Sure! The spectra are from the CPTAC2 ovarian propective dataset, though I removed all scans that matched to a standard reference database (I don't think the scan removal is the issue, since I'm also having this problem on a different dataset without removing any scans; I also checked with xmllint and it looks like the mzML pepXML files are valid). I've been running it with the philosopher pipeline, so the pepXML files were generated with MSFragger as part of that pipeline. The database is a customized variant database with contaminants and decoys added by philosopher's database tool. Are there any other specifics you'd like? I can upload my full philosopher.yml file if that would be helpful.
On Tuesday, October 20, 2020 at 1:30:44 AM UTC-4 David Shteynberg wrote: > 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.ka...@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-discu...@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/9c0b1f62-81a7-417b-9e8f-14900f87e134n%40googlegroups.com.
