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Easypqp error when making library from DIA-Umpire SE track using FragPipe #311

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sjr24 opened this issue Feb 26, 2021 · 18 comments
Closed

Easypqp error when making library from DIA-Umpire SE track using FragPipe #311

sjr24 opened this issue Feb 26, 2021 · 18 comments

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@sjr24
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sjr24 commented Feb 26, 2021

Greetings,

The following error occurs during SpecLibGen of the DIA-U track in FragPipe.

SpecLibGen [Work dir: C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU]
C:\ProgramData\Anaconda3\python.exe -u C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib..\tools\speclib\gen_con_spec_lib.py C:\Users\srice\Downloads\FragPipe-14.0\2021-02-24-decoys-reviewed-contam-UP000005640.fas C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3_calibrated.mgf;C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3_uncalibrated.mgf;C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2_calibrated.mgf;C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2_uncalibrated.mgf;C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1_calibrated.mgf;C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1_uncalibrated.mgf C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU True unused use_easypqp ciRT 7 "--rt_lowess_fraction 0.01"
Using (un)calibrated.mgfs.
Spectral library building
Commands to execute:
'C:\ProgramData\Anaconda3\Scripts\easypqp.exe' convert --pepxml 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\interact.pep.xml' --spectra 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1_uncalibrated.mgf' --exclude-range -1.5,3.5 --psms 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.psmpkl --peaks 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.peakpkl
'C:\ProgramData\Anaconda3\Scripts\easypqp.exe' convert --pepxml 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\interact.pep.xml' --spectra 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2_uncalibrated.mgf' --exclude-range -1.5,3.5 --psms 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.psmpkl --peaks 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.peakpkl
'C:\ProgramData\Anaconda3\Scripts\easypqp.exe' convert --pepxml 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\interact.pep.xml' --spectra 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3_calibrated.mgf' --exclude-range -1.5,3.5 --psms 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3.psmpkl --peaks 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3.peakpkl
'C:\ProgramData\Anaconda3\Scripts\easypqp.exe' library --psmtsv 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\psm.tsv' --peptidetsv 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\peptide.tsv' --rt_reference 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\irt.tsv' --out easypqp_lib_openswath.tsv --rt_lowess_fraction 0.01 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.psmpkl' 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.psmpkl' 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3.psmpkl' 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.peakpkl' 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.peakpkl' 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3.peakpkl'

easypqp, version 0.1.10
Executing ['C:\\ProgramData\\Anaconda3\\Scripts\\easypqp.exe', 'convert', '--pepxml', 'C:\\Users\\srice\\Downloads\\HeLa_Evosep_diaPASEF_RAW\\diaU\\interact.pep.xml', '--spectra', 'C:\\Users\\srice\\Downloads\\HeLa_Evosep_diaPASEF_RAW\\diaU\\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1_uncalibrated.mgf', '--exclude-range', '-1.5,3.5', '--psms', '20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.psmpkl', '--peaks', '20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.peakpkl']
Executing ['C:\\ProgramData\\Anaconda3\\Scripts\\easypqp.exe', 'convert', '--pepxml', 'C:\\Users\\srice\\Downloads\\HeLa_Evosep_diaPASEF_RAW\\diaU\\interact.pep.xml', '--spectra', 'C:\\Users\\srice\\Downloads\\HeLa_Evosep_diaPASEF_RAW\\diaU\\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2_uncalibrated.mgf', '--exclude-range', '-1.5,3.5', '--psms', '20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.psmpkl', '--peaks', '20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.peakpkl']
Executing ['C:\\ProgramData\\Anaconda3\\Scripts\\easypqp.exe', 'convert', '--pepxml', 'C:\\Users\\srice\\Downloads\\HeLa_Evosep_diaPASEF_RAW\\diaU\\interact.pep.xml', '--spectra', 'C:\\Users\\srice\\Downloads\\HeLa_Evosep_diaPASEF_RAW\\diaU\\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3_calibrated.mgf', '--exclude-range', '-1.5,3.5', '--psms', '20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3.psmpkl', '--peaks', '20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3.peakpkl']
EasyPQP convert error BEGIN
Info: Converting C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\interact.pep.xml.
Info: Parsing run 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.
Info: Parsing pepXML.
Info: Generate theoretical spectra.
Info: Processing spectra from file C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1_uncalibrated.mgf.
Traceback (most recent call last):
  File "c:\programdata\anaconda3\lib\runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "c:\programdata\anaconda3\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "C:\ProgramData\Anaconda3\Scripts\easypqp.exe\__main__.py", line 7, in <module>
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 782, in main
    rv = self.invoke(ctx)
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 1289, in invoke
    rv.append(sub_ctx.command.invoke(sub_ctx))
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "c:\programdata\anaconda3\lib\site-packages\easypqp\main.py", line 58, in convert
    psms, peaks = conversion(pepxmlfile, spectralfile, unimodfile, exclude_range, max_delta_unimod, max_delta_ppm, enable_unannotated, enable_massdiff, fragment_types, fragment_charges, enable_specific_losses, enable_unspecific_losses)
  File "c:\programdata\anaconda3\lib\site-packages\easypqp\convert.py", line 606, in conversion
    peaks = read_mgf(spectralfile, psms[['scan_id', 'modified_peptide', 'precursor_charge']], theoretical, max_delta_ppm)
  File "c:\programdata\anaconda3\lib\site-packages\easypqp\convert.py", line 474, in read_mgf
    mz_intensity_array = tims_data[scan_id]
KeyError: 12
EasyPQP convert error END
EasyPQP convert error BEGIN
Info: Converting C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\interact.pep.xml.
Info: Parsing run 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.
Info: Parsing pepXML.
Info: Generate theoretical spectra.
Info: Processing spectra from file C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2_uncalibrated.mgf.
Traceback (most recent call last):
  File "c:\programdata\anaconda3\lib\runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "c:\programdata\anaconda3\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "C:\ProgramData\Anaconda3\Scripts\easypqp.exe\__main__.py", line 7, in <module>
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 782, in main
    rv = self.invoke(ctx)
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 1289, in invoke
    rv.append(sub_ctx.command.invoke(sub_ctx))
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "c:\programdata\anaconda3\lib\site-packages\easypqp\main.py", line 58, in convert
    psms, peaks = conversion(pepxmlfile, spectralfile, unimodfile, exclude_range, max_delta_unimod, max_delta_ppm, enable_unannotated, enable_massdiff, fragment_types, fragment_charges, enable_specific_losses, enable_unspecific_losses)
  File "c:\programdata\anaconda3\lib\site-packages\easypqp\convert.py", line 606, in conversion
    peaks = read_mgf(spectralfile, psms[['scan_id', 'modified_peptide', 'precursor_charge']], theoretical, max_delta_ppm)
  File "c:\programdata\anaconda3\lib\site-packages\easypqp\convert.py", line 474, in read_mgf
    mz_intensity_array = tims_data[scan_id]
KeyError: 1
Traceback (most recent call last):
  File "C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\..\tools\speclib\gen_con_spec_lib.py", line 849, in <module>
    main_easypqp()
  File "C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\..\tools\speclib\gen_con_spec_lib.py", line 675, in main_easypqp
    assert all(p.returncode == 0 for p in procs)
AssertionError
EasyPQP convert error END
Process 'SpecLibGen' finished, exit code: 1
Process returned non-zero exit code, stopping
@fcyu
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fcyu commented Feb 26, 2021

Can you send us the whole log?

Best,

Fengchao

@sjr24
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sjr24 commented Feb 26, 2021 via email

@fcyu
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fcyu commented Feb 26, 2021

The log file was truncated by GitHub. Can you zip it and attach it? But I have a question: is your data from diaPASEF since your folder name is HeLa_Evosep_diaPASEF_RAW?

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Fengchao

@sjr24
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sjr24 commented Feb 26, 2021 via email

@fcyu
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fcyu commented Feb 26, 2021

OK. DIA-Umpire does not support diaPASEF.

Best,

Fengchao

@sjr24
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sjr24 commented Feb 26, 2021 via email

@fcyu
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fcyu commented Feb 26, 2021

Correct, the workflow is not compatible with diaPASEF.

Best,

Fengchao

@sjr24
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sjr24 commented Feb 26, 2021 via email

@fcyu
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fcyu commented Feb 26, 2021

You are welcome.

Best,

Fengchao

@fcyu fcyu closed this as completed Feb 26, 2021
@fcyu
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fcyu commented Feb 26, 2021

Sorry that I cannot find the zip file. Can you send them to yufe@umich.edu?

Thanks,

Fengchao

@sjr24
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sjr24 commented Feb 26, 2021 via email

@guoci
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guoci commented Feb 27, 2021

@sjr24 can you also send

C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1_uncalibrated.mgf
C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2_uncalibrated.mgf

@guoci guoci reopened this Feb 27, 2021
@sjr24
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sjr24 commented Feb 27, 2021 via email

@anesvi
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anesvi commented Feb 27, 2021 via email

@sjr24
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sjr24 commented Feb 28, 2021 via email

@anesvi
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anesvi commented Mar 1, 2021 via email

@sjr24
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sjr24 commented Mar 2, 2021 via email

@anesvi
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anesvi commented Mar 2, 2021 via email

@fcyu fcyu closed this as completed Mar 8, 2021
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@guoci @fcyu @anesvi @sjr24