Hi, I managed to solve my problem and its running successfully! I am still having slight problems with the XPress ratio, though. I'm still reading about the error that's been previously posted by others. Hopefully the solution is out there!
Thanks for the help! -Eiko On Jan 24, 7:30 pm, furukie <[email protected]> wrote: > 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 <[email protected]> > 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 <[email protected]> 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 > > ... > > read more » -- 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.
