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.
