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compomics / ms2pip

MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
https://ms2pip.readthedocs.io
Apache License 2.0
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Error when running ms2pip in the linux terminal #65

Closed MarcIsak closed 4 years ago

MarcIsak commented 4 years ago

Hi,

I tried to process a batch of .peprec files in ms2pip (those that Ralf generated for me in issue #61), to create predicted output files in spectronaut.csv format instead of just csv. I noticed that quite a few peprec files, _precursorssplit(00, 03, 04, 07, 08, 09, 11, 16, 17, 18).peprec_, generated the following error when being processed with ms2pip:

_--- Logging error --- Traceback (most recent call last): File "/usr/lib/python3.8/logging/init.py", line 1081, in emit msg = self.format(record) File "/usr/lib/python3.8/logging/init.py", line 925, in format return fmt.format(record) File "/usr/lib/python3.8/logging/init.py", line 664, in format record.message = record.getMessage() File "/usr/lib/python3.8/logging/init.py", line 369, in getMessage msg = msg % self.args TypeError: not all arguments converted during string formatting Call stack: File "/home/marc/PycharmProjects/MS2PIP/venv/bin/ms2pip", line 8, in sys.exit(main()) File "/home/marc/PycharmProjects/MS2PIP/venv/lib/python3.8/site-packages/ms2pip/main.py", line 123, in main ms2pip.run() File "/home/marc/PycharmProjects/MS2PIP/venv/lib/python3.8/site-packages/ms2pip/ms2pipC.py", line 759, in run self._read_peptide_information() File "/home/marc/PycharmProjects/MS2PIP/venv/lib/python3.8/site-packages/ms2pip/ms2pipC.py", line 842, in _read_peptideinformation logger.info( Message: 'Removed {} unsupported peptide sequences (< 3, > 99 amino acids, or containing B, J, O, U, X or Z).' Arguments: (11,)

I think that the message in this error is strange as all peptide sequences are between 7 and 50 AA, and they should not have any of the AAs: B, J, O, U, X or Z.

Any ideas? The peprec files can be found in issue #61

Best,

Marc

RalfG commented 4 years ago

Hi Marc, I checked the file with the precursors, and there are in fact peptides with B, Z and X amino acids. There does occur a bug while writing this error message, but that shouldn't influence the results. Does the script continue to run after this error message?