Open samgregoire opened 4 weeks ago
I forgot to mention that I did some initial testing on a much smaller mzML file (2G, from a thermo orbitrap MS) compared to the file I'm having the problem with (59G, from a Bruker timsTOF MS), and that both Comet and Sage were working correctly.
I'm afraid that neither SearchGUI nor PeptideShaker was developed for spectrum files as big as 59GB, hence the issues you are seeing may simply be due to the large mzML file. Would it be an option to convert the mzML to mgf and see whether that makes a difference?
As for the invalid pointer error, this comes from inside Comet and I'd recommend contacting the Comet developers directly to see if anything can be done about it: https://groups.google.com/g/comet-ms.
And I assume that there were no similar errors when running Sage? You may however consider also contacting the Sage developers (https://github.com/lazear/sage) to see if there are any limitations with regards to very large mzML files?
Hello. I'm trying to use PeptideShaker to process identification files obtained by SearchGUI using several search engines (Comet, OMSSA, Tide, X! Tandem and Sage). PeptideShaker encounters the following error when trying to process the Sage output file.
Please, ignore the fact that no PSM was found in the Comet file, I encoutered an error during the search.
I tried to run PeptideShaker without the Sage identification file and everything seems to work fine. I tried to process only the Sage identification file alone and ran into the same error. After checking, I can guarantee that the mzML file I'm using contains a 'frame=9411 scan=411' scan. Removing this specific PSM from the identification files only changes the error message to another scan title.
Please, let me know if I can provide any more useful information.
Thanks, Sam
EDIT: perhaps the problem encountered during Comet processing is actually related to this problem? I get the following error message:
I don't really understand what this means, but it seems to be related to spectra loading, which could be related to the issue I'm describing above.