levitsky
commented
2 years ago Hi @BenSamy2020,
There are two issues here. One is the very uninformative error message (I fixed it in the latest commit), the other one is the real problem: AA_stat doesn't find any files in the directory you provided. Are you sure the directory paths are correct and there are pepXML and mzML files in those folders? The command suggests that you have a separate pepXML folder and a mzML folder inside MSFragger_OpenSearch_1_Output\AA_Stat. Can you verify?
BenSamy2020
Greetings @levitsky,
Currently, I am trying to perform AA_Stat analysis using Open Search results. This Open Search was performed as per our discussion via email. The error is as following:
C:\Users\parth>AA_stat --dir D:\MSFragger_Temp\Immunopeptidomics\CRC_Immunopeptidomics\MSFragger_OpenSearch_1_Output\AA_Stat\Output --pepxml D:\MSFragger_Temp\Immunopeptidomics\CRC_Immunopeptidomics\MSFragger_OpenSearch_1_Output\AA_Stat\pepXML --mzml D:\MSFragger_Temp\Immunopeptidomics\CRC_Immunopeptidomics\MSFragger_OpenSearch_1_Output\AA_Stat\mzML --verbosity 3 INFO: [23:46:52] Starting... DEBUG: [23:46:52] Received pepxml list: ['D:\MSFragger_Temp\Immunopeptidomics\CRC_Immunopeptidomics\MSFragger_OpenSearch_1_Output\AA_Stat\pepXML'] DEBUG: [23:46:52] Found 0 files for glob .pepXML DEBUG: [23:46:52] Found 0 files for glob .pep.xml DEBUG: [23:46:52] Final pepxml list: [] DEBUG: [23:46:52] Received mzml list: ['D:\MSFragger_Temp\Immunopeptidomics\CRC_Immunopeptidomics\MSFragger_OpenSearch_1_Output\AA_Stat\mzML'] DEBUG: [23:46:52] Found 0 files for glob *.mzML DEBUG: [23:46:52] Final mzml list: [] DEBUG: [23:46:52] Received args: Namespace(params=None, dir='D:\MSFragger_Temp\Immunopeptidomics\CRC_Immunopeptidomics\MSFragger_OpenSearch_1_Output\AA_Stat\Output', verbosity=3, mgf=None, mzml=[], pepxml=[], csv=None) INFO: [23:46:52] Using default parameters for AA_stat. DEBUG: [23:46:52] defaultdict(None, {'decoy_prefix': '', 'decoy_prefixlist': ['rev', 'DECOY_'], 'FDR': 0.02, 'labels': ['M', 'D', 'Q', 'C', 'L', 'H', 'S', 'R', 'A', 'W', 'Y', 'P', 'F', 'V', 'N', 'T', 'E', 'G', 'I', 'K'], 'rule': 'trypsin', 'csv_delimiter': ',', 'proteins_delimeter': ';', 'proteins_column': 'protein', 'peptides_column': 'peptide', 'mass_shifts_column': 'massdiff', 'score_column': 'expect', 'measured_mass_column': 'precursor_neutral_mass', 'calculated_mass_column': 'calc_neutral_pep_mass', 'rt_column': 'retention_time_sec', 'next_aa_column': 'peptide_next_aa', 'prev_aa_column': 'peptide_prev_aa', 'spectrum_column': 'spectrum', 'charge_column': 'assumed_charge', 'mods_column': 'modifications', 'score_ascending': True, 'bin_width': 0.001, 'so_range': (-500.0, 500.0), 'walking_window': 0.012, 'FDR_correction': True, 'processes': 0, 'zero_window': 0.05, 'prec_acc': 0.01, 'zero bin tolerance': 0.05, 'zero min intensity': 0.05, 'min_peptides_for_mass_calibration': 100, 'specific_mass_shift_flag': False, 'specific_window': [15.975, 16.005], 'figsize': (9.0, 3.5), 'calibration': 'gauss_frequency', 'artefact_thresh': 0.5, 'html_truncate': 80, 'clustering': True, 'eps_adjust': 0.2, 'min_samples': 5.0, 'clustered_pct_min': 0.5, 'cluster_span_min': 0.1, 'shift_error': 10, 'max_deviation_sigma': 0.3, 'max_deviation_height': 0.15, 'fit batch': 900, 'ion_types': ('b', 'y'), 'frag_acc': 0.01, 'candidate threshold': 1.5, 'min_spec_matched': 4, 'force_term_loc': False, 'use_all_loc': False, 'variable_mods': 5, 'multiple_mods': True, 'fix_mod_zero_thresh': 3.0, 'min_fix_mod_pep_count_factor': 2.0, 'recommend isotope threshold': 10.0, 'min_loc_count': 10, 'window': 13, 'bins': array([-500. , -499.999 , -499.998 , ..., 499.99799998, 499.99899998, 499.99999998]), 'output directory': 'D:\MSFragger_Temp\Immunopeptidomics\CRC_Immunopeptidomics\MSFragger_OpenSearch_1_Output\AA_Stat\Output'}) Traceback (most recent call last): File "c:\users\parth\appdata\local\programs\python\python39\lib\runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "c:\users\parth\appdata\local\programs\python\python39\lib\runpy.py", line 87, in _run_code exec(code, run_globals) File "C:\Users\parth\AppData\Local\Programs\Python\Python39\Scripts\AA_stat.exe__main__.py", line 7, in
File "c:\users\parth\appdata\local\programs\python\python39\lib\site-packages\AA_stat\main.py", line 43, in main
AA_stat.AA_stat(params_dict, args)
File "c:\users\parth\appdata\local\programs\python\python39\lib\site-packages\AA_stat\AA_stat.py", line 322, in AA_stat
logger.debug('Fixed modifications: %s', params_dict['fix_mod'])
KeyError: 'fix_mod'
Please do advise me on how to troubleshoot. Thank you.
Regards, Ben