Hi Alejandro, I am trying (unsuccessfully) to replicate this behavior on a different iProphet combination of comet and xtandem results. Would it be possible for you to provide some test data so I can reproduce this specific bug in my environment?
Thanks, -David On Thu, Jun 13, 2019 at 6:24 AM Alejandro <[email protected]> wrote: > 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]> 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. 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]. >>>>> 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/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. >>> 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/6c375b42-55bf-47e2-badf-7aa9ac4b3f69%40googlegroups.com >>> <https://groups.google.com/d/msgid/spctools-discuss/6c375b42-55bf-47e2-badf-7aa9ac4b3f69%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/6d7beb83-2ddf-4128-9423-f14e4fbba0a3%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/6d7beb83-2ddf-4128-9423-f14e4fbba0a3%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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