Exception in GUI: multiprocessing/reduction.py: PermissionError: [WinError 5]

[lliligabriel]

Greetings! I am attempting to feed ms2rescore with outputs (.pin, .pepXML, .tsv`) from msfragger (part of the fragpipe workflow, but i did not use any validation tools nor any downstream software). I used top n = 5 so that the rescoring tool can have more candidates.

My regex pattern for psm_id_pattern and spectrum_id_pattern can be successfully used in parsing, both in the GUI and in the command line interface. Though the MSFragger output denotes the amino acid modification as M[147], unrecognizable by DeepLC, I can successfully fix the issue by modifying the json file.

However, I am encountering several problems in using the GUI (windows). First, the GUI cannot parse my .pepXML, so I can only use .tsv for processing. Secondly, the GUI claims that several functions in downstream processing (maybe somewhere after the DeepLC? Because I do not encounter the errors before I fix the DeepLC recognition problems.)

When I try to switch to the command line interace to manually process the rescoring pipeline, additional issues occur.

1. MS2rescore cannot recognize my .tsv file.

I can make the claim that, under the context of MSFragger outputs at least, the issue is unique to PSM with multiple candidates, since I used a smaller psm file with only 1 candidate per spectrum and did not encounter this problem.

specifically

input_psm = read_file("filename.tsv",
                      filetype='fragpipe')

File ~/miniforge3/lib/python3.12/site-packages/psm_utils/io/__init__.py:210, in read_file(filename, filetype, *args, **kwargs)
    206     raise PSMUtilsIOException(
    207         f"Filetype '{filetype}' unknown or not supported for reading."
    208     ) from e
    209 reader = reader_cls(filename, *args, **kwargs)
--> [210](https://vscode-remote+ssh-002dremote-002b172-002e28-002e40-002e2.vscode-resource.vscode-cdn.net/new_home/xinyuegu/playground/~/miniforge3/lib/python3.12/site-packages/psm_utils/io/__init__.py:210) psm_list = reader.read_file()
    211 return psm_list

File ~/miniforge3/lib/python3.12/site-packages/psm_utils/io/_base_classes.py:46, in ReaderBase.read_file(self)
     44 def read_file(self) -> PSMList:
     45     """Read full PSM file into a PSMList object."""
---> [46](https://vscode-remote+ssh-002dremote-002b172-002e28-002e40-002e2.vscode-resource.vscode-cdn.net/new_home/xinyuegu/playground/~/miniforge3/lib/python3.12/site-packages/psm_utils/io/_base_classes.py:46)     return PSMList(psm_list=[psm for psm in self.__iter__()])

File ~/miniforge3/lib/python3.12/site-packages/psm_utils/io/fragpipe.py:71, in FragPipeReader.__iter__(self)
     69 reader = csv.DictReader(msms_in, delimiter="\t")
     70 for row in reader:
---> [71](https://vscode-remote+ssh-002dremote-002b172-002e28-002e40-002e2.vscode-resource.vscode-cdn.net/new_home/xinyuegu/playground/~/miniforge3/lib/python3.12/site-packages/psm_utils/io/fragpipe.py:71)     yield self._get_peptide_spectrum_match(row)
...
     96     rescoring_features=rescoring_features,
     97     metadata={},
     98 )

KeyError: 'Modified Peptide

alternatively

input_psm = read_file("file_name.tsv",
                      filetype='tsv')

PSMUtilsIOException: Could not parse PSM from three consecutive rows. Verify that the file is formatted correctly as a psm_utils TSV file or that the correct file type reader is used.

2. when using .pepXML as psm file input and in command line interace, I am encountering issues such as (from log)

INFO     ms2rescore.feature_generators.ms2pip // Running MS²PIP for PSMs from run (1/1) `None`...                     
...
...
...
                    INFO     ms2rescore.feature_generators.deeplc // Running DeepLC for PSMs from run (1/1): `None`...                    

I am not sure whether this matters in downstream processing. After following line by line in ths ms2rescore tutorial, the psmList from readfile() function also have run = None in every entry. I found out that it can be due to the get_psm_dict() function used in initializing the psmList object, which depends on the functions parsing the input file from the psm_util package.

I have a separate issue in another ticket.

update: when trying to use the GUI, it reports errors such as [access denied]. thank you so much!

[RalfG]

Hi @lliligabriel,

Apologies for the long delay in my reply. Regarding the first issue, where the FragPipe TSV file cannot be read, this was fixed in CompOmics/psm_utils#124. Your alternative in setting the filetype to 'tsv' generates an expected error, as this is for the psm_utils TSV format, not the FragPipe one. The run value being None is not an issue. These logs are mostly useful when processing multiple MS runs in a single MS²Rescore process.

I am not sure what caused the multiprocessing permission errors. Please let me know if it still occurs with the latest version of MS²Rescore.

Thanks!
Ralf

[lliligabriel]

Thank you so much for your response! I will attempt the fragpipe tsv again soon.

Regarding the GUI - I downloaded the latest version (v3.2.0-post1) onto a Intel(R) Xeon(R) W-2295 CPU @ 3.00GHz machine and it reports

[RalfG]

Hi @lliligabriel,

Could you try again with v3.2.1?

Thanks!

[lliligabriel]

Unable to open the software this time. Looks like a hdf5 package version issue?

[RalfG]

Thanks for checking. That is strange. Perhaps it's a system-specific error.

Just to be sure, could you first completely uninstall MS²Rescore and then reinstall it?

[lliligabriel]

Re-tried and it now works! Guess it's some conflicting background issue. Thank you so much!

[RalfG]

Great new! Thanks for letting us know!