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/CACyS9bo5x-_%3D%2BFahdGxviYPLf8g00C_ikQGT7t%2BxgR_YOwTDCA%40mail.gmail.com.
