Thank you! I'm working on getting it transferred to Drive, so it might take a little while, but I'll be in touch!
On Tuesday, October 13, 2020 at 3:08:44 PM UTC-4 David Shteynberg wrote: > Hello Emily, > > If you are able to share the dataset including the pepXML file and the > database I can try to replicate the issue here and try to troubleshoot the > sticking point. > > Thanks, > -David > > On Tue, Oct 13, 2020 at 11:15 AM Emily Kawaler <e.ka...@gmail.com> wrote: > >> Hello, and thank you for your response! It doesn't look like the process >> is using too much memory (I've allocated 300 GB and it's maxing out around >> 10), and I've kicked up the minprob parameter - it's still getting stuck, >> unfortunately. >> Emily >> >> On Friday, October 9, 2020 at 2:24:37 PM UTC-4 Luis wrote: >> >>> Hello Emily, >>> >>> This is not a problem that we have seen much of. Do you know which >>> version of ProteinProphet / TPP you are using? >>> >>> One potential issue is the large number of proteins (and peptides) that >>> it is trying to process -- can you either monitor the memory usage of the >>> machine when you run this dataset, and/or try on one with more memory? >>> >>> Hope this helps, >>> --Luis >>> >>> >>> On Tue, Oct 6, 2020 at 6:32 PM Emily Kawaler <e.ka...@gmail.com> wrote: >>> >>>> Hello! I've been running ProteinProphet as part of the Philosopher >>>> pipeline for a while now with no problems. However, one of my datasets >>>> seems to be getting stuck in the middle of this function. It doesn't throw >>>> an error or anything - just stops advancing (the last >>>> line of the output is "Computing degenerate peptides for 69919 >>>> proteins: 0%...10%...20%...30%...40%...50%"). Has anyone run into this >>>> problem before? >>>> >>>> -- >>>> 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 spctools-discu...@googlegroups.com. >>>> To view this discussion on the web visit >>>> https://groups.google.com/d/msgid/spctools-discuss/be33a8fb-a6ec-41b6-a988-981161f194fcn%40googlegroups.com >>>> >>>> <https://groups.google.com/d/msgid/spctools-discuss/be33a8fb-a6ec-41b6-a988-981161f194fcn%40googlegroups.com?utm_medium=email&utm_source=footer> >>>> . >>>> >>> -- >> 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 spctools-discu...@googlegroups.com. >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/6d28e150-40f0-4747-a8a3-02630b12379dn%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/6d28e150-40f0-4747-a8a3-02630b12379dn%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- 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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/0ef57a4b-96ec-4310-8667-aa2e940e9bbfn%40googlegroups.com.
