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.
