Hi Emily, I got the data and now I am trying to understand how you are running the analysis. Can you please describe those steps?
Thank you, -David On Sat, Oct 17, 2020 at 12:54 PM Emily Kawaler <e.kawa...@gmail.com> wrote: > 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 <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/de634f4a-0057-4fc1-b135-e639c0eb77een%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/de634f4a-0057-4fc1-b135-e639c0eb77een%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/CAGJJY%3D_4bEOSa9rp9qxutryqVVzG92LRzwb2MJkipUrgRGqqyQ%40mail.gmail.com.
