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 <[email protected]> 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 <[email protected]> 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 [email protected]. >>> 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 [email protected]. > 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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D8ccGKhJLEmkkz0a%2BR6xToMOErnb3ptrsg%2B5wmewYWZHw%40mail.gmail.com.
