Hi- Thanks for the response. I always have it set to "trypsin" when converting the Sequest search results to pepXML within the TPP. Is there another place to specify enzyme? I have the same boxes checked for peptideprophet that I always used when going through the pipeline. One other thing I noticed was that in this new version of TPP I have the option of doing a 'semi-enzyme' process, which is actually what the original search is using. So I have now tried doing the pepXML conversion with straight 'trypsin' or with this extra 'semi' box checked also. Both of them create this failure. I have also tried it with specifying the sequest.params file during pepXML conversion or without specifying it, and get the same error either way. I also don't understand where "MALDI mode" comes from in the log listed below. I am not using MALDI data and I do not check the "MALDI data" box.
Any help is much appreciated!! R On Mon, Feb 27, 2012 at 11:27 AM, [email protected] < [email protected]> wrote: > Please try to rerun the pipeline once specifying the enzyme to see if that > helps. > > Sent from my Android Device > > > ----- Reply message ----- > From: "Ruby" <[email protected]> > To: "spctools-discuss" <[email protected]> > Subject: [spctools-discuss] PeptideProphet error in 4.5.2 > Date: Mon, Feb 27, 2012 7:02 am > > > 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. > > -- > 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. > -- 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.
