Hello, Thanks so much for taking a look! I think the selenocysteines ("U") are likely not the problem, since I've got those in all of my databases, including the ones that run correctly. I'm looking at 03CPTAC_OVprospective_W_PNNL_20161212_B1S3_f13.pepXML and I don't see anything odd in line 171821 ("<search_score name="nextscore" value="11.532"/>"), so I think our line numberings might not match up - what does your problematic line contain?
When I try to run it on my end, it always sticks somewhere in the 10CPTAC_OV files. Right now I'm running a working set of spectra with a database that didn't work and vice versa, so hopefully that'll help me pin down whether it's a problem with my spectra or my database - will let you know how that turns out! Emily On Thursday, October 22, 2020 at 3:09:29 PM UTC-4 David Shteynberg wrote: > 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 <e.ka...@gmail.com> 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 <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-discu...@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 >> >> <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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