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lazear/failed_run.yaml Secret

Created March 30, 2023 18:17
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failed_run.yaml
workflow:
continue_runs: false
create_database: true
import_raw_data: true
find_features: true
search_data: true
recalibrate_data: true
align: true
match: true
lfq_quantification: true
general:
n_processes: 60
modfile_hash: 72252eb041669ea9b826e49f54a4ac50
experiment:
results_path: D:\PXD003881\results.hdf
shortnames:
- B03_02_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_03_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_04_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_07_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_08_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_09_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_12_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_13_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_14_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_15_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_16_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_17_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_18_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_19_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_20_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_21_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
file_paths:
- D:\PXD003881\B03_02_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_03_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_04_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_07_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_08_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_09_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_12_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_13_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_14_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_15_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_16_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_17_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_18_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_19_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_20_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_21_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
sample_group:
- B03_02_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_03_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_04_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_07_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_08_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_09_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_12_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_13_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_14_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_15_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_16_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_17_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_18_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_19_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_20_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
- B03_21_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B
matching_group:
- 0
- 0
- 0
- 0
- 0
- 0
- 0
- 0
- 0
- 0
- 0
- 0
- 0
- 0
- 0
- 0
- 0
- 0
- 0
- 0
fraction:
- 1
- 1
- 1
- 1
- 1
- 1
- 1
- 1
- 1
- 1
- 1
- 1
- 1
- 1
- 1
- 1
- 1
- 1
- 1
- 1
database_path: D:\PXD003881\database.hdf
fasta_paths:
- D:\PXD003881\PXD003881.fasta
raw:
n_most_abundant: 400
use_profile_ms1: false
fasta:
mods_fixed:
- cC
mods_fixed_terminal: []
mods_variable:
- oxM
mods_variable_terminal: []
mods_fixed_terminal_prot: []
mods_variable_terminal_prot:
- a<^
n_missed_cleavages: 2
pep_length_min: 7
pep_length_max: 27
isoforms_max: 1024
n_modifications_max: 3
pseudo_reverse: true
AL_swap: false
KR_swap: false
protease: trypsin
spectra_block: 100000
fasta_block: 1000
save_db: true
fasta_size_max: 100
features:
max_gap: 2
centroid_tol: 8
hill_length_min: 3
hill_split_level: 1.3
iso_split_level: 1.3
hill_smoothing: 1
hill_check_large: 40
iso_charge_min: 1
iso_charge_max: 6
iso_n_seeds: 100
hill_nboot_max: 300
hill_nboot: 150
iso_mass_range: 5
iso_corr_min: 0.6
map_mz_range: 1.5
map_rt_range: 0.5
map_mob_range: 0.3
map_n_neighbors: 5
search_unidentified: false
search:
prec_tol: 20
frag_tol: 50
min_frag_hits: 7
ppm: true
calibrate: true
calibration_std_prec: 5
calibration_std_frag: 5
parallel: true
peptide_fdr: 0.01
protein_fdr: 0.01
recalibration_min: 100
score:
method: random_forest
calibration:
outlier_std: 3
calib_n_neighbors: 100
calib_mz_range: 2000
calib_rt_range: 0.5
calib_mob_range: 0.3
matching:
match_p_min: 0.05
match_d_min: 3
match_group_tol: 0
quantification:
max_lfq: true
lfq_ratio_min: 1
mode: ms1_int_sum_apex
failed:
raw_conversion: []
find_features:
- D:\PXD003881\B03_02_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_03_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_04_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_07_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_08_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_09_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_12_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_13_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_14_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_15_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_16_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_17_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_18_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_19_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_20_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_21_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
search_db:
- D:\PXD003881\B03_02_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_03_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_04_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_07_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_08_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_09_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_12_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_13_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_14_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_15_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_16_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_17_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_18_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_19_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_20_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_21_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
calibrate_hdf:
- D:\PXD003881\B03_02_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_03_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_04_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_07_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_08_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_09_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_12_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_13_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_14_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_15_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_16_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_17_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_18_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_19_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_20_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_21_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
search_db_2:
- D:\PXD003881\B03_02_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_03_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_04_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_07_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_08_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_09_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_12_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_13_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_14_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_15_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_16_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_17_150304_human_ecoli_D_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_18_150304_human_ecoli_C_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_19_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_20_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
- D:\PXD003881\B03_21_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.mzML
score_hdf: []
error: '''Dataset peptide_fdr does not exist for group / of <HDF_File D:\\PXD003881\\B03_02_150304_human_ecoli_B_3ul_3um_column_95_HCD_OT_2hrs_30B_9B.ms_data.hdf>.'''
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