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.
