Hi, so I tried running with probability filter "0" and included more files. The PepXMLViewer.cgi error did not pop out this time, however, the command still failed. When I tried to open the .shtml file, I get:-
could not delete /tmp/PepXMLViewera04956, error 13 "Permission denied" error: unable to read pepxml file: error parsing pepxml file: XML parsing error: no element found, at xml file line 357955, column 0 >From the tpp petunia, the command reads:- run_in c:/Inetpub/wwwroot/ISB/data/P00416; c:\Inetpub\tpp-bin \xinteract -NP00416.interact.pep.xml -p0 -l7 -Op -X-m1.0-L-c5-p1 c:/ Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B01Mix.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/ P00416/PHHUP00416G00336GL03B02Mix.tandem.pep.xml c:/Inetpub/wwwroot/ ISB/data/P00416/PHHUP00416G00336GL03B03Mix.tandem.pep.xml c:/Inetpub/ wwwroot/ISB/data/P00416/PHHUP00416G00336GL03B04Mix.tandem.pep.xml c:/ Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B05Mix.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/ P00416/PHHUP00416G00336GL03B06Mix.tandem.pep.xml c:/Inetpub/wwwroot/ ISB/data/P00416/PHHUP00416G00336GL03B07Mix.tandem.pep.xml c:/Inetpub/ wwwroot/ISB/data/P00416/PHHUP00416G00336GL03B08Mix.tandem.pep.xml c:/ Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B09Mix.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/ P00416/PHHUP00416G00336GL03B10Mix.tandem.pep.xml c:/Inetpub/wwwroot/ ISB/data/P00416/PHHUP00416G00336GL03B11Mix.tandem.pep.xml c:/Inetpub/ wwwroot/ISB/data/P00416/PHHUP00416G00336GL03B12Mix.tandem.pep.xml c:/ Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B13Mix.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/ P00416/PHHUP00416G00336GL03B14Mix.tandem.pep.xml c:/Inetpub/wwwroot/ ISB/data/P00416/PHHUP00416G00336GL03B15Mix.tandem.pep.xml c:/Inetpub/ wwwroot/ISB/data/P00416/PHHUP00416G00336GL03B16Mix.tandem.pep.xml c:/ Inetpub/wwwroot/ISB/data/P00416/taxonomy.xml c:\Inetpub\tpp-bin\xinteract (TPP v4.4 VUVUZELA rev 1, Build 201010121551 (MinGW)) running: "C:/Inetpub/tpp-bin/InteractParser "P00416.interact.pep.xml" "c:/Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B01Mix.tandem.pep.xml" "c:/Inetpub/wwwroot/ISB/ data/P00416/PHHUP00416G00336GL03B02Mix.tandem.pep.xml" "c:/Inetpub/ wwwroot/ISB/data/P00416/PHHUP00416G00336GL03B03Mix.tandem.pep.xml" "c:/ Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B04Mix.tandem.pep.xml" "c:/Inetpub/wwwroot/ISB/ data/P00416/PHHUP00416G00336GL03B05Mix.tandem.pep.xml" "c:/Inetpub/ wwwroot/ISB/data/P00416/PHHUP00416G00336GL03B06Mix.tandem.pep.xml" "c:/ Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B07Mix.tandem.pep.xml" "c:/Inetpub/wwwroot/ISB/ data/P00416/PHHUP00416G00336GL03B08Mix.tandem.pep.xml" "c:/Inetpub/ wwwroot/ISB/data/P00416/PHHUP00416G00336GL03B09Mix.tandem.pep.xml" "c:/ Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B10Mix.tandem.pep.xml" "c:/Inetpub/wwwroot/ISB/ data/P00416/PHHUP00416G00336GL03B11Mix.tandem.pep.xml" "c:/Inetpub/ wwwroot/ISB/data/P00416/PHHUP00416G00336GL03B12Mix.tandem.pep.xml" "c:/ Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B13Mix.tandem.pep.xml" "c:/Inetpub/wwwroot/ISB/ data/P00416/PHHUP00416G00336GL03B14Mix.tandem.pep.xml" "c:/Inetpub/ wwwroot/ISB/data/P00416/PHHUP00416G00336GL03B15Mix.tandem.pep.xml" "c:/ Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B16Mix.tandem.pep.xml" "c:/Inetpub/wwwroot/ISB/ data/P00416/taxonomy.xml" -L"7"" file 1: c:/Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B01Mix.tandem.pep.xml file 2: c:/Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B02Mix.tandem.pep.xml file 3: c:/Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B03Mix.tandem.pep.xml file 4: c:/Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B04Mix.tandem.pep.xml file 5: c:/Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B05Mix.tandem.pep.xml file 6: c:/Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B06Mix.tandem.pep.xml file 7: c:/Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B07Mix.tandem.pep.xml file 8: c:/Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B08Mix.tandem.pep.xml file 9: c:/Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B09Mix.tandem.pep.xml file 10: c:/Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B10Mix.tandem.pep.xml file 11: c:/Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B11Mix.tandem.pep.xml file 12: c:/Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B12Mix.tandem.pep.xml file 13: c:/Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B13Mix.tandem.pep.xml file 14: c:/Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B14Mix.tandem.pep.xml file 15: c:/Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B15Mix.tandem.pep.xml file 16: c:/Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B16Mix.tandem.pep.xml ...skipping 20 lines of output... Initialising statistical models ... negmean = 0.0533258 negmean = -3.85387 negmean = -3.79697 negmean = -0.2 negmean = -0.2 negmean = -0.2 negmean = -0.2 Iterations: .........10.........20.... WARNING: Mixture model quality test failed for charge (3+). model complete after 25 iterations error: no peptideprophet data written to file P00416.interact.pep.xml Error: file update failed, check file P00416.interact.pep.xml.tmp.a12568 for completeness command "C:/Inetpub/tpp-bin/PeptideProphetParser "P00416.interact.pep.xml" MINPROB=0" failed: Operation not permitted command "C:/Inetpub/tpp-bin/PeptideProphetParser "P00416.interact.pep.xml" MINPROB=0" exited with non-zero exit code: 1 QUIT - the job is incomplete command "c:\Inetpub\tpp-bin\xinteract -NP00416.interact.pep.xml -p0 - l7 -Op -X-m1.0-L-c5-p1 c:/Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B01Mix.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/ P00416/PHHUP00416G00336GL03B02Mix.tandem.pep.xml c:/Inetpub/wwwroot/ ISB/data/P00416/PHHUP00416G00336GL03B03Mix.tandem.pep.xml c:/Inetpub/ wwwroot/ISB/data/P00416/PHHUP00416G00336GL03B04Mix.tandem.pep.xml c:/ Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B05Mix.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/ P00416/PHHUP00416G00336GL03B06Mix.tandem.pep.xml c:/Inetpub/wwwroot/ ISB/data/P00416/PHHUP00416G00336GL03B07Mix.tandem.pep.xml c:/Inetpub/ wwwroot/ISB/data/P00416/PHHUP00416G00336GL03B08Mix.tandem.pep.xml c:/ Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B09Mix.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/ P00416/PHHUP00416G00336GL03B10Mix.tandem.pep.xml c:/Inetpub/wwwroot/ ISB/data/P00416/PHHUP00416G00336GL03B11Mix.tandem.pep.xml c:/Inetpub/ wwwroot/ISB/data/P00416/PHHUP00416G00336GL03B12Mix.tandem.pep.xml c:/ Inetpub/wwwroot/ISB/data/P00416/ PHHUP00416G00336GL03B13Mix.tandem.pep.xml c:/Inetpub/wwwroot/ISB/data/ P00416/PHHUP00416G00336GL03B14Mix.tandem.pep.xml c:/Inetpub/wwwroot/ ISB/data/P00416/PHHUP00416G00336GL03B15Mix.tandem.pep.xml c:/Inetpub/ wwwroot/ISB/data/P00416/PHHUP00416G00336GL03B16Mix.tandem.pep.xml c:/ Inetpub/wwwroot/ISB/data/P00416/taxonomy.xml" failed: Operation not permitted Command FAILED There is still an error. I changed the probability to "0", and used the default "0.05" TOO. Either way, it failed. I have no problem viewing the pepxml using the viewer, though. -Eiko On Jan 21, 11:20 pm, David Shteynberg <dshteynb...@systemsbiology.org> wrote: > You likely have no good hits in this dataset so the program assigns 0 > probability. If you apply a probability filter of 0 instead of 0.05 > (default) you will see all the spectra and the probability in the > pepXML. > > -David > > On Thu, Jan 20, 2011 at 11:03 PM, furukie <efur...@etc.a-star.edu.sg> wrote: > > Hi Brian, > > > the xinteract errors were always the same; > > >> run_in c:/Inetpub/wwwroot/ISB/data/Test; c:\Inetpub\tpp-bin\xinteract > >> -Ninteract.pep.xml -p0.05 -l7 -O c:/Inetpub/wwwroot/ISB/data/Test/ > >> PHHUP00416G00336GL03B01Mix.tandem.pep.xml > > >> c:\Inetpub\tpp-bin\xinteract (TPP v4.4 VUVUZELA rev 1, Build > >> 201010121551 (MinGW)) > > >> running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" "c:/ > >> Inetpub/wwwroot/ISB/data/Test/ > >> PHHUP00416G00336GL03B01Mix.tandem.pep.xml" -L"7"" > >> file 1: c:/Inetpub/wwwroot/ISB/data/Test/ > >> PHHUP00416G00336GL03B01Mix.tandem.pep.xml > >> processed altogether 1264 results > > >> results written to file c:/Inetpub/wwwroot/ISB/data/Test/ > >> interact.pep.xml > > >> direct your browser tohttp://localhost/ISB/data/Test/interact.pep.shtml > > >> command completed in 0 sec > > >> running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" > >> MINPROB=0.05" > >> (X! Tandem (k-score)) > >> init with X! Tandem (k-score) trypsin > >> MS Instrument info: Manufacturer: Waters, Model: q-tof micro, > >> Ionization: ESI, Analyzer: TOFMS, Detector: unknown > > >> ...skipping 20 lines of output... > > >> => Total of 0 hits. > >> command completed in 0 sec > > >> running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml"" > >> command completed in 0 sec > > >> running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" "c:/ > >> Inetpub/wwwroot/ISB/data/dbase/ipi.HUMAN.v3.62mod.fasta"" > >> - Searching the tree... > >> - Linking duplicate entries... - Printing results... > > >> - Building Commentz-Walter keyword tree...command completed in 3 > >> sec > > >> running: "C:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/ > >> wwwroot/ISB/data/Test/interact.pep.xml" > > >> command "C:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/ > >> wwwroot/ISB/data/Test/interact.pep.xml" failed: Unknown error > > >> command "C:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/ > >> wwwroot/ISB/data/Test/interact.pep.xml" exited with non-zero exit > >> code: -1073741819 > >> QUIT - the job is incomplete > > >> command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -O > >> c:/Inetpub/wwwroot/ISB/data/Test/ > >> PHHUP00416G00336GL03B01Mix.tandem.pep.xml" failed: Unknown error > > >> Command FAILED > > > I am unable to tell where the problem lies here, too. Let me know what > > you think. > > > Thank you! > > > -Eiko > > > -- > > You received this message because you are subscribed to the Google Groups > > "spctools-discuss" group. > > To post to this group, send email to spctools-discuss@googlegroups.com. > > To unsubscribe from this group, send email to > > spctools-discuss+unsubscr...@googlegroups.com. > > For more options, visit this group > > athttp://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 spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
