Hi Emily, I analyzed the search results that you sent and I am seeing some strange things in at least one of the files you gave me. This may be causing some of the problems you saw. In file 03CPTAC_OVprospective_W_PNNL_20161212_B1S3_f13.pepXML on line 171821 there are some strange characters (possibly binary) that are tripping up the TPP. I think these might be caused by a bug in an analysis tool upstream of the TPP. Not sure if there are other mistakes of this sort. Also I found some 'U' amino acids in the database which the TPP complains about having a mass of 0.
I hope this helps you somewhat. Let me know what you find on your end. Cheers, -David On Tue, Oct 20, 2020 at 1:42 PM Emily Kawaler <[email protected]> wrote: > 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 <[email protected]> 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 <[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 >>> <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 [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/9c0b1f62-81a7-417b-9e8f-14900f87e134n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/9c0b1f62-81a7-417b-9e8f-14900f87e134n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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