I've uploaded the pepXML files, the parameters I used, and the database here. <https://drive.google.com/drive/folders/1gJoi9fqsmIYg_0tl_2Ur-n04MJyuotyc?usp=sharing> Please let me know if I should be uploading anything else! Thank you!
On Saturday, October 17, 2020 at 12:04:21 AM UTC-4 Emily Kawaler wrote: > 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 <[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/de634f4a-0057-4fc1-b135-e639c0eb77een%40googlegroups.com.
