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0:00:00.015058 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.015090 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.015120 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.015152 PROGRESS:            |_|                           
0:00:00.015178 PROGRESS: 
0:00:00.015201 PROGRESS: version: 1.10.3
0:00:00.015244 INFO: hostname: thestral
0:00:00.015324 INFO: date: 2025-04-16 21:46:31
0:00:00.015347 INFO: ================ AlphaX Environment ===============
0:00:00.015374 INFO: alphatims       : 1.0.8
0:00:00.015395 INFO: alpharaw        : 0.4.5
0:00:00.015414 INFO: alphabase       : 1.5.0
0:00:00.015436 INFO: alphapeptdeep   : 1.3.0
0:00:00.015455 INFO: directlfq       : 0.2.19
0:00:00.015500 INFO: ===================================================
0:00:00.015521 INFO: ================= Pip Environment =================
0:00:00.079612 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
0:00:00.079775 INFO: ===================================================
0:00:00.079814 INFO: Running step 'library'
0:00:00.079907 INFO: loading config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:00:00.091890 INFO: loading additional config provided via CLI
0:00:00.092006 INFO: loading additional config provided via CLI parameters
0:00:00.092281 INFO: Updating config with 'user defined'
0:00:00.092385 INFO: Updating config with 'user defined (cli)'
0:00:00.092431 INFO: ├──version: 1
0:00:00.092461 INFO: ├──workflow_name: None
0:00:00.092485 INFO: ├──output_directory: None
0:00:00.092506 INFO: ├──library_path: None
0:00:00.092527 INFO: ├──raw_paths:
0:00:00.092550 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
0:00:00.092575 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
0:00:00.092594 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
0:00:00.092619 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
0:00:00.092639 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
0:00:00.092659 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
0:00:00.092679 INFO: ├──fasta_paths:
0:00:00.092701 INFO: │   [32;20m- ./ProteoBenchFASTA_DDAQuantification.fasta [user defined (cli), default: None][0m
0:00:00.092723 INFO: ├──quant_directory: None
0:00:00.092744 INFO: ├──general
0:00:00.092766 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
0:00:00.092786 INFO: │   ├──transfer_step_enabled: False
0:00:00.092807 INFO: │   [32;20m├──mbr_step_enabled: False [user defined, default: True][0m
0:00:00.092828 INFO: │   ├──reuse_calibration: False
0:00:00.092849 INFO: │   ├──reuse_quant: False
0:00:00.092868 INFO: │   ├──astral_ms1: False
0:00:00.092888 INFO: │   ├──log_level: INFO
0:00:00.092909 INFO: │   ├──mmap_detector_events: False
0:00:00.092930 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
0:00:00.092951 INFO: │   ├──save_library: True
0:00:00.092971 INFO: │   └──save_mbr_library: True
0:00:00.092990 INFO: ├──library_loading
0:00:00.093011 INFO: │   └──rt_heuristic: 180
0:00:00.093030 INFO: ├──library_prediction
0:00:00.093050 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.093070 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.093094 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.093118 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
0:00:00.093139 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.093160 INFO: │   ├──missed_cleavages: 1
0:00:00.093179 INFO: │   ├──precursor_len:
0:00:00.093199 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.093220 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.093240 INFO: │   ├──precursor_charge:
0:00:00.093261 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.093282 INFO: │   │   [32;20m- 4[0m
0:00:00.093302 INFO: │   ├──precursor_mz:
0:00:00.093322 INFO: │   │   [32;20m- 400[0m
0:00:00.093341 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
0:00:00.093360 INFO: │   ├──fragment_mz:
0:00:00.093380 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
0:00:00.093400 INFO: │   │   [32;20m- 2000[0m
0:00:00.093421 INFO: │   ├──nce: 25
0:00:00.093444 INFO: │   ├──fragment_types:
0:00:00.093464 INFO: │   │   [32;20m- b[0m
0:00:00.093483 INFO: │   │   [32;20m- y[0m
0:00:00.093504 INFO: │   ├──max_fragment_charge: 2
0:00:00.093524 INFO: │   [32;20m├──instrument: Astral [user defined, default: Lumos][0m
0:00:00.093544 INFO: │   ├──peptdeep_model_path: None
0:00:00.093564 INFO: │   └──peptdeep_model_type: generic
0:00:00.093583 INFO: ├──custom_modifications:
0:00:00.093610 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.093629 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.093650 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.093669 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.093688 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.093707 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.093728 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.093749 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.093770 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.093790 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.093810 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.093828 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.093850 INFO: │   ├──name: Label:13C(12)@K
0:00:00.093870 INFO: │   └──composition: C(12)
0:00:00.093888 INFO: ├──search
0:00:00.093908 INFO: │   [32;20m├──target_ms1_tolerance: 10 [user defined, default: 5][0m
0:00:00.093927 INFO: │   [32;20m├──target_ms2_tolerance: 15 [user defined, default: 10][0m
0:00:00.093947 INFO: │   ├──target_rt_tolerance: 0
0:00:00.093966 INFO: │   ├──target_mobility_tolerance: 0
0:00:00.093988 INFO: │   ├──quant_window: 3
0:00:00.094009 INFO: │   [32;20m├──target_num_candidates: 2 [user defined, default: 3][0m
0:00:00.094029 INFO: │   ├──channel_filter: 
0:00:00.094050 INFO: │   ├──exclude_shared_ions: True
0:00:00.094071 INFO: │   ├──compete_for_fragments: True
0:00:00.094090 INFO: │   ├──quant_all: True
0:00:00.094111 INFO: │   ├──top_k_fragments: 12
0:00:00.094131 INFO: │   └──experimental_xic: True
0:00:00.094151 INFO: ├──calibration
0:00:00.094170 INFO: │   ├──batch_size: 8000
0:00:00.094190 INFO: │   ├──optimization_lock_target: 200
0:00:00.094208 INFO: │   ├──max_steps: 20
0:00:00.094228 INFO: │   ├──min_steps: 2
0:00:00.094248 INFO: │   ├──max_skips: 1
0:00:00.094267 INFO: │   ├──norm_rt_mode: linear
0:00:00.094287 INFO: │   ├──max_fragments: 5000
0:00:00.094311 INFO: │   └──min_correlation: 0.7
0:00:00.094341 INFO: ├──search_initial
0:00:00.094361 INFO: │   ├──initial_num_candidates: 1
0:00:00.094381 INFO: │   ├──initial_ms1_tolerance: 30
0:00:00.094399 INFO: │   ├──initial_ms2_tolerance: 30
0:00:00.094419 INFO: │   ├──initial_mobility_tolerance: 0.1
0:00:00.094439 INFO: │   └──initial_rt_tolerance: 0.5
0:00:00.094458 INFO: ├──selection_config
0:00:00.094479 INFO: │   ├──peak_len_rt: 10.0
0:00:00.094500 INFO: │   ├──sigma_scale_rt: 0.5
0:00:00.094521 INFO: │   ├──peak_len_mobility: 0.01
0:00:00.094541 INFO: │   ├──sigma_scale_mobility: 1.0
0:00:00.094564 INFO: │   ├──top_k_precursors: 3
0:00:00.094584 INFO: │   ├──kernel_size: 30
0:00:00.094603 INFO: │   ├──f_mobility: 1.0
0:00:00.094625 INFO: │   ├──f_rt: 0.99
0:00:00.094646 INFO: │   ├──center_fraction: 0.5
0:00:00.094667 INFO: │   ├──min_size_mobility: 8
0:00:00.094687 INFO: │   ├──min_size_rt: 3
0:00:00.094707 INFO: │   ├──max_size_mobility: 20
0:00:00.094727 INFO: │   ├──max_size_rt: 15
0:00:00.094747 INFO: │   ├──group_channels: False
0:00:00.094767 INFO: │   ├──use_weighted_score: True
0:00:00.094787 INFO: │   ├──join_close_candidates: False
0:00:00.094807 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
0:00:00.094828 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
0:00:00.094849 INFO: ├──scoring_config
0:00:00.094869 INFO: │   ├──score_grouped: False
0:00:00.094888 INFO: │   ├──top_k_isotopes: 3
0:00:00.094908 INFO: │   ├──reference_channel: -1
0:00:00.094929 INFO: │   ├──precursor_mz_tolerance: 10
0:00:00.094948 INFO: │   └──fragment_mz_tolerance: 15
0:00:00.094967 INFO: ├──library_multiplexing
0:00:00.094992 INFO: │   ├──enabled: False
0:00:00.095012 INFO: │   ├──input_channel: 0
0:00:00.095031 INFO: │   └──multiplex_mapping:
0:00:00.095050 INFO: ├──multiplexing
0:00:00.095070 INFO: │   ├──enabled: False
0:00:00.095089 INFO: │   ├──target_channels: 4,8
0:00:00.095108 INFO: │   ├──decoy_channel: 12
0:00:00.095128 INFO: │   ├──reference_channel: 0
0:00:00.095148 INFO: │   └──competetive_scoring: True
0:00:00.095166 INFO: ├──fdr
0:00:00.095186 INFO: │   ├──fdr: 0.01
0:00:00.095205 INFO: │   ├──group_level: proteins
0:00:00.095225 INFO: │   ├──inference_strategy: heuristic
0:00:00.095244 INFO: │   ├──competetive_scoring: True
0:00:00.095263 INFO: │   ├──keep_decoys: False
0:00:00.095282 INFO: │   ├──channel_wise_fdr: False
0:00:00.095302 INFO: │   ├──enable_two_step_classifier: False
0:00:00.095321 INFO: │   ├──two_step_classifier_max_iterations: 5
0:00:00.095340 INFO: │   └──enable_nn_hyperparameter_tuning: False
0:00:00.095360 INFO: ├──search_output
0:00:00.095380 INFO: │   ├──file_format: tsv
0:00:00.095399 INFO: │   ├──peptide_level_lfq: False
0:00:00.095419 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
0:00:00.095439 INFO: │   ├──min_k_fragments: 12
0:00:00.095459 INFO: │   ├──min_correlation: 0.9
0:00:00.095480 INFO: │   ├──num_samples_quadratic: 50
0:00:00.095499 INFO: │   ├──min_nonnan: 3
0:00:00.095519 INFO: │   ├──normalize_lfq: True
0:00:00.095538 INFO: │   └──save_fragment_quant_matrix: False
0:00:00.095558 INFO: ├──optimization
0:00:00.095580 INFO: │   ├──order_of_optimization: None
0:00:00.095599 INFO: │   ├──ms2_error
0:00:00.095620 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.095640 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.095660 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.095680 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.095701 INFO: │   │   ├──try_narrower_values: True
0:00:00.095720 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.095739 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.095760 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.095781 INFO: │   ├──ms1_error
0:00:00.095800 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.095820 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.095840 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.095860 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.095881 INFO: │   │   ├──try_narrower_values: False
0:00:00.095901 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.095921 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.095941 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.095960 INFO: │   ├──mobility_error
0:00:00.095979 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.095999 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.096018 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.096038 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.096057 INFO: │   │   ├──try_narrower_values: False
0:00:00.096076 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.096097 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.096119 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.096139 INFO: │   └──rt_error
0:00:00.096163 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.096183 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.096204 INFO: │       ├──automatic_update_percentile_range: 0.99
0:00:00.096224 INFO: │       ├──automatic_update_factor: 1.1
0:00:00.096243 INFO: │       ├──try_narrower_values: True
0:00:00.096270 INFO: │       ├──maximal_decrease: 0.2
0:00:00.096290 INFO: │       ├──favour_narrower_optimum: True
0:00:00.096310 INFO: │       └──maximum_decrease_from_maximum: 0.1
0:00:00.096329 INFO: ├──optimization_manager
0:00:00.096349 INFO: │   ├──fwhm_rt: 5
0:00:00.096369 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.096389 INFO: │   └──score_cutoff: 0
0:00:00.096408 INFO: ├──transfer_library
0:00:00.096428 INFO: │   ├──enabled: False
0:00:00.096448 INFO: │   ├──fragment_types:
0:00:00.096467 INFO: │   │   [32;20m- b[0m
0:00:00.096486 INFO: │   │   [32;20m- y[0m
0:00:00.096505 INFO: │   ├──max_charge: 2
0:00:00.096525 INFO: │   ├──top_k_samples: 3
0:00:00.096544 INFO: │   ├──norm_delta_max: True
0:00:00.096564 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.096584 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.096603 INFO: └──transfer_learning
0:00:00.096623 INFO:     ├──enabled: False
0:00:00.096642 INFO:     ├──batch_size: 2000
0:00:00.096661 INFO:     ├──max_lr: 0.0001
0:00:00.096681 INFO:     ├──train_fraction: 0.7
0:00:00.096700 INFO:     ├──validation_fraction: 0.2
0:00:00.096720 INFO:     ├──test_fraction: 0.1
0:00:00.096740 INFO:     ├──test_interval: 1
0:00:00.096759 INFO:     ├──lr_patience: 3
0:00:00.096778 INFO:     ├──epochs: 51
0:00:00.096798 INFO:     ├──warmup_epochs: 5
0:00:00.096817 INFO:     ├──nce: 25
0:00:00.096837 INFO:     [32;20m└──instrument: Astral [user defined, default: Lumos][0m
0:00:00.102285 INFO: Registering 7 custom modifications
0:00:00.151698 PROGRESS: No library provided. Building library from fasta files.
0:00:00.153116 INFO: Running FastaDigest
0:00:01.352670 INFO: Digesting fasta file
0:00:14.177633 INFO: Adding modifications
0:02:38.418051 INFO: Removing non-canonical amino acids
0:02:44.816441 INFO: Fasta library contains 5,215,079 precursors
0:02:44.816680 PROGRESS: Predicting library properties.
0:02:44.816754 INFO: Running PeptDeepPrediction
0:02:44.816846 INFO: Device set to cpu
0:02:45.777749 INFO: Loading PeptDeep models of type generic
0:02:46.565768 INFO: Predicting RT, MS2 and mobility
0:02:46.565942 INFO: Using multiprocessing with 100 processes ...
0:02:46.979528 INFO: Predicting rt,ms2,mobility ...
0:11:03.443822 INFO: Adding fragment mz information
0:11:04.062199 INFO: Adding fragment intensity information
0:11:04.668163 INFO: Adding precursor information
0:11:05.488293 INFO: Running PrecursorInitializer
0:11:05.527033 INFO: Running AnnotateFasta
0:11:05.902878 INFO: Dropping decoys from input library before annotation
0:12:01.801176 INFO: Running IsotopeGenerator
0:12:41.279065 INFO: Running RTNormalization
0:12:41.279767 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:12:41.279954 INFO: Saving library to run_output_Astral/alphadia_1.10_noMBR/speclib.hdf
0:13:43.301130 INFO: Running DecoyGenerator
0:16:52.851084 INFO: Running FlattenLibrary
0:17:43.296695 INFO: Running InitFlatColumns
0:17:43.673846 INFO: Running LogFlatLibraryStats
0:17:43.674079 INFO: ============ Library Stats ============
0:17:43.674124 INFO: Number of precursors: 10,400,392
0:17:46.669507 INFO: 	thereof targets:5,215,079
0:17:46.669745 INFO: 	thereof decoys: 5,185,313
0:17:46.752843 INFO: Number of elution groups: 5,215,079
0:17:46.753032 INFO: 	average size: 1.99
0:17:47.391776 INFO: Number of proteins: 117,993
0:17:47.445234 INFO: Number of channels: 1 ([0])
0:17:47.445541 INFO: Isotopes Distribution for 4 isotopes
0:17:47.445587 INFO: =======================================
0:17:47.461874 INFO: Searching 6 files:
0:17:47.462080 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
0:17:47.462114 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
0:17:47.462142 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
0:17:47.462167 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
0:17:47.462207 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
0:17:47.462234 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
0:17:47.462261 INFO: Using 1 fasta files:
0:17:47.462292 INFO:   ./ProteoBenchFASTA_DDAQuantification.fasta
0:17:47.462345 INFO: Using library: None
0:17:47.462373 INFO: Saving output to: run_output_Astral/alphadia_1.10_noMBR
0:17:47.462419 PROGRESS: Starting Search Workflows
0:17:47.462570 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:17:47.462691 INFO: Quantification results path: run_output_Astral/alphadia_1.10_noMBR/quant
0:17:47.462804 INFO: Creating parent folder for workflows at run_output_Astral/alphadia_1.10_noMBR/quant
0:17:47.463009 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1 at run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:17:47.463788 INFO: Initializing RawFileManager
0:18:21.380768 INFO: Determining DIA cycle
0:18:22.117790 INFO: Found cycle with start 0.00 min and length 303.
0:18:22.439735 INFO: RT (min)            : 0.0 - 26.9
0:18:22.439882 INFO: RT duration (sec)   : 1611.2
0:18:22.439922 INFO: RT duration (min)   : 26.9
0:18:22.439955 INFO: Cycle len (scans)   : 303
0:18:22.439983 INFO: Cycle len (sec)     : 1.65
0:18:22.440012 INFO: Number of cycles    : 977
0:18:22.440041 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:18:24.899731 INFO: Initializing CalibrationManager
0:18:24.902179 INFO: Loading calibration config
0:18:24.902424 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6'}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6'}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed']}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed']}], 'name': 'precursor'}]
0:18:24.902538 INFO: Calibration group :fragment, found 1 estimator(s)
0:18:24.902726 INFO: Calibration group :precursor, found 3 estimator(s)
0:18:24.902884 INFO: Disabling ion mobility calibration
0:18:24.902932 INFO: removed mobility estimator from group precursor
0:18:24.903658 INFO: Initializing OptimizationManager
0:18:24.903875 INFO: initial parameter: ms1_error = 30
0:18:24.903956 INFO: initial parameter: ms2_error = 30
0:18:24.904044 INFO: initial parameter: rt_error = 805.5992431640625
0:18:24.904115 INFO: initial parameter: mobility_error = 0.1
0:18:24.904176 INFO: initial parameter: column_type = library
0:18:24.904236 INFO: initial parameter: num_candidates = 1
0:18:24.904292 INFO: initial parameter: classifier_version = -1
0:18:24.904351 INFO: initial parameter: fwhm_rt = 5
0:18:24.904408 INFO: initial parameter: fwhm_mobility = 0.01
0:18:24.904465 INFO: initial parameter: score_cutoff = 0
0:18:24.904562 INFO: Initializing TimingManager
0:18:24.904664 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:18:24.904854 INFO: FDRManager not loaded from disk.
0:18:24.904887 INFO: Initializing FDRManager
0:18:24.904941 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:18:27.553444 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
0:18:31.694924 PROGRESS: Starting initial search for precursors.
0:18:33.483052 INFO: Starting optimization step 0.
0:18:33.483473 PROGRESS: === Extracting elution groups 0 to 8000 ===
0:18:33.483593 PROGRESS: Extracting batch of 15798 precursors
0:18:36.315848 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:18:36.317624 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:18:36.317731 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:18:36.317767 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:18:43.315870 INFO: Starting candidate selection
0:21:04.712004 INFO: Starting candidate scoring
0:34:41.595911 INFO: Finished candidate processing
0:34:41.596266 INFO: Collecting candidate features
0:34:42.591682 INFO: Collecting fragment features
0:34:46.107866 INFO: Finished candidate scoring
0:34:46.146303 PROGRESS: === Extracted 15759 precursors and 155907 fragments ===
0:34:46.147167 INFO: performing precursor FDR with 47 features
0:34:46.147267 INFO: Decoy channel: -1
0:34:46.147302 INFO: Competetive: True
0:34:46.163548 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:53.177548 INFO: Test AUC: 0.488
0:34:53.178092 INFO: Train AUC: 0.501
0:34:53.178201 INFO: AUC difference: 2.49%
0:34:54.857289 INFO: Resetting torch num_threads to 100
0:34:54.861980 INFO: === FDR correction performed with classifier version -1 ===
0:34:54.863378 PROGRESS: ============================= Precursor FDR =============================
0:34:54.863526 PROGRESS: Total precursors accumulated: 2
0:34:54.863636 PROGRESS: Target precursors: 2 (100.00%)
0:34:54.863728 PROGRESS: Decoy precursors: 0 (0.00%)
0:34:54.863817 PROGRESS: 
0:34:54.863899 PROGRESS: Precursor Summary:
0:34:54.865453 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
0:34:54.865601 PROGRESS: 
0:34:54.865700 PROGRESS: Protein Summary:
0:34:54.867372 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
0:34:54.867528 PROGRESS: =========================================================================
0:34:55.134041 INFO: Starting optimization step 1.
0:34:55.134421 PROGRESS: === Extracting elution groups 8000 to 24000 ===
0:34:55.134526 PROGRESS: Extracting batch of 31672 precursors
0:34:55.153054 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:34:55.153246 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:34:55.153297 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:34:55.153328 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:34:55.153735 INFO: Starting candidate selection
0:34:58.061439 INFO: Starting candidate scoring
0:34:58.401305 INFO: Finished candidate processing
0:34:58.401575 INFO: Collecting candidate features
0:34:58.563537 INFO: Collecting fragment features
0:34:58.609276 INFO: Finished candidate scoring
0:34:58.682841 PROGRESS: === Extracted 47360 precursors and 468670 fragments ===
0:34:58.694859 INFO: performing precursor FDR with 47 features
0:34:58.695091 INFO: Decoy channel: -1
0:34:58.695147 INFO: Competetive: True
0:34:58.748881 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:00.012814 INFO: Test AUC: 0.541
0:35:00.013109 INFO: Train AUC: 0.547
0:35:00.013167 INFO: AUC difference: 1.01%
0:35:00.166086 INFO: Resetting torch num_threads to 100
0:35:00.179990 INFO: === FDR correction performed with classifier version -1 ===
0:35:00.181251 PROGRESS: ============================= Precursor FDR =============================
0:35:00.181393 PROGRESS: Total precursors accumulated: 2
0:35:00.181477 PROGRESS: Target precursors: 2 (100.00%)
0:35:00.181547 PROGRESS: Decoy precursors: 0 (0.00%)
0:35:00.181610 PROGRESS: 
0:35:00.181670 PROGRESS: Precursor Summary:
0:35:00.183047 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
0:35:00.183168 PROGRESS: 
0:35:00.183243 PROGRESS: Protein Summary:
0:35:00.184722 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
0:35:00.184840 PROGRESS: =========================================================================
0:35:00.561137 INFO: Starting optimization step 2.
0:35:00.561675 PROGRESS: === Extracting elution groups 24000 to 56000 ===
0:35:00.561800 PROGRESS: Extracting batch of 63174 precursors
0:35:00.600900 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:35:00.601177 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:00.601367 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:35:00.601434 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:35:00.601938 INFO: Starting candidate selection
0:35:04.904833 INFO: Starting candidate scoring
0:35:05.398004 INFO: Finished candidate processing
0:35:05.398378 INFO: Collecting candidate features
0:35:05.676355 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 63031)
0:35:05.682921 INFO: Collecting fragment features
0:35:05.754140 INFO: Finished candidate scoring
0:35:05.920418 PROGRESS: === Extracted 110391 precursors and 1091621 fragments ===
0:35:05.949924 INFO: performing precursor FDR with 47 features
0:35:05.950269 INFO: Decoy channel: -1
0:35:05.950301 INFO: Competetive: True
0:35:06.071635 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:06.110607 WARNING: dropped 1 decoy PSMs due to missing features
0:35:08.321440 INFO: Test AUC: 0.557
0:35:08.321712 INFO: Train AUC: 0.573
0:35:08.321761 INFO: AUC difference: 2.87%
0:35:08.483370 INFO: Resetting torch num_threads to 100
0:35:08.503294 INFO: === FDR correction performed with classifier version -1 ===
0:35:08.505496 PROGRESS: ============================= Precursor FDR =============================
0:35:08.505684 PROGRESS: Total precursors accumulated: 3
0:35:08.505777 PROGRESS: Target precursors: 3 (100.00%)
0:35:08.505867 PROGRESS: Decoy precursors: 0 (0.00%)
0:35:08.505937 PROGRESS: 
0:35:08.506005 PROGRESS: Precursor Summary:
0:35:08.507530 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
0:35:08.507668 PROGRESS: 
0:35:08.507750 PROGRESS: Protein Summary:
0:35:08.509342 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
0:35:08.509475 PROGRESS: =========================================================================
0:35:09.050054 INFO: Starting optimization step 3.
0:35:09.050562 PROGRESS: === Extracting elution groups 56000 to 120000 ===
0:35:09.050719 PROGRESS: Extracting batch of 126509 precursors
0:35:09.122877 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:35:09.123061 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:09.123115 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:35:09.123146 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:35:09.123675 INFO: Starting candidate selection
0:35:17.912044 INFO: Starting candidate scoring
0:35:18.957006 INFO: Finished candidate processing
0:35:18.957219 INFO: Collecting candidate features
0:35:19.487108 INFO: Collecting fragment features
0:35:19.609123 INFO: Finished candidate scoring
0:35:19.954230 PROGRESS: === Extracted 236534 precursors and 2337116 fragments ===
0:35:20.014455 INFO: performing precursor FDR with 47 features
0:35:20.014648 INFO: Decoy channel: -1
0:35:20.014688 INFO: Competetive: True
0:35:20.266768 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:20.354139 WARNING: dropped 1 decoy PSMs due to missing features
0:35:25.815637 INFO: Test AUC: 0.558
0:35:25.815847 INFO: Train AUC: 0.581
0:35:25.815883 INFO: AUC difference: 3.87%
0:35:25.940839 INFO: Resetting torch num_threads to 100
0:35:25.961381 INFO: === FDR correction performed with classifier version -1 ===
0:35:25.962952 PROGRESS: ============================= Precursor FDR =============================
0:35:25.963141 PROGRESS: Total precursors accumulated: 1
0:35:25.963211 PROGRESS: Target precursors: 1 (100.00%)
0:35:25.963268 PROGRESS: Decoy precursors: 0 (0.00%)
0:35:25.963319 PROGRESS: 
0:35:25.963367 PROGRESS: Precursor Summary:
0:35:25.964559 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:35:25.964693 PROGRESS: 
0:35:25.964763 PROGRESS: Protein Summary:
0:35:25.965913 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:35:25.966025 PROGRESS: =========================================================================
0:35:26.550847 INFO: Starting optimization step 4.
0:35:26.551483 PROGRESS: === Extracting elution groups 120000 to 248000 ===
0:35:26.551647 PROGRESS: Extracting batch of 252969 precursors
0:35:26.667424 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:35:26.667610 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:26.667659 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:35:26.667691 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:35:26.668116 INFO: Starting candidate selection
0:35:43.245145 INFO: Starting candidate scoring
0:35:44.774600 INFO: Finished candidate processing
0:35:44.774701 INFO: Collecting candidate features
0:35:45.461117 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 252311)
0:35:45.472510 INFO: Collecting fragment features
0:35:45.641721 INFO: Finished candidate scoring
0:35:46.049986 PROGRESS: === Extracted 488845 precursors and 4824410 fragments ===
0:35:46.108735 INFO: performing precursor FDR with 47 features
0:35:46.108872 INFO: Decoy channel: -1
0:35:46.108900 INFO: Competetive: True
0:35:46.355828 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:46.445304 WARNING: dropped 3 decoy PSMs due to missing features
0:35:54.996581 INFO: Test AUC: 0.565
0:35:54.996819 INFO: Train AUC: 0.584
0:35:54.996855 INFO: AUC difference: 3.26%
0:35:55.126989 INFO: Resetting torch num_threads to 100
0:35:55.158472 INFO: === FDR correction performed with classifier version -1 ===
0:35:55.159413 PROGRESS: ============================= Precursor FDR =============================
0:35:55.159512 PROGRESS: Total precursors accumulated: 5
0:35:55.159572 PROGRESS: Target precursors: 5 (100.00%)
0:35:55.159623 PROGRESS: Decoy precursors: 0 (0.00%)
0:35:55.159667 PROGRESS: 
0:35:55.159709 PROGRESS: Precursor Summary:
0:35:55.160672 PROGRESS: Channel   0:	 0.05 FDR:     5; 0.01 FDR:     5; 0.001 FDR:     5
0:35:55.160764 PROGRESS: 
0:35:55.160820 PROGRESS: Protein Summary:
0:35:55.161873 PROGRESS: Channel   0:	 0.05 FDR:     5; 0.01 FDR:     5; 0.001 FDR:     5
0:35:55.161960 PROGRESS: =========================================================================
0:35:55.878102 INFO: Starting optimization step 5.
0:35:55.878397 PROGRESS: === Extracting elution groups 248000 to 504000 ===
0:35:55.878484 PROGRESS: Extracting batch of 505926 precursors
0:35:55.990952 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:35:55.991085 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:35:55.991126 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:35:55.991150 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:35:55.991487 INFO: Starting candidate selection
0:36:28.034921 INFO: Starting candidate scoring
0:36:32.228334 INFO: Finished candidate processing
0:36:32.228527 INFO: Collecting candidate features
0:36:33.870640 WARNING: intensity_correlation has 5 NaNs ( 0.00 % out of 504656)
0:36:33.890379 INFO: Collecting fragment features
0:36:34.239379 INFO: Finished candidate scoring
0:36:34.989918 PROGRESS: === Extracted 993501 precursors and 9804968 fragments ===
0:36:35.110183 INFO: performing precursor FDR with 47 features
0:36:35.110315 INFO: Decoy channel: -1
0:36:35.110353 INFO: Competetive: True
0:36:35.577814 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:35.751553 WARNING: dropped 8 decoy PSMs due to missing features
0:37:01.352167 INFO: Test AUC: 0.570
0:37:01.352440 INFO: Train AUC: 0.581
0:37:01.352485 INFO: AUC difference: 1.97%
0:37:01.593224 INFO: Resetting torch num_threads to 100
0:37:01.739609 INFO: === FDR correction performed with classifier version -1 ===
0:37:01.740943 PROGRESS: ============================= Precursor FDR =============================
0:37:01.741051 PROGRESS: Total precursors accumulated: 2
0:37:01.741119 PROGRESS: Target precursors: 2 (100.00%)
0:37:01.741172 PROGRESS: Decoy precursors: 0 (0.00%)
0:37:01.741219 PROGRESS: 
0:37:01.741274 PROGRESS: Precursor Summary:
0:37:01.742308 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
0:37:01.742420 PROGRESS: 
0:37:01.742478 PROGRESS: Protein Summary:
0:37:01.743560 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
0:37:01.743661 PROGRESS: =========================================================================
0:37:03.535224 INFO: Starting optimization step 6.
0:37:03.535671 PROGRESS: === Extracting elution groups 504000 to 1016000 ===
0:37:03.535766 PROGRESS: Extracting batch of 1011981 precursors
0:37:03.946118 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:37:03.946359 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:37:03.946424 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:37:03.946455 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:37:03.947021 INFO: Starting candidate selection
0:38:07.437686 INFO: Starting candidate scoring
0:38:15.522724 INFO: Finished candidate processing
0:38:15.523086 INFO: Collecting candidate features
0:38:19.307650 WARNING: intensity_correlation has 7 NaNs ( 0.00 % out of 1009427)
0:38:19.352494 INFO: Collecting fragment features
0:38:20.364280 INFO: Finished candidate scoring
0:38:22.599487 PROGRESS: === Extracted 2002928 precursors and 19769299 fragments ===
0:38:23.016010 INFO: performing precursor FDR with 47 features
0:38:23.016162 INFO: Decoy channel: -1
0:38:23.016199 INFO: Competetive: True
0:38:24.689166 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:25.456244 WARNING: dropped 1 target PSMs due to missing features
0:38:25.456452 WARNING: dropped 14 decoy PSMs due to missing features
0:39:15.399197 INFO: Test AUC: 0.573
0:39:15.399568 INFO: Train AUC: 0.580
0:39:15.399615 INFO: AUC difference: 1.17%
0:39:15.776068 INFO: Resetting torch num_threads to 100
0:39:16.060425 INFO: === FDR correction performed with classifier version -1 ===
0:39:16.061869 PROGRESS: ============================= Precursor FDR =============================
0:39:16.062012 PROGRESS: Total precursors accumulated: 4
0:39:16.062099 PROGRESS: Target precursors: 4 (100.00%)
0:39:16.062171 PROGRESS: Decoy precursors: 0 (0.00%)
0:39:16.062238 PROGRESS: 
0:39:16.062309 PROGRESS: Precursor Summary:
0:39:16.063795 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
0:39:16.063907 PROGRESS: 
0:39:16.063970 PROGRESS: Protein Summary:
0:39:16.065494 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
0:39:16.065612 PROGRESS: =========================================================================
0:39:19.291116 INFO: Starting optimization step 7.
0:39:19.291498 PROGRESS: === Extracting elution groups 1016000 to 2040000 ===
0:39:19.291621 PROGRESS: Extracting batch of 2023640 precursors
0:39:20.037379 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:39:20.037601 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:39:20.037669 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:39:20.037704 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:39:20.038190 INFO: Starting candidate selection
0:41:23.188750 INFO: Starting candidate scoring
0:41:40.714364 INFO: Finished candidate processing
0:41:40.714739 INFO: Collecting candidate features
0:41:48.678871 WARNING: intensity_correlation has 21 NaNs ( 0.00 % out of 2018533)
0:41:48.804221 INFO: Collecting fragment features
0:41:51.372717 INFO: Finished candidate scoring
0:41:56.392699 PROGRESS: === Extracted 4021461 precursors and 39686175 fragments ===
0:41:57.090559 INFO: performing precursor FDR with 47 features
0:41:57.090724 INFO: Decoy channel: -1
0:41:57.090755 INFO: Competetive: True
0:42:01.238421 INFO: Setting torch num_threads to 2 for FDR classification task
0:42:03.064658 WARNING: dropped 8 target PSMs due to missing features
0:42:03.064872 WARNING: dropped 28 decoy PSMs due to missing features
0:43:42.781951 INFO: Test AUC: 0.579
0:43:42.782224 INFO: Train AUC: 0.584
0:43:42.782274 INFO: AUC difference: 0.82%
0:43:43.378232 INFO: Resetting torch num_threads to 100
0:43:43.808290 INFO: === FDR correction performed with classifier version -1 ===
0:43:43.809750 PROGRESS: ============================= Precursor FDR =============================
0:43:43.809900 PROGRESS: Total precursors accumulated: 701
0:43:43.809998 PROGRESS: Target precursors: 641 (91.44%)
0:43:43.810068 PROGRESS: Decoy precursors: 60 (8.56%)
0:43:43.810130 PROGRESS: 
0:43:43.810189 PROGRESS: Precursor Summary:
0:43:43.811632 PROGRESS: Channel   0:	 0.05 FDR:   298; 0.01 FDR:    75; 0.001 FDR:    75
0:43:43.811751 PROGRESS: 
0:43:43.811823 PROGRESS: Protein Summary:
0:43:43.813340 PROGRESS: Channel   0:	 0.05 FDR:   286; 0.01 FDR:    75; 0.001 FDR:    75
0:43:43.813470 PROGRESS: =========================================================================
0:43:49.086477 INFO: Starting optimization step 8.
0:43:49.086974 PROGRESS: === Extracting elution groups 2040000 to 4088000 ===
0:43:49.087099 PROGRESS: Extracting batch of 4047585 precursors
0:43:50.403666 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:43:50.404189 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:43:50.404392 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
0:43:50.404504 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:43:50.405135 INFO: Starting candidate selection
0:47:51.337231 INFO: Starting candidate scoring
0:48:34.138317 INFO: Finished candidate processing
0:48:34.138627 INFO: Collecting candidate features
0:48:43.757883 WARNING: intensity_correlation has 39 NaNs ( 0.00 % out of 4037525)
0:48:43.889278 INFO: Collecting fragment features
0:48:47.739509 INFO: Finished candidate scoring
0:48:56.888632 PROGRESS: === Extracted 8058986 precursors and 79522759 fragments ===
0:48:58.315204 INFO: performing precursor FDR with 47 features
0:48:58.315373 INFO: Decoy channel: -1
0:48:58.315411 INFO: Competetive: True
0:49:03.752965 INFO: Setting torch num_threads to 2 for FDR classification task
0:49:06.181820 WARNING: dropped 20 target PSMs due to missing features
0:49:06.181980 WARNING: dropped 55 decoy PSMs due to missing features
0:52:24.995821 INFO: Test AUC: 0.581
0:52:24.996043 INFO: Train AUC: 0.586
0:52:24.996079 INFO: AUC difference: 1.00%
0:52:25.643814 INFO: Resetting torch num_threads to 100
0:52:26.329625 INFO: === FDR correction performed with classifier version -1 ===
0:52:26.335428 PROGRESS: ============================= Precursor FDR =============================
0:52:26.335669 PROGRESS: Total precursors accumulated: 5,547
0:52:26.335776 PROGRESS: Target precursors: 5,094 (91.83%)
0:52:26.335867 PROGRESS: Decoy precursors: 453 (8.17%)
0:52:26.335949 PROGRESS: 
0:52:26.336028 PROGRESS: Precursor Summary:
0:52:26.340256 PROGRESS: Channel   0:	 0.05 FDR: 4,082; 0.01 FDR: 2,937; 0.001 FDR: 1,712
0:52:26.340400 PROGRESS: 
0:52:26.340470 PROGRESS: Protein Summary:
0:52:26.344770 PROGRESS: Channel   0:	 0.05 FDR: 2,577; 0.01 FDR: 1,853; 0.001 FDR: 1,200
0:52:26.344897 PROGRESS: =========================================================================
0:52:27.735859 INFO: fragments_df_filtered: 5000
0:52:30.218885 INFO: calibration group: precursor, fitting mz estimator 
0:52:30.765069 INFO: calibration group: precursor, fitting rt estimator 
0:52:31.411324 INFO: calibration group: fragment, fitting mz estimator 
0:52:32.068068 INFO: calibration group: precursor, predicting mz
0:52:32.286013 INFO: calibration group: precursor, predicting rt
0:52:33.178078 INFO: calibration group: fragment, predicting mz
0:52:35.155083 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:52:35.155496 INFO: Starting optimization step 9.
0:52:35.155616 PROGRESS: === Extracting elution groups 0 to 504000 ===
0:52:35.155725 PROGRESS: Extracting batch of 996048 precursors
0:52:35.438035 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:52:35.438288 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:52:35.438356 INFO: FWHM in RT is 2.86 seconds, sigma is 0.37
0:52:35.438396 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:52:35.438748 INFO: Starting candidate selection
0:53:28.004252 INFO: Starting candidate scoring
0:53:44.022002 INFO: Finished candidate processing
0:53:44.022540 INFO: Collecting candidate features
0:53:49.293530 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 1987016)
0:53:49.402739 INFO: Collecting fragment features
0:53:51.432855 INFO: Finished candidate scoring
0:53:54.304723 PROGRESS: === Extracted 1987016 precursors and 19337157 fragments ===
0:53:54.305875 INFO: performing precursor FDR with 47 features
0:53:54.306056 INFO: Decoy channel: -1
0:53:54.306205 INFO: Competetive: True
0:53:55.316157 INFO: Setting torch num_threads to 2 for FDR classification task
0:53:55.936759 WARNING: dropped 1 target PSMs due to missing features
0:53:55.937109 WARNING: dropped 2 decoy PSMs due to missing features
0:54:45.736195 INFO: Test AUC: 0.580
0:54:45.736472 INFO: Train AUC: 0.589
0:54:45.736517 INFO: AUC difference: 1.37%
0:54:46.086816 INFO: Resetting torch num_threads to 100
0:54:46.183638 INFO: === FDR correction performed with classifier version 8 ===
0:54:46.185466 PROGRESS: ============================= Precursor FDR =============================
0:54:46.185671 PROGRESS: Total precursors accumulated: 1,237
0:54:46.185777 PROGRESS: Target precursors: 1,127 (91.11%)
0:54:46.185857 PROGRESS: Decoy precursors: 110 (8.89%)
0:54:46.185920 PROGRESS: 
0:54:46.185983 PROGRESS: Precursor Summary:
0:54:46.187916 PROGRESS: Channel   0:	 0.05 FDR:   842; 0.01 FDR:   525; 0.001 FDR:   362
0:54:46.188069 PROGRESS: 
0:54:46.188152 PROGRESS: Protein Summary:
0:54:46.190214 PROGRESS: Channel   0:	 0.05 FDR:   751; 0.01 FDR:   463; 0.001 FDR:   324
0:54:46.190357 PROGRESS: =========================================================================
0:54:46.320037 INFO: fragments_df_filtered: 5000
0:54:47.476409 INFO: calibration group: precursor, fitting mz estimator 
0:54:47.583771 INFO: calibration group: precursor, fitting rt estimator 
0:54:47.751726 INFO: calibration group: fragment, fitting mz estimator 
0:54:48.596026 INFO: calibration group: precursor, predicting mz
0:54:48.708124 INFO: calibration group: precursor, predicting rt
0:54:49.099039 INFO: calibration group: fragment, predicting mz
0:54:50.016016 INFO: === checking if optimization conditions were reached ===
0:54:50.019401 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
0:54:50.020764 PROGRESS: ❌ ms1_error      : 14.5804 > 10.0000 or insufficient steps taken.
0:54:50.020893 INFO: ==============================================
0:54:50.021190 INFO: Starting optimization step 10.
0:54:50.021431 PROGRESS: === Extracting elution groups 0 to 248000 ===
0:54:50.021675 PROGRESS: Extracting batch of 490122 precursors
0:54:50.222262 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:54:50.222605 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:54:50.222749 INFO: FWHM in RT is 2.89 seconds, sigma is 0.37
0:54:50.222842 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:54:50.223308 INFO: Starting candidate selection
0:55:21.197696 INFO: Starting candidate scoring
0:55:27.899240 INFO: Finished candidate processing
0:55:27.899457 INFO: Collecting candidate features
0:55:30.270227 WARNING: intensity_correlation has 18 NaNs ( 0.00 % out of 977312)
0:55:30.308465 INFO: Collecting fragment features
0:55:31.009557 INFO: Finished candidate scoring
0:55:31.719199 PROGRESS: === Extracted 977312 precursors and 8429216 fragments ===
0:55:31.719870 INFO: performing precursor FDR with 47 features
0:55:31.719948 INFO: Decoy channel: -1
0:55:31.719981 INFO: Competetive: True
0:55:32.200418 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:32.529688 WARNING: dropped 8 target PSMs due to missing features
0:55:32.529874 WARNING: dropped 10 decoy PSMs due to missing features
0:55:57.062742 INFO: Test AUC: 0.576
0:55:57.063016 INFO: Train AUC: 0.589
0:55:57.063066 INFO: AUC difference: 2.24%
0:55:57.391996 INFO: Resetting torch num_threads to 100
0:55:57.600598 INFO: === FDR correction performed with classifier version 9 ===
0:55:57.602022 PROGRESS: ============================= Precursor FDR =============================
0:55:57.602198 PROGRESS: Total precursors accumulated: 968
0:55:57.602275 PROGRESS: Target precursors: 879 (90.81%)
0:55:57.609784 PROGRESS: Decoy precursors: 89 (9.19%)
0:55:57.609918 PROGRESS: 
0:55:57.609985 PROGRESS: Precursor Summary:
0:55:57.630449 PROGRESS: Channel   0:	 0.05 FDR:   643; 0.01 FDR:   523; 0.001 FDR:   347
0:55:57.634066 PROGRESS: 
0:55:57.635136 PROGRESS: Protein Summary:
0:55:57.637516 PROGRESS: Channel   0:	 0.05 FDR:   590; 0.01 FDR:   481; 0.001 FDR:   327
0:55:57.646654 PROGRESS: =========================================================================
0:55:57.747885 INFO: fragments_df_filtered: 5000
0:55:58.588424 INFO: calibration group: precursor, fitting mz estimator 
0:55:59.520687 INFO: calibration group: precursor, fitting rt estimator 
0:55:59.920242 INFO: calibration group: fragment, fitting mz estimator 
0:56:01.066386 INFO: calibration group: precursor, predicting mz
0:56:01.191213 INFO: calibration group: precursor, predicting rt
0:56:01.398890 INFO: calibration group: fragment, predicting mz
0:56:01.990685 INFO: === checking if optimization conditions were reached ===
0:56:01.993745 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
0:56:01.995115 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
0:56:01.995240 INFO: ==============================================
0:56:01.995521 PROGRESS: Optimization finished for ms2_error, ms1_error.
0:56:02.544223 INFO: calibration group: precursor, predicting mz
0:56:02.608930 INFO: calibration group: precursor, predicting rt
0:56:02.859652 INFO: calibration group: fragment, predicting mz
0:56:03.307219 INFO: Starting optimization step 0.
0:56:03.307573 PROGRESS: === Extracting elution groups 0 to 120000 ===
0:56:03.307698 PROGRESS: Extracting batch of 237153 precursors
0:56:03.377669 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:56:03.377826 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:56:03.377877 INFO: FWHM in RT is 2.61 seconds, sigma is 0.34
0:56:03.377908 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:56:03.378249 INFO: Starting candidate selection
0:56:17.724705 INFO: Starting candidate scoring
0:56:21.253740 INFO: Finished candidate processing
0:56:21.253953 INFO: Collecting candidate features
0:56:22.329837 WARNING: intensity_correlation has 7 NaNs ( 0.00 % out of 472908)
0:56:22.348987 INFO: Collecting fragment features
0:56:22.634089 INFO: Finished candidate scoring
0:56:23.233085 PROGRESS: === Extracted 472908 precursors and 4063359 fragments ===
0:56:23.233623 INFO: performing precursor FDR with 47 features
0:56:23.233680 INFO: Decoy channel: -1
0:56:23.233705 INFO: Competetive: True
0:56:23.427330 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:23.594029 WARNING: dropped 1 target PSMs due to missing features
0:56:23.594210 WARNING: dropped 6 decoy PSMs due to missing features
0:56:35.345833 INFO: Test AUC: 0.573
0:56:35.346085 INFO: Train AUC: 0.595
0:56:35.346129 INFO: AUC difference: 3.67%
0:56:35.526779 INFO: Resetting torch num_threads to 100
0:56:35.553216 INFO: === FDR correction performed with classifier version 10 ===
0:56:35.554732 PROGRESS: ============================= Precursor FDR =============================
0:56:35.554924 PROGRESS: Total precursors accumulated: 647
0:56:35.555006 PROGRESS: Target precursors: 586 (90.57%)
0:56:35.555072 PROGRESS: Decoy precursors: 61 (9.43%)
0:56:35.555136 PROGRESS: 
0:56:35.555197 PROGRESS: Precursor Summary:
0:56:35.556800 PROGRESS: Channel   0:	 0.05 FDR:   372; 0.01 FDR:   214; 0.001 FDR:   198
0:56:35.556937 PROGRESS: 
0:56:35.557009 PROGRESS: Protein Summary:
0:56:35.558724 PROGRESS: Channel   0:	 0.05 FDR:   355; 0.01 FDR:   204; 0.001 FDR:   190
0:56:35.558860 PROGRESS: =========================================================================
0:56:35.590659 INFO: fragments_df_filtered: 2279
0:56:36.100163 INFO: calibration group: precursor, fitting mz estimator 
0:56:36.201680 INFO: calibration group: precursor, fitting rt estimator 
0:56:36.327134 INFO: calibration group: fragment, fitting mz estimator 
0:56:36.669555 INFO: calibration group: precursor, predicting mz
0:56:36.750695 INFO: calibration group: precursor, predicting rt
0:56:36.966853 INFO: calibration group: fragment, predicting mz
0:56:37.348728 INFO: === checking if optimization conditions were reached ===
0:56:37.349339 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:56:37.351989 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 284.5215.
0:56:37.352132 INFO: ==============================================
0:56:37.352406 INFO: Starting optimization step 1.
0:56:37.352644 PROGRESS: === Extracting elution groups 0 to 120000 ===
0:56:37.352885 PROGRESS: Extracting batch of 237153 precursors
0:56:37.420294 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:56:37.420439 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:56:37.420481 INFO: FWHM in RT is 2.53 seconds, sigma is 0.33
0:56:37.420504 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:56:37.420841 INFO: Starting candidate selection
0:56:46.239565 INFO: Starting candidate scoring
0:56:49.013865 INFO: Finished candidate processing
0:56:49.014020 INFO: Collecting candidate features
0:56:50.125700 WARNING: intensity_correlation has 32 NaNs ( 0.01 % out of 471450)
0:56:50.145476 INFO: Collecting fragment features
0:56:50.433777 INFO: Finished candidate scoring
0:56:50.773532 PROGRESS: === Extracted 471450 precursors and 3963475 fragments ===
0:56:50.775712 INFO: performing precursor FDR with 47 features
0:56:50.775775 INFO: Decoy channel: -1
0:56:50.775805 INFO: Competetive: True
0:56:50.948840 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:51.058822 WARNING: dropped 15 target PSMs due to missing features
0:56:51.058984 WARNING: dropped 17 decoy PSMs due to missing features
0:57:02.486652 INFO: Test AUC: 0.572
0:57:02.486833 INFO: Train AUC: 0.591
0:57:02.486881 INFO: AUC difference: 3.21%
0:57:02.670373 INFO: Resetting torch num_threads to 100
0:57:02.697436 INFO: === FDR correction performed with classifier version 10 ===
0:57:02.698995 PROGRESS: ============================= Precursor FDR =============================
0:57:02.699192 PROGRESS: Total precursors accumulated: 682
0:57:02.699307 PROGRESS: Target precursors: 620 (90.91%)
0:57:02.699405 PROGRESS: Decoy precursors: 62 (9.09%)
0:57:02.699493 PROGRESS: 
0:57:02.699576 PROGRESS: Precursor Summary:
0:57:02.701457 PROGRESS: Channel   0:	 0.05 FDR:   422; 0.01 FDR:   309; 0.001 FDR:   161
0:57:02.701596 PROGRESS: 
0:57:02.701695 PROGRESS: Protein Summary:
0:57:02.703802 PROGRESS: Channel   0:	 0.05 FDR:   405; 0.01 FDR:   294; 0.001 FDR:   153
0:57:02.703960 PROGRESS: =========================================================================
0:57:02.735755 INFO: fragments_df_filtered: 2980
0:57:03.353073 INFO: calibration group: precursor, fitting mz estimator 
0:57:03.509210 INFO: calibration group: precursor, fitting rt estimator 
0:57:03.628107 INFO: calibration group: fragment, fitting mz estimator 
0:57:03.984832 INFO: calibration group: precursor, predicting mz
0:57:04.039239 INFO: calibration group: precursor, predicting rt
0:57:04.252167 INFO: calibration group: fragment, predicting mz
0:57:04.760514 INFO: === checking if optimization conditions were reached ===
0:57:04.761118 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:57:04.763874 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 261.2541.
0:57:04.764015 INFO: ==============================================
0:57:04.764319 INFO: Starting optimization step 2.
0:57:04.764575 PROGRESS: === Extracting elution groups 0 to 120000 ===
0:57:04.764837 PROGRESS: Extracting batch of 237153 precursors
0:57:04.861028 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:57:04.861346 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:57:04.861470 INFO: FWHM in RT is 2.51 seconds, sigma is 0.32
0:57:04.861558 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:57:04.861982 INFO: Starting candidate selection
0:57:16.235004 INFO: Starting candidate scoring
0:57:19.085146 INFO: Finished candidate processing
0:57:19.085281 INFO: Collecting candidate features
0:57:20.155078 WARNING: intensity_correlation has 42 NaNs ( 0.01 % out of 471258)
0:57:20.175285 INFO: Collecting fragment features
0:57:20.490962 INFO: Finished candidate scoring
0:57:21.186574 PROGRESS: === Extracted 471258 precursors and 3943601 fragments ===
0:57:21.187813 INFO: performing precursor FDR with 47 features
0:57:21.187952 INFO: Decoy channel: -1
0:57:21.188064 INFO: Competetive: True
0:57:21.437269 INFO: Setting torch num_threads to 2 for FDR classification task
0:57:21.605413 WARNING: dropped 20 target PSMs due to missing features
0:57:21.605781 WARNING: dropped 22 decoy PSMs due to missing features
0:57:35.788556 INFO: Test AUC: 0.571
0:57:35.788931 INFO: Train AUC: 0.591
0:57:35.788997 INFO: AUC difference: 3.40%
0:57:35.990466 INFO: Resetting torch num_threads to 100
0:57:36.015331 INFO: === FDR correction performed with classifier version 10 ===
0:57:36.016719 PROGRESS: ============================= Precursor FDR =============================
0:57:36.017010 PROGRESS: Total precursors accumulated: 653
0:57:36.017151 PROGRESS: Target precursors: 592 (90.66%)
0:57:36.017273 PROGRESS: Decoy precursors: 61 (9.34%)
0:57:36.017391 PROGRESS: 
0:57:36.017496 PROGRESS: Precursor Summary:
0:57:36.019035 PROGRESS: Channel   0:	 0.05 FDR:   413; 0.01 FDR:   264; 0.001 FDR:   196
0:57:36.019281 PROGRESS: 
0:57:36.019399 PROGRESS: Protein Summary:
0:57:36.021270 PROGRESS: Channel   0:	 0.05 FDR:   395; 0.01 FDR:   251; 0.001 FDR:   186
0:57:36.021582 PROGRESS: =========================================================================
0:57:36.049834 INFO: fragments_df_filtered: 2692
0:57:36.716559 INFO: calibration group: precursor, fitting mz estimator 
0:57:36.900674 INFO: calibration group: precursor, fitting rt estimator 
0:57:37.046001 INFO: calibration group: fragment, fitting mz estimator 
0:57:37.511455 INFO: calibration group: precursor, predicting mz
0:57:37.719646 INFO: calibration group: precursor, predicting rt
0:57:37.951251 INFO: calibration group: fragment, predicting mz
0:57:38.521380 INFO: === checking if optimization conditions were reached ===
0:57:38.521982 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:57:38.525166 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 163.2874.
0:57:38.525409 INFO: ==============================================
0:57:38.529919 INFO: Starting optimization step 3.
0:57:38.530300 PROGRESS: === Extracting elution groups 0 to 120000 ===
0:57:38.530648 PROGRESS: Extracting batch of 237153 precursors
0:57:38.630323 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:57:38.630843 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:57:38.631003 INFO: FWHM in RT is 2.51 seconds, sigma is 0.32
0:57:38.631100 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:57:38.631585 INFO: Starting candidate selection
0:57:47.395234 INFO: Starting candidate scoring
0:57:50.245912 INFO: Finished candidate processing
0:57:50.246049 INFO: Collecting candidate features
0:57:51.454582 WARNING: intensity_correlation has 54 NaNs ( 0.01 % out of 470242)
0:57:51.488459 INFO: Collecting fragment features
0:57:51.925195 INFO: Finished candidate scoring
0:57:52.665870 PROGRESS: === Extracted 470242 precursors and 3872087 fragments ===
0:57:52.666818 INFO: performing precursor FDR with 47 features
0:57:52.666933 INFO: Decoy channel: -1
0:57:52.667020 INFO: Competetive: True
0:57:52.943166 INFO: Setting torch num_threads to 2 for FDR classification task
0:57:53.113808 WARNING: dropped 25 target PSMs due to missing features
0:57:53.114152 WARNING: dropped 29 decoy PSMs due to missing features
0:58:06.284909 INFO: Test AUC: 0.571
0:58:06.285168 INFO: Train AUC: 0.590
0:58:06.285216 INFO: AUC difference: 3.21%
0:58:07.550221 INFO: Resetting torch num_threads to 100
0:58:07.577753 INFO: === FDR correction performed with classifier version 10 ===
0:58:07.579255 PROGRESS: ============================= Precursor FDR =============================
0:58:07.579582 PROGRESS: Total precursors accumulated: 683
0:58:07.579688 PROGRESS: Target precursors: 618 (90.48%)
0:58:07.579757 PROGRESS: Decoy precursors: 65 (9.52%)
0:58:07.579821 PROGRESS: 
0:58:07.579885 PROGRESS: Precursor Summary:
0:58:07.581591 PROGRESS: Channel   0:	 0.05 FDR:   428; 0.01 FDR:   242; 0.001 FDR:   229
0:58:07.581839 PROGRESS: 
0:58:07.581922 PROGRESS: Protein Summary:
0:58:07.583724 PROGRESS: Channel   0:	 0.05 FDR:   410; 0.01 FDR:   229; 0.001 FDR:   216
0:58:07.583960 PROGRESS: =========================================================================
0:58:07.606517 INFO: fragments_df_filtered: 2558
0:58:08.091200 INFO: calibration group: precursor, fitting mz estimator 
0:58:08.202660 INFO: calibration group: precursor, fitting rt estimator 
0:58:08.367339 INFO: calibration group: fragment, fitting mz estimator 
0:58:08.731218 INFO: calibration group: precursor, predicting mz
0:58:08.812594 INFO: calibration group: precursor, predicting rt
0:58:09.046454 INFO: calibration group: fragment, predicting mz
0:58:09.562791 INFO: === checking if optimization conditions were reached ===
0:58:09.563248 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:58:09.566254 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 120.1343.
0:58:09.566349 INFO: ==============================================
0:58:09.566496 INFO: Starting optimization step 4.
0:58:09.566583 PROGRESS: === Extracting elution groups 0 to 120000 ===
0:58:09.566665 PROGRESS: Extracting batch of 237153 precursors
0:58:09.665395 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:58:09.665567 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:58:09.665616 INFO: FWHM in RT is 2.50 seconds, sigma is 0.32
0:58:09.665647 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:58:09.666023 INFO: Starting candidate selection
0:58:18.221905 INFO: Starting candidate scoring
0:58:20.874865 INFO: Finished candidate processing
0:58:20.874980 INFO: Collecting candidate features
0:58:22.179437 WARNING: intensity_correlation has 70 NaNs ( 0.01 % out of 469184)
0:58:22.209693 INFO: Collecting fragment features
0:58:22.619533 INFO: Finished candidate scoring
0:58:23.329966 PROGRESS: === Extracted 469184 precursors and 3776452 fragments ===
0:58:23.330957 INFO: performing precursor FDR with 47 features
0:58:23.331113 INFO: Decoy channel: -1
0:58:23.331207 INFO: Competetive: True
0:58:23.597613 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:23.775692 WARNING: dropped 33 target PSMs due to missing features
0:58:23.776044 WARNING: dropped 37 decoy PSMs due to missing features
0:58:35.773963 INFO: Test AUC: 0.570
0:58:35.774225 INFO: Train AUC: 0.588
0:58:35.774277 INFO: AUC difference: 3.01%
0:58:35.968486 INFO: Resetting torch num_threads to 100
0:58:35.994757 INFO: === FDR correction performed with classifier version 10 ===
0:58:35.997873 PROGRESS: ============================= Precursor FDR =============================
0:58:35.998134 PROGRESS: Total precursors accumulated: 769
0:58:35.998237 PROGRESS: Target precursors: 699 (90.90%)
0:58:35.998334 PROGRESS: Decoy precursors: 70 (9.10%)
0:58:35.998429 PROGRESS: 
0:58:35.998517 PROGRESS: Precursor Summary:
0:58:36.000303 PROGRESS: Channel   0:	 0.05 FDR:   482; 0.01 FDR:   283; 0.001 FDR:   206
0:58:36.000472 PROGRESS: 
0:58:36.000567 PROGRESS: Protein Summary:
0:58:36.002503 PROGRESS: Channel   0:	 0.05 FDR:   464; 0.01 FDR:   269; 0.001 FDR:   195
0:58:36.002660 PROGRESS: =========================================================================
0:58:36.034121 INFO: fragments_df_filtered: 2839
0:58:36.694279 INFO: calibration group: precursor, fitting mz estimator 
0:58:36.807620 INFO: calibration group: precursor, fitting rt estimator 
0:58:36.966118 INFO: calibration group: fragment, fitting mz estimator 
0:58:37.321584 INFO: calibration group: precursor, predicting mz
0:58:37.382400 INFO: calibration group: precursor, predicting rt
0:58:37.632377 INFO: calibration group: fragment, predicting mz
0:58:38.128062 INFO: === checking if optimization conditions were reached ===
0:58:38.129583 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:58:38.131996 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 119.9098.
0:58:38.132065 INFO: ==============================================
0:58:38.132183 INFO: Starting optimization step 5.
0:58:38.132279 PROGRESS: === Extracting elution groups 0 to 120000 ===
0:58:38.132365 PROGRESS: Extracting batch of 237153 precursors
0:58:38.199896 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:58:38.200051 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:58:38.200093 INFO: FWHM in RT is 2.54 seconds, sigma is 0.33
0:58:38.200117 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:58:38.200484 INFO: Starting candidate selection
0:58:46.422803 INFO: Starting candidate scoring
0:58:49.353635 INFO: Finished candidate processing
0:58:49.355059 INFO: Collecting candidate features
0:58:50.744341 WARNING: intensity_correlation has 66 NaNs ( 0.01 % out of 469124)
0:58:50.774159 INFO: Collecting fragment features
0:58:51.168973 INFO: Finished candidate scoring
0:58:51.650323 PROGRESS: === Extracted 469124 precursors and 3779530 fragments ===
0:58:51.650902 INFO: performing precursor FDR with 47 features
0:58:51.650954 INFO: Decoy channel: -1
0:58:51.650985 INFO: Competetive: True
0:58:51.898165 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:52.065916 WARNING: dropped 38 target PSMs due to missing features
0:58:52.066130 WARNING: dropped 28 decoy PSMs due to missing features
0:59:06.514303 INFO: Test AUC: 0.569
0:59:06.514597 INFO: Train AUC: 0.587
0:59:06.514643 INFO: AUC difference: 3.03%
0:59:06.711231 INFO: Resetting torch num_threads to 100
0:59:06.738287 INFO: === FDR correction performed with classifier version 10 ===
0:59:06.739905 PROGRESS: ============================= Precursor FDR =============================
0:59:06.740124 PROGRESS: Total precursors accumulated: 726
0:59:06.740234 PROGRESS: Target precursors: 658 (90.63%)
0:59:06.740320 PROGRESS: Decoy precursors: 68 (9.37%)
0:59:06.740404 PROGRESS: 
0:59:06.740479 PROGRESS: Precursor Summary:
0:59:06.742194 PROGRESS: Channel   0:	 0.05 FDR:   441; 0.01 FDR:   283; 0.001 FDR:   234
0:59:06.742375 PROGRESS: 
0:59:06.742471 PROGRESS: Protein Summary:
0:59:06.744376 PROGRESS: Channel   0:	 0.05 FDR:   422; 0.01 FDR:   270; 0.001 FDR:   222
0:59:06.744823 PROGRESS: =========================================================================
0:59:06.777135 INFO: fragments_df_filtered: 2843
0:59:07.449200 INFO: calibration group: precursor, fitting mz estimator 
0:59:07.847039 INFO: calibration group: precursor, fitting rt estimator 
0:59:07.974244 INFO: calibration group: fragment, fitting mz estimator 
0:59:08.429785 INFO: calibration group: precursor, predicting mz
0:59:08.508469 INFO: calibration group: precursor, predicting rt
0:59:08.765070 INFO: calibration group: fragment, predicting mz
0:59:09.304020 INFO: === checking if optimization conditions were reached ===
0:59:09.304699 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:59:09.306620 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 119.9098 found after 6 searches.
0:59:09.306762 INFO: ==============================================
0:59:09.307034 PROGRESS: Optimization finished for rt_error.
0:59:10.087536 INFO: calibration group: precursor, predicting mz
0:59:10.145671 INFO: calibration group: precursor, predicting rt
0:59:10.430830 INFO: calibration group: fragment, predicting mz
0:59:10.952082 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:59:10.952370 PROGRESS: ==============================================
0:59:10.952480 PROGRESS: ms2_error      : 15.0000
0:59:10.952565 PROGRESS: ms1_error      : 10.0000
0:59:10.952640 PROGRESS: rt_error       : 119.9098
0:59:10.952726 PROGRESS: ==============================================
0:59:10.953736 INFO: calibration group: precursor, predicting mz
0:59:12.890142 INFO: calibration group: precursor, predicting rt
0:59:21.015791 INFO: calibration group: fragment, predicting mz
0:59:40.994518 PROGRESS: Extracting batch of 10183864 precursors
0:59:44.540708 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
0:59:44.540904 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:59:44.540974 INFO: FWHM in RT is 2.51 seconds, sigma is 0.32
0:59:44.541011 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:59:44.541566 INFO: Starting candidate selection
1:04:55.844163 INFO: Applying score cutoff of 47.57281446838379
1:04:56.483637 INFO: Removed 9041179 precursors with score below cutoff
1:04:59.825037 INFO: Starting candidate scoring
1:07:05.513930 INFO: Finished candidate processing
1:07:05.514314 INFO: Collecting candidate features
1:07:57.464251 WARNING: intensity_correlation has 41 NaNs ( 0.00 % out of 11277641)
1:07:58.034816 INFO: Collecting fragment features
1:08:25.681341 INFO: Finished candidate scoring
1:08:41.690555 INFO: === FDR correction performed with classifier version 16 ===
1:08:41.694656 INFO: performing precursor FDR with 47 features
1:08:41.694772 INFO: Decoy channel: -1
1:08:41.694821 INFO: Competetive: True
1:08:46.244979 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:49.499863 WARNING: dropped 23 target PSMs due to missing features
1:08:49.500089 WARNING: dropped 18 decoy PSMs due to missing features
1:14:28.379638 INFO: Test AUC: 0.576
1:14:28.380217 INFO: Train AUC: 0.580
1:14:28.380352 INFO: AUC difference: 0.79%
1:14:29.498719 INFO: Resetting torch num_threads to 100
1:14:30.139529 INFO: Removing fragments below FDR threshold
1:14:31.203380 PROGRESS: ============================= Precursor FDR =============================
1:14:31.204209 PROGRESS: Total precursors accumulated: 12,899
1:14:31.204454 PROGRESS: Target precursors: 12,772 (99.02%)
1:14:31.204670 PROGRESS: Decoy precursors: 127 (0.98%)
1:14:31.204884 PROGRESS: 
1:14:31.205093 PROGRESS: Precursor Summary:
1:14:31.214042 PROGRESS: Channel   0:	 0.05 FDR: 12,772; 0.01 FDR: 12,772; 0.001 FDR: 8,057
1:14:31.214656 PROGRESS: 
1:14:31.214893 PROGRESS: Protein Summary:
1:14:31.228274 PROGRESS: Channel   0:	 0.05 FDR: 5,367; 0.01 FDR: 5,367; 0.001 FDR: 3,810
1:14:31.228880 PROGRESS: =========================================================================
1:14:31.874073 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:14:32.610090 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:14:32.610694 INFO: Quantification results path: run_output_Astral/alphadia_1.10_noMBR/quant
1:14:32.610949 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2 at run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:14:32.612577 INFO: Initializing RawFileManager
1:15:26.371506 INFO: Determining DIA cycle
1:15:26.391246 INFO: Found cycle with start 0.00 min and length 303.
1:15:26.656271 INFO: RT (min)            : 0.0 - 26.9
1:15:26.656396 INFO: RT duration (sec)   : 1611.2
1:15:26.656439 INFO: RT duration (min)   : 26.9
1:15:26.656477 INFO: Cycle len (scans)   : 303
1:15:26.656508 INFO: Cycle len (sec)     : 1.65
1:15:26.656537 INFO: Number of cycles    : 978
1:15:26.656567 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:15:28.434138 INFO: Initializing CalibrationManager
1:15:28.434731 INFO: Loading calibration config
1:15:28.436632 INFO: Calibration config: [{'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}], 'name': 'fragment'}, {'estimators': [{'input_columns': ['mz_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mz', 'output_columns': ['mz_calibrated'], 'target_columns': ['mz_observed'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'input_columns': ['rt_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'name': 'rt', 'output_columns': ['rt_calibrated'], 'target_columns': ['rt_observed'], 'function': LOESSRegression()}, {'input_columns': ['mobility_library'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'name': 'mobility', 'output_columns': ['mobility_calibrated'], 'target_columns': ['mobility_observed'], 'function': LOESSRegression(n_kernels=2)}], 'name': 'precursor'}]
1:15:28.436781 INFO: Calibration group :fragment, found 1 estimator(s)
1:15:28.436913 INFO: Calibration group :precursor, found 3 estimator(s)
1:15:28.437043 INFO: Disabling ion mobility calibration
1:15:28.437083 INFO: removed mobility estimator from group precursor
1:15:28.437316 INFO: Initializing OptimizationManager
1:15:28.437503 INFO: initial parameter: ms1_error = 30
1:15:28.438962 INFO: initial parameter: ms2_error = 30
1:15:28.439050 INFO: initial parameter: rt_error = 805.6019897460938
1:15:28.439110 INFO: initial parameter: mobility_error = 0.1
1:15:28.439167 INFO: initial parameter: column_type = library
1:15:28.439220 INFO: initial parameter: num_candidates = 1
1:15:28.439277 INFO: initial parameter: classifier_version = -1
1:15:28.439334 INFO: initial parameter: fwhm_rt = 5
1:15:28.439394 INFO: initial parameter: fwhm_mobility = 0.01
1:15:28.439448 INFO: initial parameter: score_cutoff = 0
1:15:28.439545 INFO: Initializing TimingManager
1:15:28.439631 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:15:28.439797 INFO: FDRManager not loaded from disk.
1:15:28.439827 INFO: Initializing FDRManager
1:15:28.439881 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:15:30.692938 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
1:15:33.749424 PROGRESS: Starting initial search for precursors.
1:15:34.208591 INFO: Starting optimization step 0.
1:15:34.209172 PROGRESS: === Extracting elution groups 0 to 8000 ===
1:15:34.209455 PROGRESS: Extracting batch of 15798 precursors
1:15:34.218554 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:15:34.218759 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:15:34.218872 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:15:34.218964 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:15:34.219466 INFO: Starting candidate selection
1:15:35.983867 INFO: Starting candidate scoring
1:15:36.189784 INFO: Finished candidate processing
1:15:36.189932 INFO: Collecting candidate features
1:15:36.233040 INFO: Collecting fragment features
1:15:36.248628 INFO: Finished candidate scoring
1:15:36.257215 PROGRESS: === Extracted 15757 precursors and 155591 fragments ===
1:15:36.257627 INFO: performing precursor FDR with 47 features
1:15:36.257668 INFO: Decoy channel: -1
1:15:36.257693 INFO: Competetive: True
1:15:36.262871 INFO: Setting torch num_threads to 2 for FDR classification task
1:15:36.537216 INFO: Test AUC: 0.524
1:15:36.537388 INFO: Train AUC: 0.529
1:15:36.537427 INFO: AUC difference: 0.92%
1:15:36.628890 INFO: Resetting torch num_threads to 100
1:15:36.630784 INFO: === FDR correction performed with classifier version -1 ===
1:15:36.633396 PROGRESS: ============================= Precursor FDR =============================
1:15:36.633593 PROGRESS: Total precursors accumulated: 7,973
1:15:36.633671 PROGRESS: Target precursors: 4,305 (53.99%)
1:15:36.633746 PROGRESS: Decoy precursors: 3,668 (46.01%)
1:15:36.633826 PROGRESS: 
1:15:36.633897 PROGRESS: Precursor Summary:
1:15:36.634979 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:15:36.635103 PROGRESS: 
1:15:36.635188 PROGRESS: Protein Summary:
1:15:36.636275 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:15:36.636381 PROGRESS: =========================================================================
1:15:36.757840 INFO: Starting optimization step 1.
1:15:36.758191 PROGRESS: === Extracting elution groups 8000 to 24000 ===
1:15:36.758288 PROGRESS: Extracting batch of 31672 precursors
1:15:36.767740 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:15:36.767879 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:15:36.767925 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:15:36.767954 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:15:36.768216 INFO: Starting candidate selection
1:15:39.241097 INFO: Starting candidate scoring
1:15:39.537811 INFO: Finished candidate processing
1:15:39.537941 INFO: Collecting candidate features
1:15:39.640091 INFO: Collecting fragment features
1:15:39.673862 INFO: Finished candidate scoring
1:15:39.714975 PROGRESS: === Extracted 47355 precursors and 467062 fragments ===
1:15:39.723765 INFO: performing precursor FDR with 47 features
1:15:39.723895 INFO: Decoy channel: -1
1:15:39.723933 INFO: Competetive: True
1:15:39.765194 INFO: Setting torch num_threads to 2 for FDR classification task
1:15:40.803075 INFO: Test AUC: 0.545
1:15:40.803231 INFO: Train AUC: 0.560
1:15:40.803270 INFO: AUC difference: 2.69%
1:15:40.937822 INFO: Resetting torch num_threads to 100
1:15:40.966279 INFO: === FDR correction performed with classifier version -1 ===
1:15:40.967691 PROGRESS: ============================= Precursor FDR =============================
1:15:40.967869 PROGRESS: Total precursors accumulated: 2
1:15:40.967960 PROGRESS: Target precursors: 2 (100.00%)
1:15:40.968039 PROGRESS: Decoy precursors: 0 (0.00%)
1:15:40.968107 PROGRESS: 
1:15:40.968170 PROGRESS: Precursor Summary:
1:15:40.969683 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:15:40.969810 PROGRESS: 
1:15:40.969886 PROGRESS: Protein Summary:
1:15:40.971438 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:15:40.971558 PROGRESS: =========================================================================
1:15:41.259572 INFO: Starting optimization step 2.
1:15:41.259922 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1:15:41.260013 PROGRESS: Extracting batch of 63174 precursors
1:15:41.311238 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:15:41.311407 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:15:41.311458 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:15:41.311489 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:15:41.311806 INFO: Starting candidate selection
1:15:45.609255 INFO: Starting candidate scoring
1:15:46.364179 INFO: Finished candidate processing
1:15:46.364320 INFO: Collecting candidate features
1:15:46.592623 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 63026)
1:15:46.601062 INFO: Collecting fragment features
1:15:46.673033 INFO: Finished candidate scoring
1:15:46.799263 PROGRESS: === Extracted 110381 precursors and 1088001 fragments ===
1:15:46.817383 INFO: performing precursor FDR with 47 features
1:15:46.817559 INFO: Decoy channel: -1
1:15:46.817596 INFO: Competetive: True
1:15:46.919680 INFO: Setting torch num_threads to 2 for FDR classification task
1:15:46.955858 WARNING: dropped 1 decoy PSMs due to missing features
1:15:49.224796 INFO: Test AUC: 0.549
1:15:49.225053 INFO: Train AUC: 0.580
1:15:49.225133 INFO: AUC difference: 5.29%
1:15:49.225202 WARNING: AUC difference > 5%. This may indicate overfitting.
1:15:49.328889 INFO: Resetting torch num_threads to 100
1:15:49.337649 INFO: === FDR correction performed with classifier version -1 ===
1:15:49.338784 PROGRESS: ============================= Precursor FDR =============================
1:15:49.339000 PROGRESS: Total precursors accumulated: 3
1:15:49.339167 PROGRESS: Target precursors: 3 (100.00%)
1:15:49.339323 PROGRESS: Decoy precursors: 0 (0.00%)
1:15:49.339475 PROGRESS: 
1:15:49.339623 PROGRESS: Precursor Summary:
1:15:49.340763 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1:15:49.340968 PROGRESS: 
1:15:49.341131 PROGRESS: Protein Summary:
1:15:49.342360 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1:15:49.342582 PROGRESS: =========================================================================
1:15:49.673765 INFO: Starting optimization step 3.
1:15:49.674257 PROGRESS: === Extracting elution groups 56000 to 120000 ===
1:15:49.674495 PROGRESS: Extracting batch of 126509 precursors
1:15:49.712877 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:15:49.713030 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:15:49.713086 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:15:49.713119 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:15:49.713484 INFO: Starting candidate selection
1:15:57.843240 INFO: Starting candidate scoring
1:15:58.723565 INFO: Finished candidate processing
1:15:58.723701 INFO: Collecting candidate features
1:15:59.042516 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 126143)
1:15:59.054030 INFO: Collecting fragment features
1:15:59.151453 INFO: Finished candidate scoring
1:15:59.323668 PROGRESS: === Extracted 236524 precursors and 2330696 fragments ===
1:15:59.354636 INFO: performing precursor FDR with 47 features
1:15:59.354772 INFO: Decoy channel: -1
1:15:59.354802 INFO: Competetive: True
1:15:59.481913 INFO: Setting torch num_threads to 2 for FDR classification task
1:15:59.527666 WARNING: dropped 2 decoy PSMs due to missing features
1:16:04.465406 INFO: Test AUC: 0.557
1:16:04.465560 INFO: Train AUC: 0.586
1:16:04.465611 INFO: AUC difference: 5.00%
1:16:04.591809 INFO: Resetting torch num_threads to 100
1:16:04.620384 INFO: === FDR correction performed with classifier version -1 ===
1:16:04.621681 PROGRESS: ============================= Precursor FDR =============================
1:16:04.621862 PROGRESS: Total precursors accumulated: 8
1:16:04.621952 PROGRESS: Target precursors: 8 (100.00%)
1:16:04.622022 PROGRESS: Decoy precursors: 0 (0.00%)
1:16:04.622085 PROGRESS: 
1:16:04.622145 PROGRESS: Precursor Summary:
1:16:04.623329 PROGRESS: Channel   0:	 0.05 FDR:     8; 0.01 FDR:     8; 0.001 FDR:     8
1:16:04.623447 PROGRESS: 
1:16:04.623523 PROGRESS: Protein Summary:
1:16:04.624692 PROGRESS: Channel   0:	 0.05 FDR:     8; 0.01 FDR:     8; 0.001 FDR:     8
1:16:04.624800 PROGRESS: =========================================================================
1:16:05.121016 INFO: Starting optimization step 4.
1:16:05.121359 PROGRESS: === Extracting elution groups 120000 to 248000 ===
1:16:05.121495 PROGRESS: Extracting batch of 252969 precursors
1:16:05.190725 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:16:05.190881 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:16:05.190954 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:16:05.190986 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:16:05.191351 INFO: Starting candidate selection
1:16:25.151349 INFO: Starting candidate scoring
1:16:26.837934 INFO: Finished candidate processing
1:16:26.838154 INFO: Collecting candidate features
1:16:27.606731 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 252319)
1:16:27.619017 INFO: Collecting fragment features
1:16:27.804100 INFO: Finished candidate scoring
1:16:28.160901 PROGRESS: === Extracted 488843 precursors and 4811908 fragments ===
1:16:28.230253 INFO: performing precursor FDR with 47 features
1:16:28.230428 INFO: Decoy channel: -1
1:16:28.230455 INFO: Competetive: True
1:16:28.601918 INFO: Setting torch num_threads to 2 for FDR classification task
1:16:28.755194 WARNING: dropped 3 decoy PSMs due to missing features
1:16:41.582491 INFO: Test AUC: 0.559
1:16:41.582701 INFO: Train AUC: 0.588
1:16:41.582748 INFO: AUC difference: 4.88%
1:16:41.768176 INFO: Resetting torch num_threads to 100
1:16:41.846679 INFO: === FDR correction performed with classifier version -1 ===
1:16:41.848070 PROGRESS: ============================= Precursor FDR =============================
1:16:41.848249 PROGRESS: Total precursors accumulated: 4
1:16:41.848336 PROGRESS: Target precursors: 4 (100.00%)
1:16:41.848405 PROGRESS: Decoy precursors: 0 (0.00%)
1:16:41.848469 PROGRESS: 
1:16:41.848530 PROGRESS: Precursor Summary:
1:16:41.849972 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
1:16:41.850092 PROGRESS: 
1:16:41.850166 PROGRESS: Protein Summary:
1:16:41.851641 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
1:16:41.851761 PROGRESS: =========================================================================
1:16:42.983536 INFO: Starting optimization step 5.
1:16:42.984112 PROGRESS: === Extracting elution groups 248000 to 504000 ===
1:16:42.984224 PROGRESS: Extracting batch of 505926 precursors
1:16:43.179523 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:16:43.179689 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:16:43.179746 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:16:43.179777 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:16:43.180278 INFO: Starting candidate selection
1:17:15.202899 INFO: Starting candidate scoring
1:17:19.860648 INFO: Finished candidate processing
1:17:19.860949 INFO: Collecting candidate features
1:17:21.315859 WARNING: intensity_correlation has 9 NaNs ( 0.00 % out of 504644)
1:17:21.335165 INFO: Collecting fragment features
1:17:21.715002 INFO: Finished candidate scoring
1:17:22.567662 PROGRESS: === Extracted 993487 precursors and 9777687 fragments ===
1:17:22.706024 INFO: performing precursor FDR with 47 features
1:17:22.706182 INFO: Decoy channel: -1
1:17:22.706215 INFO: Competetive: True
1:17:23.255532 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:23.535125 WARNING: dropped 6 target PSMs due to missing features
1:17:23.535327 WARNING: dropped 6 decoy PSMs due to missing features
1:17:48.724892 INFO: Test AUC: 0.569
1:17:48.725134 INFO: Train AUC: 0.583
1:17:48.725170 INFO: AUC difference: 2.32%
1:17:48.907956 INFO: Resetting torch num_threads to 100
1:17:49.030042 INFO: === FDR correction performed with classifier version -1 ===
1:17:49.031862 PROGRESS: ============================= Precursor FDR =============================
1:17:49.032257 PROGRESS: Total precursors accumulated: 7
1:17:49.032547 PROGRESS: Target precursors: 7 (100.00%)
1:17:49.032843 PROGRESS: Decoy precursors: 0 (0.00%)
1:17:49.033108 PROGRESS: 
1:17:49.033368 PROGRESS: Precursor Summary:
1:17:49.035156 PROGRESS: Channel   0:	 0.05 FDR:     7; 0.01 FDR:     7; 0.001 FDR:     7
1:17:49.035533 PROGRESS: 
1:17:49.035891 PROGRESS: Protein Summary:
1:17:49.037537 PROGRESS: Channel   0:	 0.05 FDR:     7; 0.01 FDR:     7; 0.001 FDR:     7
1:17:49.037903 PROGRESS: =========================================================================
1:17:50.656065 INFO: Starting optimization step 6.
1:17:50.656629 PROGRESS: === Extracting elution groups 504000 to 1016000 ===
1:17:50.656863 PROGRESS: Extracting batch of 1011981 precursors
1:17:51.031193 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:17:51.031501 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:17:51.031639 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:17:51.031739 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:17:51.032212 INFO: Starting candidate selection
1:18:50.398580 INFO: Starting candidate scoring
1:18:58.916488 INFO: Finished candidate processing
1:18:58.916636 INFO: Collecting candidate features
1:19:02.405422 WARNING: intensity_correlation has 9 NaNs ( 0.00 % out of 1009421)
1:19:02.463189 INFO: Collecting fragment features
1:19:03.557785 INFO: Finished candidate scoring
1:19:05.638016 PROGRESS: === Extracted 2002908 precursors and 19715832 fragments ===
1:19:05.917851 INFO: performing precursor FDR with 47 features
1:19:05.917994 INFO: Decoy channel: -1
1:19:05.918033 INFO: Competetive: True
1:19:07.135997 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:07.842720 WARNING: dropped 13 target PSMs due to missing features
1:19:07.842919 WARNING: dropped 8 decoy PSMs due to missing features
1:19:54.160156 INFO: Test AUC: 0.571
1:19:54.160409 INFO: Train AUC: 0.580
1:19:54.160454 INFO: AUC difference: 1.48%
1:19:54.505383 INFO: Resetting torch num_threads to 100
1:19:54.952962 INFO: === FDR correction performed with classifier version -1 ===
1:19:54.955111 PROGRESS: ============================= Precursor FDR =============================
1:19:54.955509 PROGRESS: Total precursors accumulated: 863
1:19:54.955792 PROGRESS: Target precursors: 792 (91.77%)
1:19:54.956046 PROGRESS: Decoy precursors: 71 (8.23%)
1:19:54.956286 PROGRESS: 
1:19:54.956526 PROGRESS: Precursor Summary:
1:19:54.958846 PROGRESS: Channel   0:	 0.05 FDR:   564; 0.01 FDR:   202; 0.001 FDR:    69
1:19:54.959147 PROGRESS: 
1:19:54.959383 PROGRESS: Protein Summary:
1:19:54.961715 PROGRESS: Channel   0:	 0.05 FDR:   507; 0.01 FDR:   189; 0.001 FDR:    69
1:19:54.962028 PROGRESS: =========================================================================
1:19:55.256178 INFO: fragments_df_filtered: 1983
1:19:58.121613 INFO: calibration group: precursor, fitting mz estimator 
1:19:58.373746 INFO: calibration group: precursor, fitting rt estimator 
1:19:58.607566 INFO: calibration group: fragment, fitting mz estimator 
1:19:58.877455 INFO: calibration group: precursor, predicting mz
1:19:59.382714 INFO: calibration group: precursor, predicting rt
1:20:01.084330 INFO: calibration group: fragment, predicting mz
1:20:04.984086 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:20:04.984406 INFO: Starting optimization step 7.
1:20:04.984826 PROGRESS: === Extracting elution groups 0 to 1016000 ===
1:20:04.984909 PROGRESS: Extracting batch of 2008029 precursors
1:20:05.532413 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:20:05.532570 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:20:05.532610 INFO: FWHM in RT is 3.06 seconds, sigma is 0.39
1:20:05.532635 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:20:05.532973 INFO: Starting candidate selection
1:21:32.633747 INFO: Starting candidate scoring
1:22:04.726907 INFO: Finished candidate processing
1:22:04.727245 INFO: Collecting candidate features
1:22:13.885526 WARNING: intensity_correlation has 23809 NaNs ( 0.77 % out of 3082795)
1:22:13.890234 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 3082795)
1:22:14.056488 INFO: Collecting fragment features
1:22:17.332805 INFO: Finished candidate scoring
1:22:23.029333 PROGRESS: === Extracted 3082795 precursors and 24577727 fragments ===
1:22:23.030071 INFO: performing precursor FDR with 47 features
1:22:23.030149 INFO: Decoy channel: -1
1:22:23.030184 INFO: Competetive: True
1:22:24.583560 INFO: Setting torch num_threads to 2 for FDR classification task
1:22:25.486828 WARNING: dropped 12170 target PSMs due to missing features
1:22:25.487019 WARNING: dropped 11639 decoy PSMs due to missing features
1:23:41.145783 INFO: Test AUC: 0.571
1:23:41.147412 INFO: Train AUC: 0.576
1:23:41.147473 INFO: AUC difference: 0.82%
1:23:41.610817 INFO: Resetting torch num_threads to 100
1:23:41.744802 INFO: === FDR correction performed with classifier version 6 ===
1:23:41.746970 PROGRESS: ============================= Precursor FDR =============================
1:23:41.747196 PROGRESS: Total precursors accumulated: 1,755
1:23:41.747290 PROGRESS: Target precursors: 1,603 (91.34%)
1:23:41.747363 PROGRESS: Decoy precursors: 152 (8.66%)
1:23:41.747445 PROGRESS: 
1:23:41.747511 PROGRESS: Precursor Summary:
1:23:41.749777 PROGRESS: Channel   0:	 0.05 FDR: 1,241; 0.01 FDR:   801; 0.001 FDR:   353
1:23:41.749950 PROGRESS: 
1:23:41.750026 PROGRESS: Protein Summary:
1:23:41.752442 PROGRESS: Channel   0:	 0.05 FDR: 1,027; 0.01 FDR:   681; 0.001 FDR:   322
1:23:41.752589 PROGRESS: =========================================================================
1:23:41.895304 INFO: fragments_df_filtered: 5000
1:23:43.679783 INFO: calibration group: precursor, fitting mz estimator 
1:23:44.183345 INFO: calibration group: precursor, fitting rt estimator 
1:23:44.761049 INFO: calibration group: fragment, fitting mz estimator 
1:23:45.697695 INFO: calibration group: precursor, predicting mz
1:23:46.254922 INFO: calibration group: precursor, predicting rt
1:23:47.395352 INFO: calibration group: fragment, predicting mz
1:23:49.433958 INFO: === checking if optimization conditions were reached ===
1:23:49.438144 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1:23:49.439825 PROGRESS: ❌ ms1_error      : 13.6245 > 10.0000 or insufficient steps taken.
1:23:49.439955 INFO: ==============================================
1:23:49.440247 INFO: Starting optimization step 8.
1:23:49.440495 PROGRESS: === Extracting elution groups 0 to 504000 ===
1:23:49.440754 PROGRESS: Extracting batch of 996048 precursors
1:23:50.092459 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:23:50.092936 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:23:50.093059 INFO: FWHM in RT is 2.82 seconds, sigma is 0.36
1:23:50.093151 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:23:50.093646 INFO: Starting candidate selection
1:24:52.165624 INFO: Starting candidate scoring
1:25:04.566705 INFO: Finished candidate processing
1:25:04.566915 INFO: Collecting candidate features
1:25:10.291892 WARNING: intensity_correlation has 408 NaNs ( 0.02 % out of 1952006)
1:25:10.295057 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 1952006)
1:25:10.405761 INFO: Collecting fragment features
1:25:12.325781 INFO: Finished candidate scoring
1:25:15.196309 PROGRESS: === Extracted 1952006 precursors and 15976274 fragments ===
1:25:15.201005 INFO: performing precursor FDR with 47 features
1:25:15.201085 INFO: Decoy channel: -1
1:25:15.201120 INFO: Competetive: True
1:25:16.120688 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:16.728494 WARNING: dropped 217 target PSMs due to missing features
1:25:16.728683 WARNING: dropped 191 decoy PSMs due to missing features
1:26:08.464434 INFO: Test AUC: 0.572
1:26:08.465659 INFO: Train AUC: 0.580
1:26:08.465707 INFO: AUC difference: 1.36%
1:26:08.717471 INFO: Resetting torch num_threads to 100
1:26:08.802537 INFO: === FDR correction performed with classifier version 7 ===
1:26:08.804923 PROGRESS: ============================= Precursor FDR =============================
1:26:08.805148 PROGRESS: Total precursors accumulated: 1,743
1:26:08.805258 PROGRESS: Target precursors: 1,592 (91.34%)
1:26:08.805348 PROGRESS: Decoy precursors: 151 (8.66%)
1:26:08.805426 PROGRESS: 
1:26:08.805505 PROGRESS: Precursor Summary:
1:26:08.807759 PROGRESS: Channel   0:	 0.05 FDR: 1,165; 0.01 FDR:   815; 0.001 FDR:   532
1:26:08.807893 PROGRESS: 
1:26:08.807976 PROGRESS: Protein Summary:
1:26:08.810212 PROGRESS: Channel   0:	 0.05 FDR: 1,014; 0.01 FDR:   715; 0.001 FDR:   478
1:26:08.810347 PROGRESS: =========================================================================
1:26:08.905243 INFO: fragments_df_filtered: 5000
1:26:10.099167 INFO: calibration group: precursor, fitting mz estimator 
1:26:10.314570 INFO: calibration group: precursor, fitting rt estimator 
1:26:10.516036 INFO: calibration group: fragment, fitting mz estimator 
1:26:11.306337 INFO: calibration group: precursor, predicting mz
1:26:11.405481 INFO: calibration group: precursor, predicting rt
1:26:11.823996 INFO: calibration group: fragment, predicting mz
1:26:12.827119 INFO: === checking if optimization conditions were reached ===
1:26:12.830473 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1:26:12.831943 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
1:26:12.832076 INFO: ==============================================
1:26:12.832387 PROGRESS: Optimization finished for ms2_error, ms1_error.
1:26:13.864999 INFO: calibration group: precursor, predicting mz
1:26:14.003855 INFO: calibration group: precursor, predicting rt
1:26:14.431814 INFO: calibration group: fragment, predicting mz
1:26:15.356366 INFO: Starting optimization step 0.
1:26:15.356738 PROGRESS: === Extracting elution groups 0 to 248000 ===
1:26:15.356851 PROGRESS: Extracting batch of 490122 precursors
1:26:15.552552 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:26:15.552733 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:26:15.552783 INFO: FWHM in RT is 2.66 seconds, sigma is 0.34
1:26:15.552813 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:26:15.553247 INFO: Starting candidate selection
1:26:46.857809 INFO: Starting candidate scoring
1:26:52.726110 INFO: Finished candidate processing
1:26:52.726428 INFO: Collecting candidate features
1:26:55.345863 WARNING: intensity_correlation has 11 NaNs ( 0.00 % out of 977327)
1:26:55.383484 INFO: Collecting fragment features
1:26:56.071270 INFO: Finished candidate scoring
1:26:57.100077 PROGRESS: === Extracted 977327 precursors and 8365993 fragments ===
1:26:57.100749 INFO: performing precursor FDR with 47 features
1:26:57.100825 INFO: Decoy channel: -1
1:26:57.100856 INFO: Competetive: True
1:26:57.588493 INFO: Setting torch num_threads to 2 for FDR classification task
1:26:57.917344 WARNING: dropped 7 target PSMs due to missing features
1:26:57.917576 WARNING: dropped 4 decoy PSMs due to missing features
1:27:21.209840 INFO: Test AUC: 0.573
1:27:21.210075 INFO: Train AUC: 0.585
1:27:21.210112 INFO: AUC difference: 2.10%
1:27:21.380289 INFO: Resetting torch num_threads to 100
1:27:21.412990 INFO: === FDR correction performed with classifier version 8 ===
1:27:21.414207 PROGRESS: ============================= Precursor FDR =============================
1:27:21.414379 PROGRESS: Total precursors accumulated: 921
1:27:21.414453 PROGRESS: Target precursors: 854 (92.73%)
1:27:21.414508 PROGRESS: Decoy precursors: 67 (7.27%)
1:27:21.414557 PROGRESS: 
1:27:21.414603 PROGRESS: Precursor Summary:
1:27:21.416048 PROGRESS: Channel   0:	 0.05 FDR:   763; 0.01 FDR:   536; 0.001 FDR:   366
1:27:21.416167 PROGRESS: 
1:27:21.416225 PROGRESS: Protein Summary:
1:27:21.417710 PROGRESS: Channel   0:	 0.05 FDR:   717; 0.01 FDR:   497; 0.001 FDR:   343
1:27:21.417820 PROGRESS: =========================================================================
1:27:21.458509 INFO: fragments_df_filtered: 5000
1:27:21.975970 INFO: calibration group: precursor, fitting mz estimator 
1:27:22.061124 INFO: calibration group: precursor, fitting rt estimator 
1:27:22.145191 INFO: calibration group: fragment, fitting mz estimator 
1:27:22.922087 INFO: calibration group: precursor, predicting mz
1:27:23.184749 INFO: calibration group: precursor, predicting rt
1:27:23.530238 INFO: calibration group: fragment, predicting mz
1:27:24.106551 INFO: === checking if optimization conditions were reached ===
1:27:24.107193 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:27:24.110134 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 449.1144.
1:27:24.110304 INFO: ==============================================
1:27:24.110625 INFO: Starting optimization step 1.
1:27:24.110902 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:27:24.111173 PROGRESS: Extracting batch of 237153 precursors
1:27:24.213162 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:27:24.213463 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:27:24.213600 INFO: FWHM in RT is 2.68 seconds, sigma is 0.34
1:27:24.213701 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:27:24.214163 INFO: Starting candidate selection
1:27:37.267484 INFO: Starting candidate scoring
1:27:40.160900 INFO: Finished candidate processing
1:27:40.160993 INFO: Collecting candidate features
1:27:41.022253 WARNING: intensity_correlation has 5 NaNs ( 0.00 % out of 472904)
1:27:41.040631 INFO: Collecting fragment features
1:27:41.326376 INFO: Finished candidate scoring
1:27:41.757975 PROGRESS: === Extracted 472904 precursors and 4060401 fragments ===
1:27:41.758427 INFO: performing precursor FDR with 47 features
1:27:41.758473 INFO: Decoy channel: -1
1:27:41.758499 INFO: Competetive: True
1:27:41.968652 INFO: Setting torch num_threads to 2 for FDR classification task
1:27:42.114665 WARNING: dropped 2 target PSMs due to missing features
1:27:42.114822 WARNING: dropped 3 decoy PSMs due to missing features
1:27:59.325214 INFO: Test AUC: 0.574
1:27:59.325479 INFO: Train AUC: 0.588
1:27:59.325522 INFO: AUC difference: 2.52%
1:27:59.500671 INFO: Resetting torch num_threads to 100
1:27:59.527451 INFO: === FDR correction performed with classifier version 8 ===
1:27:59.528877 PROGRESS: ============================= Precursor FDR =============================
1:27:59.529078 PROGRESS: Total precursors accumulated: 545
1:27:59.529163 PROGRESS: Target precursors: 503 (92.29%)
1:27:59.529229 PROGRESS: Decoy precursors: 42 (7.71%)
1:27:59.529288 PROGRESS: 
1:27:59.529345 PROGRESS: Precursor Summary:
1:27:59.530977 PROGRESS: Channel   0:	 0.05 FDR:   425; 0.01 FDR:   311; 0.001 FDR:   253
1:27:59.531136 PROGRESS: 
1:27:59.531212 PROGRESS: Protein Summary:
1:27:59.532952 PROGRESS: Channel   0:	 0.05 FDR:   408; 0.01 FDR:   297; 0.001 FDR:   242
1:27:59.533098 PROGRESS: =========================================================================
1:27:59.567159 INFO: fragments_df_filtered: 2938
1:28:00.204471 INFO: calibration group: precursor, fitting mz estimator 
1:28:00.661188 INFO: calibration group: precursor, fitting rt estimator 
1:28:00.847389 INFO: calibration group: fragment, fitting mz estimator 
1:28:01.240954 INFO: calibration group: precursor, predicting mz
1:28:01.313340 INFO: calibration group: precursor, predicting rt
1:28:01.511210 INFO: calibration group: fragment, predicting mz
1:28:02.116461 INFO: === checking if optimization conditions were reached ===
1:28:02.116844 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:28:02.119401 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 403.9399.
1:28:02.119473 INFO: ==============================================
1:28:02.119589 INFO: Starting optimization step 2.
1:28:02.119669 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:28:02.119759 PROGRESS: Extracting batch of 237153 precursors
1:28:02.189197 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:28:02.189358 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:28:02.189406 INFO: FWHM in RT is 2.56 seconds, sigma is 0.33
1:28:02.189430 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:28:02.189773 INFO: Starting candidate selection
1:28:12.902064 INFO: Starting candidate scoring
1:28:15.895999 INFO: Finished candidate processing
1:28:15.896133 INFO: Collecting candidate features
1:28:16.978404 WARNING: intensity_correlation has 9 NaNs ( 0.00 % out of 472898)
1:28:17.000157 INFO: Collecting fragment features
1:28:17.343403 INFO: Finished candidate scoring
1:28:18.030578 PROGRESS: === Extracted 472898 precursors and 4051663 fragments ===
1:28:18.031228 INFO: performing precursor FDR with 47 features
1:28:18.031281 INFO: Decoy channel: -1
1:28:18.031312 INFO: Competetive: True
1:28:18.312124 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:18.432244 WARNING: dropped 5 target PSMs due to missing features
1:28:18.432410 WARNING: dropped 4 decoy PSMs due to missing features
1:28:29.406810 INFO: Test AUC: 0.572
1:28:29.407110 INFO: Train AUC: 0.589
1:28:29.407164 INFO: AUC difference: 2.82%
1:28:30.882915 INFO: Resetting torch num_threads to 100
1:28:30.970609 INFO: === FDR correction performed with classifier version 8 ===
1:28:30.972047 PROGRESS: ============================= Precursor FDR =============================
1:28:30.972260 PROGRESS: Total precursors accumulated: 578
1:28:30.972347 PROGRESS: Target precursors: 527 (91.18%)
1:28:30.972415 PROGRESS: Decoy precursors: 51 (8.82%)
1:28:30.972477 PROGRESS: 
1:28:30.972536 PROGRESS: Precursor Summary:
1:28:30.974165 PROGRESS: Channel   0:	 0.05 FDR:   365; 0.01 FDR:   257; 0.001 FDR:   252
1:28:30.974315 PROGRESS: 
1:28:30.974410 PROGRESS: Protein Summary:
1:28:30.976208 PROGRESS: Channel   0:	 0.05 FDR:   354; 0.01 FDR:   247; 0.001 FDR:   243
1:28:30.976339 PROGRESS: =========================================================================
1:28:31.005930 INFO: fragments_df_filtered: 2594
1:28:31.744750 INFO: calibration group: precursor, fitting mz estimator 
1:28:31.955709 INFO: calibration group: precursor, fitting rt estimator 
1:28:32.150904 INFO: calibration group: fragment, fitting mz estimator 
1:28:32.548996 INFO: calibration group: precursor, predicting mz
1:28:32.632186 INFO: calibration group: precursor, predicting rt
1:28:32.925906 INFO: calibration group: fragment, predicting mz
1:28:33.442506 INFO: === checking if optimization conditions were reached ===
1:28:33.443063 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:28:33.446845 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 385.6580.
1:28:33.446925 INFO: ==============================================
1:28:33.447057 INFO: Starting optimization step 3.
1:28:33.447148 PROGRESS: === Extracting elution groups 0 to 120000 ===
1:28:33.447258 PROGRESS: Extracting batch of 237153 precursors
1:28:33.632343 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:28:33.632526 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:28:33.632578 INFO: FWHM in RT is 2.42 seconds, sigma is 0.31
1:28:33.632608 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:28:33.633105 INFO: Starting candidate selection
1:28:44.906706 INFO: Starting candidate scoring
1:28:48.330694 INFO: Finished candidate processing
1:28:48.330845 INFO: Collecting candidate features
1:28:49.865778 WARNING: intensity_correlation has 9 NaNs ( 0.00 % out of 472687)
1:28:49.896244 INFO: Collecting fragment features
1:28:50.307992 INFO: Finished candidate scoring
1:28:50.764681 PROGRESS: === Extracted 472687 precursors and 4018585 fragments ===
1:28:50.765295 INFO: performing precursor FDR with 47 features
1:28:50.765347 INFO: Decoy channel: -1
1:28:50.765381 INFO: Competetive: True
1:28:51.013004 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:51.171381 WARNING: dropped 6 target PSMs due to missing features
1:28:51.171568 WARNING: dropped 3 decoy PSMs due to missing features
1:29:02.845849 INFO: Test AUC: 0.569
1:29:02.846168 INFO: Train AUC: 0.589
1:29:02.846269 INFO: AUC difference: 3.42%
1:29:03.115425 INFO: Resetting torch num_threads to 100
1:29:03.139832 INFO: === FDR correction performed with classifier version 8 ===
1:29:03.141342 PROGRESS: ============================= Precursor FDR =============================
1:29:03.141677 PROGRESS: Total precursors accumulated: 543
1:29:03.141892 PROGRESS: Target precursors: 496 (91.34%)
1:29:03.142090 PROGRESS: Decoy precursors: 47 (8.66%)
1:29:03.142279 PROGRESS: 
1:29:03.142492 PROGRESS: Precursor Summary:
1:29:03.144219 PROGRESS: Channel   0:	 0.05 FDR:   376; 0.01 FDR:   297; 0.001 FDR:   278
1:29:03.144512 PROGRESS: 
1:29:03.144715 PROGRESS: Protein Summary:
1:29:03.146555 PROGRESS: Channel   0:	 0.05 FDR:   365; 0.01 FDR:   286; 0.001 FDR:   267
1:29:03.146844 PROGRESS: =========================================================================
1:29:03.184455 INFO: fragments_df_filtered: 2812
1:29:03.870115 INFO: calibration group: precursor, fitting mz estimator 
1:29:04.718105 INFO: calibration group: precursor, fitting rt estimator 
1:29:05.469050 INFO: calibration group: fragment, fitting mz estimator 
1:29:06.665511 INFO: calibration group: precursor, predicting mz
1:29:06.935650 INFO: calibration group: precursor, predicting rt
1:29:07.297503 INFO: calibration group: fragment, predicting mz
1:29:08.058088 INFO: === checking if optimization conditions were reached ===
1:29:08.058593 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:29:08.060287 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 385.6580 found after 4 searches.
1:29:08.060347 INFO: ==============================================
1:29:08.060473 PROGRESS: Optimization finished for rt_error.
1:29:08.501922 INFO: calibration group: precursor, predicting mz
1:29:08.545591 INFO: calibration group: precursor, predicting rt
1:29:08.771910 INFO: calibration group: fragment, predicting mz
1:29:09.719458 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:29:09.719907 PROGRESS: ==============================================
1:29:09.720163 PROGRESS: ms2_error      : 15.0000
1:29:09.720364 PROGRESS: ms1_error      : 10.0000
1:29:09.720554 PROGRESS: rt_error       : 385.6580
1:29:09.720733 PROGRESS: ==============================================
1:29:09.722205 INFO: calibration group: precursor, predicting mz
1:29:11.702118 INFO: calibration group: precursor, predicting rt
1:29:19.142135 INFO: calibration group: fragment, predicting mz
1:29:39.277497 PROGRESS: Extracting batch of 10183864 precursors
1:29:42.706706 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:29:42.706926 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:42.707001 INFO: FWHM in RT is 2.66 seconds, sigma is 0.34
1:29:42.707043 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:29:42.707592 INFO: Starting candidate selection
1:36:03.023236 INFO: Applying score cutoff of 49.152306793212894
1:36:03.843275 INFO: Removed 5572120 precursors with score below cutoff
1:36:07.138107 INFO: Starting candidate scoring
1:38:13.250582 INFO: Finished candidate processing
1:38:13.250892 INFO: Collecting candidate features
1:39:15.817368 WARNING: intensity_correlation has 22 NaNs ( 0.00 % out of 14746937)
1:39:16.867386 INFO: Collecting fragment features
1:40:05.074296 INFO: Finished candidate scoring
1:40:23.547287 INFO: === FDR correction performed with classifier version 12 ===
1:40:23.555871 INFO: performing precursor FDR with 47 features
1:40:23.555961 INFO: Decoy channel: -1
1:40:23.556000 INFO: Competetive: True
1:40:28.682256 INFO: Setting torch num_threads to 2 for FDR classification task
1:40:31.378683 WARNING: dropped 9 target PSMs due to missing features
1:40:31.378838 WARNING: dropped 13 decoy PSMs due to missing features
1:47:23.511955 INFO: Test AUC: 0.556
1:47:23.512253 INFO: Train AUC: 0.579
1:47:23.512330 INFO: AUC difference: 3.92%
1:47:24.963506 INFO: Resetting torch num_threads to 100
1:47:25.388282 INFO: Removing fragments below FDR threshold
1:47:27.292783 PROGRESS: ============================= Precursor FDR =============================
1:47:27.293392 PROGRESS: Total precursors accumulated: 10,938
1:47:27.293499 PROGRESS: Target precursors: 10,830 (99.01%)
1:47:27.293582 PROGRESS: Decoy precursors: 108 (0.99%)
1:47:27.293667 PROGRESS: 
1:47:27.293746 PROGRESS: Precursor Summary:
1:47:27.302271 PROGRESS: Channel   0:	 0.05 FDR: 10,830; 0.01 FDR: 10,830; 0.001 FDR: 7,772
1:47:27.302577 PROGRESS: 
1:47:27.302670 PROGRESS: Protein Summary:
1:47:27.314582 PROGRESS: Channel   0:	 0.05 FDR: 4,989; 0.01 FDR: 4,989; 0.001 FDR: 3,770
1:47:27.314869 PROGRESS: =========================================================================
1:47:28.054647 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:47:28.957174 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:47:28.957512 INFO: Quantification results path: run_output_Astral/alphadia_1.10_noMBR/quant
1:47:28.957694 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3 at run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:47:28.959026 INFO: Initializing RawFileManager
1:48:24.792424 INFO: Determining DIA cycle
1:48:24.811194 INFO: Found cycle with start 0.00 min and length 303.
1:48:25.186442 INFO: RT (min)            : 0.0 - 26.9
1:48:25.186574 INFO: RT duration (sec)   : 1611.2
1:48:25.186611 INFO: RT duration (min)   : 26.9
1:48:25.186643 INFO: Cycle len (scans)   : 303
1:48:25.186670 INFO: Cycle len (sec)     : 1.65
1:48:25.186699 INFO: Number of cycles    : 977
1:48:25.186726 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:48:27.494099 INFO: Initializing CalibrationManager
1:48:27.494507 INFO: Loading calibration config
1:48:27.495268 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'}]
1:48:27.495471 INFO: Calibration group :fragment, found 1 estimator(s)
1:48:27.495615 INFO: Calibration group :precursor, found 3 estimator(s)
1:48:27.495807 INFO: Disabling ion mobility calibration
1:48:27.495844 INFO: removed mobility estimator from group precursor
1:48:27.496192 INFO: Initializing OptimizationManager
1:48:27.496423 INFO: initial parameter: ms1_error = 30
1:48:27.496501 INFO: initial parameter: ms2_error = 30
1:48:27.496569 INFO: initial parameter: rt_error = 805.6004638671875
1:48:27.496627 INFO: initial parameter: mobility_error = 0.1
1:48:27.496683 INFO: initial parameter: column_type = library
1:48:27.496737 INFO: initial parameter: num_candidates = 1
1:48:27.496794 INFO: initial parameter: classifier_version = -1
1:48:27.496851 INFO: initial parameter: fwhm_rt = 5
1:48:27.496922 INFO: initial parameter: fwhm_mobility = 0.01
1:48:27.496978 INFO: initial parameter: score_cutoff = 0
1:48:27.497057 INFO: Initializing TimingManager
1:48:27.497126 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:48:27.497244 INFO: FDRManager not loaded from disk.
1:48:27.497272 INFO: Initializing FDRManager
1:48:27.497321 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1:48:29.859979 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
1:48:33.241374 PROGRESS: Starting initial search for precursors.
1:48:33.737392 INFO: Starting optimization step 0.
1:48:33.737662 PROGRESS: === Extracting elution groups 0 to 8000 ===
1:48:33.737746 PROGRESS: Extracting batch of 15798 precursors
1:48:33.744510 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:48:33.744597 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:48:33.744637 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:48:33.744663 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:48:33.744987 INFO: Starting candidate selection
1:48:35.690636 INFO: Starting candidate scoring
1:48:35.953061 INFO: Finished candidate processing
1:48:35.953222 INFO: Collecting candidate features
1:48:36.028010 INFO: Collecting fragment features
1:48:36.051815 INFO: Finished candidate scoring
1:48:36.073006 PROGRESS: === Extracted 15761 precursors and 155907 fragments ===
1:48:36.073545 INFO: performing precursor FDR with 47 features
1:48:36.073600 INFO: Decoy channel: -1
1:48:36.073635 INFO: Competetive: True
1:48:36.081978 INFO: Setting torch num_threads to 2 for FDR classification task
1:48:36.403813 INFO: Test AUC: 0.498
1:48:36.403992 INFO: Train AUC: 0.502
1:48:36.404041 INFO: AUC difference: 0.75%
1:48:36.543900 INFO: Resetting torch num_threads to 100
1:48:36.557056 INFO: === FDR correction performed with classifier version -1 ===
1:48:36.562198 PROGRESS: ============================= Precursor FDR =============================
1:48:36.562963 PROGRESS: Total precursors accumulated: 7,977
1:48:36.563381 PROGRESS: Target precursors: 4,030 (50.52%)
1:48:36.563740 PROGRESS: Decoy precursors: 3,947 (49.48%)
1:48:36.564083 PROGRESS: 
1:48:36.564410 PROGRESS: Precursor Summary:
1:48:36.566352 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:48:36.566827 PROGRESS: 
1:48:36.567157 PROGRESS: Protein Summary:
1:48:36.569527 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:48:36.569980 PROGRESS: =========================================================================
1:48:36.772441 INFO: Starting optimization step 1.
1:48:36.773275 PROGRESS: === Extracting elution groups 8000 to 24000 ===
1:48:36.773627 PROGRESS: Extracting batch of 31672 precursors
1:48:36.790202 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:48:36.790665 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:48:36.790843 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:48:36.791006 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:48:36.791420 INFO: Starting candidate selection
1:48:40.621270 INFO: Starting candidate scoring
1:48:41.095200 INFO: Finished candidate processing
1:48:41.095349 INFO: Collecting candidate features
1:48:41.232903 INFO: Collecting fragment features
1:48:41.272506 INFO: Finished candidate scoring
1:48:41.326852 PROGRESS: === Extracted 47359 precursors and 468229 fragments ===
1:48:41.335235 INFO: performing precursor FDR with 47 features
1:48:41.335329 INFO: Decoy channel: -1
1:48:41.335362 INFO: Competetive: True
1:48:41.387543 INFO: Setting torch num_threads to 2 for FDR classification task
1:48:42.551819 INFO: Test AUC: 0.523
1:48:42.551951 INFO: Train AUC: 0.532
1:48:42.551985 INFO: AUC difference: 1.60%
1:48:42.673433 INFO: Resetting torch num_threads to 100
1:48:42.680049 INFO: === FDR correction performed with classifier version -1 ===
1:48:42.680931 PROGRESS: ============================= Precursor FDR =============================
1:48:42.681030 PROGRESS: Total precursors accumulated: 5
1:48:42.681095 PROGRESS: Target precursors: 5 (100.00%)
1:48:42.681148 PROGRESS: Decoy precursors: 0 (0.00%)
1:48:42.681204 PROGRESS: 
1:48:42.681270 PROGRESS: Precursor Summary:
1:48:42.682407 PROGRESS: Channel   0:	 0.05 FDR:     5; 0.01 FDR:     5; 0.001 FDR:     5
1:48:42.682506 PROGRESS: 
1:48:42.682575 PROGRESS: Protein Summary:
1:48:42.684227 PROGRESS: Channel   0:	 0.05 FDR:     5; 0.01 FDR:     5; 0.001 FDR:     5
1:48:42.684594 PROGRESS: =========================================================================
1:48:42.969813 INFO: Starting optimization step 2.
1:48:42.970739 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1:48:42.971106 PROGRESS: Extracting batch of 63174 precursors
1:48:43.001821 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:48:43.002454 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:48:43.002725 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:48:43.002909 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:48:43.003545 INFO: Starting candidate selection
1:48:47.703171 INFO: Starting candidate scoring
1:48:48.294137 INFO: Finished candidate processing
1:48:48.294266 INFO: Collecting candidate features
1:48:48.441150 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 63031)
1:48:48.450477 INFO: Collecting fragment features
1:48:48.510465 INFO: Finished candidate scoring
1:48:48.574101 PROGRESS: === Extracted 110390 precursors and 1090572 fragments ===
1:48:48.593981 INFO: performing precursor FDR with 47 features
1:48:48.594199 INFO: Decoy channel: -1
1:48:48.594251 INFO: Competetive: True
1:48:48.663900 INFO: Setting torch num_threads to 2 for FDR classification task
1:48:48.690518 WARNING: dropped 1 target PSMs due to missing features
1:48:48.690647 WARNING: dropped 1 decoy PSMs due to missing features
1:48:51.281013 INFO: Test AUC: 0.552
1:48:51.281169 INFO: Train AUC: 0.567
1:48:51.281203 INFO: AUC difference: 2.55%
1:48:51.389846 INFO: Resetting torch num_threads to 100
1:48:51.432895 INFO: === FDR correction performed with classifier version -1 ===
1:48:51.434193 PROGRESS: ============================= Precursor FDR =============================
1:48:51.434386 PROGRESS: Total precursors accumulated: 3
1:48:51.434470 PROGRESS: Target precursors: 3 (100.00%)
1:48:51.434526 PROGRESS: Decoy precursors: 0 (0.00%)
1:48:51.434575 PROGRESS: 
1:48:51.434623 PROGRESS: Precursor Summary:
1:48:51.435766 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1:48:51.435880 PROGRESS: 
1:48:51.435939 PROGRESS: Protein Summary:
1:48:51.437093 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
1:48:51.437200 PROGRESS: =========================================================================
1:48:51.895364 INFO: Starting optimization step 3.
1:48:51.896280 PROGRESS: === Extracting elution groups 56000 to 120000 ===
1:48:51.896687 PROGRESS: Extracting batch of 126509 precursors
1:48:51.951751 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:48:51.952173 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:48:51.952338 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:48:51.952433 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:48:51.953041 INFO: Starting candidate selection
1:48:59.812785 INFO: Starting candidate scoring
1:49:01.159544 INFO: Finished candidate processing
1:49:01.159698 INFO: Collecting candidate features
1:49:01.665046 INFO: Collecting fragment features
1:49:01.791514 INFO: Finished candidate scoring
1:49:02.047088 PROGRESS: === Extracted 236534 precursors and 2334782 fragments ===
1:49:02.095168 INFO: performing precursor FDR with 47 features
1:49:02.095378 INFO: Decoy channel: -1
1:49:02.095413 INFO: Competetive: True
1:49:02.263854 INFO: Setting torch num_threads to 2 for FDR classification task
1:49:02.327794 WARNING: dropped 1 target PSMs due to missing features
1:49:02.328090 WARNING: dropped 1 decoy PSMs due to missing features
1:49:12.576304 INFO: Test AUC: 0.557
1:49:12.576523 INFO: Train AUC: 0.575
1:49:12.576576 INFO: AUC difference: 3.14%
1:49:12.742280 INFO: Resetting torch num_threads to 100
1:49:12.775007 INFO: === FDR correction performed with classifier version -1 ===
1:49:12.824443 PROGRESS: ============================= Precursor FDR =============================
1:49:12.825156 PROGRESS: Total precursors accumulated: 118,109
1:49:12.825510 PROGRESS: Target precursors: 69,718 (59.03%)
1:49:12.825810 PROGRESS: Decoy precursors: 48,391 (40.97%)
1:49:12.826110 PROGRESS: 
1:49:12.826374 PROGRESS: Precursor Summary:
1:49:12.829712 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:49:12.830082 PROGRESS: 
1:49:12.830355 PROGRESS: Protein Summary:
1:49:12.833022 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:49:12.833348 PROGRESS: =========================================================================
1:49:13.567163 INFO: Starting optimization step 4.
1:49:13.567653 PROGRESS: === Extracting elution groups 120000 to 248000 ===
1:49:13.567807 PROGRESS: Extracting batch of 252969 precursors
1:49:13.678416 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:49:13.678586 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:49:13.678639 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:49:13.678668 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:49:13.679087 INFO: Starting candidate selection
1:49:28.560749 INFO: Starting candidate scoring
1:49:30.431976 INFO: Finished candidate processing
1:49:30.432076 INFO: Collecting candidate features
1:49:31.019912 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 252312)
1:49:31.030974 INFO: Collecting fragment features
1:49:31.211456 INFO: Finished candidate scoring
1:49:31.506598 PROGRESS: === Extracted 488846 precursors and 4820206 fragments ===
1:49:31.565272 INFO: performing precursor FDR with 47 features
1:49:31.565402 INFO: Decoy channel: -1
1:49:31.565428 INFO: Competetive: True
1:49:31.914141 INFO: Setting torch num_threads to 2 for FDR classification task
1:49:32.097841 WARNING: dropped 2 target PSMs due to missing features
1:49:32.098104 WARNING: dropped 3 decoy PSMs due to missing features
1:49:46.745115 INFO: Test AUC: 0.564
1:49:46.745809 INFO: Train AUC: 0.577
1:49:46.745960 INFO: AUC difference: 2.28%
1:49:47.039903 INFO: Resetting torch num_threads to 100
1:49:47.189603 INFO: === FDR correction performed with classifier version -1 ===
1:49:47.198760 PROGRESS: ============================= Precursor FDR =============================
1:49:47.199239 PROGRESS: Total precursors accumulated: 14
1:49:47.199319 PROGRESS: Target precursors: 13 (92.86%)
1:49:47.199387 PROGRESS: Decoy precursors: 1 (7.14%)
1:49:47.199443 PROGRESS: 
1:49:47.199497 PROGRESS: Precursor Summary:
1:49:47.200770 PROGRESS: Channel   0:	 0.05 FDR:     9; 0.01 FDR:     9; 0.001 FDR:     9
1:49:47.200910 PROGRESS: 
1:49:47.200971 PROGRESS: Protein Summary:
1:49:47.202106 PROGRESS: Channel   0:	 0.05 FDR:     9; 0.01 FDR:     9; 0.001 FDR:     9
1:49:47.202221 PROGRESS: =========================================================================
1:49:49.385385 INFO: Starting optimization step 5.
1:49:49.385890 PROGRESS: === Extracting elution groups 248000 to 504000 ===
1:49:49.386015 PROGRESS: Extracting batch of 505926 precursors
1:49:49.866453 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:49:49.866817 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:49:49.866918 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:49:49.866956 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:49:49.867747 INFO: Starting candidate selection
1:50:21.129119 INFO: Starting candidate scoring
1:50:25.349288 INFO: Finished candidate processing
1:50:25.349565 INFO: Collecting candidate features
1:50:27.442490 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 504666)
1:50:27.475016 INFO: Collecting fragment features
1:50:28.061030 INFO: Finished candidate scoring
1:50:29.631595 PROGRESS: === Extracted 993512 precursors and 9795771 fragments ===
1:50:29.927160 INFO: performing precursor FDR with 47 features
1:50:29.927372 INFO: Decoy channel: -1
1:50:29.927412 INFO: Competetive: True
1:50:30.973648 INFO: Setting torch num_threads to 2 for FDR classification task
1:50:31.345925 WARNING: dropped 3 target PSMs due to missing features
1:50:31.346148 WARNING: dropped 6 decoy PSMs due to missing features
1:51:02.524204 INFO: Test AUC: 0.568
1:51:02.526718 INFO: Train AUC: 0.580
1:51:02.526822 INFO: AUC difference: 1.98%
1:51:02.801648 INFO: Resetting torch num_threads to 100
1:51:02.940416 INFO: === FDR correction performed with classifier version -1 ===
1:51:02.942992 PROGRESS: ============================= Precursor FDR =============================
1:51:02.943360 PROGRESS: Total precursors accumulated: 9
1:51:02.943618 PROGRESS: Target precursors: 9 (100.00%)
1:51:02.943861 PROGRESS: Decoy precursors: 0 (0.00%)
1:51:02.944098 PROGRESS: 
1:51:02.944333 PROGRESS: Precursor Summary:
1:51:02.945859 PROGRESS: Channel   0:	 0.05 FDR:     9; 0.01 FDR:     9; 0.001 FDR:     9
1:51:02.946164 PROGRESS: 
1:51:02.946430 PROGRESS: Protein Summary:
1:51:02.948079 PROGRESS: Channel   0:	 0.05 FDR:     9; 0.01 FDR:     9; 0.001 FDR:     9
1:51:02.948373 PROGRESS: =========================================================================
1:51:05.335778 INFO: Starting optimization step 6.
1:51:05.336518 PROGRESS: === Extracting elution groups 504000 to 1016000 ===
1:51:05.336771 PROGRESS: Extracting batch of 1011981 precursors
1:51:05.769780 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:51:05.770036 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:51:05.770109 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:51:05.770141 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:51:05.770633 INFO: Starting candidate selection
1:52:05.431535 INFO: Starting candidate scoring
1:52:12.722287 INFO: Finished candidate processing
1:52:12.722618 INFO: Collecting candidate features
1:52:15.204378 WARNING: intensity_correlation has 6 NaNs ( 0.00 % out of 1009407)
1:52:15.238654 INFO: Collecting fragment features
1:52:15.973563 INFO: Finished candidate scoring
1:52:17.558155 PROGRESS: === Extracted 2002919 precursors and 19750767 fragments ===
1:52:17.784027 INFO: performing precursor FDR with 47 features
1:52:17.784165 INFO: Decoy channel: -1
1:52:17.784194 INFO: Competetive: True
1:52:18.718973 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:19.128046 WARNING: dropped 6 target PSMs due to missing features
1:52:19.128194 WARNING: dropped 9 decoy PSMs due to missing features
1:52:54.807793 INFO: Test AUC: 0.575
1:52:54.808002 INFO: Train AUC: 0.580
1:52:54.808036 INFO: AUC difference: 0.89%
1:52:55.036414 INFO: Resetting torch num_threads to 100
1:52:55.139264 INFO: === FDR correction performed with classifier version -1 ===
1:52:55.140141 PROGRESS: ============================= Precursor FDR =============================
1:52:55.140241 PROGRESS: Total precursors accumulated: 100
1:52:55.140302 PROGRESS: Target precursors: 91 (91.00%)
1:52:55.140354 PROGRESS: Decoy precursors: 9 (9.00%)
1:52:55.140400 PROGRESS: 
1:52:55.140445 PROGRESS: Precursor Summary:
1:52:55.141331 PROGRESS: Channel   0:	 0.05 FDR:    48; 0.01 FDR:    27; 0.001 FDR:    27
1:52:55.141421 PROGRESS: 
1:52:55.141477 PROGRESS: Protein Summary:
1:52:55.142428 PROGRESS: Channel   0:	 0.05 FDR:    48; 0.01 FDR:    27; 0.001 FDR:    27
1:52:55.142518 PROGRESS: =========================================================================
1:52:56.924678 INFO: Starting optimization step 7.
1:52:56.924962 PROGRESS: === Extracting elution groups 1016000 to 2040000 ===
1:52:56.925056 PROGRESS: Extracting batch of 2023640 precursors
1:52:57.371252 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:52:57.371375 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:52:57.371413 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
1:52:57.371436 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:52:57.371728 INFO: Starting candidate selection
1:55:03.093795 INFO: Starting candidate scoring
1:55:17.247681 INFO: Finished candidate processing
1:55:17.247980 INFO: Collecting candidate features
1:55:21.841850 WARNING: intensity_correlation has 13 NaNs ( 0.00 % out of 2018543)
1:55:21.907666 INFO: Collecting fragment features
1:55:23.458623 INFO: Finished candidate scoring
1:55:26.639584 PROGRESS: === Extracted 4021462 precursors and 39653295 fragments ===
1:55:27.080167 INFO: performing precursor FDR with 47 features
1:55:27.080305 INFO: Decoy channel: -1
1:55:27.080335 INFO: Competetive: True
1:55:29.066747 INFO: Setting torch num_threads to 2 for FDR classification task
1:55:29.999068 WARNING: dropped 13 target PSMs due to missing features
1:55:29.999250 WARNING: dropped 15 decoy PSMs due to missing features
1:56:39.857815 INFO: Test AUC: 0.580
1:56:39.858030 INFO: Train AUC: 0.584
1:56:39.858064 INFO: AUC difference: 0.64%
1:56:40.218430 INFO: Resetting torch num_threads to 100
1:56:40.409934 INFO: === FDR correction performed with classifier version -1 ===
1:56:40.411263 PROGRESS: ============================= Precursor FDR =============================
1:56:40.411368 PROGRESS: Total precursors accumulated: 2,468
1:56:40.411429 PROGRESS: Target precursors: 2,271 (92.02%)
1:56:40.411480 PROGRESS: Decoy precursors: 197 (7.98%)
1:56:40.411526 PROGRESS: 
1:56:40.411573 PROGRESS: Precursor Summary:
1:56:40.413205 PROGRESS: Channel   0:	 0.05 FDR: 1,727; 0.01 FDR: 1,310; 0.001 FDR:   895
1:56:40.413300 PROGRESS: 
1:56:40.413353 PROGRESS: Protein Summary:
1:56:40.415145 PROGRESS: Channel   0:	 0.05 FDR: 1,340; 0.01 FDR: 1,010; 0.001 FDR:   717
1:56:40.415248 PROGRESS: =========================================================================
1:56:40.867801 INFO: fragments_df_filtered: 5000
1:56:42.035782 INFO: calibration group: precursor, fitting mz estimator 
1:56:42.126649 INFO: calibration group: precursor, fitting rt estimator 
1:56:42.187194 INFO: calibration group: fragment, fitting mz estimator 
1:56:42.597705 INFO: calibration group: precursor, predicting mz
1:56:42.773767 INFO: calibration group: precursor, predicting rt
1:56:43.442572 INFO: calibration group: fragment, predicting mz
1:56:44.976591 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:56:44.976887 INFO: Starting optimization step 8.
1:56:44.976970 PROGRESS: === Extracting elution groups 0 to 504000 ===
1:56:44.977049 PROGRESS: Extracting batch of 996048 precursors
1:56:45.219167 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:56:45.219297 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:56:45.219927 INFO: FWHM in RT is 3.02 seconds, sigma is 0.39
1:56:45.219956 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:56:45.220271 INFO: Starting candidate selection
1:57:35.886179 INFO: Starting candidate scoring
1:57:49.655759 INFO: Finished candidate processing
1:57:49.656061 INFO: Collecting candidate features
1:57:53.502443 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 1986994)
1:57:53.571328 INFO: Collecting fragment features
1:57:54.933171 INFO: Finished candidate scoring
1:57:56.517485 PROGRESS: === Extracted 1986994 precursors and 19335353 fragments ===
1:57:56.517987 INFO: performing precursor FDR with 47 features
1:57:56.518027 INFO: Decoy channel: -1
1:57:56.518053 INFO: Competetive: True
1:57:57.113818 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:57.435993 WARNING: dropped 3 decoy PSMs due to missing features
1:58:39.200713 INFO: Test AUC: 0.580
1:58:39.200970 INFO: Train AUC: 0.586
1:58:39.201009 INFO: AUC difference: 1.11%
1:58:39.428759 INFO: Resetting torch num_threads to 100
1:58:39.634652 INFO: === FDR correction performed with classifier version 7 ===
1:58:39.636011 PROGRESS: ============================= Precursor FDR =============================
1:58:39.636159 PROGRESS: Total precursors accumulated: 1,110
1:58:39.636242 PROGRESS: Target precursors: 1,013 (91.26%)
1:58:39.636296 PROGRESS: Decoy precursors: 97 (8.74%)
1:58:39.636341 PROGRESS: 
1:58:39.636386 PROGRESS: Precursor Summary:
1:58:39.637690 PROGRESS: Channel   0:	 0.05 FDR:   724; 0.01 FDR:   463; 0.001 FDR:   350
1:58:39.637795 PROGRESS: 
1:58:39.637852 PROGRESS: Protein Summary:
1:58:39.639220 PROGRESS: Channel   0:	 0.05 FDR:   653; 0.01 FDR:   421; 0.001 FDR:   328
1:58:39.639318 PROGRESS: =========================================================================
1:58:39.712696 INFO: fragments_df_filtered: 5000
1:58:40.511006 INFO: calibration group: precursor, fitting mz estimator 
1:58:40.553205 INFO: calibration group: precursor, fitting rt estimator 
1:58:40.593278 INFO: calibration group: fragment, fitting mz estimator 
1:58:40.942247 INFO: calibration group: precursor, predicting mz
1:58:41.009869 INFO: calibration group: precursor, predicting rt
1:58:41.335899 INFO: calibration group: fragment, predicting mz
1:58:42.657774 INFO: === checking if optimization conditions were reached ===
1:58:42.660177 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1:58:42.661532 PROGRESS: ❌ ms1_error      : 13.0327 > 10.0000 or insufficient steps taken.
1:58:42.661871 INFO: ==============================================
1:58:42.662200 INFO: Starting optimization step 9.
1:58:42.662486 PROGRESS: === Extracting elution groups 0 to 248000 ===
1:58:42.663532 PROGRESS: Extracting batch of 490122 precursors
1:58:42.836638 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:58:42.836771 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:58:42.836809 INFO: FWHM in RT is 2.83 seconds, sigma is 0.36
1:58:42.836833 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:58:42.837130 INFO: Starting candidate selection
1:59:07.721114 INFO: Starting candidate scoring
1:59:14.613353 INFO: Finished candidate processing
1:59:14.613462 INFO: Collecting candidate features
1:59:16.524115 WARNING: intensity_correlation has 19 NaNs ( 0.00 % out of 977238)
1:59:16.558854 INFO: Collecting fragment features
1:59:17.185141 INFO: Finished candidate scoring
1:59:17.937093 PROGRESS: === Extracted 977238 precursors and 8397869 fragments ===
1:59:17.937587 INFO: performing precursor FDR with 47 features
1:59:17.937628 INFO: Decoy channel: -1
1:59:17.937653 INFO: Competetive: True
1:59:18.223866 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:18.399977 WARNING: dropped 11 target PSMs due to missing features
1:59:18.400125 WARNING: dropped 8 decoy PSMs due to missing features
1:59:43.424676 INFO: Test AUC: 0.575
1:59:43.424955 INFO: Train AUC: 0.584
1:59:43.425001 INFO: AUC difference: 1.57%
1:59:43.664622 INFO: Resetting torch num_threads to 100
1:59:43.709662 INFO: === FDR correction performed with classifier version 8 ===
1:59:43.711356 PROGRESS: ============================= Precursor FDR =============================
1:59:43.711506 PROGRESS: Total precursors accumulated: 891
1:59:43.711581 PROGRESS: Target precursors: 813 (91.25%)
1:59:43.711646 PROGRESS: Decoy precursors: 78 (8.75%)
1:59:43.711705 PROGRESS: 
1:59:43.711766 PROGRESS: Precursor Summary:
1:59:43.713324 PROGRESS: Channel   0:	 0.05 FDR:   548; 0.01 FDR:   331; 0.001 FDR:   223
1:59:43.713461 PROGRESS: 
1:59:43.713530 PROGRESS: Protein Summary:
1:59:43.715316 PROGRESS: Channel   0:	 0.05 FDR:   507; 0.01 FDR:   313; 0.001 FDR:   213
1:59:43.715443 PROGRESS: =========================================================================
1:59:43.782005 INFO: fragments_df_filtered: 3658
1:59:44.975378 INFO: calibration group: precursor, fitting mz estimator 
1:59:45.167835 INFO: calibration group: precursor, fitting rt estimator 
1:59:45.301900 INFO: calibration group: fragment, fitting mz estimator 
1:59:45.665379 INFO: calibration group: precursor, predicting mz
1:59:46.112996 INFO: calibration group: precursor, predicting rt
1:59:46.545856 INFO: calibration group: fragment, predicting mz
1:59:47.582241 INFO: === checking if optimization conditions were reached ===
1:59:47.584743 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1:59:47.586051 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
1:59:47.586120 INFO: ==============================================
1:59:47.586299 PROGRESS: Optimization finished for ms2_error, ms1_error.
1:59:48.873994 INFO: calibration group: precursor, predicting mz
1:59:48.978091 INFO: calibration group: precursor, predicting rt
1:59:49.393353 INFO: calibration group: fragment, predicting mz
1:59:50.417616 INFO: Starting optimization step 0.
1:59:50.417988 PROGRESS: === Extracting elution groups 0 to 248000 ===
1:59:50.418126 PROGRESS: Extracting batch of 490122 precursors
1:59:50.823752 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
1:59:50.824075 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:50.824133 INFO: FWHM in RT is 2.73 seconds, sigma is 0.35
1:59:50.824166 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:59:50.824675 INFO: Starting candidate selection
2:00:16.725387 INFO: Starting candidate scoring
2:00:24.199264 INFO: Finished candidate processing
2:00:24.202360 INFO: Collecting candidate features
2:00:27.795904 WARNING: intensity_correlation has 15 NaNs ( 0.00 % out of 977291)
2:00:27.864356 INFO: Collecting fragment features
2:00:28.975904 INFO: Finished candidate scoring
2:00:30.503453 PROGRESS: === Extracted 977291 precursors and 8386708 fragments ===
2:00:30.504175 INFO: performing precursor FDR with 47 features
2:00:30.504228 INFO: Decoy channel: -1
2:00:30.504265 INFO: Competetive: True
2:00:30.979115 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:31.330799 WARNING: dropped 8 target PSMs due to missing features
2:00:31.330994 WARNING: dropped 7 decoy PSMs due to missing features
2:00:55.699573 INFO: Test AUC: 0.577
2:00:55.699889 INFO: Train AUC: 0.587
2:00:55.699939 INFO: AUC difference: 1.58%
2:00:55.958015 INFO: Resetting torch num_threads to 100
2:00:56.021495 INFO: === FDR correction performed with classifier version 9 ===
2:00:56.023163 PROGRESS: ============================= Precursor FDR =============================
2:00:56.023314 PROGRESS: Total precursors accumulated: 1,018
2:00:56.023401 PROGRESS: Target precursors: 929 (91.26%)
2:00:56.023475 PROGRESS: Decoy precursors: 89 (8.74%)
2:00:56.023539 PROGRESS: 
2:00:56.023599 PROGRESS: Precursor Summary:
2:00:56.025235 PROGRESS: Channel   0:	 0.05 FDR:   656; 0.01 FDR:   375; 0.001 FDR:   274
2:00:56.025367 PROGRESS: 
2:00:56.025446 PROGRESS: Protein Summary:
2:00:56.027357 PROGRESS: Channel   0:	 0.05 FDR:   614; 0.01 FDR:   352; 0.001 FDR:   264
2:00:56.027490 PROGRESS: =========================================================================
2:00:56.111923 INFO: fragments_df_filtered: 4095
2:00:57.577495 INFO: calibration group: precursor, fitting mz estimator 
2:00:57.711522 INFO: calibration group: precursor, fitting rt estimator 
2:00:57.776793 INFO: calibration group: fragment, fitting mz estimator 
2:00:58.133261 INFO: calibration group: precursor, predicting mz
2:00:58.230650 INFO: calibration group: precursor, predicting rt
2:00:58.629277 INFO: calibration group: fragment, predicting mz
2:00:59.640612 INFO: === checking if optimization conditions were reached ===
2:00:59.642489 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2:00:59.646043 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 178.8928.
2:00:59.646142 INFO: ==============================================
2:00:59.646387 INFO: Starting optimization step 1.
2:00:59.646500 PROGRESS: === Extracting elution groups 0 to 248000 ===
2:00:59.646615 PROGRESS: Extracting batch of 490122 precursors
2:01:00.067037 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:01:00.067446 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:00.067564 INFO: FWHM in RT is 2.59 seconds, sigma is 0.33
2:01:00.067659 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:01:00.068305 INFO: Starting candidate selection
2:01:22.384032 INFO: Starting candidate scoring
2:01:30.245883 INFO: Finished candidate processing
2:01:30.246151 INFO: Collecting candidate features
2:01:32.852143 WARNING: intensity_correlation has 118 NaNs ( 0.01 % out of 970945)
2:01:32.888850 INFO: Collecting fragment features
2:01:33.519921 INFO: Finished candidate scoring
2:01:34.571874 PROGRESS: === Extracted 970945 precursors and 7951897 fragments ===
2:01:34.572345 INFO: performing precursor FDR with 47 features
2:01:34.572386 INFO: Decoy channel: -1
2:01:34.572411 INFO: Competetive: True
2:01:34.864629 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:35.043155 WARNING: dropped 61 target PSMs due to missing features
2:01:35.043276 WARNING: dropped 57 decoy PSMs due to missing features
2:02:01.001374 INFO: Test AUC: 0.564
2:02:01.001662 INFO: Train AUC: 0.571
2:02:01.001711 INFO: AUC difference: 1.22%
2:02:01.264261 INFO: Resetting torch num_threads to 100
2:02:01.440871 INFO: === FDR correction performed with classifier version 9 ===
2:02:01.442609 PROGRESS: ============================= Precursor FDR =============================
2:02:01.442771 PROGRESS: Total precursors accumulated: 903
2:02:01.442872 PROGRESS: Target precursors: 824 (91.25%)
2:02:01.442965 PROGRESS: Decoy precursors: 79 (8.75%)
2:02:01.443044 PROGRESS: 
2:02:01.443121 PROGRESS: Precursor Summary:
2:02:01.444999 PROGRESS: Channel   0:	 0.05 FDR:   658; 0.01 FDR:   467; 0.001 FDR:   245
2:02:01.445132 PROGRESS: 
2:02:01.445218 PROGRESS: Protein Summary:
2:02:01.447351 PROGRESS: Channel   0:	 0.05 FDR:   608; 0.01 FDR:   437; 0.001 FDR:   235
2:02:01.447526 PROGRESS: =========================================================================
2:02:01.505242 INFO: fragments_df_filtered: 4863
2:02:02.364091 INFO: calibration group: precursor, fitting mz estimator 
2:02:02.533718 INFO: calibration group: precursor, fitting rt estimator 
2:02:02.643744 INFO: calibration group: fragment, fitting mz estimator 
2:02:03.109189 INFO: calibration group: precursor, predicting mz
2:02:03.156759 INFO: calibration group: precursor, predicting rt
2:02:03.327542 INFO: calibration group: fragment, predicting mz
2:02:03.800758 INFO: === checking if optimization conditions were reached ===
2:02:03.801290 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2:02:03.804167 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 128.4309.
2:02:03.804246 INFO: ==============================================
2:02:03.804394 INFO: Starting optimization step 2.
2:02:03.804492 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:02:03.804595 PROGRESS: Extracting batch of 237153 precursors
2:02:03.932072 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:02:03.932261 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:02:03.932316 INFO: FWHM in RT is 2.57 seconds, sigma is 0.33
2:02:03.932349 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:02:03.932827 INFO: Starting candidate selection
2:02:14.249667 INFO: Starting candidate scoring
2:02:17.870163 INFO: Finished candidate processing
2:02:17.870480 INFO: Collecting candidate features
2:02:19.659247 WARNING: intensity_correlation has 81 NaNs ( 0.02 % out of 468653)
2:02:19.691576 INFO: Collecting fragment features
2:02:20.167351 INFO: Finished candidate scoring
2:02:21.058492 PROGRESS: === Extracted 468653 precursors and 3771768 fragments ===
2:02:21.059191 INFO: performing precursor FDR with 47 features
2:02:21.059245 INFO: Decoy channel: -1
2:02:21.059279 INFO: Competetive: True
2:02:21.339963 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:21.489990 WARNING: dropped 40 target PSMs due to missing features
2:02:21.490206 WARNING: dropped 41 decoy PSMs due to missing features
2:02:33.854564 INFO: Test AUC: 0.572
2:02:33.854863 INFO: Train AUC: 0.587
2:02:33.854914 INFO: AUC difference: 2.50%
2:02:34.051263 INFO: Resetting torch num_threads to 100
2:02:34.077534 INFO: === FDR correction performed with classifier version 9 ===
2:02:34.079113 PROGRESS: ============================= Precursor FDR =============================
2:02:34.079309 PROGRESS: Total precursors accumulated: 626
2:02:34.079393 PROGRESS: Target precursors: 567 (90.58%)
2:02:34.079460 PROGRESS: Decoy precursors: 59 (9.42%)
2:02:34.079517 PROGRESS: 
2:02:34.079576 PROGRESS: Precursor Summary:
2:02:34.080999 PROGRESS: Channel   0:	 0.05 FDR:   428; 0.01 FDR:   268; 0.001 FDR:   228
2:02:34.081140 PROGRESS: 
2:02:34.081197 PROGRESS: Protein Summary:
2:02:34.082771 PROGRESS: Channel   0:	 0.05 FDR:   409; 0.01 FDR:   258; 0.001 FDR:   221
2:02:34.082910 PROGRESS: =========================================================================
2:02:34.105139 INFO: fragments_df_filtered: 2729
2:02:34.874093 INFO: calibration group: precursor, fitting mz estimator 
2:02:35.013673 INFO: calibration group: precursor, fitting rt estimator 
2:02:35.140228 INFO: calibration group: fragment, fitting mz estimator 
2:02:35.413688 INFO: calibration group: precursor, predicting mz
2:02:35.460086 INFO: calibration group: precursor, predicting rt
2:02:35.633137 INFO: calibration group: fragment, predicting mz
2:02:36.080632 INFO: === checking if optimization conditions were reached ===
2:02:36.081239 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2:02:36.083680 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 105.7286.
2:02:36.083828 INFO: ==============================================
2:02:36.084124 INFO: Starting optimization step 3.
2:02:36.084383 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:02:36.084642 PROGRESS: Extracting batch of 237153 precursors
2:02:36.190890 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:02:36.191081 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:02:36.191145 INFO: FWHM in RT is 2.53 seconds, sigma is 0.33
2:02:36.191178 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:02:36.191642 INFO: Starting candidate selection
2:02:46.438517 INFO: Starting candidate scoring
2:02:50.256016 INFO: Finished candidate processing
2:02:50.258589 INFO: Collecting candidate features
2:02:52.058217 WARNING: intensity_correlation has 74 NaNs ( 0.02 % out of 468274)
2:02:52.096207 INFO: Collecting fragment features
2:02:52.570164 INFO: Finished candidate scoring
2:02:53.614537 PROGRESS: === Extracted 468274 precursors and 3771178 fragments ===
2:02:53.615314 INFO: performing precursor FDR with 47 features
2:02:53.615371 INFO: Decoy channel: -1
2:02:53.615402 INFO: Competetive: True
2:02:53.942194 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:54.122779 WARNING: dropped 34 target PSMs due to missing features
2:02:54.123001 WARNING: dropped 40 decoy PSMs due to missing features
2:03:06.113061 INFO: Test AUC: 0.570
2:03:06.113333 INFO: Train AUC: 0.587
2:03:06.113380 INFO: AUC difference: 2.89%
2:03:06.292947 INFO: Resetting torch num_threads to 100
2:03:06.308874 INFO: === FDR correction performed with classifier version 9 ===
2:03:06.310105 PROGRESS: ============================= Precursor FDR =============================
2:03:06.310297 PROGRESS: Total precursors accumulated: 650
2:03:06.310380 PROGRESS: Target precursors: 590 (90.77%)
2:03:06.310437 PROGRESS: Decoy precursors: 60 (9.23%)
2:03:06.310483 PROGRESS: 
2:03:06.310529 PROGRESS: Precursor Summary:
2:03:06.311705 PROGRESS: Channel   0:	 0.05 FDR:   392; 0.01 FDR:   271; 0.001 FDR:   155
2:03:06.311826 PROGRESS: 
2:03:06.311883 PROGRESS: Protein Summary:
2:03:06.313090 PROGRESS: Channel   0:	 0.05 FDR:   376; 0.01 FDR:   261; 0.001 FDR:   151
2:03:06.313194 PROGRESS: =========================================================================
2:03:06.332736 INFO: fragments_df_filtered: 2748
2:03:07.140143 INFO: calibration group: precursor, fitting mz estimator 
2:03:07.220641 INFO: calibration group: precursor, fitting rt estimator 
2:03:07.289260 INFO: calibration group: fragment, fitting mz estimator 
2:03:07.543272 INFO: calibration group: precursor, predicting mz
2:03:07.588384 INFO: calibration group: precursor, predicting rt
2:03:07.749098 INFO: calibration group: fragment, predicting mz
2:03:08.163094 INFO: === checking if optimization conditions were reached ===
2:03:08.163459 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2:03:08.165835 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 96.4908.
2:03:08.165897 INFO: ==============================================
2:03:08.166002 INFO: Starting optimization step 4.
2:03:08.166084 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:03:08.166160 PROGRESS: Extracting batch of 237153 precursors
2:03:08.240327 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:03:08.240485 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:03:08.240533 INFO: FWHM in RT is 2.63 seconds, sigma is 0.34
2:03:08.240563 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:03:08.240937 INFO: Starting candidate selection
2:03:18.198667 INFO: Starting candidate scoring
2:03:21.960128 INFO: Finished candidate processing
2:03:21.960404 INFO: Collecting candidate features
2:03:23.440722 WARNING: intensity_correlation has 87 NaNs ( 0.02 % out of 468121)
2:03:23.475850 INFO: Collecting fragment features
2:03:23.904685 INFO: Finished candidate scoring
2:03:24.684626 PROGRESS: === Extracted 468121 precursors and 3753764 fragments ===
2:03:24.685391 INFO: performing precursor FDR with 47 features
2:03:24.685452 INFO: Decoy channel: -1
2:03:24.685503 INFO: Competetive: True
2:03:24.985600 INFO: Setting torch num_threads to 2 for FDR classification task
2:03:25.215420 WARNING: dropped 40 target PSMs due to missing features
2:03:25.215629 WARNING: dropped 47 decoy PSMs due to missing features
2:03:37.140182 INFO: Test AUC: 0.570
2:03:37.140445 INFO: Train AUC: 0.586
2:03:37.140513 INFO: AUC difference: 2.65%
2:03:37.316543 INFO: Resetting torch num_threads to 100
2:03:37.413897 INFO: === FDR correction performed with classifier version 9 ===
2:03:37.415260 PROGRESS: ============================= Precursor FDR =============================
2:03:37.415388 PROGRESS: Total precursors accumulated: 603
2:03:37.415453 PROGRESS: Target precursors: 549 (91.04%)
2:03:37.415506 PROGRESS: Decoy precursors: 54 (8.96%)
2:03:37.415555 PROGRESS: 
2:03:37.415602 PROGRESS: Precursor Summary:
2:03:37.416663 PROGRESS: Channel   0:	 0.05 FDR:   386; 0.01 FDR:   285; 0.001 FDR:   185
2:03:37.416768 PROGRESS: 
2:03:37.416835 PROGRESS: Protein Summary:
2:03:37.418259 PROGRESS: Channel   0:	 0.05 FDR:   369; 0.01 FDR:   275; 0.001 FDR:   180
2:03:37.418377 PROGRESS: =========================================================================
2:03:37.451540 INFO: fragments_df_filtered: 2826
2:03:38.290688 INFO: calibration group: precursor, fitting mz estimator 
2:03:38.508281 INFO: calibration group: precursor, fitting rt estimator 
2:03:40.326557 INFO: calibration group: fragment, fitting mz estimator 
2:03:40.654816 INFO: calibration group: precursor, predicting mz
2:03:40.741348 INFO: calibration group: precursor, predicting rt
2:03:40.912832 INFO: calibration group: fragment, predicting mz
2:03:41.437294 INFO: === checking if optimization conditions were reached ===
2:03:41.437662 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2:03:41.439888 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 86.8718.
2:03:41.439943 INFO: ==============================================
2:03:41.440033 INFO: Starting optimization step 5.
2:03:41.440098 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:03:41.440168 PROGRESS: Extracting batch of 237153 precursors
2:03:41.518913 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:03:41.519158 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:03:41.519204 INFO: FWHM in RT is 2.66 seconds, sigma is 0.34
2:03:41.519234 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:03:41.519660 INFO: Starting candidate selection
2:03:51.703068 INFO: Starting candidate scoring
2:03:55.531446 INFO: Finished candidate processing
2:03:55.531600 INFO: Collecting candidate features
2:03:57.151468 WARNING: intensity_correlation has 93 NaNs ( 0.02 % out of 467195)
2:03:57.174654 INFO: Collecting fragment features
2:03:57.626057 INFO: Finished candidate scoring
2:03:58.326895 PROGRESS: === Extracted 467195 precursors and 3670318 fragments ===
2:03:58.327632 INFO: performing precursor FDR with 47 features
2:03:58.327688 INFO: Decoy channel: -1
2:03:58.327726 INFO: Competetive: True
2:03:58.622543 INFO: Setting torch num_threads to 2 for FDR classification task
2:03:58.808775 WARNING: dropped 48 target PSMs due to missing features
2:03:58.808959 WARNING: dropped 45 decoy PSMs due to missing features
2:04:10.876458 INFO: Test AUC: 0.569
2:04:10.876608 INFO: Train AUC: 0.585
2:04:10.876642 INFO: AUC difference: 2.68%
2:04:11.053683 INFO: Resetting torch num_threads to 100
2:04:11.136109 INFO: === FDR correction performed with classifier version 9 ===
2:04:11.137494 PROGRESS: ============================= Precursor FDR =============================
2:04:11.137726 PROGRESS: Total precursors accumulated: 600
2:04:11.137806 PROGRESS: Target precursors: 546 (91.00%)
2:04:11.137863 PROGRESS: Decoy precursors: 54 (9.00%)
2:04:11.137913 PROGRESS: 
2:04:11.137962 PROGRESS: Precursor Summary:
2:04:11.139546 PROGRESS: Channel   0:	 0.05 FDR:   426; 0.01 FDR:   311; 0.001 FDR:   190
2:04:11.139720 PROGRESS: 
2:04:11.139784 PROGRESS: Protein Summary:
2:04:11.141356 PROGRESS: Channel   0:	 0.05 FDR:   412; 0.01 FDR:   299; 0.001 FDR:   184
2:04:11.141482 PROGRESS: =========================================================================
2:04:11.165481 INFO: fragments_df_filtered: 2945
2:04:11.849812 INFO: calibration group: precursor, fitting mz estimator 
2:04:11.937678 INFO: calibration group: precursor, fitting rt estimator 
2:04:11.993329 INFO: calibration group: fragment, fitting mz estimator 
2:04:12.268110 INFO: calibration group: precursor, predicting mz
2:04:12.303916 INFO: calibration group: precursor, predicting rt
2:04:12.471102 INFO: calibration group: fragment, predicting mz
2:04:12.878773 INFO: === checking if optimization conditions were reached ===
2:04:12.879420 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2:04:12.882374 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 86.4919.
2:04:12.882502 INFO: ==============================================
2:04:12.882743 INFO: Starting optimization step 6.
2:04:12.882954 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:04:12.883176 PROGRESS: Extracting batch of 237153 precursors
2:04:12.968100 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:04:12.968271 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:04:12.968315 INFO: FWHM in RT is 2.69 seconds, sigma is 0.35
2:04:12.968339 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:04:12.968724 INFO: Starting candidate selection
2:04:22.927284 INFO: Starting candidate scoring
2:04:26.758857 INFO: Finished candidate processing
2:04:26.759130 INFO: Collecting candidate features
2:04:28.544758 WARNING: intensity_correlation has 107 NaNs ( 0.02 % out of 467308)
2:04:28.576777 INFO: Collecting fragment features
2:04:29.060697 INFO: Finished candidate scoring
2:04:29.915127 PROGRESS: === Extracted 467308 precursors and 3680037 fragments ===
2:04:29.915892 INFO: performing precursor FDR with 47 features
2:04:29.915951 INFO: Decoy channel: -1
2:04:29.915987 INFO: Competetive: True
2:04:30.214571 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:30.388425 WARNING: dropped 55 target PSMs due to missing features
2:04:30.388595 WARNING: dropped 52 decoy PSMs due to missing features
2:04:42.949335 INFO: Test AUC: 0.570
2:04:42.949618 INFO: Train AUC: 0.586
2:04:42.949666 INFO: AUC difference: 2.69%
2:04:43.149846 INFO: Resetting torch num_threads to 100
2:04:43.181675 INFO: === FDR correction performed with classifier version 9 ===
2:04:43.183403 PROGRESS: ============================= Precursor FDR =============================
2:04:43.183558 PROGRESS: Total precursors accumulated: 589
2:04:43.183651 PROGRESS: Target precursors: 536 (91.00%)
2:04:43.183719 PROGRESS: Decoy precursors: 53 (9.00%)
2:04:43.183779 PROGRESS: 
2:04:43.183836 PROGRESS: Precursor Summary:
2:04:43.185539 PROGRESS: Channel   0:	 0.05 FDR:   397; 0.01 FDR:   261; 0.001 FDR:   234
2:04:43.185688 PROGRESS: 
2:04:43.185761 PROGRESS: Protein Summary:
2:04:43.187608 PROGRESS: Channel   0:	 0.05 FDR:   380; 0.01 FDR:   249; 0.001 FDR:   224
2:04:43.187957 PROGRESS: =========================================================================
2:04:43.219745 INFO: fragments_df_filtered: 2595
2:04:43.963028 INFO: calibration group: precursor, fitting mz estimator 
2:04:44.031324 INFO: calibration group: precursor, fitting rt estimator 
2:04:44.098808 INFO: calibration group: fragment, fitting mz estimator 
2:04:44.303945 INFO: calibration group: precursor, predicting mz
2:04:44.363462 INFO: calibration group: precursor, predicting rt
2:04:44.554024 INFO: calibration group: fragment, predicting mz
2:04:45.015733 INFO: === checking if optimization conditions were reached ===
2:04:45.016210 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
2:04:45.017681 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 86.8718 found after 7 searches.
2:04:45.017739 INFO: ==============================================
2:04:45.017840 PROGRESS: Optimization finished for rt_error.
2:04:45.510987 INFO: calibration group: precursor, predicting mz
2:04:45.560048 INFO: calibration group: precursor, predicting rt
2:04:45.774128 INFO: calibration group: fragment, predicting mz
2:04:46.317469 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:04:46.317819 PROGRESS: ==============================================
2:04:46.317926 PROGRESS: ms2_error      : 15.0000
2:04:46.318008 PROGRESS: ms1_error      : 10.0000
2:04:46.318076 PROGRESS: rt_error       : 86.8718
2:04:46.318142 PROGRESS: ==============================================
2:04:46.319914 INFO: calibration group: precursor, predicting mz
2:04:48.372416 INFO: calibration group: precursor, predicting rt
2:04:56.853903 INFO: calibration group: fragment, predicting mz
2:05:17.694989 PROGRESS: Extracting batch of 10183864 precursors
2:05:21.367988 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:05:21.368147 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:05:21.368193 INFO: FWHM in RT is 2.69 seconds, sigma is 0.35
2:05:21.368218 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:05:21.368702 INFO: Starting candidate selection
2:12:09.947850 INFO: Applying score cutoff of 35.52879024505615
2:12:10.763141 INFO: Removed 5208481 precursors with score below cutoff
2:12:14.494321 INFO: Starting candidate scoring
2:14:12.840433 INFO: Finished candidate processing
2:14:12.840852 INFO: Collecting candidate features
2:15:09.704208 WARNING: intensity_correlation has 407 NaNs ( 0.00 % out of 15106023)
2:15:10.915665 INFO: Collecting fragment features
2:15:45.548057 INFO: Finished candidate scoring
2:16:14.902205 INFO: === FDR correction performed with classifier version 15 ===
2:16:14.915061 INFO: performing precursor FDR with 47 features
2:16:14.915279 INFO: Decoy channel: -1
2:16:14.915331 INFO: Competetive: True
2:16:22.156738 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:26.737539 WARNING: dropped 226 target PSMs due to missing features
2:16:26.737780 WARNING: dropped 181 decoy PSMs due to missing features
2:24:54.988083 INFO: Test AUC: 0.574
2:24:54.988456 INFO: Train AUC: 0.577
2:24:54.988517 INFO: AUC difference: 0.61%
2:24:56.354119 INFO: Resetting torch num_threads to 100
2:24:56.871250 INFO: Removing fragments below FDR threshold
2:24:58.305430 PROGRESS: ============================= Precursor FDR =============================
2:24:58.305830 PROGRESS: Total precursors accumulated: 11,448
2:24:58.305906 PROGRESS: Target precursors: 11,335 (99.01%)
2:24:58.305967 PROGRESS: Decoy precursors: 113 (0.99%)
2:24:58.306021 PROGRESS: 
2:24:58.306072 PROGRESS: Precursor Summary:
2:24:58.311514 PROGRESS: Channel   0:	 0.05 FDR: 11,335; 0.01 FDR: 11,335; 0.001 FDR: 7,262
2:24:58.311786 PROGRESS: 
2:24:58.311855 PROGRESS: Protein Summary:
2:24:58.319840 PROGRESS: Channel   0:	 0.05 FDR: 4,905; 0.01 FDR: 4,905; 0.001 FDR: 3,602
2:24:58.320107 PROGRESS: =========================================================================
2:24:58.815399 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:24:59.660366 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:24:59.660585 INFO: Quantification results path: run_output_Astral/alphadia_1.10_noMBR/quant
2:24:59.660690 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1 at run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:24:59.661563 INFO: Initializing RawFileManager
2:25:36.147812 INFO: Determining DIA cycle
2:25:36.169445 INFO: Found cycle with start 0.00 min and length 303.
2:25:36.489217 INFO: RT (min)            : 0.0 - 26.9
2:25:36.489351 INFO: RT duration (sec)   : 1611.2
2:25:36.489388 INFO: RT duration (min)   : 26.9
2:25:36.489422 INFO: Cycle len (scans)   : 303
2:25:36.489448 INFO: Cycle len (sec)     : 1.65
2:25:36.489473 INFO: Number of cycles    : 977
2:25:36.489498 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:25:38.916894 INFO: Initializing CalibrationManager
2:25:38.917353 INFO: Loading calibration config
2:25:38.918291 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'}]
2:25:38.918432 INFO: Calibration group :fragment, found 1 estimator(s)
2:25:38.918573 INFO: Calibration group :precursor, found 3 estimator(s)
2:25:38.918685 INFO: Disabling ion mobility calibration
2:25:38.918722 INFO: removed mobility estimator from group precursor
2:25:38.918963 INFO: Initializing OptimizationManager
2:25:38.919126 INFO: initial parameter: ms1_error = 30
2:25:38.919206 INFO: initial parameter: ms2_error = 30
2:25:38.919270 INFO: initial parameter: rt_error = 805.5982666015625
2:25:38.919330 INFO: initial parameter: mobility_error = 0.1
2:25:38.919385 INFO: initial parameter: column_type = library
2:25:38.919441 INFO: initial parameter: num_candidates = 1
2:25:38.919500 INFO: initial parameter: classifier_version = -1
2:25:38.919561 INFO: initial parameter: fwhm_rt = 5
2:25:38.919618 INFO: initial parameter: fwhm_mobility = 0.01
2:25:38.919673 INFO: initial parameter: score_cutoff = 0
2:25:38.919756 INFO: Initializing TimingManager
2:25:38.919835 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:25:38.920002 INFO: FDRManager not loaded from disk.
2:25:38.920037 INFO: Initializing FDRManager
2:25:38.920090 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
2:25:41.342013 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
2:25:44.994426 PROGRESS: Starting initial search for precursors.
2:25:45.624865 INFO: Starting optimization step 0.
2:25:45.625231 PROGRESS: === Extracting elution groups 0 to 8000 ===
2:25:45.625347 PROGRESS: Extracting batch of 15798 precursors
2:25:45.637072 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:25:45.637259 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:25:45.637318 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:25:45.637354 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:25:45.637859 INFO: Starting candidate selection
2:25:47.749845 INFO: Starting candidate scoring
2:25:47.922008 INFO: Finished candidate processing
2:25:47.922123 INFO: Collecting candidate features
2:25:47.985790 WARNING: intensity_correlation has 1 NaNs ( 0.01 % out of 15759)
2:25:47.992258 INFO: Collecting fragment features
2:25:48.019143 INFO: Finished candidate scoring
2:25:48.038010 PROGRESS: === Extracted 15759 precursors and 156806 fragments ===
2:25:48.038921 INFO: performing precursor FDR with 47 features
2:25:48.038984 INFO: Decoy channel: -1
2:25:48.039019 INFO: Competetive: True
2:25:48.049892 INFO: Setting torch num_threads to 2 for FDR classification task
2:25:48.057191 WARNING: dropped 1 decoy PSMs due to missing features
2:25:48.306053 INFO: Test AUC: 0.525
2:25:48.306222 INFO: Train AUC: 0.510
2:25:48.306268 INFO: AUC difference: 2.99%
2:25:48.443563 INFO: Resetting torch num_threads to 100
2:25:48.445722 INFO: === FDR correction performed with classifier version -1 ===
2:25:48.446887 PROGRESS: ============================= Precursor FDR =============================
2:25:48.447044 PROGRESS: Total precursors accumulated: 5
2:25:48.447123 PROGRESS: Target precursors: 5 (100.00%)
2:25:48.447192 PROGRESS: Decoy precursors: 0 (0.00%)
2:25:48.447253 PROGRESS: 
2:25:48.447315 PROGRESS: Precursor Summary:
2:25:48.448658 PROGRESS: Channel   0:	 0.05 FDR:     5; 0.01 FDR:     5; 0.001 FDR:     5
2:25:48.448783 PROGRESS: 
2:25:48.448854 PROGRESS: Protein Summary:
2:25:48.450268 PROGRESS: Channel   0:	 0.05 FDR:     5; 0.01 FDR:     5; 0.001 FDR:     5
2:25:48.451598 PROGRESS: =========================================================================
2:25:48.646187 INFO: Starting optimization step 1.
2:25:48.646577 PROGRESS: === Extracting elution groups 8000 to 24000 ===
2:25:48.646693 PROGRESS: Extracting batch of 31672 precursors
2:25:48.664627 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:25:48.664807 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:25:48.664864 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:25:48.664908 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:25:48.665293 INFO: Starting candidate selection
2:25:51.456657 INFO: Starting candidate scoring
2:25:51.764659 INFO: Finished candidate processing
2:25:51.764828 INFO: Collecting candidate features
2:25:51.916070 INFO: Collecting fragment features
2:25:51.957640 INFO: Finished candidate scoring
2:25:52.040949 PROGRESS: === Extracted 47353 precursors and 471562 fragments ===
2:25:52.055131 INFO: performing precursor FDR with 47 features
2:25:52.055353 INFO: Decoy channel: -1
2:25:52.055409 INFO: Competetive: True
2:25:52.116883 INFO: Setting torch num_threads to 2 for FDR classification task
2:25:52.136549 WARNING: dropped 1 decoy PSMs due to missing features
2:25:53.206712 INFO: Test AUC: 0.549
2:25:53.206884 INFO: Train AUC: 0.557
2:25:53.206932 INFO: AUC difference: 1.58%
2:25:53.360252 INFO: Resetting torch num_threads to 100
2:25:53.367892 INFO: === FDR correction performed with classifier version -1 ===
2:25:53.369279 PROGRESS: ============================= Precursor FDR =============================
2:25:53.369470 PROGRESS: Total precursors accumulated: 1
2:25:53.369559 PROGRESS: Target precursors: 1 (100.00%)
2:25:53.369630 PROGRESS: Decoy precursors: 0 (0.00%)
2:25:53.369696 PROGRESS: 
2:25:53.369759 PROGRESS: Precursor Summary:
2:25:53.371313 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:25:53.371470 PROGRESS: 
2:25:53.371547 PROGRESS: Protein Summary:
2:25:53.373037 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:25:53.373176 PROGRESS: =========================================================================
2:25:53.690892 INFO: Starting optimization step 2.
2:25:53.691336 PROGRESS: === Extracting elution groups 24000 to 56000 ===
2:25:53.691477 PROGRESS: Extracting batch of 63174 precursors
2:25:53.723574 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:25:53.723804 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:25:53.723888 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:25:53.723937 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:25:53.724466 INFO: Starting candidate selection
2:25:57.830824 INFO: Starting candidate scoring
2:25:58.324515 INFO: Finished candidate processing
2:25:58.324644 INFO: Collecting candidate features
2:25:58.515072 INFO: Collecting fragment features
2:25:58.570896 INFO: Finished candidate scoring
2:25:58.705548 PROGRESS: === Extracted 110381 precursors and 1098084 fragments ===
2:25:58.730253 INFO: performing precursor FDR with 47 features
2:25:58.730452 INFO: Decoy channel: -1
2:25:58.730491 INFO: Competetive: True
2:25:58.846883 INFO: Setting torch num_threads to 2 for FDR classification task
2:25:58.887659 WARNING: dropped 1 decoy PSMs due to missing features
2:26:01.126378 INFO: Test AUC: 0.558
2:26:01.126538 INFO: Train AUC: 0.572
2:26:01.126573 INFO: AUC difference: 2.45%
2:26:01.242111 INFO: Resetting torch num_threads to 100
2:26:01.280924 INFO: === FDR correction performed with classifier version -1 ===
2:26:01.282115 PROGRESS: ============================= Precursor FDR =============================
2:26:01.282231 PROGRESS: Total precursors accumulated: 3
2:26:01.282299 PROGRESS: Target precursors: 3 (100.00%)
2:26:01.282372 PROGRESS: Decoy precursors: 0 (0.00%)
2:26:01.282429 PROGRESS: 
2:26:01.282478 PROGRESS: Precursor Summary:
2:26:01.283570 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
2:26:01.283675 PROGRESS: 
2:26:01.283736 PROGRESS: Protein Summary:
2:26:01.284893 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
2:26:01.285015 PROGRESS: =========================================================================
2:26:01.701061 INFO: Starting optimization step 3.
2:26:01.701568 PROGRESS: === Extracting elution groups 56000 to 120000 ===
2:26:01.701742 PROGRESS: Extracting batch of 126509 precursors
2:26:01.745762 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:26:01.745930 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:26:01.745978 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:26:01.746004 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:26:01.746498 INFO: Starting candidate selection
2:26:10.713465 INFO: Starting candidate scoring
2:26:11.809706 INFO: Finished candidate processing
2:26:11.809849 INFO: Collecting candidate features
2:26:12.330719 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 126139)
2:26:12.348840 INFO: Collecting fragment features
2:26:12.510393 INFO: Finished candidate scoring
2:26:12.854745 PROGRESS: === Extracted 236520 precursors and 2351100 fragments ===
2:26:12.902251 INFO: performing precursor FDR with 47 features
2:26:12.902447 INFO: Decoy channel: -1
2:26:12.902485 INFO: Competetive: True
2:26:13.159546 INFO: Setting torch num_threads to 2 for FDR classification task
2:26:13.257718 WARNING: dropped 1 target PSMs due to missing features
2:26:13.257912 WARNING: dropped 1 decoy PSMs due to missing features
2:26:19.902168 INFO: Test AUC: 0.565
2:26:19.902523 INFO: Train AUC: 0.581
2:26:19.902577 INFO: AUC difference: 2.86%
2:26:20.084929 INFO: Resetting torch num_threads to 100
2:26:20.118999 INFO: === FDR correction performed with classifier version -1 ===
2:26:20.120679 PROGRESS: ============================= Precursor FDR =============================
2:26:20.120854 PROGRESS: Total precursors accumulated: 3
2:26:20.120935 PROGRESS: Target precursors: 3 (100.00%)
2:26:20.121004 PROGRESS: Decoy precursors: 0 (0.00%)
2:26:20.121064 PROGRESS: 
2:26:20.121124 PROGRESS: Precursor Summary:
2:26:20.122489 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
2:26:20.122612 PROGRESS: 
2:26:20.122685 PROGRESS: Protein Summary:
2:26:20.124155 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
2:26:20.124276 PROGRESS: =========================================================================
2:26:20.942699 INFO: Starting optimization step 4.
2:26:20.943674 PROGRESS: === Extracting elution groups 120000 to 248000 ===
2:26:20.944183 PROGRESS: Extracting batch of 252969 precursors
2:26:21.068720 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:26:21.069072 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:26:21.069192 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:26:21.069285 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:26:21.069839 INFO: Starting candidate selection
2:26:36.706421 INFO: Starting candidate scoring
2:26:38.828722 INFO: Finished candidate processing
2:26:38.828963 INFO: Collecting candidate features
2:26:39.735171 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 252312)
2:26:39.748734 INFO: Collecting fragment features
2:26:39.973056 INFO: Finished candidate scoring
2:26:40.551089 PROGRESS: === Extracted 488832 precursors and 4855020 fragments ===
2:26:40.640468 INFO: performing precursor FDR with 47 features
2:26:40.640639 INFO: Decoy channel: -1
2:26:40.640672 INFO: Competetive: True
2:26:40.966308 INFO: Setting torch num_threads to 2 for FDR classification task
2:26:41.096196 WARNING: dropped 2 target PSMs due to missing features
2:26:41.096360 WARNING: dropped 2 decoy PSMs due to missing features
2:26:53.502639 INFO: Test AUC: 0.563
2:26:53.502798 INFO: Train AUC: 0.584
2:26:53.502834 INFO: AUC difference: 3.62%
2:26:53.659529 INFO: Resetting torch num_threads to 100
2:26:53.792658 INFO: === FDR correction performed with classifier version -1 ===
2:26:53.793604 PROGRESS: ============================= Precursor FDR =============================
2:26:53.793721 PROGRESS: Total precursors accumulated: 271
2:26:53.793788 PROGRESS: Target precursors: 249 (91.88%)
2:26:53.793848 PROGRESS: Decoy precursors: 22 (8.12%)
2:26:53.793899 PROGRESS: 
2:26:53.793950 PROGRESS: Precursor Summary:
2:26:53.795009 PROGRESS: Channel   0:	 0.05 FDR:   155; 0.01 FDR:    35; 0.001 FDR:    35
2:26:53.795121 PROGRESS: 
2:26:53.795183 PROGRESS: Protein Summary:
2:26:53.796329 PROGRESS: Channel   0:	 0.05 FDR:   153; 0.01 FDR:    34; 0.001 FDR:    34
2:26:53.796440 PROGRESS: =========================================================================
2:26:54.808257 INFO: Starting optimization step 5.
2:26:54.808770 PROGRESS: === Extracting elution groups 248000 to 504000 ===
2:26:54.808901 PROGRESS: Extracting batch of 505926 precursors
2:26:55.029101 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:26:55.029293 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:26:55.029368 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:26:55.029405 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:26:55.030044 INFO: Starting candidate selection
2:27:23.708109 INFO: Starting candidate scoring
2:27:27.756989 INFO: Finished candidate processing
2:27:27.757151 INFO: Collecting candidate features
2:27:29.825758 WARNING: intensity_correlation has 5 NaNs ( 0.00 % out of 504636)
2:27:29.859779 INFO: Collecting fragment features
2:27:30.348773 INFO: Finished candidate scoring
2:27:31.569587 PROGRESS: === Extracted 993468 precursors and 9865012 fragments ===
2:27:31.808134 INFO: performing precursor FDR with 47 features
2:27:31.808370 INFO: Decoy channel: -1
2:27:31.808409 INFO: Competetive: True
2:27:32.826097 INFO: Setting torch num_threads to 2 for FDR classification task
2:27:33.209853 WARNING: dropped 4 target PSMs due to missing features
2:27:33.210036 WARNING: dropped 5 decoy PSMs due to missing features
2:27:58.080107 INFO: Test AUC: 0.569
2:27:58.080343 INFO: Train AUC: 0.582
2:27:58.080382 INFO: AUC difference: 2.22%
2:27:58.268936 INFO: Resetting torch num_threads to 100
2:27:58.356375 INFO: === FDR correction performed with classifier version -1 ===
2:27:58.357828 PROGRESS: ============================= Precursor FDR =============================
2:27:58.358078 PROGRESS: Total precursors accumulated: 1,401
2:27:58.358252 PROGRESS: Target precursors: 1,277 (91.15%)
2:27:58.358458 PROGRESS: Decoy precursors: 124 (8.85%)
2:27:58.358557 PROGRESS: 
2:27:58.358629 PROGRESS: Precursor Summary:
2:27:58.360076 PROGRESS: Channel   0:	 0.05 FDR:   909; 0.01 FDR:   596; 0.001 FDR:   401
2:27:58.360192 PROGRESS: 
2:27:58.360268 PROGRESS: Protein Summary:
2:27:58.361909 PROGRESS: Channel   0:	 0.05 FDR:   784; 0.01 FDR:   522; 0.001 FDR:   363
2:27:58.362039 PROGRESS: =========================================================================
2:27:58.537113 INFO: fragments_df_filtered: 5000
2:27:59.550139 INFO: calibration group: precursor, fitting mz estimator 
2:27:59.714741 INFO: calibration group: precursor, fitting rt estimator 
2:27:59.865076 INFO: calibration group: fragment, fitting mz estimator 
2:28:00.360497 INFO: calibration group: precursor, predicting mz
2:28:00.485628 INFO: calibration group: precursor, predicting rt
2:28:00.933637 INFO: calibration group: fragment, predicting mz
2:28:01.858534 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:28:01.859068 INFO: Starting optimization step 6.
2:28:01.859184 PROGRESS: === Extracting elution groups 0 to 248000 ===
2:28:01.859308 PROGRESS: Extracting batch of 490122 precursors
2:28:02.086725 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:28:02.087189 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:28:02.087297 INFO: FWHM in RT is 2.92 seconds, sigma is 0.38
2:28:02.087374 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:28:02.087848 INFO: Starting candidate selection
2:28:28.716527 INFO: Starting candidate scoring
2:28:36.057079 INFO: Finished candidate processing
2:28:36.057230 INFO: Collecting candidate features
2:28:39.514263 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 977726)
2:28:39.575376 INFO: Collecting fragment features
2:28:40.771650 INFO: Finished candidate scoring
2:28:41.936095 PROGRESS: === Extracted 977726 precursors and 9613164 fragments ===
2:28:41.937453 INFO: performing precursor FDR with 47 features
2:28:41.937691 INFO: Decoy channel: -1
2:28:41.937801 INFO: Competetive: True
2:28:42.466711 INFO: Setting torch num_threads to 2 for FDR classification task
2:28:42.821037 WARNING: dropped 2 target PSMs due to missing features
2:28:42.821415 WARNING: dropped 2 decoy PSMs due to missing features
2:29:06.857526 INFO: Test AUC: 0.568
2:29:06.857755 INFO: Train AUC: 0.583
2:29:06.857804 INFO: AUC difference: 2.53%
2:29:07.085566 INFO: Resetting torch num_threads to 100
2:29:07.150160 INFO: === FDR correction performed with classifier version 5 ===
2:29:07.152183 PROGRESS: ============================= Precursor FDR =============================
2:29:07.152422 PROGRESS: Total precursors accumulated: 975
2:29:07.152524 PROGRESS: Target precursors: 890 (91.28%)
2:29:07.152602 PROGRESS: Decoy precursors: 85 (8.72%)
2:29:07.152689 PROGRESS: 
2:29:07.152761 PROGRESS: Precursor Summary:
2:29:07.154851 PROGRESS: Channel   0:	 0.05 FDR:   721; 0.01 FDR:   514; 0.001 FDR:   339
2:29:07.155027 PROGRESS: 
2:29:07.155113 PROGRESS: Protein Summary:
2:29:07.157447 PROGRESS: Channel   0:	 0.05 FDR:   654; 0.01 FDR:   477; 0.001 FDR:   324
2:29:07.157595 PROGRESS: =========================================================================
2:29:07.225945 INFO: fragments_df_filtered: 5000
2:29:08.043113 INFO: calibration group: precursor, fitting mz estimator 
2:29:08.188636 INFO: calibration group: precursor, fitting rt estimator 
2:29:08.306298 INFO: calibration group: fragment, fitting mz estimator 
2:29:10.200539 INFO: calibration group: precursor, predicting mz
2:29:10.292338 INFO: calibration group: precursor, predicting rt
2:29:10.487457 INFO: calibration group: fragment, predicting mz
2:29:10.913809 INFO: === checking if optimization conditions were reached ===
2:29:10.916780 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
2:29:10.918052 PROGRESS: ❌ ms1_error      : 13.2433 > 10.0000 or insufficient steps taken.
2:29:10.918111 INFO: ==============================================
2:29:10.918223 INFO: Starting optimization step 7.
2:29:10.918304 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:29:10.926481 PROGRESS: Extracting batch of 237153 precursors
2:29:11.000828 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:29:11.000978 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:29:11.001017 INFO: FWHM in RT is 2.89 seconds, sigma is 0.37
2:29:11.001044 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:29:11.001339 INFO: Starting candidate selection
2:29:23.855233 INFO: Starting candidate scoring
2:29:27.060564 INFO: Finished candidate processing
2:29:27.060699 INFO: Collecting candidate features
2:29:27.991259 WARNING: intensity_correlation has 12 NaNs ( 0.00 % out of 472854)
2:29:28.009775 INFO: Collecting fragment features
2:29:28.297253 INFO: Finished candidate scoring
2:29:28.669014 PROGRESS: === Extracted 472854 precursors and 4119962 fragments ===
2:29:28.669511 INFO: performing precursor FDR with 47 features
2:29:28.669563 INFO: Decoy channel: -1
2:29:28.669587 INFO: Competetive: True
2:29:28.819339 INFO: Setting torch num_threads to 2 for FDR classification task
2:29:28.910126 WARNING: dropped 8 target PSMs due to missing features
2:29:28.910285 WARNING: dropped 4 decoy PSMs due to missing features
2:29:37.065621 INFO: Test AUC: 0.563
2:29:37.065819 INFO: Train AUC: 0.585
2:29:37.065852 INFO: AUC difference: 3.84%
2:29:37.186905 INFO: Resetting torch num_threads to 100
2:29:37.200410 INFO: === FDR correction performed with classifier version 6 ===
2:29:37.201313 PROGRESS: ============================= Precursor FDR =============================
2:29:37.201442 PROGRESS: Total precursors accumulated: 718
2:29:37.201503 PROGRESS: Target precursors: 654 (91.09%)
2:29:37.201555 PROGRESS: Decoy precursors: 64 (8.91%)
2:29:37.201601 PROGRESS: 
2:29:37.201646 PROGRESS: Precursor Summary:
2:29:37.202816 PROGRESS: Channel   0:	 0.05 FDR:   517; 0.01 FDR:   380; 0.001 FDR:   257
2:29:37.202921 PROGRESS: 
2:29:37.202978 PROGRESS: Protein Summary:
2:29:37.204223 PROGRESS: Channel   0:	 0.05 FDR:   483; 0.01 FDR:   358; 0.001 FDR:   247
2:29:37.204317 PROGRESS: =========================================================================
2:29:37.233274 INFO: fragments_df_filtered: 4028
2:29:37.670118 INFO: calibration group: precursor, fitting mz estimator 
2:29:37.826931 INFO: calibration group: precursor, fitting rt estimator 
2:29:37.884824 INFO: calibration group: fragment, fitting mz estimator 
2:29:38.192574 INFO: calibration group: precursor, predicting mz
2:29:38.231694 INFO: calibration group: precursor, predicting rt
2:29:38.390814 INFO: calibration group: fragment, predicting mz
2:29:38.728971 INFO: === checking if optimization conditions were reached ===
2:29:38.731481 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
2:29:38.732627 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
2:29:38.732684 INFO: ==============================================
2:29:38.732799 PROGRESS: Optimization finished for ms2_error, ms1_error.
2:29:39.110909 INFO: calibration group: precursor, predicting mz
2:29:39.143547 INFO: calibration group: precursor, predicting rt
2:29:39.293426 INFO: calibration group: fragment, predicting mz
2:29:39.628945 INFO: Starting optimization step 0.
2:29:39.629305 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:29:39.629415 PROGRESS: Extracting batch of 237153 precursors
2:29:39.694711 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:29:39.694839 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:29:39.694879 INFO: FWHM in RT is 2.74 seconds, sigma is 0.35
2:29:39.694901 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:29:39.695223 INFO: Starting candidate selection
2:29:51.911163 INFO: Starting candidate scoring
2:29:55.303940 INFO: Finished candidate processing
2:29:55.304041 INFO: Collecting candidate features
2:29:56.101962 WARNING: intensity_correlation has 9 NaNs ( 0.00 % out of 472890)
2:29:56.120375 INFO: Collecting fragment features
2:29:56.384675 INFO: Finished candidate scoring
2:29:56.606485 PROGRESS: === Extracted 472890 precursors and 4112939 fragments ===
2:29:56.606957 INFO: performing precursor FDR with 47 features
2:29:56.606998 INFO: Decoy channel: -1
2:29:56.607025 INFO: Competetive: True
2:29:56.745073 INFO: Setting torch num_threads to 2 for FDR classification task
2:29:56.830055 WARNING: dropped 6 target PSMs due to missing features
2:29:56.830198 WARNING: dropped 3 decoy PSMs due to missing features
2:30:04.777014 INFO: Test AUC: 0.568
2:30:04.777202 INFO: Train AUC: 0.589
2:30:04.777237 INFO: AUC difference: 3.52%
2:30:04.905452 INFO: Resetting torch num_threads to 100
2:30:04.917980 INFO: === FDR correction performed with classifier version 7 ===
2:30:04.918918 PROGRESS: ============================= Precursor FDR =============================
2:30:04.919052 PROGRESS: Total precursors accumulated: 813
2:30:04.919114 PROGRESS: Target precursors: 741 (91.14%)
2:30:04.919166 PROGRESS: Decoy precursors: 72 (8.86%)
2:30:04.919210 PROGRESS: 
2:30:04.919255 PROGRESS: Precursor Summary:
2:30:04.920416 PROGRESS: Channel   0:	 0.05 FDR:   634; 0.01 FDR:   412; 0.001 FDR:   246
2:30:04.920516 PROGRESS: 
2:30:04.920569 PROGRESS: Protein Summary:
2:30:04.921855 PROGRESS: Channel   0:	 0.05 FDR:   591; 0.01 FDR:   386; 0.001 FDR:   239
2:30:04.921951 PROGRESS: =========================================================================
2:30:04.939312 INFO: fragments_df_filtered: 4325
2:30:05.367154 INFO: calibration group: precursor, fitting mz estimator 
2:30:05.419149 INFO: calibration group: precursor, fitting rt estimator 
2:30:05.472326 INFO: calibration group: fragment, fitting mz estimator 
2:30:05.812525 INFO: calibration group: precursor, predicting mz
2:30:05.843801 INFO: calibration group: precursor, predicting rt
2:30:05.991993 INFO: calibration group: fragment, predicting mz
2:30:06.336040 INFO: === checking if optimization conditions were reached ===
2:30:06.336350 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2:30:06.338270 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 247.5350.
2:30:06.338325 INFO: ==============================================
2:30:06.338430 INFO: Starting optimization step 1.
2:30:06.338497 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:30:06.338578 PROGRESS: Extracting batch of 237153 precursors
2:30:06.395587 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:30:06.395728 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:30:06.395769 INFO: FWHM in RT is 2.70 seconds, sigma is 0.35
2:30:06.395790 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:30:06.396092 INFO: Starting candidate selection
2:30:18.513508 INFO: Starting candidate scoring
2:30:22.778451 INFO: Finished candidate processing
2:30:22.778660 INFO: Collecting candidate features
2:30:23.824049 WARNING: intensity_correlation has 86 NaNs ( 0.02 % out of 469551)
2:30:23.824706 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 469551)
2:30:23.842968 INFO: Collecting fragment features
2:30:24.103051 INFO: Finished candidate scoring
2:30:24.588272 PROGRESS: === Extracted 469551 precursors and 3939354 fragments ===
2:30:24.588767 INFO: performing precursor FDR with 47 features
2:30:24.588814 INFO: Decoy channel: -1
2:30:24.588839 INFO: Competetive: True
2:30:24.730480 INFO: Setting torch num_threads to 2 for FDR classification task
2:30:24.814434 WARNING: dropped 41 target PSMs due to missing features
2:30:24.814569 WARNING: dropped 45 decoy PSMs due to missing features
2:30:32.527828 INFO: Test AUC: 0.564
2:30:32.528158 INFO: Train AUC: 0.585
2:30:32.528221 INFO: AUC difference: 3.64%
2:30:32.759110 INFO: Resetting torch num_threads to 100
2:30:32.790701 INFO: === FDR correction performed with classifier version 7 ===
2:30:32.795212 PROGRESS: ============================= Precursor FDR =============================
2:30:32.795466 PROGRESS: Total precursors accumulated: 907
2:30:32.795574 PROGRESS: Target precursors: 825 (90.96%)
2:30:32.795652 PROGRESS: Decoy precursors: 82 (9.04%)
2:30:32.795722 PROGRESS: 
2:30:32.795789 PROGRESS: Precursor Summary:
2:30:32.797913 PROGRESS: Channel   0:	 0.05 FDR:   676; 0.01 FDR:   407; 0.001 FDR:   240
2:30:32.798090 PROGRESS: 
2:30:32.798176 PROGRESS: Protein Summary:
2:30:32.800689 PROGRESS: Channel   0:	 0.05 FDR:   631; 0.01 FDR:   381; 0.001 FDR:   235
2:30:32.800880 PROGRESS: =========================================================================
2:30:32.829680 INFO: fragments_df_filtered: 4336
2:30:33.485725 INFO: calibration group: precursor, fitting mz estimator 
2:30:33.630804 INFO: calibration group: precursor, fitting rt estimator 
2:30:33.692213 INFO: calibration group: fragment, fitting mz estimator 
2:30:34.068694 INFO: calibration group: precursor, predicting mz
2:30:34.147864 INFO: calibration group: precursor, predicting rt
2:30:34.336553 INFO: calibration group: fragment, predicting mz
2:30:34.726620 INFO: === checking if optimization conditions were reached ===
2:30:34.727214 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2:30:34.729867 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 114.4056.
2:30:34.730010 INFO: ==============================================
2:30:34.730276 INFO: Starting optimization step 2.
2:30:34.730511 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:30:34.730742 PROGRESS: Extracting batch of 237153 precursors
2:30:34.807404 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:30:34.807670 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:30:34.807767 INFO: FWHM in RT is 2.70 seconds, sigma is 0.35
2:30:34.807852 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:30:34.808242 INFO: Starting candidate selection
2:30:44.950791 INFO: Starting candidate scoring
2:30:48.992489 INFO: Finished candidate processing
2:30:48.992710 INFO: Collecting candidate features
2:30:50.686374 WARNING: intensity_correlation has 149 NaNs ( 0.03 % out of 467474)
2:30:50.720610 INFO: Collecting fragment features
2:30:51.059501 INFO: Finished candidate scoring
2:30:51.546095 PROGRESS: === Extracted 467474 precursors and 3752786 fragments ===
2:30:51.548560 INFO: performing precursor FDR with 47 features
2:30:51.548633 INFO: Decoy channel: -1
2:30:51.548665 INFO: Competetive: True
2:30:51.733094 INFO: Setting torch num_threads to 2 for FDR classification task
2:30:51.888921 WARNING: dropped 75 target PSMs due to missing features
2:30:51.889201 WARNING: dropped 74 decoy PSMs due to missing features
2:31:03.776648 INFO: Test AUC: 0.558
2:31:03.776816 INFO: Train AUC: 0.582
2:31:03.776863 INFO: AUC difference: 4.15%
2:31:04.007011 INFO: Resetting torch num_threads to 100
2:31:04.042239 INFO: === FDR correction performed with classifier version 7 ===
2:31:04.044481 PROGRESS: ============================= Precursor FDR =============================
2:31:04.044761 PROGRESS: Total precursors accumulated: 1,074
2:31:04.044933 PROGRESS: Target precursors: 975 (90.78%)
2:31:04.045079 PROGRESS: Decoy precursors: 99 (9.22%)
2:31:04.045187 PROGRESS: 
2:31:04.045280 PROGRESS: Precursor Summary:
2:31:04.047703 PROGRESS: Channel   0:	 0.05 FDR:   709; 0.01 FDR:   387; 0.001 FDR:   330
2:31:04.047921 PROGRESS: 
2:31:04.048027 PROGRESS: Protein Summary:
2:31:04.050446 PROGRESS: Channel   0:	 0.05 FDR:   659; 0.01 FDR:   367; 0.001 FDR:   317
2:31:04.050647 PROGRESS: =========================================================================
2:31:04.095956 INFO: fragments_df_filtered: 3983
2:31:04.906803 INFO: calibration group: precursor, fitting mz estimator 
2:31:05.155915 INFO: calibration group: precursor, fitting rt estimator 
2:31:05.236170 INFO: calibration group: fragment, fitting mz estimator 
2:31:05.575944 INFO: calibration group: precursor, predicting mz
2:31:05.667645 INFO: calibration group: precursor, predicting rt
2:31:05.875804 INFO: calibration group: fragment, predicting mz
2:31:06.289031 INFO: === checking if optimization conditions were reached ===
2:31:06.290025 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2:31:06.293466 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 91.0761.
2:31:06.293879 INFO: ==============================================
2:31:06.294233 INFO: Starting optimization step 3.
2:31:06.294558 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:31:06.294964 PROGRESS: Extracting batch of 237153 precursors
2:31:06.558382 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:31:06.558602 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:31:06.558679 INFO: FWHM in RT is 2.71 seconds, sigma is 0.35
2:31:06.558715 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:31:06.559127 INFO: Starting candidate selection
2:31:16.570346 INFO: Starting candidate scoring
2:31:20.124997 INFO: Finished candidate processing
2:31:20.125166 INFO: Collecting candidate features
2:31:21.425056 WARNING: intensity_correlation has 159 NaNs ( 0.03 % out of 466469)
2:31:21.449942 INFO: Collecting fragment features
2:31:21.832549 INFO: Finished candidate scoring
2:31:22.474438 PROGRESS: === Extracted 466469 precursors and 3682712 fragments ===
2:31:22.475336 INFO: performing precursor FDR with 47 features
2:31:22.475486 INFO: Decoy channel: -1
2:31:22.475566 INFO: Competetive: True
2:31:22.718101 INFO: Setting torch num_threads to 2 for FDR classification task
2:31:22.879891 WARNING: dropped 88 target PSMs due to missing features
2:31:22.880188 WARNING: dropped 71 decoy PSMs due to missing features
2:31:34.736187 INFO: Test AUC: 0.562
2:31:34.736489 INFO: Train AUC: 0.579
2:31:34.736535 INFO: AUC difference: 2.96%
2:31:34.925746 INFO: Resetting torch num_threads to 100
2:31:34.947616 INFO: === FDR correction performed with classifier version 7 ===
2:31:34.949315 PROGRESS: ============================= Precursor FDR =============================
2:31:34.949538 PROGRESS: Total precursors accumulated: 1,017
2:31:34.949626 PROGRESS: Target precursors: 924 (90.86%)
2:31:34.949694 PROGRESS: Decoy precursors: 93 (9.14%)
2:31:34.949753 PROGRESS: 
2:31:34.949810 PROGRESS: Precursor Summary:
2:31:34.951524 PROGRESS: Channel   0:	 0.05 FDR:   709; 0.01 FDR:   453; 0.001 FDR:   342
2:31:34.951679 PROGRESS: 
2:31:34.951752 PROGRESS: Protein Summary:
2:31:34.953201 PROGRESS: Channel   0:	 0.05 FDR:   663; 0.01 FDR:   427; 0.001 FDR:   327
2:31:34.953315 PROGRESS: =========================================================================
2:31:34.973321 INFO: fragments_df_filtered: 4555
2:31:35.450567 INFO: calibration group: precursor, fitting mz estimator 
2:31:35.655112 INFO: calibration group: precursor, fitting rt estimator 
2:31:35.722084 INFO: calibration group: fragment, fitting mz estimator 
2:31:36.193484 INFO: calibration group: precursor, predicting mz
2:31:36.213124 INFO: calibration group: precursor, predicting rt
2:31:36.378514 INFO: calibration group: fragment, predicting mz
2:31:36.603696 INFO: === checking if optimization conditions were reached ===
2:31:36.604271 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2:31:36.607007 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 72.5543.
2:31:36.607152 INFO: ==============================================
2:31:36.607414 INFO: Starting optimization step 4.
2:31:36.607651 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:31:36.607893 PROGRESS: Extracting batch of 110644 precursors
2:31:36.765469 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:31:36.765784 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:31:36.765876 INFO: FWHM in RT is 2.66 seconds, sigma is 0.34
2:31:36.765941 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:31:36.766357 INFO: Starting candidate selection
2:31:41.498175 INFO: Starting candidate scoring
2:31:43.217931 INFO: Finished candidate processing
2:31:43.218075 INFO: Collecting candidate features
2:31:43.767849 WARNING: intensity_correlation has 81 NaNs ( 0.04 % out of 217433)
2:31:43.781279 INFO: Collecting fragment features
2:31:43.958391 INFO: Finished candidate scoring
2:31:44.157536 PROGRESS: === Extracted 217433 precursors and 1681345 fragments ===
2:31:44.158605 INFO: performing precursor FDR with 47 features
2:31:44.158731 INFO: Decoy channel: -1
2:31:44.158823 INFO: Competetive: True
2:31:44.307858 INFO: Setting torch num_threads to 2 for FDR classification task
2:31:44.396424 WARNING: dropped 38 target PSMs due to missing features
2:31:44.396910 WARNING: dropped 43 decoy PSMs due to missing features
2:31:49.974828 INFO: Test AUC: 0.558
2:31:49.975079 INFO: Train AUC: 0.586
2:31:49.975118 INFO: AUC difference: 4.83%
2:31:50.106887 INFO: Resetting torch num_threads to 100
2:31:50.119035 INFO: === FDR correction performed with classifier version 7 ===
2:31:50.120414 PROGRESS: ============================= Precursor FDR =============================
2:31:50.120746 PROGRESS: Total precursors accumulated: 526
2:31:50.120981 PROGRESS: Target precursors: 478 (90.87%)
2:31:50.121189 PROGRESS: Decoy precursors: 48 (9.13%)
2:31:50.121386 PROGRESS: 
2:31:50.121581 PROGRESS: Precursor Summary:
2:31:50.123054 PROGRESS: Channel   0:	 0.05 FDR:   347; 0.01 FDR:   207; 0.001 FDR:   191
2:31:50.123352 PROGRESS: 
2:31:50.123570 PROGRESS: Protein Summary:
2:31:50.125196 PROGRESS: Channel   0:	 0.05 FDR:   338; 0.01 FDR:   202; 0.001 FDR:   186
2:31:50.125482 PROGRESS: =========================================================================
2:31:50.137734 INFO: fragments_df_filtered: 2118
2:31:50.497455 INFO: calibration group: precursor, fitting mz estimator 
2:31:50.671177 INFO: calibration group: precursor, fitting rt estimator 
2:31:50.723764 INFO: calibration group: fragment, fitting mz estimator 
2:31:50.937027 INFO: calibration group: precursor, predicting mz
2:31:50.953108 INFO: calibration group: precursor, predicting rt
2:31:51.058409 INFO: calibration group: fragment, predicting mz
2:31:51.269359 INFO: === checking if optimization conditions were reached ===
2:31:51.269918 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2:31:51.272557 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 67.4231.
2:31:51.272689 INFO: ==============================================
2:31:51.272945 INFO: Starting optimization step 5.
2:31:51.273161 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:31:51.273390 PROGRESS: Extracting batch of 110644 precursors
2:31:51.316756 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:31:51.316898 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:31:51.316953 INFO: FWHM in RT is 2.81 seconds, sigma is 0.36
2:31:51.316983 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:31:51.317338 INFO: Starting candidate selection
2:31:55.981646 INFO: Starting candidate scoring
2:31:57.731722 INFO: Finished candidate processing
2:31:57.731982 INFO: Collecting candidate features
2:31:58.492422 WARNING: intensity_correlation has 87 NaNs ( 0.04 % out of 217493)
2:31:58.507398 INFO: Collecting fragment features
2:31:58.677699 INFO: Finished candidate scoring
2:31:58.880448 PROGRESS: === Extracted 217493 precursors and 1668797 fragments ===
2:31:58.881174 INFO: performing precursor FDR with 47 features
2:31:58.881229 INFO: Decoy channel: -1
2:31:58.881267 INFO: Competetive: True
2:31:59.011886 INFO: Setting torch num_threads to 2 for FDR classification task
2:31:59.089774 WARNING: dropped 46 target PSMs due to missing features
2:31:59.090144 WARNING: dropped 41 decoy PSMs due to missing features
2:32:04.346821 INFO: Test AUC: 0.559
2:32:04.346991 INFO: Train AUC: 0.586
2:32:04.347031 INFO: AUC difference: 4.63%
2:32:04.494064 INFO: Resetting torch num_threads to 100
2:32:04.508588 INFO: === FDR correction performed with classifier version 7 ===
2:32:04.509784 PROGRESS: ============================= Precursor FDR =============================
2:32:04.509932 PROGRESS: Total precursors accumulated: 610
2:32:04.510009 PROGRESS: Target precursors: 555 (90.98%)
2:32:04.510075 PROGRESS: Decoy precursors: 55 (9.02%)
2:32:04.510134 PROGRESS: 
2:32:04.510192 PROGRESS: Precursor Summary:
2:32:04.511640 PROGRESS: Channel   0:	 0.05 FDR:   446; 0.01 FDR:   270; 0.001 FDR:   264
2:32:04.511758 PROGRESS: 
2:32:04.511830 PROGRESS: Protein Summary:
2:32:04.513456 PROGRESS: Channel   0:	 0.05 FDR:   433; 0.01 FDR:   263; 0.001 FDR:   257
2:32:04.513571 PROGRESS: =========================================================================
2:32:04.528772 INFO: fragments_df_filtered: 2643
2:32:04.920295 INFO: calibration group: precursor, fitting mz estimator 
2:32:05.088278 INFO: calibration group: precursor, fitting rt estimator 
2:32:05.181629 INFO: calibration group: fragment, fitting mz estimator 
2:32:05.390589 INFO: calibration group: precursor, predicting mz
2:32:05.409817 INFO: calibration group: precursor, predicting rt
2:32:05.587446 INFO: calibration group: fragment, predicting mz
2:32:05.835521 INFO: === checking if optimization conditions were reached ===
2:32:05.835926 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2:32:05.838529 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 66.2123.
2:32:05.838598 INFO: ==============================================
2:32:05.838717 INFO: Starting optimization step 6.
2:32:05.838798 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:32:05.838880 PROGRESS: Extracting batch of 110644 precursors
2:32:05.882658 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:32:05.883035 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:32:05.883166 INFO: FWHM in RT is 2.71 seconds, sigma is 0.35
2:32:05.883274 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:32:05.883830 INFO: Starting candidate selection
2:32:10.634279 INFO: Starting candidate scoring
2:32:12.361334 INFO: Finished candidate processing
2:32:12.361454 INFO: Collecting candidate features
2:32:12.911088 WARNING: intensity_correlation has 84 NaNs ( 0.04 % out of 217283)
2:32:12.929329 INFO: Collecting fragment features
2:32:13.125192 INFO: Finished candidate scoring
2:32:13.436590 PROGRESS: === Extracted 217283 precursors and 1683364 fragments ===
2:32:13.437012 INFO: performing precursor FDR with 47 features
2:32:13.437053 INFO: Decoy channel: -1
2:32:13.437078 INFO: Competetive: True
2:32:13.572278 INFO: Setting torch num_threads to 2 for FDR classification task
2:32:13.649841 WARNING: dropped 47 target PSMs due to missing features
2:32:13.650059 WARNING: dropped 37 decoy PSMs due to missing features
2:32:18.336728 INFO: Test AUC: 0.550
2:32:18.336956 INFO: Train AUC: 0.588
2:32:18.336996 INFO: AUC difference: 6.46%
2:32:18.337024 WARNING: AUC difference > 5%. This may indicate overfitting.
2:32:18.488832 INFO: Resetting torch num_threads to 100
2:32:18.503603 INFO: === FDR correction performed with classifier version 7 ===
2:32:18.504525 PROGRESS: ============================= Precursor FDR =============================
2:32:18.504627 PROGRESS: Total precursors accumulated: 637
2:32:18.504691 PROGRESS: Target precursors: 579 (90.89%)
2:32:18.504755 PROGRESS: Decoy precursors: 58 (9.11%)
2:32:18.504804 PROGRESS: 
2:32:18.504850 PROGRESS: Precursor Summary:
2:32:18.505847 PROGRESS: Channel   0:	 0.05 FDR:   368; 0.01 FDR:   217; 0.001 FDR:   211
2:32:18.505950 PROGRESS: 
2:32:18.506013 PROGRESS: Protein Summary:
2:32:18.507691 PROGRESS: Channel   0:	 0.05 FDR:   358; 0.01 FDR:   211; 0.001 FDR:   206
2:32:18.507812 PROGRESS: =========================================================================
2:32:18.520878 INFO: fragments_df_filtered: 2212
2:32:18.837556 INFO: calibration group: precursor, fitting mz estimator 
2:32:19.094994 INFO: calibration group: precursor, fitting rt estimator 
2:32:19.224499 INFO: calibration group: fragment, fitting mz estimator 
2:32:19.635269 INFO: calibration group: precursor, predicting mz
2:32:19.651580 INFO: calibration group: precursor, predicting rt
2:32:19.779413 INFO: calibration group: fragment, predicting mz
2:32:20.021600 INFO: === checking if optimization conditions were reached ===
2:32:20.022009 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
2:32:20.023615 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 67.4231 found after 7 searches.
2:32:20.023681 INFO: ==============================================
2:32:20.023793 PROGRESS: Optimization finished for rt_error.
2:32:20.336214 INFO: calibration group: precursor, predicting mz
2:32:20.353512 INFO: calibration group: precursor, predicting rt
2:32:20.442001 INFO: calibration group: fragment, predicting mz
2:32:20.703956 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:32:20.704243 PROGRESS: ==============================================
2:32:20.705034 PROGRESS: ms2_error      : 15.0000
2:32:20.705130 PROGRESS: ms1_error      : 10.0000
2:32:20.705195 PROGRESS: rt_error       : 67.4231
2:32:20.705251 PROGRESS: ==============================================
2:32:20.707490 INFO: calibration group: precursor, predicting mz
2:32:22.417467 INFO: calibration group: precursor, predicting rt
2:32:30.488248 INFO: calibration group: fragment, predicting mz
2:32:50.417404 PROGRESS: Extracting batch of 10183864 precursors
2:32:54.216813 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:32:54.217242 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:32:54.217363 INFO: FWHM in RT is 2.71 seconds, sigma is 0.35
2:32:54.217444 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:32:54.218049 INFO: Starting candidate selection
2:39:40.350643 INFO: Applying score cutoff of 44.24824793243408
2:39:40.829966 INFO: Removed 10067347 precursors with score below cutoff
2:39:44.407190 INFO: Starting candidate scoring
2:41:02.628484 INFO: Finished candidate processing
2:41:02.628845 INFO: Collecting candidate features
2:41:35.136272 WARNING: intensity_correlation has 193 NaNs ( 0.00 % out of 10248398)
2:41:35.862506 INFO: Collecting fragment features
2:41:48.661504 INFO: Finished candidate scoring
2:42:11.740169 INFO: === FDR correction performed with classifier version 13 ===
2:42:11.746720 INFO: performing precursor FDR with 47 features
2:42:11.746881 INFO: Decoy channel: -1
2:42:11.746925 INFO: Competetive: True
2:42:17.234546 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:20.546703 WARNING: dropped 116 target PSMs due to missing features
2:42:20.547280 WARNING: dropped 77 decoy PSMs due to missing features
2:47:36.173002 INFO: Test AUC: 0.580
2:47:36.173331 INFO: Train AUC: 0.584
2:47:36.173398 INFO: AUC difference: 0.76%
2:47:37.435717 INFO: Resetting torch num_threads to 100
2:47:37.917407 INFO: Removing fragments below FDR threshold
2:47:38.974788 PROGRESS: ============================= Precursor FDR =============================
2:47:38.975483 PROGRESS: Total precursors accumulated: 26,844
2:47:38.975759 PROGRESS: Target precursors: 26,579 (99.01%)
2:47:38.975993 PROGRESS: Decoy precursors: 265 (0.99%)
2:47:38.976215 PROGRESS: 
2:47:38.976432 PROGRESS: Precursor Summary:
2:47:39.007298 PROGRESS: Channel   0:	 0.05 FDR: 26,579; 0.01 FDR: 26,579; 0.001 FDR: 18,455
2:47:39.007950 PROGRESS: 
2:47:39.008185 PROGRESS: Protein Summary:
2:47:39.051761 PROGRESS: Channel   0:	 0.05 FDR: 7,790; 0.01 FDR: 7,790; 0.001 FDR: 5,942
2:47:39.052419 PROGRESS: =========================================================================
2:47:40.204077 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:47:41.001338 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:47:41.001815 INFO: Quantification results path: run_output_Astral/alphadia_1.10_noMBR/quant
2:47:41.001972 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2 at run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:47:41.003238 INFO: Initializing RawFileManager
2:48:17.529154 INFO: Determining DIA cycle
2:48:17.548157 INFO: Found cycle with start 0.00 min and length 303.
2:48:17.911044 INFO: RT (min)            : 0.0 - 26.9
2:48:17.911170 INFO: RT duration (sec)   : 1611.2
2:48:17.911246 INFO: RT duration (min)   : 26.9
2:48:17.911301 INFO: Cycle len (scans)   : 303
2:48:17.911339 INFO: Cycle len (sec)     : 1.65
2:48:17.911374 INFO: Number of cycles    : 977
2:48:17.911411 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:48:20.024980 INFO: Initializing CalibrationManager
2:48:20.025384 INFO: Loading calibration config
2:48:20.026442 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'}]
2:48:20.026587 INFO: Calibration group :fragment, found 1 estimator(s)
2:48:20.026727 INFO: Calibration group :precursor, found 3 estimator(s)
2:48:20.026877 INFO: Disabling ion mobility calibration
2:48:20.026928 INFO: removed mobility estimator from group precursor
2:48:20.027196 INFO: Initializing OptimizationManager
2:48:20.027391 INFO: initial parameter: ms1_error = 30
2:48:20.027505 INFO: initial parameter: ms2_error = 30
2:48:20.027596 INFO: initial parameter: rt_error = 805.6002197265625
2:48:20.027673 INFO: initial parameter: mobility_error = 0.1
2:48:20.027757 INFO: initial parameter: column_type = library
2:48:20.027845 INFO: initial parameter: num_candidates = 1
2:48:20.027918 INFO: initial parameter: classifier_version = -1
2:48:20.027993 INFO: initial parameter: fwhm_rt = 5
2:48:20.028075 INFO: initial parameter: fwhm_mobility = 0.01
2:48:20.028137 INFO: initial parameter: score_cutoff = 0
2:48:20.028245 INFO: Initializing TimingManager
2:48:20.028337 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:48:20.028497 INFO: FDRManager not loaded from disk.
2:48:20.028540 INFO: Initializing FDRManager
2:48:20.028596 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
2:48:24.337630 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
2:48:28.271293 PROGRESS: Starting initial search for precursors.
2:48:28.722152 INFO: Starting optimization step 0.
2:48:28.722735 PROGRESS: === Extracting elution groups 0 to 8000 ===
2:48:28.722899 PROGRESS: Extracting batch of 15798 precursors
2:48:28.736388 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:48:28.736564 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:48:28.736620 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:48:28.736655 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:48:28.737187 INFO: Starting candidate selection
2:48:30.321522 INFO: Starting candidate scoring
2:48:30.482987 INFO: Finished candidate processing
2:48:30.483104 INFO: Collecting candidate features
2:48:30.541604 INFO: Collecting fragment features
2:48:30.563366 INFO: Finished candidate scoring
2:48:30.584737 PROGRESS: === Extracted 15759 precursors and 157072 fragments ===
2:48:30.585171 INFO: performing precursor FDR with 47 features
2:48:30.585212 INFO: Decoy channel: -1
2:48:30.585238 INFO: Competetive: True
2:48:30.594021 INFO: Setting torch num_threads to 2 for FDR classification task
2:48:30.846787 INFO: Test AUC: 0.512
2:48:30.846980 INFO: Train AUC: 0.548
2:48:30.847032 INFO: AUC difference: 6.50%
2:48:30.847075 WARNING: AUC difference > 5%. This may indicate overfitting.
2:48:30.982554 INFO: Resetting torch num_threads to 100
2:48:30.985190 INFO: === FDR correction performed with classifier version -1 ===
2:48:30.986597 PROGRESS: ============================= Precursor FDR =============================
2:48:30.986816 PROGRESS: Total precursors accumulated: 1
2:48:30.986964 PROGRESS: Target precursors: 1 (100.00%)
2:48:30.987083 PROGRESS: Decoy precursors: 0 (0.00%)
2:48:30.987193 PROGRESS: 
2:48:30.987276 PROGRESS: Precursor Summary:
2:48:30.988850 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:48:30.989008 PROGRESS: 
2:48:30.989127 PROGRESS: Protein Summary:
2:48:30.990431 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:48:30.990565 PROGRESS: =========================================================================
2:48:31.158611 INFO: Starting optimization step 1.
2:48:31.158999 PROGRESS: === Extracting elution groups 8000 to 24000 ===
2:48:31.159110 PROGRESS: Extracting batch of 31672 precursors
2:48:31.175013 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:48:31.175171 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:48:31.175217 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:48:31.175248 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:48:31.175598 INFO: Starting candidate selection
2:48:33.569116 INFO: Starting candidate scoring
2:48:33.854420 INFO: Finished candidate processing
2:48:33.854539 INFO: Collecting candidate features
2:48:33.975875 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 31600)
2:48:33.982603 INFO: Collecting fragment features
2:48:34.023231 INFO: Finished candidate scoring
2:48:34.095286 PROGRESS: === Extracted 47359 precursors and 471784 fragments ===
2:48:34.112587 INFO: performing precursor FDR with 47 features
2:48:34.112747 INFO: Decoy channel: -1
2:48:34.112777 INFO: Competetive: True
2:48:34.143637 INFO: Setting torch num_threads to 2 for FDR classification task
2:48:34.160657 WARNING: dropped 1 decoy PSMs due to missing features
2:48:35.211831 INFO: Test AUC: 0.542
2:48:35.212172 INFO: Train AUC: 0.574
2:48:35.212286 INFO: AUC difference: 5.56%
2:48:35.212380 WARNING: AUC difference > 5%. This may indicate overfitting.
2:48:35.351785 INFO: Resetting torch num_threads to 100
2:48:35.359384 INFO: === FDR correction performed with classifier version -1 ===
2:48:35.361081 PROGRESS: ============================= Precursor FDR =============================
2:48:35.361230 PROGRESS: Total precursors accumulated: 2
2:48:35.361296 PROGRESS: Target precursors: 2 (100.00%)
2:48:35.361349 PROGRESS: Decoy precursors: 0 (0.00%)
2:48:35.361397 PROGRESS: 
2:48:35.361443 PROGRESS: Precursor Summary:
2:48:35.362565 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
2:48:35.362664 PROGRESS: 
2:48:35.362724 PROGRESS: Protein Summary:
2:48:35.364048 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
2:48:35.364161 PROGRESS: =========================================================================
2:48:35.625395 INFO: Starting optimization step 2.
2:48:35.625833 PROGRESS: === Extracting elution groups 24000 to 56000 ===
2:48:35.625932 PROGRESS: Extracting batch of 63174 precursors
2:48:35.660393 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:48:35.660577 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:48:35.660622 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:48:35.660652 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:48:35.661028 INFO: Starting candidate selection
2:48:39.710308 INFO: Starting candidate scoring
2:48:40.281097 INFO: Finished candidate processing
2:48:40.281220 INFO: Collecting candidate features
2:48:40.542658 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 63023)
2:48:40.551463 INFO: Collecting fragment features
2:48:40.626060 INFO: Finished candidate scoring
2:48:40.767509 PROGRESS: === Extracted 110382 precursors and 1098658 fragments ===
2:48:40.791694 INFO: performing precursor FDR with 47 features
2:48:40.791865 INFO: Decoy channel: -1
2:48:40.791899 INFO: Competetive: True
2:48:40.907148 INFO: Setting torch num_threads to 2 for FDR classification task
2:48:40.943145 WARNING: dropped 2 target PSMs due to missing features
2:48:40.943296 WARNING: dropped 1 decoy PSMs due to missing features
2:48:43.932331 INFO: Test AUC: 0.553
2:48:43.932609 INFO: Train AUC: 0.588
2:48:43.932651 INFO: AUC difference: 5.92%
2:48:43.932683 WARNING: AUC difference > 5%. This may indicate overfitting.
2:48:44.090920 INFO: Resetting torch num_threads to 100
2:48:44.110112 INFO: === FDR correction performed with classifier version -1 ===
2:48:44.111771 PROGRESS: ============================= Precursor FDR =============================
2:48:44.111938 PROGRESS: Total precursors accumulated: 3
2:48:44.112026 PROGRESS: Target precursors: 3 (100.00%)
2:48:44.112106 PROGRESS: Decoy precursors: 0 (0.00%)
2:48:44.112175 PROGRESS: 
2:48:44.112242 PROGRESS: Precursor Summary:
2:48:44.113772 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
2:48:44.113916 PROGRESS: 
2:48:44.113998 PROGRESS: Protein Summary:
2:48:44.115613 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
2:48:44.115744 PROGRESS: =========================================================================
2:48:44.650464 INFO: Starting optimization step 3.
2:48:44.650954 PROGRESS: === Extracting elution groups 56000 to 120000 ===
2:48:44.651082 PROGRESS: Extracting batch of 126509 precursors
2:48:44.719284 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:48:44.719496 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:48:44.719572 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:48:44.719612 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:48:44.720098 INFO: Starting candidate selection
2:48:52.809738 INFO: Starting candidate scoring
2:48:53.881639 INFO: Finished candidate processing
2:48:53.882422 INFO: Collecting candidate features
2:48:54.268587 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 126136)
2:48:54.278490 INFO: Collecting fragment features
2:48:54.432504 INFO: Finished candidate scoring
2:48:54.867496 PROGRESS: === Extracted 236518 precursors and 2353323 fragments ===
2:48:54.935783 INFO: performing precursor FDR with 47 features
2:48:54.936019 INFO: Decoy channel: -1
2:48:54.936083 INFO: Competetive: True
2:48:55.187748 INFO: Setting torch num_threads to 2 for FDR classification task
2:48:55.266026 WARNING: dropped 3 target PSMs due to missing features
2:48:55.266227 WARNING: dropped 1 decoy PSMs due to missing features
2:49:01.801349 INFO: Test AUC: 0.557
2:49:01.801639 INFO: Train AUC: 0.589
2:49:01.801685 INFO: AUC difference: 5.38%
2:49:01.801719 WARNING: AUC difference > 5%. This may indicate overfitting.
2:49:01.983086 INFO: Resetting torch num_threads to 100
2:49:02.020203 INFO: === FDR correction performed with classifier version -1 ===
2:49:02.021808 PROGRESS: ============================= Precursor FDR =============================
2:49:02.022013 PROGRESS: Total precursors accumulated: 3
2:49:02.022111 PROGRESS: Target precursors: 3 (100.00%)
2:49:02.022194 PROGRESS: Decoy precursors: 0 (0.00%)
2:49:02.022268 PROGRESS: 
2:49:02.022360 PROGRESS: Precursor Summary:
2:49:02.023986 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
2:49:02.024129 PROGRESS: 
2:49:02.024217 PROGRESS: Protein Summary:
2:49:02.026122 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
2:49:02.026260 PROGRESS: =========================================================================
2:49:02.863108 INFO: Starting optimization step 4.
2:49:02.863545 PROGRESS: === Extracting elution groups 120000 to 248000 ===
2:49:02.863695 PROGRESS: Extracting batch of 252969 precursors
2:49:02.988528 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:49:02.988818 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:49:02.988877 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:49:02.988914 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:49:02.989380 INFO: Starting candidate selection
2:49:18.733282 INFO: Starting candidate scoring
2:49:20.826743 INFO: Finished candidate processing
2:49:20.826899 INFO: Collecting candidate features
2:49:22.078516 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 252313)
2:49:22.100780 INFO: Collecting fragment features
2:49:22.448197 INFO: Finished candidate scoring
2:49:23.272268 PROGRESS: === Extracted 488831 precursors and 4859774 fragments ===
2:49:23.397608 INFO: performing precursor FDR with 47 features
2:49:23.397881 INFO: Decoy channel: -1
2:49:23.397927 INFO: Competetive: True
2:49:23.975326 INFO: Setting torch num_threads to 2 for FDR classification task
2:49:24.193408 WARNING: dropped 3 target PSMs due to missing features
2:49:24.193611 WARNING: dropped 2 decoy PSMs due to missing features
2:49:37.728197 INFO: Test AUC: 0.566
2:49:37.728374 INFO: Train AUC: 0.588
2:49:37.728422 INFO: AUC difference: 3.68%
2:49:37.928083 INFO: Resetting torch num_threads to 100
2:49:38.117759 INFO: === FDR correction performed with classifier version -1 ===
2:49:38.119365 PROGRESS: ============================= Precursor FDR =============================
2:49:38.119566 PROGRESS: Total precursors accumulated: 504
2:49:38.119678 PROGRESS: Target precursors: 463 (91.87%)
2:49:38.119762 PROGRESS: Decoy precursors: 41 (8.13%)
2:49:38.119845 PROGRESS: 
2:49:38.119921 PROGRESS: Precursor Summary:
2:49:38.121418 PROGRESS: Channel   0:	 0.05 FDR:   325; 0.01 FDR:     0; 0.001 FDR:     0
2:49:38.121605 PROGRESS: 
2:49:38.121700 PROGRESS: Protein Summary:
2:49:38.123378 PROGRESS: Channel   0:	 0.05 FDR:   305; 0.01 FDR:     0; 0.001 FDR:     0
2:49:38.123544 PROGRESS: =========================================================================
2:49:39.750908 INFO: Starting optimization step 5.
2:49:39.754842 PROGRESS: === Extracting elution groups 248000 to 504000 ===
2:49:39.755135 PROGRESS: Extracting batch of 505926 precursors
2:49:39.954432 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:49:39.954630 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:49:39.954692 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
2:49:39.954726 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:49:39.955536 INFO: Starting candidate selection
2:50:11.785252 INFO: Starting candidate scoring
2:50:15.969386 INFO: Finished candidate processing
2:50:15.969745 INFO: Collecting candidate features
2:50:18.013306 WARNING: intensity_correlation has 7 NaNs ( 0.00 % out of 504627)
2:50:18.048309 INFO: Collecting fragment features
2:50:18.669464 INFO: Finished candidate scoring
2:50:20.109989 PROGRESS: === Extracted 993458 precursors and 9874555 fragments ===
2:50:20.351739 INFO: performing precursor FDR with 47 features
2:50:20.352159 INFO: Decoy channel: -1
2:50:20.352215 INFO: Competetive: True
2:50:21.506077 INFO: Setting torch num_threads to 2 for FDR classification task
2:50:21.963011 WARNING: dropped 5 target PSMs due to missing features
2:50:21.963263 WARNING: dropped 7 decoy PSMs due to missing features
2:50:51.020084 INFO: Test AUC: 0.569
2:50:51.020551 INFO: Train AUC: 0.584
2:50:51.020667 INFO: AUC difference: 2.64%
2:50:51.294255 INFO: Resetting torch num_threads to 100
2:50:51.458783 INFO: === FDR correction performed with classifier version -1 ===
2:50:51.463061 PROGRESS: ============================= Precursor FDR =============================
2:50:51.463421 PROGRESS: Total precursors accumulated: 1,133
2:50:51.463505 PROGRESS: Target precursors: 1,034 (91.26%)
2:50:51.463573 PROGRESS: Decoy precursors: 99 (8.74%)
2:50:51.463634 PROGRESS: 
2:50:51.463693 PROGRESS: Precursor Summary:
2:50:51.466073 PROGRESS: Channel   0:	 0.05 FDR:   857; 0.01 FDR:   676; 0.001 FDR:   459
2:50:51.466292 PROGRESS: 
2:50:51.466387 PROGRESS: Protein Summary:
2:50:51.468617 PROGRESS: Channel   0:	 0.05 FDR:   723; 0.01 FDR:   562; 0.001 FDR:   400
2:50:51.468764 PROGRESS: =========================================================================
2:50:51.691511 INFO: fragments_df_filtered: 5000
2:50:53.382714 INFO: calibration group: precursor, fitting mz estimator 
2:50:53.480698 INFO: calibration group: precursor, fitting rt estimator 
2:50:53.571582 INFO: calibration group: fragment, fitting mz estimator 
2:50:54.252844 INFO: calibration group: precursor, predicting mz
2:50:54.358530 INFO: calibration group: precursor, predicting rt
2:50:54.765308 INFO: calibration group: fragment, predicting mz
2:50:55.756187 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:50:55.757305 INFO: Starting optimization step 6.
2:50:55.757524 PROGRESS: === Extracting elution groups 0 to 248000 ===
2:50:55.757720 PROGRESS: Extracting batch of 490122 precursors
2:50:56.101541 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:50:56.101854 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:50:56.101932 INFO: FWHM in RT is 2.91 seconds, sigma is 0.38
2:50:56.101975 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:50:56.102557 INFO: Starting candidate selection
2:51:23.101092 INFO: Starting candidate scoring
2:51:30.922722 INFO: Finished candidate processing
2:51:30.922913 INFO: Collecting candidate features
2:51:34.425924 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 977692)
2:51:34.492461 INFO: Collecting fragment features
2:51:35.726602 INFO: Finished candidate scoring
2:51:37.413983 PROGRESS: === Extracted 977692 precursors and 9636785 fragments ===
2:51:37.414593 INFO: performing precursor FDR with 47 features
2:51:37.414643 INFO: Decoy channel: -1
2:51:37.414681 INFO: Competetive: True
2:51:38.043576 INFO: Setting torch num_threads to 2 for FDR classification task
2:51:38.294425 WARNING: dropped 1 decoy PSMs due to missing features
2:51:58.296062 INFO: Test AUC: 0.567
2:51:58.296266 INFO: Train AUC: 0.584
2:51:58.296298 INFO: AUC difference: 2.91%
2:51:58.448744 INFO: Resetting torch num_threads to 100
2:51:58.475173 INFO: === FDR correction performed with classifier version 5 ===
2:51:58.476246 PROGRESS: ============================= Precursor FDR =============================
2:51:58.476384 PROGRESS: Total precursors accumulated: 905
2:51:58.476446 PROGRESS: Target precursors: 824 (91.05%)
2:51:58.476498 PROGRESS: Decoy precursors: 81 (8.95%)
2:51:58.476544 PROGRESS: 
2:51:58.476599 PROGRESS: Precursor Summary:
2:51:58.477872 PROGRESS: Channel   0:	 0.05 FDR:   683; 0.01 FDR:   480; 0.001 FDR:   354
2:51:58.477983 PROGRESS: 
2:51:58.478039 PROGRESS: Protein Summary:
2:51:58.479386 PROGRESS: Channel   0:	 0.05 FDR:   617; 0.01 FDR:   435; 0.001 FDR:   326
2:51:58.479486 PROGRESS: =========================================================================
2:51:58.519360 INFO: fragments_df_filtered: 5000
2:51:58.972529 INFO: calibration group: precursor, fitting mz estimator 
2:51:59.063471 INFO: calibration group: precursor, fitting rt estimator 
2:51:59.112866 INFO: calibration group: fragment, fitting mz estimator 
2:51:59.550666 INFO: calibration group: precursor, predicting mz
2:51:59.597738 INFO: calibration group: precursor, predicting rt
2:51:59.752225 INFO: calibration group: fragment, predicting mz
2:52:00.123149 INFO: === checking if optimization conditions were reached ===
2:52:00.126192 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
2:52:00.127677 PROGRESS: ❌ ms1_error      : 14.2429 > 10.0000 or insufficient steps taken.
2:52:00.127749 INFO: ==============================================
2:52:00.127904 INFO: Starting optimization step 7.
2:52:00.128007 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:52:00.128114 PROGRESS: Extracting batch of 237153 precursors
2:52:00.188613 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:52:00.188749 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:52:00.188787 INFO: FWHM in RT is 2.84 seconds, sigma is 0.37
2:52:00.188810 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:52:00.189100 INFO: Starting candidate selection
2:52:12.354514 INFO: Starting candidate scoring
2:52:15.552285 INFO: Finished candidate processing
2:52:15.552572 INFO: Collecting candidate features
2:52:17.058035 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 472852)
2:52:17.077491 INFO: Collecting fragment features
2:52:17.364116 INFO: Finished candidate scoring
2:52:17.627282 PROGRESS: === Extracted 472852 precursors and 4136948 fragments ===
2:52:17.627799 INFO: performing precursor FDR with 47 features
2:52:17.627846 INFO: Decoy channel: -1
2:52:17.627871 INFO: Competetive: True
2:52:17.782324 INFO: Setting torch num_threads to 2 for FDR classification task
2:52:17.891966 WARNING: dropped 1 target PSMs due to missing features
2:52:17.892099 WARNING: dropped 1 decoy PSMs due to missing features
2:52:28.748648 INFO: Test AUC: 0.563
2:52:28.748833 INFO: Train AUC: 0.586
2:52:28.748936 INFO: AUC difference: 3.96%
2:52:28.954054 INFO: Resetting torch num_threads to 100
2:52:29.066986 INFO: === FDR correction performed with classifier version 6 ===
2:52:29.068550 PROGRESS: ============================= Precursor FDR =============================
2:52:29.068750 PROGRESS: Total precursors accumulated: 724
2:52:29.068850 PROGRESS: Target precursors: 659 (91.02%)
2:52:29.068928 PROGRESS: Decoy precursors: 65 (8.98%)
2:52:29.068997 PROGRESS: 
2:52:29.069064 PROGRESS: Precursor Summary:
2:52:29.070932 PROGRESS: Channel   0:	 0.05 FDR:   499; 0.01 FDR:   317; 0.001 FDR:     0
2:52:29.071264 PROGRESS: 
2:52:29.071340 PROGRESS: Protein Summary:
2:52:29.073449 PROGRESS: Channel   0:	 0.05 FDR:   469; 0.01 FDR:   301; 0.001 FDR:     0
2:52:29.073608 PROGRESS: =========================================================================
2:52:29.108289 INFO: fragments_df_filtered: 3551
2:52:29.806295 INFO: calibration group: precursor, fitting mz estimator 
2:52:30.285211 INFO: calibration group: precursor, fitting rt estimator 
2:52:30.430006 INFO: calibration group: fragment, fitting mz estimator 
2:52:30.877249 INFO: calibration group: precursor, predicting mz
2:52:30.925018 INFO: calibration group: precursor, predicting rt
2:52:31.110979 INFO: calibration group: fragment, predicting mz
2:52:31.786985 INFO: === checking if optimization conditions were reached ===
2:52:31.789297 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
2:52:31.790302 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
2:52:31.790367 INFO: ==============================================
2:52:31.790478 PROGRESS: Optimization finished for ms2_error, ms1_error.
2:52:32.247988 INFO: calibration group: precursor, predicting mz
2:52:32.342848 INFO: calibration group: precursor, predicting rt
2:52:32.563460 INFO: calibration group: fragment, predicting mz
2:52:33.083628 INFO: Starting optimization step 0.
2:52:33.084016 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:52:33.084147 PROGRESS: Extracting batch of 237153 precursors
2:52:33.193353 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:52:33.193582 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:52:33.193648 INFO: FWHM in RT is 2.74 seconds, sigma is 0.35
2:52:33.193688 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:52:33.194158 INFO: Starting candidate selection
2:52:56.928184 INFO: Starting candidate scoring
2:53:01.169726 INFO: Finished candidate processing
2:53:01.170038 INFO: Collecting candidate features
2:53:02.882822 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 472934)
2:53:02.915585 INFO: Collecting fragment features
2:53:03.371210 INFO: Finished candidate scoring
2:53:04.115507 PROGRESS: === Extracted 472934 precursors and 4130574 fragments ===
2:53:04.116210 INFO: performing precursor FDR with 47 features
2:53:04.116264 INFO: Decoy channel: -1
2:53:04.116297 INFO: Competetive: True
2:53:04.384935 INFO: Setting torch num_threads to 2 for FDR classification task
2:53:04.552469 WARNING: dropped 1 target PSMs due to missing features
2:53:04.552677 WARNING: dropped 2 decoy PSMs due to missing features
2:53:15.297377 INFO: Test AUC: 0.565
2:53:15.297533 INFO: Train AUC: 0.592
2:53:15.297564 INFO: AUC difference: 4.56%
2:53:15.462028 INFO: Resetting torch num_threads to 100
2:53:15.511924 INFO: === FDR correction performed with classifier version 7 ===
2:53:15.513246 PROGRESS: ============================= Precursor FDR =============================
2:53:15.513386 PROGRESS: Total precursors accumulated: 845
2:53:15.513466 PROGRESS: Target precursors: 768 (90.89%)
2:53:15.513533 PROGRESS: Decoy precursors: 77 (9.11%)
2:53:15.513593 PROGRESS: 
2:53:15.513652 PROGRESS: Precursor Summary:
2:53:15.515174 PROGRESS: Channel   0:	 0.05 FDR:   547; 0.01 FDR:   366; 0.001 FDR:   209
2:53:15.515297 PROGRESS: 
2:53:15.515377 PROGRESS: Protein Summary:
2:53:15.517129 PROGRESS: Channel   0:	 0.05 FDR:   519; 0.01 FDR:   346; 0.001 FDR:   205
2:53:15.517245 PROGRESS: =========================================================================
2:53:15.561128 INFO: fragments_df_filtered: 3977
2:53:16.229707 INFO: calibration group: precursor, fitting mz estimator 
2:53:16.364576 INFO: calibration group: precursor, fitting rt estimator 
2:53:16.489845 INFO: calibration group: fragment, fitting mz estimator 
2:53:16.805425 INFO: calibration group: precursor, predicting mz
2:53:16.844085 INFO: calibration group: precursor, predicting rt
2:53:17.083789 INFO: calibration group: fragment, predicting mz
2:53:17.652545 INFO: === checking if optimization conditions were reached ===
2:53:17.652876 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2:53:17.654904 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 266.8344.
2:53:17.654963 INFO: ==============================================
2:53:17.655056 INFO: Starting optimization step 1.
2:53:17.655125 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:53:17.655206 PROGRESS: Extracting batch of 237153 precursors
2:53:17.714987 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:53:17.715121 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:53:17.715162 INFO: FWHM in RT is 2.69 seconds, sigma is 0.35
2:53:17.715184 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:53:17.715490 INFO: Starting candidate selection
2:53:28.823203 INFO: Starting candidate scoring
2:53:33.136833 INFO: Finished candidate processing
2:53:33.137080 INFO: Collecting candidate features
2:53:34.564884 WARNING: intensity_correlation has 44 NaNs ( 0.01 % out of 470436)
2:53:34.590350 INFO: Collecting fragment features
2:53:34.970279 INFO: Finished candidate scoring
2:53:35.551355 PROGRESS: === Extracted 470436 precursors and 3982446 fragments ===
2:53:35.552048 INFO: performing precursor FDR with 47 features
2:53:35.552120 INFO: Decoy channel: -1
2:53:35.552151 INFO: Competetive: True
2:53:35.792233 INFO: Setting torch num_threads to 2 for FDR classification task
2:53:35.944677 WARNING: dropped 24 target PSMs due to missing features
2:53:35.944865 WARNING: dropped 20 decoy PSMs due to missing features
2:53:49.762762 INFO: Test AUC: 0.562
2:53:49.764065 INFO: Train AUC: 0.589
2:53:49.764123 INFO: AUC difference: 4.48%
2:53:49.955001 INFO: Resetting torch num_threads to 100
2:53:50.003865 INFO: === FDR correction performed with classifier version 7 ===
2:53:50.005238 PROGRESS: ============================= Precursor FDR =============================
2:53:50.005379 PROGRESS: Total precursors accumulated: 865
2:53:50.005461 PROGRESS: Target precursors: 788 (91.10%)
2:53:50.005542 PROGRESS: Decoy precursors: 77 (8.90%)
2:53:50.005613 PROGRESS: 
2:53:50.005677 PROGRESS: Precursor Summary:
2:53:50.007329 PROGRESS: Channel   0:	 0.05 FDR:   613; 0.01 FDR:   411; 0.001 FDR:   273
2:53:50.007452 PROGRESS: 
2:53:50.007526 PROGRESS: Protein Summary:
2:53:50.009382 PROGRESS: Channel   0:	 0.05 FDR:   578; 0.01 FDR:   389; 0.001 FDR:   265
2:53:50.009499 PROGRESS: =========================================================================
2:53:50.039114 INFO: fragments_df_filtered: 4397
2:53:50.753088 INFO: calibration group: precursor, fitting mz estimator 
2:53:50.933382 INFO: calibration group: precursor, fitting rt estimator 
2:53:51.011605 INFO: calibration group: fragment, fitting mz estimator 
2:53:51.409156 INFO: calibration group: precursor, predicting mz
2:53:51.549130 INFO: calibration group: precursor, predicting rt
2:53:51.824704 INFO: calibration group: fragment, predicting mz
2:53:52.320536 INFO: === checking if optimization conditions were reached ===
2:53:52.321262 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2:53:52.324861 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 182.9259.
2:53:52.325269 INFO: ==============================================
2:53:52.325827 INFO: Starting optimization step 2.
2:53:52.326154 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:53:52.326479 PROGRESS: Extracting batch of 237153 precursors
2:53:52.437846 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:53:52.438229 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:53:52.438378 INFO: FWHM in RT is 2.70 seconds, sigma is 0.35
2:53:52.438492 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:53:52.439024 INFO: Starting candidate selection
2:54:04.785607 INFO: Starting candidate scoring
2:54:11.606419 INFO: Finished candidate processing
2:54:11.607166 INFO: Collecting candidate features
2:54:14.270176 WARNING: intensity_correlation has 71 NaNs ( 0.02 % out of 468999)
2:54:14.305313 INFO: Collecting fragment features
2:54:14.871539 INFO: Finished candidate scoring
2:54:16.511706 PROGRESS: === Extracted 468999 precursors and 3860259 fragments ===
2:54:16.513203 INFO: performing precursor FDR with 47 features
2:54:16.513293 INFO: Decoy channel: -1
2:54:16.513328 INFO: Competetive: True
2:54:16.932627 INFO: Setting torch num_threads to 2 for FDR classification task
2:54:17.139345 WARNING: dropped 34 target PSMs due to missing features
2:54:17.139642 WARNING: dropped 37 decoy PSMs due to missing features
2:54:30.049439 INFO: Test AUC: 0.557
2:54:30.049666 INFO: Train AUC: 0.586
2:54:30.049702 INFO: AUC difference: 5.01%
2:54:30.049728 WARNING: AUC difference > 5%. This may indicate overfitting.
2:54:30.182041 INFO: Resetting torch num_threads to 100
2:54:30.303065 INFO: === FDR correction performed with classifier version 7 ===
2:54:30.304254 PROGRESS: ============================= Precursor FDR =============================
2:54:30.304363 PROGRESS: Total precursors accumulated: 938
2:54:30.304440 PROGRESS: Target precursors: 854 (91.04%)
2:54:30.304495 PROGRESS: Decoy precursors: 84 (8.96%)
2:54:30.304541 PROGRESS: 
2:54:30.304586 PROGRESS: Precursor Summary:
2:54:30.305631 PROGRESS: Channel   0:	 0.05 FDR:   618; 0.01 FDR:   335; 0.001 FDR:     0
2:54:30.305724 PROGRESS: 
2:54:30.305785 PROGRESS: Protein Summary:
2:54:30.307034 PROGRESS: Channel   0:	 0.05 FDR:   577; 0.01 FDR:   321; 0.001 FDR:     0
2:54:30.307131 PROGRESS: =========================================================================
2:54:30.340271 INFO: fragments_df_filtered: 3694
2:54:31.261542 INFO: calibration group: precursor, fitting mz estimator 
2:54:31.431576 INFO: calibration group: precursor, fitting rt estimator 
2:54:31.553315 INFO: calibration group: fragment, fitting mz estimator 
2:54:31.876071 INFO: calibration group: precursor, predicting mz
2:54:31.972014 INFO: calibration group: precursor, predicting rt
2:54:32.182302 INFO: calibration group: fragment, predicting mz
2:54:32.693335 INFO: === checking if optimization conditions were reached ===
2:54:32.694131 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2:54:32.698248 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 107.8424.
2:54:32.698769 INFO: ==============================================
2:54:32.699324 INFO: Starting optimization step 3.
2:54:32.699455 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:54:32.699567 PROGRESS: Extracting batch of 237153 precursors
2:54:32.788972 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:54:32.789141 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:54:32.789185 INFO: FWHM in RT is 2.76 seconds, sigma is 0.36
2:54:32.789209 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:54:32.789616 INFO: Starting candidate selection
2:54:43.077273 INFO: Starting candidate scoring
2:54:46.437223 INFO: Finished candidate processing
2:54:46.437455 INFO: Collecting candidate features
2:54:47.730420 WARNING: intensity_correlation has 79 NaNs ( 0.02 % out of 468051)
2:54:49.626240 INFO: Collecting fragment features
2:54:50.113313 INFO: Finished candidate scoring
2:54:50.967621 PROGRESS: === Extracted 468051 precursors and 3742476 fragments ===
2:54:50.968428 INFO: performing precursor FDR with 47 features
2:54:50.968548 INFO: Decoy channel: -1
2:54:50.968640 INFO: Competetive: True
2:54:51.244089 INFO: Setting torch num_threads to 2 for FDR classification task
2:54:51.405662 WARNING: dropped 42 target PSMs due to missing features
2:54:51.405993 WARNING: dropped 37 decoy PSMs due to missing features
2:55:03.422850 INFO: Test AUC: 0.558
2:55:03.423129 INFO: Train AUC: 0.583
2:55:03.423185 INFO: AUC difference: 4.24%
2:55:03.615850 INFO: Resetting torch num_threads to 100
2:55:03.643695 INFO: === FDR correction performed with classifier version 7 ===
2:55:03.645270 PROGRESS: ============================= Precursor FDR =============================
2:55:03.645431 PROGRESS: Total precursors accumulated: 902
2:55:03.645516 PROGRESS: Target precursors: 822 (91.13%)
2:55:03.645587 PROGRESS: Decoy precursors: 80 (8.87%)
2:55:03.645653 PROGRESS: 
2:55:03.645716 PROGRESS: Precursor Summary:
2:55:03.647597 PROGRESS: Channel   0:	 0.05 FDR:   608; 0.01 FDR:   412; 0.001 FDR:   235
2:55:03.647750 PROGRESS: 
2:55:03.647837 PROGRESS: Protein Summary:
2:55:03.649877 PROGRESS: Channel   0:	 0.05 FDR:   568; 0.01 FDR:   386; 0.001 FDR:   229
2:55:03.650006 PROGRESS: =========================================================================
2:55:03.678171 INFO: fragments_df_filtered: 4311
2:55:04.366005 INFO: calibration group: precursor, fitting mz estimator 
2:55:04.666516 INFO: calibration group: precursor, fitting rt estimator 
2:55:04.799592 INFO: calibration group: fragment, fitting mz estimator 
2:55:05.482314 INFO: calibration group: precursor, predicting mz
2:55:05.614700 INFO: calibration group: precursor, predicting rt
2:55:05.863259 INFO: calibration group: fragment, predicting mz
2:55:06.505521 INFO: === checking if optimization conditions were reached ===
2:55:06.506246 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2:55:06.509629 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 68.0758.
2:55:06.509848 INFO: ==============================================
2:55:06.510201 INFO: Starting optimization step 4.
2:55:06.510514 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:55:06.511296 PROGRESS: Extracting batch of 237153 precursors
2:55:06.624444 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:55:06.624797 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:55:06.624914 INFO: FWHM in RT is 2.80 seconds, sigma is 0.36
2:55:06.625008 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:55:06.625504 INFO: Starting candidate selection
2:55:18.473664 INFO: Starting candidate scoring
2:55:24.579210 INFO: Finished candidate processing
2:55:24.579366 INFO: Collecting candidate features
2:55:25.884155 WARNING: intensity_correlation has 107 NaNs ( 0.02 % out of 466316)
2:55:25.916941 INFO: Collecting fragment features
2:55:26.350230 INFO: Finished candidate scoring
2:55:26.961378 PROGRESS: === Extracted 466316 precursors and 3635189 fragments ===
2:55:26.962103 INFO: performing precursor FDR with 47 features
2:55:26.962171 INFO: Decoy channel: -1
2:55:26.962223 INFO: Competetive: True
2:55:27.214684 INFO: Setting torch num_threads to 2 for FDR classification task
2:55:27.373997 WARNING: dropped 58 target PSMs due to missing features
2:55:27.374203 WARNING: dropped 49 decoy PSMs due to missing features
2:55:40.168333 INFO: Test AUC: 0.557
2:55:40.168609 INFO: Train AUC: 0.582
2:55:40.168657 INFO: AUC difference: 4.19%
2:55:40.360265 INFO: Resetting torch num_threads to 100
2:55:40.388077 INFO: === FDR correction performed with classifier version 7 ===
2:55:40.389585 PROGRESS: ============================= Precursor FDR =============================
2:55:40.389731 PROGRESS: Total precursors accumulated: 891
2:55:40.389842 PROGRESS: Target precursors: 809 (90.80%)
2:55:40.389919 PROGRESS: Decoy precursors: 82 (9.20%)
2:55:40.389991 PROGRESS: 
2:55:40.390054 PROGRESS: Precursor Summary:
2:55:40.391807 PROGRESS: Channel   0:	 0.05 FDR:   593; 0.01 FDR:   424; 0.001 FDR:   137
2:55:40.391938 PROGRESS: 
2:55:40.392017 PROGRESS: Protein Summary:
2:55:40.393919 PROGRESS: Channel   0:	 0.05 FDR:   555; 0.01 FDR:   397; 0.001 FDR:   136
2:55:40.394040 PROGRESS: =========================================================================
2:55:40.422845 INFO: fragments_df_filtered: 4349
2:55:41.150143 INFO: calibration group: precursor, fitting mz estimator 
2:55:41.486698 INFO: calibration group: precursor, fitting rt estimator 
2:55:41.681810 INFO: calibration group: fragment, fitting mz estimator 
2:55:42.451348 INFO: calibration group: precursor, predicting mz
2:55:42.613868 INFO: calibration group: precursor, predicting rt
2:55:42.896284 INFO: calibration group: fragment, predicting mz
2:55:43.457799 INFO: === checking if optimization conditions were reached ===
2:55:43.458234 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2:55:43.460765 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 58.4249.
2:55:43.460827 INFO: ==============================================
2:55:43.460933 INFO: Starting optimization step 5.
2:55:43.461004 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:55:43.461081 PROGRESS: Extracting batch of 237153 precursors
2:55:43.526900 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:55:43.527051 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:55:43.527092 INFO: FWHM in RT is 2.76 seconds, sigma is 0.36
2:55:43.527117 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:55:43.527449 INFO: Starting candidate selection
2:55:53.589000 INFO: Starting candidate scoring
2:55:59.812876 INFO: Finished candidate processing
2:55:59.813299 INFO: Collecting candidate features
2:56:01.303635 WARNING: intensity_correlation has 153 NaNs ( 0.03 % out of 465107)
2:56:01.337798 INFO: Collecting fragment features
2:56:01.743965 INFO: Finished candidate scoring
2:56:02.424204 PROGRESS: === Extracted 465107 precursors and 3529040 fragments ===
2:56:02.425350 INFO: performing precursor FDR with 47 features
2:56:02.425497 INFO: Decoy channel: -1
2:56:02.425617 INFO: Competetive: True
2:56:02.672058 INFO: Setting torch num_threads to 2 for FDR classification task
2:56:02.833815 WARNING: dropped 72 target PSMs due to missing features
2:56:02.834179 WARNING: dropped 81 decoy PSMs due to missing features
2:56:15.541304 INFO: Test AUC: 0.556
2:56:15.541578 INFO: Train AUC: 0.582
2:56:15.541622 INFO: AUC difference: 4.50%
2:56:15.730243 INFO: Resetting torch num_threads to 100
2:56:15.758215 INFO: === FDR correction performed with classifier version 7 ===
2:56:15.759687 PROGRESS: ============================= Precursor FDR =============================
2:56:15.759830 PROGRESS: Total precursors accumulated: 876
2:56:15.759915 PROGRESS: Target precursors: 796 (90.87%)
2:56:15.759986 PROGRESS: Decoy precursors: 80 (9.13%)
2:56:15.760052 PROGRESS: 
2:56:15.760115 PROGRESS: Precursor Summary:
2:56:15.761744 PROGRESS: Channel   0:	 0.05 FDR:   627; 0.01 FDR:   430; 0.001 FDR:   272
2:56:15.761882 PROGRESS: 
2:56:15.761958 PROGRESS: Protein Summary:
2:56:15.763797 PROGRESS: Channel   0:	 0.05 FDR:   581; 0.01 FDR:   405; 0.001 FDR:   265
2:56:15.763919 PROGRESS: =========================================================================
2:56:15.790195 INFO: fragments_df_filtered: 4450
2:56:16.222892 INFO: calibration group: precursor, fitting mz estimator 
2:56:16.462966 INFO: calibration group: precursor, fitting rt estimator 
2:56:16.563095 INFO: calibration group: fragment, fitting mz estimator 
2:56:17.170632 INFO: calibration group: precursor, predicting mz
2:56:17.190569 INFO: calibration group: precursor, predicting rt
2:56:17.290618 INFO: calibration group: fragment, predicting mz
2:56:17.506263 INFO: === checking if optimization conditions were reached ===
2:56:17.507192 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2:56:17.510191 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 56.7748.
2:56:17.510429 INFO: ==============================================
2:56:17.510762 INFO: Starting optimization step 6.
2:56:17.511053 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:56:17.511351 PROGRESS: Extracting batch of 110644 precursors
2:56:17.561560 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:56:17.563376 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:56:17.563564 INFO: FWHM in RT is 2.74 seconds, sigma is 0.35
2:56:17.563673 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:56:17.564265 INFO: Starting candidate selection
2:56:22.511233 INFO: Starting candidate scoring
2:56:24.289039 INFO: Finished candidate processing
2:56:24.289177 INFO: Collecting candidate features
2:56:24.946737 WARNING: intensity_correlation has 73 NaNs ( 0.03 % out of 217089)
2:56:24.964717 INFO: Collecting fragment features
2:56:25.161531 INFO: Finished candidate scoring
2:56:25.486629 PROGRESS: === Extracted 217089 precursors and 1641958 fragments ===
2:56:25.487281 INFO: performing precursor FDR with 47 features
2:56:25.487336 INFO: Decoy channel: -1
2:56:25.487368 INFO: Competetive: True
2:56:25.608902 INFO: Setting torch num_threads to 2 for FDR classification task
2:56:25.683896 WARNING: dropped 34 target PSMs due to missing features
2:56:25.684091 WARNING: dropped 39 decoy PSMs due to missing features
2:56:31.100248 INFO: Test AUC: 0.552
2:56:31.100435 INFO: Train AUC: 0.588
2:56:31.100490 INFO: AUC difference: 6.07%
2:56:31.100526 WARNING: AUC difference > 5%. This may indicate overfitting.
2:56:31.263238 INFO: Resetting torch num_threads to 100
2:56:31.298667 INFO: === FDR correction performed with classifier version 7 ===
2:56:31.299612 PROGRESS: ============================= Precursor FDR =============================
2:56:31.299727 PROGRESS: Total precursors accumulated: 479
2:56:31.299793 PROGRESS: Target precursors: 435 (90.81%)
2:56:31.299856 PROGRESS: Decoy precursors: 44 (9.19%)
2:56:31.299907 PROGRESS: 
2:56:31.299953 PROGRESS: Precursor Summary:
2:56:31.301064 PROGRESS: Channel   0:	 0.05 FDR:   342; 0.01 FDR:   234; 0.001 FDR:     2
2:56:31.301169 PROGRESS: 
2:56:31.301228 PROGRESS: Protein Summary:
2:56:31.302438 PROGRESS: Channel   0:	 0.05 FDR:   333; 0.01 FDR:   228; 0.001 FDR:     2
2:56:31.302542 PROGRESS: =========================================================================
2:56:31.312571 INFO: fragments_df_filtered: 2355
2:56:31.678406 INFO: calibration group: precursor, fitting mz estimator 
2:56:31.780863 INFO: calibration group: precursor, fitting rt estimator 
2:56:31.863512 INFO: calibration group: fragment, fitting mz estimator 
2:56:32.158992 INFO: calibration group: precursor, predicting mz
2:56:32.193434 INFO: calibration group: precursor, predicting rt
2:56:32.433473 INFO: calibration group: fragment, predicting mz
2:56:32.665081 INFO: === checking if optimization conditions were reached ===
2:56:32.665743 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
2:56:32.667575 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 56.7748 found after 7 searches.
2:56:32.667727 INFO: ==============================================
2:56:32.667996 PROGRESS: Optimization finished for rt_error.
2:56:33.101555 INFO: calibration group: precursor, predicting mz
2:56:33.121487 INFO: calibration group: precursor, predicting rt
2:56:33.217455 INFO: calibration group: fragment, predicting mz
2:56:33.557224 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:56:33.557845 PROGRESS: ==============================================
2:56:33.558101 PROGRESS: ms2_error      : 15.0000
2:56:33.558342 PROGRESS: ms1_error      : 10.0000
2:56:33.558578 PROGRESS: rt_error       : 56.7748
2:56:33.558797 PROGRESS: ==============================================
2:56:33.560505 INFO: calibration group: precursor, predicting mz
2:56:35.643655 INFO: calibration group: precursor, predicting rt
2:56:44.167382 INFO: calibration group: fragment, predicting mz
2:57:03.582376 PROGRESS: Extracting batch of 10183864 precursors
2:57:05.876598 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
2:57:05.876826 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:57:05.876871 INFO: FWHM in RT is 2.82 seconds, sigma is 0.36
2:57:05.876896 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:57:05.877381 INFO: Starting candidate selection
3:02:05.260805 INFO: Applying score cutoff of 42.2410219039917
3:02:05.900171 INFO: Removed 9683597 precursors with score below cutoff
3:02:09.527209 INFO: Starting candidate scoring
3:03:18.710980 INFO: Finished candidate processing
3:03:18.711407 INFO: Collecting candidate features
3:03:45.550693 WARNING: intensity_correlation has 103 NaNs ( 0.00 % out of 10629728)
3:03:45.977036 INFO: Collecting fragment features
3:03:54.449037 INFO: Finished candidate scoring
3:04:08.275581 INFO: === FDR correction performed with classifier version 14 ===
3:04:08.315180 INFO: performing precursor FDR with 47 features
3:04:08.315263 INFO: Decoy channel: -1
3:04:08.315291 INFO: Competetive: True
3:04:11.154987 INFO: Setting torch num_threads to 2 for FDR classification task
3:04:12.962125 WARNING: dropped 52 target PSMs due to missing features
3:04:12.962272 WARNING: dropped 51 decoy PSMs due to missing features
3:09:06.689581 INFO: Test AUC: 0.578
3:09:06.689901 INFO: Train AUC: 0.582
3:09:06.689983 INFO: AUC difference: 0.71%
3:09:07.809872 INFO: Resetting torch num_threads to 100
3:09:08.201322 INFO: Removing fragments below FDR threshold
3:09:09.394351 PROGRESS: ============================= Precursor FDR =============================
3:09:09.394722 PROGRESS: Total precursors accumulated: 24,514
3:09:09.394812 PROGRESS: Target precursors: 24,272 (99.01%)
3:09:09.394883 PROGRESS: Decoy precursors: 242 (0.99%)
3:09:09.394939 PROGRESS: 
3:09:09.394990 PROGRESS: Precursor Summary:
3:09:09.408009 PROGRESS: Channel   0:	 0.05 FDR: 24,272; 0.01 FDR: 24,272; 0.001 FDR: 16,266
3:09:09.408360 PROGRESS: 
3:09:09.408426 PROGRESS: Protein Summary:
3:09:09.428603 PROGRESS: Channel   0:	 0.05 FDR: 7,151; 0.01 FDR: 7,151; 0.001 FDR: 5,380
3:09:09.428958 PROGRESS: =========================================================================
3:09:09.903237 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:09:10.864934 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:09:10.865366 INFO: Quantification results path: run_output_Astral/alphadia_1.10_noMBR/quant
3:09:10.865553 INFO: Creating workflow folder for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3 at run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:09:10.866807 INFO: Initializing RawFileManager
3:09:58.665468 INFO: Determining DIA cycle
3:09:58.685226 INFO: Found cycle with start 0.00 min and length 303.
3:09:58.969865 INFO: RT (min)            : 0.0 - 26.9
3:09:58.969995 INFO: RT duration (sec)   : 1611.2
3:09:58.970036 INFO: RT duration (min)   : 26.9
3:09:58.970070 INFO: Cycle len (scans)   : 303
3:09:58.970099 INFO: Cycle len (sec)     : 1.65
3:09:58.970127 INFO: Number of cycles    : 978
3:09:58.970155 INFO: MS2 range (m/z)     : 380.4 - 980.7
3:10:00.964945 INFO: Initializing CalibrationManager
3:10:00.965329 INFO: Loading calibration config
3:10:00.966081 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'}]
3:10:00.966192 INFO: Calibration group :fragment, found 1 estimator(s)
3:10:00.966299 INFO: Calibration group :precursor, found 3 estimator(s)
3:10:00.966401 INFO: Disabling ion mobility calibration
3:10:00.966436 INFO: removed mobility estimator from group precursor
3:10:00.966628 INFO: Initializing OptimizationManager
3:10:00.966773 INFO: initial parameter: ms1_error = 30
3:10:00.969010 INFO: initial parameter: ms2_error = 30
3:10:00.969109 INFO: initial parameter: rt_error = 805.611083984375
3:10:00.969177 INFO: initial parameter: mobility_error = 0.1
3:10:00.969239 INFO: initial parameter: column_type = library
3:10:00.969300 INFO: initial parameter: num_candidates = 1
3:10:00.969360 INFO: initial parameter: classifier_version = -1
3:10:00.969420 INFO: initial parameter: fwhm_rt = 5
3:10:00.969481 INFO: initial parameter: fwhm_mobility = 0.01
3:10:00.969539 INFO: initial parameter: score_cutoff = 0
3:10:00.969624 INFO: Initializing TimingManager
3:10:00.969702 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:10:00.969829 INFO: FDRManager not loaded from disk.
3:10:00.969862 INFO: Initializing FDRManager
3:10:00.969910 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
3:10:03.257207 PROGRESS: 5,117,285 target precursors potentially observable (97,794 removed)
3:10:06.777645 PROGRESS: Starting initial search for precursors.
3:10:07.346137 INFO: Starting optimization step 0.
3:10:07.346606 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:10:07.346728 PROGRESS: Extracting batch of 15798 precursors
3:10:07.355549 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:10:07.355719 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:10:07.355770 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:10:07.355801 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:10:07.356276 INFO: Starting candidate selection
3:10:09.832403 INFO: Starting candidate scoring
3:10:10.066278 INFO: Finished candidate processing
3:10:10.066433 INFO: Collecting candidate features
3:10:10.142289 INFO: Collecting fragment features
3:10:10.164184 INFO: Finished candidate scoring
3:10:10.179380 PROGRESS: === Extracted 15762 precursors and 157190 fragments ===
3:10:10.179980 INFO: performing precursor FDR with 47 features
3:10:10.180037 INFO: Decoy channel: -1
3:10:10.180070 INFO: Competetive: True
3:10:10.192584 INFO: Setting torch num_threads to 2 for FDR classification task
3:10:10.507144 INFO: Test AUC: 0.516
3:10:10.507327 INFO: Train AUC: 0.508
3:10:10.507371 INFO: AUC difference: 1.46%
3:10:10.647767 INFO: Resetting torch num_threads to 100
3:10:10.650192 INFO: === FDR correction performed with classifier version -1 ===
3:10:10.651618 PROGRESS: ============================= Precursor FDR =============================
3:10:10.651916 PROGRESS: Total precursors accumulated: 2
3:10:10.652166 PROGRESS: Target precursors: 2 (100.00%)
3:10:10.652406 PROGRESS: Decoy precursors: 0 (0.00%)
3:10:10.652633 PROGRESS: 
3:10:10.652865 PROGRESS: Precursor Summary:
3:10:10.654363 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
3:10:10.654650 PROGRESS: 
3:10:10.654899 PROGRESS: Protein Summary:
3:10:10.656543 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
3:10:10.656833 PROGRESS: =========================================================================
3:10:10.853086 INFO: Starting optimization step 1.
3:10:10.853498 PROGRESS: === Extracting elution groups 8000 to 24000 ===
3:10:10.853613 PROGRESS: Extracting batch of 31672 precursors
3:10:10.870949 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:10:10.871146 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:10:10.871202 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:10:10.871233 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:10:10.871696 INFO: Starting candidate selection
3:10:14.111585 INFO: Starting candidate scoring
3:10:14.443012 INFO: Finished candidate processing
3:10:14.443163 INFO: Collecting candidate features
3:10:14.575857 INFO: Collecting fragment features
3:10:14.613965 INFO: Finished candidate scoring
3:10:14.692627 PROGRESS: === Extracted 47361 precursors and 471773 fragments ===
3:10:14.704566 INFO: performing precursor FDR with 47 features
3:10:14.704747 INFO: Decoy channel: -1
3:10:14.704789 INFO: Competetive: True
3:10:14.760740 INFO: Setting torch num_threads to 2 for FDR classification task
3:10:15.752262 INFO: Test AUC: 0.555
3:10:15.752456 INFO: Train AUC: 0.556
3:10:15.752503 INFO: AUC difference: 0.18%
3:10:15.888404 INFO: Resetting torch num_threads to 100
3:10:15.894872 INFO: === FDR correction performed with classifier version -1 ===
3:10:15.896209 PROGRESS: ============================= Precursor FDR =============================
3:10:15.896366 PROGRESS: Total precursors accumulated: 3
3:10:15.896455 PROGRESS: Target precursors: 3 (100.00%)
3:10:15.896533 PROGRESS: Decoy precursors: 0 (0.00%)
3:10:15.896602 PROGRESS: 
3:10:15.896670 PROGRESS: Precursor Summary:
3:10:15.898001 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
3:10:15.898119 PROGRESS: 
3:10:15.898189 PROGRESS: Protein Summary:
3:10:15.899601 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
3:10:15.899719 PROGRESS: =========================================================================
3:10:16.208494 INFO: Starting optimization step 2.
3:10:16.208909 PROGRESS: === Extracting elution groups 24000 to 56000 ===
3:10:16.209075 PROGRESS: Extracting batch of 63174 precursors
3:10:16.239868 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:10:16.240046 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:10:16.240100 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:10:16.240131 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:10:16.240560 INFO: Starting candidate selection
3:10:21.279849 INFO: Starting candidate scoring
3:10:21.828335 INFO: Finished candidate processing
3:10:21.828516 INFO: Collecting candidate features
3:10:22.070704 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 63030)
3:10:22.080002 INFO: Collecting fragment features
3:10:22.151123 INFO: Finished candidate scoring
3:10:22.270773 PROGRESS: === Extracted 110391 precursors and 1098063 fragments ===
3:10:22.291970 INFO: performing precursor FDR with 47 features
3:10:22.292329 INFO: Decoy channel: -1
3:10:22.292437 INFO: Competetive: True
3:10:22.405351 INFO: Setting torch num_threads to 2 for FDR classification task
3:10:22.449389 WARNING: dropped 2 decoy PSMs due to missing features
3:10:25.222159 INFO: Test AUC: 0.547
3:10:25.222433 INFO: Train AUC: 0.579
3:10:25.222476 INFO: AUC difference: 5.57%
3:10:25.222506 WARNING: AUC difference > 5%. This may indicate overfitting.
3:10:25.370437 INFO: Resetting torch num_threads to 100
3:10:25.385463 INFO: === FDR correction performed with classifier version -1 ===
3:10:25.386908 PROGRESS: ============================= Precursor FDR =============================
3:10:25.387042 PROGRESS: Total precursors accumulated: 5
3:10:25.387121 PROGRESS: Target precursors: 5 (100.00%)
3:10:25.387188 PROGRESS: Decoy precursors: 0 (0.00%)
3:10:25.387253 PROGRESS: 
3:10:25.387327 PROGRESS: Precursor Summary:
3:10:25.388748 PROGRESS: Channel   0:	 0.05 FDR:     5; 0.01 FDR:     5; 0.001 FDR:     5
3:10:25.388882 PROGRESS: 
3:10:25.388966 PROGRESS: Protein Summary:
3:10:25.390409 PROGRESS: Channel   0:	 0.05 FDR:     5; 0.01 FDR:     5; 0.001 FDR:     5
3:10:25.390530 PROGRESS: =========================================================================
3:10:25.872471 INFO: Starting optimization step 3.
3:10:25.872952 PROGRESS: === Extracting elution groups 56000 to 120000 ===
3:10:25.873173 PROGRESS: Extracting batch of 126509 precursors
3:10:25.933043 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:10:25.933225 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:10:25.933277 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:10:25.933307 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:10:25.933744 INFO: Starting candidate selection
3:10:35.784122 INFO: Starting candidate scoring
3:10:36.891745 INFO: Finished candidate processing
3:10:36.891894 INFO: Collecting candidate features
3:10:37.340036 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 126135)
3:10:37.348477 INFO: Collecting fragment features
3:10:37.455590 INFO: Finished candidate scoring
3:10:37.653317 PROGRESS: === Extracted 236526 precursors and 2351083 fragments ===
3:10:37.690499 INFO: performing precursor FDR with 47 features
3:10:37.690665 INFO: Decoy channel: -1
3:10:37.690696 INFO: Competetive: True
3:10:37.857263 INFO: Setting torch num_threads to 2 for FDR classification task
3:10:37.935107 WARNING: dropped 3 decoy PSMs due to missing features
3:10:48.147439 INFO: Test AUC: 0.558
3:10:48.147725 INFO: Train AUC: 0.586
3:10:48.147773 INFO: AUC difference: 4.89%
3:10:48.312166 INFO: Resetting torch num_threads to 100
3:10:48.344238 INFO: === FDR correction performed with classifier version -1 ===
3:10:48.390004 PROGRESS: ============================= Precursor FDR =============================
3:10:48.390977 PROGRESS: Total precursors accumulated: 118,408
3:10:48.391315 PROGRESS: Target precursors: 70,860 (59.84%)
3:10:48.391614 PROGRESS: Decoy precursors: 47,548 (40.16%)
3:10:48.391913 PROGRESS: 
3:10:48.392238 PROGRESS: Precursor Summary:
3:10:48.395634 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:10:48.396109 PROGRESS: 
3:10:48.396407 PROGRESS: Protein Summary:
3:10:48.399004 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:10:48.399338 PROGRESS: =========================================================================
3:10:49.156077 INFO: Starting optimization step 4.
3:10:49.156901 PROGRESS: === Extracting elution groups 120000 to 248000 ===
3:10:49.157212 PROGRESS: Extracting batch of 252969 precursors
3:10:49.274206 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:10:49.274644 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:10:49.274851 INFO: FWHM in RT is 5.00 seconds, sigma is 0.64
3:10:49.274980 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:10:49.275550 INFO: Starting candidate selection
3:11:05.340499 INFO: Starting candidate scoring
3:11:07.324273 INFO: Finished candidate processing
3:11:07.324395 INFO: Collecting candidate features
3:11:08.147093 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 252312)
3:11:08.159754 INFO: Collecting fragment features
3:11:08.375941 INFO: Finished candidate scoring
3:11:08.868586 PROGRESS: === Extracted 488838 precursors and 4854756 fragments ===
3:11:08.961689 INFO: performing precursor FDR with 47 features
3:11:08.961866 INFO: Decoy channel: -1
3:11:08.961901 INFO: Competetive: True
3:11:09.361166 INFO: Setting torch num_threads to 2 for FDR classification task
3:11:09.487733 WARNING: dropped 1 target PSMs due to missing features
3:11:09.487905 WARNING: dropped 5 decoy PSMs due to missing features
3:11:23.076388 INFO: Test AUC: 0.565
3:11:23.076557 INFO: Train AUC: 0.587
3:11:23.076595 INFO: AUC difference: 3.74%
3:11:23.213780 INFO: Resetting torch num_threads to 100
3:11:23.252162 INFO: === FDR correction performed with classifier version -1 ===
3:11:23.253372 PROGRESS: ============================= Precursor FDR =============================
3:11:23.253547 PROGRESS: Total precursors accumulated: 584
3:11:23.253620 PROGRESS: Target precursors: 534 (91.44%)
3:11:23.253679 PROGRESS: Decoy precursors: 50 (8.56%)
3:11:23.253731 PROGRESS: 
3:11:23.253779 PROGRESS: Precursor Summary:
3:11:23.255092 PROGRESS: Channel   0:	 0.05 FDR:   367; 0.01 FDR:   230; 0.001 FDR:   157
3:11:23.255230 PROGRESS: 
3:11:23.255294 PROGRESS: Protein Summary:
3:11:23.256639 PROGRESS: Channel   0:	 0.05 FDR:   341; 0.01 FDR:   215; 0.001 FDR:   151
3:11:23.256759 PROGRESS: =========================================================================
3:11:23.327782 INFO: fragments_df_filtered: 2239
3:11:24.470592 INFO: calibration group: precursor, fitting mz estimator 
3:11:24.786721 INFO: calibration group: precursor, fitting rt estimator 
3:11:24.923154 INFO: calibration group: fragment, fitting mz estimator 
3:11:25.199915 INFO: calibration group: precursor, predicting mz
3:11:25.294848 INFO: calibration group: precursor, predicting rt
3:11:25.703881 INFO: calibration group: fragment, predicting mz
3:11:26.697721 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3:11:26.698141 INFO: Starting optimization step 5.
3:11:26.698235 PROGRESS: === Extracting elution groups 0 to 248000 ===
3:11:26.698346 PROGRESS: Extracting batch of 490122 precursors
3:11:27.046356 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:11:27.046525 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:11:27.046573 INFO: FWHM in RT is 2.81 seconds, sigma is 0.36
3:11:27.046601 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:11:27.046958 INFO: Starting candidate selection
3:11:57.013985 INFO: Starting candidate scoring
3:12:03.350188 INFO: Finished candidate processing
3:12:03.350413 INFO: Collecting candidate features
3:12:05.642987 WARNING: intensity_correlation has 5 NaNs ( 0.00 % out of 977727)
3:12:05.682358 INFO: Collecting fragment features
3:12:06.661606 INFO: Finished candidate scoring
3:12:08.135051 PROGRESS: === Extracted 977727 precursors and 9620719 fragments ===
3:12:08.135760 INFO: performing precursor FDR with 47 features
3:12:08.135817 INFO: Decoy channel: -1
3:12:08.135852 INFO: Competetive: True
3:12:08.649784 INFO: Setting torch num_threads to 2 for FDR classification task
3:12:08.997919 WARNING: dropped 1 target PSMs due to missing features
3:12:08.998117 WARNING: dropped 4 decoy PSMs due to missing features
3:12:34.674310 INFO: Test AUC: 0.570
3:12:34.674596 INFO: Train AUC: 0.584
3:12:34.674642 INFO: AUC difference: 2.43%
3:12:34.927918 INFO: Resetting torch num_threads to 100
3:12:35.027028 INFO: === FDR correction performed with classifier version 4 ===
3:12:35.028620 PROGRESS: ============================= Precursor FDR =============================
3:12:35.028775 PROGRESS: Total precursors accumulated: 869
3:12:35.028865 PROGRESS: Target precursors: 796 (91.60%)
3:12:35.028939 PROGRESS: Decoy precursors: 73 (8.40%)
3:12:35.029018 PROGRESS: 
3:12:35.029086 PROGRESS: Precursor Summary:
3:12:35.030859 PROGRESS: Channel   0:	 0.05 FDR:   634; 0.01 FDR:   464; 0.001 FDR:   426
3:12:35.030993 PROGRESS: 
3:12:35.031075 PROGRESS: Protein Summary:
3:12:35.033106 PROGRESS: Channel   0:	 0.05 FDR:   578; 0.01 FDR:   419; 0.001 FDR:   385
3:12:35.033237 PROGRESS: =========================================================================
3:12:35.098806 INFO: fragments_df_filtered: 5000
3:12:35.986923 INFO: calibration group: precursor, fitting mz estimator 
3:12:36.107808 INFO: calibration group: precursor, fitting rt estimator 
3:12:36.181096 INFO: calibration group: fragment, fitting mz estimator 
3:12:36.914543 INFO: calibration group: precursor, predicting mz
3:12:37.004836 INFO: calibration group: precursor, predicting rt
3:12:37.250655 INFO: calibration group: fragment, predicting mz
3:12:37.732181 INFO: === checking if optimization conditions were reached ===
3:12:37.736133 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
3:12:37.737715 PROGRESS: ❌ ms1_error      : 13.5468 > 10.0000 or insufficient steps taken.
3:12:37.737850 INFO: ==============================================
3:12:37.738186 INFO: Starting optimization step 6.
3:12:37.738482 PROGRESS: === Extracting elution groups 0 to 120000 ===
3:12:37.738749 PROGRESS: Extracting batch of 237153 precursors
3:12:37.891779 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:12:37.891966 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:12:37.892015 INFO: FWHM in RT is 2.78 seconds, sigma is 0.36
3:12:37.892041 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:12:37.892468 INFO: Starting candidate selection
3:12:58.145533 INFO: Starting candidate scoring
3:13:01.473875 INFO: Finished candidate processing
3:13:01.474013 INFO: Collecting candidate features
3:13:02.439057 WARNING: intensity_correlation has 8 NaNs ( 0.00 % out of 472884)
3:13:02.461496 INFO: Collecting fragment features
3:13:02.777469 INFO: Finished candidate scoring
3:13:03.166358 PROGRESS: === Extracted 472884 precursors and 4128128 fragments ===
3:13:03.166879 INFO: performing precursor FDR with 47 features
3:13:03.166924 INFO: Decoy channel: -1
3:13:03.166949 INFO: Competetive: True
3:13:03.345450 INFO: Setting torch num_threads to 2 for FDR classification task
3:13:03.455396 WARNING: dropped 4 target PSMs due to missing features
3:13:03.455580 WARNING: dropped 4 decoy PSMs due to missing features
3:13:14.758395 INFO: Test AUC: 0.559
3:13:14.758852 INFO: Train AUC: 0.582
3:13:14.758956 INFO: AUC difference: 3.95%
3:13:14.937293 INFO: Resetting torch num_threads to 100
3:13:14.966411 INFO: === FDR correction performed with classifier version 5 ===
3:13:14.968326 PROGRESS: ============================= Precursor FDR =============================
3:13:14.968718 PROGRESS: Total precursors accumulated: 683
3:13:14.968982 PROGRESS: Target precursors: 624 (91.36%)
3:13:14.969218 PROGRESS: Decoy precursors: 59 (8.64%)
3:13:14.969437 PROGRESS: 
3:13:14.969646 PROGRESS: Precursor Summary:
3:13:14.971430 PROGRESS: Channel   0:	 0.05 FDR:   531; 0.01 FDR:     8; 0.001 FDR:     8
3:13:14.971721 PROGRESS: 
3:13:14.971939 PROGRESS: Protein Summary:
3:13:14.973708 PROGRESS: Channel   0:	 0.05 FDR:   505; 0.01 FDR:     8; 0.001 FDR:     8
3:13:14.974011 PROGRESS: =========================================================================
3:13:15.554610 INFO: calibration group: precursor, predicting mz
3:13:15.609011 INFO: calibration group: precursor, predicting rt
3:13:15.893060 INFO: calibration group: fragment, predicting mz
3:13:16.493087 INFO: === skipping optimization until target number of precursors are found ===
3:13:16.493610 INFO: Starting optimization step 7.
3:13:16.494165 PROGRESS: === Extracting elution groups 120000 to 248000 ===
3:13:16.494526 PROGRESS: Extracting batch of 252969 precursors
3:13:16.616436 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:13:16.617177 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:13:16.617362 INFO: FWHM in RT is 2.78 seconds, sigma is 0.36
3:13:16.617608 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:13:16.618227 INFO: Starting candidate selection
3:13:36.939710 INFO: Starting candidate scoring
3:13:40.966098 INFO: Finished candidate processing
3:13:40.966414 INFO: Collecting candidate features
3:13:42.715991 WARNING: intensity_correlation has 8 NaNs ( 0.00 % out of 504455)
3:13:42.750453 INFO: Collecting fragment features
3:13:43.258337 INFO: Finished candidate scoring
3:13:44.537934 PROGRESS: === Extracted 977339 precursors and 8521631 fragments ===
3:13:44.713487 INFO: performing precursor FDR with 47 features
3:13:44.713685 INFO: Decoy channel: -1
3:13:44.713723 INFO: Competetive: True
3:13:45.576968 INFO: Setting torch num_threads to 2 for FDR classification task
3:13:45.946040 WARNING: dropped 9 target PSMs due to missing features
3:13:45.946250 WARNING: dropped 7 decoy PSMs due to missing features
3:14:07.827752 INFO: Test AUC: 0.565
3:14:07.827966 INFO: Train AUC: 0.578
3:14:07.827999 INFO: AUC difference: 2.28%
3:14:09.572570 INFO: Resetting torch num_threads to 100
3:14:09.627378 INFO: === FDR correction performed with classifier version 5 ===
3:14:09.628629 PROGRESS: ============================= Precursor FDR =============================
3:14:09.628755 PROGRESS: Total precursors accumulated: 1,402
3:14:09.628816 PROGRESS: Target precursors: 1,277 (91.08%)
3:14:09.628869 PROGRESS: Decoy precursors: 125 (8.92%)
3:14:09.628916 PROGRESS: 
3:14:09.628960 PROGRESS: Precursor Summary:
3:14:09.630229 PROGRESS: Channel   0:	 0.05 FDR: 1,051; 0.01 FDR:   615; 0.001 FDR:   435
3:14:09.630336 PROGRESS: 
3:14:09.630397 PROGRESS: Protein Summary:
3:14:09.631824 PROGRESS: Channel   0:	 0.05 FDR:   922; 0.01 FDR:   550; 0.001 FDR:   402
3:14:09.631917 PROGRESS: =========================================================================
3:14:09.729012 INFO: fragments_df_filtered: 5000
3:14:10.185397 INFO: calibration group: precursor, fitting mz estimator 
3:14:10.234697 INFO: calibration group: precursor, fitting rt estimator 
3:14:10.276426 INFO: calibration group: fragment, fitting mz estimator 
3:14:10.659989 INFO: calibration group: precursor, predicting mz
3:14:10.714973 INFO: calibration group: precursor, predicting rt
3:14:10.904115 INFO: calibration group: fragment, predicting mz
3:14:11.233105 INFO: === checking if optimization conditions were reached ===
3:14:11.235507 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
3:14:11.236557 PROGRESS: ✅ ms1_error      : 10.0000 <= 10.0000
3:14:11.236607 INFO: ==============================================
3:14:11.236720 PROGRESS: Optimization finished for ms2_error, ms1_error.
3:14:11.673505 INFO: calibration group: precursor, predicting mz
3:14:11.705425 INFO: calibration group: precursor, predicting rt
3:14:11.863143 INFO: calibration group: fragment, predicting mz
3:14:12.195799 INFO: Starting optimization step 0.
3:14:12.196172 PROGRESS: === Extracting elution groups 0 to 120000 ===
3:14:12.196267 PROGRESS: Extracting batch of 237153 precursors
3:14:12.331247 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:14:12.331381 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:14:12.331419 INFO: FWHM in RT is 2.70 seconds, sigma is 0.35
3:14:12.331442 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:14:12.331745 INFO: Starting candidate selection
3:14:24.616949 INFO: Starting candidate scoring
3:14:27.856166 INFO: Finished candidate processing
3:14:27.856270 INFO: Collecting candidate features
3:14:28.681566 WARNING: intensity_correlation has 6 NaNs ( 0.00 % out of 472912)
3:14:28.701582 INFO: Collecting fragment features
3:14:28.966252 INFO: Finished candidate scoring
3:14:29.393252 PROGRESS: === Extracted 472912 precursors and 4124011 fragments ===
3:14:29.393709 INFO: performing precursor FDR with 47 features
3:14:29.393759 INFO: Decoy channel: -1
3:14:29.393783 INFO: Competetive: True
3:14:29.532594 INFO: Setting torch num_threads to 2 for FDR classification task
3:14:29.615564 WARNING: dropped 3 target PSMs due to missing features
3:14:29.615705 WARNING: dropped 3 decoy PSMs due to missing features
3:14:40.951199 INFO: Test AUC: 0.565
3:14:40.951453 INFO: Train AUC: 0.588
3:14:40.951501 INFO: AUC difference: 3.83%
3:14:41.167889 INFO: Resetting torch num_threads to 100
3:14:41.194725 INFO: === FDR correction performed with classifier version 7 ===
3:14:41.196488 PROGRESS: ============================= Precursor FDR =============================
3:14:41.196705 PROGRESS: Total precursors accumulated: 764
3:14:41.196802 PROGRESS: Target precursors: 695 (90.97%)
3:14:41.196872 PROGRESS: Decoy precursors: 69 (9.03%)
3:14:41.196934 PROGRESS: 
3:14:41.196992 PROGRESS: Precursor Summary:
3:14:41.199078 PROGRESS: Channel   0:	 0.05 FDR:   572; 0.01 FDR:   405; 0.001 FDR:   319
3:14:41.199271 PROGRESS: 
3:14:41.199363 PROGRESS: Protein Summary:
3:14:41.201639 PROGRESS: Channel   0:	 0.05 FDR:   537; 0.01 FDR:   386; 0.001 FDR:   306
3:14:41.201784 PROGRESS: =========================================================================
3:14:41.232236 INFO: fragments_df_filtered: 4264
3:14:41.905286 INFO: calibration group: precursor, fitting mz estimator 
3:14:42.125678 INFO: calibration group: precursor, fitting rt estimator 
3:14:42.208145 INFO: calibration group: fragment, fitting mz estimator 
3:14:42.726377 INFO: calibration group: precursor, predicting mz
3:14:42.783501 INFO: calibration group: precursor, predicting rt
3:14:42.988902 INFO: calibration group: fragment, predicting mz
3:14:43.423532 INFO: === checking if optimization conditions were reached ===
3:14:43.424144 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3:14:43.426631 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 343.1633.
3:14:43.426780 INFO: ==============================================
3:14:43.427048 INFO: Starting optimization step 1.
3:14:43.427285 PROGRESS: === Extracting elution groups 0 to 120000 ===
3:14:43.427521 PROGRESS: Extracting batch of 237153 precursors
3:14:43.496815 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:14:43.496962 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:14:43.497023 INFO: FWHM in RT is 2.68 seconds, sigma is 0.35
3:14:43.497053 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:14:43.497403 INFO: Starting candidate selection
3:14:54.810347 INFO: Starting candidate scoring
3:14:58.163740 INFO: Finished candidate processing
3:14:58.163990 INFO: Collecting candidate features
3:14:59.153922 WARNING: intensity_correlation has 31 NaNs ( 0.01 % out of 471544)
3:14:59.172745 INFO: Collecting fragment features
3:14:59.441514 INFO: Finished candidate scoring
3:14:59.913584 PROGRESS: === Extracted 471544 precursors and 4045484 fragments ===
3:14:59.914103 INFO: performing precursor FDR with 47 features
3:14:59.914150 INFO: Decoy channel: -1
3:14:59.914174 INFO: Competetive: True
3:15:00.058856 INFO: Setting torch num_threads to 2 for FDR classification task
3:15:00.144194 WARNING: dropped 14 target PSMs due to missing features
3:15:00.144330 WARNING: dropped 17 decoy PSMs due to missing features
3:15:08.537524 INFO: Test AUC: 0.560
3:15:08.537718 INFO: Train AUC: 0.585
3:15:08.537753 INFO: AUC difference: 4.19%
3:15:08.659504 INFO: Resetting torch num_threads to 100
3:15:08.672186 INFO: === FDR correction performed with classifier version 7 ===
3:15:08.673109 PROGRESS: ============================= Precursor FDR =============================
3:15:08.673236 PROGRESS: Total precursors accumulated: 750
3:15:08.673301 PROGRESS: Target precursors: 681 (90.80%)
3:15:08.673352 PROGRESS: Decoy precursors: 69 (9.20%)
3:15:08.673400 PROGRESS: 
3:15:08.673446 PROGRESS: Precursor Summary:
3:15:08.674579 PROGRESS: Channel   0:	 0.05 FDR:   550; 0.01 FDR:   417; 0.001 FDR:    78
3:15:08.674683 PROGRESS: 
3:15:08.674751 PROGRESS: Protein Summary:
3:15:08.675989 PROGRESS: Channel   0:	 0.05 FDR:   519; 0.01 FDR:   394; 0.001 FDR:    78
3:15:08.676086 PROGRESS: =========================================================================
3:15:08.693537 INFO: fragments_df_filtered: 4343
3:15:09.124990 INFO: calibration group: precursor, fitting mz estimator 
3:15:09.220551 INFO: calibration group: precursor, fitting rt estimator 
3:15:09.282511 INFO: calibration group: fragment, fitting mz estimator 
3:15:09.625522 INFO: calibration group: precursor, predicting mz
3:15:09.656329 INFO: calibration group: precursor, predicting rt
3:15:09.809682 INFO: calibration group: fragment, predicting mz
3:15:10.149091 INFO: === checking if optimization conditions were reached ===
3:15:10.149439 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3:15:10.151904 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 184.6175.
3:15:10.151970 INFO: ==============================================
3:15:10.152085 INFO: Starting optimization step 2.
3:15:10.152162 PROGRESS: === Extracting elution groups 0 to 120000 ===
3:15:10.152244 PROGRESS: Extracting batch of 237153 precursors
3:15:10.213749 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:15:10.213879 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:15:10.213919 INFO: FWHM in RT is 2.69 seconds, sigma is 0.35
3:15:10.213943 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:15:10.214251 INFO: Starting candidate selection
3:15:20.629433 INFO: Starting candidate scoring
3:15:23.814964 INFO: Finished candidate processing
3:15:23.815069 INFO: Collecting candidate features
3:15:24.626883 WARNING: intensity_correlation has 66 NaNs ( 0.01 % out of 468942)
3:15:24.645152 INFO: Collecting fragment features
3:15:24.905006 INFO: Finished candidate scoring
3:15:25.202415 PROGRESS: === Extracted 468942 precursors and 3877893 fragments ===
3:15:25.202885 INFO: performing precursor FDR with 47 features
3:15:25.202935 INFO: Decoy channel: -1
3:15:25.202961 INFO: Competetive: True
3:15:25.341227 INFO: Setting torch num_threads to 2 for FDR classification task
3:15:25.423610 WARNING: dropped 31 target PSMs due to missing features
3:15:25.423753 WARNING: dropped 35 decoy PSMs due to missing features
3:15:34.705680 INFO: Test AUC: 0.561
3:15:34.706084 INFO: Train AUC: 0.583
3:15:34.706201 INFO: AUC difference: 3.82%
3:15:34.916608 INFO: Resetting torch num_threads to 100
3:15:34.945382 INFO: === FDR correction performed with classifier version 7 ===
3:15:34.946995 PROGRESS: ============================= Precursor FDR =============================
3:15:34.947348 PROGRESS: Total precursors accumulated: 1,015
3:15:34.947597 PROGRESS: Target precursors: 922 (90.84%)
3:15:34.947834 PROGRESS: Decoy precursors: 93 (9.16%)
3:15:34.948069 PROGRESS: 
3:15:34.948309 PROGRESS: Precursor Summary:
3:15:34.950289 PROGRESS: Channel   0:	 0.05 FDR:   686; 0.01 FDR:   461; 0.001 FDR:   230
3:15:34.950605 PROGRESS: 
3:15:34.950857 PROGRESS: Protein Summary:
3:15:34.953112 PROGRESS: Channel   0:	 0.05 FDR:   638; 0.01 FDR:   438; 0.001 FDR:   222
3:15:34.953418 PROGRESS: =========================================================================
3:15:34.983088 INFO: fragments_df_filtered: 4727
3:15:35.434184 INFO: calibration group: precursor, fitting mz estimator 
3:15:35.572697 INFO: calibration group: precursor, fitting rt estimator 
3:15:35.670571 INFO: calibration group: fragment, fitting mz estimator 
3:15:36.312785 INFO: calibration group: precursor, predicting mz
3:15:36.329899 INFO: calibration group: precursor, predicting rt
3:15:36.427313 INFO: calibration group: fragment, predicting mz
3:15:36.646093 INFO: === checking if optimization conditions were reached ===
3:15:36.646745 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3:15:36.649658 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 121.2785.
3:15:36.649817 INFO: ==============================================
3:15:36.650101 INFO: Starting optimization step 3.
3:15:36.650351 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:15:36.650614 PROGRESS: Extracting batch of 110644 precursors
3:15:36.702804 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:15:36.702978 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:15:36.703063 INFO: FWHM in RT is 2.67 seconds, sigma is 0.34
3:15:36.703104 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:15:36.703508 INFO: Starting candidate selection
3:15:42.447286 INFO: Starting candidate scoring
3:15:46.295746 INFO: Finished candidate processing
3:15:46.296027 INFO: Collecting candidate features
3:15:47.007781 WARNING: intensity_correlation has 37 NaNs ( 0.02 % out of 218542)
3:15:47.008464 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 218542)
3:15:47.025884 INFO: Collecting fragment features
3:15:47.225537 INFO: Finished candidate scoring
3:15:47.439636 PROGRESS: === Extracted 218542 precursors and 1753017 fragments ===
3:15:47.440317 INFO: performing precursor FDR with 47 features
3:15:47.440372 INFO: Decoy channel: -1
3:15:47.440406 INFO: Competetive: True
3:15:47.565177 INFO: Setting torch num_threads to 2 for FDR classification task
3:15:47.639200 WARNING: dropped 15 target PSMs due to missing features
3:15:47.639380 WARNING: dropped 22 decoy PSMs due to missing features
3:15:54.716988 INFO: Test AUC: 0.562
3:15:54.717160 INFO: Train AUC: 0.588
3:15:54.717200 INFO: AUC difference: 4.42%
3:15:54.856866 INFO: Resetting torch num_threads to 100
3:15:54.925835 INFO: === FDR correction performed with classifier version 7 ===
3:15:54.927541 PROGRESS: ============================= Precursor FDR =============================
3:15:54.928455 PROGRESS: Total precursors accumulated: 489
3:15:54.928563 PROGRESS: Target precursors: 447 (91.41%)
3:15:54.928634 PROGRESS: Decoy precursors: 42 (8.59%)
3:15:54.928698 PROGRESS: 
3:15:54.928760 PROGRESS: Precursor Summary:
3:15:54.930388 PROGRESS: Channel   0:	 0.05 FDR:   329; 0.01 FDR:   227; 0.001 FDR:   181
3:15:54.930553 PROGRESS: 
3:15:54.930632 PROGRESS: Protein Summary:
3:15:54.932248 PROGRESS: Channel   0:	 0.05 FDR:   318; 0.01 FDR:   218; 0.001 FDR:   177
3:15:54.932407 PROGRESS: =========================================================================
3:15:54.945630 INFO: fragments_df_filtered: 2305
3:15:55.371477 INFO: calibration group: precursor, fitting mz estimator 
3:15:55.710715 INFO: calibration group: precursor, fitting rt estimator 
3:15:55.882149 INFO: calibration group: fragment, fitting mz estimator 
3:15:56.139981 INFO: calibration group: precursor, predicting mz
3:15:56.167865 INFO: calibration group: precursor, predicting rt
3:15:56.342029 INFO: calibration group: fragment, predicting mz
3:15:56.676813 INFO: === checking if optimization conditions were reached ===
3:15:56.677503 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3:15:56.681111 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 72.7116.
3:15:56.681312 INFO: ==============================================
3:15:56.681629 INFO: Starting optimization step 4.
3:15:56.681893 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:15:56.682153 PROGRESS: Extracting batch of 110644 precursors
3:15:56.741054 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:15:56.741414 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:15:56.741572 INFO: FWHM in RT is 2.64 seconds, sigma is 0.34
3:15:56.741673 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:15:56.742224 INFO: Starting candidate selection
3:16:01.585629 INFO: Starting candidate scoring
3:16:04.154567 INFO: Finished candidate processing
3:16:04.156072 INFO: Collecting candidate features
3:16:04.802341 WARNING: intensity_correlation has 53 NaNs ( 0.02 % out of 217540)
3:16:04.802998 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 217540)
3:16:04.820978 INFO: Collecting fragment features
3:16:05.004856 INFO: Finished candidate scoring
3:16:05.320952 PROGRESS: === Extracted 217540 precursors and 1651195 fragments ===
3:16:05.321504 INFO: performing precursor FDR with 47 features
3:16:05.321557 INFO: Decoy channel: -1
3:16:05.321589 INFO: Competetive: True
3:16:05.439708 INFO: Setting torch num_threads to 2 for FDR classification task
3:16:05.513255 WARNING: dropped 28 target PSMs due to missing features
3:16:05.513449 WARNING: dropped 25 decoy PSMs due to missing features
3:16:11.382174 INFO: Test AUC: 0.556
3:16:11.382487 INFO: Train AUC: 0.586
3:16:11.382600 INFO: AUC difference: 5.10%
3:16:11.382689 WARNING: AUC difference > 5%. This may indicate overfitting.
3:16:11.534018 INFO: Resetting torch num_threads to 100
3:16:11.547945 INFO: === FDR correction performed with classifier version 7 ===
3:16:11.549442 PROGRESS: ============================= Precursor FDR =============================
3:16:11.549720 PROGRESS: Total precursors accumulated: 454
3:16:11.549946 PROGRESS: Target precursors: 416 (91.63%)
3:16:11.550158 PROGRESS: Decoy precursors: 38 (8.37%)
3:16:11.550391 PROGRESS: 
3:16:11.550617 PROGRESS: Precursor Summary:
3:16:11.552180 PROGRESS: Channel   0:	 0.05 FDR:   325; 0.01 FDR:   224; 0.001 FDR:   218
3:16:11.552453 PROGRESS: 
3:16:11.552682 PROGRESS: Protein Summary:
3:16:11.554493 PROGRESS: Channel   0:	 0.05 FDR:   314; 0.01 FDR:   217; 0.001 FDR:   211
3:16:11.554815 PROGRESS: =========================================================================
3:16:11.568651 INFO: fragments_df_filtered: 2280
3:16:11.929827 INFO: calibration group: precursor, fitting mz estimator 
3:16:12.178163 INFO: calibration group: precursor, fitting rt estimator 
3:16:12.345938 INFO: calibration group: fragment, fitting mz estimator 
3:16:12.738818 INFO: calibration group: precursor, predicting mz
3:16:12.759506 INFO: calibration group: precursor, predicting rt
3:16:12.867058 INFO: calibration group: fragment, predicting mz
3:16:13.205587 INFO: === checking if optimization conditions were reached ===
3:16:13.206271 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3:16:13.209166 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 58.4833.
3:16:13.209353 INFO: ==============================================
3:16:13.209663 INFO: Starting optimization step 5.
3:16:13.209914 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:16:13.210158 PROGRESS: Extracting batch of 110644 precursors
3:16:13.260797 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:16:13.261134 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:16:13.261255 INFO: FWHM in RT is 2.70 seconds, sigma is 0.35
3:16:13.261357 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:16:13.261780 INFO: Starting candidate selection
3:16:17.826474 INFO: Starting candidate scoring
3:16:19.825480 INFO: Finished candidate processing
3:16:19.825627 INFO: Collecting candidate features
3:16:20.425652 WARNING: intensity_correlation has 79 NaNs ( 0.04 % out of 217043)
3:16:20.426215 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 217043)
3:16:20.440636 INFO: Collecting fragment features
3:16:20.606057 INFO: Finished candidate scoring
3:16:20.825705 PROGRESS: === Extracted 217043 precursors and 1618665 fragments ===
3:16:20.826292 INFO: performing precursor FDR with 47 features
3:16:20.826351 INFO: Decoy channel: -1
3:16:20.826382 INFO: Competetive: True
3:16:20.947568 INFO: Setting torch num_threads to 2 for FDR classification task
3:16:21.019814 WARNING: dropped 41 target PSMs due to missing features
3:16:21.020005 WARNING: dropped 38 decoy PSMs due to missing features
3:16:26.325568 INFO: Test AUC: 0.552
3:16:26.330394 INFO: Train AUC: 0.584
3:16:26.330517 INFO: AUC difference: 5.53%
3:16:26.330547 WARNING: AUC difference > 5%. This may indicate overfitting.
3:16:26.539814 INFO: Resetting torch num_threads to 100
3:16:26.616096 INFO: === FDR correction performed with classifier version 7 ===
3:16:26.617281 PROGRESS: ============================= Precursor FDR =============================
3:16:26.617405 PROGRESS: Total precursors accumulated: 461
3:16:26.617485 PROGRESS: Target precursors: 421 (91.32%)
3:16:26.617550 PROGRESS: Decoy precursors: 40 (8.68%)
3:16:26.617609 PROGRESS: 
3:16:26.617670 PROGRESS: Precursor Summary:
3:16:26.619054 PROGRESS: Channel   0:	 0.05 FDR:   347; 0.01 FDR:   206; 0.001 FDR:     0
3:16:26.619179 PROGRESS: 
3:16:26.619252 PROGRESS: Protein Summary:
3:16:26.620799 PROGRESS: Channel   0:	 0.05 FDR:   335; 0.01 FDR:   201; 0.001 FDR:     0
3:16:26.620917 PROGRESS: =========================================================================
3:16:26.633847 INFO: fragments_df_filtered: 2114
3:16:27.060694 INFO: calibration group: precursor, fitting mz estimator 
3:16:27.356007 INFO: calibration group: precursor, fitting rt estimator 
3:16:27.594092 INFO: calibration group: fragment, fitting mz estimator 
3:16:27.991566 INFO: calibration group: precursor, predicting mz
3:16:28.011504 INFO: calibration group: precursor, predicting rt
3:16:28.230135 INFO: calibration group: fragment, predicting mz
3:16:28.557225 INFO: === checking if optimization conditions were reached ===
3:16:28.557602 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3:16:28.560187 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 53.3452.
3:16:28.560253 INFO: ==============================================
3:16:28.560358 INFO: Starting optimization step 6.
3:16:28.560442 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:16:28.560527 PROGRESS: Extracting batch of 110644 precursors
3:16:28.602550 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:16:28.602703 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:16:28.602752 INFO: FWHM in RT is 2.70 seconds, sigma is 0.35
3:16:28.602777 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:16:28.603134 INFO: Starting candidate selection
3:16:33.433455 INFO: Starting candidate scoring
3:16:35.527144 INFO: Finished candidate processing
3:16:35.527280 INFO: Collecting candidate features
3:16:36.186236 WARNING: intensity_correlation has 93 NaNs ( 0.04 % out of 216585)
3:16:36.186896 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 216585)
3:16:36.204151 INFO: Collecting fragment features
3:16:36.393108 INFO: Finished candidate scoring
3:16:36.590828 PROGRESS: === Extracted 216585 precursors and 1603335 fragments ===
3:16:36.591454 INFO: performing precursor FDR with 47 features
3:16:36.591529 INFO: Decoy channel: -1
3:16:36.591578 INFO: Competetive: True
3:16:36.700401 INFO: Setting torch num_threads to 2 for FDR classification task
3:16:36.770595 WARNING: dropped 51 target PSMs due to missing features
3:16:36.770798 WARNING: dropped 42 decoy PSMs due to missing features
3:16:42.777442 INFO: Test AUC: 0.554
3:16:42.777723 INFO: Train AUC: 0.584
3:16:42.777771 INFO: AUC difference: 5.05%
3:16:42.777808 WARNING: AUC difference > 5%. This may indicate overfitting.
3:16:42.960739 INFO: Resetting torch num_threads to 100
3:16:42.974818 INFO: === FDR correction performed with classifier version 7 ===
3:16:42.976218 PROGRESS: ============================= Precursor FDR =============================
3:16:42.976438 PROGRESS: Total precursors accumulated: 451
3:16:42.976528 PROGRESS: Target precursors: 411 (91.13%)
3:16:42.976602 PROGRESS: Decoy precursors: 40 (8.87%)
3:16:42.976670 PROGRESS: 
3:16:42.976739 PROGRESS: Precursor Summary:
3:16:42.978227 PROGRESS: Channel   0:	 0.05 FDR:   330; 0.01 FDR:   246; 0.001 FDR:   197
3:16:42.978405 PROGRESS: 
3:16:42.978490 PROGRESS: Protein Summary:
3:16:42.980105 PROGRESS: Channel   0:	 0.05 FDR:   318; 0.01 FDR:   240; 0.001 FDR:   193
3:16:42.980263 PROGRESS: =========================================================================
3:16:42.992942 INFO: fragments_df_filtered: 2451
3:16:43.360418 INFO: calibration group: precursor, fitting mz estimator 
3:16:43.586425 INFO: calibration group: precursor, fitting rt estimator 
3:16:43.776926 INFO: calibration group: fragment, fitting mz estimator 
3:16:44.192546 INFO: calibration group: precursor, predicting mz
3:16:44.209656 INFO: calibration group: precursor, predicting rt
3:16:44.298606 INFO: calibration group: fragment, predicting mz
3:16:44.565079 INFO: === checking if optimization conditions were reached ===
3:16:44.565903 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
3:16:44.568880 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 52.5484.
3:16:44.568969 INFO: ==============================================
3:16:44.569137 INFO: Starting optimization step 7.
3:16:44.569257 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:16:44.569363 PROGRESS: Extracting batch of 110644 precursors
3:16:44.615129 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:16:44.615351 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:16:44.615421 INFO: FWHM in RT is 2.72 seconds, sigma is 0.35
3:16:44.615464 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:16:44.615916 INFO: Starting candidate selection
3:16:48.946827 INFO: Starting candidate scoring
3:16:52.271547 INFO: Finished candidate processing
3:16:52.271826 INFO: Collecting candidate features
3:16:52.900668 WARNING: intensity_correlation has 69 NaNs ( 0.03 % out of 216384)
3:16:52.924015 INFO: Collecting fragment features
3:16:53.106047 INFO: Finished candidate scoring
3:16:53.245738 PROGRESS: === Extracted 216384 precursors and 1626616 fragments ===
3:16:53.246594 INFO: performing precursor FDR with 47 features
3:16:53.246739 INFO: Decoy channel: -1
3:16:53.246853 INFO: Competetive: True
3:16:53.397710 INFO: Setting torch num_threads to 2 for FDR classification task
3:16:53.470314 WARNING: dropped 34 target PSMs due to missing features
3:16:53.470659 WARNING: dropped 35 decoy PSMs due to missing features
3:16:59.241275 INFO: Test AUC: 0.556
3:16:59.241856 INFO: Train AUC: 0.585
3:16:59.241976 INFO: AUC difference: 5.04%
3:16:59.242070 WARNING: AUC difference > 5%. This may indicate overfitting.
3:16:59.402814 INFO: Resetting torch num_threads to 100
3:16:59.416300 INFO: === FDR correction performed with classifier version 7 ===
3:16:59.417844 PROGRESS: ============================= Precursor FDR =============================
3:16:59.418172 PROGRESS: Total precursors accumulated: 483
3:16:59.418421 PROGRESS: Target precursors: 439 (90.89%)
3:16:59.418666 PROGRESS: Decoy precursors: 44 (9.11%)
3:16:59.418895 PROGRESS: 
3:16:59.419118 PROGRESS: Precursor Summary:
3:16:59.420667 PROGRESS: Channel   0:	 0.05 FDR:   321; 0.01 FDR:   193; 0.001 FDR:    18
3:16:59.420950 PROGRESS: 
3:16:59.421194 PROGRESS: Protein Summary:
3:16:59.422916 PROGRESS: Channel   0:	 0.05 FDR:   312; 0.01 FDR:   188; 0.001 FDR:    18
3:16:59.423223 PROGRESS: =========================================================================
3:16:59.881903 INFO: calibration group: precursor, predicting mz
3:16:59.904364 INFO: calibration group: precursor, predicting rt
3:17:00.145749 INFO: calibration group: fragment, predicting mz
3:17:00.497627 INFO: === skipping optimization until target number of precursors are found ===
3:17:00.509920 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
3:17:00.510309 INFO: Starting optimization step 8.
3:17:00.510733 PROGRESS: === Extracting elution groups 56000 to 120000 ===
3:17:00.511061 PROGRESS: Extracting batch of 126509 precursors
3:17:00.561666 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:17:00.562014 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:17:00.562150 INFO: FWHM in RT is 2.72 seconds, sigma is 0.35
3:17:00.562245 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:17:00.562741 INFO: Starting candidate selection
3:17:04.355201 INFO: Starting candidate scoring
3:17:07.073430 INFO: Finished candidate processing
3:17:07.073607 INFO: Collecting candidate features
3:17:07.835950 WARNING: intensity_correlation has 92 NaNs ( 0.04 % out of 247043)
3:17:07.857320 INFO: Collecting fragment features
3:17:08.077755 INFO: Finished candidate scoring
3:17:08.501599 PROGRESS: === Extracted 463427 precursors and 3482787 fragments ===
3:17:08.573624 INFO: performing precursor FDR with 47 features
3:17:08.573802 INFO: Decoy channel: -1
3:17:08.573844 INFO: Competetive: True
3:17:08.969667 INFO: Setting torch num_threads to 2 for FDR classification task
3:17:09.133365 WARNING: dropped 80 target PSMs due to missing features
3:17:09.133573 WARNING: dropped 81 decoy PSMs due to missing features
3:17:21.284991 INFO: Test AUC: 0.557
3:17:21.285303 INFO: Train AUC: 0.578
3:17:21.285352 INFO: AUC difference: 3.64%
3:17:21.493758 INFO: Resetting torch num_threads to 100
3:17:21.544641 INFO: === FDR correction performed with classifier version 7 ===
3:17:21.546668 PROGRESS: ============================= Precursor FDR =============================
3:17:21.546890 PROGRESS: Total precursors accumulated: 993
3:17:21.547004 PROGRESS: Target precursors: 905 (91.14%)
3:17:21.547101 PROGRESS: Decoy precursors: 88 (8.86%)
3:17:21.547179 PROGRESS: 
3:17:21.547261 PROGRESS: Precursor Summary:
3:17:21.549119 PROGRESS: Channel   0:	 0.05 FDR:   741; 0.01 FDR:   446; 0.001 FDR:     7
3:17:21.549250 PROGRESS: 
3:17:21.549328 PROGRESS: Protein Summary:
3:17:21.551324 PROGRESS: Channel   0:	 0.05 FDR:   688; 0.01 FDR:   418; 0.001 FDR:     7
3:17:21.551463 PROGRESS: =========================================================================
3:17:21.607644 INFO: fragments_df_filtered: 4476
3:17:22.022707 INFO: calibration group: precursor, fitting mz estimator 
3:17:22.230998 INFO: calibration group: precursor, fitting rt estimator 
3:17:22.414174 INFO: calibration group: fragment, fitting mz estimator 
3:17:23.061255 INFO: calibration group: precursor, predicting mz
3:17:23.080177 INFO: calibration group: precursor, predicting rt
3:17:23.250511 INFO: calibration group: fragment, predicting mz
3:17:23.557158 INFO: === checking if optimization conditions were reached ===
3:17:23.557826 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
3:17:23.559707 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 53.3452 found after 8 searches.
3:17:23.559840 INFO: ==============================================
3:17:23.560127 PROGRESS: Optimization finished for rt_error.
3:17:23.901125 INFO: calibration group: precursor, predicting mz
3:17:23.921121 INFO: calibration group: precursor, predicting rt
3:17:24.086198 INFO: calibration group: fragment, predicting mz
3:17:24.446282 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:17:24.446866 PROGRESS: ==============================================
3:17:24.447132 PROGRESS: ms2_error      : 15.0000
3:17:24.447381 PROGRESS: ms1_error      : 10.0000
3:17:24.447616 PROGRESS: rt_error       : 53.3452
3:17:24.447842 PROGRESS: ==============================================
3:17:24.450967 INFO: calibration group: precursor, predicting mz
3:17:26.206346 INFO: calibration group: precursor, predicting rt
3:17:34.144587 INFO: calibration group: fragment, predicting mz
3:17:54.711704 PROGRESS: Extracting batch of 10183864 precursors
3:17:58.115034 INFO: Duty cycle consists of 303 frames, 1.65 seconds cycle time
3:17:58.115469 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:17:58.115594 INFO: FWHM in RT is 2.72 seconds, sigma is 0.35
3:17:58.115691 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:17:58.116320 INFO: Starting candidate selection
3:23:02.704343 INFO: Applying score cutoff of 44.32123649597168
3:23:03.188515 INFO: Removed 10766109 precursors with score below cutoff
3:23:05.874737 INFO: Starting candidate scoring
3:24:06.739738 INFO: Finished candidate processing
3:24:06.740131 INFO: Collecting candidate features
3:24:40.121269 WARNING: intensity_correlation has 70 NaNs ( 0.00 % out of 9546843)
3:24:40.733243 INFO: Collecting fragment features
3:24:51.570342 INFO: Finished candidate scoring
3:25:07.075467 INFO: === FDR correction performed with classifier version 14 ===
3:25:07.081896 INFO: performing precursor FDR with 47 features
3:25:07.082024 INFO: Decoy channel: -1
3:25:07.082070 INFO: Competetive: True
3:25:11.741302 INFO: Setting torch num_threads to 2 for FDR classification task
3:25:14.701243 WARNING: dropped 36 target PSMs due to missing features
3:25:14.701455 WARNING: dropped 34 decoy PSMs due to missing features
3:29:36.708096 INFO: Test AUC: 0.578
3:29:36.708385 INFO: Train AUC: 0.582
3:29:36.708438 INFO: AUC difference: 0.64%
3:29:37.807887 INFO: Resetting torch num_threads to 100
3:29:38.141485 INFO: Removing fragments below FDR threshold
3:29:39.030694 PROGRESS: ============================= Precursor FDR =============================
3:29:39.031104 PROGRESS: Total precursors accumulated: 26,991
3:29:39.031189 PROGRESS: Target precursors: 26,724 (99.01%)
3:29:39.031275 PROGRESS: Decoy precursors: 267 (0.99%)
3:29:39.031336 PROGRESS: 
3:29:39.031396 PROGRESS: Precursor Summary:
3:29:39.054177 PROGRESS: Channel   0:	 0.05 FDR: 26,724; 0.01 FDR: 26,724; 0.001 FDR: 16,260
3:29:39.054595 PROGRESS: 
3:29:39.054678 PROGRESS: Protein Summary:
3:29:39.088833 PROGRESS: Channel   0:	 0.05 FDR: 7,745; 0.01 FDR: 7,745; 0.001 FDR: 5,565
3:29:39.089202 PROGRESS: =========================================================================
3:29:39.866043 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:30:17.489742 PROGRESS: Processing search outputs
3:30:17.490116 PROGRESS: Performing protein grouping and FDR
3:30:17.490183 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:30:17.623372 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:30:17.702670 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:30:17.725936 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:30:17.757310 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:30:17.780061 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:30:17.803069 INFO: Building combined output
3:30:18.075889 INFO: Performing protein inference
3:30:18.204167 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
3:30:33.254924 INFO: Performing protein FDR
3:30:42.403317 INFO: Normalizing q-values using 9,864 targets and 1,002 decoys
3:30:42.440416 INFO: Test AUC: 0.888
3:30:42.440564 INFO: Train AUC: 0.880
3:30:42.440605 INFO: AUC difference: 0.96%
3:30:42.854958 PROGRESS: ================ Protein FDR =================
3:30:42.855160 PROGRESS: Unique protein groups in output
3:30:42.855201 PROGRESS:   1% protein FDR: 6,074
3:30:42.855227 PROGRESS: 
3:30:42.855250 PROGRESS: Unique precursor in output
3:30:42.855273 PROGRESS:   1% protein FDR: 33,864
3:30:42.855297 PROGRESS: ================================================
3:30:42.887095 PROGRESS: Building search statistics
3:30:42.934810 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
3:30:42.935350 INFO: Initializing OptimizationManager
3:30:42.935900 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
3:30:42.936119 INFO: Initializing CalibrationManager
3:30:42.936669 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
3:30:42.936897 INFO: Initializing RawFileManager
3:30:42.948775 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
3:30:42.949242 INFO: Initializing OptimizationManager
3:30:42.949722 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
3:30:42.949939 INFO: Initializing CalibrationManager
3:30:42.950407 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
3:30:42.950634 INFO: Initializing RawFileManager
3:30:42.962181 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
3:30:42.962652 INFO: Initializing OptimizationManager
3:30:42.963123 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
3:30:42.963337 INFO: Initializing CalibrationManager
3:30:42.963794 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
3:30:42.964023 INFO: Initializing RawFileManager
3:30:42.981636 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
3:30:42.982111 INFO: Initializing OptimizationManager
3:30:42.982633 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
3:30:42.982875 INFO: Initializing CalibrationManager
3:30:42.983455 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
3:30:42.983693 INFO: Initializing RawFileManager
3:30:43.001497 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
3:30:43.001960 INFO: Initializing OptimizationManager
3:30:43.002476 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
3:30:43.002719 INFO: Initializing CalibrationManager
3:30:43.003216 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
3:30:43.003454 INFO: Initializing RawFileManager
3:30:43.021343 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
3:30:43.021802 INFO: Initializing OptimizationManager
3:30:43.022313 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
3:30:43.022557 INFO: Initializing CalibrationManager
3:30:43.023014 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
3:30:43.023239 INFO: Initializing RawFileManager
3:30:43.026279 INFO: Writing stat output to disk
3:30:43.026449 INFO: Saving run_output_Astral/alphadia_1.10_noMBR/stat.tsv to disk
3:30:43.032216 PROGRESS: Building internal statistics
3:30:43.032642 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
3:30:43.032754 INFO: Initializing TimingManager
3:30:43.033316 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
3:30:43.033427 INFO: Initializing TimingManager
3:30:43.033709 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
3:30:43.033813 INFO: Initializing TimingManager
3:30:43.034084 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
3:30:43.034202 INFO: Initializing TimingManager
3:30:43.034481 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
3:30:43.034587 INFO: Initializing TimingManager
3:30:43.034849 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.10_noMBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
3:30:43.034950 INFO: Initializing TimingManager
3:30:43.035592 INFO: Writing internal output to disk
3:30:43.035712 INFO: Saving run_output_Astral/alphadia_1.10_noMBR/internal.tsv to disk
3:30:43.036910 PROGRESS: Performing label free quantification
3:30:43.071985 INFO: Accumulating fragment data
3:30:43.072187 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:30:43.378029 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:30:43.646812 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:30:43.921380 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:30:44.507615 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:30:45.107639 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:30:45.884567 PROGRESS: Performing label free quantification on the precursor level
3:30:45.884749 INFO: Filtering fragments by quality
3:30:46.016941 INFO: Performing label-free quantification using directLFQ
3:30:47.655275 INFO: 33864 lfq-groups total
3:31:50.342246 INFO: using 100 processes
3:31:50.485133 INFO: lfq-object 0
3:31:50.544088 INFO: lfq-object 100
3:31:50.614530 INFO: lfq-object 200
3:31:50.685040 INFO: lfq-object 300
3:31:50.769452 INFO: lfq-object 400
3:31:50.822022 INFO: lfq-object 500
3:31:50.848588 INFO: lfq-object 600
3:31:50.935478 INFO: lfq-object 700
3:31:51.005947 INFO: lfq-object 800
3:31:51.093514 INFO: lfq-object 900
3:31:51.142095 INFO: lfq-object 1000
3:31:51.232822 INFO: lfq-object 1100
3:31:51.239574 INFO: lfq-object 1200
3:31:51.325127 INFO: lfq-object 1300
3:31:51.395581 INFO: lfq-object 1400
3:31:51.450034 INFO: lfq-object 1500
3:31:51.526361 INFO: lfq-object 1700
3:31:51.553530 INFO: lfq-object 1600
3:31:51.619206 INFO: lfq-object 1800
3:31:51.697564 INFO: lfq-object 1900
3:31:51.739030 INFO: lfq-object 2000
3:31:51.818839 INFO: lfq-object 2100
3:31:51.882943 INFO: lfq-object 2300
3:31:51.889607 INFO: lfq-object 2200
3:31:51.983029 INFO: lfq-object 2400
3:31:52.069586 INFO: lfq-object 2500
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3:31:52.368068 INFO: lfq-object 3000
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3:31:52.930218 INFO: lfq-object 4000
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3:31:53.550309 INFO: lfq-object 5100
3:31:53.572483 INFO: lfq-object 5000
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3:32:04.627071 INFO: lfq-object 18500
3:32:04.688209 INFO: lfq-object 18700
3:32:04.705332 INFO: lfq-object 18600
3:32:04.757922 INFO: lfq-object 18800
3:32:04.814641 INFO: lfq-object 18900
3:32:04.883099 INFO: lfq-object 19000
3:32:04.953113 INFO: lfq-object 19100
3:32:04.981821 INFO: lfq-object 19300
3:32:05.001100 INFO: lfq-object 19200
3:32:05.065185 INFO: lfq-object 19400
3:32:05.134227 INFO: lfq-object 19500
3:32:05.194244 INFO: lfq-object 19600
3:32:05.275323 INFO: lfq-object 19700
3:32:05.331676 INFO: lfq-object 19900
3:32:05.333710 INFO: lfq-object 19800
3:32:05.371646 INFO: lfq-object 20000
3:32:05.453941 INFO: lfq-object 20100
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3:32:05.560364 INFO: lfq-object 20400
3:32:05.589085 INFO: lfq-object 20300
3:32:05.634550 INFO: lfq-object 20500
3:32:05.698741 INFO: lfq-object 20600
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3:32:08.724064 INFO: lfq-object 21200
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3:32:10.508793 INFO: lfq-object 24300
3:32:10.575618 INFO: lfq-object 24500
3:32:10.659880 INFO: lfq-object 24600
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3:32:10.861562 INFO: lfq-object 25000
3:32:10.867295 INFO: lfq-object 24900
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3:32:11.025986 INFO: lfq-object 25200
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3:32:12.034452 INFO: lfq-object 27000
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3:32:12.231248 INFO: lfq-object 27400
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3:32:12.660038 INFO: lfq-object 28100
3:32:12.738538 INFO: lfq-object 28200
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3:32:13.049775 INFO: lfq-object 28800
3:32:13.055614 INFO: lfq-object 28900
3:32:13.123370 INFO: lfq-object 29000
3:32:13.211085 INFO: lfq-object 29100
3:32:13.252386 INFO: lfq-object 29200
3:32:13.314680 INFO: lfq-object 29300
3:32:13.338857 INFO: lfq-object 29400
3:32:13.356009 INFO: lfq-object 29500
3:32:13.417216 INFO: lfq-object 29600
3:32:13.480591 INFO: lfq-object 29700
3:32:13.542711 INFO: lfq-object 29800
3:32:13.603435 INFO: lfq-object 29900
3:32:13.697552 INFO: lfq-object 30000
3:32:13.708208 INFO: lfq-object 30100
3:32:13.801824 INFO: lfq-object 30200
3:32:13.872139 INFO: lfq-object 30300
3:32:13.932098 INFO: lfq-object 30400
3:32:13.975637 INFO: lfq-object 30600
3:32:13.985495 INFO: lfq-object 30500
3:32:14.052784 INFO: lfq-object 30700
3:32:14.126962 INFO: lfq-object 30800
3:32:14.196235 INFO: lfq-object 30900
3:32:14.261352 INFO: lfq-object 31000
3:32:14.315785 INFO: lfq-object 31200
3:32:14.332623 INFO: lfq-object 31100
3:32:14.401691 INFO: lfq-object 31300
3:32:14.461788 INFO: lfq-object 31400
3:32:14.539499 INFO: lfq-object 31500
3:32:14.607233 INFO: lfq-object 31600
3:32:14.646469 INFO: lfq-object 31700
3:32:14.661777 INFO: lfq-object 31800
3:32:14.735867 INFO: lfq-object 31900
3:32:14.813750 INFO: lfq-object 32000
3:32:14.886391 INFO: lfq-object 32100
3:32:14.912677 INFO: lfq-object 32300
3:32:14.947991 INFO: lfq-object 32200
3:32:14.999331 INFO: lfq-object 32400
3:32:15.067307 INFO: lfq-object 32500
3:32:15.141309 INFO: lfq-object 32600
3:32:15.201366 INFO: lfq-object 32700
3:32:15.256050 INFO: lfq-object 32900
3:32:15.272379 INFO: lfq-object 32800
3:32:15.336662 INFO: lfq-object 33000
3:32:15.402400 INFO: lfq-object 33100
3:32:15.471249 INFO: lfq-object 33200
3:32:15.546983 INFO: lfq-object 33300
3:32:15.590878 INFO: lfq-object 33500
3:32:15.604736 INFO: lfq-object 33400
3:32:15.654649 INFO: lfq-object 33600
3:32:15.713982 INFO: lfq-object 33700
3:32:15.794399 INFO: lfq-object 33800
3:32:23.681829 INFO: Writing precursor output to disk
3:32:23.682121 INFO: Saving run_output_Astral/alphadia_1.10_noMBR/precursor.matrix.tsv to disk
3:32:24.057623 PROGRESS: Performing label free quantification on the pg level
3:32:24.057802 INFO: Filtering fragments by quality
3:32:24.213192 INFO: Performing label-free quantification using directLFQ
3:32:24.375512 INFO: 6074 lfq-groups total
3:33:30.666803 INFO: using 100 processes
3:33:30.706450 INFO: lfq-object 0
3:33:30.787586 INFO: lfq-object 100
3:33:30.909129 INFO: lfq-object 200
3:33:30.981348 INFO: lfq-object 300
3:33:31.016102 INFO: lfq-object 400
3:33:31.146048 INFO: lfq-object 500
3:33:31.393839 INFO: lfq-object 600
3:33:31.584266 INFO: lfq-object 700
3:33:31.631232 INFO: lfq-object 800
3:33:31.711223 INFO: lfq-object 900
3:33:31.831492 INFO: lfq-object 1000
3:33:31.948485 INFO: lfq-object 1100
3:33:32.010879 INFO: lfq-object 1200
3:33:32.087354 INFO: lfq-object 1300
3:33:32.228556 INFO: lfq-object 1500
3:33:32.288178 INFO: lfq-object 1600
3:33:32.363605 INFO: lfq-object 1700
3:33:32.364314 INFO: lfq-object 1400
3:33:32.445179 INFO: lfq-object 1800
3:33:32.533959 INFO: lfq-object 1900
3:33:32.580128 INFO: lfq-object 2000
3:33:32.648513 INFO: lfq-object 2100
3:33:32.752164 INFO: lfq-object 2200
3:33:32.843115 INFO: lfq-object 2300
3:33:32.872043 INFO: lfq-object 2400
3:33:32.951192 INFO: lfq-object 2500
3:33:33.035912 INFO: lfq-object 2600
3:33:33.098061 INFO: lfq-object 2700
3:33:33.142805 INFO: lfq-object 2800
3:33:33.214408 INFO: lfq-object 2900
3:33:33.284856 INFO: lfq-object 3000
3:33:33.379487 INFO: lfq-object 3100
3:33:33.407607 INFO: lfq-object 3200
3:33:33.485472 INFO: lfq-object 3300
3:33:33.545654 INFO: lfq-object 3400
3:33:33.633862 INFO: lfq-object 3500
3:33:33.709707 INFO: lfq-object 3600
3:33:33.800239 INFO: lfq-object 3700
3:33:33.880290 INFO: lfq-object 3800
3:33:33.985018 INFO: lfq-object 3900
3:33:34.116261 INFO: lfq-object 4000
3:33:34.192963 INFO: lfq-object 4100
3:33:34.283244 INFO: lfq-object 4200
3:33:34.351800 INFO: lfq-object 4300
3:33:34.403979 INFO: lfq-object 4400
3:33:34.513861 INFO: lfq-object 4500
3:33:34.591000 INFO: lfq-object 4600
3:33:34.650730 INFO: lfq-object 4700
3:33:34.695841 INFO: lfq-object 4800
3:33:34.781861 INFO: lfq-object 4900
3:33:34.849262 INFO: lfq-object 5000
3:33:34.902647 INFO: lfq-object 5100
3:33:34.960758 INFO: lfq-object 5200
3:33:35.031251 INFO: lfq-object 5300
3:33:35.097475 INFO: lfq-object 5400
3:33:35.187227 INFO: lfq-object 5500
3:33:35.219547 INFO: lfq-object 5600
3:33:35.292407 INFO: lfq-object 5700
3:33:35.356655 INFO: lfq-object 5800
3:33:35.482352 INFO: lfq-object 6000
3:33:35.649305 INFO: lfq-object 5900
3:33:39.622209 INFO: Writing pg output to disk
3:33:39.622618 INFO: Saving run_output_Astral/alphadia_1.10_noMBR/pg.matrix.tsv to disk
3:33:39.760297 INFO: Writing psm output to disk
3:33:39.760461 INFO: Saving run_output_Astral/alphadia_1.10_noMBR/precursors.tsv to disk
3:33:55.050792 PROGRESS: Building spectral library
3:33:55.108383 INFO: Building MBR spectral library
3:33:55.108741 INFO: Running MbrLibraryBuilder
3:33:57.483754 INFO: MBR spectral library contains 33,864 precursors, 6,074 proteins
3:33:57.483968 INFO: Writing MBR spectral library to disk
3:33:58.067541 PROGRESS: =================== Search Finished ===================
3:33:59.793274 WARNING: WARNING: Temp mmap arrays were written to /tmp/temp_mmap_3womrqe0. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 699,911,065,600
