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 <javascript:>> > 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 <javascript:>. >> To post to this group, send email to spctools...@googlegroups.com >> <javascript:>. >> 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. For more options, visit https://groups.google.com/d/optout.
