XPRESS had a bug in TPP 4.4.0 which was addressed in TPP 4.4.1. What solution to what problem are you looking for?
On Tue, Jan 25, 2011 at 2:18 AM, furukie <[email protected]> wrote: > 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. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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