quantms utils Acetyl Unimod:1 error #466

ypriverol · 2024-12-26T09:15:17Z

Description of the bug

Workflow execution completed unsuccessfully
The exit status of the task that caused the workflow execution to fail was: 1

Error executing process > 'BIGBIO_QUANTMS:QUANTMS:DIA:DIANNCONVERT (PXD048325-Hela.sdrf)'

Caused by:
  Process `BIGBIO_QUANTMS:QUANTMS:DIA:DIANNCONVERT (PXD048325-Hela.sdrf)` terminated with an error exit status (1)


Command executed:

  quantmsutilsc diann2mztab \
      --folder ./ \
      --exp_design PXD048325-Hela.sdrf_openms_design.tsv \
      --diann_version ./version/versions.yml \
      --dia_params "40.0;ppm;40.0;ppm;Trypsin;Carbamidomethyl (C);Acetyl (Any N-term),Oxidation (M)" \
      --charge 4 \
      --missed_cleavages 1 \
      --qvalue_threshold 0.01 \
       \
      2>&1 | tee convert_report.log
  
  cat <<-END_VERSIONS > versions.yml
  "BIGBIO_QUANTMS:QUANTMS:DIA:DIANNCONVERT":
      quantms-utils: $(pip show quantms-utils | grep "Version" | awk -F ': ' '{print $2}')
  END_VERSIONS

Command exit status:
  1

Command output:
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLATAPPHVTVVR:1445.7990694133002
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDATLYEQVLLEK:1719.8930919875
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDLSGPNVDVDVPDVNLEGPDAK:2563.228972550601
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDLTK:774.4123388501998
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDLTKR:930.5134502329998
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDLVTMDYAAQK:1552.7443181752
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDVSGPK:900.4552670415999
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDVSGPKVDLDTPDLDLHGPEGK:2602.2762567101013
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDVSGPKVDLDVPDVNLEGPDAK:2577.281007742001
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDVSGPKVDLDVPDVNLEGPEGK:2577.281007742001
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDVSGPKVDLEGPDVNLEGPEGK:2549.249707614401
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDVSGPKVDVDLPDVNLEGPDAK:2577.281007742001
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDVSGPKVDVDVPDVNLEGPDAK:2563.265357678201
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDVSGPKVDVEC(UniMod:4)PDVNLEGPEGK:2638.243242440101
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDVSGPKVDVEVPDVSLEGPEGK:2550.270108710101
  Traceback (most recent call last):
    File "/usr/local/bin/quantmsutilsc", line 10, in <module>
      sys.exit(main())
               ^^^^^^
    File "/usr/local/lib/python3.12/site-packages/quantmsutils/quantmsutilsc.py", line 36, in main
      cli()
    File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1157, in __call__
      return self.main(*args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1078, in main
      rv = self.invoke(ctx)
           ^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1688, in invoke
      return _process_result(sub_ctx.command.invoke(sub_ctx))
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1434, in invoke
      return ctx.invoke(self.callback, **ctx.params)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/click/core.py", line 783, in invoke
      return __callback(*args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/click/decorators.py", line 33, in new_func
      return f(get_current_context(), *args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/quantmsutils/diann/diann2mztab.py", line 84, in diann2mztab
      report = diann_directory.main_report_df(qvalue_threshold=qvalue_threshold)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/quantmsutils/diann/diann2mztab.py", line 481, in main_report_df
      k: compute_mass_modified_peptide(k) for k in report["Modified.Sequence"].unique()
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/quantmsutils/diann/diann2mztab.py", line 299, in compute_mass_modified_peptide
      mass = AASequence.fromString(new_peptide_seq).getMonoWeight()
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "pyopenms/_pyopenms_5.pyx", line 31, in pyopenms._pyopenms_5.__static_AASequence_fromString
  RuntimeError: the value 'UniMod:1' was used but is not valid; Cannot convert string to peptide modification. No modification matches in our database.

Command wrapper:
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLATAPPHVTVVR:1445.7990694133002
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDATLYEQVLLEK:1719.8930919875
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDLSGPNVDVDVPDVNLEGPDAK:2563.228972550601
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDLTK:774.4123388501998
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDLTKR:930.5134502329998
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDLVTMDYAAQK:1552.7443181752
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDVSGPK:900.4552670415999
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDVSGPKVDLDTPDLDLHGPEGK:2602.2762567101013
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDVSGPKVDLDVPDVNLEGPDAK:2577.281007742001
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDVSGPKVDLDVPDVNLEGPEGK:2577.281007742001
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDVSGPKVDLEGPDVNLEGPEGK:2549.249707614401
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDVSGPKVDVDLPDVNLEGPDAK:2577.281007742001
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDVSGPKVDVDVPDVNLEGPDAK:2563.265357678201
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDVSGPKVDVEC(UniMod:4)PDVNLEGPEGK:2638.243242440101
  2024-12-26 00:51:36,655 [compute_mass_modified_peptide] - ADLDVSGPKVDVEVPDVSLEGPEGK:2550.270108710101
  Traceback (most recent call last):
    File "/usr/local/bin/quantmsutilsc", line 10, in <module>
      sys.exit(main())
               ^^^^^^
    File "/usr/local/lib/python3.12/site-packages/quantmsutils/quantmsutilsc.py", line 36, in main
      cli()
    File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1157, in __call__
      return self.main(*args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1078, in main
      rv = self.invoke(ctx)
           ^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1688, in invoke
      return _process_result(sub_ctx.command.invoke(sub_ctx))
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1434, in invoke
      return ctx.invoke(self.callback, **ctx.params)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/click/core.py", line 783, in invoke
      return __callback(*args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/click/decorators.py", line 33, in new_func
      return f(get_current_context(), *args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/quantmsutils/diann/diann2mztab.py", line 84, in diann2mztab
      report = diann_directory.main_report_df(qvalue_threshold=qvalue_threshold)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/quantmsutils/diann/diann2mztab.py", line 481, in main_report_df
      k: compute_mass_modified_peptide(k) for k in report["Modified.Sequence"].unique()
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/quantmsutils/diann/diann2mztab.py", line 299, in compute_mass_modified_peptide
      mass = AASequence.fromString(new_peptide_seq).getMonoWeight()
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "pyopenms/_pyopenms_5.pyx", line 31, in pyopenms._pyopenms_5.__static_AASequence_fromString
  RuntimeError: the value 'UniMod:1' was used but is not valid; Cannot convert string to peptide modification. No modification matches in our database.

Work dir:
  /hps/nobackup/juan/pride/reanalysis/absolute-expression/cell-lines/PXD048325/work/5f/cfc150c913dda165696db769016216

Container:
  /hps/nobackup/juan/pride/reanalysis/singularity/depot.galaxyproject.org-singularity-quantms-utils-0.0.18--pyh7e72e81_0.img

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Command used and terminal output

No response

Relevant files

No response

System information

No response

The text was updated successfully, but these errors were encountered:

daichengxin · 2024-12-30T01:36:12Z

Amino acid Acetyl (not in peptide N-term) is not supported in pyopenms modification database like these: APLLA(UniMod:1)VTR、ASGN(UniMod:1)YATVLSHNPETKK. There are 162 modiified peptides in this DIA-NN results like these. DIA-NN modification parameters passed is --var-mod Acetyl,42.010565,Any N-term

ypriverol · 2024-12-30T08:18:29Z

@vdemichev have you seen this problem before, when searching with the parameter --var-mod Acetyl,42.010565,Any N-term, we got a lot of peptides with Acetyl in the middle of the sequence (e.g. ASGN(UniMod:1)YATVLSHNPETKK)

vdemichev · 2024-12-30T08:25:15Z

--var-mod Acetyl,42.010565,Any N-term

Hi both, that's incorrect syntax, should be --var-mod Acetyl,42.010565,n

Best,
Vadim

ypriverol · 2024-12-31T23:51:14Z

Solved, acetylation: NT=Acetyl;MT=Variable;PP=Any N-term;AC=UNIMOD:1

ypriverol added the bug Something isn't working label Dec 26, 2024

ypriverol assigned ypriverol and daichengxin Dec 26, 2024

ypriverol closed this as completed Dec 31, 2024

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quantms utils Acetyl Unimod:1 error #466

quantms utils Acetyl Unimod:1 error #466

ypriverol commented Dec 26, 2024

daichengxin commented Dec 30, 2024

ypriverol commented Dec 30, 2024

vdemichev commented Dec 30, 2024

ypriverol commented Dec 31, 2024

quantms utils Acetyl Unimod:1 error #466

quantms utils Acetyl Unimod:1 error #466

Comments

ypriverol commented Dec 26, 2024

Description of the bug

Command used and terminal output

Relevant files

System information

daichengxin commented Dec 30, 2024

ypriverol commented Dec 30, 2024

vdemichev commented Dec 30, 2024

ypriverol commented Dec 31, 2024