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]> 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] [ > [email protected]] on behalf of David Shteynberg [ > [email protected]] > *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]> 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]. >> 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. >> > > -- > 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. > > -- > 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. > -- 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.
