Hello, Can you check that the comet results files are complete and valid? An easy way to check this is to try to open those files in the PepXMLViewer (before running PeptideProphet); make sure you can open a few spectra using the "ions" link. If this fails, you may want to check the logs of the comet searches -- do they have any errors?
Cheers, --Luis On Thu, Mar 9, 2017 at 12:28 PM, Murielle Ålund <[email protected]> wrote: > Hi, > > I am running PeptideProphet on both .tandem.pep.xml and .comet.pep.xml > files using TPP v.4.8.0. It runs fine for all my .tandem files and half of > the .comet files, but I get the following error message for the remaining > .comet files and cannot figure out how they differ from the other files: > > > running: " /PepXMLViewer.cgi -I filename.comet.pep.xml" > Segmentation fault (core dumped) > > command "/PepXMLViewer.cgi -I filename.comet.pep.xml" exited with non-zero > exit code: 35584 > QUIT - the job is incomplete > > > > > In each case a high number of decoys and non-decoys are found, but I get 0 > hits in the actual analysis. > > Any help is appreciated, thanks! > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
