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0:00:00.000222 PROGRESS: 
0:00:00.000242 PROGRESS: version: 1.8.2
0:00:00.000271 PROGRESS: hostname: thestral
0:00:00.000316 PROGRESS: date: 2024-11-17 22:07:32
0:00:00.000341 PROGRESS: =================== Environment ===================
0:00:00.000363 PROGRESS: alphatims       : 1.0.8
0:00:00.000383 PROGRESS: alpharaw        : 0.4.5
0:00:00.000412 PROGRESS: alphabase       : 1.4.0
0:00:00.000431 PROGRESS: alphapeptdeep   : 1.3.0
0:00:00.000450 PROGRESS: directlfq       : 0.2.19
0:00:00.000468 PROGRESS: ===================================================
0:00:00.000499 INFO: loading default config from /home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:00:00.014780 INFO: ├──version: 1 (default)
0:00:00.014840 INFO: ├──general
0:00:00.014874 INFO: │   ├──thread_count: 10 (default)
0:00:00.014902 INFO: │   ├──thread_count: 50 (user defined)
0:00:00.014929 INFO: │   ├──reuse_calibration: False (default)
0:00:00.014952 INFO: │   ├──reuse_quant: False (default)
0:00:00.014977 INFO: │   ├──astral_ms1: False (default)
0:00:00.015001 INFO: │   ├──log_level: INFO (default)
0:00:00.015023 INFO: │   ├──wsl: False (default)
0:00:00.015045 INFO: │   ├──mmap_detector_events: False (default)
0:00:00.015066 INFO: │   ├──use_gpu: True (default)
0:00:00.015088 INFO: │   ├──use_gpu: False (user defined)
0:00:00.015109 INFO: │   ├──save_library: True (default)
0:00:00.015130 INFO: │   └──save_mbr_library: True (default)
0:00:00.015152 INFO: ├──library_loading
0:00:00.015174 INFO: │   └──rt_heuristic: 180 (default)
0:00:00.015195 INFO: ├──library_prediction
0:00:00.015218 INFO: │   ├──predict: False (default)
0:00:00.015239 INFO: │   ├──enzyme: trypsin (default)
0:00:00.015260 INFO: │   ├──fixed_modifications: Carbamidomethyl@C (default)
0:00:00.015281 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term (default)
0:00:00.015302 INFO: │   ├──variable_modifications: Oxidation@M (user defined)
0:00:00.015323 INFO: │   ├──max_var_mod_num: 2 (default)
0:00:00.015344 INFO: │   ├──max_var_mod_num: 1 (user defined)
0:00:00.015364 INFO: │   ├──missed_cleavages: 1 (default)
0:00:00.015385 INFO: │   ├──precursor_len
0:00:00.015407 INFO: │   │   ├──7 (default)
0:00:00.015429 INFO: │   │   └──35 (default)
0:00:00.015449 INFO: │   │   └──30 (user defined)
0:00:00.015473 INFO: │   ├──precursor_charge
0:00:00.015495 INFO: │   │   ├──2 (default)
0:00:00.015516 INFO: │   │   ├──1 (user defined)
0:00:00.015537 INFO: │   │   └──4 (default)
0:00:00.015557 INFO: │   ├──precursor_mz
0:00:00.015579 INFO: │   │   ├──400 (default)
0:00:00.015600 INFO: │   │   └──1200 (default)
0:00:00.015622 INFO: │   ├──fragment_mz
0:00:00.015644 INFO: │   │   ├──200 (default)
0:00:00.015665 INFO: │   │   └──2000 (default)
0:00:00.015689 INFO: │   ├──nce: 25.0 (default)
0:00:00.015711 INFO: │   ├──fragment_types: b;y (default)
0:00:00.015733 INFO: │   ├──max_fragment_charge: 2 (default)
0:00:00.015755 INFO: │   ├──instrument: Lumos (default)
0:00:00.015775 INFO: │   ├──instrument: timsTOF (user defined)
0:00:00.015797 INFO: │   ├──peptdeep_model_path: None (default)
0:00:00.015819 INFO: │   └──peptdeep_model_type: None (default)
0:00:00.015840 INFO: ├──custom_modififcations
0:00:00.015861 INFO: │   ├──Dimethyl:d12@K
0:00:00.015882 INFO: │   │   └──composition: H(-2)2H(8)13C(2) (default)
0:00:00.015915 INFO: │   ├──Dimethyl:d12@Any_N-term
0:00:00.015936 INFO: │   │   └──composition: H(-2)2H(8)13C(2) (default)
0:00:00.015957 INFO: │   ├──Dimethyl:d12@Protein_N-term
0:00:00.015978 INFO: │   │   └──composition: H(-2)2H(8)13C(2) (default)
0:00:00.015998 INFO: │   ├──mTRAQ:d12@K
0:00:00.016019 INFO: │   │   └──composition: H(12)C(1)13C(10)15N(2)O(1) (default)
0:00:00.016038 INFO: │   ├──mTRAQ:d12@Any_N-term
0:00:00.016059 INFO: │   │   └──composition: H(12)C(1)13C(14)15N(2)O(1) (default)
0:00:00.016078 INFO: │   ├──mTRAQ:d12@Protein_N-term
0:00:00.016099 INFO: │   │   └──composition: H(12)C(1)13C(14)15N(2)O(1) (default)
0:00:00.016119 INFO: │   └──Label:13C(12)@K
0:00:00.016139 INFO: │       └──composition: C(12) (default)
0:00:00.016160 INFO: ├──search
0:00:00.016184 INFO: │   ├──channel_filter: 0 (default)
0:00:00.016204 INFO: │   ├──channel_filter:  (user defined)
0:00:00.016225 INFO: │   ├──exclude_shared_ions: True (default)
0:00:00.016245 INFO: │   ├──compete_for_fragments: True (default)
0:00:00.016267 INFO: │   ├──target_num_candidates: 2 (default)
0:00:00.016288 INFO: │   ├──target_ms1_tolerance: 5 (default)
0:00:00.016308 INFO: │   ├──target_ms2_tolerance: 10 (default)
0:00:00.016329 INFO: │   ├──target_mobility_tolerance: 0.0 (default)
0:00:00.016351 INFO: │   ├──target_mobility_tolerance: 0.1 (user defined)
0:00:00.016372 INFO: │   ├──target_rt_tolerance: 0.0 (default)
0:00:00.016400 INFO: │   ├──target_rt_tolerance: 0.5 (user defined)
0:00:00.016421 INFO: │   ├──quant_window: 3 (default)
0:00:00.016443 INFO: │   └──quant_all: True (default)
0:00:00.016464 INFO: ├──search_advanced
0:00:00.016486 INFO: │   └──top_k_fragments: 12 (default)
0:00:00.016507 INFO: ├──calibration
0:00:00.016528 INFO: │   ├──batch_size: 8000 (default)
0:00:00.016549 INFO: │   ├──optimization_lock_target: 200 (default)
0:00:00.016569 INFO: │   ├──max_steps: 20 (default)
0:00:00.016589 INFO: │   ├──min_steps: 2 (default)
0:00:00.016609 INFO: │   ├──max_skips: 1 (default)
0:00:00.016631 INFO: │   ├──final_full_calibration: False (default)
0:00:00.016651 INFO: │   ├──norm_rt_mode: linear (default)
0:00:00.016671 INFO: │   ├──max_fragments: 5000 (default)
0:00:00.016690 INFO: │   └──min_correlation: 0.7 (default)
0:00:00.016713 INFO: ├──search_initial
0:00:00.016735 INFO: │   ├──initial_num_candidates: 1 (default)
0:00:00.016756 INFO: │   ├──initial_ms1_tolerance: 30 (default)
0:00:00.016776 INFO: │   ├──initial_ms2_tolerance: 30 (default)
0:00:00.016796 INFO: │   ├──initial_mobility_tolerance: 0.1 (default)
0:00:00.016818 INFO: │   └──initial_rt_tolerance: 0.5 (default)
0:00:00.016838 INFO: ├──selection_config
0:00:00.016859 INFO: │   ├──peak_len_rt: 10.0 (default)
0:00:00.016880 INFO: │   ├──sigma_scale_rt: 0.5 (default)
0:00:00.016900 INFO: │   ├──peak_len_mobility: 0.01 (default)
0:00:00.016921 INFO: │   ├──sigma_scale_mobility: 1.0 (default)
0:00:00.016941 INFO: │   ├──top_k_precursors: 3 (default)
0:00:00.016962 INFO: │   ├──kernel_size: 30 (default)
0:00:00.016983 INFO: │   ├──f_mobility: 1.0 (default)
0:00:00.017004 INFO: │   ├──f_rt: 0.99 (default)
0:00:00.017025 INFO: │   ├──center_fraction: 0.5 (default)
0:00:00.017045 INFO: │   ├──min_size_mobility: 8 (default)
0:00:00.017066 INFO: │   ├──min_size_rt: 3 (default)
0:00:00.017087 INFO: │   ├──max_size_mobility: 20 (default)
0:00:00.017107 INFO: │   ├──max_size_rt: 15 (default)
0:00:00.017128 INFO: │   ├──group_channels: False (default)
0:00:00.017148 INFO: │   ├──use_weighted_score: True (default)
0:00:00.017175 INFO: │   ├──join_close_candidates: False (default)
0:00:00.017196 INFO: │   ├──join_close_candidates_scan_threshold: 0.6 (default)
0:00:00.017218 INFO: │   └──join_close_candidates_cycle_threshold: 0.6 (default)
0:00:00.017238 INFO: ├──scoring_config
0:00:00.017260 INFO: │   ├──score_grouped: False (default)
0:00:00.017281 INFO: │   ├──top_k_isotopes: 3 (default)
0:00:00.017301 INFO: │   ├──reference_channel: -1 (default)
0:00:00.017321 INFO: │   ├──precursor_mz_tolerance: 10 (default)
0:00:00.017342 INFO: │   └──fragment_mz_tolerance: 15 (default)
0:00:00.017362 INFO: ├──library_multiplexing
0:00:00.017383 INFO: │   ├──enabled: False (default)
0:00:00.017404 INFO: │   ├──input_channel: 0 (default)
0:00:00.017423 INFO: │   └──multiplex_mapping
0:00:00.017444 INFO: ├──multiplexing
0:00:00.017467 INFO: │   ├──enabled: False (default)
0:00:00.017487 INFO: │   ├──target_channels: 4,8 (default)
0:00:00.017508 INFO: │   ├──decoy_channel: 12 (default)
0:00:00.017528 INFO: │   ├──reference_channel: 0 (default)
0:00:00.017548 INFO: │   ├──competetive_scoring: True (default)
0:00:00.017569 INFO: │   └──multiplexed_quant: False (user defined)
0:00:00.017590 INFO: ├──fdr
0:00:00.017613 INFO: │   ├──fdr: 0.01 (default)
0:00:00.017633 INFO: │   ├──fdr: 1.0 (user defined)
0:00:00.017654 INFO: │   ├──group_level: proteins (default)
0:00:00.017674 INFO: │   ├──competetive_scoring: True (default)
0:00:00.017695 INFO: │   ├──keep_decoys: False (default)
0:00:00.017715 INFO: │   ├──keep_decoys: True (user defined)
0:00:00.017736 INFO: │   ├──channel_wise_fdr: False (default)
0:00:00.017757 INFO: │   └──inference_strategy: heuristic (default)
0:00:00.017777 INFO: ├──search_output
0:00:00.017799 INFO: │   ├──peptide_level_lfq: False (default)
0:00:00.017819 INFO: │   ├──precursor_level_lfq: False (default)
0:00:00.017840 INFO: │   ├──min_k_fragments: 12 (default)
0:00:00.017860 INFO: │   ├──min_correlation: 0.9 (default)
0:00:00.017881 INFO: │   ├──num_samples_quadratic: 50 (default)
0:00:00.017901 INFO: │   ├──min_nonnan: 3 (default)
0:00:00.017922 INFO: │   ├──normalize_lfq: True (default)
0:00:00.017943 INFO: │   └──file_format: tsv (default)
0:00:00.017964 INFO: ├──optimization
0:00:00.017985 INFO: │   ├──order_of_optimization: None (default)
0:00:00.018005 INFO: │   ├──ms2_error
0:00:00.018026 INFO: │   │   ├──targeted_update_percentile_range: 0.95 (default)
0:00:00.018048 INFO: │   │   ├──targeted_update_factor: 1.0 (default)
0:00:00.018068 INFO: │   │   ├──automatic_update_percentile_range: 0.99 (default)
0:00:00.018089 INFO: │   │   ├──automatic_update_factor: 1.1 (default)
0:00:00.018109 INFO: │   │   ├──try_narrower_values: True (default)
0:00:00.018129 INFO: │   │   ├──maximal_decrease: 0.5 (default)
0:00:00.018149 INFO: │   │   ├──favour_narrower_optimum: False (default)
0:00:00.018170 INFO: │   │   └──maximum_decrease_from_maximum: 0.1 (default)
0:00:00.018190 INFO: │   ├──ms1_error
0:00:00.018212 INFO: │   │   ├──targeted_update_percentile_range: 0.95 (default)
0:00:00.018232 INFO: │   │   ├──targeted_update_factor: 1.0 (default)
0:00:00.018253 INFO: │   │   ├──automatic_update_percentile_range: 0.99 (default)
0:00:00.018273 INFO: │   │   ├──automatic_update_factor: 1.1 (default)
0:00:00.018294 INFO: │   │   ├──try_narrower_values: False (default)
0:00:00.018315 INFO: │   │   ├──maximal_decrease: 0.2 (default)
0:00:00.018336 INFO: │   │   ├──favour_narrower_optimum: False (default)
0:00:00.018358 INFO: │   │   └──maximum_decrease_from_maximum: 0.1 (default)
0:00:00.018379 INFO: │   ├──mobility_error
0:00:00.018403 INFO: │   │   ├──targeted_update_percentile_range: 0.95 (default)
0:00:00.018423 INFO: │   │   ├──targeted_update_factor: 1.0 (default)
0:00:00.018444 INFO: │   │   ├──automatic_update_percentile_range: 0.99 (default)
0:00:00.018464 INFO: │   │   ├──automatic_update_factor: 1.1 (default)
0:00:00.018485 INFO: │   │   ├──try_narrower_values: False (default)
0:00:00.018506 INFO: │   │   ├──maximal_decrease: 0.2 (default)
0:00:00.018527 INFO: │   │   ├──favour_narrower_optimum: False (default)
0:00:00.018548 INFO: │   │   └──maximum_decrease_from_maximum: 0.1 (default)
0:00:00.018569 INFO: │   └──rt_error
0:00:00.018592 INFO: │       ├──targeted_update_percentile_range: 0.95 (default)
0:00:00.018612 INFO: │       ├──targeted_update_factor: 1.0 (default)
0:00:00.018633 INFO: │       ├──automatic_update_percentile_range: 0.99 (default)
0:00:00.018655 INFO: │       ├──automatic_update_factor: 1.1 (default)
0:00:00.018676 INFO: │       ├──try_narrower_values: True (default)
0:00:00.018697 INFO: │       ├──maximal_decrease: 0.2 (default)
0:00:00.018717 INFO: │       ├──favour_narrower_optimum: True (default)
0:00:00.018738 INFO: │       └──maximum_decrease_from_maximum: 0.1 (default)
0:00:00.018758 INFO: ├──optimization_manager
0:00:00.018779 INFO: │   ├──fwhm_rt: 5 (default)
0:00:00.018800 INFO: │   ├──fwhm_mobility: 0.01 (default)
0:00:00.018821 INFO: │   └──score_cutoff: 0 (default)
0:00:00.018840 INFO: ├──transfer_library
0:00:00.018862 INFO: │   ├──enabled: False (default)
0:00:00.018882 INFO: │   ├──fragment_types: b;y (default)
0:00:00.018902 INFO: │   ├──max_charge: 2 (default)
0:00:00.018922 INFO: │   ├──top_k_samples: 3 (default)
0:00:00.018942 INFO: │   ├──norm_delta_max: True (default)
0:00:00.018963 INFO: │   ├──precursor_correlation_cutoff: 0.5 (default)
0:00:00.018984 INFO: │   └──fragment_correlation_ratio: 0.75 (default)
0:00:00.019004 INFO: ├──transfer_learning
0:00:00.019028 INFO: │   ├──enabled: False (default)
0:00:00.019048 INFO: │   ├──batch_size: 2000 (default)
0:00:00.019069 INFO: │   ├──max_lr: 0.0001 (default)
0:00:00.019089 INFO: │   ├──train_fraction: 0.7 (default)
0:00:00.019109 INFO: │   ├──validation_fraction: 0.2 (default)
0:00:00.019130 INFO: │   ├──test_fraction: 0.1 (default)
0:00:00.019150 INFO: │   ├──test_interval: 1 (default)
0:00:00.019171 INFO: │   ├──lr_patience: 3 (default)
0:00:00.019191 INFO: │   ├──epochs: 51 (default)
0:00:00.019211 INFO: │   ├──warmup_epochs: 5 (default)
0:00:00.019233 INFO: │   ├──nce: 25 (default)
0:00:00.019253 INFO: │   ├──instrument: Lumos (default)
0:00:00.019273 INFO: │   ├──instrument: timsTOF (user defined)
0:00:00.019295 INFO: │   └──train_ratio: 0.7 (user defined)
0:00:00.019315 INFO: ├──calibration_manager
0:00:00.019339 INFO: │   ├──0
0:00:00.019360 INFO: │   │   ├──name: fragment (default)
0:00:00.019380 INFO: │   │   └──estimators
0:00:00.019401 INFO: │   │       └──0
0:00:00.019422 INFO: │   │           ├──name: mz (default)
0:00:00.019443 INFO: │   │           ├──model: LOESSRegression (default)
0:00:00.019463 INFO: │   │           ├──model_args
0:00:00.019485 INFO: │   │           │   └──n_kernels: 2 (default)
0:00:00.019505 INFO: │   │           ├──input_columns
0:00:00.019526 INFO: │   │           │   └──mz_library (default)
0:00:00.019545 INFO: │   │           ├──target_columns
0:00:00.019566 INFO: │   │           │   └──mz_observed (default)
0:00:00.019586 INFO: │   │           ├──output_columns
0:00:00.019608 INFO: │   │           │   └──mz_calibrated (default)
0:00:00.019629 INFO: │   │           └──transform_deviation: 1e6 (default)
0:00:00.019654 INFO: │   └──1
0:00:00.019676 INFO: │       ├──name: precursor (default)
0:00:00.019696 INFO: │       └──estimators
0:00:00.019717 INFO: │           ├──0
0:00:00.019737 INFO: │           │   ├──name: mz (default)
0:00:00.019758 INFO: │           │   ├──model: LOESSRegression (default)
0:00:00.019778 INFO: │           │   ├──model_args
0:00:00.019799 INFO: │           │   │   └──n_kernels: 2 (default)
0:00:00.019820 INFO: │           │   ├──input_columns
0:00:00.019841 INFO: │           │   │   └──mz_library (default)
0:00:00.019861 INFO: │           │   ├──target_columns
0:00:00.019881 INFO: │           │   │   └──mz_observed (default)
0:00:00.019902 INFO: │           │   ├──output_columns
0:00:00.019922 INFO: │           │   │   └──mz_calibrated (default)
0:00:00.019944 INFO: │           │   └──transform_deviation: 1e6 (default)
0:00:00.019965 INFO: │           ├──1
0:00:00.019986 INFO: │           │   ├──name: rt (default)
0:00:00.020006 INFO: │           │   ├──model: LOESSRegression (default)
0:00:00.020027 INFO: │           │   ├──model_args
0:00:00.020048 INFO: │           │   │   └──n_kernels: 6 (default)
0:00:00.020068 INFO: │           │   ├──input_columns
0:00:00.020090 INFO: │           │   │   └──rt_library (default)
0:00:00.020126 INFO: │           │   ├──target_columns
0:00:00.020148 INFO: │           │   │   └──rt_observed (default)
0:00:00.020168 INFO: │           │   └──output_columns
0:00:00.020189 INFO: │           │       └──rt_calibrated (default)
0:00:00.020209 INFO: │           └──2
0:00:00.020231 INFO: │               ├──name: mobility (default)
0:00:00.020251 INFO: │               ├──model: LOESSRegression (default)
0:00:00.020271 INFO: │               ├──model_args
0:00:00.020292 INFO: │               │   └──n_kernels: 2 (default)
0:00:00.020312 INFO: │               ├──input_columns
0:00:00.020333 INFO: │               │   └──mobility_library (default)
0:00:00.020353 INFO: │               ├──target_columns
0:00:00.020374 INFO: │               │   └──mobility_observed (default)
0:00:00.020400 INFO: │               └──output_columns
0:00:00.020419 INFO: │                   └──mobility_calibrated (default)
0:00:00.020441 INFO: └──name: Phospho_diaPASEF (user defined)
0:00:00.020547 INFO: Registering 7 custom modifications
0:00:00.050082 INFO: Running DynamicLoader
0:00:00.050188 INFO: Loading .tsv library from /home/sander/apps/slim/experiment_1/human_pasef_phospho-enriched/speclibs/Human_PhophoE_005_speclib.spectronaut.tsv
425921518 Entries with unknown modifications are removed
1:59:54.495143 INFO: Running PrecursorInitializer
1:59:54.508298 INFO: Running AnnotateFasta
1:59:54.662044 INFO: Dropping decoys from input library before annotation
2:00:09.389579 INFO: Running IsotopeGenerator
2:00:22.105720 INFO: Running RTNormalization
2:00:22.163032 INFO: Saving library to /home/sander/apps/slim/experiment_1/human_pasef_phospho-enriched/results_alphadia/speclib.hdf
2:00:42.945565 INFO: Running DecoyGenerator
2:01:51.118583 INFO: Running FlattenLibrary
2:02:27.857380 INFO: Running InitFlatColumns
2:02:28.063893 INFO: Running LogFlatLibraryStats
2:02:28.064033 INFO: ============ Library Stats ============
2:02:28.064073 INFO: Number of precursors: 8,536,704
2:02:29.082793 INFO: 	thereof targets:4,269,623
2:02:29.082938 INFO: 	thereof decoys: 4,267,081
2:02:29.151954 INFO: Number of elution groups: 4,269,623
2:02:29.152081 INFO: 	average size: 2.00
2:02:29.437873 INFO: Number of proteins: 39,194
2:02:29.458676 INFO: Number of channels: 1 ([0])
2:02:29.458843 INFO: Isotopes Distribution for 4 isotopes
2:02:29.458870 INFO: =======================================
2:02:29.461188 PROGRESS: Starting Search Workflows
2:02:29.461468 PROGRESS: Loading raw file 1/4: Tims_Phospho-Enriched_03
2:02:29.461784 INFO: Creating workflow folder for Tims_Phospho-Enriched_03 at /home/sander/apps/slim/experiment_1/human_pasef_phospho-enriched/results_alphadia/.progress/Tims_Phospho-Enriched_03
2:02:29.462315 INFO: Importing data from /home/sander/apps/slim/experiment_1/human_pasef_phospho-enriched/raw_ms/Tims_Phospho-Enriched_03.d
2:02:29.462483 INFO: Using .d import for /home/sander/apps/slim/experiment_1/human_pasef_phospho-enriched/raw_ms/Tims_Phospho-Enriched_03.d
2:02:29.462526 INFO: Reading frame metadata for /home/sander/apps/slim/experiment_1/human_pasef_phospho-enriched/raw_ms/Tims_Phospho-Enriched_03.d
2:02:29.689181 INFO: Reading 33,961 frames with 1,153,733,648 detector events for /home/sander/apps/slim/experiment_1/human_pasef_phospho-enriched/raw_ms/Tims_Phospho-Enriched_03.d
2:02:35.076281 INFO: Indexing /home/sander/apps/slim/experiment_1/human_pasef_phospho-enriched/raw_ms/Tims_Phospho-Enriched_03.d...
2:02:35.078954 INFO: Opening handle for /home/sander/apps/slim/experiment_1/human_pasef_phospho-enriched/raw_ms/Tims_Phospho-Enriched_03.d
2:02:35.081700 INFO: Fetching mobility values from /home/sander/apps/slim/experiment_1/human_pasef_phospho-enriched/raw_ms/Tims_Phospho-Enriched_03.d
2:02:35.081975 INFO: Closing handle for /home/sander/apps/slim/experiment_1/human_pasef_phospho-enriched/raw_ms/Tims_Phospho-Enriched_03.d
2:02:35.082261 INFO: Opening handle for /home/sander/apps/slim/experiment_1/human_pasef_phospho-enriched/raw_ms/Tims_Phospho-Enriched_03.d
2:02:35.083631 INFO: Fetching mz values from /home/sander/apps/slim/experiment_1/human_pasef_phospho-enriched/raw_ms/Tims_Phospho-Enriched_03.d
2:02:35.090722 INFO: Closing handle for /home/sander/apps/slim/experiment_1/human_pasef_phospho-enriched/raw_ms/Tims_Phospho-Enriched_03.d
2:02:35.090873 INFO: Indexing quadrupole dimension
2:02:35.328897 INFO: Transposing detector events
2:02:40.670774 INFO: Finished transposing data
2:02:40.687475 INFO: Successfully imported data from /home/sander/apps/slim/experiment_1/human_pasef_phospho-enriched/raw_ms/Tims_Phospho-Enriched_03.d
2:02:40.687663 INFO: ============ Raw file stats ============
2:02:40.687845 INFO: RT (min)            : 0.0 - 60.0
2:02:40.687908 INFO: RT duration (sec)   : 3601.3
2:02:40.687953 INFO: RT duration (min)   : 60.0
2:02:40.688183 INFO: Cycle len (scans)   : 13
2:02:40.688254 INFO: Cycle len (sec)     : 1.38
2:02:40.688302 INFO: Number of cycles    : 2612
2:02:40.688492 INFO: MS2 range (m/z)     : 400.2 - 1399.3
2:02:40.688554 INFO: ========================================
2:02:41.505035 INFO: Initializing CalibrationManager
2:02:41.505321 INFO: Loading calibration config
2:02:41.505431 INFO: Calibration config: [{'name': 'fragment', 'estimators': [{'name': 'mz', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'transform_deviation': '1e6'}]}, {'name': 'precursor', 'estimators': [{'name': 'mz', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'transform_deviation': '1e6'}, {'name': 'rt', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated']}, {'name': 'mobility', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated']}]}]
2:02:41.505497 INFO: Calibration group :fragment, found 1 estimator(s)
2:02:41.505599 INFO: Calibration group :precursor, found 3 estimator(s)
2:02:41.505721 INFO: Initializing OptimizationManager
2:02:41.505815 INFO: initial parameter: ms1_error = 30
2:02:41.505861 INFO: initial parameter: ms2_error = 30
2:02:41.505909 INFO: initial parameter: rt_error = 1800.6459615
2:02:41.505951 INFO: initial parameter: mobility_error = 0.1
2:02:41.505990 INFO: initial parameter: column_type = library
2:02:41.506048 INFO: initial parameter: num_candidates = 1
2:02:41.506089 INFO: initial parameter: classifier_version = -1
2:02:41.506129 INFO: initial parameter: fwhm_rt = 5
2:02:41.506167 INFO: initial parameter: fwhm_mobility = 0.01
2:02:41.506203 INFO: initial parameter: score_cutoff = 0
2:02:41.506258 INFO: Initializing TimingManager
2:02:41.506304 PROGRESS: Initializing workflow Tims_Phospho-Enriched_03
2:02:41.506355 INFO: Initializing FDRManager
2:02:41.506389 INFO: Loading classifier store from /home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
2:02:42.348281 PROGRESS: 3,549,653 target precursors potentially observable (719,970 removed)
2:02:43.415973 PROGRESS: Starting initial search for precursors.
2:02:44.297474 INFO: Starting optimization step 0.
2:02:44.297714 PROGRESS: === Extracting elution groups 0 to 8000 ===
2:02:44.297781 PROGRESS: Extracting batch of 15810 precursors
2:02:46.268863 INFO: Duty cycle consists of 13 frames, 1.38 seconds cycle time
2:02:46.268974 INFO: Duty cycle consists of 919 scans, 0.00103 1/K_0 resolution
2:02:46.269006 INFO: FWHM in RT is 5.00 seconds, sigma is 0.77
2:02:46.269029 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.13
2:02:49.760001 INFO: Starting candidate selection
2:04:13.548206 ERROR: Search for Tims_Phospho-Enriched_03 failed with error: No objects to concatenate
Traceback (most recent call last):
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/alphadia/planning.py", line 338, in run
    workflow.search_parameter_optimization()
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/alphadia/workflow/peptidecentric.py", line 433, in search_parameter_optimization
    precursor_df = self._process_batch()
                   ^^^^^^^^^^^^^^^^^^^^^
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/alphadia/workflow/peptidecentric.py", line 512, in _process_batch
    feature_df, fragment_df = self.extract_batch(
                              ^^^^^^^^^^^^^^^^^^^
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/alphadia/workflow/peptidecentric.py", line 772, in extract_batch
    sns.histplot(candidates_df, x="score", hue="decoy", bins=100)
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/seaborn/distributions.py", line 1416, in histplot
    p.plot_univariate_histogram(
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/seaborn/distributions.py", line 665, in plot_univariate_histogram
    hist_metadata = pd.concat([
                    ^^^^^^^^^^^
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/pandas/core/reshape/concat.py", line 382, in concat
    op = _Concatenator(
         ^^^^^^^^^^^^^^
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/pandas/core/reshape/concat.py", line 445, in __init__
    objs, keys = self._clean_keys_and_objs(objs, keys)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/pandas/core/reshape/concat.py", line 507, in _clean_keys_and_objs
    raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate
2:04:13.551034 ERROR: No objects to concatenate
2:04:13.551198 INFO: Finished workflow for Tims_Phospho-Enriched_03
2:04:13.552615 INFO: Traceback (most recent call last):
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/alphadia/cli.py", line 342, in run
    plan.run()
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/alphadia/planning.py", line 365, in run
    raise e
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/alphadia/planning.py", line 338, in run
    workflow.search_parameter_optimization()
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/alphadia/workflow/peptidecentric.py", line 433, in search_parameter_optimization
    precursor_df = self._process_batch()
                   ^^^^^^^^^^^^^^^^^^^^^
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/alphadia/workflow/peptidecentric.py", line 512, in _process_batch
    feature_df, fragment_df = self.extract_batch(
                              ^^^^^^^^^^^^^^^^^^^
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/alphadia/workflow/peptidecentric.py", line 772, in extract_batch
    sns.histplot(candidates_df, x="score", hue="decoy", bins=100)
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/seaborn/distributions.py", line 1416, in histplot
    p.plot_univariate_histogram(
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/seaborn/distributions.py", line 665, in plot_univariate_histogram
    hist_metadata = pd.concat([
                    ^^^^^^^^^^^
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/pandas/core/reshape/concat.py", line 382, in concat
    op = _Concatenator(
         ^^^^^^^^^^^^^^
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/pandas/core/reshape/concat.py", line 445, in __init__
    objs, keys = self._clean_keys_and_objs(objs, keys)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/sander/miniconda3/envs/alphadia/lib/python3.11/site-packages/pandas/core/reshape/concat.py", line 507, in _clean_keys_and_objs
    raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate

2:04:13.552676 ERROR: No objects to concatenate
2:06:41.431217 WARNING: WARNING: Temp mmap arrays were written to /tmp/temp_mmap_l1ygvc1i. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 805,756,198,912