I was able to replicate the error on a different dataset. I will work on a solution in the coming days, meanwhile the older version of iProphet will work just fine. The new version will be faster when it's released but results shouldn't change.
Cheers, David On Mon, Jun 3, 2019, 4:45 AM Alejandro <agomeza...@gmail.com> wrote: > Hi David, > > I installed the revision 7931 and it gives the same error: > > Running FPKM NSS NRS NSE NSI NSM NSP Model EM: > Computing NSS values ... > > Creating 1 threads > Wait for threads to finish ... > .... done > Computing NRS values ... > > Creating 1 threads > Wait for threads to finish ... > 0--------------------------------------------------50------------------------------------------------100% > ..................................................................................................... > done > Computing NSE values ... > > Creating 1 threads > Wait for threads to finish ... > 0--------------------------------------------------50------------------------------------------------100% > ..................................................................................................... > done > Computing NSI values ... > > Creating 1 threads > Wait for threads to finish ... > 0--------------------------------------------------50------------------------------------------------100% > ..................................................................................................... > done > Computing NSM values ... > > Creating 1 threads > Wait for threads to finish ... > 0--------------------------------------------------50------------------------------------------------100% > ..................................................................................................... > done > Computing NSP values ... > Creating 1 threads > Wait for threads to finish ... > 0--------------------------------------------------50------------------------------------------------100% > ..................................................................................................... > done > FPKM values are unavailable ... > Iterations: DEBUG HERE ... > Segmentation fault (core dumped) > > > *Command FAILED* > RETURN CODE:35584 > > I also tested in each file alone and I can run iProphet succesfully. > However combining files from MSGF and Comet fails. > > Best, > > Alejandro > > On Sunday, June 2, 2019 at 4:43:45 AM UTC+2, David Shteynberg wrote: >> >> Hello Alejandro, >> >> It appears that you are coming across an iProphet error in that svn code >> revision. Are you willing to test if the latest revision (7931) fails in >> the same way on your data? Otherwise, if you are able to share the data I >> can attempt to replicate the error myself and correct the bug. >> >> Thanks, >> -David >> >> On Sat, Jun 1, 2019 at 4:28 PM Alejandro <agome...@gmail.com> wrote: >> >>> Hello all, >>> >>> I'm having trouble running TPP 5.2 in general in Ubuntu 18.04. I >>> followed the compilation guideline, and after using svn checkout -r 7922 >>> (as recommended by Eric) it went ahead, although I still have some things >>> that are broken, like checking for the ions in the pepxml file. I get the >>> following error: >>> >>> Error - scan 10000 is an *MS1* scan in the mzXML file >>>> /home/laptop/Documents/TPP_data/tests/QuickYeastUPS1/UPS1_50000amol_R1.mzML >>> >>> >>> I can click on the Spectrum and see the peptide table but whenever I >>> click on the ions I see that error. >>> >>> More importantly, I can run Comet followed by PeptideProphet, iProphet >>> and ProteinProphet and it all goes fine. I can do the same with MSGF+ >>> (PeptideProphet, iProphet and ProteinProphet). However, when I try to >>> combine both PeptideProphet files (from Comet and MSGF+) I always get the >>> following error: >>> >>> >>> *EXECUTING: cd /home/laptop/Documents/TPP_data/TH129_134/comsgf ; >>> /usr/local/tpp/bin/InterProphetParser >>> /home/laptop/Documents/TPP_data/TH129_134/Comet/interact_comet.pep.xml >>> /home/laptop/Documents/TPP_data/TH129_134/MSGF/interact_p005.pep.xml >>> interact.ipro.pep.xml * >>> >>> Running FPKM NSS NRS NSE NSI NSM NSP Model EM: >>> Computing NSS values ... >>> >>> Creating 1 threads >>> Wait for threads to finish ... >>> .... done >>> Computing NRS values ... >>> >>> Creating 1 threads >>> Wait for threads to finish ... >>> 0--------------------------------------------------50------------------------------------------------100% >>> ..................................................................................................... >>> done >>> Computing NSE values ... >>> >>> Creating 1 threads >>> Wait for threads to finish ... >>> 0--------------------------------------------------50------------------------------------------------100% >>> ..................................................................................................... >>> done >>> Computing NSI values ... >>> >>> Creating 1 threads >>> Wait for threads to finish ... >>> 0--------------------------------------------------50------------------------------------------------100% >>> ..................................................................................................... >>> done >>> Computing NSM values ... >>> >>> Creating 1 threads >>> Wait for threads to finish ... >>> 0--------------------------------------------------50------------------------------------------------100% >>> ..................................................................................................... >>> done >>> Computing NSP values ... >>> Creating 1 threads >>> Wait for threads to finish ... >>> 0--------------------------------------------------50------------------------------------------------100% >>> ..................................................................................................... >>> done >>> FPKM values are unavailable ... >>> Iterations: DEBUG HERE ... >>> Segmentation fault (core dumped) >>> >>> >>> *Command FAILED* >>> RETURN CODE:35584 >>> >>> I have tried to disable FPKM, but gives the same error. Odd is that I >>> can run iProphet on each and runs fine, including FPKM. >>> >>> My samples are dimethylated samples, and was searched using static >>> modifications, doing one search for Light and one search for Heavy, and >>> then both files combined with PeptideProphet., like so: >>> *xinteract -Ninteract_comet.pep.xml -p0.05 -l7 -PPM -OAPd -dDECOY >>> H_TH189.pep.xml L_TH189.pep.xml * >>> I have also tried using -p0 but gives in the end the same error when >>> combining both search engines. >>> >>> In TPP 5.1 the combination works, however I'm trying to use the new >>> Xpress which uses the intensity for quantitation, and in TPP 5.1 the >>> intensities are not passed to the proteins. >>> >>> Any help would be appreciated. Thanks, >>> >>> Alejandro >>> >>> -- >>> 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...@googlegroups.com. >>> To post to this group, send email to spctools...@googlegroups.com. >>> Visit this group at https://groups.google.com/group/spctools-discuss. >>> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/spctools-discuss/38e40045-66e2-4d7e-8acf-4a9995047464%40googlegroups.com >>> <https://groups.google.com/d/msgid/spctools-discuss/38e40045-66e2-4d7e-8acf-4a9995047464%40googlegroups.com?utm_medium=email&utm_source=footer> >>> . >>> For more options, visit https://groups.google.com/d/optout. >>> >> -- > 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 post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at https://groups.google.com/group/spctools-discuss. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/161a30c8-2fa3-4a20-9683-c726ad147c14%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/161a30c8-2fa3-4a20-9683-c726ad147c14%40googlegroups.com?utm_medium=email&utm_source=footer> > . > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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