Hi David, No, I haven't moved the files. I grep mzML and it has 4 instances, one for Heavy, one for Light for Comet, as well as one Heavy and one Light for MSGF. Running each independently (Comet or MSGF+) generates no error.
Thanks, Alejandro On Tuesday, June 11, 2019 at 4:27:28 PM UTC+2, David Shteynberg wrote: > > Hi Alejandro, > > It appears that XPress runs for awhile then crashes in the middle of the > file. This may indicate that different ms run in the pepxml file reference > different mzML files to extract the data, and some of those mzML references > could be incorrect. Have you moved the files around after processing? Can > you grep your file for mzML and make sure the paths are valid? Otherwise, > I would have to play with your data to troubleshoot the issue. > > Thanks, > David > > On Mon, Jun 10, 2019, 3:58 PM Alejandro <[email protected] <javascript:>> > wrote: > >> 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 <[email protected]> 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 <[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. >>>> 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/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. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To post to this group, send email to [email protected] >> <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/156c48b8-2602-4c6e-8fd0-f6aaf9b8667c%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/156c48b8-2602-4c6e-8fd0-f6aaf9b8667c%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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