Hi David, The test didn't went forward not because of TPP but because of how MSGF+ encodes the modifications. I have to troubleshoot that first. However, I don't know if that will make a big change. In TPP 5.1 and below I can do XPRESS quantitation when running iProphet of both results (Comet and MSGF). I can also do it separately in TPP 5.2 : Comet > PeptideProphet > iProphet > Xpress or MSGF > PeptideProphet > iProphet > Xpress, is just when I do iProphet of the combined Comet/MSGF+ plus Xpress that it hangs. I can also run PeptideProphet with Xpress in each (Comet or MSGF) and then combine them with iProphet and I get the quantitation results in the combined iProphet file. Just I would have to run Xpress on each search engine result.
Best, Alejandro On Tuesday, June 11, 2019 at 7:48:13 PM UTC+2, David Shteynberg wrote: > > 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 <[email protected] > <javascript:>> 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 <[email protected]> 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. 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