Hi David, I re-mapped it and now is working. A step forward. Now, I'm running XPRESS and I get an error when running it within iProphet, I use:
/usr/local/tpp/bin/XPressPeptideParser interact.ipro.pep.xml -m10 -a -c5 -H -b -i -nn,6.031817 -nK,6.031817 And get always: *EXECUTING: cd /home/laptop/Documents/TPP_data/TH189/comsgf ; /usr/local/tpp/bin/XPressPeptideParser interact.ipro.pep.xml -m20 -a -c5 -H -b -i -nn,6.031817 -nK,6.031817 * .................................................. 1k .................................................. 2k .....................Segmentation fault (core dumped) *Command FAILED* RETURN CODE:35584 I can run XPRESS successfully the same way, in either the Comet (PeptideProphet and iProphet) or the MSGF run separately. I can then run iPropeht on both PeptideProphet files and import the XPRESS file with success. However if I run XPRESS at the iProphet step when combining both files it gives that error. Best, Alejandro On Monday, June 10, 2019 at 6:49:43 PM UTC+2, David Shteynberg wrote: > > Hello Alejandro, > > This is a new issue so that's good, as we have made some progress. I am > not sure why ProteinProphet is telling you you have two different databases > referenced by your two searches. Can you either post your pep.xml input > file and database for me to test with ProteinProphet or post all relevant > lines referencing the database from your input files? A single file > pep.xml may contain multiple MS runs and they would all have to reference > the same database in the same way. Based on my understanding of how you've > run iProphet, I expect that you'd have a single input file to > ProteinProphet. Can you remap this file against the database and run > ProteinProphet on that? > > Thanks, > -David > > > On Mon, Jun 10, 2019 at 9:33 AM Alejandro <agome...@gmail.com > <javascript:>> wrote: > >> 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> 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. >>>> 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/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...@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/b3b5fb8b-17e5-4c64-9964-80ca01349db6%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/b3b5fb8b-17e5-4c64-9964-80ca01349db6%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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