Hi Alejandro, XPress might be getting confused with the way you've done the search. Can you redo the search once, using variable heavy label modification and see if it lets you quantify the results?
Thanks, -David On Tue, Jun 11, 2019 at 9:53 AM Alejandro <agomeza...@gmail.com> wrote: > 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 <agome...@gmail.com> 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 <agome...@gmail.com> 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. 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