I have been using TPP 4.0 for over a year with no issues. Last week I upgraded to 4.5.2 and can't get PeptideProphet to work. I"m not doing anything in terms of how I proceed through the pipeline and what settings I use. I get the following error and I get it whether I try to do the pep.XML conversion in this version of TPP, or whether I use pepXML files generated using the previous version of TPP (and which worked fine in peptideprophet before). Any help would be much appreciated!
Command 1 [Mon Feb 27 08:52:22 2012] [ Show / Hide ] run_in c:/Inetpub/wwwroot/ISB/data/Olaf/OR_8; c:\Inetpub\tpp-bin \xinteract -Now_8_1-3.pep.xml -p0.05 -l7 -OAgx -I1 - OT2_Gundry_2012-02-21_OR-08_1.pep.xml - OT2_Gundry_2012-02-21_OR-08_2.pep.xml - OT2_Gundry_2012-02-21_OR-08_3.pep.xml c:\Inetpub\tpp-bin\xinteract (TPP v4.5 RAPTURE rev 2, Build 201202031108 (MinGW)) running: "C:/Inetpub/tpp-bin/InteractParser "ow_8_1-3.pep.xml" -L"7"" processed altogether 0 results ERROR: output file created, c:/Inetpub/wwwroot/ISB/data/Olaf/OR_8/ ow_8_1-3.pep.xml, appears incomplete. Please check the input files for completeness. results written to file c:/Inetpub/wwwroot/ISB/data/Olaf/OR_8/ ow_8_1-3.pep.xml direct your browser to http://localhost/ISB/data/Olaf/OR_8/ow_8_1-3.pep.shtml command completed in 0 sec running: "C:/Inetpub/tpp-bin/DatabaseParser "ow_8_1-3.pep.xml"" command completed in 0 sec No single database specified (by -D option or in .pep.xml file). RefreshParser skipped. running: "C:/Inetpub/tpp-bin/PeptideProphetParser "ow_8_1-3.pep.xml" MINPROB=0.05 ACCMASS GLYC EXCLUDE IGNORECHG=1 NEGGAMMA NONEGINIT DECOYPROBS RT EXCLUDE MALDI LEAVE NEGGAMMA NONEGINIT DECOYPROBS RT EXCLUDE MALDI LEAVE NEGGAMMA NONEGINIT DECOYPROBS RT EXCLUDE MALDI LEAVE" using Accurate Mass Bins using RT using N-glyc info maldi mode Ignoring charge 1+ spectra. Using hardcoded values to initialize the distributions. Using Gamma Distribution to model the negative hits. MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN Error: file update failed (did not find closing tag "</ msms_pipeline_analysis>"), check file ow_8_1-3.pep.xml.tmp.a04004 for completeness error: no peptideprophet data written to file ow_8_1-3.pep.xml command "C:/Inetpub/tpp-bin/PeptideProphetParser "ow_8_1-3.pep.xml" MINPROB=0.05 ACCMASS GLYC EXCLUDE IGNORECHG=1 NEGGAMMA NONEGINIT DECOYPROBS RT EXCLUDE MALDI LEAVE NEGGAMMA NONEGINIT DECOYPROBS RT EXCLUDE MALDI LEAVE NEGGAMMA NONEGINIT DECOYPROBS RT EXCLUDE MALDI LEAVE" failed: Operation not permitted command "C:/Inetpub/tpp-bin/PeptideProphetParser "ow_8_1-3.pep.xml" MINPROB=0.05 ACCMASS GLYC EXCLUDE IGNORECHG=1 NEGGAMMA NONEGINIT DECOYPROBS RT EXCLUDE MALDI LEAVE NEGGAMMA NONEGINIT DECOYPROBS RT EXCLUDE MALDI LEAVE NEGGAMMA NONEGINIT DECOYPROBS RT EXCLUDE MALDI LEAVE" exited with non-zero exit code: 1 QUIT - the job is incomplete command "c:\Inetpub\tpp-bin\xinteract -Now_8_1-3.pep.xml -p0.05 -l7 - OAgx -I1 -OT2_Gundry_2012-02-21_OR-08_1.pep.xml - OT2_Gundry_2012-02-21_OR-08_2.pep.xml - OT2_Gundry_2012-02-21_OR-08_3.pep.xml" failed: Operation not permitted Command FAILED -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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.
