Can ypu post your msgf and comet results for me to download and test. Please let me know. Also if you are at ASMS, stip by our booth and I can get your dataset to test there.
Cheers, David On Mon, Jun 3, 2019, 4:45 AM Alejandro <[email protected]> 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 <[email protected]> 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 [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 >>> <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 [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/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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