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 [email protected]. To post to this group, send email to [email protected]. 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. For more options, visit https://groups.google.com/d/optout.
