HI David, Sorry for the late reply, I was out of town.
Thanks for looking into it. I recompiled and installed the revision 7932. It now runs iProphet with those files! However, ProteinProphet now fails with the following error: COMMAND 1 [MON JUN 10 18:28:57 2019] show *EXECUTING: cd /home/laptop/Documents/TPP_data/TH189 ; /usr/local/tpp/bin/ProteinProphet /home/laptop/Documents/TPP_data/TH189/interact_comsgf_v2.ipro.pep.xml /home/laptop/Documents/TPP_data/TH189/interact_comsgf.prot.xml IPROPHET * ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.2.1-dev Flammagenitus, Build 201906101745-7932 (Linux-x86_64)) (no FPKM) (using iProphet probs) (using degen pep info) Reading in /home/laptop/Documents/TPP_data/TH189/interact_comsgf_v2.ipro.pep.xml...Error: multiple databases referenced by /home/laptop/Documents/TPP_data/TH189/interact_comsgf_v2.ipro.pep.xml Use RefreshParser to update all input files to common database *Command FAILED* RETURN CODE:256 I have double check the Comet and MSGF pep.xml files and they map to the same database, using the same structure. In any case I remap the files, and it stills gives me the same error. Best, Alejandro On Tuesday, June 4, 2019 at 2:58:12 AM UTC+2, David Shteynberg wrote: > > Hello Alejandro, > > I have committed a fix for this problem. Would you mind seeing if it > works on your end? The revision number is 7932. Thanks for reporting the > issue and helping to make the TPP better. > > Cheers, > -David > > > > On Mon, Jun 3, 2019 at 1:45 AM Alejandro <agome...@gmail.com <javascript:>> > 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...@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/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. 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/b3b5fb8b-17e5-4c64-9964-80ca01349db6%40googlegroups.com. For more options, visit https://groups.google.com/d/optout.
