Hello David, Thank you for your quick fix! It seems that fixed PeptideProphet, but now ProteinProphet is failing:
running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/Kac.GluC.all.interact.pep.xml" command completed in 4 sec running: "C:/Inetpub/tpp-bin/ProteinProphet "Kac.GluC.all.interact.pep.xml" "Kac.GluC.all.interact.prot.xml" XML" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v4.8.0 PHILAE, Build 201411201551-6764 (mingw-i686)) (xml input) (no FPKM) (report Protein Length) (using degen pep info) . . . reading in c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/kac.gluc.all.interact.pep.xml. . . . . . read in 0 1+, 8221 2+, 10337 3+, 5278 4+, 1927 5+, 139 6+, 47 7+ spectra with min prob 0.05 This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information. command "C:/Inetpub/tpp-bin/ProteinProphet "Kac.GluC.all.interact.pep.xml" "Kac.GluC.all.interact.prot.xml" XML" failed: Unknown error command "C:/Inetpub/tpp-bin/ProteinProphet "Kac.GluC.all.interact.pep.xml" "Kac.GluC.all.interact.prot.xml" XML" exited with non-zero exit code: 255 QUIT - the job is incomplete *Command FAILED* RETURN CODE:65280 On Friday, July 24, 2015 at 1:07:43 PM UTC-7, David Shteynberg wrote: > > Hello Jesse, > > I tracked this issue to a problem with InteractParser.exe, there was a bug > that I patched. Unfortunately, while sourceforge is restoring services SVN > is not yet available for me to commit the code. Meanwhile, I have built a > windows binary that you can use instead of your current copy of > InteractParser.exe. Please download the windows binary from my dropbox at > this link https://dl.dropboxusercontent.com/u/21286225/InteractParser.exe > to replace your existing copy, then rerun the xinteract command. > > Please let me know if for some reason it fails for you. > > Thank you, > -David > > On Thu, Jul 23, 2015 at 2:00 PM, Jesse G Meyer <[email protected] > <javascript:>> wrote: > >> Hi David, >> >> I just sent you a link to the files with my new email address. I tried >> without the pI model and I got the same error. I suspect a problem with >> the network settings on the computers at work. >> >> Thanks for looking into this for me. >> >> Best, >> Jesse >> ------------------------------ >> *From:* [email protected] <javascript:> [ >> [email protected] <javascript:>] on behalf of David >> Shteynberg [[email protected] <javascript:>] >> *Sent:* Thursday, July 23, 2015 11:58 AM >> *To:* spctools-discuss >> *Subject:* Re: [spctools-discuss] Re: Processing MSGF+ searches >> >> Hello Jesse, >> >> >> I am not sure that I can pinpoint the error without access to your >> file. Is this possible? Otherwise you can try the analysis with the >> following PeptideProphetParser options removing PI model which has not been >> extensively tested through MSGF+ and could be the culprit. >> >> PeptideProphetParser >> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml" MINPROB=0.0 CLEVEL=2.5 >> PPM DECOYPROBS ACCMASS NONTT NONPARAM DECOY=XXX_ IGNORECHG=1 >> >> If this works then the problem is with the pI model. >> >> Let me know if you can forward me your test.interact.pep.xml file to >> test with. >> >> Thank you, >> -David >> >> On Wed, Jul 22, 2015 at 7:57 PM, Jesse <[email protected] <javascript:>> >> wrote: >> >>> Hi David, >>> >>> I'm having problems recently running PeptideProphet on MSGF+ search >>> output of GluC digests. I tried the perl script you suggest but I'm not >>> sure if it does anything because I'm not sure what it is supposed to do. >>> That line is meant to replace a single "\" with "-", correct? It seems to >>> start OK but then it quits. The GUI then prints return code: 65280. If >>> you could make a quick suggestion as to whether you think the problem is my >>> pep.xml files again or my install I would greatly appreciate it. I tried >>> both the development release and 4.8. >>> >>> C:/TPP/bin/xinteract (TPP v5.0.0a2 Development, Build xxxx-xxxx (x86_64)) >>> PPM mode in Accurate Mass Model ... >>> PPM mode in Accurate Mass Model ... >>> >>> running: "C:/TPP/bin/InteractParser >>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml" >>> "150624_0002_CR1_GluC_Xyl_0p4_rep1b.pep.XML" >>> "150624_0003_CR1_GluC_Xyl_4_rep1.pep.XML" >>> "150624_0004_CR1_GluC_Glc_0p4_rep1.pep.XML" >>> "150624_0005_CR1_GluC_Glc_4_rep1.pep.XML" >>> "150624_0007_CR1_GluC_Xyl_0p4_rep2.pep.XML" >>> "150624_0008_CR1_GluC_Xyl_4_rep2.pep.XML" >>> "150624_0009_CR1_GluC_Glc_0p4_rep2.pep.XML" >>> "150624_0010_CR1_GluC_Glc_4_rep2.pep.XML" >>> "150624_0012_CR1_GluC_Xyl_0p4_rep3.pep.XML" >>> "150624_0014_CR1_GluC_Xyl_4_rep3.pep.XML" >>> "150624_0015_CR1_GluC_Glc_0p4_rep3.pep.XML" >>> "150624_0016_CR1_GluC_Glc_4_rep3.pep.XML" -L"7" -E"nonspecific"" >>> file 1: 150624_0002_CR1_GluC_Xyl_0p4_rep1b.pep.XMLWARNING: empty raw_data >>> in msms_run_summary tag ... trying mzML ... >>> Failed to open input file >>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0002_CR1_GluC_Xyl_0p4_rep1b.mzML'.WARNING: >>> cannot open data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0002_CR1_GluC_Xyl_0p4_rep1b.mzML >>> in msms_run_summary tag ...... trying .mzXML ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0002_CR1_GluC_Xyl_0p4_rep1b.mzXML >>> in msms_run_summary tag ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0002_CR1_GluC_Xyl_0p4_rep1b.mzXML >>> in msms_run_summary tag ... >>> file 2: 150624_0003_CR1_GluC_Xyl_4_rep1.pep.XMLWARNING: empty raw_data in >>> msms_run_summary tag ... trying mzML ... >>> Failed to open input file >>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0003_CR1_GluC_Xyl_4_rep1.mzML'.WARNING: >>> cannot open data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0003_CR1_GluC_Xyl_4_rep1.mzML >>> in msms_run_summary tag ...... trying .mzXML ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0003_CR1_GluC_Xyl_4_rep1.mzXML >>> in msms_run_summary tag ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0003_CR1_GluC_Xyl_4_rep1.mzXML >>> in msms_run_summary tag ... >>> file 3: 150624_0004_CR1_GluC_Glc_0p4_rep1.pep.XMLWARNING: empty raw_data >>> in msms_run_summary tag ... trying mzML ... >>> Failed to open input file >>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0004_CR1_GluC_Glc_0p4_rep1.mzML'.WARNING: >>> cannot open data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0004_CR1_GluC_Glc_0p4_rep1.mzML >>> in msms_run_summary tag ...... trying .mzXML ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0004_CR1_GluC_Glc_0p4_rep1.mzXML >>> in msms_run_summary tag ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0004_CR1_GluC_Glc_0p4_rep1.mzXML >>> in msms_run_summary tag ... >>> file 4: 150624_0005_CR1_GluC_Glc_4_rep1.pep.XMLWARNING: empty raw_data in >>> msms_run_summary tag ... trying mzML ... >>> Failed to open input file >>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0005_CR1_GluC_Glc_4_rep1.mzML'.WARNING: >>> cannot open data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0005_CR1_GluC_Glc_4_rep1.mzML >>> in msms_run_summary tag ...... trying .mzXML ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0005_CR1_GluC_Glc_4_rep1.mzXML >>> in msms_run_summary tag ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0005_CR1_GluC_Glc_4_rep1.mzXML >>> in msms_run_summary tag ... >>> file 5: 150624_0007_CR1_GluC_Xyl_0p4_rep2.pep.XMLWARNING: empty raw_data >>> in msms_run_summary tag ... trying mzML ... >>> Failed to open input file >>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0007_CR1_GluC_Xyl_0p4_rep2.mzML'.WARNING: >>> cannot open data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0007_CR1_GluC_Xyl_0p4_rep2.mzML >>> in msms_run_summary tag ...... trying .mzXML ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0007_CR1_GluC_Xyl_0p4_rep2.mzXML >>> in msms_run_summary tag ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0007_CR1_GluC_Xyl_0p4_rep2.mzXML >>> in msms_run_summary tag ... >>> file 6: 150624_0008_CR1_GluC_Xyl_4_rep2.pep.XMLWARNING: empty raw_data in >>> msms_run_summary tag ... trying mzML ... >>> Failed to open input file >>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0008_CR1_GluC_Xyl_4_rep2.mzML'.WARNING: >>> cannot open data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0008_CR1_GluC_Xyl_4_rep2.mzML >>> in msms_run_summary tag ...... trying .mzXML ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0008_CR1_GluC_Xyl_4_rep2.mzXML >>> in msms_run_summary tag ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0008_CR1_GluC_Xyl_4_rep2.mzXML >>> in msms_run_summary tag ... >>> file 7: 150624_0009_CR1_GluC_Glc_0p4_rep2.pep.XMLWARNING: empty raw_data >>> in msms_run_summary tag ... trying mzML ... >>> Failed to open input file >>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0009_CR1_GluC_Glc_0p4_rep2.mzML'.WARNING: >>> cannot open data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0009_CR1_GluC_Glc_0p4_rep2.mzML >>> in msms_run_summary tag ...... trying .mzXML ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0009_CR1_GluC_Glc_0p4_rep2.mzXML >>> in msms_run_summary tag ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0009_CR1_GluC_Glc_0p4_rep2.mzXML >>> in msms_run_summary tag ... >>> file 8: 150624_0010_CR1_GluC_Glc_4_rep2.pep.XMLWARNING: empty raw_data in >>> msms_run_summary tag ... trying mzML ... >>> Failed to open input file >>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0010_CR1_GluC_Glc_4_rep2.mzML'.WARNING: >>> cannot open data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0010_CR1_GluC_Glc_4_rep2.mzML >>> in msms_run_summary tag ...... trying .mzXML ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0010_CR1_GluC_Glc_4_rep2.mzXML >>> in msms_run_summary tag ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0010_CR1_GluC_Glc_4_rep2.mzXML >>> in msms_run_summary tag ... >>> file 9: 150624_0012_CR1_GluC_Xyl_0p4_rep3.pep.XMLWARNING: empty raw_data >>> in msms_run_summary tag ... trying mzML ... >>> Failed to open input file >>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0012_CR1_GluC_Xyl_0p4_rep3.mzML'.WARNING: >>> cannot open data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0012_CR1_GluC_Xyl_0p4_rep3.mzML >>> in msms_run_summary tag ...... trying .mzXML ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0012_CR1_GluC_Xyl_0p4_rep3.mzXML >>> in msms_run_summary tag ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0012_CR1_GluC_Xyl_0p4_rep3.mzXML >>> in msms_run_summary tag ... >>> file 10: 150624_0014_CR1_GluC_Xyl_4_rep3.pep.XMLWARNING: empty raw_data in >>> msms_run_summary tag ... trying mzML ... >>> Failed to open input file >>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0014_CR1_GluC_Xyl_4_rep3.mzML'.WARNING: >>> cannot open data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0014_CR1_GluC_Xyl_4_rep3.mzML >>> in msms_run_summary tag ...... trying .mzXML ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0014_CR1_GluC_Xyl_4_rep3.mzXML >>> in msms_run_summary tag ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0014_CR1_GluC_Xyl_4_rep3.mzXML >>> in msms_run_summary tag ... >>> file 11: 150624_0015_CR1_GluC_Glc_0p4_rep3.pep.XMLWARNING: empty raw_data >>> in msms_run_summary tag ... trying mzML ... >>> Failed to open input file >>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0015_CR1_GluC_Glc_0p4_rep3.mzML'.WARNING: >>> cannot open data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0015_CR1_GluC_Glc_0p4_rep3.mzML >>> in msms_run_summary tag ...... trying .mzXML ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0015_CR1_GluC_Glc_0p4_rep3.mzXML >>> in msms_run_summary tag ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0015_CR1_GluC_Glc_0p4_rep3.mzXML >>> in msms_run_summary tag ... >>> file 12: 150624_0016_CR1_GluC_Glc_4_rep3.pep.XMLWARNING: empty raw_data in >>> msms_run_summary tag ... trying mzML ... >>> Failed to open input file >>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0016_CR1_GluC_Glc_4_rep3.mzML'.WARNING: >>> cannot open data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0016_CR1_GluC_Glc_4_rep3.mzML >>> in msms_run_summary tag ...... trying .mzXML ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0016_CR1_GluC_Glc_4_rep3.mzXML >>> in msms_run_summary tag ... >>> SUCCESS: CORRECTED data file >>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0016_CR1_GluC_Glc_4_rep3.mzXML >>> in msms_run_summary tag ... >>> processed altogether 186504 results >>> INFO: Results written to file: >>> C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml >>> command completed in 86 sec >>> >>> running: "C:/TPP/bin/DatabaseParser >>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml"" >>> command completed in 2 sec >>> >>> running: "C:/TPP/bin/RefreshParser >>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml" "C:\Jesse\Ecoli.fasta"" >>> - Searching the tree...opening "c:/Jesse/Ecoli.fasta" as >>> "c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/Ecoli.fasta" >>> >>> - Linking duplicate entries... - Printing results... >>> >>> - Building Commentz-Walter keyword tree...command completed in 22 sec >>> >>> running: "C:/TPP/bin/PeptideProphetParser >>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml" MINPROB=0.05 CLEVEL=2.5 >>> PPM PPM ACCMASS PI NONTT NONPARAM DECOY=XXX_ IGNORECHG=1" >>> using Accurate Mass Bins >>> using PPM mass difference >>> using pI >>> Using Decoy Label "XXX_". >>> Ignoring charge 1+ spectra. >>> Not using ntt model >>> Using non-parametric distributions >>> (MS-GF+)WARNING: Support of MSGF+ may not be full. There exist known >>> issues with the way MSGF+ encodes certain modifications in pep.xml that may >>> not be correct. Also, high-scoring DECOY have been observed in MSGF+ >>> analysis. The user is encouraged to be vigilant in comparing model >>> estimated error-rates to the DECOY-estimated error-rates to make sure the >>> two agree and set CLEVEL parameter accordingly: see >>> http://tools.proteomecenter.org/wiki/index.php?title=TPP:Frequently_Asked_Questions#What_is_CLEVEL_and_when_do_I_use_it.3F >>> adding Accurate Mass mixture distr >>> adding pI mixture distr >>> init with MS-GF+ nonspecific >>> >>> command "C:/TPP/bin/PeptideProphetParser >>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml" MINPROB=0.05 CLEVEL=2.5 >>> PPM PPM ACCMASS PI NONTT NONPARAM DECOY=XXX_ IGNORECHG=1" failed: Unknown >>> error >>> >>> command "C:/TPP/bin/PeptideProphetParser >>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml" MINPROB=0.05 CLEVEL=2.5 >>> PPM PPM ACCMASS PI NONTT NONPARAM DECOY=XXX_ IGNORECHG=1" exited with >>> non-zero exit code: 255 >>> QUIT - the job is incomplete >>> >>> >>> On Thursday, July 9, 2015 at 2:33:16 PM UTC-7, [email protected] wrote: >>>> >>>> Hi David, >>>> >>>> I can cope with the command line. Thanks for the info I never would >>>> have worked that one out... >>>> >>>> Peter >>>> >>>> On Thursday, July 9, 2015 at 2:55:41 PM UTC+10, [email protected] >>>> wrote: >>>>> >>>>> Hi, >>>>> >>>>> >>>>> I want to use the TPP to combine, Mascot, X!Tandem and MSGF+ searches >>>>> (amongst other things). I'm having trouble getting around some of the >>>>> basics. I have successfully used the TPP in the past to process samples, >>>>> but only with Mascot data. >>>>> >>>>> Once I get my MSGF+ output files converted to pepXML I should be >>>>> fine. I cannot work out how I get the MSGF+ files converted. The output >>>>> generated by MSGF+ is an mzid file. I am also unclear as to where the >>>>> database (with decoys) and mzXML files, used for searching, need to be >>>>> located when generating this pepXML file. I have noticed error messages >>>>> in >>>>> the logs about accessing the database and mzXML file. I am generally >>>>> using >>>>> the Petunia interface as it's much nicer to work with multiple files. >>>>> >>>>> >>>>> Thanks, >>>>> >>>>> >>>>> Peter >>>>> >>>> -- >>> 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 http://groups.google.com/group/spctools-discuss. >>> 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 http://groups.google.com/group/spctools-discuss. >> 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 http://groups.google.com/group/spctools-discuss. >> 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 http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
