0:00:00.000030 INFO: Moved old log file ./run_output/alphadia_1.10_defaultMBRTransfer/log.txt to run_output/alphadia_1.10_defaultMBRTransfer/log.1.bkp.txt
0:00:00.013781 PROGRESS:           _      _         ___ ___   _   
0:00:00.013845 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.013874 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.013904 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.013927 PROGRESS:            |_|                           
0:00:00.013948 PROGRESS: 
0:00:00.013974 PROGRESS: version: 1.10.3
0:00:00.014007 INFO: hostname: thestral
0:00:00.014056 INFO: date: 2025-04-18 10:14:07
0:00:00.014079 INFO: ================ AlphaX Environment ===============
0:00:00.014099 INFO: alphatims       : 1.0.8
0:00:00.014118 INFO: alpharaw        : 0.4.5
0:00:00.014136 INFO: alphabase       : 1.5.0
0:00:00.014153 INFO: alphapeptdeep   : 1.3.0
0:00:00.014171 INFO: directlfq       : 0.2.19
0:00:00.014188 INFO: ===================================================
0:00:00.014205 INFO: ================= Pip Environment =================
0:00:00.071044 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
0:00:00.071134 INFO: ===================================================
0:00:00.071163 INFO: Running step 'library'
0:00:00.071224 INFO: loading config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:00:00.081814 INFO: loading additional config provided via CLI
0:00:00.081873 INFO: loading additional config provided via CLI parameters
0:00:00.082100 INFO: Updating config with 'user defined'
0:00:00.082183 INFO: Updating config with 'user defined (cli)'
0:00:00.082208 INFO: Updating config with 'multistep search'
0:00:00.082243 INFO: ├──version: 1
0:00:00.082269 INFO: ├──workflow_name: None
0:00:00.082292 INFO: [32;20m├──output_directory: run_output/alphadia_1.10_defaultMBRTransfer/library [multistep search, default: None][0m
0:00:00.082314 INFO: ├──library_path: None
0:00:00.082336 INFO: ├──raw_paths:
0:00:00.082356 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d [user defined (cli), default: None][0m
0:00:00.082376 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d [user defined (cli), default: None][0m
0:00:00.082397 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d [user defined (cli), default: None][0m
0:00:00.082417 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d [user defined (cli), default: None][0m
0:00:00.082435 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d [user defined (cli), default: None][0m
0:00:00.082454 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d [user defined (cli), default: None][0m
0:00:00.082473 INFO: ├──fasta_paths:
0:00:00.082491 INFO: │   [32;20m- ./ProteoBenchFASTA_DDAQuantification.fasta [user defined (cli), default: None][0m
0:00:00.082512 INFO: ├──quant_directory: None
0:00:00.082530 INFO: ├──general
0:00:00.082552 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
0:00:00.082571 INFO: │   ├──transfer_step_enabled: False
0:00:00.082590 INFO: │   ├──mbr_step_enabled: True
0:00:00.082608 INFO: │   ├──reuse_calibration: False
0:00:00.082626 INFO: │   ├──reuse_quant: False
0:00:00.082645 INFO: │   ├──astral_ms1: False
0:00:00.082663 INFO: │   ├──log_level: INFO
0:00:00.082680 INFO: │   ├──mmap_detector_events: False
0:00:00.082702 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
0:00:00.082721 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.082740 INFO: │   └──save_mbr_library: True
0:00:00.082758 INFO: ├──library_loading
0:00:00.082777 INFO: │   └──rt_heuristic: 180
0:00:00.082794 INFO: ├──library_prediction
0:00:00.082814 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.082835 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.082854 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.082872 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
0:00:00.082892 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.082910 INFO: │   ├──missed_cleavages: 1
0:00:00.082928 INFO: │   ├──precursor_len:
0:00:00.082947 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.082967 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.082986 INFO: │   ├──precursor_charge:
0:00:00.083004 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.083023 INFO: │   │   [32;20m- 4[0m
0:00:00.083040 INFO: │   ├──precursor_mz:
0:00:00.083058 INFO: │   │   [32;20m- 400[0m
0:00:00.083076 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
0:00:00.083095 INFO: │   ├──fragment_mz:
0:00:00.083113 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
0:00:00.083132 INFO: │   │   [32;20m- 2000[0m
0:00:00.083152 INFO: │   ├──nce: 25
0:00:00.083170 INFO: │   ├──fragment_types:
0:00:00.083188 INFO: │   │   [32;20m- b[0m
0:00:00.083214 INFO: │   │   [32;20m- y[0m
0:00:00.083232 INFO: │   ├──max_fragment_charge: 2
0:00:00.083250 INFO: │   [32;20m├──instrument: timsTOF [user defined, default: Lumos][0m
0:00:00.083268 INFO: │   ├──peptdeep_model_path: None
0:00:00.083287 INFO: │   └──peptdeep_model_type: generic
0:00:00.083304 INFO: ├──custom_modifications:
0:00:00.083323 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.083342 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.083362 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.083380 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.083398 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.083416 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.083435 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.083452 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.083471 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.083488 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.083506 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.083524 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.083542 INFO: │   ├──name: Label:13C(12)@K
0:00:00.083565 INFO: │   └──composition: C(12)
0:00:00.083582 INFO: ├──search
0:00:00.083602 INFO: │   [32;20m├──target_ms1_tolerance: 10 [user defined, default: 5][0m
0:00:00.083621 INFO: │   [32;20m├──target_ms2_tolerance: 15 [user defined, default: 10][0m
0:00:00.083640 INFO: │   ├──target_rt_tolerance: 0
0:00:00.083658 INFO: │   ├──target_mobility_tolerance: 0
0:00:00.083676 INFO: │   ├──quant_window: 3
0:00:00.083696 INFO: │   [32;20m├──target_num_candidates: 2 [user defined, default: 3][0m
0:00:00.083717 INFO: │   ├──channel_filter: 
0:00:00.083735 INFO: │   ├──exclude_shared_ions: True
0:00:00.083754 INFO: │   ├──compete_for_fragments: True
0:00:00.083771 INFO: │   ├──quant_all: True
0:00:00.083790 INFO: │   ├──top_k_fragments: 12
0:00:00.083807 INFO: │   └──experimental_xic: True
0:00:00.083824 INFO: ├──calibration
0:00:00.083843 INFO: │   ├──batch_size: 8000
0:00:00.083862 INFO: │   ├──optimization_lock_target: 200
0:00:00.083880 INFO: │   ├──max_steps: 20
0:00:00.083899 INFO: │   ├──min_steps: 2
0:00:00.083917 INFO: │   ├──max_skips: 1
0:00:00.083935 INFO: │   ├──norm_rt_mode: linear
0:00:00.083952 INFO: │   ├──max_fragments: 5000
0:00:00.083975 INFO: │   └──min_correlation: 0.7
0:00:00.083992 INFO: ├──search_initial
0:00:00.084009 INFO: │   ├──initial_num_candidates: 1
0:00:00.084026 INFO: │   ├──initial_ms1_tolerance: 30
0:00:00.084044 INFO: │   ├──initial_ms2_tolerance: 30
0:00:00.084063 INFO: │   ├──initial_mobility_tolerance: 0.1
0:00:00.084082 INFO: │   └──initial_rt_tolerance: 0.5
0:00:00.084126 INFO: ├──selection_config
0:00:00.084146 INFO: │   ├──peak_len_rt: 10.0
0:00:00.084165 INFO: │   ├──sigma_scale_rt: 0.5
0:00:00.084186 INFO: │   ├──peak_len_mobility: 0.01
0:00:00.084204 INFO: │   ├──sigma_scale_mobility: 1.0
0:00:00.084224 INFO: │   ├──top_k_precursors: 3
0:00:00.084242 INFO: │   ├──kernel_size: 30
0:00:00.084261 INFO: │   ├──f_mobility: 1.0
0:00:00.084281 INFO: │   ├──f_rt: 0.99
0:00:00.084300 INFO: │   ├──center_fraction: 0.5
0:00:00.084319 INFO: │   ├──min_size_mobility: 8
0:00:00.084337 INFO: │   ├──min_size_rt: 3
0:00:00.084355 INFO: │   ├──max_size_mobility: 20
0:00:00.084374 INFO: │   ├──max_size_rt: 15
0:00:00.084393 INFO: │   ├──group_channels: False
0:00:00.084411 INFO: │   ├──use_weighted_score: True
0:00:00.084430 INFO: │   ├──join_close_candidates: False
0:00:00.084449 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
0:00:00.084467 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
0:00:00.084492 INFO: ├──scoring_config
0:00:00.084512 INFO: │   ├──score_grouped: False
0:00:00.084530 INFO: │   ├──top_k_isotopes: 3
0:00:00.084548 INFO: │   ├──reference_channel: -1
0:00:00.084566 INFO: │   ├──precursor_mz_tolerance: 10
0:00:00.084583 INFO: │   └──fragment_mz_tolerance: 15
0:00:00.084601 INFO: ├──library_multiplexing
0:00:00.084619 INFO: │   ├──enabled: False
0:00:00.084640 INFO: │   ├──input_channel: 0
0:00:00.084658 INFO: │   └──multiplex_mapping:
0:00:00.084675 INFO: ├──multiplexing
0:00:00.084693 INFO: │   ├──enabled: False
0:00:00.084711 INFO: │   ├──target_channels: 4,8
0:00:00.084728 INFO: │   ├──decoy_channel: 12
0:00:00.084745 INFO: │   ├──reference_channel: 0
0:00:00.084764 INFO: │   └──competetive_scoring: True
0:00:00.084781 INFO: ├──fdr
0:00:00.084800 INFO: │   ├──fdr: 0.01
0:00:00.084818 INFO: │   ├──group_level: proteins
0:00:00.084838 INFO: │   ├──inference_strategy: heuristic
0:00:00.084856 INFO: │   ├──competetive_scoring: True
0:00:00.084876 INFO: │   ├──keep_decoys: False
0:00:00.084894 INFO: │   ├──channel_wise_fdr: False
0:00:00.084912 INFO: │   ├──enable_two_step_classifier: False
0:00:00.084932 INFO: │   ├──two_step_classifier_max_iterations: 5
0:00:00.084952 INFO: │   └──enable_nn_hyperparameter_tuning: False
0:00:00.084968 INFO: ├──search_output
0:00:00.084988 INFO: │   ├──file_format: tsv
0:00:00.085007 INFO: │   ├──peptide_level_lfq: False
0:00:00.085027 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
0:00:00.085046 INFO: │   ├──min_k_fragments: 12
0:00:00.085064 INFO: │   ├──min_correlation: 0.9
0:00:00.085082 INFO: │   ├──num_samples_quadratic: 50
0:00:00.085100 INFO: │   ├──min_nonnan: 3
0:00:00.085118 INFO: │   ├──normalize_lfq: True
0:00:00.085137 INFO: │   └──save_fragment_quant_matrix: False
0:00:00.085155 INFO: ├──optimization
0:00:00.085174 INFO: │   ├──order_of_optimization: None
0:00:00.085191 INFO: │   ├──ms2_error
0:00:00.085209 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.085228 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.085246 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.085263 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.085282 INFO: │   │   ├──try_narrower_values: True
0:00:00.085300 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.085318 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.085336 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.085355 INFO: │   ├──ms1_error
0:00:00.085373 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.085390 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.085409 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.085429 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.085447 INFO: │   │   ├──try_narrower_values: False
0:00:00.085465 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.085484 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.085502 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.085519 INFO: │   ├──mobility_error
0:00:00.085538 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.085557 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.085575 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.085594 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.085613 INFO: │   │   ├──try_narrower_values: False
0:00:00.085631 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.085649 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.085668 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.085691 INFO: │   └──rt_error
0:00:00.085711 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.085729 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.085747 INFO: │       ├──automatic_update_percentile_range: 0.99
0:00:00.085765 INFO: │       ├──automatic_update_factor: 1.1
0:00:00.085782 INFO: │       ├──try_narrower_values: True
0:00:00.085803 INFO: │       ├──maximal_decrease: 0.2
0:00:00.085820 INFO: │       ├──favour_narrower_optimum: True
0:00:00.085837 INFO: │       └──maximum_decrease_from_maximum: 0.1
0:00:00.085854 INFO: ├──optimization_manager
0:00:00.085873 INFO: │   ├──fwhm_rt: 5
0:00:00.085890 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.085908 INFO: │   └──score_cutoff: 0
0:00:00.085925 INFO: ├──transfer_library
0:00:00.085943 INFO: │   ├──enabled: False
0:00:00.085960 INFO: │   ├──fragment_types:
0:00:00.085977 INFO: │   │   [32;20m- b[0m
0:00:00.085995 INFO: │   │   [32;20m- y[0m
0:00:00.086012 INFO: │   ├──max_charge: 2
0:00:00.086030 INFO: │   ├──top_k_samples: 3
0:00:00.086048 INFO: │   ├──norm_delta_max: True
0:00:00.086066 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.086084 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.086102 INFO: └──transfer_learning
0:00:00.086121 INFO:     ├──enabled: False
0:00:00.086138 INFO:     ├──batch_size: 2000
0:00:00.086156 INFO:     ├──max_lr: 0.0001
0:00:00.086174 INFO:     ├──train_fraction: 0.7
0:00:00.086193 INFO:     ├──validation_fraction: 0.2
0:00:00.086210 INFO:     ├──test_fraction: 0.1
0:00:00.086229 INFO:     ├──test_interval: 1
0:00:00.086247 INFO:     ├──lr_patience: 3
0:00:00.086264 INFO:     ├──epochs: 51
0:00:00.086282 INFO:     ├──warmup_epochs: 5
0:00:00.086299 INFO:     ├──nce: 25
0:00:00.086320 INFO:     [32;20m└──instrument: timsTOF [user defined, default: Lumos][0m
0:00:00.090935 INFO: Moved existing config file run_output/alphadia_1.10_defaultMBRTransfer/library/frozen_config.yaml to run_output/alphadia_1.10_defaultMBRTransfer/library/frozen_config.0.bkp.yaml
0:00:00.091071 INFO: Registering 7 custom modifications
0:00:00.117816 PROGRESS: No library provided. Building library from fasta files.
0:00:00.117902 INFO: Running FastaDigest
0:00:00.963677 INFO: Digesting fasta file
0:00:07.449559 INFO: Adding modifications
0:01:33.019191 INFO: Removing non-canonical amino acids
0:01:39.154832 INFO: Fasta library contains 5,215,079 precursors
0:01:39.155063 PROGRESS: Predicting library properties.
0:01:39.155129 INFO: Running PeptDeepPrediction
0:01:39.155205 INFO: Device set to cpu
0:01:40.063421 INFO: Loading PeptDeep models of type generic
0:01:40.827416 INFO: Predicting RT, MS2 and mobility
0:01:40.827580 INFO: Using multiprocessing with 100 processes ...
0:01:41.198892 INFO: Predicting rt,ms2,mobility ...
0:07:09.234442 INFO: Adding fragment mz information
0:07:09.515614 INFO: Adding fragment intensity information
0:07:09.795415 INFO: Adding precursor information
0:07:10.168978 INFO: Running PrecursorInitializer
0:07:10.190934 INFO: Running AnnotateFasta
0:07:10.338822 INFO: Dropping decoys from input library before annotation
0:07:37.007220 INFO: Running IsotopeGenerator
0:08:02.192073 INFO: Running RTNormalization
0:08:02.192614 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:08:02.192716 INFO: Saving library to run_output/alphadia_1.10_defaultMBRTransfer/library/speclib.hdf
0:08:33.621171 INFO: Running DecoyGenerator
0:10:24.584504 INFO: Running FlattenLibrary
0:10:52.298342 INFO: Running InitFlatColumns
0:10:52.512543 INFO: Running LogFlatLibraryStats
0:10:52.512681 INFO: ============ Library Stats ============
0:10:52.512725 INFO: Number of precursors: 10,400,392
0:10:53.957826 INFO: 	thereof targets:5,215,079
0:10:53.957978 INFO: 	thereof decoys: 5,185,313
0:10:54.029934 INFO: Number of elution groups: 5,215,079
0:10:54.030078 INFO: 	average size: 1.99
0:10:54.360658 INFO: Number of proteins: 117,993
0:10:54.385849 INFO: Number of channels: 1 ([0])
0:10:54.386011 INFO: Isotopes Distribution for 4 isotopes
0:10:54.386040 INFO: =======================================
0:10:54.393687 INFO: Searching 6 files:
0:10:54.393789 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:10:54.393810 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
0:10:54.393828 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
0:10:54.393846 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
0:10:54.393864 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
0:10:54.393881 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
0:10:54.393903 INFO: Using 1 fasta files:
0:10:54.393922 INFO:   ./ProteoBenchFASTA_DDAQuantification.fasta
0:10:54.393945 INFO: Using library: None
0:10:54.393964 INFO: Saving output to: run_output/alphadia_1.10_defaultMBRTransfer/library
0:10:54.393988 PROGRESS: Starting Search Workflows
0:10:54.394051 PROGRESS: Loading raw file 1/6: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
0:10:54.394099 INFO: Quantification results path: run_output/alphadia_1.10_defaultMBRTransfer/library/quant
0:10:54.394667 INFO: Initializing RawFileManager
0:10:54.394769 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:10:54.394813 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:10:54.394842 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:10:54.604594 INFO: Reading 39,128 frames with 2,835,410,867 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:11:02.202339 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d...
0:11:02.208422 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:11:02.223111 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:11:02.223434 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:11:02.223739 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:11:02.225228 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:11:02.233973 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:11:02.234151 INFO: Indexing quadrupole dimension
0:11:02.722251 INFO: Transposing detector events
0:11:12.114819 INFO: Finished transposing data
0:11:12.151342 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:11:12.152265 INFO: RT (min)            : 0.0 - 70.0
0:11:12.152364 INFO: RT duration (sec)   : 4199.9
0:11:12.152419 INFO: RT duration (min)   : 70.0
0:11:12.152467 INFO: Cycle len (scans)   : 9
0:11:12.152513 INFO: Cycle len (sec)     : 0.97
0:11:12.152557 INFO: Number of cycles    : 4347
0:11:12.152604 INFO: MS2 range (m/z)     : 400.0 - 1000.0
0:11:13.394270 INFO: Initializing CalibrationManager
0:11:13.394558 INFO: Loading calibration config
0:11:13.394660 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'}]
0:11:13.395188 INFO: Calibration group :fragment, found 1 estimator(s)
0:11:13.395311 INFO: Calibration group :precursor, found 3 estimator(s)
0:11:13.395436 INFO: Initializing OptimizationManager
0:11:13.395531 INFO: initial parameter: ms1_error = 30
0:11:13.395585 INFO: initial parameter: ms2_error = 30
0:11:13.395633 INFO: initial parameter: rt_error = 2099.928159
0:11:13.395686 INFO: initial parameter: mobility_error = 0.1
0:11:13.395735 INFO: initial parameter: column_type = library
0:11:13.395778 INFO: initial parameter: num_candidates = 1
0:11:13.395821 INFO: initial parameter: classifier_version = -1
0:11:13.395865 INFO: initial parameter: fwhm_rt = 5
0:11:13.395906 INFO: initial parameter: fwhm_mobility = 0.01
0:11:13.395947 INFO: initial parameter: score_cutoff = 0
0:11:13.396012 INFO: Initializing TimingManager
0:11:13.396071 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
0:11:13.396187 INFO: FDRManager not loaded from disk.
0:11:13.396214 INFO: Initializing FDRManager
0:11:13.396253 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:11:14.713257 PROGRESS: 5,215,079 target precursors potentially observable (0 removed)
0:11:16.596484 PROGRESS: Starting initial search for precursors.
0:11:17.525935 INFO: Starting optimization step 0.
0:11:17.526314 PROGRESS: === Extracting elution groups 0 to 8000 ===
0:11:17.526407 PROGRESS: Extracting batch of 15764 precursors
0:11:19.664520 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:11:19.664665 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:11:19.664702 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:11:19.664724 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:11:23.477867 INFO: Starting candidate selection
0:14:19.445550 INFO: Starting candidate scoring
0:22:05.974109 INFO: Finished candidate processing
0:22:05.974319 INFO: Collecting candidate features
0:22:06.583860 WARNING: intensity_correlation has 1 NaNs ( 0.01 % out of 13753)
0:22:06.587468 INFO: Collecting fragment features
0:22:09.064791 INFO: Finished candidate scoring
0:22:09.078527 PROGRESS: === Extracted 13753 precursors and 137923 fragments ===
0:22:09.078910 INFO: performing precursor FDR with 47 features
0:22:09.078952 INFO: Decoy channel: -1
0:22:09.078978 INFO: Competetive: True
0:22:09.082835 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:09.085307 WARNING: dropped 1 decoy PSMs due to missing features
0:22:09.731423 INFO: Test AUC: 0.528
0:22:09.731545 INFO: Train AUC: 0.537
0:22:09.731576 INFO: AUC difference: 1.74%
0:22:09.814678 INFO: Resetting torch num_threads to 128
0:22:09.815104 INFO: === FDR correction performed with classifier version -1 ===
0:22:09.816987 PROGRESS: ============================= Precursor FDR =============================
0:22:09.817087 PROGRESS: Total precursors accumulated: 7,052
0:22:09.817148 PROGRESS: Target precursors: 3,895 (55.23%)
0:22:09.817201 PROGRESS: Decoy precursors: 3,157 (44.77%)
0:22:09.817247 PROGRESS: 
0:22:09.817293 PROGRESS: Precursor Summary:
0:22:09.818175 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:09.818263 PROGRESS: 
0:22:09.818319 PROGRESS: Protein Summary:
0:22:09.819246 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:22:09.819333 PROGRESS: =========================================================================
0:22:09.970968 INFO: Starting optimization step 1.
0:22:09.971225 PROGRESS: === Extracting elution groups 8000 to 24000 ===
0:22:09.971297 PROGRESS: Extracting batch of 31501 precursors
0:22:09.978669 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:22:09.978740 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:22:09.978773 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:22:09.978795 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:22:09.979606 INFO: Starting candidate selection
0:24:41.527042 INFO: Starting candidate scoring
0:24:43.001598 INFO: Finished candidate processing
0:24:43.001794 INFO: Collecting candidate features
0:24:43.092441 WARNING: intensity_correlation has 7 NaNs ( 0.03 % out of 27358)
0:24:43.092741 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 27358)
0:24:43.096730 INFO: Collecting fragment features
0:24:43.114688 INFO: Finished candidate scoring
0:24:43.202557 PROGRESS: === Extracted 41111 precursors and 410863 fragments ===
0:24:43.209769 INFO: performing precursor FDR with 47 features
0:24:43.209893 INFO: Decoy channel: -1
0:24:43.209920 INFO: Competetive: True
0:24:43.232793 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:43.242694 WARNING: dropped 4 target PSMs due to missing features
0:24:43.242840 WARNING: dropped 4 decoy PSMs due to missing features
0:24:43.980245 INFO: Test AUC: 0.546
0:24:43.980401 INFO: Train AUC: 0.563
0:24:43.980432 INFO: AUC difference: 3.06%
0:24:44.077046 INFO: Resetting torch num_threads to 128
0:24:44.080567 INFO: === FDR correction performed with classifier version -1 ===
0:24:44.084473 PROGRESS: ============================= Precursor FDR =============================
0:24:44.084633 PROGRESS: Total precursors accumulated: 21,080
0:24:44.084698 PROGRESS: Target precursors: 12,259 (58.15%)
0:24:44.084751 PROGRESS: Decoy precursors: 8,821 (41.85%)
0:24:44.084798 PROGRESS: 
0:24:44.084843 PROGRESS: Precursor Summary:
0:24:44.085827 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:24:44.085918 PROGRESS: 
0:24:44.085974 PROGRESS: Protein Summary:
0:24:44.086976 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:24:44.087065 PROGRESS: =========================================================================
0:24:44.815278 INFO: Starting optimization step 2.
0:24:44.815603 PROGRESS: === Extracting elution groups 24000 to 56000 ===
0:24:44.815711 PROGRESS: Extracting batch of 63033 precursors
0:24:44.834180 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:24:44.834335 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:24:44.834389 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:24:44.834415 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:24:44.835516 INFO: Starting candidate selection
0:29:45.821956 INFO: Starting candidate scoring
0:29:48.755748 INFO: Finished candidate processing
0:29:48.755922 INFO: Collecting candidate features
0:29:48.883509 WARNING: intensity_correlation has 9 NaNs ( 0.02 % out of 55174)
0:29:48.883821 WARNING: height_correlation has 3 NaNs ( 0.01 % out of 55174)
0:29:48.888703 INFO: Collecting fragment features
0:29:48.931378 INFO: Finished candidate scoring
0:29:49.026017 PROGRESS: === Extracted 96285 precursors and 964198 fragments ===
0:29:49.039676 INFO: performing precursor FDR with 47 features
0:29:49.039795 INFO: Decoy channel: -1
0:29:49.039821 INFO: Competetive: True
0:29:49.087311 INFO: Setting torch num_threads to 2 for FDR classification task
0:29:49.110977 WARNING: dropped 9 target PSMs due to missing features
0:29:49.111109 WARNING: dropped 9 decoy PSMs due to missing features
0:29:50.770088 INFO: Test AUC: 0.563
0:29:50.770224 INFO: Train AUC: 0.574
0:29:50.770256 INFO: AUC difference: 1.89%
0:29:50.864381 INFO: Resetting torch num_threads to 128
0:29:50.870715 INFO: === FDR correction performed with classifier version -1 ===
0:29:50.880791 PROGRESS: ============================= Precursor FDR =============================
0:29:50.881063 PROGRESS: Total precursors accumulated: 49,349
0:29:50.881129 PROGRESS: Target precursors: 29,493 (59.76%)
0:29:50.881181 PROGRESS: Decoy precursors: 19,856 (40.24%)
0:29:50.881229 PROGRESS: 
0:29:50.881276 PROGRESS: Precursor Summary:
0:29:50.882701 PROGRESS: Channel   0:	 0.05 FDR:   423; 0.01 FDR:   271; 0.001 FDR:   225
0:29:50.882796 PROGRESS: 
0:29:50.882855 PROGRESS: Protein Summary:
0:29:50.884260 PROGRESS: Channel   0:	 0.05 FDR:   405; 0.01 FDR:   267; 0.001 FDR:   222
0:29:50.884370 PROGRESS: =========================================================================
0:29:50.897003 INFO: fragments_df_filtered: 2475
0:29:51.176641 INFO: calibration group: precursor, fitting mz estimator 
0:29:51.226000 INFO: calibration group: precursor, fitting rt estimator 
0:29:51.267581 INFO: calibration group: precursor, fitting mobility estimator 
0:29:51.308072 INFO: calibration group: fragment, fitting mz estimator 
0:29:51.422474 INFO: calibration group: precursor, predicting mz
0:29:51.438483 INFO: calibration group: precursor, predicting rt
0:29:51.508970 INFO: calibration group: precursor, predicting mobility
0:29:51.525016 INFO: calibration group: fragment, predicting mz
0:29:51.660818 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:29:51.661189 INFO: Starting optimization step 3.
0:29:51.661280 PROGRESS: === Extracting elution groups 0 to 56000 ===
0:29:51.661366 PROGRESS: Extracting batch of 110298 precursors
0:29:51.692765 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:29:51.692929 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:29:51.692986 INFO: FWHM in RT is 3.39 seconds, sigma is 0.74
0:29:51.693010 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.17
0:29:51.701810 INFO: Starting candidate selection
0:38:39.434575 INFO: Starting candidate scoring
0:38:49.282892 INFO: Finished candidate processing
0:38:49.283145 INFO: Collecting candidate features
0:38:49.622775 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 189768)
0:38:49.633013 INFO: Collecting fragment features
0:38:49.744929 INFO: Finished candidate scoring
0:38:49.859496 PROGRESS: === Extracted 189768 precursors and 1932589 fragments ===
0:38:49.860208 INFO: performing precursor FDR with 47 features
0:38:49.860252 INFO: Decoy channel: -1
0:38:49.860277 INFO: Competetive: True
0:38:49.930336 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:49.971805 WARNING: dropped 1 target PSMs due to missing features
0:38:49.971936 WARNING: dropped 1 decoy PSMs due to missing features
0:38:53.411387 INFO: Test AUC: 0.564
0:38:53.411510 INFO: Train AUC: 0.588
0:38:53.411539 INFO: AUC difference: 4.02%
0:38:53.511693 INFO: Resetting torch num_threads to 128
0:38:53.518885 INFO: === FDR correction performed with classifier version 2 ===
0:38:53.529582 PROGRESS: ============================= Precursor FDR =============================
0:38:53.529853 PROGRESS: Total precursors accumulated: 50,379
0:38:53.529922 PROGRESS: Target precursors: 31,584 (62.69%)
0:38:53.529973 PROGRESS: Decoy precursors: 18,795 (37.31%)
0:38:53.530020 PROGRESS: 
0:38:53.530065 PROGRESS: Precursor Summary:
0:38:53.531455 PROGRESS: Channel   0:	 0.05 FDR:   465; 0.01 FDR:   339; 0.001 FDR:   290
0:38:53.531561 PROGRESS: 
0:38:53.531619 PROGRESS: Protein Summary:
0:38:53.533060 PROGRESS: Channel   0:	 0.05 FDR:   438; 0.01 FDR:   327; 0.001 FDR:   281
0:38:53.533154 PROGRESS: =========================================================================
0:38:53.549095 INFO: fragments_df_filtered: 4241
0:38:53.825103 INFO: calibration group: precursor, fitting mz estimator 
0:38:53.928913 INFO: calibration group: precursor, fitting rt estimator 
0:38:53.978743 INFO: calibration group: precursor, fitting mobility estimator 
0:38:54.029387 INFO: calibration group: fragment, fitting mz estimator 
0:38:54.314581 INFO: calibration group: precursor, predicting mz
0:38:54.330136 INFO: calibration group: precursor, predicting rt
0:38:54.418255 INFO: calibration group: precursor, predicting mobility
0:38:54.434721 INFO: calibration group: fragment, predicting mz
0:38:54.579550 INFO: === checking if optimization conditions were reached ===
0:38:54.582189 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
0:38:54.583344 PROGRESS: ❌ ms1_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:38:54.583401 INFO: ==============================================
0:38:54.583513 INFO: Starting optimization step 4.
0:38:54.583593 PROGRESS: === Extracting elution groups 0 to 56000 ===
0:38:54.583697 PROGRESS: Extracting batch of 110298 precursors
0:38:54.629742 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:38:54.629907 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:38:54.629963 INFO: FWHM in RT is 3.36 seconds, sigma is 0.74
0:38:54.629987 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.12
0:38:54.630892 INFO: Starting candidate selection
0:45:56.786395 WARNING: WARNING: Temp mmap arrays were written to /tmp/temp_mmap_htb5t9zl. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 697,618,354,176
