It looks like all the perl commands are failing. Please make sure that you have installed the ActivePerl perl interpreter. Then the directory where the perl binary is installed should be added to your path.
-David On Dec 3, 2012 9:41 PM, "apauls" <[email protected]> wrote: > Hello, > > I have since noticed this persistent error while analyzing a large set of > iTRAQ-labeled LCMS data. Though X!tandem search appears to work okay, it > however returns a disproportionately less number of NXT/S motif containing > peptides for a glycocapture experiment than expected. In addition, running > Xinteract returns the following error in an example batch analysis: > > > c:/Inetpub/wwwroot/ISB/data/Projects/GlycoMotif/Humans/CPTAC/batch2/cptac_batch2_interact.pep.shtml > (file not found: not created or deleted?) > > > run_in > c:/Inetpub/wwwroot/ISB/data/Projects/GlycoMotif/Humans/CPTAC/batch2; > c:\Inetpub\tpp-bin\xinteract -Ncptac_batch2_interact.pep.xml -p0.05 -l7 -O > cptac_p5p6_itraq4_glycopep.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_10.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_11.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_12.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_2.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_3.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_4.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_5.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_6.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_7.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_8.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_9.tandem.pep.xml > > > c:\Inetpub\tpp-bin\xinteract (TPP v4.5 RAPTURE rev 2, Build 201202031108 > (MinGW)) > > running: "C:/Inetpub/tpp-bin/InteractParser > "cptac_batch2_interact.pep.xml" "cptac_p5p6_itraq4_glycopep.tandem.pep.xml" > "cptac_p5p6_itraq4_glycopep_fraction_10.tandem.pep.xml" > "cptac_p5p6_itraq4_glycopep_fraction_11.tandem.pep.xml" > "cptac_p5p6_itraq4_glycopep_fraction_12.tandem.pep.xml" > "cptac_p5p6_itraq4_glycopep_fraction_2.tandem.pep.xml" > "cptac_p5p6_itraq4_glycopep_fraction_3.tandem.pep.xml" > "cptac_p5p6_itraq4_glycopep_fraction_4.tandem.pep.xml" > "cptac_p5p6_itraq4_glycopep_fraction_5.tandem.pep.xml" > "cptac_p5p6_itraq4_glycopep_fraction_6.tandem.pep.xml" > "cptac_p5p6_itraq4_glycopep_fraction_7.tandem.pep.xml" > "cptac_p5p6_itraq4_glycopep_fraction_8.tandem.pep.xml" > "cptac_p5p6_itraq4_glycopep_fraction_9.tandem.pep.xml" -L"7"" > file 1: cptac_p5p6_itraq4_glycopep.tandem.pep.xml > file 2: cptac_p5p6_itraq4_glycopep_fraction_10.tandem.pep.xml > file 3: cptac_p5p6_itraq4_glycopep_fraction_11.tandem.pep.xml > file 4: cptac_p5p6_itraq4_glycopep_fraction_12.tandem.pep.xml > file 5: cptac_p5p6_itraq4_glycopep_fraction_2.tandem.pep.xml > file 6: cptac_p5p6_itraq4_glycopep_fraction_3.tandem.pep.xml > file 7: cptac_p5p6_itraq4_glycopep_fraction_4.tandem.pep.xml > file 8: cptac_p5p6_itraq4_glycopep_fraction_5.tandem.pep.xml > file 9: cptac_p5p6_itraq4_glycopep_fraction_6.tandem.pep.xml > file 10: cptac_p5p6_itraq4_glycopep_fraction_7.tandem.pep.xml > file 11: cptac_p5p6_itraq4_glycopep_fraction_8.tandem.pep.xml > file 12: cptac_p5p6_itraq4_glycopep_fraction_9.tandem.pep.xml > processed altogether 113689 results > The system cannot find message text for message number 0x2331 in the > message file for Application. > command completed in 48 sec > > > ...skipping 22 lines of output... > > WARNING: Found semi-cleavage in refinement mode and semi-cleavage not used > in the first pass. Turning off NTT model. > WARNING: Found semi-cleavage in refinement mode and semi-cleavage not used > in the first pass. Turning off NTT model. > MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: > UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN > > PeptideProphet (TPP v4.5 RAPTURE rev 2, Build 201202031108 (MinGW)) > AKeller@ISB > read in 0 1+, 45270 2+, 53863 3+, 12778 4+, 0 5+, 0 6+, and 0 7+ spectra. > Initialising statistical models ... > Iterations: .........10.........20.........30. > model complete after 32 iterations > command completed in 21 sec > > running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i > cptac_batch2_interact.pep.xml" > The system cannot find message text for message number 0x2331 in the > message file for Application. > > command "perl C:/Inetpub/tpp-bin/ProphetModels.pl -i > cptac_batch2_interact.pep.xml" failed: Operation not permitted > > command "C:/Inetpub/tpp-bin/ProphetModels.pl -i > cptac_batch2_interact.pep.xml" exited with non-zero exit code: 1 > QUIT - the job is incomplete > > command "c:\Inetpub\tpp-bin\xinteract -Ncptac_batch2_interact.pep.xml > -p0.05 -l7 -O cptac_p5p6_itraq4_glycopep.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_10.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_11.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_12.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_2.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_3.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_4.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_5.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_6.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_7.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_8.tandem.pep.xml > cptac_p5p6_itraq4_glycopep_fraction_9.tandem.pep.xml" failed: Operation not > permitted > > Command FAILED > > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/spctools-discuss/-/THi7vPShPgMJ. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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