRESS: 
2:34:31.723076 PROGRESS: Precursor Summary:
2:34:31.724605 PROGRESS: Channel   0:	 0.05 FDR:   807; 0.01 FDR:   583; 0.001 FDR:   507
2:34:31.724717 PROGRESS: 
2:34:31.724777 PROGRESS: Protein Summary:
2:34:31.726227 PROGRESS: Channel   0:	 0.05 FDR:   724; 0.01 FDR:   526; 0.001 FDR:   462
2:34:31.726321 PROGRESS: =========================================================================
2:34:31.800464 INFO: fragments_df_filtered: 5000
2:34:32.584068 INFO: calibration group: precursor, fitting mz estimator 
2:34:32.642155 INFO: calibration group: precursor, fitting rt estimator 
2:34:32.696284 INFO: calibration group: fragment, fitting mz estimator 
2:34:33.094312 INFO: calibration group: precursor, predicting mz
2:34:33.130698 INFO: calibration group: precursor, predicting rt
2:34:33.279876 INFO: calibration group: fragment, predicting mz
2:34:33.628362 INFO: === checking if optimization conditions were reached ===
2:34:33.631249 PROGRESS: ❌ ms2_error      : 13.3896 > 8.0000 or insufficient steps taken.
2:34:33.632471 PROGRESS: ❌ ms1_error      : 13.8655 > 3.0000 or insufficient steps taken.
2:34:33.632526 INFO: ==============================================
2:34:33.632642 INFO: Starting optimization step 6.
2:34:33.632737 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:34:33.632832 PROGRESS: Extracting batch of 237213 precursors
2:34:33.745878 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:34:33.746010 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:34:33.746049 INFO: FWHM in RT is 2.93 seconds, sigma is 0.38
2:34:33.746072 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:34:33.746420 INFO: Starting candidate selection
2:34:45.387726 INFO: Starting candidate scoring
2:34:48.776486 INFO: Finished candidate processing
2:34:48.776615 INFO: Collecting candidate features
2:34:49.899616 WARNING: intensity_correlation has 10 NaNs ( 0.00 % out of 472861)
2:34:49.919424 INFO: Collecting fragment features
2:34:50.238040 INFO: Finished candidate scoring
2:34:50.715799 PROGRESS: === Extracted 472861 precursors and 3998858 fragments ===
2:34:50.716361 INFO: performing precursor FDR with 47 features
2:34:50.716413 INFO: Decoy channel: -1
2:34:50.716440 INFO: Competetive: True
2:34:50.876210 INFO: Setting torch num_threads to 2 for FDR classification task
2:34:50.977483 WARNING: dropped 6 target PSMs due to missing features
2:34:50.977709 WARNING: dropped 4 decoy PSMs due to missing features
2:34:59.148623 INFO: Test AUC: 0.558
2:34:59.148781 INFO: Train AUC: 0.587
2:34:59.148815 INFO: AUC difference: 4.87%
2:34:59.275813 INFO: Resetting torch num_threads to 100
2:34:59.289451 INFO: === FDR correction performed with classifier version 5 ===
2:34:59.290631 PROGRESS: ============================= Precursor FDR =============================
2:34:59.290757 PROGRESS: Total precursors accumulated: 805
2:34:59.290817 PROGRESS: Target precursors: 732 (90.93%)
2:34:59.290869 PROGRESS: Decoy precursors: 73 (9.07%)
2:34:59.290914 PROGRESS: 
2:34:59.290958 PROGRESS: Precursor Summary:
2:34:59.292165 PROGRESS: Channel   0:	 0.05 FDR:   605; 0.01 FDR:   407; 0.001 FDR:   284
2:34:59.292267 PROGRESS: 
2:34:59.292323 PROGRESS: Protein Summary:
2:34:59.293584 PROGRESS: Channel   0:	 0.05 FDR:   568; 0.01 FDR:   384; 0.001 FDR:   272
2:34:59.293685 PROGRESS: =========================================================================
2:34:59.311064 INFO: fragments_df_filtered: 4183
2:34:59.714749 INFO: calibration group: precursor, fitting mz estimator 
2:34:59.771024 INFO: calibration group: precursor, fitting rt estimator 
2:34:59.823024 INFO: calibration group: fragment, fitting mz estimator 
2:35:00.127565 INFO: calibration group: precursor, predicting mz
2:35:00.158253 INFO: calibration group: precursor, predicting rt
2:35:00.309003 INFO: calibration group: fragment, predicting mz
2:35:00.643425 INFO: === checking if optimization conditions were reached ===
2:35:00.645800 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
2:35:00.646766 PROGRESS: ❌ ms1_error      : 5.4791 > 3.0000 or insufficient steps taken.
2:35:00.646816 INFO: ==============================================
2:35:00.646918 INFO: Starting optimization step 7.
2:35:00.646991 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:35:00.647074 PROGRESS: Extracting batch of 237213 precursors
2:35:00.707132 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:35:00.707272 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:35:00.707519 INFO: FWHM in RT is 2.62 seconds, sigma is 0.34
2:35:00.707551 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:35:00.708156 INFO: Starting candidate selection
2:35:12.695516 INFO: Starting candidate scoring
2:35:16.266235 INFO: Finished candidate processing
2:35:16.268214 INFO: Collecting candidate features
2:35:17.216957 WARNING: intensity_correlation has 25 NaNs ( 0.01 % out of 472431)
2:35:17.235557 INFO: Collecting fragment features
2:35:17.510982 INFO: Finished candidate scoring
2:35:17.811983 PROGRESS: === Extracted 472431 precursors and 3515673 fragments ===
2:35:17.812901 INFO: performing precursor FDR with 47 features
2:35:17.812948 INFO: Decoy channel: -1
2:35:17.812973 INFO: Competetive: True
2:35:17.977482 INFO: Setting torch num_threads to 2 for FDR classification task
2:35:18.078761 WARNING: dropped 12 target PSMs due to missing features
2:35:18.078903 WARNING: dropped 13 decoy PSMs due to missing features
2:35:28.181800 INFO: Test AUC: 0.558
2:35:28.181954 INFO: Train AUC: 0.590
2:35:28.181985 INFO: AUC difference: 5.40%
2:35:28.182009 WARNING: AUC difference > 5%. This may indicate overfitting.
2:35:28.304950 INFO: Resetting torch num_threads to 100
2:35:28.322478 INFO: === FDR correction performed with classifier version 6 ===
2:35:28.323581 PROGRESS: ============================= Precursor FDR =============================
2:35:28.323713 PROGRESS: Total precursors accumulated: 1,130
2:35:28.323774 PROGRESS: Target precursors: 1,030 (91.15%)
2:35:28.323825 PROGRESS: Decoy precursors: 100 (8.85%)
2:35:28.323869 PROGRESS: 
2:35:28.323915 PROGRESS: Precursor Summary:
2:35:28.325311 PROGRESS: Channel   0:	 0.05 FDR:   809; 0.01 FDR:   523; 0.001 FDR:   314
2:35:28.325420 PROGRESS: 
2:35:28.325478 PROGRESS: Protein Summary:
2:35:28.326842 PROGRESS: Channel   0:	 0.05 FDR:   751; 0.01 FDR:   492; 0.001 FDR:   301
2:35:28.326938 PROGRESS: =========================================================================
2:35:28.355650 INFO: fragments_df_filtered: 5000
2:35:28.620211 INFO: calibration group: precursor, fitting mz estimator 
2:35:28.670706 INFO: calibration group: precursor, fitting rt estimator 
2:35:28.710204 INFO: calibration group: fragment, fitting mz estimator 
2:35:29.064667 INFO: calibration group: precursor, predicting mz
2:35:29.079967 INFO: calibration group: precursor, predicting rt
2:35:29.150423 INFO: calibration group: fragment, predicting mz
2:35:29.316625 INFO: === checking if optimization conditions were reached ===
2:35:29.316952 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
2:35:29.318451 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
2:35:29.318502 INFO: ==============================================
2:35:29.318604 PROGRESS: Optimization finished for ms2_error, ms1_error.
2:35:29.547345 INFO: calibration group: precursor, predicting mz
2:35:29.563115 INFO: calibration group: precursor, predicting rt
2:35:29.633611 INFO: calibration group: fragment, predicting mz
2:35:29.798606 INFO: Starting optimization step 0.
2:35:29.798899 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:35:29.798982 PROGRESS: Extracting batch of 110685 precursors
2:35:29.836307 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:35:29.836457 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:35:29.836500 INFO: FWHM in RT is 2.38 seconds, sigma is 0.31
2:35:29.836523 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:35:29.836854 INFO: Starting candidate selection
2:35:35.708191 INFO: Starting candidate scoring
2:35:37.424727 INFO: Finished candidate processing
2:35:37.424859 INFO: Collecting candidate features
2:35:37.867054 WARNING: intensity_correlation has 5 NaNs ( 0.00 % out of 220548)
2:35:37.878518 INFO: Collecting fragment features
2:35:38.028365 INFO: Finished candidate scoring
2:35:38.177301 PROGRESS: === Extracted 220548 precursors and 1641243 fragments ===
2:35:38.177846 INFO: performing precursor FDR with 47 features
2:35:38.177896 INFO: Decoy channel: -1
2:35:38.177920 INFO: Competetive: True
2:35:38.278227 INFO: Setting torch num_threads to 2 for FDR classification task
2:35:38.341674 WARNING: dropped 3 target PSMs due to missing features
2:35:38.341839 WARNING: dropped 2 decoy PSMs due to missing features
2:35:42.863216 INFO: Test AUC: 0.561
2:35:42.863682 INFO: Train AUC: 0.606
2:35:42.863720 INFO: AUC difference: 7.46%
2:35:42.863744 WARNING: AUC difference > 5%. This may indicate overfitting.
2:35:42.972149 INFO: Resetting torch num_threads to 100
2:35:42.984711 INFO: === FDR correction performed with classifier version 7 ===
2:35:42.985715 PROGRESS: ============================= Precursor FDR =============================
2:35:42.985834 PROGRESS: Total precursors accumulated: 650
2:35:42.985897 PROGRESS: Target precursors: 592 (91.08%)
2:35:42.985947 PROGRESS: Decoy precursors: 58 (8.92%)
2:35:42.985994 PROGRESS: 
2:35:42.986036 PROGRESS: Precursor Summary:
2:35:42.987239 PROGRESS: Channel   0:	 0.05 FDR:   467; 0.01 FDR:   265; 0.001 FDR:   157
2:35:42.987328 PROGRESS: 
2:35:42.987381 PROGRESS: Protein Summary:
2:35:42.988559 PROGRESS: Channel   0:	 0.05 FDR:   453; 0.01 FDR:   258; 0.001 FDR:   155
2:35:42.988646 PROGRESS: =========================================================================
2:35:42.999304 INFO: fragments_df_filtered: 2488
2:35:43.340000 INFO: calibration group: precursor, fitting mz estimator 
2:35:43.428786 INFO: calibration group: precursor, fitting rt estimator 
2:35:43.470442 INFO: calibration group: fragment, fitting mz estimator 
2:35:43.593814 INFO: calibration group: precursor, predicting mz
2:35:43.611259 INFO: calibration group: precursor, predicting rt
2:35:43.684048 INFO: calibration group: fragment, predicting mz
2:35:43.854205 INFO: === checking if optimization conditions were reached ===
2:35:43.854662 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2:35:43.857131 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 310.8153.
2:35:43.857197 INFO: ==============================================
2:35:43.857310 INFO: Starting optimization step 1.
2:35:43.857386 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:35:43.857476 PROGRESS: Extracting batch of 110685 precursors
2:35:43.904565 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:35:43.904731 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:35:43.904778 INFO: FWHM in RT is 2.28 seconds, sigma is 0.29
2:35:43.904801 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:35:43.905200 INFO: Starting candidate selection
2:35:49.009947 INFO: Starting candidate scoring
2:35:50.750550 INFO: Finished candidate processing
2:35:50.750664 INFO: Collecting candidate features
2:35:51.146193 WARNING: intensity_correlation has 14 NaNs ( 0.01 % out of 219951)
2:35:51.158310 INFO: Collecting fragment features
2:35:51.287163 INFO: Finished candidate scoring
2:35:51.450212 PROGRESS: === Extracted 219951 precursors and 1603046 fragments ===
2:35:51.451178 INFO: performing precursor FDR with 47 features
2:35:51.451220 INFO: Decoy channel: -1
2:35:51.451246 INFO: Competetive: True
2:35:51.533781 INFO: Setting torch num_threads to 2 for FDR classification task
2:35:51.579921 WARNING: dropped 11 target PSMs due to missing features
2:35:51.580084 WARNING: dropped 3 decoy PSMs due to missing features
2:35:55.677788 INFO: Test AUC: 0.556
2:35:55.677991 INFO: Train AUC: 0.599
2:35:55.678033 INFO: AUC difference: 7.19%
2:35:55.678056 WARNING: AUC difference > 5%. This may indicate overfitting.
2:35:55.783267 INFO: Resetting torch num_threads to 100
2:35:55.794880 INFO: === FDR correction performed with classifier version 7 ===
2:35:55.795855 PROGRESS: ============================= Precursor FDR =============================
2:35:55.795958 PROGRESS: Total precursors accumulated: 640
2:35:55.796031 PROGRESS: Target precursors: 581 (90.78%)
2:35:55.796083 PROGRESS: Decoy precursors: 59 (9.22%)
2:35:55.796131 PROGRESS: 
2:35:55.796175 PROGRESS: Precursor Summary:
2:35:55.797211 PROGRESS: Channel   0:	 0.05 FDR:   387; 0.01 FDR:   260; 0.001 FDR:   142
2:35:55.797305 PROGRESS: 
2:35:55.797361 PROGRESS: Protein Summary:
2:35:55.798475 PROGRESS: Channel   0:	 0.05 FDR:   377; 0.01 FDR:   253; 0.001 FDR:   140
2:35:55.798568 PROGRESS: =========================================================================
2:35:55.808363 INFO: fragments_df_filtered: 2467
2:35:56.189285 INFO: calibration group: precursor, fitting mz estimator 
2:35:56.264852 INFO: calibration group: precursor, fitting rt estimator 
2:35:56.441361 INFO: calibration group: fragment, fitting mz estimator 
2:35:56.663383 INFO: calibration group: precursor, predicting mz
2:35:56.687500 INFO: calibration group: precursor, predicting rt
2:35:56.782854 INFO: calibration group: fragment, predicting mz
2:35:56.967236 INFO: === checking if optimization conditions were reached ===
2:35:56.967979 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2:35:56.971259 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 231.0642.
2:35:56.971441 INFO: ==============================================
2:35:56.971750 INFO: Starting optimization step 2.
2:35:56.971996 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:35:56.972238 PROGRESS: Extracting batch of 110685 precursors
2:35:57.017791 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:35:57.018083 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:35:57.018198 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
2:35:57.018289 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:35:57.018752 INFO: Starting candidate selection
2:36:01.431905 INFO: Starting candidate scoring
2:36:03.117529 INFO: Finished candidate processing
2:36:03.117635 INFO: Collecting candidate features
2:36:03.463783 WARNING: intensity_correlation has 17 NaNs ( 0.01 % out of 219346)
2:36:03.474733 INFO: Collecting fragment features
2:36:03.588469 INFO: Finished candidate scoring
2:36:03.725753 PROGRESS: === Extracted 219346 precursors and 1572719 fragments ===
2:36:03.726172 INFO: performing precursor FDR with 47 features
2:36:03.726213 INFO: Decoy channel: -1
2:36:03.726238 INFO: Competetive: True
2:36:03.801422 INFO: Setting torch num_threads to 2 for FDR classification task
2:36:03.847003 WARNING: dropped 8 target PSMs due to missing features
2:36:03.847158 WARNING: dropped 9 decoy PSMs due to missing features
2:36:07.561916 INFO: Test AUC: 0.561
2:36:07.562062 INFO: Train AUC: 0.597
2:36:07.562093 INFO: AUC difference: 6.10%
2:36:07.562114 WARNING: AUC difference > 5%. This may indicate overfitting.
2:36:07.660879 INFO: Resetting torch num_threads to 100
2:36:07.669462 INFO: === FDR correction performed with classifier version 7 ===
2:36:07.670300 PROGRESS: ============================= Precursor FDR =============================
2:36:07.670403 PROGRESS: Total precursors accumulated: 628
2:36:07.670466 PROGRESS: Target precursors: 571 (90.92%)
2:36:07.670515 PROGRESS: Decoy precursors: 57 (9.08%)
2:36:07.670561 PROGRESS: 
2:36:07.670606 PROGRESS: Precursor Summary:
2:36:07.671702 PROGRESS: Channel   0:	 0.05 FDR:   395; 0.01 FDR:   257; 0.001 FDR:   107
2:36:07.671795 PROGRESS: 
2:36:07.671850 PROGRESS: Protein Summary:
2:36:07.673024 PROGRESS: Channel   0:	 0.05 FDR:   383; 0.01 FDR:   251; 0.001 FDR:   105
2:36:07.673118 PROGRESS: =========================================================================
2:36:07.681883 INFO: fragments_df_filtered: 2418
2:36:07.908216 INFO: calibration group: precursor, fitting mz estimator 
2:36:07.999203 INFO: calibration group: precursor, fitting rt estimator 
2:36:08.049864 INFO: calibration group: fragment, fitting mz estimator 
2:36:08.234729 INFO: calibration group: precursor, predicting mz
2:36:08.249859 INFO: calibration group: precursor, predicting rt
2:36:08.322649 INFO: calibration group: fragment, predicting mz
2:36:08.489846 INFO: === checking if optimization conditions were reached ===
2:36:08.490232 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2:36:08.492811 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 176.6789.
2:36:08.492888 INFO: ==============================================
2:36:08.493004 INFO: Starting optimization step 3.
2:36:08.493092 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:36:08.493174 PROGRESS: Extracting batch of 110685 precursors
2:36:08.541110 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:36:08.541291 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:36:08.541341 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
2:36:08.541371 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:36:08.541666 INFO: Starting candidate selection
2:36:13.455520 INFO: Starting candidate scoring
2:36:15.162874 INFO: Finished candidate processing
2:36:15.163045 INFO: Collecting candidate features
2:36:15.520226 WARNING: intensity_correlation has 33 NaNs ( 0.02 % out of 218412)
2:36:15.531405 INFO: Collecting fragment features
2:36:15.646185 INFO: Finished candidate scoring
2:36:15.907087 PROGRESS: === Extracted 218412 precursors and 1523731 fragments ===
2:36:15.907619 INFO: performing precursor FDR with 47 features
2:36:15.907657 INFO: Decoy channel: -1
2:36:15.907681 INFO: Competetive: True
2:36:15.993514 INFO: Setting torch num_threads to 2 for FDR classification task
2:36:16.037922 WARNING: dropped 17 target PSMs due to missing features
2:36:16.038088 WARNING: dropped 16 decoy PSMs due to missing features
2:36:19.544364 INFO: Test AUC: 0.554
2:36:19.545268 INFO: Train AUC: 0.593
2:36:19.545313 INFO: AUC difference: 6.55%
2:36:19.545338 WARNING: AUC difference > 5%. This may indicate overfitting.
2:36:19.645744 INFO: Resetting torch num_threads to 100
2:36:19.654152 INFO: === FDR correction performed with classifier version 7 ===
2:36:19.654994 PROGRESS: ============================= Precursor FDR =============================
2:36:19.655111 PROGRESS: Total precursors accumulated: 619
2:36:19.655171 PROGRESS: Target precursors: 565 (91.28%)
2:36:19.655232 PROGRESS: Decoy precursors: 54 (8.72%)
2:36:19.655279 PROGRESS: 
2:36:19.655323 PROGRESS: Precursor Summary:
2:36:19.656389 PROGRESS: Channel   0:	 0.05 FDR:   437; 0.01 FDR:   243; 0.001 FDR:   121
2:36:19.656484 PROGRESS: 
2:36:19.656539 PROGRESS: Protein Summary:
2:36:19.657717 PROGRESS: Channel   0:	 0.05 FDR:   421; 0.01 FDR:   238; 0.001 FDR:   118
2:36:19.657818 PROGRESS: =========================================================================
2:36:19.666559 INFO: fragments_df_filtered: 2295
2:36:19.898489 INFO: calibration group: precursor, fitting mz estimator 
2:36:22.807619 INFO: calibration group: precursor, fitting rt estimator 
2:36:22.934408 INFO: calibration group: fragment, fitting mz estimator 
2:36:23.139900 INFO: calibration group: precursor, predicting mz
2:36:23.158460 INFO: calibration group: precursor, predicting rt
2:36:23.257549 INFO: calibration group: fragment, predicting mz
2:36:23.455944 INFO: === checking if optimization conditions were reached ===
2:36:23.456657 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2:36:23.459888 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 120.1273.
2:36:23.460127 INFO: ==============================================
2:36:23.460462 INFO: Starting optimization step 4.
2:36:23.460734 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:36:23.461005 PROGRESS: Extracting batch of 110685 precursors
2:36:23.519981 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:36:23.520643 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:36:23.520940 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
2:36:23.521167 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:36:23.521814 INFO: Starting candidate selection
2:36:28.679867 INFO: Starting candidate scoring
2:36:30.852537 INFO: Finished candidate processing
2:36:30.852795 INFO: Collecting candidate features
2:36:31.528480 WARNING: intensity_correlation has 29 NaNs ( 0.01 % out of 217610)
2:36:31.542221 INFO: Collecting fragment features
2:36:31.720304 INFO: Finished candidate scoring
2:36:32.113429 PROGRESS: === Extracted 217610 precursors and 1465729 fragments ===
2:36:32.114004 INFO: performing precursor FDR with 47 features
2:36:32.114046 INFO: Decoy channel: -1
2:36:32.114071 INFO: Competetive: True
2:36:32.252955 INFO: Setting torch num_threads to 2 for FDR classification task
2:36:32.329554 WARNING: dropped 14 target PSMs due to missing features
2:36:32.329773 WARNING: dropped 15 decoy PSMs due to missing features
2:36:37.645097 INFO: Test AUC: 0.560
2:36:37.645299 INFO: Train AUC: 0.591
2:36:37.645338 INFO: AUC difference: 5.23%
2:36:37.645363 WARNING: AUC difference > 5%. This may indicate overfitting.
2:36:37.793579 INFO: Resetting torch num_threads to 100
2:36:37.846307 INFO: === FDR correction performed with classifier version 7 ===
2:36:37.848357 PROGRESS: ============================= Precursor FDR =============================
2:36:37.848598 PROGRESS: Total precursors accumulated: 563
2:36:37.848689 PROGRESS: Target precursors: 512 (90.94%)
2:36:37.848760 PROGRESS: Decoy precursors: 51 (9.06%)
2:36:37.848810 PROGRESS: 
2:36:37.848853 PROGRESS: Precursor Summary:
2:36:37.851403 PROGRESS: Channel   0:	 0.05 FDR:   383; 0.01 FDR:   247; 0.001 FDR:   181
2:36:37.851677 PROGRESS: 
2:36:37.851754 PROGRESS: Protein Summary:
2:36:37.853936 PROGRESS: Channel   0:	 0.05 FDR:   370; 0.01 FDR:   241; 0.001 FDR:   178
2:36:37.854104 PROGRESS: =========================================================================
2:36:37.864465 INFO: fragments_df_filtered: 2323
2:36:38.286542 INFO: calibration group: precursor, fitting mz estimator 
2:36:38.420328 INFO: calibration group: precursor, fitting rt estimator 
2:36:38.496196 INFO: calibration group: fragment, fitting mz estimator 
2:36:38.669001 INFO: calibration group: precursor, predicting mz
2:36:38.689425 INFO: calibration group: precursor, predicting rt
2:36:38.770864 INFO: calibration group: fragment, predicting mz
2:36:38.965937 INFO: === checking if optimization conditions were reached ===
2:36:38.966437 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2:36:38.969532 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 87.0277.
2:36:38.969641 INFO: ==============================================
2:36:38.969803 INFO: Starting optimization step 5.
2:36:38.969903 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:36:38.970008 PROGRESS: Extracting batch of 110685 precursors
2:36:39.038049 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:36:39.038357 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:36:39.038474 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
2:36:39.038521 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:36:39.039146 INFO: Starting candidate selection
2:36:43.959377 INFO: Starting candidate scoring
2:36:45.953053 INFO: Finished candidate processing
2:36:45.953339 INFO: Collecting candidate features
2:36:46.614639 WARNING: intensity_correlation has 50 NaNs ( 0.02 % out of 216415)
2:36:46.627400 INFO: Collecting fragment features
2:36:46.815278 INFO: Finished candidate scoring
2:36:47.281487 PROGRESS: === Extracted 216415 precursors and 1412887 fragments ===
2:36:47.282014 INFO: performing precursor FDR with 47 features
2:36:47.282055 INFO: Decoy channel: -1
2:36:47.282095 INFO: Competetive: True
2:36:47.432621 INFO: Setting torch num_threads to 2 for FDR classification task
2:36:47.503322 WARNING: dropped 28 target PSMs due to missing features
2:36:47.503547 WARNING: dropped 22 decoy PSMs due to missing features
2:36:52.661890 INFO: Test AUC: 0.557
2:36:52.662169 INFO: Train AUC: 0.590
2:36:52.662208 INFO: AUC difference: 5.66%
2:36:52.662236 WARNING: AUC difference > 5%. This may indicate overfitting.
2:36:52.788946 INFO: Resetting torch num_threads to 100
2:36:52.799704 INFO: === FDR correction performed with classifier version 7 ===
2:36:52.801252 PROGRESS: ============================= Precursor FDR =============================
2:36:52.801441 PROGRESS: Total precursors accumulated: 560
2:36:52.801508 PROGRESS: Target precursors: 510 (91.07%)
2:36:52.801562 PROGRESS: Decoy precursors: 50 (8.93%)
2:36:52.801635 PROGRESS: 
2:36:52.801684 PROGRESS: Precursor Summary:
2:36:52.803168 PROGRESS: Channel   0:	 0.05 FDR:   409; 0.01 FDR:   277; 0.001 FDR:    32
2:36:52.803295 PROGRESS: 
2:36:52.803351 PROGRESS: Protein Summary:
2:36:52.804829 PROGRESS: Channel   0:	 0.05 FDR:   396; 0.01 FDR:   270; 0.001 FDR:    31
2:36:52.804956 PROGRESS: =========================================================================
2:36:52.817544 INFO: fragments_df_filtered: 2478
2:36:53.215486 INFO: calibration group: precursor, fitting mz estimator 
2:36:53.298587 INFO: calibration group: precursor, fitting rt estimator 
2:36:53.348366 INFO: calibration group: fragment, fitting mz estimator 
2:36:53.552429 INFO: calibration group: precursor, predicting mz
2:36:53.575303 INFO: calibration group: precursor, predicting rt
2:36:53.693226 INFO: calibration group: fragment, predicting mz
2:36:53.878986 INFO: === checking if optimization conditions were reached ===
2:36:53.879493 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2:36:53.882753 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 67.2152.
2:36:53.882890 INFO: ==============================================
2:36:53.883090 INFO: Starting optimization step 6.
2:36:53.883190 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:36:53.883307 PROGRESS: Extracting batch of 110685 precursors
2:36:53.939047 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:36:53.939230 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:36:53.939282 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
2:36:53.939318 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:36:53.939670 INFO: Starting candidate selection
2:36:58.094833 INFO: Starting candidate scoring
2:37:00.152404 INFO: Finished candidate processing
2:37:00.152804 INFO: Collecting candidate features
2:37:00.808401 WARNING: intensity_correlation has 62 NaNs ( 0.03 % out of 215891)
2:37:00.821591 INFO: Collecting fragment features
2:37:01.013048 INFO: Finished candidate scoring
2:37:01.579937 PROGRESS: === Extracted 215891 precursors and 1384624 fragments ===
2:37:01.580506 INFO: performing precursor FDR with 47 features
2:37:01.580548 INFO: Decoy channel: -1
2:37:01.580573 INFO: Competetive: True
2:37:01.726766 INFO: Setting torch num_threads to 2 for FDR classification task
2:37:01.813945 WARNING: dropped 29 target PSMs due to missing features
2:37:01.814187 WARNING: dropped 33 decoy PSMs due to missing features
2:37:06.669513 INFO: Test AUC: 0.554
2:37:06.669746 INFO: Train AUC: 0.588
2:37:06.669783 INFO: AUC difference: 5.85%
2:37:06.669809 WARNING: AUC difference > 5%. This may indicate overfitting.
2:37:06.799742 INFO: Resetting torch num_threads to 100
2:37:06.812701 INFO: === FDR correction performed with classifier version 7 ===
2:37:06.814556 PROGRESS: ============================= Precursor FDR =============================
2:37:06.814782 PROGRESS: Total precursors accumulated: 535
2:37:06.814856 PROGRESS: Target precursors: 486 (90.84%)
2:37:06.814913 PROGRESS: Decoy precursors: 49 (9.16%)
2:37:06.814960 PROGRESS: 
2:37:06.815006 PROGRESS: Precursor Summary:
2:37:06.817368 PROGRESS: Channel   0:	 0.05 FDR:   415; 0.01 FDR:   329; 0.001 FDR:   240
2:37:06.817623 PROGRESS: 
2:37:06.817689 PROGRESS: Protein Summary:
2:37:06.819800 PROGRESS: Channel   0:	 0.05 FDR:   402; 0.01 FDR:   317; 0.001 FDR:   233
2:37:06.820007 PROGRESS: =========================================================================
2:37:06.832461 INFO: fragments_df_filtered: 2839
2:37:07.200699 INFO: calibration group: precursor, fitting mz estimator 
2:37:07.312212 INFO: calibration group: precursor, fitting rt estimator 
2:37:07.406363 INFO: calibration group: fragment, fitting mz estimator 
2:37:07.672040 INFO: calibration group: precursor, predicting mz
2:37:07.690171 INFO: calibration group: precursor, predicting rt
2:37:07.772994 INFO: calibration group: fragment, predicting mz
2:37:07.962445 INFO: === checking if optimization conditions were reached ===
2:37:07.963795 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
2:37:07.968007 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 68.9085.
2:37:07.968505 INFO: ==============================================
2:37:07.968914 INFO: Starting optimization step 7.
2:37:07.969353 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:37:07.969646 PROGRESS: Extracting batch of 110685 precursors
2:37:08.025864 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:37:08.026069 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:37:08.026155 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
2:37:08.026201 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:37:08.026694 INFO: Starting candidate selection
2:37:12.169085 INFO: Starting candidate scoring
2:37:14.238013 INFO: Finished candidate processing
2:37:14.238156 INFO: Collecting candidate features
2:37:14.866706 WARNING: intensity_correlation has 70 NaNs ( 0.03 % out of 215907)
2:37:14.879321 INFO: Collecting fragment features
2:37:15.038467 INFO: Finished candidate scoring
2:37:15.398726 PROGRESS: === Extracted 215907 precursors and 1385923 fragments ===
2:37:15.399279 INFO: performing precursor FDR with 47 features
2:37:15.399324 INFO: Decoy channel: -1
2:37:15.399361 INFO: Competetive: True
2:37:15.514976 INFO: Setting torch num_threads to 2 for FDR classification task
2:37:15.596473 WARNING: dropped 39 target PSMs due to missing features
2:37:15.596671 WARNING: dropped 31 decoy PSMs due to missing features
2:37:20.662295 INFO: Test AUC: 0.554
2:37:20.662565 INFO: Train AUC: 0.589
2:37:20.662599 INFO: AUC difference: 5.93%
2:37:20.662623 WARNING: AUC difference > 5%. This may indicate overfitting.
2:37:20.777935 INFO: Resetting torch num_threads to 100
2:37:20.790020 INFO: === FDR correction performed with classifier version 7 ===
2:37:20.791094 PROGRESS: ============================= Precursor FDR =============================
2:37:20.791207 PROGRESS: Total precursors accumulated: 556
2:37:20.791270 PROGRESS: Target precursors: 506 (91.01%)
2:37:20.791323 PROGRESS: Decoy precursors: 50 (8.99%)
2:37:20.791370 PROGRESS: 
2:37:20.791429 PROGRESS: Precursor Summary:
2:37:20.792516 PROGRESS: Channel   0:	 0.05 FDR:   430; 0.01 FDR:   305; 0.001 FDR:   268
2:37:20.792609 PROGRESS: 
2:37:20.792664 PROGRESS: Protein Summary:
2:37:20.793872 PROGRESS: Channel   0:	 0.05 FDR:   415; 0.01 FDR:   295; 0.001 FDR:   260
2:37:20.793973 PROGRESS: =========================================================================
2:37:20.805556 INFO: fragments_df_filtered: 2693
2:37:21.214522 INFO: calibration group: precursor, fitting mz estimator 
2:37:21.258459 INFO: calibration group: precursor, fitting rt estimator 
2:37:21.298037 INFO: calibration group: fragment, fitting mz estimator 
2:37:21.433325 INFO: calibration group: precursor, predicting mz
2:37:21.449738 INFO: calibration group: precursor, predicting rt
2:37:21.537567 INFO: calibration group: fragment, predicting mz
2:37:21.727476 INFO: === checking if optimization conditions were reached ===
2:37:21.727889 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
2:37:21.730176 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 67.2152 found after 8 searches.
2:37:21.730247 INFO: ==============================================
2:37:21.730377 PROGRESS: Optimization finished for rt_error.
2:37:22.087949 INFO: calibration group: precursor, predicting mz
2:37:22.104561 INFO: calibration group: precursor, predicting rt
2:37:22.178034 INFO: calibration group: fragment, predicting mz
2:37:22.391375 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:37:22.391699 PROGRESS: ==============================================
2:37:22.391781 PROGRESS: ms2_error      : 8.0000
2:37:22.391850 PROGRESS: ms1_error      : 3.0000
2:37:22.391911 PROGRESS: rt_error       : 67.2152
2:37:22.391965 PROGRESS: ==============================================
2:37:22.392987 INFO: calibration group: precursor, predicting mz
2:37:23.988460 INFO: calibration group: precursor, predicting rt
2:37:31.038204 INFO: calibration group: fragment, predicting mz
2:37:52.446736 PROGRESS: Extracting batch of 10183864 precursors
2:37:55.794677 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:37:55.795472 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:37:55.795576 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
2:37:55.795602 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:37:55.796136 INFO: Starting candidate selection
2:43:36.092691 INFO: Applying score cutoff of 13.144169914245605
2:43:36.763772 INFO: Removed 1160787 precursors with score below cutoff
2:43:39.240613 INFO: Starting candidate scoring
2:46:04.495146 INFO: Finished candidate processing
2:46:04.495444 INFO: Collecting candidate features
2:47:54.391733 WARNING: intensity_correlation has 2768 NaNs ( 0.01 % out of 19077309)
2:47:54.416736 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 19077309)
2:47:55.397358 INFO: Collecting fragment features
2:49:10.961686 INFO: Finished candidate scoring
2:50:05.835831 INFO: === FDR correction performed with classifier version 14 ===
2:50:06.119391 INFO: performing precursor FDR with 47 features
2:50:06.119600 INFO: Decoy channel: -1
2:50:06.119648 INFO: Competetive: True
2:50:18.619463 INFO: Setting torch num_threads to 2 for FDR classification task
2:50:25.194402 WARNING: dropped 1434 target PSMs due to missing features
2:50:25.194672 WARNING: dropped 1334 decoy PSMs due to missing features
2:58:12.571951 INFO: Test AUC: 0.569
2:58:12.572175 INFO: Train AUC: 0.578
2:58:12.572217 INFO: AUC difference: 1.50%
2:58:13.789038 INFO: Resetting torch num_threads to 100
2:58:14.143057 INFO: Removing fragments below FDR threshold
2:58:15.151481 PROGRESS: ============================= Precursor FDR =============================
2:58:15.151961 PROGRESS: Total precursors accumulated: 30,365
2:58:15.152033 PROGRESS: Target precursors: 30,065 (99.01%)
2:58:15.152105 PROGRESS: Decoy precursors: 300 (0.99%)
2:58:15.152156 PROGRESS: 
2:58:15.152204 PROGRESS: Precursor Summary:
2:58:15.164894 PROGRESS: Channel   0:	 0.05 FDR: 30,065; 0.01 FDR: 30,065; 0.001 FDR: 20,602
2:58:15.165220 PROGRESS: 
2:58:15.165283 PROGRESS: Protein Summary:
2:58:15.182466 PROGRESS: Channel   0:	 0.05 FDR: 8,132; 0.01 FDR: 8,132; 0.001 FDR: 6,261
2:58:15.182796 PROGRESS: =========================================================================
2:58:16.517328 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:58:43.212085 PROGRESS: Processing search outputs
2:58:43.212379 PROGRESS: Performing protein grouping and FDR
2:58:43.212434 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:58:43.276315 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:58:43.305718 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:58:43.330322 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:58:43.358758 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:58:43.388826 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:58:43.414894 INFO: Building combined output
2:58:43.777493 INFO: Performing protein inference
2:58:43.921806 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
2:58:58.108559 INFO: Performing protein FDR
2:59:01.696033 INFO: Normalizing q-values using 10,522 targets and 1,141 decoys
2:59:01.705755 INFO: Test AUC: 0.888
2:59:01.705820 INFO: Train AUC: 0.890
2:59:01.705855 INFO: AUC difference: 0.31%
2:59:01.943226 PROGRESS: ================ Protein FDR =================
2:59:01.943372 PROGRESS: Unique protein groups in output
2:59:01.943403 PROGRESS:   1% protein FDR: 6,731
2:59:01.943424 PROGRESS: 
2:59:01.943442 PROGRESS: Unique precursor in output
2:59:01.943459 PROGRESS:   1% protein FDR: 39,524
2:59:01.943479 PROGRESS: ================================================
2:59:01.966578 PROGRESS: Building search statistics
2:59:02.010180 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
2:59:02.010404 INFO: Initializing OptimizationManager
2:59:02.010700 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
2:59:02.010775 INFO: Initializing CalibrationManager
2:59:02.011039 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
2:59:02.011118 INFO: Initializing RawFileManager
2:59:02.020456 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
2:59:02.020565 INFO: Initializing OptimizationManager
2:59:02.020757 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
2:59:02.020832 INFO: Initializing CalibrationManager
2:59:02.021033 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
2:59:02.021106 INFO: Initializing RawFileManager
2:59:02.029914 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
2:59:02.030662 INFO: Initializing OptimizationManager
2:59:02.030850 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
2:59:02.030919 INFO: Initializing CalibrationManager
2:59:02.031084 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
2:59:02.031165 INFO: Initializing RawFileManager
2:59:02.043912 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
2:59:02.044086 INFO: Initializing OptimizationManager
2:59:02.044279 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
2:59:02.044345 INFO: Initializing CalibrationManager
2:59:02.044529 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
2:59:02.044598 INFO: Initializing RawFileManager
2:59:02.057653 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
2:59:02.057816 INFO: Initializing OptimizationManager
2:59:02.058025 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
2:59:02.058096 INFO: Initializing CalibrationManager
2:59:02.058293 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
2:59:02.058364 INFO: Initializing RawFileManager
2:59:02.071074 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
2:59:02.071238 INFO: Initializing OptimizationManager
2:59:02.071428 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
2:59:02.071498 INFO: Initializing CalibrationManager
2:59:02.071674 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
2:59:02.071748 INFO: Initializing RawFileManager
2:59:02.073366 INFO: Writing stat output to disk
2:59:02.073449 INFO: Saving run_output_Astral/alphadia_1.10_MBRSetValues/library/stat.tsv to disk
2:59:02.077897 PROGRESS: Building internal statistics
2:59:02.078135 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
2:59:02.078177 INFO: Initializing TimingManager
2:59:02.078414 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
2:59:02.078456 INFO: Initializing TimingManager
2:59:02.078622 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
2:59:02.078659 INFO: Initializing TimingManager
2:59:02.078820 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
2:59:02.078857 INFO: Initializing TimingManager
2:59:02.079008 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
2:59:02.079045 INFO: Initializing TimingManager
2:59:02.079194 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_MBRSetValues/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
2:59:02.079230 INFO: Initializing TimingManager
2:59:02.079576 INFO: Writing internal output to disk
2:59:02.079620 INFO: Saving run_output_Astral/alphadia_1.10_MBRSetValues/library/internal.tsv to disk
2:59:02.080020 PROGRESS: Performing label free quantification
2:59:02.103808 INFO: Accumulating fragment data
2:59:02.103962 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:59:02.296368 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:59:02.522401 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:59:02.754541 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:59:03.156500 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:59:03.625117 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:59:04.165731 PROGRESS: Performing label free quantification on the precursor level
2:59:04.165893 INFO: Filtering fragments by quality
2:59:04.270577 INFO: Performing label-free quantification using directLFQ
2:59:05.265880 INFO: 39524 lfq-groups total
3:00:11.872789 INFO: using 100 processes
3:00:14.469822 INFO: lfq-object 0
3:00:14.497711 INFO: lfq-object 100
3:00:14.523256 INFO: lfq-object 200
3:00:14.552474 INFO: lfq-object 300
3:00:14.580838 INFO: lfq-object 400
3:00:14.628093 INFO: lfq-object 500
3:00:14.646490 INFO: lfq-object 600
3:00:14.671029 INFO: lfq-object 700
3:00:14.713500 INFO: lfq-object 800
3:00:14.746070 INFO: lfq-object 900
3:00:14.775374 INFO: lfq-object 1000
3:00:14.799713 INFO: lfq-object 1100
3:00:14.830874 INFO: lfq-object 1200
3:00:14.877101 INFO: lfq-object 1300
3:00:14.923496 INFO: lfq-object 1400
3:00:14.954526 INFO: lfq-object 1500
3:00:14.970051 INFO: lfq-object 1600
3:00:15.008318 INFO: lfq-object 1700
3:00:15.048780 INFO: lfq-object 1800
3:00:15.103573 INFO: lfq-object 1900
3:00:15.147176 INFO: lfq-object 2000
3:00:15.181682 INFO: lfq-object 2100
3:00:15.235677 INFO: lfq-object 2200
3:00:15.269377 INFO: lfq-object 2300
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3:00:15.362533 INFO: lfq-object 2500
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3:00:17.110331 INFO: lfq-object 6800
3:00:17.165663 INFO: lfq-object 6900
3:00:17.182745 INFO: lfq-object 7000
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3:00:18.621456 INFO: lfq-object 10000
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3:00:22.896916 INFO: lfq-object 14000
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3:00:23.009595 INFO: lfq-object 14200
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3:00:23.405893 INFO: lfq-object 15000
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3:00:25.012944 INFO: lfq-object 18800
3:00:25.081104 INFO: lfq-object 18900
3:00:25.121752 INFO: lfq-object 19000
3:00:25.190953 INFO: lfq-object 19100
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3:00:25.361606 INFO: lfq-object 19400
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3:00:29.940491 INFO: lfq-object 24600
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3:00:30.911842 INFO: lfq-object 26900
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3:00:31.014297 INFO: lfq-object 27100
3:00:31.070531 INFO: lfq-object 27200
3:00:31.074035 INFO: lfq-object 27300
3:00:31.125294 INFO: lfq-object 27400
3:00:31.178876 INFO: lfq-object 27500
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3:00:31.983963 INFO: lfq-object 29300
3:00:32.015056 INFO: lfq-object 29400
3:00:32.063700 INFO: lfq-object 29500
3:00:32.091609 INFO: lfq-object 29700
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3:00:32.132880 INFO: lfq-object 29600
3:00:32.161968 INFO: lfq-object 29900
3:00:32.206550 INFO: lfq-object 30000
3:00:32.246049 INFO: lfq-object 30100
3:00:32.267352 INFO: lfq-object 30200
3:00:32.311484 INFO: lfq-object 30300
3:00:32.342390 INFO: lfq-object 30400
3:00:32.399037 INFO: lfq-object 30500
3:00:32.426006 INFO: lfq-object 30600
3:00:32.459760 INFO: lfq-object 30700
3:00:32.523935 INFO: lfq-object 30800
3:00:32.571310 INFO: lfq-object 30900
3:00:32.628292 INFO: lfq-object 31000
3:00:32.664341 INFO: lfq-object 31100
3:00:32.722715 INFO: lfq-object 31200
3:00:32.745211 INFO: lfq-object 31300
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3:00:33.044207 INFO: lfq-object 31900
3:00:33.066014 INFO: lfq-object 32000
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3:00:33.368245 INFO: lfq-object 32600
3:00:33.402475 INFO: lfq-object 32700
3:00:33.437869 INFO: lfq-object 32800
3:00:33.471841 INFO: lfq-object 32900
3:00:33.522005 INFO: lfq-object 33000
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3:00:33.617681 INFO: lfq-object 33200
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3:00:34.526490 INFO: lfq-object 35300
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3:00:34.864049 INFO: lfq-object 36300
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3:00:34.912188 INFO: lfq-object 36500
3:00:34.956992 INFO: lfq-object 36600
3:00:34.980130 INFO: lfq-object 36700
3:00:35.021228 INFO: lfq-object 36800
3:00:35.088322 INFO: lfq-object 37000
3:00:35.088506 INFO: lfq-object 36900
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3:00:35.216099 INFO: lfq-object 37300
3:00:35.265025 INFO: lfq-object 37400
3:00:35.289201 INFO: lfq-object 37500
3:00:35.324829 INFO: lfq-object 37600
3:00:35.398516 INFO: lfq-object 37700
3:00:35.421476 INFO: lfq-object 37800
3:00:38.400537 INFO: lfq-object 37900
3:00:38.457236 INFO: lfq-object 38000
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3:00:38.593916 INFO: lfq-object 38400
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3:00:38.799269 INFO: lfq-object 38900
3:00:38.841396 INFO: lfq-object 39000
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3:00:38.937044 INFO: lfq-object 39200
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3:00:39.011952 INFO: lfq-object 39400
3:00:39.060016 INFO: lfq-object 39500
3:00:44.861236 INFO: Writing precursor output to disk
3:00:44.861561 INFO: Saving run_output_Astral/alphadia_1.10_MBRSetValues/library/precursor.matrix.tsv to disk
3:00:45.095573 PROGRESS: Performing label free quantification on the pg level
3:00:45.095686 INFO: Filtering fragments by quality
3:00:45.231156 INFO: Performing label-free quantification using directLFQ
3:00:45.349564 INFO: 6731 lfq-groups total
3:01:52.836611 INFO: using 100 processes
3:01:52.902158 INFO: lfq-object 0
3:01:52.973734 INFO: lfq-object 100
3:01:52.994123 INFO: lfq-object 200
3:01:53.060146 INFO: lfq-object 300
3:01:53.102317 INFO: lfq-object 400
3:01:53.135857 INFO: lfq-object 500
3:01:53.180346 INFO: lfq-object 600
3:01:53.225903 INFO: lfq-object 700
3:01:53.291223 INFO: lfq-object 800
3:01:53.399061 INFO: lfq-object 1000
3:01:53.447102 INFO: lfq-object 1100
3:01:53.481172 INFO: lfq-object 1200
3:01:53.481619 INFO: lfq-object 900
3:01:53.516276 INFO: lfq-object 1300
3:01:53.579712 INFO: lfq-object 1400
3:01:53.635646 INFO: lfq-object 1500
3:01:53.677373 INFO: lfq-object 1600
3:01:53.710993 INFO: lfq-object 1700
3:01:53.767805 INFO: lfq-object 1800
3:01:53.807143 INFO: lfq-object 1900
3:01:53.848094 INFO: lfq-object 2000
3:01:53.891989 INFO: lfq-object 2100
3:01:53.931713 INFO: lfq-object 2200
3:01:53.977803 INFO: lfq-object 2300
3:01:54.037527 INFO: lfq-object 2400
3:01:54.092350 INFO: lfq-object 2500
3:01:54.168345 INFO: lfq-object 2600
3:01:54.206255 INFO: lfq-object 2700
3:01:54.245473 INFO: lfq-object 2800
3:01:54.295742 INFO: lfq-object 2900
3:01:54.344577 INFO: lfq-object 3000
3:01:54.394832 INFO: lfq-object 3100
3:01:54.422935 INFO: lfq-object 3200
3:01:54.468462 INFO: lfq-object 3300
3:01:54.512701 INFO: lfq-object 3400
3:01:54.564743 INFO: lfq-object 3500
3:01:54.628111 INFO: lfq-object 3600
3:01:54.688150 INFO: lfq-object 3800
3:01:54.733836 INFO: lfq-object 3900
3:01:54.784898 INFO: lfq-object 4000
3:01:54.795472 INFO: lfq-object 3700
3:01:54.834113 INFO: lfq-object 4100
3:01:54.868302 INFO: lfq-object 4200
3:01:54.935228 INFO: lfq-object 4300
3:01:55.046364 INFO: lfq-object 4500
3:01:55.092399 INFO: lfq-object 4600
3:01:55.098791 INFO: lfq-object 4400
3:01:55.123970 INFO: lfq-object 4700
3:01:55.169107 INFO: lfq-object 4800
3:01:55.215639 INFO: lfq-object 4900
3:01:55.246479 INFO: lfq-object 5000
3:01:55.293301 INFO: lfq-object 5100
3:01:55.348419 INFO: lfq-object 5200
3:01:55.382138 INFO: lfq-object 5300
3:01:55.430240 INFO: lfq-object 5400
3:01:55.465708 INFO: lfq-object 5500
3:01:55.511797 INFO: lfq-object 5600
3:01:55.542924 INFO: lfq-object 5700
3:01:55.575720 INFO: lfq-object 5800
3:01:55.613665 INFO: lfq-object 5900
3:01:55.685750 INFO: lfq-object 6000
3:01:55.726248 INFO: lfq-object 6100
3:01:55.773399 INFO: lfq-object 6200
3:01:55.792668 INFO: lfq-object 6300
3:01:55.846617 INFO: lfq-object 6400
3:01:55.897269 INFO: lfq-object 6500
3:01:55.933319 INFO: lfq-object 6600
3:01:55.960722 INFO: lfq-object 6700
3:01:59.263247 INFO: Writing pg output to disk
3:01:59.263448 INFO: Saving run_output_Astral/alphadia_1.10_MBRSetValues/library/pg.matrix.tsv to disk
3:01:59.408107 INFO: Writing psm output to disk
3:01:59.408276 INFO: Saving run_output_Astral/alphadia_1.10_MBRSetValues/library/precursors.tsv to disk
3:02:09.481075 PROGRESS: Building spectral library
3:02:09.524517 INFO: Building MBR spectral library
3:02:09.524659 INFO: Running MbrLibraryBuilder
3:02:11.596532 INFO: MBR spectral library contains 39,524 precursors, 6,731 proteins
3:02:11.596692 INFO: Writing MBR spectral library to disk
3:02:12.446702 PROGRESS: =================== Search Finished ===================
3:02:13.676430 INFO: Running step 'mbr'
3:02:13.679582 INFO: Extracted extra_config from previous step: defaultdict(<class 'dict'>, {'search': {'target_ms1_tolerance': 3.0, 'target_ms2_tolerance': 8.0}})
3:02:13.679773 INFO: loading config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
3:02:13.691359 INFO: loading additional config provided via CLI
3:02:13.691452 INFO: loading additional config provided via CLI parameters
3:02:13.691751 INFO: Updating config with 'user defined'
3:02:13.691839 INFO: Updating config with 'user defined (cli)'
3:02:13.691862 INFO: Updating config with 'multistep search'
3:02:13.691905 INFO: ├──version: 1
3:02:13.691931 INFO: ├──workflow_name: None
3:02:13.691957 INFO: [32;20m├──output_directory: run_output_Astral/alphadia_1.10_MBRSetValues [multistep search, default: None][0m
3:02:13.691982 INFO: [32;20m├──library_path: run_output_Astral/alphadia_1.10_MBRSetValues/library/speclib.mbr.hdf [multistep search, default: None][0m
3:02:13.692003 INFO: ├──raw_paths:
3:02:13.692023 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
3:02:13.692042 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
3:02:13.692060 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
3:02:13.692079 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
3:02:13.692097 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
3:02:13.692115 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
3:02:13.692133 INFO: ├──fasta_paths:
3:02:13.692153 INFO: ├──quant_directory: None
3:02:13.692173 INFO: ├──general
3:02:13.692192 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
3:02:13.692212 INFO: │   ├──transfer_step_enabled: False
3:02:13.692230 INFO: │   ├──mbr_step_enabled: True
3:02:13.692249 INFO: │   ├──reuse_calibration: False
3:02:13.692270 INFO: │   ├──reuse_quant: False
3:02:13.692290 INFO: │   ├──astral_ms1: False
3:02:13.692309 INFO: │   ├──log_level: INFO
3:02:13.692328 INFO: │   ├──mmap_detector_events: False
3:02:13.692361 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
3:02:13.692380 INFO: │   ├──save_library: True
3:02:13.692399 INFO: │   └──save_mbr_library: True
3:02:13.692416 INFO: ├──library_loading
3:02:13.692437 INFO: │   └──rt_heuristic: 180
3:02:13.692454 INFO: ├──library_prediction
3:02:13.692473 INFO: │   ├──enabled: False
3:02:13.692491 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
3:02:13.692509 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
3:02:13.692527 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
3:02:13.692546 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
3:02:13.692564 INFO: │   ├──missed_cleavages: 1
3:02:13.692582 INFO: │   ├──precursor_len:
3:02:13.692601 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
3:02:13.692619 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
3:02:13.692637 INFO: │   ├──precursor_charge:
3:02:13.692655 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
3:02:13.692672 INFO: │   │   [32;20m- 4[0m
3:02:13.692690 INFO: │   ├──precursor_mz:
3:02:13.692715 INFO: │   │   [32;20m- 400[0m
3:02:13.692733 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
3:02:13.692750 INFO: │   ├──fragment_mz:
3:02:13.692768 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
3:02:13.692787 INFO: │   │   [32;20m- 2000[0m
3:02:13.692806 INFO: │   ├──nce: 25
3:02:13.692824 INFO: │   ├──fragment_types:
3:02:13.692842 INFO: │   │   [32;20m- b[0m
3:02:13.692859 INFO: │   │   [32;20m- y[0m
3:02:13.692878 INFO: │   ├──max_fragment_charge: 2
3:02:13.692896 INFO: │   [32;20m├──instrument: Astral [user defined, default: Lumos][0m
3:02:13.692914 INFO: │   ├──peptdeep_model_path: None
3:02:13.692932 INFO: │   └──peptdeep_model_type: generic
3:02:13.692950 INFO: ├──custom_modifications:
3:02:13.692970 INFO: │   ├──name: Dimethyl:d12@K
3:02:13.692989 INFO: │   └──composition: H(-2)2H(8)13C(2)
3:02:13.693008 INFO: │   ├──name: Dimethyl:d12@Any_N-term
3:02:13.693026 INFO: │   └──composition: H(-2)2H(8)13C(2)
3:02:13.693044 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
3:02:13.693061 INFO: │   └──composition: H(-2)2H(8)13C(2)
3:02:13.693079 INFO: │   ├──name: mTRAQ:d12@K
3:02:13.693097 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
3:02:13.693116 INFO: │   ├──name: mTRAQ:d12@Any_N-term
3:02:13.693133 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
3:02:13.693152 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
3:02:13.693170 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
3:02:13.693187 INFO: │   ├──name: Label:13C(12)@K
3:02:13.693204 INFO: │   └──composition: C(12)
3:02:13.693221 INFO: ├──search
3:02:13.693244 INFO: │   [32;20m├──target_ms1_tolerance: 3.0 [multistep search, default: 5][0m
3:02:13.693265 INFO: │   [32;20m├──target_ms2_tolerance: 8.0 [multistep search, default: 10][0m
3:02:13.693284 INFO: │   ├──target_rt_tolerance: 0
3:02:13.693302 INFO: │   ├──target_mobility_tolerance: 0
3:02:13.693321 INFO: │   ├──quant_window: 3
3:02:13.693339 INFO: │   [32;20m├──target_num_candidates: 2 [user defined, default: 3][0m
3:02:13.693357 INFO: │   ├──channel_filter: 
3:02:13.693375 INFO: │   ├──exclude_shared_ions: True
3:02:13.693393 INFO: │   ├──compete_for_fragments: True
3:02:13.693410 INFO: │   ├──quant_all: True
3:02:13.693429 INFO: │   ├──top_k_fragments: 12
3:02:13.693447 INFO: │   └──experimental_xic: True
3:02:13.693464 INFO: ├──calibration
3:02:13.693483 INFO: │   ├──batch_size: 8000
3:02:13.693503 INFO: │   ├──optimization_lock_target: 200
3:02:13.693521 INFO: │   ├──max_steps: 20
3:02:13.693545 INFO: │   ├──min_steps: 2
3:02:13.693564 INFO: │   ├──max_skips: 1
3:02:13.693583 INFO: │   ├──norm_rt_mode: linear
3:02:13.693601 INFO: │   ├──max_fragments: 5000
3:02:13.693624 INFO: │   └──min_correlation: 0.7
3:02:13.693641 INFO: ├──search_initial
3:02:13.693659 INFO: │   ├──initial_num_candidates: 1
3:02:13.693678 INFO: │   ├──initial_ms1_tolerance: 30
3:02:13.693696 INFO: │   ├──initial_ms2_tolerance: 30
3:02:13.693714 INFO: │   ├──initial_mobility_tolerance: 0.1
3:02:13.693733 INFO: │   └──initial_rt_tolerance: 0.5
3:02:13.693750 INFO: ├──selection_config
3:02:13.693769 INFO: │   ├──peak_len_rt: 10.0
3:02:13.693787 INFO: │   ├──sigma_scale_rt: 0.5
3:02:13.693805 INFO: │   ├──peak_len_mobility: 0.01
3:02:13.693824 INFO: │   ├──sigma_scale_mobility: 1.0
3:02:13.693843 INFO: │   ├──top_k_precursors: 3
3:02:13.693861 INFO: │   ├──kernel_size: 30
3:02:13.693879 INFO: │   ├──f_mobility: 1.0
3:02:13.693897 INFO: │   ├──f_rt: 0.99
3:02:13.693915 INFO: │   ├──center_fraction: 0.5
3:02:13.693933 INFO: │   ├──min_size_mobility: 8
3:02:13.693951 INFO: │   ├──min_size_rt: 3
3:02:13.693968 INFO: │   ├──max_size_mobility: 20
3:02:13.693986 INFO: │   ├──max_size_rt: 15
3:02:13.694004 INFO: │   ├──group_channels: False
3:02:13.694022 INFO: │   ├──use_weighted_score: True
3:02:13.694040 INFO: │   ├──join_close_candidates: False
3:02:13.694058 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
3:02:13.694076 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
3:02:13.694094 INFO: ├──scoring_config
3:02:13.694113 INFO: │   ├──score_grouped: False
3:02:13.694130 INFO: │   ├──top_k_isotopes: 3
3:02:13.694148 INFO: │   ├──reference_channel: -1
3:02:13.694165 INFO: │   ├──precursor_mz_tolerance: 10
3:02:13.694183 INFO: │   └──fragment_mz_tolerance: 15
3:02:13.694201 INFO: ├──library_multiplexing
3:02:13.694219 INFO: │   ├──enabled: False
3:02:13.694237 INFO: │   ├──input_channel: 0
3:02:13.694255 INFO: │   └──multiplex_mapping:
3:02:13.694273 INFO: ├──multiplexing
3:02:13.694290 INFO: │   ├──enabled: False
3:02:13.694308 INFO: │   ├──target_channels: 4,8
3:02:13.694325 INFO: │   ├──decoy_channel: 12
3:02:13.694343 INFO: │   ├──reference_channel: 0
3:02:13.694361 INFO: │   └──competetive_scoring: True
3:02:13.694378 INFO: ├──fdr
3:02:13.694396 INFO: │   ├──fdr: 0.01
3:02:13.694414 INFO: │   ├──group_level: proteins
3:02:13.694432 INFO: │   [32;20m├──inference_strategy: library [multistep search, default: heuristic][0m
3:02:13.694451 INFO: │   ├──competetive_scoring: True
3:02:13.694468 INFO: │   ├──keep_decoys: False
3:02:13.694485 INFO: │   ├──channel_wise_fdr: False
3:02:13.694503 INFO: │   ├──enable_two_step_classifier: False
3:02:13.694521 INFO: │   ├──two_step_classifier_max_iterations: 5
3:02:13.694540 INFO: │   └──enable_nn_hyperparameter_tuning: False
3:02:13.694557 INFO: ├──search_output
3:02:13.694576 INFO: │   ├──file_format: tsv
3:02:13.694594 INFO: │   ├──peptide_level_lfq: False
3:02:13.694612 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
3:02:13.694632 INFO: │   ├──min_k_fragments: 12
3:02:13.694649 INFO: │   ├──min_correlation: 0.9
3:02:13.694668 INFO: │   ├──num_samples_quadratic: 50
3:02:13.694686 INFO: │   ├──min_nonnan: 3
3:02:13.694704 INFO: │   ├──normalize_lfq: True
3:02:13.694722 INFO: │   └──save_fragment_quant_matrix: False
3:02:13.694740 INFO: ├──optimization
3:02:13.694759 INFO: │   ├──order_of_optimization: None
3:02:13.694776 INFO: │   ├──ms2_error
3:02:13.694796 INFO: │   │   ├──targeted_update_percentile_range: 0.95
3:02:13.694819 INFO: │   │   ├──targeted_update_factor: 1.0
3:02:13.694839 INFO: │   │   ├──automatic_update_percentile_range: 0.99
3:02:13.694858 INFO: │   │   ├──automatic_update_factor: 1.1
3:02:13.694876 INFO: │   │   ├──try_narrower_values: True
3:02:13.694895 INFO: │   │   ├──maximal_decrease: 0.5
3:02:13.694912 INFO: │   │   ├──favour_narrower_optimum: False
3:02:13.694931 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
3:02:13.694948 INFO: │   ├──ms1_error
3:02:13.694968 INFO: │   │   ├──targeted_update_percentile_range: 0.95
3:02:13.694986 INFO: │   │   ├──targeted_update_factor: 1.0
3:02:13.695005 INFO: │   │   ├──automatic_update_percentile_range: 0.99
3:02:13.695023 INFO: │   │   ├──automatic_update_factor: 1.1
3:02:13.695041 INFO: │   │   ├──try_narrower_values: False
3:02:13.695060 INFO: │   │   ├──maximal_decrease: 0.2
3:02:13.695078 INFO: │   │   ├──favour_narrower_optimum: False
3:02:13.695096 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
3:02:13.695114 INFO: │   ├──mobility_error
3:02:13.695133 INFO: │   │   ├──targeted_update_percentile_range: 0.95
3:02:13.695151 INFO: │   │   ├──targeted_update_factor: 1.0
3:02:13.695169 INFO: │   │   ├──automatic_update_percentile_range: 0.99
3:02:13.695187 INFO: │   │   ├──automatic_update_factor: 1.1
3:02:13.695205 INFO: │   │   ├──try_narrower_values: False
3:02:13.695224 INFO: │   │   ├──maximal_decrease: 0.2
3:02:13.695241 INFO: │   │   ├──favour_narrower_optimum: False
3:02:13.695260 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
3:02:13.695277 INFO: │   └──rt_error
3:02:13.695295 INFO: │       ├──targeted_update_percentile_range: 0.95
3:02:13.695313 INFO: │       ├──targeted_update_factor: 1.0
3:02:13.695331 INFO: │       ├──automatic_update_percentile_range: 0.99
3:02:13.695350 INFO: │       ├──automatic_update_factor: 1.1
3:02:13.695368 INFO: │       ├──try_narrower_values: True
3:02:13.695386 INFO: │       ├──maximal_decrease: 0.2
3:02:13.695405 INFO: │       ├──favour_narrower_optimum: True
3:02:13.695423 INFO: │       └──maximum_decrease_from_maximum: 0.1
3:02:13.695441 INFO: ├──optimization_manager
3:02:13.695459 INFO: │   ├──fwhm_rt: 5
3:02:13.695477 INFO: │   ├──fwhm_mobility: 0.01
3:02:13.695496 INFO: │   └──score_cutoff: 0
3:02:13.695513 INFO: ├──transfer_library
3:02:13.695531 INFO: │   ├──enabled: False
3:02:13.695548 INFO: │   ├──fragment_types:
3:02:13.695566 INFO: │   │   [32;20m- b[0m
3:02:13.695583 INFO: │   │   [32;20m- y[0m
3:02:13.695600 INFO: │   ├──max_charge: 2
3:02:13.695617 INFO: │   ├──top_k_samples: 3
3:02:13.695635 INFO: │   ├──norm_delta_max: True
3:02:13.695652 INFO: │   ├──precursor_correlation_cutoff: 0.5
3:02:13.695670 INFO: │   └──fragment_correlation_ratio: 0.75
3:02:13.695688 INFO: └──transfer_learning
3:02:13.695706 INFO:     ├──enabled: False
3:02:13.695724 INFO:     ├──batch_size: 2000
3:02:13.695742 INFO:     ├──max_lr: 0.0001
3:02:13.695761 INFO:     ├──train_fraction: 0.7
3:02:13.695779 INFO:     ├──validation_fraction: 0.2
3:02:13.695797 INFO:     ├──test_fraction: 0.1
3:02:13.695815 INFO:     ├──test_interval: 1
3:02:13.695833 INFO:     ├──lr_patience: 3
3:02:13.695851 INFO:     ├──epochs: 51
3:02:13.695868 INFO:     ├──warmup_epochs: 5
3:02:13.695887 INFO:     ├──nce: 25
3:02:13.695904 INFO:     [32;20m└──instrument: Astral [user defined, default: Lumos][0m
3:02:13.701707 INFO: Registering 7 custom modifications
3:02:13.719077 INFO: Running DynamicLoader
3:02:13.719235 INFO: Loading .hdf library from run_output_Astral/alphadia_1.10_MBRSetValues/library/speclib.mbr.hdf
3:02:13.969225 INFO: Running PrecursorInitializer
3:02:13.969398 INFO: Running AnnotateFasta
3:02:13.969728 INFO: Dropping decoys from input library before annotation
3:02:13.978094 INFO: Running IsotopeGenerator
3:02:13.978356 WARNING: Input library already contains isotope information. Skipping isotope generation. 
 Please note that isotope generation outside of alphabase is not supported.
3:02:13.978400 INFO: Running RTNormalization
3:02:13.981064 INFO: Saving library to run_output_Astral/alphadia_1.10_MBRSetValues/speclib.hdf
3:02:14.347793 INFO: Running DecoyGenerator
3:02:33.728346 INFO: Running FlattenLibrary
3:02:34.569681 INFO: Running InitFlatColumns
3:02:34.575759 INFO: Running LogFlatLibraryStats
3:02:34.575857 INFO: ============ Library Stats ============
3:02:34.575888 INFO: Number of precursors: 79,043
3:02:34.595965 INFO: 	thereof targets:39,524
3:02:34.596115 INFO: 	thereof decoys: 39,519
3:02:34.597021 INFO: Number of elution groups: 39,524
3:02:34.597064 INFO: 	average size: 2.00
3:02:34.599897 INFO: Number of proteins: 6,731
3:02:34.600325 INFO: Number of channels: 1 ([0])
3:02:34.600408 INFO: Isotopes Distribution for 4 isotopes
3:02:34.600435 INFO: =======================================
3:02:34.600551 INFO: Searching 6 files:
3:02:34.600578 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
3:02:34.600597 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
3:02:34.600616 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
3:02:34.600633 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
3:02:34.600652 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
3:02:34.600670 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
3:02:34.600688 INFO: Using 0 fasta files:
3:02:34.600712 INFO: Using library: run_output_Astral/alphadia_1.10_MBRSetValues/library/speclib.mbr.hdf
3:02:34.600732 INFO: Saving output to: run_output_Astral/alphadia_1.10_MBRSetValues
3:02:34.600761 PROGRESS: Starting Search Workflows
3:02:34.600811 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:02:34.600860 INFO: Quantification results path: run_output_Astral/alphadia_1.10_MBRSetValues/quant
3:02:34.600933 INFO: Creating parent folder for workflows at run_output_Astral/alphadia_1.10_MBRSetValues/quant
3:02:34.601634 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1 at run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:02:34.602047 INFO: Initializing RawFileManager
3:03:05.357306 INFO: Determining DIA cycle
3:03:05.373609 INFO: Found cycle with start 0.00 min and length 303.
3:03:05.662357 INFO: RT (min)            : 0.0 - 26.9
3:03:05.662563 INFO: RT duration (sec)   : 1611.2
3:03:05.662593 INFO: RT duration (min)   : 26.9
3:03:05.662619 INFO: Cycle len (scans)   : 303
3:03:05.662641 INFO: Cycle len (sec)     : 1.65
3:03:05.662662 INFO: Number of cycles    : 977
3:03:05.662684 INFO: MS2 range (m/z)     : 380.4 - 980.7
3:03:05.676042 INFO: Initializing CalibrationManager
3:03:05.676387 INFO: Loading calibration config
3:03:05.676826 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'}]
3:03:05.676951 INFO: Calibration group :fragment, found 1 estimator(s)
3:03:05.677034 INFO: Calibration group :precursor, found 3 estimator(s)
3:03:05.677099 INFO: Disabling ion mobility calibration
3:03:05.677127 INFO: removed mobility estimator from group precursor
3:03:05.677264 INFO: Initializing OptimizationManager
3:03:05.677378 INFO: initial parameter: ms1_error = 30
3:03:05.677446 INFO: initial parameter: ms2_error = 30
3:03:05.677494 INFO: initial parameter: rt_error = 805.5992431640625
3:03:05.677539 INFO: initial parameter: mobility_error = 0.1
3:03:05.677581 INFO: initial parameter: column_type = library
3:03:05.677622 INFO: initial parameter: num_candidates = 1
3:03:05.677661 INFO: initial parameter: classifier_version = -1
3:03:05.677701 INFO: initial parameter: fwhm_rt = 5
3:03:05.677739 INFO: initial parameter: fwhm_mobility = 0.01
3:03:05.677777 INFO: initial parameter: score_cutoff = 0
3:03:05.677836 INFO: Initializing TimingManager
3:03:05.677889 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:03:05.677984 INFO: FDRManager not loaded from disk.
3:03:05.678005 INFO: Initializing FDRManager
3:03:05.678039 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
3:03:05.698086 PROGRESS: 39,524 target precursors potentially observable (0 removed)
3:03:05.722001 PROGRESS: Starting initial search for precursors.
3:03:05.741174 INFO: Starting optimization step 0.
3:03:05.741496 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:03:05.741565 PROGRESS: Extracting batch of 15945 precursors
3:03:05.748027 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:03:05.748218 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:03:05.748266 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:03:05.748291 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:03:05.748782 INFO: Starting candidate selection
3:03:06.828753 INFO: Starting candidate scoring
3:03:06.926153 INFO: Finished candidate processing
3:03:06.926273 INFO: Collecting candidate features
3:03:06.962642 INFO: Collecting fragment features
3:03:06.975147 INFO: Finished candidate scoring
3:03:06.985376 PROGRESS: === Extracted 15945 precursors and 171336 fragments ===
3:03:06.985785 INFO: performing precursor FDR with 47 features
3:03:06.985824 INFO: Decoy channel: -1
3:03:06.985850 INFO: Competetive: True
3:03:06.992872 INFO: Setting torch num_threads to 2 for FDR classification task
3:03:07.168462 INFO: Test AUC: 0.595
3:03:07.168597 INFO: Train AUC: 0.598
3:03:07.168628 INFO: AUC difference: 0.59%
3:03:07.272831 INFO: Resetting torch num_threads to 100
3:03:07.274584 INFO: === FDR correction performed with classifier version -1 ===
3:03:07.275939 PROGRESS: ============================= Precursor FDR =============================
3:03:07.276266 PROGRESS: Total precursors accumulated: 1,164
3:03:07.276544 PROGRESS: Target precursors: 1,074 (92.27%)
3:03:07.276807 PROGRESS: Decoy precursors: 90 (7.73%)
3:03:07.277072 PROGRESS: 
3:03:07.277322 PROGRESS: Precursor Summary:
3:03:07.279331 PROGRESS: Channel   0:	 0.05 FDR:   964; 0.01 FDR:   722; 0.001 FDR:   391
3:03:07.279779 PROGRESS: 
3:03:07.280046 PROGRESS: Protein Summary:
3:03:07.282231 PROGRESS: Channel   0:	 0.05 FDR:   794; 0.01 FDR:   609; 0.001 FDR:   342
3:03:07.282593 PROGRESS: =========================================================================
3:03:07.288203 INFO: fragments_df_filtered: 5000
3:03:07.302013 INFO: calibration group: precursor, fitting mz estimator 
3:03:07.368724 INFO: calibration group: precursor, fitting rt estimator 
3:03:07.427587 INFO: calibration group: fragment, fitting mz estimator 
3:03:07.847447 INFO: calibration group: precursor, predicting mz
3:03:07.850433 INFO: calibration group: precursor, predicting rt
3:03:07.859928 INFO: calibration group: fragment, predicting mz
3:03:07.885854 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3:03:07.886217 INFO: Starting optimization step 1.
3:03:07.886294 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:03:07.886356 PROGRESS: Extracting batch of 15945 precursors
3:03:07.898756 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:03:07.898863 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:03:07.898902 INFO: FWHM in RT is 2.96 seconds, sigma is 0.38
3:03:07.898929 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:03:07.899180 INFO: Starting candidate selection
3:03:08.851292 INFO: Starting candidate scoring
3:03:09.052001 INFO: Finished candidate processing
3:03:09.052156 INFO: Collecting candidate features
3:03:09.118482 INFO: Collecting fragment features
3:03:09.141594 INFO: Finished candidate scoring
3:03:09.158012 PROGRESS: === Extracted 31890 precursors and 339991 fragments ===
3:03:09.158431 INFO: performing precursor FDR with 47 features
3:03:09.158470 INFO: Decoy channel: -1
3:03:09.158494 INFO: Competetive: True
3:03:09.169255 INFO: Setting torch num_threads to 2 for FDR classification task
3:03:09.663449 INFO: Test AUC: 0.583
3:03:09.663604 INFO: Train AUC: 0.593
3:03:09.663636 INFO: AUC difference: 1.68%
3:03:09.752200 INFO: Resetting torch num_threads to 100
3:03:09.753662 INFO: === FDR correction performed with classifier version 0 ===
3:03:09.755133 PROGRESS: ============================= Precursor FDR =============================
3:03:09.755255 PROGRESS: Total precursors accumulated: 2,224
3:03:09.755315 PROGRESS: Target precursors: 2,057 (92.49%)
3:03:09.755366 PROGRESS: Decoy precursors: 167 (7.51%)
3:03:09.755412 PROGRESS: 
3:03:09.755458 PROGRESS: Precursor Summary:
3:03:09.756973 PROGRESS: Channel   0:	 0.05 FDR: 1,847; 0.01 FDR: 1,376; 0.001 FDR:   521
3:03:09.757081 PROGRESS: 
3:03:09.757139 PROGRESS: Protein Summary:
3:03:09.758928 PROGRESS: Channel   0:	 0.05 FDR: 1,396; 0.01 FDR: 1,087; 0.001 FDR:   464
3:03:09.759043 PROGRESS: =========================================================================
3:03:09.768456 INFO: fragments_df_filtered: 5000
3:03:09.781333 INFO: calibration group: precursor, fitting mz estimator 
3:03:09.937211 INFO: calibration group: precursor, fitting rt estimator 
3:03:10.033619 INFO: calibration group: fragment, fitting mz estimator 
3:03:10.455598 INFO: calibration group: precursor, predicting mz
3:03:10.458664 INFO: calibration group: precursor, predicting rt
3:03:10.469350 INFO: calibration group: fragment, predicting mz
3:03:10.577111 INFO: === checking if optimization conditions were reached ===
3:03:10.579845 PROGRESS: ❌ ms2_error      : 15.3224 > 8.0000 or insufficient steps taken.
3:03:10.581205 PROGRESS: ❌ ms1_error      : 14.2424 > 3.0000 or insufficient steps taken.
3:03:10.581263 INFO: ==============================================
3:03:10.581386 INFO: Starting optimization step 2.
3:03:10.581459 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:03:10.581524 PROGRESS: Extracting batch of 15945 precursors
3:03:10.589803 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:03:10.589878 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:03:10.589916 INFO: FWHM in RT is 2.89 seconds, sigma is 0.37
3:03:10.589943 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:03:10.590155 INFO: Starting candidate selection
3:03:12.711173 INFO: Starting candidate scoring
3:03:12.898230 INFO: Finished candidate processing
3:03:12.898341 INFO: Collecting candidate features
3:03:12.962461 INFO: Collecting fragment features
3:03:12.984639 INFO: Finished candidate scoring
3:03:13.002627 PROGRESS: === Extracted 31890 precursors and 316123 fragments ===
3:03:13.003122 INFO: performing precursor FDR with 47 features
3:03:13.003167 INFO: Decoy channel: -1
3:03:13.003191 INFO: Competetive: True
3:03:13.016213 INFO: Setting torch num_threads to 2 for FDR classification task
3:03:13.508870 INFO: Test AUC: 0.611
3:03:13.509023 INFO: Train AUC: 0.614
3:03:13.509057 INFO: AUC difference: 0.45%
3:03:13.597557 INFO: Resetting torch num_threads to 100
3:03:13.598941 INFO: === FDR correction performed with classifier version 1 ===
3:03:13.600090 PROGRESS: ============================= Precursor FDR =============================
3:03:13.600207 PROGRESS: Total precursors accumulated: 3,464
3:03:13.600270 PROGRESS: Target precursors: 3,237 (93.45%)
3:03:13.600319 PROGRESS: Decoy precursors: 227 (6.55%)
3:03:13.600363 PROGRESS: 
3:03:13.600406 PROGRESS: Precursor Summary:
3:03:13.602218 PROGRESS: Channel   0:	 0.05 FDR: 3,078; 0.01 FDR: 2,560; 0.001 FDR: 1,479
3:03:13.602342 PROGRESS: 
3:03:13.602402 PROGRESS: Protein Summary:
3:03:13.604698 PROGRESS: Channel   0:	 0.05 FDR: 2,133; 0.01 FDR: 1,838; 0.001 FDR: 1,159
3:03:13.604815 PROGRESS: =========================================================================
3:03:13.616514 INFO: fragments_df_filtered: 5000
3:03:13.629357 INFO: calibration group: precursor, fitting mz estimator 
3:03:13.775588 INFO: calibration group: precursor, fitting rt estimator 
3:03:13.965521 INFO: calibration group: fragment, fitting mz estimator 
3:03:14.383621 INFO: calibration group: precursor, predicting mz
3:03:14.386844 INFO: calibration group: precursor, predicting rt
3:03:14.396281 INFO: calibration group: fragment, predicting mz
3:03:14.442201 INFO: === checking if optimization conditions were reached ===
3:03:14.460202 PROGRESS: ❌ ms2_error      : 11.0092 > 8.0000 or insufficient steps taken.
3:03:14.462152 PROGRESS: ❌ ms1_error      : 6.6986 > 3.0000 or insufficient steps taken.
3:03:14.462222 INFO: ==============================================
3:03:14.462448 INFO: Starting optimization step 3.
3:03:14.462525 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:03:14.462595 PROGRESS: Extracting batch of 15945 precursors
3:03:14.467803 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:03:14.467869 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:03:14.467908 INFO: FWHM in RT is 2.67 seconds, sigma is 0.34
3:03:14.467938 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:03:14.468157 INFO: Starting candidate selection
3:03:15.418777 INFO: Starting candidate scoring
3:03:15.633935 INFO: Finished candidate processing
3:03:15.634102 INFO: Collecting candidate features
3:03:15.690697 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 31888)
3:03:15.695136 INFO: Collecting fragment features
3:03:15.718332 INFO: Finished candidate scoring
3:03:15.736069 PROGRESS: === Extracted 31888 precursors and 301023 fragments ===
3:03:15.736507 INFO: performing precursor FDR with 47 features
3:03:15.736545 INFO: Decoy channel: -1
3:03:15.736568 INFO: Competetive: True
3:03:15.745491 INFO: Setting torch num_threads to 2 for FDR classification task
3:03:15.750093 WARNING: dropped 1 decoy PSMs due to missing features
3:03:16.232660 INFO: Test AUC: 0.631
3:03:16.232810 INFO: Train AUC: 0.636
3:03:16.232843 INFO: AUC difference: 0.76%
3:03:16.316339 INFO: Resetting torch num_threads to 100
3:03:16.317565 INFO: === FDR correction performed with classifier version 2 ===
3:03:16.318742 PROGRESS: ============================= Precursor FDR =============================
3:03:16.318855 PROGRESS: Total precursors accumulated: 4,063
3:03:16.318916 PROGRESS: Target precursors: 3,841 (94.54%)
3:03:16.318966 PROGRESS: Decoy precursors: 222 (5.46%)
3:03:16.319015 PROGRESS: 
3:03:16.319058 PROGRESS: Precursor Summary:
3:03:16.321864 PROGRESS: Channel   0:	 0.05 FDR: 3,779; 0.01 FDR: 3,160; 0.001 FDR: 2,302
3:03:16.321975 PROGRESS: 
3:03:16.322032 PROGRESS: Protein Summary:
3:03:16.324605 PROGRESS: Channel   0:	 0.05 FDR: 2,482; 0.01 FDR: 2,170; 0.001 FDR: 1,696
3:03:16.324739 PROGRESS: =========================================================================
3:03:16.336646 INFO: fragments_df_filtered: 5000
3:03:16.348041 INFO: calibration group: precursor, fitting mz estimator 
3:03:16.597067 INFO: calibration group: precursor, fitting rt estimator 
3:03:16.839603 INFO: calibration group: fragment, fitting mz estimator 
3:03:17.252190 INFO: calibration group: precursor, predicting mz
3:03:17.255180 INFO: calibration group: precursor, predicting rt
3:03:17.264441 INFO: calibration group: fragment, predicting mz
3:03:17.289629 INFO: === checking if optimization conditions were reached ===
3:03:17.292404 PROGRESS: ❌ ms2_error      : 8.5701 > 8.0000 or insufficient steps taken.
3:03:17.294142 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
3:03:17.294209 INFO: ==============================================
3:03:17.294336 INFO: Starting optimization step 4.
3:03:17.294414 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:03:17.294485 PROGRESS: Extracting batch of 15945 precursors
3:03:17.301501 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:03:17.301620 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:03:17.301663 INFO: FWHM in RT is 2.47 seconds, sigma is 0.32
3:03:17.301694 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:03:17.301932 INFO: Starting candidate selection
3:03:18.263692 INFO: Starting candidate scoring
3:03:18.487711 INFO: Finished candidate processing
3:03:18.487842 INFO: Collecting candidate features
3:03:18.542337 WARNING: intensity_correlation has 2 NaNs ( 0.01 % out of 31883)
3:03:18.546731 INFO: Collecting fragment features
3:03:18.568982 INFO: Finished candidate scoring
3:03:18.588143 PROGRESS: === Extracted 31883 precursors and 284513 fragments ===
3:03:18.588583 INFO: performing precursor FDR with 47 features
3:03:18.588622 INFO: Decoy channel: -1
3:03:18.588648 INFO: Competetive: True
3:03:18.598549 INFO: Setting torch num_threads to 2 for FDR classification task
3:03:18.603657 WARNING: dropped 2 decoy PSMs due to missing features
3:03:19.090842 INFO: Test AUC: 0.658
3:03:19.090998 INFO: Train AUC: 0.655
3:03:19.091027 INFO: AUC difference: 0.55%
3:03:19.176845 INFO: Resetting torch num_threads to 100
3:03:19.178272 INFO: === FDR correction performed with classifier version 3 ===
3:03:19.179787 PROGRESS: ============================= Precursor FDR =============================
3:03:19.179912 PROGRESS: Total precursors accumulated: 4,451
3:03:19.179972 PROGRESS: Target precursors: 4,209 (94.56%)
3:03:19.180024 PROGRESS: Decoy precursors: 242 (5.44%)
3:03:19.180072 PROGRESS: 
3:03:19.180116 PROGRESS: Precursor Summary:
3:03:19.182374 PROGRESS: Channel   0:	 0.05 FDR: 4,154; 0.01 FDR: 3,536; 0.001 FDR: 2,628
3:03:19.182517 PROGRESS: 
3:03:19.182575 PROGRESS: Protein Summary:
3:03:19.185475 PROGRESS: Channel   0:	 0.05 FDR: 2,675; 0.01 FDR: 2,367; 0.001 FDR: 1,901
3:03:19.185602 PROGRESS: =========================================================================
3:03:19.201064 INFO: fragments_df_filtered: 5000
3:03:19.212767 INFO: calibration group: precursor, fitting mz estimator 
3:03:19.512639 INFO: calibration group: precursor, fitting rt estimator 
3:03:19.784496 INFO: calibration group: fragment, fitting mz estimator 
3:03:20.200968 INFO: calibration group: precursor, predicting mz
3:03:20.203968 INFO: calibration group: precursor, predicting rt
3:03:20.213661 INFO: calibration group: fragment, predicting mz
3:03:20.264171 INFO: === checking if optimization conditions were reached ===
3:03:20.267066 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
3:03:20.267168 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
3:03:20.267208 INFO: ==============================================
3:03:20.267372 PROGRESS: Optimization finished for ms2_error, ms1_error.
3:03:20.291024 INFO: calibration group: precursor, predicting mz
3:03:20.295034 INFO: calibration group: precursor, predicting rt
3:03:20.307396 INFO: calibration group: fragment, predicting mz
3:03:20.358086 INFO: Starting optimization step 0.
3:03:20.358532 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:03:20.358641 PROGRESS: Extracting batch of 15945 precursors
3:03:20.370637 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:03:20.370824 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:03:20.370875 INFO: FWHM in RT is 2.30 seconds, sigma is 0.30
3:03:20.370914 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:03:20.371189 INFO: Starting candidate selection
3:03:21.300080 INFO: Starting candidate scoring
3:03:21.529912 INFO: Finished candidate processing
3:03:21.530045 INFO: Collecting candidate features
3:03:21.576953 WARNING: intensity_correlation has 2 NaNs ( 0.01 % out of 31884)
3:03:21.581309 INFO: Collecting fragment features
3:03:21.602242 INFO: Finished candidate scoring
3:03:21.618133 PROGRESS: === Extracted 31884 precursors and 284564 fragments ===
3:03:21.618552 INFO: performing precursor FDR with 47 features
3:03:21.618590 INFO: Decoy channel: -1
3:03:21.618614 INFO: Competetive: True
3:03:21.628483 INFO: Setting torch num_threads to 2 for FDR classification task
3:03:21.633286 WARNING: dropped 2 decoy PSMs due to missing features
3:03:22.127321 INFO: Test AUC: 0.657
3:03:22.127490 INFO: Train AUC: 0.672
3:03:22.127521 INFO: AUC difference: 2.23%
3:03:22.208966 INFO: Resetting torch num_threads to 100
3:03:22.210356 INFO: === FDR correction performed with classifier version 4 ===
3:03:22.211883 PROGRESS: ============================= Precursor FDR =============================
3:03:22.212027 PROGRESS: Total precursors accumulated: 4,563
3:03:22.212088 PROGRESS: Target precursors: 4,322 (94.72%)
3:03:22.212139 PROGRESS: Decoy precursors: 241 (5.28%)
3:03:22.212187 PROGRESS: 
3:03:22.212233 PROGRESS: Precursor Summary:
3:03:22.214674 PROGRESS: Channel   0:	 0.05 FDR: 4,264; 0.01 FDR: 3,640; 0.001 FDR: 2,544
3:03:22.214863 PROGRESS: 
3:03:22.214923 PROGRESS: Protein Summary:
3:03:22.217779 PROGRESS: Channel   0:	 0.05 FDR: 2,723; 0.01 FDR: 2,414; 0.001 FDR: 1,847
3:03:22.217917 PROGRESS: =========================================================================
3:03:22.231995 INFO: fragments_df_filtered: 5000
3:03:22.245746 INFO: calibration group: precursor, fitting mz estimator 
3:03:22.593545 INFO: calibration group: precursor, fitting rt estimator 
3:03:22.887286 INFO: calibration group: fragment, fitting mz estimator 
3:03:23.398028 INFO: calibration group: precursor, predicting mz
3:03:23.401061 INFO: calibration group: precursor, predicting rt
3:03:23.410454 INFO: calibration group: fragment, predicting mz
3:03:23.442029 INFO: === checking if optimization conditions were reached ===
3:03:23.442374 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3:03:23.455009 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 110.1568.
3:03:23.455158 INFO: ==============================================
3:03:23.455343 INFO: Starting optimization step 1.
3:03:23.455420 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:03:23.455492 PROGRESS: Extracting batch of 15945 precursors
3:03:23.460716 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:03:23.460830 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:03:23.460879 INFO: FWHM in RT is 2.29 seconds, sigma is 0.30
3:03:23.460919 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:03:23.461152 INFO: Starting candidate selection
3:03:24.153606 INFO: Starting candidate scoring
3:03:24.339516 INFO: Finished candidate processing
3:03:24.339630 INFO: Collecting candidate features
3:03:24.395586 WARNING: intensity_correlation has 4 NaNs ( 0.01 % out of 31793)
3:03:24.405176 INFO: Collecting fragment features
3:03:24.426632 INFO: Finished candidate scoring
3:03:24.445337 PROGRESS: === Extracted 31793 precursors and 268568 fragments ===
3:03:24.445793 INFO: performing precursor FDR with 47 features
3:03:24.445833 INFO: Decoy channel: -1
3:03:24.445858 INFO: Competetive: True
3:03:24.454767 INFO: Setting torch num_threads to 2 for FDR classification task
3:03:24.460398 WARNING: dropped 1 target PSMs due to missing features
3:03:24.460536 WARNING: dropped 3 decoy PSMs due to missing features
3:03:24.966846 INFO: Test AUC: 0.694
3:03:24.966992 INFO: Train AUC: 0.701
3:03:24.967025 INFO: AUC difference: 1.05%
3:03:25.051761 INFO: Resetting torch num_threads to 100
3:03:25.053100 INFO: === FDR correction performed with classifier version 4 ===
3:03:25.054363 PROGRESS: ============================= Precursor FDR =============================
3:03:25.054463 PROGRESS: Total precursors accumulated: 4,981
3:03:25.054543 PROGRESS: Target precursors: 4,742 (95.20%)
3:03:25.054598 PROGRESS: Decoy precursors: 239 (4.80%)
3:03:25.054648 PROGRESS: 
3:03:25.054697 PROGRESS: Precursor Summary:
3:03:25.056769 PROGRESS: Channel   0:	 0.05 FDR: 4,730; 0.01 FDR: 4,123; 0.001 FDR: 2,724
3:03:25.056898 PROGRESS: 
3:03:25.056957 PROGRESS: Protein Summary:
3:03:25.059889 PROGRESS: Channel   0:	 0.05 FDR: 2,911; 0.01 FDR: 2,655; 0.001 FDR: 1,949
3:03:25.059993 PROGRESS: =========================================================================
3:03:25.076622 INFO: fragments_df_filtered: 5000
3:03:25.090100 INFO: calibration group: precursor, fitting mz estimator 
3:03:25.502537 INFO: calibration group: precursor, fitting rt estimator 
3:03:25.800624 INFO: calibration group: fragment, fitting mz estimator 
3:03:26.226824 INFO: calibration group: precursor, predicting mz
3:03:26.229765 INFO: calibration group: precursor, predicting rt
3:03:26.239254 INFO: calibration group: fragment, predicting mz
3:03:26.268469 INFO: === checking if optimization conditions were reached ===
3:03:26.268854 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3:03:26.277739 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 62.6131.
3:03:26.277908 INFO: ==============================================
3:03:26.278101 INFO: Starting optimization step 2.
3:03:26.278174 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:03:26.278239 PROGRESS: Extracting batch of 15945 precursors
3:03:26.285836 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:03:26.285978 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:03:26.286014 INFO: FWHM in RT is 2.28 seconds, sigma is 0.29
3:03:26.286040 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:03:26.286324 INFO: Starting candidate selection
3:03:26.982660 INFO: Starting candidate scoring
3:03:27.204297 INFO: Finished candidate processing
3:03:27.204429 INFO: Collecting candidate features
3:03:27.252826 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 31703)
3:03:27.257090 INFO: Collecting fragment features
3:03:27.277194 INFO: Finished candidate scoring
3:03:27.290744 PROGRESS: === Extracted 31703 precursors and 259566 fragments ===
3:03:27.291150 INFO: performing precursor FDR with 47 features
3:03:27.291187 INFO: Decoy channel: -1
3:03:27.291212 INFO: Competetive: True
3:03:27.299674 INFO: Setting torch num_threads to 2 for FDR classification task
3:03:27.304097 WARNING: dropped 1 target PSMs due to missing features
3:03:27.664026 INFO: Test AUC: 0.714
3:03:27.664161 INFO: Train AUC: 0.717
3:03:27.664191 INFO: AUC difference: 0.42%
3:03:27.745615 INFO: Resetting torch num_threads to 100
3:03:27.746806 INFO: === FDR correction performed with classifier version 4 ===
3:03:27.748142 PROGRESS: ============================= Precursor FDR =============================
3:03:27.748242 PROGRESS: Total precursors accumulated: 4,987
3:03:27.748300 PROGRESS: Target precursors: 4,777 (95.79%)
3:03:27.748351 PROGRESS: Decoy precursors: 210 (4.21%)
3:03:27.748396 PROGRESS: 
3:03:27.748440 PROGRESS: Precursor Summary:
3:03:27.750666 PROGRESS: Channel   0:	 0.05 FDR: 4,777; 0.01 FDR: 4,175; 0.001 FDR: 3,133
3:03:27.750794 PROGRESS: 
3:03:27.750851 PROGRESS: Protein Summary:
3:03:27.753879 PROGRESS: Channel   0:	 0.05 FDR: 2,943; 0.01 FDR: 2,662; 0.001 FDR: 2,155
3:03:27.753982 PROGRESS: =========================================================================
3:03:27.767776 INFO: fragments_df_filtered: 5000
3:03:27.780366 INFO: calibration group: precursor, fitting mz estimator 
3:03:28.150881 INFO: calibration group: precursor, fitting rt estimator 
3:03:28.477190 INFO: calibration group: fragment, fitting mz estimator 
3:03:28.896097 INFO: calibration group: precursor, predicting mz
3:03:28.899096 INFO: calibration group: precursor, predicting rt
3:03:28.908476 INFO: calibration group: fragment, predicting mz
3:03:28.933070 INFO: === checking if optimization conditions were reached ===
3:03:28.933430 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3:03:28.976423 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 43.7571.
3:03:28.976585 INFO: ==============================================
3:03:29.001104 INFO: Starting optimization step 3.
3:03:29.001543 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:03:29.001846 PROGRESS: Extracting batch of 15945 precursors
3:03:29.011101 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:03:29.011280 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:03:29.011409 INFO: FWHM in RT is 2.29 seconds, sigma is 0.29
3:03:29.011516 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:03:29.011821 INFO: Starting candidate selection
3:03:29.667154 INFO: Starting candidate scoring
3:03:29.895962 INFO: Finished candidate processing
3:03:29.896081 INFO: Collecting candidate features
3:03:29.948191 WARNING: intensity_correlation has 5 NaNs ( 0.02 % out of 31654)
3:03:29.958663 INFO: Collecting fragment features
3:03:29.980233 INFO: Finished candidate scoring
3:03:29.995118 PROGRESS: === Extracted 31654 precursors and 257021 fragments ===
3:03:29.995558 INFO: performing precursor FDR with 47 features
3:03:29.995595 INFO: Decoy channel: -1
3:03:29.995617 INFO: Competetive: True
3:03:30.008021 INFO: Setting torch num_threads to 2 for FDR classification task
3:03:30.014200 WARNING: dropped 2 target PSMs due to missing features
3:03:30.014339 WARNING: dropped 3 decoy PSMs due to missing features
3:03:30.518227 INFO: Test AUC: 0.720
3:03:30.518465 INFO: Train AUC: 0.722
3:03:30.518497 INFO: AUC difference: 0.29%
3:03:30.605525 INFO: Resetting torch num_threads to 100
3:03:30.607062 INFO: === FDR correction performed with classifier version 4 ===
3:03:30.608297 PROGRESS: ============================= Precursor FDR =============================
3:03:30.608397 PROGRESS: Total precursors accumulated: 5,021
3:03:30.608457 PROGRESS: Target precursors: 4,825 (96.10%)
3:03:30.608509 PROGRESS: Decoy precursors: 196 (3.90%)
3:03:30.608554 PROGRESS: 
3:03:30.608598 PROGRESS: Precursor Summary:
3:03:30.610812 PROGRESS: Channel   0:	 0.05 FDR: 4,825; 0.01 FDR: 4,130; 0.001 FDR: 3,269
3:03:30.611033 PROGRESS: 
3:03:30.611091 PROGRESS: Protein Summary:
3:03:30.615283 PROGRESS: Channel   0:	 0.05 FDR: 2,943; 0.01 FDR: 2,641; 0.001 FDR: 2,232
3:03:30.615648 PROGRESS: =========================================================================
3:03:30.630446 INFO: fragments_df_filtered: 5000
3:03:30.643579 INFO: calibration group: precursor, fitting mz estimator 
3:03:31.003386 INFO: calibration group: precursor, fitting rt estimator 
3:03:31.327612 INFO: calibration group: fragment, fitting mz estimator 
3:03:31.745284 INFO: calibration group: precursor, predicting mz
3:03:31.748234 INFO: calibration group: precursor, predicting rt
3:03:31.757564 INFO: calibration group: fragment, predicting mz
3:03:31.793939 INFO: === checking if optimization conditions were reached ===
3:03:31.794293 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3:03:31.813055 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 35.4697.
3:03:31.813186 INFO: ==============================================
3:03:31.813360 INFO: Starting optimization step 4.
3:03:31.813441 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:03:31.813523 PROGRESS: Extracting batch of 15945 precursors
3:03:31.831685 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:03:31.831825 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:03:31.831867 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
3:03:31.831896 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:03:31.832168 INFO: Starting candidate selection
3:03:32.454570 INFO: Starting candidate scoring
3:03:32.661894 INFO: Finished candidate processing
3:03:32.662026 INFO: Collecting candidate features
3:03:32.720820 WARNING: intensity_correlation has 8 NaNs ( 0.03 % out of 31537)
3:03:32.729167 INFO: Collecting fragment features
3:03:32.748822 INFO: Finished candidate scoring
3:03:32.763108 PROGRESS: === Extracted 31537 precursors and 251249 fragments ===
3:03:32.763543 INFO: performing precursor FDR with 47 features
3:03:32.763581 INFO: Decoy channel: -1
3:03:32.763604 INFO: Competetive: True
3:03:32.772175 INFO: Setting torch num_threads to 2 for FDR classification task
3:03:32.777815 WARNING: dropped 3 target PSMs due to missing features
3:03:32.777949 WARNING: dropped 5 decoy PSMs due to missing features
3:03:33.265212 INFO: Test AUC: 0.723
3:03:33.265357 INFO: Train AUC: 0.733
3:03:33.265387 INFO: AUC difference: 1.40%
3:03:33.351639 INFO: Resetting torch num_threads to 100
3:03:33.353254 INFO: === FDR correction performed with classifier version 4 ===
3:03:33.354974 PROGRESS: ============================= Precursor FDR =============================
3:03:33.355125 PROGRESS: Total precursors accumulated: 5,021
3:03:33.355187 PROGRESS: Target precursors: 4,815 (95.90%)
3:03:33.355236 PROGRESS: Decoy precursors: 206 (4.10%)
3:03:33.355283 PROGRESS: 
3:03:33.355326 PROGRESS: Precursor Summary:
3:03:33.357781 PROGRESS: Channel   0:	 0.05 FDR: 4,815; 0.01 FDR: 4,143; 0.001 FDR: 3,190
3:03:33.357919 PROGRESS: 
3:03:33.357994 PROGRESS: Protein Summary:
3:03:33.361000 PROGRESS: Channel   0:	 0.05 FDR: 2,941; 0.01 FDR: 2,645; 0.001 FDR: 2,199
3:03:33.361101 PROGRESS: =========================================================================
3:03:33.375561 INFO: fragments_df_filtered: 5000
3:03:33.394408 INFO: calibration group: precursor, fitting mz estimator 
3:03:33.804642 INFO: calibration group: precursor, fitting rt estimator 
3:03:34.130889 INFO: calibration group: fragment, fitting mz estimator 
3:03:34.574218 INFO: calibration group: precursor, predicting mz
3:03:34.577301 INFO: calibration group: precursor, predicting rt
3:03:34.586694 INFO: calibration group: fragment, predicting mz
3:03:34.628488 INFO: === checking if optimization conditions were reached ===
3:03:34.637603 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3:03:34.642150 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 29.7236.
3:03:34.642228 INFO: ==============================================
3:03:34.642348 INFO: Starting optimization step 5.
3:03:34.642422 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:03:34.642492 PROGRESS: Extracting batch of 15945 precursors
3:03:34.663546 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:03:34.663669 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:03:34.663711 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
3:03:34.663740 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:03:34.663981 INFO: Starting candidate selection
3:03:35.262827 INFO: Starting candidate scoring
3:03:35.511102 INFO: Finished candidate processing
3:03:35.511274 INFO: Collecting candidate features
3:03:35.584457 WARNING: intensity_correlation has 12 NaNs ( 0.04 % out of 31557)
3:03:35.589089 INFO: Collecting fragment features
3:03:35.609411 INFO: Finished candidate scoring
3:03:35.629452 PROGRESS: === Extracted 31557 precursors and 252524 fragments ===
3:03:35.629890 INFO: performing precursor FDR with 47 features
3:03:35.629931 INFO: Decoy channel: -1
3:03:35.629956 INFO: Competetive: True
3:03:35.639366 INFO: Setting torch num_threads to 2 for FDR classification task
3:03:35.644870 WARNING: dropped 2 target PSMs due to missing features
3:03:35.645007 WARNING: dropped 10 decoy PSMs due to missing features
3:03:36.141891 INFO: Test AUC: 0.735
3:03:36.142037 INFO: Train AUC: 0.729
3:03:36.142070 INFO: AUC difference: 0.75%
3:03:36.225424 INFO: Resetting torch num_threads to 100
3:03:36.227017 INFO: === FDR correction performed with classifier version 4 ===
3:03:36.228889 PROGRESS: ============================= Precursor FDR =============================
3:03:36.229041 PROGRESS: Total precursors accumulated: 5,027
3:03:36.229105 PROGRESS: Target precursors: 4,819 (95.86%)
3:03:36.229172 PROGRESS: Decoy precursors: 208 (4.14%)
3:03:36.229218 PROGRESS: 
3:03:36.229261 PROGRESS: Precursor Summary:
3:03:36.231852 PROGRESS: Channel   0:	 0.05 FDR: 4,819; 0.01 FDR: 4,182; 0.001 FDR: 3,240
3:03:36.231992 PROGRESS: 
3:03:36.232050 PROGRESS: Protein Summary:
3:03:36.235080 PROGRESS: Channel   0:	 0.05 FDR: 2,949; 0.01 FDR: 2,662; 0.001 FDR: 2,214
3:03:36.235186 PROGRESS: =========================================================================
3:03:36.253143 INFO: fragments_df_filtered: 5000
3:03:36.267347 INFO: calibration group: precursor, fitting mz estimator 
3:03:36.601025 INFO: calibration group: precursor, fitting rt estimator 
3:03:36.933017 INFO: calibration group: fragment, fitting mz estimator 
3:03:37.360008 INFO: calibration group: precursor, predicting mz
3:03:37.363079 INFO: calibration group: precursor, predicting rt
3:03:37.372515 INFO: calibration group: fragment, predicting mz
3:03:37.419326 INFO: === checking if optimization conditions were reached ===
3:03:37.419598 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3:03:37.424201 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 25.4297.
3:03:37.424271 INFO: ==============================================
3:03:37.424381 INFO: Starting optimization step 6.
3:03:37.424456 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:03:37.424526 PROGRESS: Extracting batch of 15945 precursors
3:03:37.445330 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:03:37.445413 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:03:37.445453 INFO: FWHM in RT is 2.26 seconds, sigma is 0.29
3:03:37.445483 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:03:37.445793 INFO: Starting candidate selection
3:03:38.117321 INFO: Starting candidate scoring
3:03:38.340726 INFO: Finished candidate processing
3:03:38.340855 INFO: Collecting candidate features
3:03:38.406034 WARNING: intensity_correlation has 11 NaNs ( 0.04 % out of 30628)
3:03:38.417127 INFO: Collecting fragment features
3:03:38.442884 INFO: Finished candidate scoring
3:03:38.457152 PROGRESS: === Extracted 30628 precursors and 237447 fragments ===
3:03:38.457691 INFO: performing precursor FDR with 47 features
3:03:38.457738 INFO: Decoy channel: -1
3:03:38.457763 INFO: Competetive: True
3:03:38.470605 INFO: Setting torch num_threads to 2 for FDR classification task
3:03:38.476552 WARNING: dropped 4 target PSMs due to missing features
3:03:38.476687 WARNING: dropped 7 decoy PSMs due to missing features
3:03:38.823557 INFO: Test AUC: 0.723
3:03:38.823704 INFO: Train AUC: 0.736
3:03:38.823736 INFO: AUC difference: 1.83%
3:03:38.905406 INFO: Resetting torch num_threads to 100
3:03:38.906482 INFO: === FDR correction performed with classifier version 4 ===
3:03:38.907661 PROGRESS: ============================= Precursor FDR =============================
3:03:38.907756 PROGRESS: Total precursors accumulated: 5,008
3:03:38.907816 PROGRESS: Target precursors: 4,790 (95.65%)
3:03:38.907866 PROGRESS: Decoy precursors: 218 (4.35%)
3:03:38.907911 PROGRESS: 
3:03:38.907954 PROGRESS: Precursor Summary:
3:03:38.910120 PROGRESS: Channel   0:	 0.05 FDR: 4,790; 0.01 FDR: 3,987; 0.001 FDR: 1,924
3:03:38.910224 PROGRESS: 
3:03:38.910279 PROGRESS: Protein Summary:
3:03:38.913044 PROGRESS: Channel   0:	 0.05 FDR: 2,933; 0.01 FDR: 2,583; 0.001 FDR: 1,476
3:03:38.913144 PROGRESS: =========================================================================
3:03:38.925962 INFO: fragments_df_filtered: 5000
3:03:38.941504 INFO: calibration group: precursor, fitting mz estimator 
3:03:39.245496 INFO: calibration group: precursor, fitting rt estimator 
3:03:39.559600 INFO: calibration group: fragment, fitting mz estimator 
3:03:39.976332 INFO: calibration group: precursor, predicting mz
3:03:39.979289 INFO: calibration group: precursor, predicting rt
3:03:39.988266 INFO: calibration group: fragment, predicting mz
3:03:40.065994 INFO: === checking if optimization conditions were reached ===
3:03:40.066562 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
3:03:40.071249 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 20.7626.
3:03:40.071406 INFO: ==============================================
3:03:40.071708 INFO: Starting optimization step 7.
3:03:40.071949 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:03:40.072184 PROGRESS: Extracting batch of 15945 precursors
3:03:40.080324 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:03:40.080718 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:03:40.080882 INFO: FWHM in RT is 2.26 seconds, sigma is 0.29
3:03:40.081006 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:03:40.081525 INFO: Starting candidate selection
3:03:40.733171 INFO: Starting candidate scoring
3:03:40.960084 INFO: Finished candidate processing
3:03:40.960254 INFO: Collecting candidate features
3:03:41.014770 WARNING: intensity_correlation has 22 NaNs ( 0.07 % out of 30669)
3:03:41.025768 INFO: Collecting fragment features
3:03:41.046959 INFO: Finished candidate scoring
3:03:41.061010 PROGRESS: === Extracted 30669 precursors and 239001 fragments ===
3:03:41.061575 INFO: performing precursor FDR with 47 features
3:03:41.061621 INFO: Decoy channel: -1
3:03:41.061646 INFO: Competetive: True
3:03:41.073105 INFO: Setting torch num_threads to 2 for FDR classification task
3:03:41.078464 WARNING: dropped 7 target PSMs due to missing features
3:03:41.078597 WARNING: dropped 15 decoy PSMs due to missing features
3:03:41.473486 INFO: Test AUC: 0.748
3:03:41.473638 INFO: Train AUC: 0.734
3:03:41.473670 INFO: AUC difference: 1.87%
3:03:41.560552 INFO: Resetting torch num_threads to 100
3:03:41.562186 INFO: === FDR correction performed with classifier version 4 ===
3:03:41.564098 PROGRESS: ============================= Precursor FDR =============================
3:03:41.564251 PROGRESS: Total precursors accumulated: 4,977
3:03:41.564315 PROGRESS: Target precursors: 4,761 (95.66%)
3:03:41.564367 PROGRESS: Decoy precursors: 216 (4.34%)
3:03:41.564413 PROGRESS: 
3:03:41.564459 PROGRESS: Precursor Summary:
3:03:41.567183 PROGRESS: Channel   0:	 0.05 FDR: 4,761; 0.01 FDR: 4,049; 0.001 FDR: 2,964
3:03:41.567332 PROGRESS: 
3:03:41.567389 PROGRESS: Protein Summary:
3:03:41.570369 PROGRESS: Channel   0:	 0.05 FDR: 2,907; 0.01 FDR: 2,596; 0.001 FDR: 2,055
3:03:41.570484 PROGRESS: =========================================================================
3:03:41.583828 INFO: fragments_df_filtered: 5000
3:03:41.595839 INFO: calibration group: precursor, fitting mz estimator 
3:03:41.907478 INFO: calibration group: precursor, fitting rt estimator 
3:03:42.218066 INFO: calibration group: fragment, fitting mz estimator 
3:03:42.636603 INFO: calibration group: precursor, predicting mz
3:03:42.639563 INFO: calibration group: precursor, predicting rt
3:03:42.648640 INFO: calibration group: fragment, predicting mz
3:03:42.720498 INFO: === checking if optimization conditions were reached ===
3:03:42.725583 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
3:03:42.749756 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 19.0672.
3:03:42.749913 INFO: ==============================================
3:03:42.750103 INFO: Starting optimization step 8.
3:03:42.750172 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:03:42.750235 PROGRESS: Extracting batch of 15945 precursors
3:03:42.754206 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:03:42.754270 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:03:42.754303 INFO: FWHM in RT is 2.25 seconds, sigma is 0.29
3:03:42.754327 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:03:42.754516 INFO: Starting candidate selection
3:03:43.406883 INFO: Starting candidate scoring
3:03:43.662405 INFO: Finished candidate processing
3:03:43.662525 INFO: Collecting candidate features
3:03:43.716190 WARNING: intensity_correlation has 18 NaNs ( 0.06 % out of 30693)
3:03:43.721928 INFO: Collecting fragment features
3:03:43.740781 INFO: Finished candidate scoring
3:03:43.757723 PROGRESS: === Extracted 30693 precursors and 239691 fragments ===
3:03:43.758167 INFO: performing precursor FDR with 47 features
3:03:43.758209 INFO: Decoy channel: -1
3:03:43.758237 INFO: Competetive: True
3:03:43.769705 INFO: Setting torch num_threads to 2 for FDR classification task
3:03:43.776327 WARNING: dropped 9 target PSMs due to missing features
3:03:43.776465 WARNING: dropped 9 decoy PSMs due to missing features
3:03:44.168524 INFO: Test AUC: 0.740
3:03:44.168691 INFO: Train AUC: 0.742
3:03:44.168737 INFO: AUC difference: 0.31%
3:03:44.254247 INFO: Resetting torch num_threads to 100
3:03:44.255790 INFO: === FDR correction performed with classifier version 4 ===
3:03:44.257718 PROGRESS: ============================= Precursor FDR =============================
3:03:44.257888 PROGRESS: Total precursors accumulated: 4,956
3:03:44.257952 PROGRESS: Target precursors: 4,751 (95.86%)
3:03:44.258003 PROGRESS: Decoy precursors: 205 (4.14%)
3:03:44.258048 PROGRESS: 
3:03:44.258092 PROGRESS: Precursor Summary:
3:03:44.260663 PROGRESS: Channel   0:	 0.05 FDR: 4,751; 0.01 FDR: 4,073; 0.001 FDR: 2,609
3:03:44.260833 PROGRESS: 
3:03:44.260890 PROGRESS: Protein Summary:
3:03:44.263783 PROGRESS: Channel   0:	 0.05 FDR: 2,915; 0.01 FDR: 2,606; 0.001 FDR: 1,873
3:03:44.263913 PROGRESS: =========================================================================
3:03:44.277209 INFO: fragments_df_filtered: 5000
3:03:44.289445 INFO: calibration group: precursor, fitting mz estimator 
3:03:44.636539 INFO: calibration group: precursor, fitting rt estimator 
3:03:44.955613 INFO: calibration group: fragment, fitting mz estimator 
3:03:45.375257 INFO: calibration group: precursor, predicting mz
3:03:45.378297 INFO: calibration group: precursor, predicting rt
3:03:45.387498 INFO: calibration group: fragment, predicting mz
3:03:45.414401 INFO: === checking if optimization conditions were reached ===
3:03:45.414964 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
3:03:45.421187 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 18.9213.
3:03:45.421390 INFO: ==============================================
3:03:45.421621 INFO: Starting optimization step 9.
3:03:45.421702 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:03:45.421780 PROGRESS: Extracting batch of 15945 precursors
3:03:45.432813 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:03:45.433013 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:03:45.433057 INFO: FWHM in RT is 2.26 seconds, sigma is 0.29
3:03:45.433083 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:03:45.433673 INFO: Starting candidate selection
3:03:46.081166 INFO: Starting candidate scoring
3:03:46.305034 INFO: Finished candidate processing
3:03:46.305153 INFO: Collecting candidate features
3:03:46.354473 WARNING: intensity_correlation has 15 NaNs ( 0.05 % out of 30679)
3:03:46.358851 INFO: Collecting fragment features
3:03:46.380156 INFO: Finished candidate scoring
3:03:46.393698 PROGRESS: === Extracted 30679 precursors and 239689 fragments ===
3:03:46.394132 INFO: performing precursor FDR with 47 features
3:03:46.394170 INFO: Decoy channel: -1
3:03:46.394194 INFO: Competetive: True
3:03:46.404894 INFO: Setting torch num_threads to 2 for FDR classification task
3:03:46.410324 WARNING: dropped 4 target PSMs due to missing features
3:03:46.410462 WARNING: dropped 11 decoy PSMs due to missing features
3:03:46.797320 INFO: Test AUC: 0.743
3:03:46.797492 INFO: Train AUC: 0.737
3:03:46.797523 INFO: AUC difference: 0.88%
3:03:48.745255 INFO: Resetting torch num_threads to 100
3:03:48.746940 INFO: === FDR correction performed with classifier version 4 ===
3:03:48.748657 PROGRESS: ============================= Precursor FDR =============================
3:03:48.748801 PROGRESS: Total precursors accumulated: 4,939
3:03:48.748872 PROGRESS: Target precursors: 4,739 (95.95%)
3:03:48.748922 PROGRESS: Decoy precursors: 200 (4.05%)
3:03:48.748966 PROGRESS: 
3:03:48.749009 PROGRESS: Precursor Summary:
3:03:48.751367 PROGRESS: Channel   0:	 0.05 FDR: 4,739; 0.01 FDR: 4,162; 0.001 FDR: 3,359
3:03:48.751648 PROGRESS: 
3:03:48.751709 PROGRESS: Protein Summary:
3:03:48.755724 PROGRESS: Channel   0:	 0.05 FDR: 2,913; 0.01 FDR: 2,657; 0.001 FDR: 2,264
3:03:48.755904 PROGRESS: =========================================================================
3:03:48.771667 INFO: fragments_df_filtered: 5000
3:03:48.785615 INFO: calibration group: precursor, fitting mz estimator 
3:03:49.120967 INFO: calibration group: precursor, fitting rt estimator 
3:03:49.451759 INFO: calibration group: fragment, fitting mz estimator 
3:03:49.881300 INFO: calibration group: precursor, predicting mz
3:03:49.884401 INFO: calibration group: precursor, predicting rt
3:03:49.893871 INFO: calibration group: fragment, predicting mz
3:03:49.973173 INFO: === checking if optimization conditions were reached ===
3:03:49.973665 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
3:03:49.975147 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 18.9213 found after 10 searches.
3:03:49.975208 INFO: ==============================================
3:03:49.975329 PROGRESS: Optimization finished for rt_error.
3:03:50.003916 INFO: calibration group: precursor, predicting mz
3:03:50.007037 INFO: calibration group: precursor, predicting rt
3:03:50.016267 INFO: calibration group: fragment, predicting mz
3:03:50.095167 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:03:50.095448 PROGRESS: ==============================================
3:03:50.095528 PROGRESS: ms2_error      : 8.0000
3:03:50.095590 PROGRESS: ms1_error      : 3.0000
3:03:50.095646 PROGRESS: rt_error       : 18.9213
3:03:50.095696 PROGRESS: ==============================================
3:03:50.096692 INFO: calibration group: precursor, predicting mz
3:03:50.108041 INFO: calibration group: precursor, predicting rt
3:03:50.163196 INFO: calibration group: fragment, predicting mz
3:03:50.295798 PROGRESS: Extracting batch of 78739 precursors
3:03:50.346222 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:03:50.346372 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:03:50.346410 INFO: FWHM in RT is 2.25 seconds, sigma is 0.29
3:03:50.346434 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:03:50.346719 INFO: Starting candidate selection
3:03:53.276155 INFO: Applying score cutoff of 10.806270468711853
3:03:53.279435 INFO: Removed 4150 precursors with score below cutoff
3:03:53.312932 INFO: Starting candidate scoring
3:03:54.361927 INFO: Finished candidate processing
3:03:54.362058 INFO: Collecting candidate features
3:03:54.576648 WARNING: intensity_correlation has 30 NaNs ( 0.02 % out of 148925)
3:03:54.585297 INFO: Collecting fragment features
3:03:54.678787 INFO: Finished candidate scoring
3:03:54.752446 INFO: === FDR correction performed with classifier version 14 ===
3:03:54.753505 INFO: performing precursor FDR with 47 features
3:03:54.753540 INFO: Decoy channel: -1
3:03:54.753566 INFO: Competetive: True
3:03:54.803000 INFO: Setting torch num_threads to 2 for FDR classification task
3:03:54.826596 WARNING: dropped 10 target PSMs due to missing features
3:03:54.826751 WARNING: dropped 20 decoy PSMs due to missing features
3:03:57.304136 INFO: Test AUC: 0.759
3:03:57.304288 INFO: Train AUC: 0.763
3:03:57.304319 INFO: AUC difference: 0.50%
3:03:57.402968 INFO: Resetting torch num_threads to 100
3:03:57.409744 INFO: Removing fragments below FDR threshold
3:03:57.435525 PROGRESS: ============================= Precursor FDR =============================
3:03:57.435827 PROGRESS: Total precursors accumulated: 21,577
3:03:57.435893 PROGRESS: Target precursors: 21,364 (99.01%)
3:03:57.435943 PROGRESS: Decoy precursors: 213 (0.99%)
3:03:57.435989 PROGRESS: 
3:03:57.436034 PROGRESS: Precursor Summary:
3:03:57.442954 PROGRESS: Channel   0:	 0.05 FDR: 21,364; 0.01 FDR: 21,364; 0.001 FDR: 16,242
3:03:57.443187 PROGRESS: 
3:03:57.443246 PROGRESS: Protein Summary:
3:03:57.453417 PROGRESS: Channel   0:	 0.05 FDR: 5,914; 0.01 FDR: 5,914; 0.001 FDR: 5,356
3:03:57.453642 PROGRESS: =========================================================================
3:03:57.698262 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:03:57.710883 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:03:57.711058 INFO: Quantification results path: run_output_Astral/alphadia_1.10_MBRSetValues/quant
3:03:57.711147 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2 at run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:03:57.711910 INFO: Initializing RawFileManager
3:04:28.224407 INFO: Determining DIA cycle
3:04:28.240998 INFO: Found cycle with start 0.00 min and length 303.
3:04:28.492812 INFO: RT (min)            : 0.0 - 26.9
3:04:28.492918 INFO: RT duration (sec)   : 1611.2
3:04:28.492946 INFO: RT duration (min)   : 26.9
3:04:28.492970 INFO: Cycle len (scans)   : 303
3:04:28.492991 INFO: Cycle len (sec)     : 1.65
3:04:28.493010 INFO: Number of cycles    : 978
3:04:28.493029 INFO: MS2 range (m/z)     : 380.4 - 980.7
3:04:28.513176 INFO: Initializing CalibrationManager
3:04:28.513782 INFO: Loading calibration config
3:04:28.514290 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'}]
3:04:28.514391 INFO: Calibration group :fragment, found 1 estimator(s)
3:04:28.514467 INFO: Calibration group :precursor, found 3 estimator(s)
3:04:28.514547 INFO: Disabling ion mobility calibration
3:04:28.514575 INFO: removed mobility estimator from group precursor
3:04:28.514905 INFO: Initializing OptimizationManager
3:04:28.515044 INFO: initial parameter: ms1_error = 30
3:04:28.515124 INFO: initial parameter: ms2_error = 30
3:04:28.515182 INFO: initial parameter: rt_error = 805.6019897460938
3:04:28.515237 INFO: initial parameter: mobility_error = 0.1
3:04:28.515280 INFO: initial parameter: column_type = library
3:04:28.515321 INFO: initial parameter: num_candidates = 1
3:04:28.515365 INFO: initial parameter: classifier_version = -1
3:04:28.515409 INFO: initial parameter: fwhm_rt = 5
3:04:28.515452 INFO: initial parameter: fwhm_mobility = 0.01
3:04:28.515491 INFO: initial parameter: score_cutoff = 0
3:04:28.515557 INFO: Initializing TimingManager
3:04:28.515617 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:04:28.515733 INFO: FDRManager not loaded from disk.
3:04:28.515762 INFO: Initializing FDRManager
3:04:28.515792 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
3:04:28.534112 PROGRESS: 39,524 target precursors potentially observable (0 removed)
3:04:28.558380 PROGRESS: Starting initial search for precursors.
3:04:28.575896 INFO: Starting optimization step 0.
3:04:28.576207 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:04:28.576278 PROGRESS: Extracting batch of 15945 precursors
3:04:28.580017 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:04:28.580102 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:04:28.580136 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:04:28.580158 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:04:28.580367 INFO: Starting candidate selection
3:04:29.565317 INFO: Starting candidate scoring
3:04:29.666011 INFO: Finished candidate processing
3:04:29.666130 INFO: Collecting candidate features
3:04:29.707646 INFO: Collecting fragment features
3:04:29.718974 INFO: Finished candidate scoring
3:04:29.728886 PROGRESS: === Extracted 15945 precursors and 171194 fragments ===
3:04:29.729314 INFO: performing precursor FDR with 47 features
3:04:29.729351 INFO: Decoy channel: -1
3:04:29.729374 INFO: Competetive: True
3:04:29.736755 INFO: Setting torch num_threads to 2 for FDR classification task
3:04:29.950051 INFO: Test AUC: 0.574
3:04:29.950185 INFO: Train AUC: 0.566
3:04:29.950215 INFO: AUC difference: 1.40%
3:04:30.035506 INFO: Resetting torch num_threads to 100
3:04:30.036829 INFO: === FDR correction performed with classifier version -1 ===
3:04:30.039273 PROGRESS: ============================= Precursor FDR =============================
3:04:30.039527 PROGRESS: Total precursors accumulated: 7,980
3:04:30.039593 PROGRESS: Target precursors: 4,608 (57.74%)
3:04:30.039644 PROGRESS: Decoy precursors: 3,372 (42.26%)
3:04:30.039690 PROGRESS: 
3:04:30.039733 PROGRESS: Precursor Summary:
3:04:30.040731 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:04:30.040828 PROGRESS: 
3:04:30.040882 PROGRESS: Protein Summary:
3:04:30.041873 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:04:30.041961 PROGRESS: =========================================================================
3:04:30.070482 INFO: Starting optimization step 1.
3:04:30.070786 PROGRESS: === Extracting elution groups 8000 to 24000 ===
3:04:30.070856 PROGRESS: Extracting batch of 31875 precursors
3:04:30.078699 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:04:30.078838 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:04:30.078871 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:04:30.078895 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:04:30.079119 INFO: Starting candidate selection
3:04:31.972077 INFO: Starting candidate scoring
3:04:32.189621 INFO: Finished candidate processing
3:04:32.189933 INFO: Collecting candidate features
3:04:32.251519 INFO: Collecting fragment features
3:04:32.273418 INFO: Finished candidate scoring
3:04:32.308266 PROGRESS: === Extracted 47820 precursors and 513950 fragments ===
3:04:32.315738 INFO: performing precursor FDR with 47 features
3:04:32.315891 INFO: Decoy channel: -1
3:04:32.315917 INFO: Competetive: True
3:04:32.333903 INFO: Setting torch num_threads to 2 for FDR classification task
3:04:33.045482 INFO: Test AUC: 0.625
3:04:33.045620 INFO: Train AUC: 0.620
3:04:33.045651 INFO: AUC difference: 0.77%
3:04:33.132310 INFO: Resetting torch num_threads to 100
3:04:33.135161 INFO: === FDR correction performed with classifier version -1 ===
3:04:33.136739 PROGRESS: ============================= Precursor FDR =============================
3:04:33.136902 PROGRESS: Total precursors accumulated: 4,002
3:04:33.136964 PROGRESS: Target precursors: 3,697 (92.38%)
3:04:33.137014 PROGRESS: Decoy precursors: 305 (7.62%)
3:04:33.137061 PROGRESS: 
3:04:33.137105 PROGRESS: Precursor Summary:
3:04:33.139240 PROGRESS: Channel   0:	 0.05 FDR: 3,391; 0.01 FDR: 2,631; 0.001 FDR: 1,611
3:04:33.139468 PROGRESS: 
3:04:33.139529 PROGRESS: Protein Summary:
3:04:33.142727 PROGRESS: Channel   0:	 0.05 FDR: 2,093; 0.01 FDR: 1,709; 0.001 FDR: 1,129
3:04:33.143013 PROGRESS: =========================================================================
3:04:33.155836 INFO: fragments_df_filtered: 5000
3:04:33.169972 INFO: calibration group: precursor, fitting mz estimator 
3:04:33.379492 INFO: calibration group: precursor, fitting rt estimator 
3:04:33.525552 INFO: calibration group: fragment, fitting mz estimator 
3:04:33.941265 INFO: calibration group: precursor, predicting mz
3:04:33.944250 INFO: calibration group: precursor, predicting rt
3:04:33.953809 INFO: calibration group: fragment, predicting mz
3:04:33.982506 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3:04:33.982829 INFO: Starting optimization step 2.
3:04:33.982912 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:04:33.982986 PROGRESS: Extracting batch of 15945 precursors
3:04:33.989996 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:04:33.990076 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:04:33.990114 INFO: FWHM in RT is 2.97 seconds, sigma is 0.38
3:04:33.990143 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:04:33.990378 INFO: Starting candidate selection
3:04:35.034898 INFO: Starting candidate scoring
3:04:35.260319 INFO: Finished candidate processing
3:04:35.260454 INFO: Collecting candidate features
3:04:35.324828 INFO: Collecting fragment features
3:04:35.347580 INFO: Finished candidate scoring
3:04:35.363899 PROGRESS: === Extracted 31890 precursors and 339300 fragments ===
3:04:35.364321 INFO: performing precursor FDR with 47 features
3:04:35.364359 INFO: Decoy channel: -1
3:04:35.364384 INFO: Competetive: True
3:04:35.374501 INFO: Setting torch num_threads to 2 for FDR classification task
3:04:35.860770 INFO: Test AUC: 0.623
3:04:35.860917 INFO: Train AUC: 0.624
3:04:35.860950 INFO: AUC difference: 0.09%
3:04:35.948777 INFO: Resetting torch num_threads to 100
3:04:35.950153 INFO: === FDR correction performed with classifier version 1 ===
3:04:35.951089 PROGRESS: ============================= Precursor FDR =============================
3:04:35.951190 PROGRESS: Total precursors accumulated: 2,222
3:04:35.951249 PROGRESS: Target precursors: 2,059 (92.66%)
3:04:35.951298 PROGRESS: Decoy precursors: 163 (7.34%)
3:04:35.951343 PROGRESS: 
3:04:35.951388 PROGRESS: Precursor Summary:
3:04:35.952779 PROGRESS: Channel   0:	 0.05 FDR: 1,867; 0.01 FDR: 1,401; 0.001 FDR:   681
3:04:35.952882 PROGRESS: 
3:04:35.952953 PROGRESS: Protein Summary:
3:04:35.954698 PROGRESS: Channel   0:	 0.05 FDR: 1,428; 0.01 FDR: 1,111; 0.001 FDR:   589
3:04:35.954791 PROGRESS: =========================================================================
3:04:35.963441 INFO: fragments_df_filtered: 5000
3:04:35.981618 INFO: calibration group: precursor, fitting mz estimator 
3:04:36.100296 INFO: calibration group: precursor, fitting rt estimator 
3:04:36.213380 INFO: calibration group: fragment, fitting mz estimator 
3:04:36.636482 INFO: calibration group: precursor, predicting mz
3:04:36.639541 INFO: calibration group: precursor, predicting rt
3:04:36.649472 INFO: calibration group: fragment, predicting mz
3:04:36.680243 INFO: === checking if optimization conditions were reached ===
3:04:36.708014 PROGRESS: ❌ ms2_error      : 15.9493 > 8.0000 or insufficient steps taken.
3:04:36.709944 PROGRESS: ❌ ms1_error      : 14.0136 > 3.0000 or insufficient steps taken.
3:04:36.710028 INFO: ==============================================
3:04:36.710226 INFO: Starting optimization step 3.
3:04:36.710305 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:04:36.710377 PROGRESS: Extracting batch of 15945 precursors
3:04:36.729528 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:04:36.729722 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:04:36.729774 INFO: FWHM in RT is 2.93 seconds, sigma is 0.38
3:04:36.729810 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:04:36.730117 INFO: Starting candidate selection
3:04:37.739560 INFO: Starting candidate scoring
3:04:37.970558 INFO: Finished candidate processing
3:04:37.970686 INFO: Collecting candidate features
3:04:38.028075 INFO: Collecting fragment features
3:04:38.048614 INFO: Finished candidate scoring
3:04:38.063690 PROGRESS: === Extracted 31887 precursors and 314810 fragments ===
3:04:38.064104 INFO: performing precursor FDR with 47 features
3:04:38.064158 INFO: Decoy channel: -1
3:04:38.064181 INFO: Competetive: True
3:04:38.072305 INFO: Setting torch num_threads to 2 for FDR classification task
3:04:38.542718 INFO: Test AUC: 0.646
3:04:38.542858 INFO: Train AUC: 0.653
3:04:38.542889 INFO: AUC difference: 0.98%
3:04:38.635699 INFO: Resetting torch num_threads to 100
3:04:38.636877 INFO: === FDR correction performed with classifier version 2 ===
3:04:38.637898 PROGRESS: ============================= Precursor FDR =============================
3:04:38.637993 PROGRESS: Total precursors accumulated: 3,415
3:04:38.638050 PROGRESS: Target precursors: 3,188 (93.35%)
3:04:38.638102 PROGRESS: Decoy precursors: 227 (6.65%)
3:04:38.638148 PROGRESS: 
3:04:38.638191 PROGRESS: Precursor Summary:
3:04:38.639811 PROGRESS: Channel   0:	 0.05 FDR: 3,032; 0.01 FDR: 2,330; 0.001 FDR: 1,124
3:04:38.639911 PROGRESS: 
3:04:38.639966 PROGRESS: Protein Summary:
3:04:38.642119 PROGRESS: Channel   0:	 0.05 FDR: 2,083; 0.01 FDR: 1,695; 0.001 FDR:   924
3:04:38.642226 PROGRESS: =========================================================================
3:04:38.651937 INFO: fragments_df_filtered: 5000
3:04:38.663512 INFO: calibration group: precursor, fitting mz estimator 
3:04:38.823006 INFO: calibration group: precursor, fitting rt estimator 
3:04:38.984701 INFO: calibration group: fragment, fitting mz estimator 
3:04:39.402542 INFO: calibration group: precursor, predicting mz
3:04:39.405668 INFO: calibration group: precursor, predicting rt
3:04:39.415033 INFO: calibration group: fragment, predicting mz
3:04:39.474838 INFO: === checking if optimization conditions were reached ===
3:04:39.494202 PROGRESS: ❌ ms2_error      : 10.3487 > 8.0000 or insufficient steps taken.
3:04:39.496203 PROGRESS: ❌ ms1_error      : 6.6667 > 3.0000 or insufficient steps taken.
3:04:39.496288 INFO: ==============================================
3:04:39.496484 INFO: Starting optimization step 4.
3:04:39.496561 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:04:39.496633 PROGRESS: Extracting batch of 15945 precursors
3:04:39.504446 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:04:39.504531 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:04:39.504570 INFO: FWHM in RT is 2.68 seconds, sigma is 0.34
3:04:39.504597 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:04:39.504824 INFO: Starting candidate selection
3:04:40.385525 INFO: Starting candidate scoring
3:04:40.601043 INFO: Finished candidate processing
3:04:40.601261 INFO: Collecting candidate features
3:04:40.657211 INFO: Collecting fragment features
3:04:40.681202 INFO: Finished candidate scoring
3:04:40.696294 PROGRESS: === Extracted 31888 precursors and 294452 fragments ===
3:04:40.696748 INFO: performing precursor FDR with 47 features
3:04:40.696789 INFO: Decoy channel: -1
3:04:40.696813 INFO: Competetive: True
3:04:40.705106 INFO: Setting torch num_threads to 2 for FDR classification task
3:04:41.182380 INFO: Test AUC: 0.665
3:04:41.182519 INFO: Train AUC: 0.678
3:04:41.182552 INFO: AUC difference: 1.87%
3:04:41.264475 INFO: Resetting torch num_threads to 100
3:04:41.265592 INFO: === FDR correction performed with classifier version 3 ===
3:04:41.266643 PROGRESS: ============================= Precursor FDR =============================
3:04:41.266736 PROGRESS: Total precursors accumulated: 4,070
3:04:41.266797 PROGRESS: Target precursors: 3,827 (94.03%)
3:04:41.266847 PROGRESS: Decoy precursors: 243 (5.97%)
3:04:41.266893 PROGRESS: 
3:04:41.266936 PROGRESS: Precursor Summary:
3:04:41.268901 PROGRESS: Channel   0:	 0.05 FDR: 3,729; 0.01 FDR: 3,053; 0.001 FDR: 2,123
3:04:41.268998 PROGRESS: 
3:04:41.269055 PROGRESS: Protein Summary:
3:04:41.272271 PROGRESS: Channel   0:	 0.05 FDR: 2,421; 0.01 FDR: 2,088; 0.001 FDR: 1,575
3:04:41.272370 PROGRESS: =========================================================================
3:04:41.284323 INFO: fragments_df_filtered: 5000
3:04:41.295524 INFO: calibration group: precursor, fitting mz estimator 
3:04:41.492658 INFO: calibration group: precursor, fitting rt estimator 
3:04:41.718611 INFO: calibration group: fragment, fitting mz estimator 
3:04:42.137583 INFO: calibration group: precursor, predicting mz
3:04:42.140692 INFO: calibration group: precursor, predicting rt
3:04:42.150834 INFO: calibration group: fragment, predicting mz
3:04:42.174191 INFO: === checking if optimization conditions were reached ===
3:04:42.176652 PROGRESS: ❌ ms2_error      : 8.0262 > 8.0000 or insufficient steps taken.
3:04:42.202740 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
3:04:42.202863 INFO: ==============================================
3:04:42.203037 INFO: Starting optimization step 5.
3:04:42.203115 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:04:42.203187 PROGRESS: Extracting batch of 15945 precursors
3:04:42.254260 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:04:42.254396 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:04:42.254432 INFO: FWHM in RT is 2.49 seconds, sigma is 0.32
3:04:42.254455 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:04:42.254667 INFO: Starting candidate selection
3:04:43.220138 INFO: Starting candidate scoring
3:04:43.430637 INFO: Finished candidate processing
3:04:43.430742 INFO: Collecting candidate features
3:04:43.483755 INFO: Collecting fragment features
3:04:43.504560 INFO: Finished candidate scoring
3:04:43.518238 PROGRESS: === Extracted 31879 precursors and 283916 fragments ===
3:04:43.518655 INFO: performing precursor FDR with 47 features
3:04:43.518693 INFO: Decoy channel: -1
3:04:43.518717 INFO: Competetive: True
3:04:43.526657 INFO: Setting torch num_threads to 2 for FDR classification task
3:04:43.953605 INFO: Test AUC: 0.682
3:04:43.953735 INFO: Train AUC: 0.697
3:04:43.953764 INFO: AUC difference: 2.09%
3:04:44.036882 INFO: Resetting torch num_threads to 100
3:04:44.038099 INFO: === FDR correction performed with classifier version 4 ===
3:04:44.039371 PROGRESS: ============================= Precursor FDR =============================
3:04:44.039480 PROGRESS: Total precursors accumulated: 4,493
3:04:44.039539 PROGRESS: Target precursors: 4,260 (94.81%)
3:04:44.039589 PROGRESS: Decoy precursors: 233 (5.19%)
3:04:44.039633 PROGRESS: 
3:04:44.039676 PROGRESS: Precursor Summary:
3:04:44.041751 PROGRESS: Channel   0:	 0.05 FDR: 4,225; 0.01 FDR: 3,482; 0.001 FDR: 2,499
3:04:44.041883 PROGRESS: 
3:04:44.041944 PROGRESS: Protein Summary:
3:04:44.044645 PROGRESS: Channel   0:	 0.05 FDR: 2,678; 0.01 FDR: 2,316; 0.001 FDR: 1,791
3:04:44.044768 PROGRESS: =========================================================================
3:04:44.057034 INFO: fragments_df_filtered: 5000
3:04:44.069068 INFO: calibration group: precursor, fitting mz estimator 
3:04:44.325767 INFO: calibration group: precursor, fitting rt estimator 
3:04:44.588114 INFO: calibration group: fragment, fitting mz estimator 
3:04:45.015631 INFO: calibration group: precursor, predicting mz
3:04:45.018508 INFO: calibration group: precursor, predicting rt
3:04:45.027825 INFO: calibration group: fragment, predicting mz
3:04:45.054820 INFO: === checking if optimization conditions were reached ===
3:04:45.056958 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
3:04:45.057024 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
3:04:45.057057 INFO: ==============================================
3:04:45.057156 PROGRESS: Optimization finished for ms2_error, ms1_error.
3:04:45.092635 INFO: calibration group: precursor, predicting mz
3:04:45.095874 INFO: calibration group: precursor, predicting rt
3:04:45.115230 INFO: calibration group: fragment, predicting mz
3:04:45.149055 INFO: Starting optimization step 0.
3:04:45.149268 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:04:45.149352 PROGRESS: Extracting batch of 15945 precursors
3:04:45.154642 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:04:45.154725 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:04:45.154767 INFO: FWHM in RT is 2.31 seconds, sigma is 0.30
3:04:45.154797 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:04:45.155018 INFO: Starting candidate selection
3:04:46.186561 INFO: Starting candidate scoring
3:04:46.413496 INFO: Finished candidate processing
3:04:46.413638 INFO: Collecting candidate features
3:04:46.479821 INFO: Collecting fragment features
3:04:46.501982 INFO: Finished candidate scoring
3:04:46.516531 PROGRESS: === Extracted 31880 precursors and 283428 fragments ===
3:04:46.516994 INFO: performing precursor FDR with 47 features
3:04:46.517044 INFO: Decoy channel: -1
3:04:46.517069 INFO: Competetive: True
3:04:46.531582 INFO: Setting torch num_threads to 2 for FDR classification task
3:04:47.023583 INFO: Test AUC: 0.682
3:04:47.023714 INFO: Train AUC: 0.707
3:04:47.023744 INFO: AUC difference: 3.54%
3:04:47.107346 INFO: Resetting torch num_threads to 100
3:04:47.108533 INFO: === FDR correction performed with classifier version 5 ===
3:04:47.109851 PROGRESS: ============================= Precursor FDR =============================
3:04:47.109980 PROGRESS: Total precursors accumulated: 4,569
3:04:47.110044 PROGRESS: Target precursors: 4,326 (94.68%)
3:04:47.110106 PROGRESS: Decoy precursors: 243 (5.32%)
3:04:47.110163 PROGRESS: 
3:04:47.110237 PROGRESS: Precursor Summary:
3:04:47.112924 PROGRESS: Channel   0:	 0.05 FDR: 4,247; 0.01 FDR: 3,518; 0.001 FDR: 2,690
3:04:47.113071 PROGRESS: 
3:04:47.113130 PROGRESS: Protein Summary:
3:04:47.116059 PROGRESS: Channel   0:	 0.05 FDR: 2,684; 0.01 FDR: 2,327; 0.001 FDR: 1,901
3:04:47.116158 PROGRESS: =========================================================================
3:04:47.130430 INFO: fragments_df_filtered: 5000
3:04:47.145489 INFO: calibration group: precursor, fitting mz estimator 
3:04:47.405098 INFO: calibration group: precursor, fitting rt estimator 
3:04:47.670252 INFO: calibration group: fragment, fitting mz estimator 
3:04:48.091559 INFO: calibration group: precursor, predicting mz
3:04:48.094505 INFO: calibration group: precursor, predicting rt
3:04:48.103976 INFO: calibration group: fragment, predicting mz
3:04:48.130245 INFO: === checking if optimization conditions were reached ===
3:04:48.130652 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3:04:48.135293 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 85.1328.
3:04:48.135461 INFO: ==============================================
3:04:48.135673 INFO: Starting optimization step 1.
3:04:48.135752 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:04:48.135829 PROGRESS: Extracting batch of 15945 precursors
3:04:48.146233 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:04:48.146393 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:04:48.146439 INFO: FWHM in RT is 2.30 seconds, sigma is 0.30
3:04:48.146464 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:04:48.146815 INFO: Starting candidate selection
3:04:48.891280 INFO: Starting candidate scoring
3:04:49.092891 INFO: Finished candidate processing
3:04:49.093027 INFO: Collecting candidate features
3:04:49.141043 WARNING: intensity_correlation has 4 NaNs ( 0.01 % out of 31762)
3:04:49.145379 INFO: Collecting fragment features
3:04:49.166797 INFO: Finished candidate scoring
3:04:49.180456 PROGRESS: === Extracted 31762 precursors and 264219 fragments ===
3:04:49.180882 INFO: performing precursor FDR with 47 features
3:04:49.180921 INFO: Decoy channel: -1
3:04:49.180945 INFO: Competetive: True
3:04:49.190781 INFO: Setting torch num_threads to 2 for FDR classification task
3:04:49.196326 WARNING: dropped 1 target PSMs due to missing features
3:04:49.196448 WARNING: dropped 3 decoy PSMs due to missing features
3:04:49.551332 INFO: Test AUC: 0.731
3:04:49.551480 INFO: Train AUC: 0.737
3:04:49.551509 INFO: AUC difference: 0.83%
3:04:49.634584 INFO: Resetting torch num_threads to 100
3:04:49.635823 INFO: === FDR correction performed with classifier version 5 ===
3:04:49.637025 PROGRESS: ============================= Precursor FDR =============================
3:04:49.637120 PROGRESS: Total precursors accumulated: 5,026
3:04:49.637179 PROGRESS: Target precursors: 4,785 (95.20%)
3:04:49.637249 PROGRESS: Decoy precursors: 241 (4.80%)
3:04:49.637294 PROGRESS: 
3:04:49.637338 PROGRESS: Precursor Summary:
3:04:49.639475 PROGRESS: Channel   0:	 0.05 FDR: 4,778; 0.01 FDR: 4,138; 0.001 FDR: 3,275
3:04:49.639585 PROGRESS: 
3:04:49.639641 PROGRESS: Protein Summary:
3:04:49.642578 PROGRESS: Channel   0:	 0.05 FDR: 2,941; 0.01 FDR: 2,656; 0.001 FDR: 2,229
3:04:49.642684 PROGRESS: =========================================================================
3:04:49.656562 INFO: fragments_df_filtered: 5000
3:04:49.669398 INFO: calibration group: precursor, fitting mz estimator 
3:04:50.069868 INFO: calibration group: precursor, fitting rt estimator 
3:04:50.408206 INFO: calibration group: fragment, fitting mz estimator 
3:04:50.834471 INFO: calibration group: precursor, predicting mz
3:04:50.837368 INFO: calibration group: precursor, predicting rt
3:04:50.846538 INFO: calibration group: fragment, predicting mz
3:04:50.876348 INFO: === checking if optimization conditions were reached ===
3:04:50.876556 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3:04:50.880656 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 44.9009.
3:04:50.880738 INFO: ==============================================
3:04:50.880845 INFO: Starting optimization step 2.
3:04:50.880923 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:04:50.880993 PROGRESS: Extracting batch of 15945 precursors
3:04:50.898343 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:04:50.898424 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:04:50.898464 INFO: FWHM in RT is 2.28 seconds, sigma is 0.29
3:04:50.898493 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:04:50.898708 INFO: Starting candidate selection
3:04:51.519415 INFO: Starting candidate scoring
3:04:51.754115 INFO: Finished candidate processing
3:04:51.754244 INFO: Collecting candidate features
3:04:51.809242 WARNING: intensity_correlation has 5 NaNs ( 0.02 % out of 31694)
3:04:51.813578 INFO: Collecting fragment features
3:04:51.833234 INFO: Finished candidate scoring
3:04:51.847202 PROGRESS: === Extracted 31694 precursors and 257073 fragments ===
3:04:51.847622 INFO: performing precursor FDR with 47 features
3:04:51.847662 INFO: Decoy channel: -1
3:04:51.847687 INFO: Competetive: True
3:04:51.856328 INFO: Setting torch num_threads to 2 for FDR classification task
3:04:51.862402 WARNING: dropped 2 target PSMs due to missing features
3:04:51.862555 WARNING: dropped 3 decoy PSMs due to missing features
3:04:52.355288 INFO: Test AUC: 0.747
3:04:52.355427 INFO: Train AUC: 0.746
3:04:52.355459 INFO: AUC difference: 0.16%
3:04:52.442641 INFO: Resetting torch num_threads to 100
3:04:52.443959 INFO: === FDR correction performed with classifier version 5 ===
3:04:52.445228 PROGRESS: ============================= Precursor FDR =============================
3:04:52.445327 PROGRESS: Total precursors accumulated: 5,165
3:04:52.445389 PROGRESS: Target precursors: 4,930 (95.45%)
3:04:52.445439 PROGRESS: Decoy precursors: 235 (4.55%)
3:04:52.445484 PROGRESS: 
3:04:52.445529 PROGRESS: Precursor Summary:
3:04:52.448113 PROGRESS: Channel   0:	 0.05 FDR: 4,930; 0.01 FDR: 4,238; 0.001 FDR: 3,309
3:04:52.448223 PROGRESS: 
3:04:52.448280 PROGRESS: Protein Summary:
3:04:52.451272 PROGRESS: Channel   0:	 0.05 FDR: 3,000; 0.01 FDR: 2,698; 0.001 FDR: 2,247
3:04:52.451376 PROGRESS: =========================================================================
3:04:52.465725 INFO: fragments_df_filtered: 5000
3:04:52.477664 INFO: calibration group: precursor, fitting mz estimator 
3:04:52.824223 INFO: calibration group: precursor, fitting rt estimator 
3:04:53.167962 INFO: calibration group: fragment, fitting mz estimator 
3:04:53.631908 INFO: calibration group: precursor, predicting mz
3:04:53.634856 INFO: calibration group: precursor, predicting rt
3:04:53.644400 INFO: calibration group: fragment, predicting mz
3:04:53.671566 INFO: === checking if optimization conditions were reached ===
3:04:53.672047 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3:04:53.677449 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 27.9685.
3:04:53.677546 INFO: ==============================================
3:04:53.677703 INFO: Starting optimization step 3.
3:04:53.677783 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:04:53.677855 PROGRESS: Extracting batch of 15945 precursors
3:04:53.685907 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:04:53.686018 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:04:53.686056 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
3:04:53.686082 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:04:53.686363 INFO: Starting candidate selection
3:04:54.385404 INFO: Starting candidate scoring
3:04:54.618297 INFO: Finished candidate processing
3:04:54.618422 INFO: Collecting candidate features
3:04:54.678457 WARNING: intensity_correlation has 6 NaNs ( 0.02 % out of 31593)
3:04:54.685743 INFO: Collecting fragment features
3:04:54.704944 INFO: Finished candidate scoring
3:04:54.719914 PROGRESS: === Extracted 31593 precursors and 253543 fragments ===
3:04:54.720381 INFO: performing precursor FDR with 47 features
3:04:54.720425 INFO: Decoy channel: -1
3:04:54.720450 INFO: Competetive: True
3:04:54.733851 INFO: Setting torch num_threads to 2 for FDR classification task
3:04:54.739872 WARNING: dropped 1 target PSMs due to missing features
3:04:54.740028 WARNING: dropped 5 decoy PSMs due to missing features
3:04:55.230870 INFO: Test AUC: 0.750
3:04:55.231033 INFO: Train AUC: 0.752
3:04:55.231064 INFO: AUC difference: 0.25%
3:04:55.315748 INFO: Resetting torch num_threads to 100
3:04:55.317061 INFO: === FDR correction performed with classifier version 5 ===
3:04:55.318613 PROGRESS: ============================= Precursor FDR =============================
3:04:55.318741 PROGRESS: Total precursors accumulated: 5,212
3:04:55.318802 PROGRESS: Target precursors: 4,992 (95.78%)
3:04:55.318853 PROGRESS: Decoy precursors: 220 (4.22%)
3:04:55.318899 PROGRESS: 
3:04:55.318944 PROGRESS: Precursor Summary:
3:04:55.321385 PROGRESS: Channel   0:	 0.05 FDR: 4,992; 0.01 FDR: 4,359; 0.001 FDR: 3,364
3:04:55.321520 PROGRESS: 
3:04:55.321576 PROGRESS: Protein Summary:
3:04:55.324672 PROGRESS: Channel   0:	 0.05 FDR: 3,022; 0.01 FDR: 2,747; 0.001 FDR: 2,279
3:04:55.324796 PROGRESS: =========================================================================
3:04:55.339352 INFO: fragments_df_filtered: 5000
3:04:55.352332 INFO: calibration group: precursor, fitting mz estimator 
3:04:55.766475 INFO: calibration group: precursor, fitting rt estimator 
3:04:56.130779 INFO: calibration group: fragment, fitting mz estimator 
3:04:56.561014 INFO: calibration group: precursor, predicting mz
3:04:56.563971 INFO: calibration group: precursor, predicting rt
3:04:56.573088 INFO: calibration group: fragment, predicting mz
3:04:56.612415 INFO: === checking if optimization conditions were reached ===
3:04:56.612760 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3:04:56.617325 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 23.2311.
3:04:56.617398 INFO: ==============================================
3:04:56.617517 INFO: Starting optimization step 4.
3:04:56.617591 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:04:56.617659 PROGRESS: Extracting batch of 15945 precursors
3:04:56.623443 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:04:56.623516 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:04:56.623554 INFO: FWHM in RT is 2.26 seconds, sigma is 0.29
3:04:56.623581 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:04:56.623793 INFO: Starting candidate selection
3:04:57.325079 INFO: Starting candidate scoring
3:04:57.595652 INFO: Finished candidate processing
3:04:57.595762 INFO: Collecting candidate features
3:04:57.656041 WARNING: intensity_correlation has 12 NaNs ( 0.04 % out of 30751)
3:04:57.660495 INFO: Collecting fragment features
3:04:57.680510 INFO: Finished candidate scoring
3:04:57.695044 PROGRESS: === Extracted 30751 precursors and 240425 fragments ===
3:04:57.695433 INFO: performing precursor FDR with 47 features
3:04:57.695471 INFO: Decoy channel: -1
3:04:57.695493 INFO: Competetive: True
3:04:57.703516 INFO: Setting torch num_threads to 2 for FDR classification task
3:04:57.709614 WARNING: dropped 3 target PSMs due to missing features
3:04:57.709749 WARNING: dropped 9 decoy PSMs due to missing features
3:04:58.133868 INFO: Test AUC: 0.744
3:04:58.134029 INFO: Train AUC: 0.762
3:04:58.134059 INFO: AUC difference: 2.47%
3:04:58.224063 INFO: Resetting torch num_threads to 100
3:04:58.225572 INFO: === FDR correction performed with classifier version 5 ===
3:04:58.227358 PROGRESS: ============================= Precursor FDR =============================
3:04:58.227506 PROGRESS: Total precursors accumulated: 5,349
3:04:58.227569 PROGRESS: Target precursors: 5,107 (95.48%)
3:04:58.227619 PROGRESS: Decoy precursors: 242 (4.52%)
3:04:58.227663 PROGRESS: 
3:04:58.227706 PROGRESS: Precursor Summary:
3:04:58.230294 PROGRESS: Channel   0:	 0.05 FDR: 5,107; 0.01 FDR: 4,448; 0.001 FDR: 3,253
3:04:58.230462 PROGRESS: 
3:04:58.230520 PROGRESS: Protein Summary:
3:04:58.233602 PROGRESS: Channel   0:	 0.05 FDR: 3,073; 0.01 FDR: 2,785; 0.001 FDR: 2,208
3:04:58.233707 PROGRESS: =========================================================================
3:04:58.247339 INFO: fragments_df_filtered: 5000
3:04:58.259069 INFO: calibration group: precursor, fitting mz estimator 
3:04:58.621228 INFO: calibration group: precursor, fitting rt estimator 
3:04:58.999913 INFO: calibration group: fragment, fitting mz estimator 
3:04:59.454976 INFO: calibration group: precursor, predicting mz
3:04:59.458012 INFO: calibration group: precursor, predicting rt
3:04:59.467378 INFO: calibration group: fragment, predicting mz
3:04:59.496742 INFO: === checking if optimization conditions were reached ===
3:04:59.497086 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3:04:59.501678 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 16.3592.
3:04:59.501783 INFO: ==============================================
3:04:59.501931 INFO: Starting optimization step 5.
3:04:59.502008 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:04:59.502076 PROGRESS: Extracting batch of 15945 precursors
3:04:59.507267 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:04:59.507351 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:04:59.507395 INFO: FWHM in RT is 2.25 seconds, sigma is 0.29
3:04:59.507423 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:04:59.507645 INFO: Starting candidate selection
3:05:00.171734 INFO: Starting candidate scoring
3:05:00.383035 INFO: Finished candidate processing
3:05:00.383152 INFO: Collecting candidate features
3:05:00.433391 WARNING: intensity_correlation has 15 NaNs ( 0.05 % out of 30795)
3:05:00.437650 INFO: Collecting fragment features
3:05:00.456368 INFO: Finished candidate scoring
3:05:00.470869 PROGRESS: === Extracted 30795 precursors and 242066 fragments ===
3:05:00.471292 INFO: performing precursor FDR with 47 features
3:05:00.471330 INFO: Decoy channel: -1
3:05:00.471354 INFO: Competetive: True
3:05:00.479984 INFO: Setting torch num_threads to 2 for FDR classification task
3:05:00.485594 WARNING: dropped 6 target PSMs due to missing features
3:05:00.485744 WARNING: dropped 9 decoy PSMs due to missing features
3:05:00.884508 INFO: Test AUC: 0.768
3:05:00.884660 INFO: Train AUC: 0.768
3:05:00.884691 INFO: AUC difference: 0.02%
3:05:00.968250 INFO: Resetting torch num_threads to 100
3:05:00.969669 INFO: === FDR correction performed with classifier version 5 ===
3:05:00.971316 PROGRESS: ============================= Precursor FDR =============================
3:05:00.971450 PROGRESS: Total precursors accumulated: 5,365
3:05:00.971512 PROGRESS: Target precursors: 5,133 (95.68%)
3:05:00.971582 PROGRESS: Decoy precursors: 232 (4.32%)
3:05:00.971629 PROGRESS: 
3:05:00.971673 PROGRESS: Precursor Summary:
3:05:00.974136 PROGRESS: Channel   0:	 0.05 FDR: 5,133; 0.01 FDR: 4,463; 0.001 FDR: 3,420
3:05:00.974279 PROGRESS: 
3:05:00.974335 PROGRESS: Protein Summary:
3:05:00.977428 PROGRESS: Channel   0:	 0.05 FDR: 3,089; 0.01 FDR: 2,793; 0.001 FDR: 2,295
3:05:00.977543 PROGRESS: =========================================================================
3:05:00.992148 INFO: fragments_df_filtered: 5000
3:05:01.005212 INFO: calibration group: precursor, fitting mz estimator 
3:05:01.459179 INFO: calibration group: precursor, fitting rt estimator 
3:05:03.841913 INFO: calibration group: fragment, fitting mz estimator 
3:05:04.267259 INFO: calibration group: precursor, predicting mz
3:05:04.270350 INFO: calibration group: precursor, predicting rt
3:05:04.280566 INFO: calibration group: fragment, predicting mz
3:05:04.305247 INFO: === checking if optimization conditions were reached ===
3:05:04.305567 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3:05:04.310540 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 16.2407.
3:05:04.310616 INFO: ==============================================
3:05:04.310730 INFO: Starting optimization step 6.
3:05:04.310804 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:05:04.310873 PROGRESS: Extracting batch of 15945 precursors
3:05:04.316198 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:05:04.316265 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:05:04.316303 INFO: FWHM in RT is 2.23 seconds, sigma is 0.29
3:05:04.316334 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:05:04.316539 INFO: Starting candidate selection
3:05:05.001058 INFO: Starting candidate scoring
3:05:05.190485 INFO: Finished candidate processing
3:05:05.190653 INFO: Collecting candidate features
3:05:05.239763 WARNING: intensity_correlation has 15 NaNs ( 0.05 % out of 30792)
3:05:05.243997 INFO: Collecting fragment features
3:05:05.265190 INFO: Finished candidate scoring
3:05:05.281360 PROGRESS: === Extracted 30792 precursors and 242102 fragments ===
3:05:05.281764 INFO: performing precursor FDR with 47 features
3:05:05.281801 INFO: Decoy channel: -1
3:05:05.281824 INFO: Competetive: True
3:05:05.289863 INFO: Setting torch num_threads to 2 for FDR classification task
3:05:05.294835 WARNING: dropped 5 target PSMs due to missing features
3:05:05.294937 WARNING: dropped 10 decoy PSMs due to missing features
3:05:05.596299 INFO: Test AUC: 0.762
3:05:05.596437 INFO: Train AUC: 0.770
3:05:05.596467 INFO: AUC difference: 1.02%
3:05:05.685594 INFO: Resetting torch num_threads to 100
3:05:05.686942 INFO: === FDR correction performed with classifier version 5 ===
3:05:05.688350 PROGRESS: ============================= Precursor FDR =============================
3:05:05.688451 PROGRESS: Total precursors accumulated: 5,365
3:05:05.688509 PROGRESS: Target precursors: 5,136 (95.73%)
3:05:05.688560 PROGRESS: Decoy precursors: 229 (4.27%)
3:05:05.688606 PROGRESS: 
3:05:05.688649 PROGRESS: Precursor Summary:
3:05:05.690898 PROGRESS: Channel   0:	 0.05 FDR: 5,136; 0.01 FDR: 4,443; 0.001 FDR: 3,051
3:05:05.691020 PROGRESS: 
3:05:05.691089 PROGRESS: Protein Summary:
3:05:05.694288 PROGRESS: Channel   0:	 0.05 FDR: 3,087; 0.01 FDR: 2,783; 0.001 FDR: 2,100
3:05:05.694391 PROGRESS: =========================================================================
3:05:05.708849 INFO: fragments_df_filtered: 5000
3:05:05.721513 INFO: calibration group: precursor, fitting mz estimator 
3:05:06.148037 INFO: calibration group: precursor, fitting rt estimator 
3:05:06.512428 INFO: calibration group: fragment, fitting mz estimator 
3:05:06.941208 INFO: calibration group: precursor, predicting mz
3:05:06.944323 INFO: calibration group: precursor, predicting rt
3:05:06.953929 INFO: calibration group: fragment, predicting mz
3:05:06.977235 INFO: === checking if optimization conditions were reached ===
3:05:06.977601 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
3:05:06.979023 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 16.2407 found after 7 searches.
3:05:06.979082 INFO: ==============================================
3:05:06.979185 PROGRESS: Optimization finished for rt_error.
3:05:06.995859 INFO: calibration group: precursor, predicting mz
3:05:06.999360 INFO: calibration group: precursor, predicting rt
3:05:07.009746 INFO: calibration group: fragment, predicting mz
3:05:07.071131 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:05:07.071649 PROGRESS: ==============================================
3:05:07.071789 PROGRESS: ms2_error      : 8.0000
3:05:07.071918 PROGRESS: ms1_error      : 3.0000
3:05:07.072046 PROGRESS: rt_error       : 16.2407
3:05:07.072157 PROGRESS: ==============================================
3:05:07.074278 INFO: calibration group: precursor, predicting mz
3:05:07.086330 INFO: calibration group: precursor, predicting rt
3:05:07.132156 INFO: calibration group: fragment, predicting mz
3:05:07.255135 PROGRESS: Extracting batch of 78739 precursors
3:05:07.282221 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:05:07.282944 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:05:07.283049 INFO: FWHM in RT is 2.25 seconds, sigma is 0.29
3:05:07.283137 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:05:07.283823 INFO: Starting candidate selection
3:05:10.301610 INFO: Applying score cutoff of 7.940015068054199
3:05:10.306288 INFO: Removed 2224 precursors with score below cutoff
3:05:10.339487 INFO: Starting candidate scoring
3:05:11.511187 INFO: Finished candidate processing
3:05:11.511354 INFO: Collecting candidate features
3:05:11.875320 WARNING: intensity_correlation has 41 NaNs ( 0.03 % out of 150959)
3:05:11.886491 INFO: Collecting fragment features
3:05:11.996615 INFO: Finished candidate scoring
3:05:12.086196 INFO: === FDR correction performed with classifier version 12 ===
3:05:12.087277 INFO: performing precursor FDR with 47 features
3:05:12.087312 INFO: Decoy channel: -1
3:05:12.087336 INFO: Competetive: True
3:05:12.140072 INFO: Setting torch num_threads to 2 for FDR classification task
3:05:12.167974 WARNING: dropped 15 target PSMs due to missing features
3:05:12.168157 WARNING: dropped 26 decoy PSMs due to missing features
3:05:14.867453 INFO: Test AUC: 0.783
3:05:14.867610 INFO: Train AUC: 0.790
3:05:14.867647 INFO: AUC difference: 0.92%
3:05:14.966317 INFO: Resetting torch num_threads to 100
3:05:14.973487 INFO: Removing fragments below FDR threshold
3:05:14.999910 PROGRESS: ============================= Precursor FDR =============================
3:05:15.000262 PROGRESS: Total precursors accumulated: 22,638
3:05:15.000331 PROGRESS: Target precursors: 22,414 (99.01%)
3:05:15.000382 PROGRESS: Decoy precursors: 224 (0.99%)
3:05:15.000429 PROGRESS: 
3:05:15.000473 PROGRESS: Precursor Summary:
3:05:15.009101 PROGRESS: Channel   0:	 0.05 FDR: 22,414; 0.01 FDR: 22,414; 0.001 FDR: 19,563
3:05:15.009428 PROGRESS: 
3:05:15.009489 PROGRESS: Protein Summary:
3:05:15.021423 PROGRESS: Channel   0:	 0.05 FDR: 6,045; 0.01 FDR: 6,045; 0.001 FDR: 5,783
3:05:15.021712 PROGRESS: =========================================================================
3:05:15.284919 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:05:15.297599 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:05:15.297767 INFO: Quantification results path: run_output_Astral/alphadia_1.10_MBRSetValues/quant
3:05:15.297852 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3 at run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:05:15.298636 INFO: Initializing RawFileManager
3:05:45.064976 INFO: Determining DIA cycle
3:05:45.080886 INFO: Found cycle with start 0.00 min and length 303.
3:05:45.343373 INFO: RT (min)            : 0.0 - 26.9
3:05:45.343475 INFO: RT duration (sec)   : 1611.2
3:05:45.343516 INFO: RT duration (min)   : 26.9
3:05:45.343541 INFO: Cycle len (scans)   : 303
3:05:45.343560 INFO: Cycle len (sec)     : 1.65
3:05:45.343578 INFO: Number of cycles    : 977
3:05:45.343596 INFO: MS2 range (m/z)     : 380.4 - 980.7
3:05:45.370959 INFO: Initializing CalibrationManager
3:05:45.371346 INFO: Loading calibration config
3:05:45.371995 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'}]
3:05:45.372092 INFO: Calibration group :fragment, found 1 estimator(s)
3:05:45.372182 INFO: Calibration group :precursor, found 3 estimator(s)
3:05:45.372253 INFO: Disabling ion mobility calibration
3:05:45.372277 INFO: removed mobility estimator from group precursor
3:05:45.372422 INFO: Initializing OptimizationManager
3:05:45.372543 INFO: initial parameter: ms1_error = 30
3:05:45.372615 INFO: initial parameter: ms2_error = 30
3:05:45.372661 INFO: initial parameter: rt_error = 805.6004638671875
3:05:45.372710 INFO: initial parameter: mobility_error = 0.1
3:05:45.372753 INFO: initial parameter: column_type = library
3:05:45.372792 INFO: initial parameter: num_candidates = 1
3:05:45.372831 INFO: initial parameter: classifier_version = -1
3:05:45.372871 INFO: initial parameter: fwhm_rt = 5
3:05:45.372911 INFO: initial parameter: fwhm_mobility = 0.01
3:05:45.372950 INFO: initial parameter: score_cutoff = 0
3:05:45.373012 INFO: Initializing TimingManager
3:05:45.373066 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:05:45.373167 INFO: FDRManager not loaded from disk.
3:05:45.373190 INFO: Initializing FDRManager
3:05:45.373222 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
3:05:45.395806 PROGRESS: 39,524 target precursors potentially observable (0 removed)
3:05:45.424343 PROGRESS: Starting initial search for precursors.
3:05:45.440804 INFO: Starting optimization step 0.
3:05:45.441100 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:05:45.441175 PROGRESS: Extracting batch of 15945 precursors
3:05:45.445660 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:05:45.445743 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:05:45.445787 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:05:45.445810 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:05:45.446136 INFO: Starting candidate selection
3:05:46.498430 INFO: Starting candidate scoring
3:05:46.606175 INFO: Finished candidate processing
3:05:46.606294 INFO: Collecting candidate features
3:05:46.643526 INFO: Collecting fragment features
3:05:46.659564 INFO: Finished candidate scoring
3:05:46.672778 PROGRESS: === Extracted 15945 precursors and 171355 fragments ===
3:05:46.673233 INFO: performing precursor FDR with 47 features
3:05:46.673273 INFO: Decoy channel: -1
3:05:46.673297 INFO: Competetive: True
3:05:46.678857 INFO: Setting torch num_threads to 2 for FDR classification task
3:05:46.859963 INFO: Test AUC: 0.594
3:05:46.860108 INFO: Train AUC: 0.599
3:05:46.860138 INFO: AUC difference: 0.85%
3:05:46.949548 INFO: Resetting torch num_threads to 100
3:05:46.950914 INFO: === FDR correction performed with classifier version -1 ===
3:05:46.952099 PROGRESS: ============================= Precursor FDR =============================
3:05:46.952254 PROGRESS: Total precursors accumulated: 1,072
3:05:46.952319 PROGRESS: Target precursors: 985 (91.88%)
3:05:46.952370 PROGRESS: Decoy precursors: 87 (8.12%)
3:05:46.952417 PROGRESS: 
3:05:46.952462 PROGRESS: Precursor Summary:
3:05:46.953880 PROGRESS: Channel   0:	 0.05 FDR:   863; 0.01 FDR:   658; 0.001 FDR:   316
3:05:46.954034 PROGRESS: 
3:05:46.954092 PROGRESS: Protein Summary:
3:05:46.955691 PROGRESS: Channel   0:	 0.05 FDR:   722; 0.01 FDR:   566; 0.001 FDR:   287
3:05:46.955823 PROGRESS: =========================================================================
3:05:46.959628 INFO: fragments_df_filtered: 5000
3:05:46.972042 INFO: calibration group: precursor, fitting mz estimator 
3:05:47.034437 INFO: calibration group: precursor, fitting rt estimator 
3:05:47.093171 INFO: calibration group: fragment, fitting mz estimator 
3:05:47.512419 INFO: calibration group: precursor, predicting mz
3:05:47.515409 INFO: calibration group: precursor, predicting rt
3:05:47.525410 INFO: calibration group: fragment, predicting mz
3:05:47.550778 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3:05:47.551245 INFO: Starting optimization step 1.
3:05:47.551327 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:05:47.551397 PROGRESS: Extracting batch of 15945 precursors
3:05:47.563310 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:05:47.563512 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:05:47.563563 INFO: FWHM in RT is 2.94 seconds, sigma is 0.38
3:05:47.563589 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:05:47.563937 INFO: Starting candidate selection
3:05:48.576382 INFO: Starting candidate scoring
3:05:48.792180 INFO: Finished candidate processing
3:05:48.792298 INFO: Collecting candidate features
3:05:48.861531 INFO: Collecting fragment features
3:05:48.887775 INFO: Finished candidate scoring
3:05:48.906032 PROGRESS: === Extracted 31890 precursors and 339709 fragments ===
3:05:48.906456 INFO: performing precursor FDR with 47 features
3:05:48.906492 INFO: Decoy channel: -1
3:05:48.906515 INFO: Competetive: True
3:05:48.915524 INFO: Setting torch num_threads to 2 for FDR classification task
3:05:49.410728 INFO: Test AUC: 0.606
3:05:49.410873 INFO: Train AUC: 0.617
3:05:49.410904 INFO: AUC difference: 1.73%
3:05:49.499912 INFO: Resetting torch num_threads to 100
3:05:49.501564 INFO: === FDR correction performed with classifier version 0 ===
3:05:49.502966 PROGRESS: ============================= Precursor FDR =============================
3:05:49.503141 PROGRESS: Total precursors accumulated: 1,910
3:05:49.503216 PROGRESS: Target precursors: 1,763 (92.30%)
3:05:49.503268 PROGRESS: Decoy precursors: 147 (7.70%)
3:05:49.503317 PROGRESS: 
3:05:49.503361 PROGRESS: Precursor Summary:
3:05:49.505239 PROGRESS: Channel   0:	 0.05 FDR: 1,611; 0.01 FDR: 1,219; 0.001 FDR:    62
3:05:49.505392 PROGRESS: 
3:05:49.505449 PROGRESS: Protein Summary:
3:05:49.507313 PROGRESS: Channel   0:	 0.05 FDR: 1,244; 0.01 FDR:   964; 0.001 FDR:    60
3:05:49.508568 PROGRESS: =========================================================================
3:05:49.516823 INFO: fragments_df_filtered: 5000
3:05:49.534766 INFO: calibration group: precursor, fitting mz estimator 
3:05:49.650965 INFO: calibration group: precursor, fitting rt estimator 
3:05:49.805285 INFO: calibration group: fragment, fitting mz estimator 
3:05:50.250331 INFO: calibration group: precursor, predicting mz
3:05:50.253209 INFO: calibration group: precursor, predicting rt
3:05:50.263190 INFO: calibration group: fragment, predicting mz
3:05:50.304412 INFO: === checking if optimization conditions were reached ===
3:05:50.307485 PROGRESS: ❌ ms2_error      : 14.9663 > 8.0000 or insufficient steps taken.
3:05:50.315375 PROGRESS: ❌ ms1_error      : 13.6941 > 3.0000 or insufficient steps taken.
3:05:50.315554 INFO: ==============================================
3:05:50.315880 INFO: Starting optimization step 2.
3:05:50.315967 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:05:50.316046 PROGRESS: Extracting batch of 15945 precursors
3:05:50.322089 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:05:50.322177 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:05:50.322216 INFO: FWHM in RT is 2.89 seconds, sigma is 0.37
3:05:50.322244 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:05:50.322463 INFO: Starting candidate selection
3:05:51.272446 INFO: Starting candidate scoring
3:05:51.480300 INFO: Finished candidate processing
3:05:51.480426 INFO: Collecting candidate features
3:05:51.534389 INFO: Collecting fragment features
3:05:51.555053 INFO: Finished candidate scoring
3:05:51.569837 PROGRESS: === Extracted 31887 precursors and 312181 fragments ===
3:05:51.570265 INFO: performing precursor FDR with 47 features
3:05:51.570302 INFO: Decoy channel: -1
3:05:51.570325 INFO: Competetive: True
3:05:51.578624 INFO: Setting torch num_threads to 2 for FDR classification task
3:05:52.103492 INFO: Test AUC: 0.637
3:05:52.103646 INFO: Train AUC: 0.649
3:05:52.103677 INFO: AUC difference: 1.82%
3:05:52.195622 INFO: Resetting torch num_threads to 100
3:05:52.196995 INFO: === FDR correction performed with classifier version 1 ===
3:05:52.198071 PROGRESS: ============================= Precursor FDR =============================
3:05:52.198167 PROGRESS: Total precursors accumulated: 3,241
3:05:52.198225 PROGRESS: Target precursors: 3,020 (93.18%)
3:05:52.198274 PROGRESS: Decoy precursors: 221 (6.82%)
3:05:52.198319 PROGRESS: 
3:05:52.198363 PROGRESS: Precursor Summary:
3:05:52.200022 PROGRESS: Channel   0:	 0.05 FDR: 2,831; 0.01 FDR: 2,221; 0.001 FDR: 1,514
3:05:52.200128 PROGRESS: 
3:05:52.200184 PROGRESS: Protein Summary:
3:05:52.202345 PROGRESS: Channel   0:	 0.05 FDR: 1,973; 0.01 FDR: 1,621; 0.001 FDR: 1,179
3:05:52.202452 PROGRESS: =========================================================================
3:05:52.213358 INFO: fragments_df_filtered: 5000
3:05:52.227882 INFO: calibration group: precursor, fitting mz estimator 
3:05:52.381941 INFO: calibration group: precursor, fitting rt estimator 
3:05:52.584353 INFO: calibration group: fragment, fitting mz estimator 
3:05:53.026857 INFO: calibration group: precursor, predicting mz
3:05:53.029807 INFO: calibration group: precursor, predicting rt
3:05:53.039753 INFO: calibration group: fragment, predicting mz
3:05:53.072313 INFO: === checking if optimization conditions were reached ===
3:05:53.075055 PROGRESS: ❌ ms2_error      : 9.8037 > 8.0000 or insufficient steps taken.
3:05:53.076656 PROGRESS: ❌ ms1_error      : 6.2155 > 3.0000 or insufficient steps taken.
3:05:53.076738 INFO: ==============================================
3:05:53.076918 INFO: Starting optimization step 3.
3:05:53.077003 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:05:53.077082 PROGRESS: Extracting batch of 15945 precursors
3:05:53.096572 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:05:53.096781 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:05:53.096822 INFO: FWHM in RT is 2.63 seconds, sigma is 0.34
3:05:53.096851 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:05:53.097173 INFO: Starting candidate selection
3:05:54.022810 INFO: Starting candidate scoring
3:05:54.223701 INFO: Finished candidate processing
3:05:54.223826 INFO: Collecting candidate features
3:05:54.275143 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 31881)
3:05:54.281597 INFO: Collecting fragment features
3:05:54.302545 INFO: Finished candidate scoring
3:05:54.318031 PROGRESS: === Extracted 31881 precursors and 288961 fragments ===
3:05:54.318449 INFO: performing precursor FDR with 47 features
3:05:54.318489 INFO: Decoy channel: -1
3:05:54.318514 INFO: Competetive: True
3:05:54.329462 INFO: Setting torch num_threads to 2 for FDR classification task
3:05:54.336352 WARNING: dropped 1 decoy PSMs due to missing features
3:05:54.814885 INFO: Test AUC: 0.658
3:05:54.815021 INFO: Train AUC: 0.676
3:05:54.815052 INFO: AUC difference: 2.71%
3:05:54.900903 INFO: Resetting torch num_threads to 100
3:05:54.902291 INFO: === FDR correction performed with classifier version 2 ===
3:05:54.903939 PROGRESS: ============================= Precursor FDR =============================
3:05:54.904063 PROGRESS: Total precursors accumulated: 3,969
3:05:54.904122 PROGRESS: Target precursors: 3,722 (93.78%)
3:05:54.904171 PROGRESS: Decoy precursors: 247 (6.22%)
3:05:54.904217 PROGRESS: 
3:05:54.904258 PROGRESS: Precursor Summary:
3:05:54.906446 PROGRESS: Channel   0:	 0.05 FDR: 3,591; 0.01 FDR: 3,007; 0.001 FDR: 1,760
3:05:54.906572 PROGRESS: 
3:05:54.906628 PROGRESS: Protein Summary:
3:05:54.909265 PROGRESS: Channel   0:	 0.05 FDR: 2,387; 0.01 FDR: 2,085; 0.001 FDR: 1,365
3:05:54.909387 PROGRESS: =========================================================================
3:05:54.922168 INFO: fragments_df_filtered: 5000
3:05:54.934942 INFO: calibration group: precursor, fitting mz estimator 
3:05:55.160864 INFO: calibration group: precursor, fitting rt estimator 
3:05:55.383038 INFO: calibration group: fragment, fitting mz estimator 
3:05:55.870938 INFO: calibration group: precursor, predicting mz
3:05:55.873870 INFO: calibration group: precursor, predicting rt
3:05:55.883037 INFO: calibration group: fragment, predicting mz
3:05:55.947551 INFO: === checking if optimization conditions were reached ===
3:05:55.966308 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
3:05:55.968046 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
3:05:55.968107 INFO: ==============================================
3:05:55.968301 PROGRESS: Optimization finished for ms2_error, ms1_error.
3:05:56.000132 INFO: calibration group: precursor, predicting mz
3:05:56.003964 INFO: calibration group: precursor, predicting rt
3:05:56.014932 INFO: calibration group: fragment, predicting mz
3:05:56.046484 INFO: Starting optimization step 0.
3:05:56.046840 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:05:56.046926 PROGRESS: Extracting batch of 15945 precursors
3:05:56.052616 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:05:56.052731 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:05:56.052772 INFO: FWHM in RT is 2.41 seconds, sigma is 0.31
3:05:56.052800 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:05:56.053070 INFO: Starting candidate selection
3:05:56.973269 INFO: Starting candidate scoring
3:05:57.194273 INFO: Finished candidate processing
3:05:57.194392 INFO: Collecting candidate features
3:05:57.247578 INFO: Collecting fragment features
3:05:57.268180 INFO: Finished candidate scoring
3:05:57.283494 PROGRESS: === Extracted 31883 precursors and 284250 fragments ===
3:05:57.283933 INFO: performing precursor FDR with 47 features
3:05:57.283970 INFO: Decoy channel: -1
3:05:57.283993 INFO: Competetive: True
3:05:57.293071 INFO: Setting torch num_threads to 2 for FDR classification task
3:05:57.770777 INFO: Test AUC: 0.672
3:05:57.770932 INFO: Train AUC: 0.684
3:05:57.770963 INFO: AUC difference: 1.76%
3:05:57.856332 INFO: Resetting torch num_threads to 100
3:05:57.857670 INFO: === FDR correction performed with classifier version 3 ===
3:05:57.859030 PROGRESS: ============================= Precursor FDR =============================
3:05:57.859154 PROGRESS: Total precursors accumulated: 4,226
3:05:57.859219 PROGRESS: Target precursors: 3,991 (94.44%)
3:05:57.859271 PROGRESS: Decoy precursors: 235 (5.56%)
3:05:57.859316 PROGRESS: 
3:05:57.859361 PROGRESS: Precursor Summary:
3:05:57.861471 PROGRESS: Channel   0:	 0.05 FDR: 3,896; 0.01 FDR: 3,247; 0.001 FDR: 2,392
3:05:57.861621 PROGRESS: 
3:05:57.861678 PROGRESS: Protein Summary:
3:05:57.864474 PROGRESS: Channel   0:	 0.05 FDR: 2,551; 0.01 FDR: 2,232; 0.001 FDR: 1,752
3:05:57.864587 PROGRESS: =========================================================================
3:05:57.877362 INFO: fragments_df_filtered: 5000
3:05:57.890910 INFO: calibration group: precursor, fitting mz estimator 
3:05:58.141474 INFO: calibration group: precursor, fitting rt estimator 
3:05:58.385257 INFO: calibration group: fragment, fitting mz estimator 
3:05:58.809261 INFO: calibration group: precursor, predicting mz
3:05:58.812273 INFO: calibration group: precursor, predicting rt
3:05:58.821758 INFO: calibration group: fragment, predicting mz
3:05:58.844189 INFO: === checking if optimization conditions were reached ===
3:05:58.844551 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3:05:58.848405 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 59.8850.
3:05:58.848485 INFO: ==============================================
3:05:58.848609 INFO: Starting optimization step 1.
3:05:58.848684 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:05:58.848766 PROGRESS: Extracting batch of 15945 precursors
3:05:58.854993 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:05:58.855093 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:05:58.855131 INFO: FWHM in RT is 2.28 seconds, sigma is 0.29
3:05:58.855159 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:05:58.855403 INFO: Starting candidate selection
3:05:59.566201 INFO: Starting candidate scoring
3:05:59.760330 INFO: Finished candidate processing
3:05:59.760461 INFO: Collecting candidate features
3:05:59.812472 WARNING: intensity_correlation has 5 NaNs ( 0.02 % out of 31726)
3:05:59.817212 INFO: Collecting fragment features
3:05:59.836998 INFO: Finished candidate scoring
3:05:59.851042 PROGRESS: === Extracted 31726 precursors and 259957 fragments ===
3:05:59.851453 INFO: performing precursor FDR with 47 features
3:05:59.851494 INFO: Decoy channel: -1
3:05:59.851517 INFO: Competetive: True
3:05:59.859948 INFO: Setting torch num_threads to 2 for FDR classification task
3:05:59.864991 WARNING: dropped 2 target PSMs due to missing features
3:05:59.865102 WARNING: dropped 3 decoy PSMs due to missing features
3:06:00.362127 INFO: Test AUC: 0.738
3:06:00.362274 INFO: Train AUC: 0.731
3:06:00.362304 INFO: AUC difference: 1.01%
3:06:00.448168 INFO: Resetting torch num_threads to 100
3:06:00.449896 INFO: === FDR correction performed with classifier version 3 ===
3:06:00.451757 PROGRESS: ============================= Precursor FDR =============================
3:06:00.451934 PROGRESS: Total precursors accumulated: 4,841
3:06:00.452006 PROGRESS: Target precursors: 4,600 (95.02%)
3:06:00.452058 PROGRESS: Decoy precursors: 241 (4.98%)
3:06:00.452105 PROGRESS: 
3:06:00.452150 PROGRESS: Precursor Summary:
3:06:00.454639 PROGRESS: Channel   0:	 0.05 FDR: 4,581; 0.01 FDR: 3,858; 0.001 FDR: 2,482
3:06:00.454824 PROGRESS: 
3:06:00.454885 PROGRESS: Protein Summary:
3:06:00.457766 PROGRESS: Channel   0:	 0.05 FDR: 2,875; 0.01 FDR: 2,539; 0.001 FDR: 1,805
3:06:00.457898 PROGRESS: =========================================================================
3:06:00.471238 INFO: fragments_df_filtered: 5000
3:06:00.483928 INFO: calibration group: precursor, fitting mz estimator 
3:06:00.784821 INFO: calibration group: precursor, fitting rt estimator 
3:06:01.084543 INFO: calibration group: fragment, fitting mz estimator 
3:06:01.510830 INFO: calibration group: precursor, predicting mz
3:06:01.513835 INFO: calibration group: precursor, predicting rt
3:06:01.523173 INFO: calibration group: fragment, predicting mz
3:06:01.577483 INFO: === checking if optimization conditions were reached ===
3:06:01.578031 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3:06:01.583933 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 24.5690.
3:06:01.584085 INFO: ==============================================
3:06:01.584295 INFO: Starting optimization step 2.
3:06:01.584383 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:06:01.584467 PROGRESS: Extracting batch of 15945 precursors
3:06:01.596064 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:06:01.596258 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:06:01.596316 INFO: FWHM in RT is 2.27 seconds, sigma is 0.29
3:06:01.596357 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:06:01.596763 INFO: Starting candidate selection
3:06:02.289484 INFO: Starting candidate scoring
3:06:02.487389 INFO: Finished candidate processing
3:06:02.487507 INFO: Collecting candidate features
3:06:02.543688 WARNING: intensity_correlation has 17 NaNs ( 0.06 % out of 30738)
3:06:02.548137 INFO: Collecting fragment features
3:06:02.566683 INFO: Finished candidate scoring
3:06:02.581056 PROGRESS: === Extracted 30738 precursors and 239719 fragments ===
3:06:02.581458 INFO: performing precursor FDR with 47 features
3:06:02.581496 INFO: Decoy channel: -1
3:06:02.581520 INFO: Competetive: True
3:06:02.590075 INFO: Setting torch num_threads to 2 for FDR classification task
3:06:02.595883 WARNING: dropped 5 target PSMs due to missing features
3:06:02.596068 WARNING: dropped 12 decoy PSMs due to missing features
3:06:02.989652 INFO: Test AUC: 0.747
3:06:02.989797 INFO: Train AUC: 0.761
3:06:02.989828 INFO: AUC difference: 1.81%
3:06:03.075606 INFO: Resetting torch num_threads to 100
3:06:03.076920 INFO: === FDR correction performed with classifier version 3 ===
3:06:03.078254 PROGRESS: ============================= Precursor FDR =============================
3:06:03.078360 PROGRESS: Total precursors accumulated: 5,190
3:06:03.078420 PROGRESS: Target precursors: 4,937 (95.13%)
3:06:03.078471 PROGRESS: Decoy precursors: 253 (4.87%)
3:06:03.078515 PROGRESS: 
3:06:03.078559 PROGRESS: Precursor Summary:
3:06:03.080630 PROGRESS: Channel   0:	 0.05 FDR: 4,919; 0.01 FDR: 4,213; 0.001 FDR: 2,607
3:06:03.080762 PROGRESS: 
3:06:03.080820 PROGRESS: Protein Summary:
3:06:03.083714 PROGRESS: Channel   0:	 0.05 FDR: 3,000; 0.01 FDR: 2,685; 0.001 FDR: 1,868
3:06:03.083818 PROGRESS: =========================================================================
3:06:03.097048 INFO: fragments_df_filtered: 5000
3:06:03.112481 INFO: calibration group: precursor, fitting mz estimator 
3:06:03.480924 INFO: calibration group: precursor, fitting rt estimator 
3:06:03.814440 INFO: calibration group: fragment, fitting mz estimator 
3:06:04.233526 INFO: calibration group: precursor, predicting mz
3:06:04.236467 INFO: calibration group: precursor, predicting rt
3:06:04.245482 INFO: calibration group: fragment, predicting mz
3:06:04.322060 INFO: === checking if optimization conditions were reached ===
3:06:04.322349 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3:06:04.346242 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 15.3852.
3:06:04.346349 INFO: ==============================================
3:06:04.346485 INFO: Starting optimization step 3.
3:06:04.346559 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:06:04.346626 PROGRESS: Extracting batch of 15945 precursors
3:06:04.350294 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:06:04.350352 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:06:04.350389 INFO: FWHM in RT is 2.24 seconds, sigma is 0.29
3:06:04.350418 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:06:04.350593 INFO: Starting candidate selection
3:06:05.015428 INFO: Starting candidate scoring
3:06:05.224937 INFO: Finished candidate processing
3:06:05.225064 INFO: Collecting candidate features
3:06:05.274851 WARNING: intensity_correlation has 13 NaNs ( 0.04 % out of 30860)
3:06:05.279196 INFO: Collecting fragment features
3:06:05.297055 INFO: Finished candidate scoring
3:06:05.311157 PROGRESS: === Extracted 30860 precursors and 243160 fragments ===
3:06:05.311579 INFO: performing precursor FDR with 47 features
3:06:05.311616 INFO: Decoy channel: -1
3:06:05.311640 INFO: Competetive: True
3:06:05.320614 INFO: Setting torch num_threads to 2 for FDR classification task
3:06:05.326158 WARNING: dropped 6 target PSMs due to missing features
3:06:05.326311 WARNING: dropped 7 decoy PSMs due to missing features
3:06:05.712215 INFO: Test AUC: 0.764
3:06:05.712374 INFO: Train AUC: 0.766
3:06:05.712405 INFO: AUC difference: 0.21%
3:06:05.796569 INFO: Resetting torch num_threads to 100
3:06:05.797877 INFO: === FDR correction performed with classifier version 3 ===
3:06:05.799358 PROGRESS: ============================= Precursor FDR =============================
3:06:05.799478 PROGRESS: Total precursors accumulated: 5,137
3:06:05.799539 PROGRESS: Target precursors: 4,900 (95.39%)
3:06:05.799591 PROGRESS: Decoy precursors: 237 (4.61%)
3:06:05.799636 PROGRESS: 
3:06:05.799680 PROGRESS: Precursor Summary:
3:06:05.801971 PROGRESS: Channel   0:	 0.05 FDR: 4,900; 0.01 FDR: 4,265; 0.001 FDR: 3,093
3:06:05.802135 PROGRESS: 
3:06:05.802193 PROGRESS: Protein Summary:
3:06:05.805337 PROGRESS: Channel   0:	 0.05 FDR: 3,003; 0.01 FDR: 2,725; 0.001 FDR: 2,138
3:06:05.805472 PROGRESS: =========================================================================
3:06:05.819404 INFO: fragments_df_filtered: 5000
3:06:05.832647 INFO: calibration group: precursor, fitting mz estimator 
3:06:06.219473 INFO: calibration group: precursor, fitting rt estimator 
3:06:06.558518 INFO: calibration group: fragment, fitting mz estimator 
3:06:07.026443 INFO: calibration group: precursor, predicting mz
3:06:07.029362 INFO: calibration group: precursor, predicting rt
3:06:07.038366 INFO: calibration group: fragment, predicting mz
3:06:07.067294 INFO: === checking if optimization conditions were reached ===
3:06:07.067805 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3:06:07.073644 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 16.5297.
3:06:07.073823 INFO: ==============================================
3:06:07.074025 INFO: Starting optimization step 4.
3:06:07.074102 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:06:07.074171 PROGRESS: Extracting batch of 15945 precursors
3:06:07.079706 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:06:07.079771 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:06:07.079808 INFO: FWHM in RT is 2.24 seconds, sigma is 0.29
3:06:07.079835 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:06:07.080046 INFO: Starting candidate selection
3:06:07.753948 INFO: Starting candidate scoring
3:06:07.957212 INFO: Finished candidate processing
3:06:07.957328 INFO: Collecting candidate features
3:06:08.003268 WARNING: intensity_correlation has 15 NaNs ( 0.05 % out of 30845)
3:06:08.007564 INFO: Collecting fragment features
3:06:08.025531 INFO: Finished candidate scoring
3:06:08.039446 PROGRESS: === Extracted 30845 precursors and 242918 fragments ===
3:06:08.039876 INFO: performing precursor FDR with 47 features
3:06:08.039914 INFO: Decoy channel: -1
3:06:08.039939 INFO: Competetive: True
3:06:08.048428 INFO: Setting torch num_threads to 2 for FDR classification task
3:06:08.053827 WARNING: dropped 6 target PSMs due to missing features
3:06:08.053968 WARNING: dropped 9 decoy PSMs due to missing features
3:06:08.439405 INFO: Test AUC: 0.763
3:06:08.439558 INFO: Train AUC: 0.762
3:06:08.439591 INFO: AUC difference: 0.08%
3:06:08.521666 INFO: Resetting torch num_threads to 100
3:06:08.522806 INFO: === FDR correction performed with classifier version 3 ===
3:06:08.524027 PROGRESS: ============================= Precursor FDR =============================
3:06:08.524120 PROGRESS: Total precursors accumulated: 5,166
3:06:08.524179 PROGRESS: Target precursors: 4,923 (95.30%)
3:06:08.524229 PROGRESS: Decoy precursors: 243 (4.70%)
3:06:08.524275 PROGRESS: 
3:06:08.524319 PROGRESS: Precursor Summary:
3:06:08.526484 PROGRESS: Channel   0:	 0.05 FDR: 4,923; 0.01 FDR: 4,221; 0.001 FDR: 3,164
3:06:08.526602 PROGRESS: 
3:06:08.526662 PROGRESS: Protein Summary:
3:06:08.529701 PROGRESS: Channel   0:	 0.05 FDR: 3,009; 0.01 FDR: 2,706; 0.001 FDR: 2,181
3:06:08.529808 PROGRESS: =========================================================================
3:06:08.543176 INFO: fragments_df_filtered: 5000
3:06:08.555037 INFO: calibration group: precursor, fitting mz estimator 
3:06:08.868388 INFO: calibration group: precursor, fitting rt estimator 
3:06:09.206143 INFO: calibration group: fragment, fitting mz estimator 
3:06:09.623653 INFO: calibration group: precursor, predicting mz
3:06:09.626603 INFO: calibration group: precursor, predicting rt
3:06:09.635849 INFO: calibration group: fragment, predicting mz
3:06:09.664430 INFO: === checking if optimization conditions were reached ===
3:06:09.664717 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3:06:09.669022 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 16.6350.
3:06:09.669097 INFO: ==============================================
3:06:09.669214 INFO: Starting optimization step 5.
3:06:09.669290 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:06:09.669358 PROGRESS: Extracting batch of 15945 precursors
3:06:09.687337 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:06:09.687438 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:06:09.687479 INFO: FWHM in RT is 2.24 seconds, sigma is 0.29
3:06:09.687508 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:06:09.687746 INFO: Starting candidate selection
3:06:10.365317 INFO: Starting candidate scoring
3:06:10.569898 INFO: Finished candidate processing
3:06:10.570135 INFO: Collecting candidate features
3:06:10.617668 WARNING: intensity_correlation has 14 NaNs ( 0.05 % out of 30843)
3:06:10.621940 INFO: Collecting fragment features
3:06:10.640138 INFO: Finished candidate scoring
3:06:10.654428 PROGRESS: === Extracted 30843 precursors and 242830 fragments ===
3:06:10.654856 INFO: performing precursor FDR with 47 features
3:06:10.654894 INFO: Decoy channel: -1
3:06:10.654918 INFO: Competetive: True
3:06:10.664685 INFO: Setting torch num_threads to 2 for FDR classification task
3:06:10.671253 WARNING: dropped 6 target PSMs due to missing features
3:06:10.671399 WARNING: dropped 8 decoy PSMs due to missing features
3:06:11.063633 INFO: Test AUC: 0.761
3:06:11.063783 INFO: Train AUC: 0.762
3:06:11.063813 INFO: AUC difference: 0.21%
3:06:11.150753 INFO: Resetting torch num_threads to 100
3:06:11.152093 INFO: === FDR correction performed with classifier version 3 ===
3:06:11.153333 PROGRESS: ============================= Precursor FDR =============================
3:06:11.153426 PROGRESS: Total precursors accumulated: 5,168
3:06:11.153486 PROGRESS: Target precursors: 4,933 (95.45%)
3:06:11.153537 PROGRESS: Decoy precursors: 235 (4.55%)
3:06:11.153584 PROGRESS: 
3:06:11.153628 PROGRESS: Precursor Summary:
3:06:11.155702 PROGRESS: Channel   0:	 0.05 FDR: 4,933; 0.01 FDR: 4,248; 0.001 FDR: 3,134
3:06:11.155870 PROGRESS: 
3:06:11.155950 PROGRESS: Protein Summary:
3:06:11.159169 PROGRESS: Channel   0:	 0.05 FDR: 3,020; 0.01 FDR: 2,714; 0.001 FDR: 2,157
3:06:11.159288 PROGRESS: =========================================================================
3:06:11.175268 INFO: fragments_df_filtered: 5000
3:06:11.188118 INFO: calibration group: precursor, fitting mz estimator 
3:06:11.520041 INFO: calibration group: precursor, fitting rt estimator 
3:06:11.859260 INFO: calibration group: fragment, fitting mz estimator 
3:06:12.278248 INFO: calibration group: precursor, predicting mz
3:06:12.281242 INFO: calibration group: precursor, predicting rt
3:06:12.290361 INFO: calibration group: fragment, predicting mz
3:06:12.318269 INFO: === checking if optimization conditions were reached ===
3:06:12.318469 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3:06:12.319719 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 15.3852 found after 6 searches.
3:06:12.319782 INFO: ==============================================
3:06:12.319880 PROGRESS: Optimization finished for rt_error.
3:06:12.355201 INFO: calibration group: precursor, predicting mz
3:06:12.358469 INFO: calibration group: precursor, predicting rt
3:06:12.378286 INFO: calibration group: fragment, predicting mz
3:06:12.451831 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:06:12.452126 PROGRESS: ==============================================
3:06:12.452217 PROGRESS: ms2_error      : 8.0000
3:06:12.452295 PROGRESS: ms1_error      : 3.0000
3:06:12.452367 PROGRESS: rt_error       : 15.3852
3:06:12.452447 PROGRESS: ==============================================
3:06:12.453426 INFO: calibration group: precursor, predicting mz
3:06:12.464334 INFO: calibration group: precursor, predicting rt
3:06:12.515579 INFO: calibration group: fragment, predicting mz
3:06:12.649771 PROGRESS: Extracting batch of 78739 precursors
3:06:12.675240 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:06:12.675558 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:06:12.675666 INFO: FWHM in RT is 2.24 seconds, sigma is 0.29
3:06:12.675759 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:06:12.676093 INFO: Starting candidate selection
3:06:15.682963 INFO: Applying score cutoff of 12.125768646240234
3:06:15.686953 INFO: Removed 5061 precursors with score below cutoff
3:06:15.728431 INFO: Starting candidate scoring
3:06:16.772435 INFO: Finished candidate processing
3:06:16.772620 INFO: Collecting candidate features
3:06:17.012040 WARNING: intensity_correlation has 37 NaNs ( 0.02 % out of 148497)
3:06:17.020906 INFO: Collecting fragment features
3:06:17.120517 INFO: Finished candidate scoring
3:06:17.202829 INFO: === FDR correction performed with classifier version 7 ===
3:06:17.203581 INFO: performing precursor FDR with 47 features
3:06:17.203616 INFO: Decoy channel: -1
3:06:17.203639 INFO: Competetive: True
3:06:17.254023 INFO: Setting torch num_threads to 2 for FDR classification task
3:06:17.277324 WARNING: dropped 13 target PSMs due to missing features
3:06:17.277500 WARNING: dropped 24 decoy PSMs due to missing features
3:06:19.838379 INFO: Test AUC: 0.777
3:06:19.838932 INFO: Train AUC: 0.781
3:06:19.838968 INFO: AUC difference: 0.56%
3:06:19.935819 INFO: Resetting torch num_threads to 100
3:06:19.943706 INFO: Removing fragments below FDR threshold
3:06:19.970178 PROGRESS: ============================= Precursor FDR =============================
3:06:19.970497 PROGRESS: Total precursors accumulated: 22,070
3:06:19.970563 PROGRESS: Target precursors: 21,852 (99.01%)
3:06:19.970623 PROGRESS: Decoy precursors: 218 (0.99%)
3:06:19.970670 PROGRESS: 
3:06:19.970714 PROGRESS: Precursor Summary:
3:06:19.982260 PROGRESS: Channel   0:	 0.05 FDR: 21,852; 0.01 FDR: 21,852; 0.001 FDR: 17,794
3:06:19.982661 PROGRESS: 
3:06:19.982723 PROGRESS: Protein Summary:
3:06:19.997886 PROGRESS: Channel   0:	 0.05 FDR: 5,951; 0.01 FDR: 5,951; 0.001 FDR: 5,537
3:06:19.998178 PROGRESS: =========================================================================
3:06:20.262404 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:06:20.277530 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:06:20.277708 INFO: Quantification results path: run_output_Astral/alphadia_1.10_MBRSetValues/quant
3:06:20.277796 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1 at run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:06:20.278920 INFO: Initializing RawFileManager
3:06:47.321495 INFO: Determining DIA cycle
3:06:47.337839 INFO: Found cycle with start 0.00 min and length 303.
3:06:47.522080 INFO: RT (min)            : 0.0 - 26.9
3:06:47.522202 INFO: RT duration (sec)   : 1611.2
3:06:47.522232 INFO: RT duration (min)   : 26.9
3:06:47.522256 INFO: Cycle len (scans)   : 303
3:06:47.522276 INFO: Cycle len (sec)     : 1.65
3:06:47.522294 INFO: Number of cycles    : 977
3:06:47.522313 INFO: MS2 range (m/z)     : 380.4 - 980.7
3:06:47.552433 INFO: Initializing CalibrationManager
3:06:47.552805 INFO: Loading calibration config
3:06:47.553786 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'}]
3:06:47.554205 INFO: Calibration group :fragment, found 1 estimator(s)
3:06:47.554334 INFO: Calibration group :precursor, found 3 estimator(s)
3:06:47.554462 INFO: Disabling ion mobility calibration
3:06:47.554493 INFO: removed mobility estimator from group precursor
3:06:47.554688 INFO: Initializing OptimizationManager
3:06:47.554810 INFO: initial parameter: ms1_error = 30
3:06:47.554871 INFO: initial parameter: ms2_error = 30
3:06:47.554921 INFO: initial parameter: rt_error = 805.5982666015625
3:06:47.554970 INFO: initial parameter: mobility_error = 0.1
3:06:47.555012 INFO: initial parameter: column_type = library
3:06:47.555053 INFO: initial parameter: num_candidates = 1
3:06:47.555092 INFO: initial parameter: classifier_version = -1
3:06:47.555133 INFO: initial parameter: fwhm_rt = 5
3:06:47.555174 INFO: initial parameter: fwhm_mobility = 0.01
3:06:47.555213 INFO: initial parameter: score_cutoff = 0
3:06:47.555285 INFO: Initializing TimingManager
3:06:47.555342 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:06:47.555448 INFO: FDRManager not loaded from disk.
3:06:47.555472 INFO: Initializing FDRManager
3:06:47.555526 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
3:06:47.579835 PROGRESS: 39,524 target precursors potentially observable (0 removed)
3:06:47.609099 PROGRESS: Starting initial search for precursors.
3:06:47.631127 INFO: Starting optimization step 0.
3:06:47.631410 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:06:47.631500 PROGRESS: Extracting batch of 15945 precursors
3:06:47.636978 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:06:47.637045 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:06:47.637103 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:06:47.637127 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:06:47.637549 INFO: Starting candidate selection
3:06:48.620606 INFO: Starting candidate scoring
3:06:48.730384 INFO: Finished candidate processing
3:06:48.731472 INFO: Collecting candidate features
3:06:48.765896 INFO: Collecting fragment features
3:06:48.777993 INFO: Finished candidate scoring
3:06:48.785768 PROGRESS: === Extracted 15945 precursors and 172869 fragments ===
3:06:48.786124 INFO: performing precursor FDR with 47 features
3:06:48.786161 INFO: Decoy channel: -1
3:06:48.786185 INFO: Competetive: True
3:06:48.790217 INFO: Setting torch num_threads to 2 for FDR classification task
3:06:48.990487 INFO: Test AUC: 0.654
3:06:48.990613 INFO: Train AUC: 0.669
3:06:48.990644 INFO: AUC difference: 2.26%
3:06:49.069764 INFO: Resetting torch num_threads to 100
3:06:49.070725 INFO: === FDR correction performed with classifier version -1 ===
3:06:49.072234 PROGRESS: ============================= Precursor FDR =============================
3:06:49.072342 PROGRESS: Total precursors accumulated: 7,988
3:06:49.072401 PROGRESS: Target precursors: 5,420 (67.85%)
3:06:49.072450 PROGRESS: Decoy precursors: 2,568 (32.15%)
3:06:49.072495 PROGRESS: 
3:06:49.072537 PROGRESS: Precursor Summary:
3:06:49.073455 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:06:49.073561 PROGRESS: 
3:06:49.073618 PROGRESS: Protein Summary:
3:06:49.074585 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:06:49.074673 PROGRESS: =========================================================================
3:06:49.095947 INFO: Starting optimization step 1.
3:06:49.096236 PROGRESS: === Extracting elution groups 8000 to 24000 ===
3:06:49.096304 PROGRESS: Extracting batch of 31875 precursors
3:06:49.102968 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:06:49.103067 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:06:49.103101 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:06:49.103123 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:06:49.103326 INFO: Starting candidate selection
3:06:50.890875 INFO: Starting candidate scoring
3:06:53.446628 INFO: Finished candidate processing
3:06:53.446749 INFO: Collecting candidate features
3:06:53.510442 INFO: Collecting fragment features
3:06:53.547014 INFO: Finished candidate scoring
3:06:53.576094 PROGRESS: === Extracted 47820 precursors and 518604 fragments ===
3:06:53.583788 INFO: performing precursor FDR with 47 features
3:06:53.583876 INFO: Decoy channel: -1
3:06:53.583902 INFO: Competetive: True
3:06:53.606915 INFO: Setting torch num_threads to 2 for FDR classification task
3:06:54.519384 INFO: Test AUC: 0.726
3:06:54.519531 INFO: Train AUC: 0.734
3:06:54.519561 INFO: AUC difference: 1.10%
3:06:54.606831 INFO: Resetting torch num_threads to 100
3:06:54.609694 INFO: === FDR correction performed with classifier version -1 ===
3:06:54.611861 PROGRESS: ============================= Precursor FDR =============================
3:06:54.611984 PROGRESS: Total precursors accumulated: 9,555
3:06:54.612043 PROGRESS: Target precursors: 8,974 (93.92%)
3:06:54.612094 PROGRESS: Decoy precursors: 581 (6.08%)
3:06:54.612141 PROGRESS: 
3:06:54.612187 PROGRESS: Precursor Summary:
3:06:54.616274 PROGRESS: Channel   0:	 0.05 FDR: 8,690; 0.01 FDR: 7,445; 0.001 FDR: 5,181
3:06:54.616411 PROGRESS: 
3:06:54.616470 PROGRESS: Protein Summary:
3:06:54.620997 PROGRESS: Channel   0:	 0.05 FDR: 3,725; 0.01 FDR: 3,353; 0.001 FDR: 2,597
3:06:54.621114 PROGRESS: =========================================================================
3:06:54.647449 INFO: fragments_df_filtered: 5000
3:06:54.664596 INFO: calibration group: precursor, fitting mz estimator 
3:06:55.389508 INFO: calibration group: precursor, fitting rt estimator 
3:06:56.153059 INFO: calibration group: fragment, fitting mz estimator 
3:06:56.503925 INFO: calibration group: precursor, predicting mz
3:06:56.507014 INFO: calibration group: precursor, predicting rt
3:06:56.516286 INFO: calibration group: fragment, predicting mz
3:06:56.537243 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3:06:56.537463 INFO: Starting optimization step 2.
3:06:56.537548 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:06:56.537618 PROGRESS: Extracting batch of 15945 precursors
3:06:56.546340 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:06:56.546430 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:06:56.546468 INFO: FWHM in RT is 3.00 seconds, sigma is 0.39
3:06:56.546496 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:06:56.546751 INFO: Starting candidate selection
3:06:57.504014 INFO: Starting candidate scoring
3:06:57.685562 INFO: Finished candidate processing
3:06:57.685674 INFO: Collecting candidate features
3:06:57.734267 INFO: Collecting fragment features
3:06:57.754181 INFO: Finished candidate scoring
3:06:57.771437 PROGRESS: === Extracted 31890 precursors and 342242 fragments ===
3:06:57.771851 INFO: performing precursor FDR with 47 features
3:06:57.771894 INFO: Decoy channel: -1
3:06:57.771928 INFO: Competetive: True
3:06:57.780187 INFO: Setting torch num_threads to 2 for FDR classification task
3:06:58.300806 INFO: Test AUC: 0.697
3:06:58.300942 INFO: Train AUC: 0.697
3:06:58.300973 INFO: AUC difference: 0.02%
3:06:58.384440 INFO: Resetting torch num_threads to 100
3:06:58.385661 INFO: === FDR correction performed with classifier version 1 ===
3:06:58.386858 PROGRESS: ============================= Precursor FDR =============================
3:06:58.386954 PROGRESS: Total precursors accumulated: 4,653
3:06:58.387013 PROGRESS: Target precursors: 4,430 (95.21%)
3:06:58.387063 PROGRESS: Decoy precursors: 223 (4.79%)
3:06:58.387110 PROGRESS: 
3:06:58.387154 PROGRESS: Precursor Summary:
3:06:58.389116 PROGRESS: Channel   0:	 0.05 FDR: 4,429; 0.01 FDR: 3,621; 0.001 FDR: 1,378
3:06:58.389220 PROGRESS: 
3:06:58.389284 PROGRESS: Protein Summary:
3:06:58.391926 PROGRESS: Channel   0:	 0.05 FDR: 2,705; 0.01 FDR: 2,311; 0.001 FDR: 1,064
3:06:58.392025 PROGRESS: =========================================================================
3:06:58.407126 INFO: fragments_df_filtered: 5000
3:06:58.419198 INFO: calibration group: precursor, fitting mz estimator 
3:06:58.684753 INFO: calibration group: precursor, fitting rt estimator 
3:06:58.960538 INFO: calibration group: fragment, fitting mz estimator 
3:06:59.377006 INFO: calibration group: precursor, predicting mz
3:06:59.379852 INFO: calibration group: precursor, predicting rt
3:06:59.388633 INFO: calibration group: fragment, predicting mz
3:06:59.408649 INFO: === checking if optimization conditions were reached ===
3:06:59.410791 PROGRESS: ❌ ms2_error      : 19.1903 > 8.0000 or insufficient steps taken.
3:06:59.412503 PROGRESS: ❌ ms1_error      : 13.6198 > 3.0000 or insufficient steps taken.
3:06:59.412561 INFO: ==============================================
3:06:59.412667 INFO: Starting optimization step 3.
3:06:59.412754 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:06:59.412824 PROGRESS: Extracting batch of 15945 precursors
3:06:59.418615 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:06:59.418687 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:06:59.418725 INFO: FWHM in RT is 2.99 seconds, sigma is 0.38
3:06:59.418754 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:06:59.418961 INFO: Starting candidate selection
3:07:00.333695 INFO: Starting candidate scoring
3:07:00.528174 INFO: Finished candidate processing
3:07:00.528296 INFO: Collecting candidate features
3:07:00.577693 INFO: Collecting fragment features
3:07:00.597125 INFO: Finished candidate scoring
3:07:00.613872 PROGRESS: === Extracted 31889 precursors and 329179 fragments ===
3:07:00.614263 INFO: performing precursor FDR with 47 features
3:07:00.614303 INFO: Decoy channel: -1
3:07:00.614329 INFO: Competetive: True
3:07:00.622309 INFO: Setting torch num_threads to 2 for FDR classification task
3:07:01.136171 INFO: Test AUC: 0.725
3:07:01.136311 INFO: Train AUC: 0.729
3:07:01.136342 INFO: AUC difference: 0.46%
3:07:01.220263 INFO: Resetting torch num_threads to 100
3:07:01.221489 INFO: === FDR correction performed with classifier version 2 ===
3:07:01.222793 PROGRESS: ============================= Precursor FDR =============================
3:07:01.222891 PROGRESS: Total precursors accumulated: 5,611
3:07:01.222952 PROGRESS: Target precursors: 5,415 (96.51%)
3:07:01.223003 PROGRESS: Decoy precursors: 196 (3.49%)
3:07:01.223051 PROGRESS: 
3:07:01.223094 PROGRESS: Precursor Summary:
3:07:01.225291 PROGRESS: Channel   0:	 0.05 FDR: 5,415; 0.01 FDR: 4,765; 0.001 FDR: 2,750
3:07:01.225409 PROGRESS: 
3:07:01.225468 PROGRESS: Protein Summary:
3:07:01.228603 PROGRESS: Channel   0:	 0.05 FDR: 3,116; 0.01 FDR: 2,845; 0.001 FDR: 1,876
3:07:01.228712 PROGRESS: =========================================================================
3:07:01.245875 INFO: fragments_df_filtered: 5000
3:07:01.257707 INFO: calibration group: precursor, fitting mz estimator 
3:07:01.644051 INFO: calibration group: precursor, fitting rt estimator 
3:07:02.046349 INFO: calibration group: fragment, fitting mz estimator 
3:07:02.463723 INFO: calibration group: precursor, predicting mz
3:07:02.466560 INFO: calibration group: precursor, predicting rt
3:07:02.475263 INFO: calibration group: fragment, predicting mz
3:07:02.494225 INFO: === checking if optimization conditions were reached ===
3:07:02.496355 PROGRESS: ❌ ms2_error      : 14.6323 > 8.0000 or insufficient steps taken.
3:07:02.498169 PROGRESS: ❌ ms1_error      : 6.0988 > 3.0000 or insufficient steps taken.
3:07:02.498232 INFO: ==============================================
3:07:02.498338 INFO: Starting optimization step 4.
3:07:02.498416 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:07:02.498485 PROGRESS: Extracting batch of 15945 precursors
3:07:02.504059 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:07:02.504127 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:07:02.504166 INFO: FWHM in RT is 2.80 seconds, sigma is 0.36
3:07:02.504195 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:07:02.504401 INFO: Starting candidate selection
3:07:03.412074 INFO: Starting candidate scoring
3:07:03.642550 INFO: Finished candidate processing
3:07:03.642655 INFO: Collecting candidate features
3:07:03.691912 INFO: Collecting fragment features
3:07:03.712364 INFO: Finished candidate scoring
3:07:03.728371 PROGRESS: === Extracted 31888 precursors and 317074 fragments ===
3:07:03.728773 INFO: performing precursor FDR with 47 features
3:07:03.728815 INFO: Decoy channel: -1
3:07:03.728840 INFO: Competetive: True
3:07:03.736841 INFO: Setting torch num_threads to 2 for FDR classification task
3:07:04.250140 INFO: Test AUC: 0.739
3:07:04.250278 INFO: Train AUC: 0.751
3:07:04.250308 INFO: AUC difference: 1.58%
3:07:04.333635 INFO: Resetting torch num_threads to 100
3:07:04.334843 INFO: === FDR correction performed with classifier version 3 ===
3:07:04.336265 PROGRESS: ============================= Precursor FDR =============================
3:07:04.336364 PROGRESS: Total precursors accumulated: 6,224
3:07:04.336424 PROGRESS: Target precursors: 6,029 (96.87%)
3:07:04.336474 PROGRESS: Decoy precursors: 195 (3.13%)
3:07:04.336518 PROGRESS: 
3:07:04.336560 PROGRESS: Precursor Summary:
3:07:04.338940 PROGRESS: Channel   0:	 0.05 FDR: 6,029; 0.01 FDR: 5,543; 0.001 FDR: 3,522
3:07:04.339055 PROGRESS: 
3:07:04.339113 PROGRESS: Protein Summary:
3:07:04.342613 PROGRESS: Channel   0:	 0.05 FDR: 3,366; 0.01 FDR: 3,171; 0.001 FDR: 2,291
3:07:04.342719 PROGRESS: =========================================================================
3:07:04.362804 INFO: fragments_df_filtered: 5000
3:07:04.374720 INFO: calibration group: precursor, fitting mz estimator 
3:07:04.864113 INFO: calibration group: precursor, fitting rt estimator 
3:07:05.370316 INFO: calibration group: fragment, fitting mz estimator 
3:07:05.785797 INFO: calibration group: precursor, predicting mz
3:07:05.788711 INFO: calibration group: precursor, predicting rt
3:07:05.797532 INFO: calibration group: fragment, predicting mz
3:07:05.819567 INFO: === checking if optimization conditions were reached ===
3:07:05.822435 PROGRESS: ❌ ms2_error      : 11.7157 > 8.0000 or insufficient steps taken.
3:07:05.824430 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
3:07:05.824494 INFO: ==============================================
3:07:05.824620 INFO: Starting optimization step 5.
3:07:05.824697 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:07:05.824785 PROGRESS: Extracting batch of 15945 precursors
3:07:05.831860 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:07:05.831931 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:07:05.831970 INFO: FWHM in RT is 2.65 seconds, sigma is 0.34
3:07:05.832001 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:07:05.832203 INFO: Starting candidate selection
3:07:06.748265 INFO: Starting candidate scoring
3:07:06.989626 INFO: Finished candidate processing
3:07:06.989736 INFO: Collecting candidate features
3:07:07.037999 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 31884)
3:07:07.042383 INFO: Collecting fragment features
3:07:07.062534 INFO: Finished candidate scoring
3:07:07.078531 PROGRESS: === Extracted 31884 precursors and 307823 fragments ===
3:07:07.078946 INFO: performing precursor FDR with 47 features
3:07:07.078986 INFO: Decoy channel: -1
3:07:07.079010 INFO: Competetive: True
3:07:07.087050 INFO: Setting torch num_threads to 2 for FDR classification task
3:07:07.091197 WARNING: dropped 1 target PSMs due to missing features
3:07:07.603882 INFO: Test AUC: 0.759
3:07:07.604015 INFO: Train AUC: 0.771
3:07:07.604046 INFO: AUC difference: 1.54%
3:07:07.687492 INFO: Resetting torch num_threads to 100
3:07:07.688701 INFO: === FDR correction performed with classifier version 4 ===
3:07:07.690099 PROGRESS: ============================= Precursor FDR =============================
3:07:07.690195 PROGRESS: Total precursors accumulated: 6,616
3:07:07.690254 PROGRESS: Target precursors: 6,455 (97.57%)
3:07:07.690305 PROGRESS: Decoy precursors: 161 (2.43%)
3:07:07.690351 PROGRESS: 
3:07:07.690394 PROGRESS: Precursor Summary:
3:07:07.693032 PROGRESS: Channel   0:	 0.05 FDR: 6,455; 0.01 FDR: 6,209; 0.001 FDR: 4,317
3:07:07.693149 PROGRESS: 
3:07:07.693203 PROGRESS: Protein Summary:
3:07:07.696939 PROGRESS: Channel   0:	 0.05 FDR: 3,512; 0.01 FDR: 3,414; 0.001 FDR: 2,662
3:07:07.697057 PROGRESS: =========================================================================
3:07:07.717619 INFO: fragments_df_filtered: 5000
3:07:07.729776 INFO: calibration group: precursor, fitting mz estimator 
3:07:08.331708 INFO: calibration group: precursor, fitting rt estimator 
3:07:08.949821 INFO: calibration group: fragment, fitting mz estimator 
3:07:09.363292 INFO: calibration group: precursor, predicting mz
3:07:09.366174 INFO: calibration group: precursor, predicting rt
3:07:09.374983 INFO: calibration group: fragment, predicting mz
3:07:09.400225 INFO: === checking if optimization conditions were reached ===
3:07:09.403086 PROGRESS: ❌ ms2_error      : 9.7494 > 8.0000 or insufficient steps taken.
3:07:09.403157 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
3:07:09.403194 INFO: ==============================================
3:07:09.403298 INFO: Starting optimization step 6.
3:07:09.403381 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:07:09.403454 PROGRESS: Extracting batch of 15945 precursors
3:07:09.415359 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:07:09.415456 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:07:09.415506 INFO: FWHM in RT is 2.48 seconds, sigma is 0.32
3:07:09.415543 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:07:09.415772 INFO: Starting candidate selection
3:07:10.338197 INFO: Starting candidate scoring
3:07:10.588393 INFO: Finished candidate processing
3:07:10.588512 INFO: Collecting candidate features
3:07:10.646436 WARNING: intensity_correlation has 2 NaNs ( 0.01 % out of 31881)
3:07:10.651102 INFO: Collecting fragment features
3:07:10.682919 INFO: Finished candidate scoring
3:07:10.700866 PROGRESS: === Extracted 31881 precursors and 297879 fragments ===
3:07:10.701401 INFO: performing precursor FDR with 47 features
3:07:10.701442 INFO: Decoy channel: -1
3:07:10.701467 INFO: Competetive: True
3:07:10.719128 INFO: Setting torch num_threads to 2 for FDR classification task
3:07:10.725891 WARNING: dropped 1 target PSMs due to missing features
3:07:10.726005 WARNING: dropped 1 decoy PSMs due to missing features
3:07:11.375081 INFO: Test AUC: 0.779
3:07:11.375270 INFO: Train AUC: 0.775
3:07:11.375302 INFO: AUC difference: 0.51%
3:07:11.464728 INFO: Resetting torch num_threads to 100
3:07:11.466435 INFO: === FDR correction performed with classifier version 5 ===
3:07:11.467957 PROGRESS: ============================= Precursor FDR =============================
3:07:11.468063 PROGRESS: Total precursors accumulated: 6,798
3:07:11.468121 PROGRESS: Target precursors: 6,655 (97.90%)
3:07:11.468173 PROGRESS: Decoy precursors: 143 (2.10%)
3:07:11.468220 PROGRESS: 
3:07:11.468266 PROGRESS: Precursor Summary:
3:07:11.471166 PROGRESS: Channel   0:	 0.05 FDR: 6,655; 0.01 FDR: 6,460; 0.001 FDR: 5,314
3:07:11.471288 PROGRESS: 
3:07:11.471344 PROGRESS: Protein Summary:
3:07:11.475512 PROGRESS: Channel   0:	 0.05 FDR: 3,583; 0.01 FDR: 3,507; 0.001 FDR: 3,084
3:07:11.475633 PROGRESS: =========================================================================
3:07:11.497629 INFO: fragments_df_filtered: 5000
3:07:11.516986 INFO: calibration group: precursor, fitting mz estimator 
3:07:12.160420 INFO: calibration group: precursor, fitting rt estimator 
3:07:12.784596 INFO: calibration group: fragment, fitting mz estimator 
3:07:13.220197 INFO: calibration group: precursor, predicting mz
3:07:13.223593 INFO: calibration group: precursor, predicting rt
3:07:13.233040 INFO: calibration group: fragment, predicting mz
3:07:13.254116 INFO: === checking if optimization conditions were reached ===
3:07:13.256062 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
3:07:13.256120 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
3:07:13.256155 INFO: ==============================================
3:07:13.256271 PROGRESS: Optimization finished for ms2_error, ms1_error.
3:07:13.273039 INFO: calibration group: precursor, predicting mz
3:07:13.276000 INFO: calibration group: precursor, predicting rt
3:07:13.284919 INFO: calibration group: fragment, predicting mz
3:07:13.306432 INFO: Starting optimization step 0.
3:07:13.306627 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:07:13.306731 PROGRESS: Extracting batch of 15945 precursors
3:07:13.312459 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:07:13.312519 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:07:13.312570 INFO: FWHM in RT is 2.41 seconds, sigma is 0.31
3:07:13.312600 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:07:13.312938 INFO: Starting candidate selection
3:07:14.231475 INFO: Starting candidate scoring
3:07:14.431794 INFO: Finished candidate processing
3:07:14.431911 INFO: Collecting candidate features
3:07:14.481708 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 31871)
3:07:14.486053 INFO: Collecting fragment features
3:07:14.510210 INFO: Finished candidate scoring
3:07:14.526153 PROGRESS: === Extracted 31871 precursors and 292487 fragments ===
3:07:14.526576 INFO: performing precursor FDR with 47 features
3:07:14.526612 INFO: Decoy channel: -1
3:07:14.526637 INFO: Competetive: True
3:07:14.538216 INFO: Setting torch num_threads to 2 for FDR classification task
3:07:14.543245 WARNING: dropped 1 target PSMs due to missing features
3:07:15.162268 INFO: Test AUC: 0.782
3:07:15.162393 INFO: Train AUC: 0.789
3:07:15.162423 INFO: AUC difference: 0.92%
3:07:15.249729 INFO: Resetting torch num_threads to 100
3:07:15.251270 INFO: === FDR correction performed with classifier version 6 ===
3:07:15.252854 PROGRESS: ============================= Precursor FDR =============================
3:07:15.252953 PROGRESS: Total precursors accumulated: 6,967
3:07:15.253013 PROGRESS: Target precursors: 6,825 (97.96%)
3:07:15.253061 PROGRESS: Decoy precursors: 142 (2.04%)
3:07:15.253107 PROGRESS: 
3:07:15.253150 PROGRESS: Precursor Summary:
3:07:15.255973 PROGRESS: Channel   0:	 0.05 FDR: 6,825; 0.01 FDR: 6,659; 0.001 FDR: 5,414
3:07:15.256094 PROGRESS: 
3:07:15.256150 PROGRESS: Protein Summary:
3:07:15.260414 PROGRESS: Channel   0:	 0.05 FDR: 3,661; 0.01 FDR: 3,593; 0.001 FDR: 3,148
3:07:15.260520 PROGRESS: =========================================================================
3:07:15.282629 INFO: fragments_df_filtered: 5000
3:07:15.297171 INFO: calibration group: precursor, fitting mz estimator 
3:07:16.062252 INFO: calibration group: precursor, fitting rt estimator 
3:07:16.767941 INFO: calibration group: fragment, fitting mz estimator 
3:07:17.190106 INFO: calibration group: precursor, predicting mz
3:07:17.194753 INFO: calibration group: precursor, predicting rt
3:07:17.205124 INFO: calibration group: fragment, predicting mz
3:07:17.231990 INFO: === checking if optimization conditions were reached ===
3:07:17.232368 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3:07:17.238581 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 88.6150.
3:07:17.238671 INFO: ==============================================
3:07:17.238796 INFO: Starting optimization step 1.
3:07:17.238884 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:07:17.238983 PROGRESS: Extracting batch of 15945 precursors
3:07:17.245993 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:07:17.246198 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:07:17.246305 INFO: FWHM in RT is 2.36 seconds, sigma is 0.30
3:07:17.246399 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:07:17.246688 INFO: Starting candidate selection
3:07:17.882647 INFO: Starting candidate scoring
3:07:18.117154 INFO: Finished candidate processing
3:07:18.117291 INFO: Collecting candidate features
3:07:18.174690 WARNING: intensity_correlation has 2 NaNs ( 0.01 % out of 31756)
3:07:18.181819 INFO: Collecting fragment features
3:07:18.201510 INFO: Finished candidate scoring
3:07:18.218318 PROGRESS: === Extracted 31756 precursors and 274099 fragments ===
3:07:18.218720 INFO: performing precursor FDR with 47 features
3:07:18.218763 INFO: Decoy channel: -1
3:07:18.218787 INFO: Competetive: True
3:07:18.228209 INFO: Setting torch num_threads to 2 for FDR classification task
3:07:18.233011 WARNING: dropped 2 decoy PSMs due to missing features
3:07:18.792614 INFO: Test AUC: 0.827
3:07:18.792782 INFO: Train AUC: 0.828
3:07:18.792814 INFO: AUC difference: 0.16%
3:07:18.884113 INFO: Resetting torch num_threads to 100
3:07:18.885619 INFO: === FDR correction performed with classifier version 6 ===
3:07:18.887365 PROGRESS: ============================= Precursor FDR =============================
3:07:18.887477 PROGRESS: Total precursors accumulated: 7,493
3:07:18.887539 PROGRESS: Target precursors: 7,396 (98.71%)
3:07:18.887593 PROGRESS: Decoy precursors: 97 (1.29%)
3:07:18.887640 PROGRESS: 
3:07:18.887685 PROGRESS: Precursor Summary:
3:07:18.890934 PROGRESS: Channel   0:	 0.05 FDR: 7,396; 0.01 FDR: 7,279; 0.001 FDR: 6,027
3:07:18.891064 PROGRESS: 
3:07:18.891120 PROGRESS: Protein Summary:
3:07:18.895583 PROGRESS: Channel   0:	 0.05 FDR: 3,860; 0.01 FDR: 3,825; 0.001 FDR: 3,362
3:07:18.895691 PROGRESS: =========================================================================
3:07:18.920179 INFO: fragments_df_filtered: 5000
3:07:18.933151 INFO: calibration group: precursor, fitting mz estimator 
3:07:19.686532 INFO: calibration group: precursor, fitting rt estimator 
3:07:20.490608 INFO: calibration group: fragment, fitting mz estimator 
3:07:20.909588 INFO: calibration group: precursor, predicting mz
3:07:20.912535 INFO: calibration group: precursor, predicting rt
3:07:20.922494 INFO: calibration group: fragment, predicting mz
3:07:20.942595 INFO: === checking if optimization conditions were reached ===
3:07:20.942788 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3:07:20.948862 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 30.9061.
3:07:20.948929 INFO: ==============================================
3:07:20.949036 INFO: Starting optimization step 2.
3:07:20.949110 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:07:20.949175 PROGRESS: Extracting batch of 15945 precursors
3:07:20.955825 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:07:20.955895 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:07:20.955932 INFO: FWHM in RT is 2.34 seconds, sigma is 0.30
3:07:20.955960 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:07:20.956197 INFO: Starting candidate selection
3:07:21.545821 INFO: Starting candidate scoring
3:07:21.776910 INFO: Finished candidate processing
3:07:21.777031 INFO: Collecting candidate features
3:07:21.827261 WARNING: intensity_correlation has 9 NaNs ( 0.03 % out of 31566)
3:07:21.831663 INFO: Collecting fragment features
3:07:21.849896 INFO: Finished candidate scoring
3:07:21.864225 PROGRESS: === Extracted 31566 precursors and 264576 fragments ===
3:07:21.864620 INFO: performing precursor FDR with 47 features
3:07:21.864659 INFO: Decoy channel: -1
3:07:21.864683 INFO: Competetive: True
3:07:21.873108 INFO: Setting torch num_threads to 2 for FDR classification task
3:07:21.878577 WARNING: dropped 2 target PSMs due to missing features
3:07:21.878701 WARNING: dropped 7 decoy PSMs due to missing features
3:07:22.428666 INFO: Test AUC: 0.837
3:07:22.428810 INFO: Train AUC: 0.851
3:07:22.428858 INFO: AUC difference: 1.62%
3:07:22.516272 INFO: Resetting torch num_threads to 100
3:07:22.517570 INFO: === FDR correction performed with classifier version 6 ===
3:07:22.519051 PROGRESS: ============================= Precursor FDR =============================
3:07:22.519148 PROGRESS: Total precursors accumulated: 7,554
3:07:22.519208 PROGRESS: Target precursors: 7,476 (98.97%)
3:07:22.519260 PROGRESS: Decoy precursors: 78 (1.03%)
3:07:22.519304 PROGRESS: 
3:07:22.519349 PROGRESS: Precursor Summary:
3:07:22.522216 PROGRESS: Channel   0:	 0.05 FDR: 7,476; 0.01 FDR: 7,467; 0.001 FDR: 6,544
3:07:22.522331 PROGRESS: 
3:07:22.522387 PROGRESS: Protein Summary:
3:07:22.526639 PROGRESS: Channel   0:	 0.05 FDR: 3,888; 0.01 FDR: 3,886; 0.001 FDR: 3,554
3:07:22.526750 PROGRESS: =========================================================================
3:07:22.551304 INFO: fragments_df_filtered: 5000
3:07:22.563684 INFO: calibration group: precursor, fitting mz estimator 
3:07:23.364353 INFO: calibration group: precursor, fitting rt estimator 
3:07:24.194615 INFO: calibration group: fragment, fitting mz estimator 
3:07:24.582808 INFO: calibration group: precursor, predicting mz
3:07:24.585786 INFO: calibration group: precursor, predicting rt
3:07:24.594728 INFO: calibration group: fragment, predicting mz
3:07:24.614226 INFO: === checking if optimization conditions were reached ===
3:07:24.614425 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3:07:24.620825 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 21.5110.
3:07:24.620897 INFO: ==============================================
3:07:24.621011 INFO: Starting optimization step 3.
3:07:24.621089 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:07:24.621158 PROGRESS: Extracting batch of 15945 precursors
3:07:24.626774 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:07:24.626849 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:07:24.626887 INFO: FWHM in RT is 2.34 seconds, sigma is 0.30
3:07:24.626915 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:07:24.627126 INFO: Starting candidate selection
3:07:25.208994 INFO: Starting candidate scoring
3:07:25.409192 INFO: Finished candidate processing
3:07:25.409308 INFO: Collecting candidate features
3:07:25.462243 WARNING: intensity_correlation has 11 NaNs ( 0.04 % out of 30740)
3:07:25.466526 INFO: Collecting fragment features
3:07:25.485879 INFO: Finished candidate scoring
3:07:25.500989 PROGRESS: === Extracted 30740 precursors and 252245 fragments ===
3:07:25.501398 INFO: performing precursor FDR with 47 features
3:07:25.501437 INFO: Decoy channel: -1
3:07:25.501464 INFO: Competetive: True
3:07:25.510476 INFO: Setting torch num_threads to 2 for FDR classification task
3:07:25.515954 WARNING: dropped 4 target PSMs due to missing features
3:07:25.516064 WARNING: dropped 7 decoy PSMs due to missing features
3:07:26.019044 INFO: Test AUC: 0.848
3:07:26.019183 INFO: Train AUC: 0.858
3:07:26.019213 INFO: AUC difference: 1.22%
3:07:26.105994 INFO: Resetting torch num_threads to 100
3:07:26.107462 INFO: === FDR correction performed with classifier version 6 ===
3:07:26.108974 PROGRESS: ============================= Precursor FDR =============================
3:07:26.109074 PROGRESS: Total precursors accumulated: 7,566
3:07:26.109135 PROGRESS: Target precursors: 7,497 (99.09%)
3:07:26.109186 PROGRESS: Decoy precursors: 69 (0.91%)
3:07:26.109232 PROGRESS: 
3:07:26.109277 PROGRESS: Precursor Summary:
3:07:26.112171 PROGRESS: Channel   0:	 0.05 FDR: 7,497; 0.01 FDR: 7,497; 0.001 FDR: 6,528
3:07:26.112293 PROGRESS: 
3:07:26.112354 PROGRESS: Protein Summary:
3:07:26.116904 PROGRESS: Channel   0:	 0.05 FDR: 3,897; 0.01 FDR: 3,897; 0.001 FDR: 3,552
3:07:26.117011 PROGRESS: =========================================================================
3:07:26.143522 INFO: fragments_df_filtered: 5000
3:07:26.156784 INFO: calibration group: precursor, fitting mz estimator 
3:07:26.957205 INFO: calibration group: precursor, fitting rt estimator 
3:07:27.775061 INFO: calibration group: fragment, fitting mz estimator 
3:07:28.196610 INFO: calibration group: precursor, predicting mz
3:07:28.199630 INFO: calibration group: precursor, predicting rt
3:07:28.208730 INFO: calibration group: fragment, predicting mz
3:07:28.228784 INFO: === checking if optimization conditions were reached ===
3:07:28.228956 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3:07:28.234465 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 16.1658.
3:07:28.234529 INFO: ==============================================
3:07:28.234627 INFO: Starting optimization step 4.
3:07:28.234694 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:07:28.234752 PROGRESS: Extracting batch of 15945 precursors
3:07:28.239594 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:07:28.239656 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:07:28.239688 INFO: FWHM in RT is 2.34 seconds, sigma is 0.30
3:07:28.239712 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:07:28.239903 INFO: Starting candidate selection
3:07:28.808211 INFO: Starting candidate scoring
3:07:29.034493 INFO: Finished candidate processing
3:07:29.035700 INFO: Collecting candidate features
3:07:29.083355 WARNING: intensity_correlation has 17 NaNs ( 0.06 % out of 30751)
3:07:29.087699 INFO: Collecting fragment features
3:07:29.106293 INFO: Finished candidate scoring
3:07:29.121404 PROGRESS: === Extracted 30751 precursors and 253937 fragments ===
3:07:29.121819 INFO: performing precursor FDR with 47 features
3:07:29.121857 INFO: Decoy channel: -1
3:07:29.121882 INFO: Competetive: True
3:07:29.130710 INFO: Setting torch num_threads to 2 for FDR classification task
3:07:29.136107 WARNING: dropped 7 target PSMs due to missing features
3:07:29.136221 WARNING: dropped 10 decoy PSMs due to missing features
3:07:29.636339 INFO: Test AUC: 0.871
3:07:29.636478 INFO: Train AUC: 0.873
3:07:29.636509 INFO: AUC difference: 0.25%
3:07:29.721547 INFO: Resetting torch num_threads to 100
3:07:29.722998 INFO: === FDR correction performed with classifier version 6 ===
3:07:29.724505 PROGRESS: ============================= Precursor FDR =============================
3:07:29.724600 PROGRESS: Total precursors accumulated: 7,543
3:07:29.724659 PROGRESS: Target precursors: 7,480 (99.16%)
3:07:29.724717 PROGRESS: Decoy precursors: 63 (0.84%)
3:07:29.724767 PROGRESS: 
3:07:29.724813 PROGRESS: Precursor Summary:
3:07:29.727755 PROGRESS: Channel   0:	 0.05 FDR: 7,480; 0.01 FDR: 7,480; 0.001 FDR: 6,449
3:07:29.727869 PROGRESS: 
3:07:29.727924 PROGRESS: Protein Summary:
3:07:29.732405 PROGRESS: Channel   0:	 0.05 FDR: 3,885; 0.01 FDR: 3,885; 0.001 FDR: 3,523
3:07:29.732515 PROGRESS: =========================================================================
3:07:29.756585 INFO: fragments_df_filtered: 5000
3:07:29.770253 INFO: calibration group: precursor, fitting mz estimator 
3:07:30.570254 INFO: calibration group: precursor, fitting rt estimator 
3:07:31.387141 INFO: calibration group: fragment, fitting mz estimator 
3:07:31.807420 INFO: calibration group: precursor, predicting mz
3:07:31.810368 INFO: calibration group: precursor, predicting rt
3:07:31.819451 INFO: calibration group: fragment, predicting mz
3:07:31.839862 INFO: === checking if optimization conditions were reached ===
3:07:31.840059 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3:07:31.846225 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 18.6962.
3:07:31.846295 INFO: ==============================================
3:07:31.846402 INFO: Starting optimization step 5.
3:07:31.846477 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:07:31.846561 PROGRESS: Extracting batch of 15945 precursors
3:07:31.853515 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:07:31.853591 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:07:31.853632 INFO: FWHM in RT is 2.34 seconds, sigma is 0.30
3:07:31.853661 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:07:31.853892 INFO: Starting candidate selection
3:07:32.421034 INFO: Starting candidate scoring
3:07:32.650327 INFO: Finished candidate processing
3:07:32.650462 INFO: Collecting candidate features
3:07:32.699346 WARNING: intensity_correlation has 15 NaNs ( 0.05 % out of 30741)
3:07:32.706791 INFO: Collecting fragment features
3:07:32.725382 INFO: Finished candidate scoring
3:07:32.741287 PROGRESS: === Extracted 30741 precursors and 253458 fragments ===
3:07:32.741686 INFO: performing precursor FDR with 47 features
3:07:32.741726 INFO: Decoy channel: -1
3:07:32.741750 INFO: Competetive: True
3:07:32.750405 INFO: Setting torch num_threads to 2 for FDR classification task
3:07:32.755854 WARNING: dropped 3 target PSMs due to missing features
3:07:32.755960 WARNING: dropped 12 decoy PSMs due to missing features
3:07:33.245331 INFO: Test AUC: 0.863
3:07:33.245466 INFO: Train AUC: 0.868
3:07:33.245497 INFO: AUC difference: 0.56%
3:07:33.330586 INFO: Resetting torch num_threads to 100
3:07:33.332039 INFO: === FDR correction performed with classifier version 6 ===
3:07:33.333686 PROGRESS: ============================= Precursor FDR =============================
3:07:33.333786 PROGRESS: Total precursors accumulated: 7,544
3:07:33.333846 PROGRESS: Target precursors: 7,471 (99.03%)
3:07:33.333896 PROGRESS: Decoy precursors: 73 (0.97%)
3:07:33.333943 PROGRESS: 
3:07:33.333987 PROGRESS: Precursor Summary:
3:07:33.336990 PROGRESS: Channel   0:	 0.05 FDR: 7,471; 0.01 FDR: 7,471; 0.001 FDR: 6,478
3:07:33.337101 PROGRESS: 
3:07:33.337170 PROGRESS: Protein Summary:
3:07:33.341787 PROGRESS: Channel   0:	 0.05 FDR: 3,882; 0.01 FDR: 3,882; 0.001 FDR: 3,544
3:07:33.341896 PROGRESS: =========================================================================
3:07:33.365925 INFO: fragments_df_filtered: 5000
3:07:33.380216 INFO: calibration group: precursor, fitting mz estimator 
3:07:34.188906 INFO: calibration group: precursor, fitting rt estimator 
3:07:34.971668 INFO: calibration group: fragment, fitting mz estimator 
3:07:35.403886 INFO: calibration group: precursor, predicting mz
3:07:35.407440 INFO: calibration group: precursor, predicting rt
3:07:35.417619 INFO: calibration group: fragment, predicting mz
3:07:35.436559 INFO: === checking if optimization conditions were reached ===
3:07:35.436768 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3:07:35.443184 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 18.2895.
3:07:35.443263 INFO: ==============================================
3:07:35.443384 INFO: Starting optimization step 6.
3:07:35.443457 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:07:35.443525 PROGRESS: Extracting batch of 15945 precursors
3:07:35.451262 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:07:35.451331 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:07:35.451368 INFO: FWHM in RT is 2.34 seconds, sigma is 0.30
3:07:35.451396 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:07:35.451620 INFO: Starting candidate selection
3:07:36.022583 INFO: Starting candidate scoring
3:07:36.251504 INFO: Finished candidate processing
3:07:36.251631 INFO: Collecting candidate features
3:07:36.299915 WARNING: intensity_correlation has 21 NaNs ( 0.07 % out of 30733)
3:07:36.304206 INFO: Collecting fragment features
3:07:36.322452 INFO: Finished candidate scoring
3:07:36.338310 PROGRESS: === Extracted 30733 precursors and 253562 fragments ===
3:07:36.338724 INFO: performing precursor FDR with 47 features
3:07:36.338764 INFO: Decoy channel: -1
3:07:36.338789 INFO: Competetive: True
3:07:36.347364 INFO: Setting torch num_threads to 2 for FDR classification task
3:07:36.353046 WARNING: dropped 3 target PSMs due to missing features
3:07:36.353173 WARNING: dropped 18 decoy PSMs due to missing features
3:07:36.848803 INFO: Test AUC: 0.866
3:07:36.848942 INFO: Train AUC: 0.868
3:07:36.848971 INFO: AUC difference: 0.19%
3:07:36.933868 INFO: Resetting torch num_threads to 100
3:07:36.935335 INFO: === FDR correction performed with classifier version 6 ===
3:07:36.936776 PROGRESS: ============================= Precursor FDR =============================
3:07:36.936874 PROGRESS: Total precursors accumulated: 7,550
3:07:36.936933 PROGRESS: Target precursors: 7,478 (99.05%)
3:07:36.936984 PROGRESS: Decoy precursors: 72 (0.95%)
3:07:36.937028 PROGRESS: 
3:07:36.937071 PROGRESS: Precursor Summary:
3:07:36.940086 PROGRESS: Channel   0:	 0.05 FDR: 7,478; 0.01 FDR: 7,478; 0.001 FDR: 6,240
3:07:36.940202 PROGRESS: 
3:07:36.940259 PROGRESS: Protein Summary:
3:07:36.944802 PROGRESS: Channel   0:	 0.05 FDR: 3,878; 0.01 FDR: 3,878; 0.001 FDR: 3,460
3:07:36.944915 PROGRESS: =========================================================================
3:07:36.969566 INFO: fragments_df_filtered: 5000
3:07:36.983436 INFO: calibration group: precursor, fitting mz estimator 
3:07:37.799151 INFO: calibration group: precursor, fitting rt estimator 
3:07:38.641654 INFO: calibration group: fragment, fitting mz estimator 
3:07:39.092404 INFO: calibration group: precursor, predicting mz
3:07:39.096758 INFO: calibration group: precursor, predicting rt
3:07:39.107017 INFO: calibration group: fragment, predicting mz
3:07:39.126015 INFO: === checking if optimization conditions were reached ===
3:07:39.126231 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
3:07:39.127603 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 16.1658 found after 7 searches.
3:07:39.127659 INFO: ==============================================
3:07:39.127758 PROGRESS: Optimization finished for rt_error.
3:07:39.146487 INFO: calibration group: precursor, predicting mz
3:07:39.149747 INFO: calibration group: precursor, predicting rt
3:07:39.159363 INFO: calibration group: fragment, predicting mz
3:07:39.213253 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:07:39.213471 PROGRESS: ==============================================
3:07:39.213551 PROGRESS: ms2_error      : 8.0000
3:07:39.213619 PROGRESS: ms1_error      : 3.0000
3:07:39.213713 PROGRESS: rt_error       : 16.1658
3:07:39.213781 PROGRESS: ==============================================
3:07:39.215175 INFO: calibration group: precursor, predicting mz
3:07:39.226053 INFO: calibration group: precursor, predicting rt
3:07:39.269008 INFO: calibration group: fragment, predicting mz
3:07:39.398135 PROGRESS: Extracting batch of 78739 precursors
3:07:39.423636 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:07:39.423791 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:07:39.423832 INFO: FWHM in RT is 2.34 seconds, sigma is 0.30
3:07:39.423858 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:07:39.424151 INFO: Starting candidate selection
3:07:41.837552 INFO: Applying score cutoff of 19.9167350063324
3:07:41.841058 INFO: Removed 14337 precursors with score below cutoff
3:07:41.876598 INFO: Starting candidate scoring
3:07:42.901321 INFO: Finished candidate processing
3:07:42.901440 INFO: Collecting candidate features
3:07:43.126678 WARNING: intensity_correlation has 11 NaNs ( 0.01 % out of 139212)
3:07:43.134951 INFO: Collecting fragment features
3:07:43.225581 INFO: Finished candidate scoring
3:07:43.320854 INFO: === FDR correction performed with classifier version 11 ===
3:07:43.321596 INFO: performing precursor FDR with 47 features
3:07:43.321631 INFO: Decoy channel: -1
3:07:43.321654 INFO: Competetive: True
3:07:43.369727 INFO: Setting torch num_threads to 2 for FDR classification task
3:07:43.395347 WARNING: dropped 4 target PSMs due to missing features
3:07:43.395500 WARNING: dropped 7 decoy PSMs due to missing features
3:07:43.395562 WARNING: FDR calculation for 73807 target and 65394 decoy PSMs
3:07:43.395598 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
3:07:46.542968 INFO: Test AUC: 0.896
3:07:46.543112 INFO: Train AUC: 0.899
3:07:46.543143 INFO: AUC difference: 0.29%
3:07:46.634055 INFO: Resetting torch num_threads to 100
3:07:46.641670 INFO: Removing fragments below FDR threshold
3:07:46.669500 PROGRESS: ============================= Precursor FDR =============================
3:07:46.669788 PROGRESS: Total precursors accumulated: 37,329
3:07:46.669860 PROGRESS: Target precursors: 36,973 (99.05%)
3:07:46.669912 PROGRESS: Decoy precursors: 356 (0.95%)
3:07:46.669961 PROGRESS: 
3:07:46.670010 PROGRESS: Precursor Summary:
3:07:46.685099 PROGRESS: Channel   0:	 0.05 FDR: 36,973; 0.01 FDR: 36,973; 0.001 FDR: 34,025
3:07:46.685397 PROGRESS: 
3:07:46.685460 PROGRESS: Protein Summary:
3:07:46.707390 PROGRESS: Channel   0:	 0.05 FDR: 6,696; 0.01 FDR: 6,696; 0.001 FDR: 6,619
3:07:46.707648 PROGRESS: =========================================================================
3:07:47.098317 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:07:47.113959 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:07:47.114134 INFO: Quantification results path: run_output_Astral/alphadia_1.10_MBRSetValues/quant
3:07:47.114213 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2 at run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:07:47.114863 INFO: Initializing RawFileManager
3:08:13.809334 INFO: Determining DIA cycle
3:08:13.827026 INFO: Found cycle with start 0.00 min and length 303.
3:08:14.007122 INFO: RT (min)            : 0.0 - 26.9
3:08:14.007240 INFO: RT duration (sec)   : 1611.2
3:08:14.007270 INFO: RT duration (min)   : 26.9
3:08:14.007294 INFO: Cycle len (scans)   : 303
3:08:14.007314 INFO: Cycle len (sec)     : 1.65
3:08:14.007333 INFO: Number of cycles    : 977
3:08:14.007353 INFO: MS2 range (m/z)     : 380.4 - 980.7
3:08:14.035212 INFO: Initializing CalibrationManager
3:08:14.035543 INFO: Loading calibration config
3:08:14.036092 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'}]
3:08:14.036183 INFO: Calibration group :fragment, found 1 estimator(s)
3:08:14.036276 INFO: Calibration group :precursor, found 3 estimator(s)
3:08:14.036385 INFO: Disabling ion mobility calibration
3:08:14.036417 INFO: removed mobility estimator from group precursor
3:08:14.036576 INFO: Initializing OptimizationManager
3:08:14.036696 INFO: initial parameter: ms1_error = 30
3:08:14.036775 INFO: initial parameter: ms2_error = 30
3:08:14.036839 INFO: initial parameter: rt_error = 805.6002197265625
3:08:14.036895 INFO: initial parameter: mobility_error = 0.1
3:08:14.036945 INFO: initial parameter: column_type = library
3:08:14.036988 INFO: initial parameter: num_candidates = 1
3:08:14.037030 INFO: initial parameter: classifier_version = -1
3:08:14.037071 INFO: initial parameter: fwhm_rt = 5
3:08:14.037115 INFO: initial parameter: fwhm_mobility = 0.01
3:08:14.037163 INFO: initial parameter: score_cutoff = 0
3:08:14.037221 INFO: Initializing TimingManager
3:08:14.037284 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:08:14.037370 INFO: FDRManager not loaded from disk.
3:08:14.037394 INFO: Initializing FDRManager
3:08:14.037424 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
3:08:14.058670 PROGRESS: 39,524 target precursors potentially observable (0 removed)
3:08:14.084826 PROGRESS: Starting initial search for precursors.
3:08:14.099696 INFO: Starting optimization step 0.
3:08:14.099958 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:08:14.100030 PROGRESS: Extracting batch of 15945 precursors
3:08:14.103614 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:08:14.103680 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:08:14.103718 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:08:14.103740 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:08:14.103991 INFO: Starting candidate selection
3:08:15.123111 INFO: Starting candidate scoring
3:08:15.248273 INFO: Finished candidate processing
3:08:15.248391 INFO: Collecting candidate features
3:08:15.285576 INFO: Collecting fragment features
3:08:15.297821 INFO: Finished candidate scoring
3:08:15.306616 PROGRESS: === Extracted 15945 precursors and 172975 fragments ===
3:08:15.307016 INFO: performing precursor FDR with 47 features
3:08:15.307058 INFO: Decoy channel: -1
3:08:15.307085 INFO: Competetive: True
3:08:15.311372 INFO: Setting torch num_threads to 2 for FDR classification task
3:08:15.449351 INFO: Test AUC: 0.681
3:08:15.449485 INFO: Train AUC: 0.687
3:08:15.449517 INFO: AUC difference: 0.79%
3:08:15.533148 INFO: Resetting torch num_threads to 100
3:08:15.534397 INFO: === FDR correction performed with classifier version -1 ===
3:08:15.535594 PROGRESS: ============================= Precursor FDR =============================
3:08:15.535687 PROGRESS: Total precursors accumulated: 2,740
3:08:15.535748 PROGRESS: Target precursors: 2,558 (93.36%)
3:08:15.535800 PROGRESS: Decoy precursors: 182 (6.64%)
3:08:15.535847 PROGRESS: 
3:08:15.535892 PROGRESS: Precursor Summary:
3:08:15.537515 PROGRESS: Channel   0:	 0.05 FDR: 2,346; 0.01 FDR: 1,918; 0.001 FDR:   375
3:08:15.537611 PROGRESS: 
3:08:15.537667 PROGRESS: Protein Summary:
3:08:15.539469 PROGRESS: Channel   0:	 0.05 FDR: 1,648; 0.01 FDR: 1,392; 0.001 FDR:   340
3:08:15.539564 PROGRESS: =========================================================================
3:08:15.545894 INFO: fragments_df_filtered: 5000
3:08:15.560099 INFO: calibration group: precursor, fitting mz estimator 
3:08:18.525022 INFO: calibration group: precursor, fitting rt estimator 
3:08:18.643612 INFO: calibration group: fragment, fitting mz estimator 
3:08:18.996058 INFO: calibration group: precursor, predicting mz
3:08:19.000282 INFO: calibration group: precursor, predicting rt
3:08:19.009935 INFO: calibration group: fragment, predicting mz
3:08:19.034412 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3:08:19.034653 INFO: Starting optimization step 1.
3:08:19.034765 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:08:19.034851 PROGRESS: Extracting batch of 15945 precursors
3:08:19.043376 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:08:19.043470 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:08:19.043523 INFO: FWHM in RT is 2.96 seconds, sigma is 0.38
3:08:19.043565 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:08:19.043840 INFO: Starting candidate selection
3:08:19.990407 INFO: Starting candidate scoring
3:08:20.209431 INFO: Finished candidate processing
3:08:20.209546 INFO: Collecting candidate features
3:08:20.262100 INFO: Collecting fragment features
3:08:20.286567 INFO: Finished candidate scoring
3:08:20.305149 PROGRESS: === Extracted 31890 precursors and 342971 fragments ===
3:08:20.305535 INFO: performing precursor FDR with 47 features
3:08:20.305586 INFO: Decoy channel: -1
3:08:20.305611 INFO: Competetive: True
3:08:20.317278 INFO: Setting torch num_threads to 2 for FDR classification task
3:08:20.701778 INFO: Test AUC: 0.688
3:08:20.701912 INFO: Train AUC: 0.674
3:08:20.701945 INFO: AUC difference: 2.12%
3:08:20.786044 INFO: Resetting torch num_threads to 100
3:08:20.787377 INFO: === FDR correction performed with classifier version 0 ===
3:08:20.788637 PROGRESS: ============================= Precursor FDR =============================
3:08:20.788750 PROGRESS: Total precursors accumulated: 4,342
3:08:20.788812 PROGRESS: Target precursors: 4,113 (94.73%)
3:08:20.788862 PROGRESS: Decoy precursors: 229 (5.27%)
3:08:20.788908 PROGRESS: 
3:08:20.788951 PROGRESS: Precursor Summary:
3:08:20.790798 PROGRESS: Channel   0:	 0.05 FDR: 4,067; 0.01 FDR: 3,339; 0.001 FDR:   283
3:08:20.790894 PROGRESS: 
3:08:20.790949 PROGRESS: Protein Summary:
3:08:20.793320 PROGRESS: Channel   0:	 0.05 FDR: 2,574; 0.01 FDR: 2,188; 0.001 FDR:   253
3:08:20.793416 PROGRESS: =========================================================================
3:08:20.808097 INFO: fragments_df_filtered: 5000
3:08:20.822308 INFO: calibration group: precursor, fitting mz estimator 
3:08:21.101076 INFO: calibration group: precursor, fitting rt estimator 
3:08:21.351344 INFO: calibration group: fragment, fitting mz estimator 
3:08:21.765323 INFO: calibration group: precursor, predicting mz
3:08:21.768366 INFO: calibration group: precursor, predicting rt
3:08:21.777239 INFO: calibration group: fragment, predicting mz
3:08:21.798359 INFO: === checking if optimization conditions were reached ===
3:08:21.800777 PROGRESS: ❌ ms2_error      : 18.5688 > 8.0000 or insufficient steps taken.
3:08:21.802473 PROGRESS: ❌ ms1_error      : 13.0541 > 3.0000 or insufficient steps taken.
3:08:21.802535 INFO: ==============================================
3:08:21.802649 INFO: Starting optimization step 2.
3:08:21.802727 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:08:21.802797 PROGRESS: Extracting batch of 15945 precursors
3:08:21.808346 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:08:21.808422 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:08:21.808464 INFO: FWHM in RT is 2.95 seconds, sigma is 0.38
3:08:21.808493 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:08:21.808722 INFO: Starting candidate selection
3:08:22.707237 INFO: Starting candidate scoring
3:08:22.944477 INFO: Finished candidate processing
3:08:22.944624 INFO: Collecting candidate features
3:08:23.004046 INFO: Collecting fragment features
3:08:23.025538 INFO: Finished candidate scoring
3:08:23.043887 PROGRESS: === Extracted 31890 precursors and 328250 fragments ===
3:08:23.044328 INFO: performing precursor FDR with 47 features
3:08:23.044370 INFO: Decoy channel: -1
3:08:23.044396 INFO: Competetive: True
3:08:23.054431 INFO: Setting torch num_threads to 2 for FDR classification task
3:08:23.672736 INFO: Test AUC: 0.710
3:08:23.672883 INFO: Train AUC: 0.717
3:08:23.672915 INFO: AUC difference: 0.97%
3:08:23.757276 INFO: Resetting torch num_threads to 100
3:08:23.758973 INFO: === FDR correction performed with classifier version 1 ===
3:08:23.760422 PROGRESS: ============================= Precursor FDR =============================
3:08:23.760547 PROGRESS: Total precursors accumulated: 5,399
3:08:23.760607 PROGRESS: Target precursors: 5,190 (96.13%)
3:08:23.760658 PROGRESS: Decoy precursors: 209 (3.87%)
3:08:23.760712 PROGRESS: 
3:08:23.760761 PROGRESS: Precursor Summary:
3:08:23.763364 PROGRESS: Channel   0:	 0.05 FDR: 5,190; 0.01 FDR: 4,640; 0.001 FDR: 3,116
3:08:23.763503 PROGRESS: 
3:08:23.763560 PROGRESS: Protein Summary:
3:08:23.766924 PROGRESS: Channel   0:	 0.05 FDR: 3,052; 0.01 FDR: 2,831; 0.001 FDR: 2,067
3:08:23.767036 PROGRESS: =========================================================================
3:08:23.784793 INFO: fragments_df_filtered: 5000
3:08:23.798875 INFO: calibration group: precursor, fitting mz estimator 
3:08:24.172118 INFO: calibration group: precursor, fitting rt estimator 
3:08:24.558273 INFO: calibration group: fragment, fitting mz estimator 
3:08:24.975391 INFO: calibration group: precursor, predicting mz
3:08:24.978542 INFO: calibration group: precursor, predicting rt
3:08:24.987387 INFO: calibration group: fragment, predicting mz
3:08:25.008265 INFO: === checking if optimization conditions were reached ===
3:08:25.010143 PROGRESS: ❌ ms2_error      : 14.0461 > 8.0000 or insufficient steps taken.
3:08:25.011670 PROGRESS: ❌ ms1_error      : 6.1280 > 3.0000 or insufficient steps taken.
3:08:25.011720 INFO: ==============================================
3:08:25.011822 INFO: Starting optimization step 3.
3:08:25.011890 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:08:25.011946 PROGRESS: Extracting batch of 15945 precursors
3:08:25.016466 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:08:25.016531 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:08:25.016563 INFO: FWHM in RT is 2.77 seconds, sigma is 0.36
3:08:25.016586 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:08:25.016789 INFO: Starting candidate selection
3:08:25.905793 INFO: Starting candidate scoring
3:08:26.134484 INFO: Finished candidate processing
3:08:26.134619 INFO: Collecting candidate features
3:08:26.187556 INFO: Collecting fragment features
3:08:26.207956 INFO: Finished candidate scoring
3:08:26.225678 PROGRESS: === Extracted 31889 precursors and 318384 fragments ===
3:08:26.226088 INFO: performing precursor FDR with 47 features
3:08:26.226130 INFO: Decoy channel: -1
3:08:26.226156 INFO: Competetive: True
3:08:26.235822 INFO: Setting torch num_threads to 2 for FDR classification task
3:08:26.855741 INFO: Test AUC: 0.731
3:08:26.855881 INFO: Train AUC: 0.742
3:08:26.855912 INFO: AUC difference: 1.53%
3:08:26.941397 INFO: Resetting torch num_threads to 100
3:08:26.942909 INFO: === FDR correction performed with classifier version 2 ===
3:08:26.944373 PROGRESS: ============================= Precursor FDR =============================
3:08:26.944489 PROGRESS: Total precursors accumulated: 6,029
3:08:26.944548 PROGRESS: Target precursors: 5,869 (97.35%)
3:08:26.944597 PROGRESS: Decoy precursors: 160 (2.65%)
3:08:26.944647 PROGRESS: 
3:08:26.944693 PROGRESS: Precursor Summary:
3:08:26.947551 PROGRESS: Channel   0:	 0.05 FDR: 5,869; 0.01 FDR: 5,478; 0.001 FDR: 3,738
3:08:26.947684 PROGRESS: 
3:08:26.947739 PROGRESS: Protein Summary:
3:08:26.951412 PROGRESS: Channel   0:	 0.05 FDR: 3,301; 0.01 FDR: 3,153; 0.001 FDR: 2,399
3:08:26.951533 PROGRESS: =========================================================================
3:08:26.975833 INFO: fragments_df_filtered: 5000
3:08:26.989360 INFO: calibration group: precursor, fitting mz estimator 
3:08:27.435241 INFO: calibration group: precursor, fitting rt estimator 
3:08:27.930856 INFO: calibration group: fragment, fitting mz estimator 
3:08:28.346458 INFO: calibration group: precursor, predicting mz
3:08:28.349584 INFO: calibration group: precursor, predicting rt
3:08:28.358492 INFO: calibration group: fragment, predicting mz
3:08:28.379254 INFO: === checking if optimization conditions were reached ===
3:08:28.381561 PROGRESS: ❌ ms2_error      : 11.6168 > 8.0000 or insufficient steps taken.
3:08:28.383499 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
3:08:28.383561 INFO: ==============================================
3:08:28.383683 INFO: Starting optimization step 4.
3:08:28.383761 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:08:28.383828 PROGRESS: Extracting batch of 15945 precursors
3:08:28.390149 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:08:28.390223 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:08:28.390260 INFO: FWHM in RT is 2.62 seconds, sigma is 0.34
3:08:28.390288 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:08:28.390536 INFO: Starting candidate selection
3:08:29.306641 INFO: Starting candidate scoring
3:08:29.506145 INFO: Finished candidate processing
3:08:29.506271 INFO: Collecting candidate features
3:08:29.561346 INFO: Collecting fragment features
3:08:29.582502 INFO: Finished candidate scoring
3:08:29.600211 PROGRESS: === Extracted 31888 precursors and 308677 fragments ===
3:08:29.600638 INFO: performing precursor FDR with 47 features
3:08:29.600678 INFO: Decoy channel: -1
3:08:29.600712 INFO: Competetive: True
3:08:29.611039 INFO: Setting torch num_threads to 2 for FDR classification task
3:08:30.219197 INFO: Test AUC: 0.743
3:08:30.219338 INFO: Train AUC: 0.758
3:08:30.219368 INFO: AUC difference: 2.03%
3:08:30.302033 INFO: Resetting torch num_threads to 100
3:08:30.303556 INFO: === FDR correction performed with classifier version 3 ===
3:08:30.305794 PROGRESS: ============================= Precursor FDR =============================
3:08:30.305903 PROGRESS: Total precursors accumulated: 6,363
3:08:30.305963 PROGRESS: Target precursors: 6,199 (97.42%)
3:08:30.306015 PROGRESS: Decoy precursors: 164 (2.58%)
3:08:30.306061 PROGRESS: 
3:08:30.306110 PROGRESS: Precursor Summary:
3:08:30.309519 PROGRESS: Channel   0:	 0.05 FDR: 6,199; 0.01 FDR: 5,868; 0.001 FDR: 3,839
3:08:30.309648 PROGRESS: 
3:08:30.309706 PROGRESS: Protein Summary:
3:08:30.313320 PROGRESS: Channel   0:	 0.05 FDR: 3,437; 0.01 FDR: 3,316; 0.001 FDR: 2,466
3:08:30.313431 PROGRESS: =========================================================================
3:08:30.334704 INFO: fragments_df_filtered: 5000
3:08:30.348245 INFO: calibration group: precursor, fitting mz estimator 
3:08:30.884170 INFO: calibration group: precursor, fitting rt estimator 
3:08:31.438644 INFO: calibration group: fragment, fitting mz estimator 
3:08:31.851432 INFO: calibration group: precursor, predicting mz
3:08:31.854552 INFO: calibration group: precursor, predicting rt
3:08:31.863499 INFO: calibration group: fragment, predicting mz
3:08:31.883973 INFO: === checking if optimization conditions were reached ===
3:08:31.885823 PROGRESS: ❌ ms2_error      : 9.6409 > 8.0000 or insufficient steps taken.
3:08:31.885883 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
3:08:31.885911 INFO: ==============================================
3:08:31.886009 INFO: Starting optimization step 5.
3:08:31.886075 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:08:31.886135 PROGRESS: Extracting batch of 15945 precursors
3:08:31.890692 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:08:31.890753 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:08:31.890786 INFO: FWHM in RT is 2.47 seconds, sigma is 0.32
3:08:31.890812 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:08:31.891007 INFO: Starting candidate selection
3:08:32.868297 INFO: Starting candidate scoring
3:08:33.056782 INFO: Finished candidate processing
3:08:33.056904 INFO: Collecting candidate features
3:08:33.111778 INFO: Collecting fragment features
3:08:33.133015 INFO: Finished candidate scoring
3:08:33.150229 PROGRESS: === Extracted 31886 precursors and 298904 fragments ===
3:08:33.150636 INFO: performing precursor FDR with 47 features
3:08:33.150675 INFO: Decoy channel: -1
3:08:33.150700 INFO: Competetive: True
3:08:33.167273 INFO: Setting torch num_threads to 2 for FDR classification task
3:08:33.784922 INFO: Test AUC: 0.770
3:08:33.785068 INFO: Train AUC: 0.765
3:08:33.785098 INFO: AUC difference: 0.63%
3:08:33.870313 INFO: Resetting torch num_threads to 100
3:08:33.872075 INFO: === FDR correction performed with classifier version 4 ===
3:08:33.873682 PROGRESS: ============================= Precursor FDR =============================
3:08:33.873803 PROGRESS: Total precursors accumulated: 6,621
3:08:33.873862 PROGRESS: Target precursors: 6,459 (97.55%)
3:08:33.873914 PROGRESS: Decoy precursors: 162 (2.45%)
3:08:33.873961 PROGRESS: 
3:08:33.874006 PROGRESS: Precursor Summary:
3:08:33.877103 PROGRESS: Channel   0:	 0.05 FDR: 6,459; 0.01 FDR: 6,166; 0.001 FDR: 4,867
3:08:33.877236 PROGRESS: 
3:08:33.877293 PROGRESS: Protein Summary:
3:08:33.881433 PROGRESS: Channel   0:	 0.05 FDR: 3,517; 0.01 FDR: 3,417; 0.001 FDR: 2,919
3:08:33.881571 PROGRESS: =========================================================================
3:08:33.903188 INFO: fragments_df_filtered: 5000
3:08:33.918892 INFO: calibration group: precursor, fitting mz estimator 
3:08:34.501875 INFO: calibration group: precursor, fitting rt estimator 
3:08:35.069953 INFO: calibration group: fragment, fitting mz estimator 
3:08:35.417477 INFO: calibration group: precursor, predicting mz
3:08:35.420564 INFO: calibration group: precursor, predicting rt
3:08:35.429476 INFO: calibration group: fragment, predicting mz
3:08:35.452611 INFO: === checking if optimization conditions were reached ===
3:08:35.454435 PROGRESS: ❌ ms2_error      : 8.0201 > 8.0000 or insufficient steps taken.
3:08:35.454496 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
3:08:35.454523 INFO: ==============================================
3:08:35.454607 INFO: Starting optimization step 6.
3:08:35.454674 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:08:35.454730 PROGRESS: Extracting batch of 15945 precursors
3:08:35.459209 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:08:35.459271 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:08:35.459305 INFO: FWHM in RT is 2.40 seconds, sigma is 0.31
3:08:35.459328 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:08:35.459526 INFO: Starting candidate selection
3:08:36.356967 INFO: Starting candidate scoring
3:08:36.564553 INFO: Finished candidate processing
3:08:36.564674 INFO: Collecting candidate features
3:08:36.618202 INFO: Collecting fragment features
3:08:36.639067 INFO: Finished candidate scoring
3:08:36.655665 PROGRESS: === Extracted 31883 precursors and 293635 fragments ===
3:08:36.656073 INFO: performing precursor FDR with 47 features
3:08:36.656112 INFO: Decoy channel: -1
3:08:36.656136 INFO: Competetive: True
3:08:36.665324 INFO: Setting torch num_threads to 2 for FDR classification task
3:08:37.270261 INFO: Test AUC: 0.771
3:08:37.270408 INFO: Train AUC: 0.774
3:08:37.270439 INFO: AUC difference: 0.37%
3:08:37.354258 INFO: Resetting torch num_threads to 100
3:08:37.355747 INFO: === FDR correction performed with classifier version 5 ===
3:08:37.357183 PROGRESS: ============================= Precursor FDR =============================
3:08:37.357290 PROGRESS: Total precursors accumulated: 6,730
3:08:37.357351 PROGRESS: Target precursors: 6,580 (97.77%)
3:08:37.357401 PROGRESS: Decoy precursors: 150 (2.23%)
3:08:37.357447 PROGRESS: 
3:08:37.357491 PROGRESS: Precursor Summary:
3:08:37.360230 PROGRESS: Channel   0:	 0.05 FDR: 6,580; 0.01 FDR: 6,355; 0.001 FDR: 5,248
3:08:37.360352 PROGRESS: 
3:08:37.360410 PROGRESS: Protein Summary:
3:08:37.364509 PROGRESS: Channel   0:	 0.05 FDR: 3,571; 0.01 FDR: 3,483; 0.001 FDR: 3,089
3:08:37.364620 PROGRESS: =========================================================================
3:08:37.386214 INFO: fragments_df_filtered: 5000
3:08:37.399480 INFO: calibration group: precursor, fitting mz estimator 
3:08:38.008448 INFO: calibration group: precursor, fitting rt estimator 
3:08:38.639844 INFO: calibration group: fragment, fitting mz estimator 
3:08:39.058704 INFO: calibration group: precursor, predicting mz
3:08:39.061818 INFO: calibration group: precursor, predicting rt
3:08:39.070758 INFO: calibration group: fragment, predicting mz
3:08:39.091297 INFO: === checking if optimization conditions were reached ===
3:08:39.093458 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
3:08:39.093529 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
3:08:39.093561 INFO: ==============================================
3:08:39.093663 PROGRESS: Optimization finished for ms2_error, ms1_error.
3:08:39.111066 INFO: calibration group: precursor, predicting mz
3:08:39.114401 INFO: calibration group: precursor, predicting rt
3:08:39.124344 INFO: calibration group: fragment, predicting mz
3:08:39.148514 INFO: Starting optimization step 0.
3:08:39.148717 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:08:39.148803 PROGRESS: Extracting batch of 15945 precursors
3:08:39.155023 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:08:39.155105 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:08:39.155157 INFO: FWHM in RT is 2.36 seconds, sigma is 0.30
3:08:39.155187 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:08:39.155443 INFO: Starting candidate selection
3:08:40.097798 INFO: Starting candidate scoring
3:08:40.294738 INFO: Finished candidate processing
3:08:40.294858 INFO: Collecting candidate features
3:08:40.347730 INFO: Collecting fragment features
3:08:40.367285 INFO: Finished candidate scoring
3:08:40.383422 PROGRESS: === Extracted 31884 precursors and 293491 fragments ===
3:08:40.383840 INFO: performing precursor FDR with 47 features
3:08:40.383879 INFO: Decoy channel: -1
3:08:40.383903 INFO: Competetive: True
3:08:40.392837 INFO: Setting torch num_threads to 2 for FDR classification task
3:08:40.997779 INFO: Test AUC: 0.772
3:08:40.997924 INFO: Train AUC: 0.778
3:08:40.997954 INFO: AUC difference: 0.81%
3:08:41.081393 INFO: Resetting torch num_threads to 100
3:08:41.082908 INFO: === FDR correction performed with classifier version 6 ===
3:08:41.084479 PROGRESS: ============================= Precursor FDR =============================
3:08:41.084581 PROGRESS: Total precursors accumulated: 6,756
3:08:41.084641 PROGRESS: Target precursors: 6,611 (97.85%)
3:08:41.084692 PROGRESS: Decoy precursors: 145 (2.15%)
3:08:41.084747 PROGRESS: 
3:08:41.084791 PROGRESS: Precursor Summary:
3:08:41.087517 PROGRESS: Channel   0:	 0.05 FDR: 6,611; 0.01 FDR: 6,415; 0.001 FDR: 5,199
3:08:41.087649 PROGRESS: 
3:08:41.087708 PROGRESS: Protein Summary:
3:08:41.091793 PROGRESS: Channel   0:	 0.05 FDR: 3,587; 0.01 FDR: 3,504; 0.001 FDR: 3,074
3:08:41.091900 PROGRESS: =========================================================================
3:08:41.112943 INFO: fragments_df_filtered: 5000
3:08:41.126196 INFO: calibration group: precursor, fitting mz estimator 
3:08:41.744425 INFO: calibration group: precursor, fitting rt estimator 
3:08:42.383399 INFO: calibration group: fragment, fitting mz estimator 
3:08:42.804451 INFO: calibration group: precursor, predicting mz
3:08:42.807529 INFO: calibration group: precursor, predicting rt
3:08:42.816465 INFO: calibration group: fragment, predicting mz
3:08:42.836847 INFO: === checking if optimization conditions were reached ===
3:08:42.837030 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3:08:42.842354 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 75.7492.
3:08:42.842428 INFO: ==============================================
3:08:42.842542 INFO: Starting optimization step 1.
3:08:42.842618 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:08:42.842686 PROGRESS: Extracting batch of 15945 precursors
3:08:42.848851 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:08:42.848929 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:08:42.848969 INFO: FWHM in RT is 2.36 seconds, sigma is 0.30
3:08:42.848998 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:08:42.849228 INFO: Starting candidate selection
3:08:43.470924 INFO: Starting candidate scoring
3:08:43.686393 INFO: Finished candidate processing
3:08:43.686534 INFO: Collecting candidate features
3:08:43.735933 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 31710)
3:08:43.743313 INFO: Collecting fragment features
3:08:43.762290 INFO: Finished candidate scoring
3:08:43.778835 PROGRESS: === Extracted 31710 precursors and 271115 fragments ===
3:08:43.779236 INFO: performing precursor FDR with 47 features
3:08:43.779272 INFO: Decoy channel: -1
3:08:43.779295 INFO: Competetive: True
3:08:43.788458 INFO: Setting torch num_threads to 2 for FDR classification task
3:08:43.792962 WARNING: dropped 1 decoy PSMs due to missing features
3:08:44.406091 INFO: Test AUC: 0.816
3:08:44.406238 INFO: Train AUC: 0.820
3:08:44.406268 INFO: AUC difference: 0.49%
3:08:44.490181 INFO: Resetting torch num_threads to 100
3:08:44.491681 INFO: === FDR correction performed with classifier version 6 ===
3:08:44.493203 PROGRESS: ============================= Precursor FDR =============================
3:08:44.493317 PROGRESS: Total precursors accumulated: 7,319
3:08:44.493376 PROGRESS: Target precursors: 7,220 (98.65%)
3:08:44.493427 PROGRESS: Decoy precursors: 99 (1.35%)
3:08:44.493475 PROGRESS: 
3:08:44.493517 PROGRESS: Precursor Summary:
3:08:44.496415 PROGRESS: Channel   0:	 0.05 FDR: 7,220; 0.01 FDR: 7,126; 0.001 FDR: 5,785
3:08:44.496543 PROGRESS: 
3:08:44.496600 PROGRESS: Protein Summary:
3:08:44.501005 PROGRESS: Channel   0:	 0.05 FDR: 3,809; 0.01 FDR: 3,779; 0.001 FDR: 3,320
3:08:44.501138 PROGRESS: =========================================================================
3:08:44.525745 INFO: fragments_df_filtered: 5000
3:08:44.540834 INFO: calibration group: precursor, fitting mz estimator 
3:08:45.299222 INFO: calibration group: precursor, fitting rt estimator 
3:08:46.066453 INFO: calibration group: fragment, fitting mz estimator 
3:08:46.487153 INFO: calibration group: precursor, predicting mz
3:08:46.490312 INFO: calibration group: precursor, predicting rt
3:08:46.499362 INFO: calibration group: fragment, predicting mz
3:08:46.519449 INFO: === checking if optimization conditions were reached ===
3:08:46.519622 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3:08:46.524937 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 32.3250.
3:08:46.524999 INFO: ==============================================
3:08:46.525093 INFO: Starting optimization step 2.
3:08:46.525159 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:08:46.525218 PROGRESS: Extracting batch of 15945 precursors
3:08:46.529822 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:08:46.529889 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:08:46.529921 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
3:08:46.529946 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:08:46.530144 INFO: Starting candidate selection
3:08:47.174413 INFO: Starting candidate scoring
3:08:47.384226 INFO: Finished candidate processing
3:08:47.384348 INFO: Collecting candidate features
3:08:47.432579 WARNING: intensity_correlation has 5 NaNs ( 0.02 % out of 31557)
3:08:47.436951 INFO: Collecting fragment features
3:08:47.456459 INFO: Finished candidate scoring
3:08:47.471735 PROGRESS: === Extracted 31557 precursors and 263056 fragments ===
3:08:47.472155 INFO: performing precursor FDR with 47 features
3:08:47.472194 INFO: Decoy channel: -1
3:08:47.472219 INFO: Competetive: True
3:08:47.481292 INFO: Setting torch num_threads to 2 for FDR classification task
3:08:47.485821 WARNING: dropped 5 decoy PSMs due to missing features
3:08:48.091263 INFO: Test AUC: 0.829
3:08:48.091409 INFO: Train AUC: 0.836
3:08:48.091440 INFO: AUC difference: 0.81%
3:08:48.175949 INFO: Resetting torch num_threads to 100
3:08:48.177462 INFO: === FDR correction performed with classifier version 6 ===
3:08:48.178946 PROGRESS: ============================= Precursor FDR =============================
3:08:48.179053 PROGRESS: Total precursors accumulated: 7,358
3:08:48.179114 PROGRESS: Target precursors: 7,264 (98.72%)
3:08:48.179165 PROGRESS: Decoy precursors: 94 (1.28%)
3:08:48.179210 PROGRESS: 
3:08:48.179252 PROGRESS: Precursor Summary:
3:08:48.182158 PROGRESS: Channel   0:	 0.05 FDR: 7,264; 0.01 FDR: 7,211; 0.001 FDR: 6,213
3:08:48.182275 PROGRESS: 
3:08:48.182341 PROGRESS: Protein Summary:
3:08:48.186762 PROGRESS: Channel   0:	 0.05 FDR: 3,830; 0.01 FDR: 3,813; 0.001 FDR: 3,469
3:08:48.186872 PROGRESS: =========================================================================
3:08:48.210005 INFO: fragments_df_filtered: 5000
3:08:48.223430 INFO: calibration group: precursor, fitting mz estimator 
3:08:48.957527 INFO: calibration group: precursor, fitting rt estimator 
3:08:49.740531 INFO: calibration group: fragment, fitting mz estimator 
3:08:50.214351 INFO: calibration group: precursor, predicting mz
3:08:50.217346 INFO: calibration group: precursor, predicting rt
3:08:50.226267 INFO: calibration group: fragment, predicting mz
3:08:50.245432 INFO: === checking if optimization conditions were reached ===
3:08:50.245620 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3:08:50.251647 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 19.8690.
3:08:50.251711 INFO: ==============================================
3:08:50.251815 INFO: Starting optimization step 3.
3:08:50.251892 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:08:50.251960 PROGRESS: Extracting batch of 15945 precursors
3:08:50.257399 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:08:50.257470 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:08:50.257509 INFO: FWHM in RT is 2.32 seconds, sigma is 0.30
3:08:50.257538 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:08:50.257749 INFO: Starting candidate selection
3:08:50.804830 INFO: Starting candidate scoring
3:08:51.001233 INFO: Finished candidate processing
3:08:51.001357 INFO: Collecting candidate features
3:08:51.060827 WARNING: intensity_correlation has 14 NaNs ( 0.05 % out of 30701)
3:08:51.065104 INFO: Collecting fragment features
3:08:51.083494 INFO: Finished candidate scoring
3:08:51.097501 PROGRESS: === Extracted 30701 precursors and 251296 fragments ===
3:08:51.097917 INFO: performing precursor FDR with 47 features
3:08:51.097959 INFO: Decoy channel: -1
3:08:51.097984 INFO: Competetive: True
3:08:51.106949 INFO: Setting torch num_threads to 2 for FDR classification task
3:08:51.112299 WARNING: dropped 3 target PSMs due to missing features
3:08:51.112412 WARNING: dropped 11 decoy PSMs due to missing features
3:08:51.602009 INFO: Test AUC: 0.850
3:08:51.602155 INFO: Train AUC: 0.852
3:08:51.602184 INFO: AUC difference: 0.24%
3:08:51.685681 INFO: Resetting torch num_threads to 100
3:08:51.687223 INFO: === FDR correction performed with classifier version 6 ===
3:08:51.688765 PROGRESS: ============================= Precursor FDR =============================
3:08:51.688890 PROGRESS: Total precursors accumulated: 7,360
3:08:51.688958 PROGRESS: Target precursors: 7,271 (98.79%)
3:08:51.689034 PROGRESS: Decoy precursors: 89 (1.21%)
3:08:51.689101 PROGRESS: 
3:08:51.689163 PROGRESS: Precursor Summary:
3:08:51.692193 PROGRESS: Channel   0:	 0.05 FDR: 7,271; 0.01 FDR: 7,202; 0.001 FDR: 6,084
3:08:51.692327 PROGRESS: 
3:08:51.692404 PROGRESS: Protein Summary:
3:08:51.696884 PROGRESS: Channel   0:	 0.05 FDR: 3,827; 0.01 FDR: 3,804; 0.001 FDR: 3,426
3:08:51.697009 PROGRESS: =========================================================================
3:08:51.719594 INFO: fragments_df_filtered: 5000
3:08:51.733001 INFO: calibration group: precursor, fitting mz estimator 
3:08:52.492177 INFO: calibration group: precursor, fitting rt estimator 
3:08:53.261015 INFO: calibration group: fragment, fitting mz estimator 
3:08:53.699481 INFO: calibration group: precursor, predicting mz
3:08:53.702491 INFO: calibration group: precursor, predicting rt
3:08:53.711532 INFO: calibration group: fragment, predicting mz
3:08:53.732696 INFO: === checking if optimization conditions were reached ===
3:08:53.733050 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3:08:53.740234 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 15.5306.
3:08:53.740385 INFO: ==============================================
3:08:53.740581 INFO: Starting optimization step 4.
3:08:53.740664 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:08:53.740780 PROGRESS: Extracting batch of 15945 precursors
3:08:53.749246 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:08:53.749409 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:08:53.749450 INFO: FWHM in RT is 2.32 seconds, sigma is 0.30
3:08:53.749481 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:08:53.749790 INFO: Starting candidate selection
3:08:54.322083 INFO: Starting candidate scoring
3:08:54.517427 INFO: Finished candidate processing
3:08:54.517558 INFO: Collecting candidate features
3:08:54.566627 WARNING: intensity_correlation has 13 NaNs ( 0.04 % out of 30761)
3:08:54.570975 INFO: Collecting fragment features
3:08:54.589435 INFO: Finished candidate scoring
3:08:54.605254 PROGRESS: === Extracted 30761 precursors and 252772 fragments ===
3:08:54.605659 INFO: performing precursor FDR with 47 features
3:08:54.605702 INFO: Decoy channel: -1
3:08:54.605729 INFO: Competetive: True
3:08:54.614997 INFO: Setting torch num_threads to 2 for FDR classification task
3:08:54.620591 WARNING: dropped 3 target PSMs due to missing features
3:08:54.620713 WARNING: dropped 10 decoy PSMs due to missing features
3:08:55.194157 INFO: Test AUC: 0.864
3:08:55.194303 INFO: Train AUC: 0.862
3:08:55.194333 INFO: AUC difference: 0.25%
3:08:55.279336 INFO: Resetting torch num_threads to 100
3:08:55.280817 INFO: === FDR correction performed with classifier version 6 ===
3:08:55.282328 PROGRESS: ============================= Precursor FDR =============================
3:08:55.282424 PROGRESS: Total precursors accumulated: 7,335
3:08:55.282483 PROGRESS: Target precursors: 7,241 (98.72%)
3:08:55.282533 PROGRESS: Decoy precursors: 94 (1.28%)
3:08:55.282579 PROGRESS: 
3:08:55.282621 PROGRESS: Precursor Summary:
3:08:55.285683 PROGRESS: Channel   0:	 0.05 FDR: 7,241; 0.01 FDR: 7,143; 0.001 FDR: 5,977
3:08:55.285798 PROGRESS: 
3:08:55.285852 PROGRESS: Protein Summary:
3:08:55.290279 PROGRESS: Channel   0:	 0.05 FDR: 3,823; 0.01 FDR: 3,787; 0.001 FDR: 3,387
3:08:55.290388 PROGRESS: =========================================================================
3:08:55.314713 INFO: fragments_df_filtered: 5000
3:08:55.330375 INFO: calibration group: precursor, fitting mz estimator 
3:08:56.037892 INFO: calibration group: precursor, fitting rt estimator 
3:08:56.744455 INFO: calibration group: fragment, fitting mz estimator 
3:08:57.168894 INFO: calibration group: precursor, predicting mz
3:08:57.171993 INFO: calibration group: precursor, predicting rt
3:08:57.181121 INFO: calibration group: fragment, predicting mz
3:08:57.234969 INFO: === checking if optimization conditions were reached ===
3:08:57.235564 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3:08:57.242510 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 17.1173.
3:08:57.242687 INFO: ==============================================
3:08:57.242966 INFO: Starting optimization step 5.
3:08:57.243186 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:08:57.243426 PROGRESS: Extracting batch of 15945 precursors
3:08:57.250224 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:08:57.250370 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:08:57.250474 INFO: FWHM in RT is 2.32 seconds, sigma is 0.30
3:08:57.250566 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:08:57.250864 INFO: Starting candidate selection
3:08:57.826007 INFO: Starting candidate scoring
3:08:58.068353 INFO: Finished candidate processing
3:08:58.068471 INFO: Collecting candidate features
3:08:58.120949 WARNING: intensity_correlation has 14 NaNs ( 0.05 % out of 30762)
3:08:58.131909 INFO: Collecting fragment features
3:08:58.151632 INFO: Finished candidate scoring
3:08:58.164927 PROGRESS: === Extracted 30762 precursors and 252396 fragments ===
3:08:58.165349 INFO: performing precursor FDR with 47 features
3:08:58.165390 INFO: Decoy channel: -1
3:08:58.165414 INFO: Competetive: True
3:08:58.173625 INFO: Setting torch num_threads to 2 for FDR classification task
3:08:58.179256 WARNING: dropped 4 target PSMs due to missing features
3:08:58.179389 WARNING: dropped 10 decoy PSMs due to missing features
3:08:58.591647 INFO: Test AUC: 0.859
3:08:58.591782 INFO: Train AUC: 0.859
3:08:58.591813 INFO: AUC difference: 0.03%
3:08:58.675190 INFO: Resetting torch num_threads to 100
3:08:58.676462 INFO: === FDR correction performed with classifier version 6 ===
3:08:58.677962 PROGRESS: ============================= Precursor FDR =============================
3:08:58.678062 PROGRESS: Total precursors accumulated: 7,348
3:08:58.678138 PROGRESS: Target precursors: 7,258 (98.78%)
3:08:58.678191 PROGRESS: Decoy precursors: 90 (1.22%)
3:08:58.678238 PROGRESS: 
3:08:58.678285 PROGRESS: Precursor Summary:
3:08:58.681179 PROGRESS: Channel   0:	 0.05 FDR: 7,258; 0.01 FDR: 7,164; 0.001 FDR: 6,192
3:08:58.681291 PROGRESS: 
3:08:58.681349 PROGRESS: Protein Summary:
3:08:58.685650 PROGRESS: Channel   0:	 0.05 FDR: 3,819; 0.01 FDR: 3,790; 0.001 FDR: 3,460
3:08:58.685754 PROGRESS: =========================================================================
3:08:58.708989 INFO: fragments_df_filtered: 5000
3:08:58.721137 INFO: calibration group: precursor, fitting mz estimator 
3:08:59.418748 INFO: calibration group: precursor, fitting rt estimator 
3:09:00.165250 INFO: calibration group: fragment, fitting mz estimator 
3:09:00.580910 INFO: calibration group: precursor, predicting mz
3:09:00.583792 INFO: calibration group: precursor, predicting rt
3:09:00.592607 INFO: calibration group: fragment, predicting mz
3:09:00.617202 INFO: === checking if optimization conditions were reached ===
3:09:00.617637 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3:09:00.625404 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 16.7919.
3:09:00.625503 INFO: ==============================================
3:09:00.625673 INFO: Starting optimization step 6.
3:09:00.625792 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:09:00.625904 PROGRESS: Extracting batch of 15945 precursors
3:09:00.634531 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:09:00.634623 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:09:00.634684 INFO: FWHM in RT is 2.32 seconds, sigma is 0.30
3:09:00.634727 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:09:00.635005 INFO: Starting candidate selection
3:09:01.185706 INFO: Starting candidate scoring
3:09:01.410238 INFO: Finished candidate processing
3:09:01.410359 INFO: Collecting candidate features
3:09:01.466002 WARNING: intensity_correlation has 13 NaNs ( 0.04 % out of 30736)
3:09:01.470321 INFO: Collecting fragment features
3:09:01.488582 INFO: Finished candidate scoring
3:09:01.504479 PROGRESS: === Extracted 30736 precursors and 252295 fragments ===
3:09:01.504912 INFO: performing precursor FDR with 47 features
3:09:01.504956 INFO: Decoy channel: -1
3:09:01.504983 INFO: Competetive: True
3:09:01.514003 INFO: Setting torch num_threads to 2 for FDR classification task
3:09:01.519444 WARNING: dropped 5 target PSMs due to missing features
3:09:01.519558 WARNING: dropped 8 decoy PSMs due to missing features
3:09:01.849043 INFO: Test AUC: 0.856
3:09:01.849218 INFO: Train AUC: 0.861
3:09:01.849249 INFO: AUC difference: 0.52%
3:09:01.940194 INFO: Resetting torch num_threads to 100
3:09:01.942159 INFO: === FDR correction performed with classifier version 6 ===
3:09:01.943945 PROGRESS: ============================= Precursor FDR =============================
3:09:01.944051 PROGRESS: Total precursors accumulated: 7,336
3:09:01.944112 PROGRESS: Target precursors: 7,223 (98.46%)
3:09:01.944164 PROGRESS: Decoy precursors: 113 (1.54%)
3:09:01.944210 PROGRESS: 
3:09:01.944256 PROGRESS: Precursor Summary:
3:09:01.947293 PROGRESS: Channel   0:	 0.05 FDR: 7,223; 0.01 FDR: 7,131; 0.001 FDR: 5,933
3:09:01.947418 PROGRESS: 
3:09:01.947474 PROGRESS: Protein Summary:
3:09:01.952003 PROGRESS: Channel   0:	 0.05 FDR: 3,818; 0.01 FDR: 3,783; 0.001 FDR: 3,362
3:09:01.952130 PROGRESS: =========================================================================
3:09:01.976641 INFO: fragments_df_filtered: 5000
3:09:01.996406 INFO: calibration group: precursor, fitting mz estimator 
3:09:02.793210 INFO: calibration group: precursor, fitting rt estimator 
3:09:03.579331 INFO: calibration group: fragment, fitting mz estimator 
3:09:04.005109 INFO: calibration group: precursor, predicting mz
3:09:04.008494 INFO: calibration group: precursor, predicting rt
3:09:04.018311 INFO: calibration group: fragment, predicting mz
3:09:04.098893 INFO: === checking if optimization conditions were reached ===
3:09:04.099366 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
3:09:04.105698 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 15.5306 found after 7 searches.
3:09:04.105870 INFO: ==============================================
3:09:04.107045 PROGRESS: Optimization finished for rt_error.
3:09:04.129746 INFO: calibration group: precursor, predicting mz
3:09:04.133012 INFO: calibration group: precursor, predicting rt
3:09:04.142731 INFO: calibration group: fragment, predicting mz
3:09:04.219294 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:09:04.219598 PROGRESS: ==============================================
3:09:04.219681 PROGRESS: ms2_error      : 8.0000
3:09:04.219750 PROGRESS: ms1_error      : 3.0000
3:09:04.219813 PROGRESS: rt_error       : 15.5306
3:09:04.219868 PROGRESS: ==============================================
3:09:04.221162 INFO: calibration group: precursor, predicting mz
3:09:04.232394 INFO: calibration group: precursor, predicting rt
3:09:04.301919 INFO: calibration group: fragment, predicting mz
3:09:04.475664 PROGRESS: Extracting batch of 78739 precursors
3:09:04.543914 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:09:04.544115 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:09:04.544167 INFO: FWHM in RT is 2.32 seconds, sigma is 0.30
3:09:04.544198 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:09:04.544529 INFO: Starting candidate selection
3:09:07.056337 INFO: Applying score cutoff of 18.57264839553833
3:09:07.062697 INFO: Removed 12584 precursors with score below cutoff
3:09:07.112286 INFO: Starting candidate scoring
3:09:08.290127 INFO: Finished candidate processing
3:09:08.290277 INFO: Collecting candidate features
3:09:08.533315 WARNING: intensity_correlation has 11 NaNs ( 0.01 % out of 140993)
3:09:08.543815 INFO: Collecting fragment features
3:09:08.651276 INFO: Finished candidate scoring
3:09:08.729727 INFO: === FDR correction performed with classifier version 11 ===
3:09:08.731139 INFO: performing precursor FDR with 47 features
3:09:08.731179 INFO: Decoy channel: -1
3:09:08.731207 INFO: Competetive: True
3:09:08.800910 INFO: Setting torch num_threads to 2 for FDR classification task
3:09:08.831440 WARNING: dropped 6 target PSMs due to missing features
3:09:08.831616 WARNING: dropped 5 decoy PSMs due to missing features
3:09:08.831677 WARNING: FDR calculation for 74166 target and 66816 decoy PSMs
3:09:08.831708 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
3:09:10.910306 INFO: Test AUC: 0.884
3:09:10.910463 INFO: Train AUC: 0.888
3:09:10.910494 INFO: AUC difference: 0.47%
3:09:11.012562 INFO: Resetting torch num_threads to 100
3:09:11.022914 INFO: Removing fragments below FDR threshold
3:09:11.055700 PROGRESS: ============================= Precursor FDR =============================
3:09:11.056025 PROGRESS: Total precursors accumulated: 36,172
3:09:11.056089 PROGRESS: Target precursors: 35,814 (99.01%)
3:09:11.056138 PROGRESS: Decoy precursors: 358 (0.99%)
3:09:11.056186 PROGRESS: 
3:09:11.056230 PROGRESS: Precursor Summary:
3:09:11.073355 PROGRESS: Channel   0:	 0.05 FDR: 35,814; 0.01 FDR: 35,814; 0.001 FDR: 32,584
3:09:11.073680 PROGRESS: 
3:09:11.074485 PROGRESS: Protein Summary:
3:09:11.100634 PROGRESS: Channel   0:	 0.05 FDR: 6,701; 0.01 FDR: 6,701; 0.001 FDR: 6,608
3:09:11.101015 PROGRESS: =========================================================================
3:09:11.467692 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:09:11.496123 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:09:11.496322 INFO: Quantification results path: run_output_Astral/alphadia_1.10_MBRSetValues/quant
3:09:11.496420 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3 at run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:09:11.497232 INFO: Initializing RawFileManager
3:09:44.133049 INFO: Determining DIA cycle
3:09:44.149263 INFO: Found cycle with start 0.00 min and length 303.
3:09:44.382994 INFO: RT (min)            : 0.0 - 26.9
3:09:44.383113 INFO: RT duration (sec)   : 1611.2
3:09:44.383146 INFO: RT duration (min)   : 26.9
3:09:44.383171 INFO: Cycle len (scans)   : 303
3:09:44.383193 INFO: Cycle len (sec)     : 1.65
3:09:44.383214 INFO: Number of cycles    : 978
3:09:44.383234 INFO: MS2 range (m/z)     : 380.4 - 980.7
3:09:44.403359 INFO: Initializing CalibrationManager
3:09:44.403733 INFO: Loading calibration config
3:09:44.404524 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'}]
3:09:44.404615 INFO: Calibration group :fragment, found 1 estimator(s)
3:09:44.404753 INFO: Calibration group :precursor, found 3 estimator(s)
3:09:44.404882 INFO: Disabling ion mobility calibration
3:09:44.404925 INFO: removed mobility estimator from group precursor
3:09:44.405139 INFO: Initializing OptimizationManager
3:09:44.405257 INFO: initial parameter: ms1_error = 30
3:09:44.405329 INFO: initial parameter: ms2_error = 30
3:09:44.405381 INFO: initial parameter: rt_error = 805.611083984375
3:09:44.405426 INFO: initial parameter: mobility_error = 0.1
3:09:44.405470 INFO: initial parameter: column_type = library
3:09:44.405510 INFO: initial parameter: num_candidates = 1
3:09:44.405548 INFO: initial parameter: classifier_version = -1
3:09:44.405589 INFO: initial parameter: fwhm_rt = 5
3:09:44.405629 INFO: initial parameter: fwhm_mobility = 0.01
3:09:44.405668 INFO: initial parameter: score_cutoff = 0
3:09:44.405740 INFO: Initializing TimingManager
3:09:44.405794 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:09:44.405891 INFO: FDRManager not loaded from disk.
3:09:44.405915 INFO: Initializing FDRManager
3:09:44.405954 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
3:09:44.426431 PROGRESS: 39,524 target precursors potentially observable (0 removed)
3:09:44.451657 PROGRESS: Starting initial search for precursors.
3:09:44.469677 INFO: Starting optimization step 0.
3:09:44.469983 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:09:44.470070 PROGRESS: Extracting batch of 15945 precursors
3:09:44.476549 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:09:44.476622 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:09:44.476682 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:09:44.476714 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:09:44.477125 INFO: Starting candidate selection
3:09:45.549307 INFO: Starting candidate scoring
3:09:45.697123 INFO: Finished candidate processing
3:09:45.697241 INFO: Collecting candidate features
3:09:45.736595 INFO: Collecting fragment features
3:09:45.750403 INFO: Finished candidate scoring
3:09:45.759969 PROGRESS: === Extracted 15945 precursors and 172899 fragments ===
3:09:45.760358 INFO: performing precursor FDR with 47 features
3:09:45.760414 INFO: Decoy channel: -1
3:09:45.760438 INFO: Competetive: True
3:09:45.764746 INFO: Setting torch num_threads to 2 for FDR classification task
3:09:45.909056 INFO: Test AUC: 0.692
3:09:45.909223 INFO: Train AUC: 0.701
3:09:45.909254 INFO: AUC difference: 1.29%
3:09:45.993505 INFO: Resetting torch num_threads to 100
3:09:45.994690 INFO: === FDR correction performed with classifier version -1 ===
3:09:45.995737 PROGRESS: ============================= Precursor FDR =============================
3:09:45.995832 PROGRESS: Total precursors accumulated: 2,984
3:09:45.995893 PROGRESS: Target precursors: 2,795 (93.67%)
3:09:45.995943 PROGRESS: Decoy precursors: 189 (6.33%)
3:09:45.995989 PROGRESS: 
3:09:45.996032 PROGRESS: Precursor Summary:
3:09:45.997534 PROGRESS: Channel   0:	 0.05 FDR: 2,673; 0.01 FDR: 2,050; 0.001 FDR:   260
3:09:45.997634 PROGRESS: 
3:09:45.997690 PROGRESS: Protein Summary:
3:09:45.999545 PROGRESS: Channel   0:	 0.05 FDR: 1,848; 0.01 FDR: 1,469; 0.001 FDR:   240
3:09:45.999637 PROGRESS: =========================================================================
3:09:46.005668 INFO: fragments_df_filtered: 5000
3:09:46.017953 INFO: calibration group: precursor, fitting mz estimator 
3:09:46.240120 INFO: calibration group: precursor, fitting rt estimator 
3:09:46.408022 INFO: calibration group: fragment, fitting mz estimator 
3:09:46.832316 INFO: calibration group: precursor, predicting mz
3:09:46.835177 INFO: calibration group: precursor, predicting rt
3:09:46.844257 INFO: calibration group: fragment, predicting mz
3:09:46.870920 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3:09:46.871601 INFO: Starting optimization step 1.
3:09:46.871692 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:09:46.871787 PROGRESS: Extracting batch of 15945 precursors
3:09:46.883775 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:09:46.883943 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:09:46.883988 INFO: FWHM in RT is 2.98 seconds, sigma is 0.38
3:09:46.884017 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:09:46.884319 INFO: Starting candidate selection
3:09:47.913462 INFO: Starting candidate scoring
3:09:48.187519 INFO: Finished candidate processing
3:09:48.187642 INFO: Collecting candidate features
3:09:48.242441 INFO: Collecting fragment features
3:09:48.280585 INFO: Finished candidate scoring
3:09:48.296862 PROGRESS: === Extracted 31890 precursors and 343030 fragments ===
3:09:48.297310 INFO: performing precursor FDR with 47 features
3:09:48.297350 INFO: Decoy channel: -1
3:09:48.297374 INFO: Competetive: True
3:09:48.307561 INFO: Setting torch num_threads to 2 for FDR classification task
3:09:48.836571 INFO: Test AUC: 0.697
3:09:48.836743 INFO: Train AUC: 0.698
3:09:48.836775 INFO: AUC difference: 0.07%
3:09:48.925179 INFO: Resetting torch num_threads to 100
3:09:48.926502 INFO: === FDR correction performed with classifier version 0 ===
3:09:48.927745 PROGRESS: ============================= Precursor FDR =============================
3:09:48.927844 PROGRESS: Total precursors accumulated: 4,490
3:09:48.927903 PROGRESS: Target precursors: 4,266 (95.01%)
3:09:48.927953 PROGRESS: Decoy precursors: 224 (4.99%)
3:09:48.927998 PROGRESS: 
3:09:48.928042 PROGRESS: Precursor Summary:
3:09:48.929684 PROGRESS: Channel   0:	 0.05 FDR: 4,224; 0.01 FDR: 2,957; 0.001 FDR:     0
3:09:48.929779 PROGRESS: 
3:09:48.929834 PROGRESS: Protein Summary:
3:09:48.931976 PROGRESS: Channel   0:	 0.05 FDR: 2,628; 0.01 FDR: 1,964; 0.001 FDR:     0
3:09:48.932716 PROGRESS: =========================================================================
3:09:48.946597 INFO: fragments_df_filtered: 5000
3:09:48.960514 INFO: calibration group: precursor, fitting mz estimator 
3:09:49.219007 INFO: calibration group: precursor, fitting rt estimator 
3:09:52.346642 INFO: calibration group: fragment, fitting mz estimator 
3:09:52.766066 INFO: calibration group: precursor, predicting mz
3:09:52.769115 INFO: calibration group: precursor, predicting rt
3:09:52.778390 INFO: calibration group: fragment, predicting mz
3:09:52.884810 INFO: === checking if optimization conditions were reached ===
3:09:52.887790 PROGRESS: ❌ ms2_error      : 18.3524 > 8.0000 or insufficient steps taken.
3:09:52.889840 PROGRESS: ❌ ms1_error      : 13.5629 > 3.0000 or insufficient steps taken.
3:09:52.889976 INFO: ==============================================
3:09:52.890200 INFO: Starting optimization step 2.
3:09:52.890308 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:09:52.890397 PROGRESS: Extracting batch of 15945 precursors
3:09:52.898423 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:09:52.898573 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:09:52.898612 INFO: FWHM in RT is 2.97 seconds, sigma is 0.38
3:09:52.898639 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:09:52.898913 INFO: Starting candidate selection
3:09:53.825670 INFO: Starting candidate scoring
3:09:54.073257 INFO: Finished candidate processing
3:09:54.073406 INFO: Collecting candidate features
3:09:54.125754 INFO: Collecting fragment features
3:09:54.151114 INFO: Finished candidate scoring
3:09:54.171027 PROGRESS: === Extracted 31890 precursors and 328930 fragments ===
3:09:54.171473 INFO: performing precursor FDR with 47 features
3:09:54.171511 INFO: Decoy channel: -1
3:09:54.171536 INFO: Competetive: True
3:09:54.181026 INFO: Setting torch num_threads to 2 for FDR classification task
3:09:54.711951 INFO: Test AUC: 0.724
3:09:54.712090 INFO: Train AUC: 0.732
3:09:54.712122 INFO: AUC difference: 1.12%
3:09:54.796545 INFO: Resetting torch num_threads to 100
3:09:54.798012 INFO: === FDR correction performed with classifier version 1 ===
3:09:54.799705 PROGRESS: ============================= Precursor FDR =============================
3:09:54.799808 PROGRESS: Total precursors accumulated: 5,740
3:09:54.799866 PROGRESS: Target precursors: 5,506 (95.92%)
3:09:54.799916 PROGRESS: Decoy precursors: 234 (4.08%)
3:09:54.799962 PROGRESS: 
3:09:54.800005 PROGRESS: Precursor Summary:
3:09:54.802501 PROGRESS: Channel   0:	 0.05 FDR: 5,506; 0.01 FDR: 4,659; 0.001 FDR: 3,393
3:09:54.802624 PROGRESS: 
3:09:54.802682 PROGRESS: Protein Summary:
3:09:54.806049 PROGRESS: Channel   0:	 0.05 FDR: 3,157; 0.01 FDR: 2,798; 0.001 FDR: 2,195
3:09:54.806152 PROGRESS: =========================================================================
3:09:54.823914 INFO: fragments_df_filtered: 5000
3:09:54.837018 INFO: calibration group: precursor, fitting mz estimator 
3:09:55.286412 INFO: calibration group: precursor, fitting rt estimator 
3:09:55.680727 INFO: calibration group: fragment, fitting mz estimator 
3:09:56.141612 INFO: calibration group: precursor, predicting mz
3:09:56.144585 INFO: calibration group: precursor, predicting rt
3:09:56.153417 INFO: calibration group: fragment, predicting mz
3:09:56.212116 INFO: === checking if optimization conditions were reached ===
3:09:56.214556 PROGRESS: ❌ ms2_error      : 13.7048 > 8.0000 or insufficient steps taken.
3:09:56.216184 PROGRESS: ❌ ms1_error      : 6.0342 > 3.0000 or insufficient steps taken.
3:09:56.216238 INFO: ==============================================
3:09:56.216370 INFO: Starting optimization step 3.
3:09:56.216443 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:09:56.216500 PROGRESS: Extracting batch of 15945 precursors
3:09:56.221084 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:09:56.221139 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:09:56.221174 INFO: FWHM in RT is 2.78 seconds, sigma is 0.36
3:09:56.221196 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:09:56.221381 INFO: Starting candidate selection
3:09:57.175325 INFO: Starting candidate scoring
3:09:57.405819 INFO: Finished candidate processing
3:09:57.405939 INFO: Collecting candidate features
3:09:57.455407 INFO: Collecting fragment features
3:09:57.477178 INFO: Finished candidate scoring
3:09:57.496225 PROGRESS: === Extracted 31888 precursors and 315825 fragments ===
3:09:57.496641 INFO: performing precursor FDR with 47 features
3:09:57.496700 INFO: Decoy channel: -1
3:09:57.496736 INFO: Competetive: True
3:09:57.505552 INFO: Setting torch num_threads to 2 for FDR classification task
3:09:58.035213 INFO: Test AUC: 0.749
3:09:58.035372 INFO: Train AUC: 0.756
3:09:58.035403 INFO: AUC difference: 0.93%
3:09:58.119399 INFO: Resetting torch num_threads to 100
3:09:58.120727 INFO: === FDR correction performed with classifier version 2 ===
3:09:58.122386 PROGRESS: ============================= Precursor FDR =============================
3:09:58.122493 PROGRESS: Total precursors accumulated: 6,354
3:09:58.122553 PROGRESS: Target precursors: 6,145 (96.71%)
3:09:58.122604 PROGRESS: Decoy precursors: 209 (3.29%)
3:09:58.122650 PROGRESS: 
3:09:58.122693 PROGRESS: Precursor Summary:
3:09:58.125286 PROGRESS: Channel   0:	 0.05 FDR: 6,145; 0.01 FDR: 5,628; 0.001 FDR: 3,547
3:09:58.125415 PROGRESS: 
3:09:58.125472 PROGRESS: Protein Summary:
3:09:58.129051 PROGRESS: Channel   0:	 0.05 FDR: 3,405; 0.01 FDR: 3,213; 0.001 FDR: 2,283
3:09:58.129189 PROGRESS: =========================================================================
3:09:58.148965 INFO: fragments_df_filtered: 5000
3:09:58.162241 INFO: calibration group: precursor, fitting mz estimator 
3:09:58.687750 INFO: calibration group: precursor, fitting rt estimator 
3:09:59.211721 INFO: calibration group: fragment, fitting mz estimator 
3:09:59.626343 INFO: calibration group: precursor, predicting mz
3:09:59.629436 INFO: calibration group: precursor, predicting rt
3:09:59.638432 INFO: calibration group: fragment, predicting mz
3:09:59.667483 INFO: === checking if optimization conditions were reached ===
3:09:59.669668 PROGRESS: ❌ ms2_error      : 11.2025 > 8.0000 or insufficient steps taken.
3:09:59.671779 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
3:09:59.671842 INFO: ==============================================
3:09:59.671962 INFO: Starting optimization step 4.
3:09:59.672039 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:09:59.672107 PROGRESS: Extracting batch of 15945 precursors
3:09:59.686998 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:09:59.692540 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:09:59.692671 INFO: FWHM in RT is 2.62 seconds, sigma is 0.34
3:09:59.692906 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:09:59.693249 INFO: Starting candidate selection
3:10:00.676924 INFO: Starting candidate scoring
3:10:00.921526 INFO: Finished candidate processing
3:10:00.921654 INFO: Collecting candidate features
3:10:00.976300 INFO: Collecting fragment features
3:10:01.000430 INFO: Finished candidate scoring
3:10:01.018990 PROGRESS: === Extracted 31888 precursors and 309768 fragments ===
3:10:01.019414 INFO: performing precursor FDR with 47 features
3:10:01.019456 INFO: Decoy channel: -1
3:10:01.019482 INFO: Competetive: True
3:10:01.029039 INFO: Setting torch num_threads to 2 for FDR classification task
3:10:01.551779 INFO: Test AUC: 0.777
3:10:01.551927 INFO: Train AUC: 0.774
3:10:01.551958 INFO: AUC difference: 0.33%
3:10:01.636167 INFO: Resetting torch num_threads to 100
3:10:01.637618 INFO: === FDR correction performed with classifier version 3 ===
3:10:01.639295 PROGRESS: ============================= Precursor FDR =============================
3:10:01.639403 PROGRESS: Total precursors accumulated: 6,691
3:10:01.639462 PROGRESS: Target precursors: 6,532 (97.62%)
3:10:01.639512 PROGRESS: Decoy precursors: 159 (2.38%)
3:10:01.639556 PROGRESS: 
3:10:01.639599 PROGRESS: Precursor Summary:
3:10:01.642219 PROGRESS: Channel   0:	 0.05 FDR: 6,532; 0.01 FDR: 6,258; 0.001 FDR: 3,358
3:10:01.642343 PROGRESS: 
3:10:01.642401 PROGRESS: Protein Summary:
3:10:01.646032 PROGRESS: Channel   0:	 0.05 FDR: 3,564; 0.01 FDR: 3,455; 0.001 FDR: 2,229
3:10:01.646143 PROGRESS: =========================================================================
3:10:01.670282 INFO: fragments_df_filtered: 5000
3:10:01.685722 INFO: calibration group: precursor, fitting mz estimator 
3:10:02.520782 INFO: calibration group: precursor, fitting rt estimator 
3:10:03.382951 INFO: calibration group: fragment, fitting mz estimator 
3:10:03.857304 INFO: calibration group: precursor, predicting mz
3:10:03.860372 INFO: calibration group: precursor, predicting rt
3:10:03.870054 INFO: calibration group: fragment, predicting mz
3:10:03.954456 INFO: === checking if optimization conditions were reached ===
3:10:03.971583 PROGRESS: ❌ ms2_error      : 9.6580 > 8.0000 or insufficient steps taken.
3:10:03.971732 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
3:10:03.971764 INFO: ==============================================
3:10:03.971971 INFO: Starting optimization step 5.
3:10:03.972052 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:10:03.972119 PROGRESS: Extracting batch of 15945 precursors
3:10:03.979403 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:10:03.979476 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:10:03.979512 INFO: FWHM in RT is 2.47 seconds, sigma is 0.32
3:10:03.979535 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:10:03.979777 INFO: Starting candidate selection
3:10:04.957649 INFO: Starting candidate scoring
3:10:05.213273 INFO: Finished candidate processing
3:10:05.213411 INFO: Collecting candidate features
3:10:05.279047 INFO: Collecting fragment features
3:10:05.316234 INFO: Finished candidate scoring
3:10:05.334205 PROGRESS: === Extracted 31885 precursors and 300010 fragments ===
3:10:05.334668 INFO: performing precursor FDR with 47 features
3:10:05.334706 INFO: Decoy channel: -1
3:10:05.334730 INFO: Competetive: True
3:10:05.348544 INFO: Setting torch num_threads to 2 for FDR classification task
3:10:05.734095 INFO: Test AUC: 0.783
3:10:05.734276 INFO: Train AUC: 0.785
3:10:05.734306 INFO: AUC difference: 0.22%
3:10:05.821290 INFO: Resetting torch num_threads to 100
3:10:05.822517 INFO: === FDR correction performed with classifier version 4 ===
3:10:05.823932 PROGRESS: ============================= Precursor FDR =============================
3:10:05.824033 PROGRESS: Total precursors accumulated: 6,881
3:10:05.824093 PROGRESS: Target precursors: 6,726 (97.75%)
3:10:05.824144 PROGRESS: Decoy precursors: 155 (2.25%)
3:10:05.824189 PROGRESS: 
3:10:05.824232 PROGRESS: Precursor Summary:
3:10:05.826843 PROGRESS: Channel   0:	 0.05 FDR: 6,726; 0.01 FDR: 6,503; 0.001 FDR: 4,053
3:10:05.826965 PROGRESS: 
3:10:05.827022 PROGRESS: Protein Summary:
3:10:05.830764 PROGRESS: Channel   0:	 0.05 FDR: 3,631; 0.01 FDR: 3,549; 0.001 FDR: 2,558
3:10:05.830869 PROGRESS: =========================================================================
3:10:05.853543 INFO: fragments_df_filtered: 5000
3:10:05.870989 INFO: calibration group: precursor, fitting mz estimator 
3:10:06.505717 INFO: calibration group: precursor, fitting rt estimator 
3:10:07.173702 INFO: calibration group: fragment, fitting mz estimator 
3:10:07.614777 INFO: calibration group: precursor, predicting mz
3:10:07.618374 INFO: calibration group: precursor, predicting rt
3:10:07.628711 INFO: calibration group: fragment, predicting mz
3:10:07.676673 INFO: === checking if optimization conditions were reached ===
3:10:07.706960 PROGRESS: ❌ ms2_error      : 8.0677 > 8.0000 or insufficient steps taken.
3:10:07.707066 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
3:10:07.707103 INFO: ==============================================
3:10:07.707235 INFO: Starting optimization step 6.
3:10:07.707315 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:10:07.707388 PROGRESS: Extracting batch of 15945 precursors
3:10:07.713238 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:10:07.713300 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:10:07.713343 INFO: FWHM in RT is 2.40 seconds, sigma is 0.31
3:10:07.713370 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:10:07.713636 INFO: Starting candidate selection
3:10:08.712011 INFO: Starting candidate scoring
3:10:08.945990 INFO: Finished candidate processing
3:10:08.946102 INFO: Collecting candidate features
3:10:09.002644 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 31886)
3:10:09.007134 INFO: Collecting fragment features
3:10:09.033054 INFO: Finished candidate scoring
3:10:09.049963 PROGRESS: === Extracted 31886 precursors and 294806 fragments ===
3:10:09.050394 INFO: performing precursor FDR with 47 features
3:10:09.050435 INFO: Decoy channel: -1
3:10:09.050461 INFO: Competetive: True
3:10:09.061691 INFO: Setting torch num_threads to 2 for FDR classification task
3:10:09.066864 WARNING: dropped 1 decoy PSMs due to missing features
3:10:09.599590 INFO: Test AUC: 0.777
3:10:09.599740 INFO: Train AUC: 0.797
3:10:09.599774 INFO: AUC difference: 2.46%
3:10:09.692531 INFO: Resetting torch num_threads to 100
3:10:09.694299 INFO: === FDR correction performed with classifier version 5 ===
3:10:09.697057 PROGRESS: ============================= Precursor FDR =============================
3:10:09.697378 PROGRESS: Total precursors accumulated: 7,010
3:10:09.697458 PROGRESS: Target precursors: 6,858 (97.83%)
3:10:09.697518 PROGRESS: Decoy precursors: 152 (2.17%)
3:10:09.697571 PROGRESS: 
3:10:09.697621 PROGRESS: Precursor Summary:
3:10:09.700846 PROGRESS: Channel   0:	 0.05 FDR: 6,858; 0.01 FDR: 6,625; 0.001 FDR: 4,590
3:10:09.701014 PROGRESS: 
3:10:09.701078 PROGRESS: Protein Summary:
3:10:09.705077 PROGRESS: Channel   0:	 0.05 FDR: 3,673; 0.01 FDR: 3,586; 0.001 FDR: 2,800
3:10:09.705217 PROGRESS: =========================================================================
3:10:09.728494 INFO: fragments_df_filtered: 5000
3:10:09.741628 INFO: calibration group: precursor, fitting mz estimator 
3:10:10.432748 INFO: calibration group: precursor, fitting rt estimator 
3:10:11.107301 INFO: calibration group: fragment, fitting mz estimator 
3:10:11.519997 INFO: calibration group: precursor, predicting mz
3:10:11.523330 INFO: calibration group: precursor, predicting rt
3:10:11.533132 INFO: calibration group: fragment, predicting mz
3:10:11.560150 INFO: === checking if optimization conditions were reached ===
3:10:11.562769 PROGRESS: ✅ ms2_error      : 8.0000 <= 8.0000
3:10:11.562846 PROGRESS: ✅ ms1_error      : 3.0000 <= 3.0000
3:10:11.562882 INFO: ==============================================
3:10:11.562996 PROGRESS: Optimization finished for ms2_error, ms1_error.
3:10:11.578856 INFO: calibration group: precursor, predicting mz
3:10:11.582077 INFO: calibration group: precursor, predicting rt
3:10:11.591498 INFO: calibration group: fragment, predicting mz
3:10:11.615682 INFO: Starting optimization step 0.
3:10:11.616081 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:10:11.616304 PROGRESS: Extracting batch of 15945 precursors
3:10:11.622058 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:10:11.622193 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:10:11.622286 INFO: FWHM in RT is 2.36 seconds, sigma is 0.30
3:10:11.622366 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:10:11.622652 INFO: Starting candidate selection
3:10:12.586762 INFO: Starting candidate scoring
3:10:12.826276 INFO: Finished candidate processing
3:10:12.826401 INFO: Collecting candidate features
3:10:12.885787 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 31884)
3:10:12.890980 INFO: Collecting fragment features
3:10:12.913878 INFO: Finished candidate scoring
3:10:12.930742 PROGRESS: === Extracted 31884 precursors and 294587 fragments ===
3:10:12.931156 INFO: performing precursor FDR with 47 features
3:10:12.931193 INFO: Decoy channel: -1
3:10:12.931216 INFO: Competetive: True
3:10:12.940311 INFO: Setting torch num_threads to 2 for FDR classification task
3:10:12.945610 WARNING: dropped 1 decoy PSMs due to missing features
3:10:13.402591 INFO: Test AUC: 0.780
3:10:13.402741 INFO: Train AUC: 0.800
3:10:13.402771 INFO: AUC difference: 2.50%
3:10:13.493685 INFO: Resetting torch num_threads to 100
3:10:13.495038 INFO: === FDR correction performed with classifier version 6 ===
3:10:13.496526 PROGRESS: ============================= Precursor FDR =============================
3:10:13.496639 PROGRESS: Total precursors accumulated: 7,000
3:10:13.496709 PROGRESS: Target precursors: 6,860 (98.00%)
3:10:13.496780 PROGRESS: Decoy precursors: 140 (2.00%)
3:10:13.496827 PROGRESS: 
3:10:13.496873 PROGRESS: Precursor Summary:
3:10:13.499605 PROGRESS: Channel   0:	 0.05 FDR: 6,860; 0.01 FDR: 6,627; 0.001 FDR: 4,548
3:10:13.499743 PROGRESS: 
3:10:13.499802 PROGRESS: Protein Summary:
3:10:13.503768 PROGRESS: Channel   0:	 0.05 FDR: 3,686; 0.01 FDR: 3,600; 0.001 FDR: 2,778
3:10:13.503888 PROGRESS: =========================================================================
3:10:13.526445 INFO: fragments_df_filtered: 5000
3:10:13.539856 INFO: calibration group: precursor, fitting mz estimator 
3:10:14.288609 INFO: calibration group: precursor, fitting rt estimator 
3:10:14.973336 INFO: calibration group: fragment, fitting mz estimator 
3:10:15.409817 INFO: calibration group: precursor, predicting mz
3:10:15.412786 INFO: calibration group: precursor, predicting rt
3:10:15.421857 INFO: calibration group: fragment, predicting mz
3:10:15.447633 INFO: === checking if optimization conditions were reached ===
3:10:15.449462 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3:10:15.455959 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 62.6521.
3:10:15.456125 INFO: ==============================================
3:10:15.456335 INFO: Starting optimization step 1.
3:10:15.456413 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:10:15.456489 PROGRESS: Extracting batch of 15945 precursors
3:10:15.462231 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:10:15.462344 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:10:15.462383 INFO: FWHM in RT is 2.36 seconds, sigma is 0.30
3:10:15.462410 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:10:15.462664 INFO: Starting candidate selection
3:10:16.101420 INFO: Starting candidate scoring
3:10:16.347451 INFO: Finished candidate processing
3:10:16.347593 INFO: Collecting candidate features
3:10:16.414742 WARNING: intensity_correlation has 6 NaNs ( 0.02 % out of 31710)
3:10:16.419635 INFO: Collecting fragment features
3:10:16.440031 INFO: Finished candidate scoring
3:10:16.455848 PROGRESS: === Extracted 31710 precursors and 269828 fragments ===
3:10:16.456239 INFO: performing precursor FDR with 47 features
3:10:16.456278 INFO: Decoy channel: -1
3:10:16.456302 INFO: Competetive: True
3:10:16.467159 INFO: Setting torch num_threads to 2 for FDR classification task
3:10:16.474648 WARNING: dropped 2 target PSMs due to missing features
3:10:16.474798 WARNING: dropped 4 decoy PSMs due to missing features
3:10:16.975765 INFO: Test AUC: 0.835
3:10:16.975896 INFO: Train AUC: 0.838
3:10:16.975925 INFO: AUC difference: 0.45%
3:10:17.062459 INFO: Resetting torch num_threads to 100
3:10:17.063768 INFO: === FDR correction performed with classifier version 6 ===
3:10:17.065330 PROGRESS: ============================= Precursor FDR =============================
3:10:17.065431 PROGRESS: Total precursors accumulated: 7,552
3:10:17.065492 PROGRESS: Target precursors: 7,490 (99.18%)
3:10:17.065543 PROGRESS: Decoy precursors: 62 (0.82%)
3:10:17.065590 PROGRESS: 
3:10:17.065635 PROGRESS: Precursor Summary:
3:10:17.068545 PROGRESS: Channel   0:	 0.05 FDR: 7,490; 0.01 FDR: 7,490; 0.001 FDR: 6,491
3:10:17.068660 PROGRESS: 
3:10:17.068729 PROGRESS: Protein Summary:
3:10:17.073000 PROGRESS: Channel   0:	 0.05 FDR: 3,889; 0.01 FDR: 3,889; 0.001 FDR: 3,550
3:10:17.073105 PROGRESS: =========================================================================
3:10:17.097407 INFO: fragments_df_filtered: 5000
3:10:17.109413 INFO: calibration group: precursor, fitting mz estimator 
3:10:17.929497 INFO: calibration group: precursor, fitting rt estimator 
3:10:18.800450 INFO: calibration group: fragment, fitting mz estimator 
3:10:19.277592 INFO: calibration group: precursor, predicting mz
3:10:19.281908 INFO: calibration group: precursor, predicting rt
3:10:19.292316 INFO: calibration group: fragment, predicting mz
3:10:19.336023 INFO: === checking if optimization conditions were reached ===
3:10:19.336379 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3:10:19.343965 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 27.9230.
3:10:19.344046 INFO: ==============================================
3:10:19.344178 INFO: Starting optimization step 2.
3:10:19.344266 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:10:19.344348 PROGRESS: Extracting batch of 15945 precursors
3:10:19.351013 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:10:19.351083 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:10:19.351128 INFO: FWHM in RT is 2.34 seconds, sigma is 0.30
3:10:19.351158 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:10:19.351413 INFO: Starting candidate selection
3:10:20.037599 INFO: Starting candidate scoring
3:10:20.323129 INFO: Finished candidate processing
3:10:20.323416 INFO: Collecting candidate features
3:10:20.402220 WARNING: intensity_correlation has 5 NaNs ( 0.02 % out of 31615)
3:10:20.410675 INFO: Collecting fragment features
3:10:20.448195 INFO: Finished candidate scoring
3:10:20.496645 PROGRESS: === Extracted 31615 precursors and 264950 fragments ===
3:10:20.497160 INFO: performing precursor FDR with 47 features
3:10:20.497213 INFO: Decoy channel: -1
3:10:20.497248 INFO: Competetive: True
3:10:20.509312 INFO: Setting torch num_threads to 2 for FDR classification task
3:10:20.516656 WARNING: dropped 2 target PSMs due to missing features
3:10:20.516857 WARNING: dropped 3 decoy PSMs due to missing features
3:10:21.241933 INFO: Test AUC: 0.854
3:10:21.242108 INFO: Train AUC: 0.857
3:10:21.242139 INFO: AUC difference: 0.30%
3:10:21.331971 INFO: Resetting torch num_threads to 100
3:10:21.333371 INFO: === FDR correction performed with classifier version 6 ===
3:10:21.336937 PROGRESS: ============================= Precursor FDR =============================
3:10:21.337085 PROGRESS: Total precursors accumulated: 7,573
3:10:21.337147 PROGRESS: Target precursors: 7,521 (99.31%)
3:10:21.337199 PROGRESS: Decoy precursors: 52 (0.69%)
3:10:21.337245 PROGRESS: 
3:10:21.337290 PROGRESS: Precursor Summary:
3:10:21.340438 PROGRESS: Channel   0:	 0.05 FDR: 7,521; 0.01 FDR: 7,521; 0.001 FDR: 5,900
3:10:21.340609 PROGRESS: 
3:10:21.340682 PROGRESS: Protein Summary:
3:10:21.345076 PROGRESS: Channel   0:	 0.05 FDR: 3,908; 0.01 FDR: 3,908; 0.001 FDR: 3,332
3:10:21.345208 PROGRESS: =========================================================================
3:10:21.370375 INFO: fragments_df_filtered: 5000
3:10:21.384336 INFO: calibration group: precursor, fitting mz estimator 
3:10:22.212164 INFO: calibration group: precursor, fitting rt estimator 
3:10:23.061316 INFO: calibration group: fragment, fitting mz estimator 
3:10:23.491091 INFO: calibration group: precursor, predicting mz
3:10:23.494122 INFO: calibration group: precursor, predicting rt
3:10:23.503404 INFO: calibration group: fragment, predicting mz
3:10:23.528809 INFO: === checking if optimization conditions were reached ===
3:10:23.529239 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3:10:23.536507 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 22.9032.
3:10:23.536646 INFO: ==============================================
3:10:23.536848 INFO: Starting optimization step 3.
3:10:23.536928 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:10:23.536999 PROGRESS: Extracting batch of 15945 precursors
3:10:23.543282 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:10:23.543403 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:10:23.543442 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
3:10:23.543470 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:10:23.543716 INFO: Starting candidate selection
3:10:24.121004 INFO: Starting candidate scoring
3:10:24.356540 INFO: Finished candidate processing
3:10:24.356682 INFO: Collecting candidate features
3:10:24.428569 WARNING: intensity_correlation has 21 NaNs ( 0.07 % out of 30679)
3:10:24.433241 INFO: Collecting fragment features
3:10:24.453515 INFO: Finished candidate scoring
3:10:24.469434 PROGRESS: === Extracted 30679 precursors and 250965 fragments ===
3:10:24.469851 INFO: performing precursor FDR with 47 features
3:10:24.469890 INFO: Decoy channel: -1
3:10:24.469913 INFO: Competetive: True
3:10:24.484008 INFO: Setting torch num_threads to 2 for FDR classification task
3:10:24.493572 WARNING: dropped 3 target PSMs due to missing features
3:10:24.493707 WARNING: dropped 18 decoy PSMs due to missing features
3:10:24.914901 INFO: Test AUC: 0.852
3:10:24.915029 INFO: Train AUC: 0.863
3:10:24.915058 INFO: AUC difference: 1.27%
3:10:24.999218 INFO: Resetting torch num_threads to 100
3:10:25.000487 INFO: === FDR correction performed with classifier version 6 ===
3:10:25.002038 PROGRESS: ============================= Precursor FDR =============================
3:10:25.002152 PROGRESS: Total precursors accumulated: 7,602
3:10:25.002212 PROGRESS: Target precursors: 7,548 (99.29%)
3:10:25.002263 PROGRESS: Decoy precursors: 54 (0.71%)
3:10:25.002310 PROGRESS: 
3:10:25.002354 PROGRESS: Precursor Summary:
3:10:25.005298 PROGRESS: Channel   0:	 0.05 FDR: 7,548; 0.01 FDR: 7,548; 0.001 FDR: 6,490
3:10:25.005413 PROGRESS: 
3:10:25.005467 PROGRESS: Protein Summary:
3:10:25.009749 PROGRESS: Channel   0:	 0.05 FDR: 3,902; 0.01 FDR: 3,902; 0.001 FDR: 3,549
3:10:25.009863 PROGRESS: =========================================================================
3:10:25.034573 INFO: fragments_df_filtered: 5000
3:10:25.046939 INFO: calibration group: precursor, fitting mz estimator 
3:10:25.874285 INFO: calibration group: precursor, fitting rt estimator 
3:10:26.713063 INFO: calibration group: fragment, fitting mz estimator 
3:10:27.136569 INFO: calibration group: precursor, predicting mz
3:10:27.139536 INFO: calibration group: precursor, predicting rt
3:10:27.148753 INFO: calibration group: fragment, predicting mz
3:10:27.174496 INFO: === checking if optimization conditions were reached ===
3:10:27.174931 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3:10:27.182415 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 16.0016.
3:10:27.182599 INFO: ==============================================
3:10:27.182815 INFO: Starting optimization step 4.
3:10:27.182894 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:10:27.182965 PROGRESS: Extracting batch of 15945 precursors
3:10:27.188729 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:10:27.188805 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:10:27.188843 INFO: FWHM in RT is 2.32 seconds, sigma is 0.30
3:10:27.188871 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:10:27.189100 INFO: Starting candidate selection
3:10:27.741359 INFO: Starting candidate scoring
3:10:27.986353 INFO: Finished candidate processing
3:10:27.986487 INFO: Collecting candidate features
3:10:28.033530 WARNING: intensity_correlation has 16 NaNs ( 0.05 % out of 30711)
3:10:28.037901 INFO: Collecting fragment features
3:10:28.057035 INFO: Finished candidate scoring
3:10:28.071741 PROGRESS: === Extracted 30711 precursors and 253216 fragments ===
3:10:28.072154 INFO: performing precursor FDR with 47 features
3:10:28.072191 INFO: Decoy channel: -1
3:10:28.072216 INFO: Competetive: True
3:10:28.080583 INFO: Setting torch num_threads to 2 for FDR classification task
3:10:28.085765 WARNING: dropped 4 target PSMs due to missing features
3:10:28.085866 WARNING: dropped 12 decoy PSMs due to missing features
3:10:28.503128 INFO: Test AUC: 0.886
3:10:28.503262 INFO: Train AUC: 0.881
3:10:28.503293 INFO: AUC difference: 0.53%
3:10:28.590937 INFO: Resetting torch num_threads to 100
3:10:28.592227 INFO: === FDR correction performed with classifier version 6 ===
3:10:28.593841 PROGRESS: ============================= Precursor FDR =============================
3:10:28.593950 PROGRESS: Total precursors accumulated: 7,603
3:10:28.594013 PROGRESS: Target precursors: 7,542 (99.20%)
3:10:28.594079 PROGRESS: Decoy precursors: 61 (0.80%)
3:10:28.594124 PROGRESS: 
3:10:28.594167 PROGRESS: Precursor Summary:
3:10:28.597075 PROGRESS: Channel   0:	 0.05 FDR: 7,542; 0.01 FDR: 7,542; 0.001 FDR: 6,289
3:10:28.597195 PROGRESS: 
3:10:28.597251 PROGRESS: Protein Summary:
3:10:28.601511 PROGRESS: Channel   0:	 0.05 FDR: 3,901; 0.01 FDR: 3,901; 0.001 FDR: 3,478
3:10:28.601628 PROGRESS: =========================================================================
3:10:28.625614 INFO: fragments_df_filtered: 5000
3:10:28.640773 INFO: calibration group: precursor, fitting mz estimator 
3:10:29.481638 INFO: calibration group: precursor, fitting rt estimator 
3:10:30.326502 INFO: calibration group: fragment, fitting mz estimator 
3:10:30.760026 INFO: calibration group: precursor, predicting mz
3:10:30.763050 INFO: calibration group: precursor, predicting rt
3:10:30.772228 INFO: calibration group: fragment, predicting mz
3:10:30.829417 INFO: === checking if optimization conditions were reached ===
3:10:30.829731 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3:10:30.843093 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 17.3121.
3:10:30.843481 INFO: ==============================================
3:10:30.843836 INFO: Starting optimization step 5.
3:10:30.844120 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:10:30.844396 PROGRESS: Extracting batch of 15945 precursors
3:10:30.850887 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:10:30.851093 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:10:30.851239 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
3:10:30.851372 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:10:30.851690 INFO: Starting candidate selection
3:10:31.420325 INFO: Starting candidate scoring
3:10:31.669563 INFO: Finished candidate processing
3:10:31.669700 INFO: Collecting candidate features
3:10:31.719692 WARNING: intensity_correlation has 19 NaNs ( 0.06 % out of 30698)
3:10:31.724077 INFO: Collecting fragment features
3:10:31.743171 INFO: Finished candidate scoring
3:10:31.757433 PROGRESS: === Extracted 30698 precursors and 252863 fragments ===
3:10:31.757871 INFO: performing precursor FDR with 47 features
3:10:31.757910 INFO: Decoy channel: -1
3:10:31.757934 INFO: Competetive: True
3:10:31.766879 INFO: Setting torch num_threads to 2 for FDR classification task
3:10:31.772066 WARNING: dropped 7 target PSMs due to missing features
3:10:31.772173 WARNING: dropped 12 decoy PSMs due to missing features
3:10:32.205344 INFO: Test AUC: 0.872
3:10:32.205492 INFO: Train AUC: 0.881
3:10:32.205527 INFO: AUC difference: 1.11%
3:10:32.303294 INFO: Resetting torch num_threads to 100
3:10:32.304636 INFO: === FDR correction performed with classifier version 6 ===
3:10:32.306305 PROGRESS: ============================= Precursor FDR =============================
3:10:32.306419 PROGRESS: Total precursors accumulated: 7,599
3:10:32.306494 PROGRESS: Target precursors: 7,537 (99.18%)
3:10:32.306558 PROGRESS: Decoy precursors: 62 (0.82%)
3:10:32.306622 PROGRESS: 
3:10:32.306679 PROGRESS: Precursor Summary:
3:10:32.309705 PROGRESS: Channel   0:	 0.05 FDR: 7,537; 0.01 FDR: 7,537; 0.001 FDR: 6,664
3:10:32.309836 PROGRESS: 
3:10:32.309910 PROGRESS: Protein Summary:
3:10:32.314259 PROGRESS: Channel   0:	 0.05 FDR: 3,898; 0.01 FDR: 3,898; 0.001 FDR: 3,615
3:10:32.314383 PROGRESS: =========================================================================
3:10:32.337462 INFO: fragments_df_filtered: 5000
3:10:32.349946 INFO: calibration group: precursor, fitting mz estimator 
3:10:33.240834 INFO: calibration group: precursor, fitting rt estimator 
3:10:34.081906 INFO: calibration group: fragment, fitting mz estimator 
3:10:34.507774 INFO: calibration group: precursor, predicting mz
3:10:34.510609 INFO: calibration group: precursor, predicting rt
3:10:34.523387 INFO: calibration group: fragment, predicting mz
3:10:34.545206 INFO: === checking if optimization conditions were reached ===
3:10:34.545562 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3:10:34.552520 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 17.2093.
3:10:34.552616 INFO: ==============================================
3:10:34.552780 INFO: Starting optimization step 6.
3:10:34.552863 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:10:34.552936 PROGRESS: Extracting batch of 15945 precursors
3:10:34.560000 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:10:34.560090 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:10:34.560130 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
3:10:34.560159 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:10:34.560394 INFO: Starting candidate selection
3:10:35.130375 INFO: Starting candidate scoring
3:10:35.384865 INFO: Finished candidate processing
3:10:35.385005 INFO: Collecting candidate features
3:10:35.442044 WARNING: intensity_correlation has 16 NaNs ( 0.05 % out of 30713)
3:10:35.446311 INFO: Collecting fragment features
3:10:35.465757 INFO: Finished candidate scoring
3:10:35.480504 PROGRESS: === Extracted 30713 precursors and 252978 fragments ===
3:10:35.480905 INFO: performing precursor FDR with 47 features
3:10:35.480944 INFO: Decoy channel: -1
3:10:35.480966 INFO: Competetive: True
3:10:35.489985 INFO: Setting torch num_threads to 2 for FDR classification task
3:10:35.495436 WARNING: dropped 7 target PSMs due to missing features
3:10:35.495576 WARNING: dropped 9 decoy PSMs due to missing features
3:10:35.883774 INFO: Test AUC: 0.880
3:10:35.883917 INFO: Train AUC: 0.879
3:10:35.883946 INFO: AUC difference: 0.20%
3:10:35.966611 INFO: Resetting torch num_threads to 100
3:10:35.967768 INFO: === FDR correction performed with classifier version 6 ===
3:10:35.969181 PROGRESS: ============================= Precursor FDR =============================
3:10:35.969282 PROGRESS: Total precursors accumulated: 7,605
3:10:35.969344 PROGRESS: Target precursors: 7,547 (99.24%)
3:10:35.969393 PROGRESS: Decoy precursors: 58 (0.76%)
3:10:35.969440 PROGRESS: 
3:10:35.969484 PROGRESS: Precursor Summary:
3:10:35.972252 PROGRESS: Channel   0:	 0.05 FDR: 7,547; 0.01 FDR: 7,547; 0.001 FDR: 6,206
3:10:35.972361 PROGRESS: 
3:10:35.972418 PROGRESS: Protein Summary:
3:10:35.976643 PROGRESS: Channel   0:	 0.05 FDR: 3,902; 0.01 FDR: 3,902; 0.001 FDR: 3,453
3:10:35.976782 PROGRESS: =========================================================================
3:10:35.998782 INFO: fragments_df_filtered: 5000
3:10:36.010795 INFO: calibration group: precursor, fitting mz estimator 
3:10:36.890242 INFO: calibration group: precursor, fitting rt estimator 
3:10:37.760130 INFO: calibration group: fragment, fitting mz estimator 
3:10:38.177218 INFO: calibration group: precursor, predicting mz
3:10:38.180280 INFO: calibration group: precursor, predicting rt
3:10:38.189564 INFO: calibration group: fragment, predicting mz
3:10:38.246620 INFO: === checking if optimization conditions were reached ===
3:10:38.246954 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
3:10:38.248350 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 16.0016 found after 7 searches.
3:10:38.248409 INFO: ==============================================
3:10:38.248510 PROGRESS: Optimization finished for rt_error.
3:10:38.276724 INFO: calibration group: precursor, predicting mz
3:10:38.280563 INFO: calibration group: precursor, predicting rt
3:10:38.290450 INFO: calibration group: fragment, predicting mz
3:10:38.347029 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:10:38.347426 PROGRESS: ==============================================
3:10:38.347521 PROGRESS: ms2_error      : 8.0000
3:10:38.347594 PROGRESS: ms1_error      : 3.0000
3:10:38.347658 PROGRESS: rt_error       : 16.0016
3:10:38.347713 PROGRESS: ==============================================
3:10:38.349385 INFO: calibration group: precursor, predicting mz
3:10:38.361002 INFO: calibration group: precursor, predicting rt
3:10:38.403649 INFO: calibration group: fragment, predicting mz
3:10:38.539144 PROGRESS: Extracting batch of 78739 precursors
3:10:38.566385 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:10:38.566676 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:10:38.566785 INFO: FWHM in RT is 2.33 seconds, sigma is 0.30
3:10:38.566879 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:10:38.567239 INFO: Starting candidate selection
3:10:41.003842 INFO: Applying score cutoff of 16.880808280944823
3:10:41.008777 INFO: Removed 9890 precursors with score below cutoff
3:10:41.049418 INFO: Starting candidate scoring
3:10:42.297831 INFO: Finished candidate processing
3:10:42.298043 INFO: Collecting candidate features
3:10:42.529834 WARNING: intensity_correlation has 10 NaNs ( 0.01 % out of 143600)
3:10:42.538360 INFO: Collecting fragment features
3:10:42.637969 INFO: Finished candidate scoring
3:10:42.711572 INFO: === FDR correction performed with classifier version 11 ===
3:10:42.712286 INFO: performing precursor FDR with 47 features
3:10:42.712319 INFO: Decoy channel: -1
3:10:42.712342 INFO: Competetive: True
3:10:42.774570 INFO: Setting torch num_threads to 2 for FDR classification task
3:10:42.797709 WARNING: dropped 3 target PSMs due to missing features
3:10:42.797859 WARNING: dropped 7 decoy PSMs due to missing features
3:10:44.639648 INFO: Test AUC: 0.899
3:10:44.639798 INFO: Train AUC: 0.902
3:10:44.639828 INFO: AUC difference: 0.28%
3:10:44.732738 INFO: Resetting torch num_threads to 100
3:10:44.738986 INFO: Removing fragments below FDR threshold
3:10:44.764082 PROGRESS: ============================= Precursor FDR =============================
3:10:44.764403 PROGRESS: Total precursors accumulated: 37,703
3:10:44.764466 PROGRESS: Target precursors: 37,370 (99.12%)
3:10:44.764518 PROGRESS: Decoy precursors: 333 (0.88%)
3:10:44.764564 PROGRESS: 
3:10:44.764608 PROGRESS: Precursor Summary:
3:10:44.777348 PROGRESS: Channel   0:	 0.05 FDR: 37,370; 0.01 FDR: 37,370; 0.001 FDR: 34,210
3:10:44.777653 PROGRESS: 
3:10:44.777712 PROGRESS: Protein Summary:
3:10:44.797133 PROGRESS: Channel   0:	 0.05 FDR: 6,708; 0.01 FDR: 6,708; 0.001 FDR: 6,621
3:10:44.797404 PROGRESS: =========================================================================
3:10:45.169361 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:10:45.396743 PROGRESS: Processing search outputs
3:10:45.396894 PROGRESS: Performing protein grouping and FDR
3:10:45.396936 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:10:45.434247 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:10:45.458323 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:10:45.481261 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:10:45.525624 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:10:45.555800 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:10:45.588931 INFO: Building combined output
3:10:45.658463 INFO: Performing protein inference
3:10:45.850841 INFO: Inference strategy: library. Using library grouping for protein inference
3:10:45.852685 INFO: Performing protein FDR
3:10:48.477880 INFO: Normalizing q-values using 6,730 targets and 1,227 decoys
3:10:48.484816 INFO: Test AUC: 0.999
3:10:48.484900 INFO: Train AUC: 1.000
3:10:48.484936 INFO: AUC difference: 0.08%
3:10:48.818011 PROGRESS: ================ Protein FDR =================
3:10:48.818191 PROGRESS: Unique protein groups in output
3:10:48.818222 PROGRESS:   1% protein FDR: 6,729
3:10:48.818244 PROGRESS: 
3:10:48.818266 PROGRESS: Unique precursor in output
3:10:48.818286 PROGRESS:   1% protein FDR: 39,462
3:10:48.818308 PROGRESS: ================================================
3:10:48.854872 PROGRESS: Building search statistics
3:10:48.914156 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
3:10:48.914397 INFO: Initializing OptimizationManager
3:10:48.914670 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
3:10:48.914745 INFO: Initializing CalibrationManager
3:10:48.914995 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
3:10:48.915075 INFO: Initializing RawFileManager
3:10:48.928565 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
3:10:48.928778 INFO: Initializing OptimizationManager
3:10:48.928994 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
3:10:48.929065 INFO: Initializing CalibrationManager
3:10:48.929269 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
3:10:48.929345 INFO: Initializing RawFileManager
3:10:48.943287 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
3:10:48.943582 INFO: Initializing OptimizationManager
3:10:48.943834 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
3:10:48.943917 INFO: Initializing CalibrationManager
3:10:48.944170 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
3:10:48.944253 INFO: Initializing RawFileManager
3:10:48.964680 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
3:10:48.966081 INFO: Initializing OptimizationManager
3:10:48.966309 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
3:10:48.966399 INFO: Initializing CalibrationManager
3:10:48.966624 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
3:10:48.966698 INFO: Initializing RawFileManager
3:10:48.985222 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
3:10:48.985445 INFO: Initializing OptimizationManager
3:10:48.985670 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
3:10:48.985743 INFO: Initializing CalibrationManager
3:10:48.985948 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
3:10:48.986021 INFO: Initializing RawFileManager
3:10:49.002492 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
3:10:49.002714 INFO: Initializing OptimizationManager
3:10:49.002924 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
3:10:49.002995 INFO: Initializing CalibrationManager
3:10:49.003198 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
3:10:49.003273 INFO: Initializing RawFileManager
3:10:49.005098 INFO: Writing stat output to disk
3:10:49.005164 INFO: Saving run_output_Astral/alphadia_1.10_MBRSetValues/stat.tsv to disk
3:10:49.009979 PROGRESS: Building internal statistics
3:10:49.010219 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
3:10:49.010266 INFO: Initializing TimingManager
3:10:49.010509 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
3:10:49.010547 INFO: Initializing TimingManager
3:10:49.010716 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
3:10:49.010752 INFO: Initializing TimingManager
3:10:49.010907 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
3:10:49.010942 INFO: Initializing TimingManager
3:10:49.011094 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
3:10:49.011128 INFO: Initializing TimingManager
3:10:49.011277 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_MBRSetValues/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
3:10:49.011310 INFO: Initializing TimingManager
3:10:49.011672 INFO: Writing internal output to disk
3:10:49.011719 INFO: Saving run_output_Astral/alphadia_1.10_MBRSetValues/internal.tsv to disk
3:10:49.012180 PROGRESS: Performing label free quantification
3:10:49.057085 INFO: Accumulating fragment data
3:10:49.057276 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:10:49.082113 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:10:49.379746 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:10:49.681337 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:10:50.211913 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:10:50.695755 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:10:51.252729 PROGRESS: Performing label free quantification on the precursor level
3:10:51.252890 INFO: Filtering fragments by quality
3:10:51.359796 INFO: Performing label-free quantification using directLFQ
3:10:51.657256 INFO: 39462 lfq-groups total
3:12:06.439030 INFO: using 100 processes
3:12:06.553823 INFO: lfq-object 0
3:12:06.585701 INFO: lfq-object 100
3:12:06.624602 INFO: lfq-object 200
3:12:06.664401 INFO: lfq-object 300
3:12:06.718492 INFO: lfq-object 400
3:12:06.778590 INFO: lfq-object 500
3:12:06.803458 INFO: lfq-object 600
3:12:06.831881 INFO: lfq-object 700
3:12:06.883378 INFO: lfq-object 800
3:12:06.921975 INFO: lfq-object 900
3:12:06.970044 INFO: lfq-object 1000
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3:12:27.907639 INFO: lfq-object 36900
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3:12:28.093916 INFO: lfq-object 37300
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3:12:28.234181 INFO: lfq-object 37500
3:12:28.265707 INFO: lfq-object 37600
3:12:28.315450 INFO: lfq-object 37700
3:12:28.365871 INFO: lfq-object 37800
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3:12:28.730658 INFO: lfq-object 38800
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3:12:32.727848 INFO: lfq-object 39300
3:12:32.770624 INFO: lfq-object 39400
3:12:36.996420 INFO: Writing precursor output to disk
3:12:36.996743 INFO: Saving run_output_Astral/alphadia_1.10_MBRSetValues/precursor.matrix.tsv to disk
3:12:37.281820 PROGRESS: Performing label free quantification on the pg level
3:12:37.281950 INFO: Filtering fragments by quality
3:12:37.415358 INFO: Performing label-free quantification using directLFQ
3:12:37.556636 INFO: 6729 lfq-groups total
3:13:42.046846 INFO: using 100 processes
3:13:42.103460 INFO: lfq-object 0
3:13:42.193964 INFO: lfq-object 200
3:13:42.210001 INFO: lfq-object 100
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3:13:43.935338 INFO: lfq-object 4000
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3:13:44.288094 INFO: lfq-object 4800
3:13:44.341486 INFO: lfq-object 4900
3:13:44.396222 INFO: lfq-object 4400
3:13:44.402273 INFO: lfq-object 5000
3:13:44.432195 INFO: lfq-object 5100
3:13:44.498177 INFO: lfq-object 5200
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3:13:44.593550 INFO: lfq-object 5400
3:13:44.632457 INFO: lfq-object 5500
3:13:44.671470 INFO: lfq-object 5600
3:13:44.701958 INFO: lfq-object 5700
3:13:44.742993 INFO: lfq-object 5800
3:13:44.783257 INFO: lfq-object 5900
3:13:44.852763 INFO: lfq-object 6000
3:13:44.900578 INFO: lfq-object 6100
3:13:44.944241 INFO: lfq-object 6200
3:13:44.977754 INFO: lfq-object 6300
3:13:45.016467 INFO: lfq-object 6400
3:13:45.062242 INFO: lfq-object 6500
3:13:45.096276 INFO: lfq-object 6600
3:13:45.123545 INFO: lfq-object 6700
3:13:48.223960 INFO: Writing pg output to disk
3:13:48.224160 INFO: Saving run_output_Astral/alphadia_1.10_MBRSetValues/pg.matrix.tsv to disk
3:13:48.360584 INFO: Writing psm output to disk
3:13:48.360769 INFO: Saving run_output_Astral/alphadia_1.10_MBRSetValues/precursors.tsv to disk
3:14:00.354080 PROGRESS: Building spectral library
3:14:00.405011 INFO: Building MBR spectral library
3:14:00.405173 INFO: Running MbrLibraryBuilder
3:14:00.541780 INFO: MBR spectral library contains 39,462 precursors, 6,729 proteins
3:14:00.541934 INFO: Writing MBR spectral library to disk
3:14:00.888002 PROGRESS: =================== Search Finished ===================
3:14:00.907872 WARNING: WARNING: Temp mmap arrays were written to /tmp/temp_mmap_zhra2ri_. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 692,379,938,816
