Open prvst opened 3 weeks ago
Hi @prvst,
Seems like something goes wrong while reading the run
field from the idXML file.
@jonasscheid, would you have time to look into this? Thanks!
Best, Ralf
Can you attach the input file or a reduced version of it @prvst?
Hello, @jonasscheid. Unfortunately, I cannot share any data, but I believe to have found the source of the problem. The issue happens when you convert a MSFragger-derived pepXML file to idXML using the OpenMS IDFileConverter, several of the UserParam attributes are not ported to the new idXML, including the one below:
<UserParam type="stringList" name="spectra_data" value="[/foo/bar/file.mzML]"/>
This seems to be the line triggering the error on idxml.py:223
Perhaps making _get_run
accept empty/missing values would be a workaround here?
Hello, I'm getting this error, can you please help me locate the source of the problem?