Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

Not a problem! In the end I decided just to remove all of the titins from my database - it shouldn't have a huge effect on my results - and I was indeed able to run all of my datasets to completion. Thanks for all of your help! Emily On Friday, November 6, 2020 at 8:25:56 PM UTC-5 David Shteynb

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

Hello again Emily, Apologies for the delay but I needed a bit more time to look into this. You are absolutely right about the titins causing this issue. The problem is the significant overlap in peptides in this very large titin group. Your database contains 343 variations of titin with differe

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

Another update: I've pinpointed a much smaller database that reproduces the error when run with just 10OV - uploaded to the same folder as above, named "titins_revs.fasta" (it contains a bunch of titins and some reverse decoy sequences). Something in the titins is causing this error, I think (I'

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

Okay - When I ran the working set of spectra with the database that failed, it seems to have failed; when I ran the set of spectra that failed with a database that worked, it ran to completion. I think we can probably narrow the problem down to something in the database. On Friday, October 23,

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

While those tests are still running, I pulled out all 185 of the proteins that are in the 10OV pepXMLs but not in 01-09OV, figuring that maybe one of those is causing the error. I've uploaded that to the same folder everything else is in (it's called 10OV_uniq.fasta) - I don't see anything that

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

I just re extracted that file and I don't see the issue anymore. Perhaps this was a decompression issue. Thanks for checking. -David On Thu, Oct 22, 2020 at 12:19 PM Emily Kawaler wrote: > Hello, > Thanks so much for taking a look! I think the selenocysteines ("U") are > likely not the proble

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

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 17

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

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 17

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

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 (pos

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

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 xmlli

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

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 wrote: > I've uploaded the pepXML files, the parameters I used, and the database > here. >

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

I've uploaded the pepXML files, the parameters I used, and the database here. 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 Kawa

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

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 t

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

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 wrote: > Hello, and thank you for your response! It doesn

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

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

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

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 th

[spctools-discuss] ProteinProphet sticking in findDegenGroups3

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 "Compu