Hi Jimmy, I am able to solve the problem from the email you replied a few days ago (where I mentioned the ratio states "unavailable"). Turns out, the problem was with the unspecified mass difference in XPress! It's producing lovely ratios now!
Many thanks!!! -Eiko On Jan 26, 12:27 am, Jimmy Eng <[email protected]> wrote: > 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: > > ... > > 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.
