MSFragger - ValueError: too many values to unpack

[Evan-Raymond]

Hi there,

I've been getting the following error code from MSFragger while (I assume) its writing pepxml to disk, but I don't know enough about what the software is doing at this point to debug the error. Do you have any ideas?

Cheers,
Evan

Writing: CP_184 spectrum: 98304
concurrent.futures.process._RemoteTraceback:
"""
Traceback (most recent call last):
File "C:\Users\Core i7 PC\AppData\Local\Programs\Python\Python39\lib\concurrent\futures\process.py", line 246, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "D:\fragpipe\tools\msfragger_pep_split.py", line 370, in write_pepxml
pep_to_prot = get_pep_to_prot_mapping(infile)
File "D:\fragpipe\tools\msfragger_pep_split.py", line 341, in get_pep_to_prot_mapping
pep, prot = make_dict_entry(sh)
File "D:\fragpipe\tools\msfragger_pep_split.py", line 336, in make_dict_entry
key, = sh_peptide.findall(sh)
ValueError: too many values to unpack (expected 1)
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "D:\fragpipe\tools\msfragger_pep_split.py", line 631, in
main()
File "D:\fragpipe\tools\msfragger_pep_split.py", line 623, in main
combine_results()
File "D:\fragpipe\tools\msfragger_pep_split.py", line 477, in combine_results
e.result()
File "C:\Users\Core i7 PC\AppData\Local\Programs\Python\Python39\lib\concurrent\futures_base.py", line 439, in result
Process 'MSFragger' finished, exit code: 1
Process returned non-zero exit code, stopping

log_2024-12-30_22-45-25.zip

[guoci]

@Evan-Raymond can you send me the split_peptide_index_tempdir directory?

[Evan-Raymond]

Hi @guoci,

Thanks for getting back to me.
The split_peptide_index_tempdir file is way too big to upload, even when compressed its almost 14GB. Can I send you part of the file?

Cheers,
Evan

[guoci]

yes, can just send the pepxml files

[Evan-Raymond]

Hi @guoci

I've uploaded one of the smaller pepxml files I could find, as most are over 25 MB compressed. Please bear in mind that this is only one of 275 pepxml files split over 5 folders in the split_peptide_index_tempdir and MSFragger seemed fine with most of them, so I don't know if its a specific file thats the problem.

Cheers,
Evan

CP_484.zip

[Evan-Raymond]

Hi @guoci

Any updates on the above issue?

Cheers,
Evan