Try renaming the mzXMl file to "F030382.mzXML", maybe? On Mon, Jun 28, 2010 at 4:37 PM, Jing Wang <[email protected]> wrote:
> Hi Brian, > > I ran the Mascot search again with "trypsin" as enzyme, instead of > tryspin/P. The .dat file was able to convert to .pep.xml file successfully > (cool!). Well, there is a warning at the end of the command lines, and I > don't know how important this is. > > "....... > > 333. opening 334spectrum.0000.0000.3.out > > > > warning: cannot open "c:/Inetpub/wwwroot/ISB/data/SSM411/F030382.mzXML" > for reading MS instrument info. > > *Command Successful"* > > When I ran "Analyze Peptides" for the next step, It failed. It seemed > can't find .mzXML file (MS data?). There is the mzXML file in the same > folder. > > > see following error message: > > # Commands for session NYDW4ZIZ7 on Mon Jun 28 16:24:38 2010 > > # BEGIN COMMAND BLOCK > > ###### BEGIN Command Execution ###### > > [Mon Jun 28 16:24:38 2010] EXECUTING: run_in > c:/Inetpub/wwwroot/ISB/data/SSM411; c:\Inetpub\tpp-bin\xinteract > -NSSM411.pep.xml -p0.05 -l1 -Oi -X-m1.0-nC,9.0 -A-lC-r0.5-mC9.0 > c:/Inetpub/wwwroot/ISB/data/SSM411/F030382.pep.xml > > OUTPUT: > > > > c:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909091257 > (MinGW)) > > > > running: "C:/Inetpub/tpp-bin/InteractParser "SSM411.pep.xml" > "c:/Inetpub/wwwroot/ISB/data/SSM411/F030382.pep.xml" -L"1"" > > file 1: c:/Inetpub/wwwroot/ISB/data/SSM411/F030382.pep.xml > > processed altogether 238 results > > > > results written to file c:/Inetpub/wwwroot/ISB/data/SSM411/SSM411.pep.xml > > > direct your browser to http://localhost/ISB/data/SSM411/SSM411.pep.shtml > > > > command completed in 0 sec > > > > running: "C:/Inetpub/tpp-bin/PeptideProphetParser "SSM411.pep.xml" > MINPROB=0.05 ICAT" > > (MASCOT) (icat) > > results for charge 1: 0 id tot and 0 adj scores > > results for charge 2: 189 id tot and 55 adj scores > > results for charge 2: 21.2543 adj_ion_mean and 25.4733 adj_ion_hom mean > 23.7547id mean0.908354 correlation (r) > > 2+ ion - id = 0.988351*(ion - hom) + -3.92233 with error = 4.05281 > > mean ion - id: 21.2543, mean ion - hom: 25.4733 > > results for charge 3: 49 id tot and 16 adj scores > > results for charge 4: 0 id tot and 0 adj scores > > results for charge 5: 0 id tot and 0 adj scores > > results for charge 6: 0 id tot and 0 adj scores > > results for charge 6: -0 adj_ion_mean and -0 adj_ion_hom mean 0id meannan > correlation (r) > > results for charge 7: 0 id tot and 0 adj scores > > init with MASCOT trypsin > > MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: > UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN > > > > PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 200909091257 (MinGW)) > akel...@isb > > read in 0 1+, 188 2+, 49 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. > > Initialising statistical models ... > > Iterations: .........10.........20.... > > model complete after 25 iterations > > command completed in 0 sec > > > > running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i SSM411.pep.xml" > > Analyzing SSM411.pep.xml ... > > Parsing search results "c:/Inetpub/wwwroot/ISB/data/SSM411/F030382 > (MASCOT)"... > > => Total of 154 hits. > > command completed in 1 sec > > > > running: "C:/Inetpub/tpp-bin/XPressPeptideParser "SSM411.pep.xml" -m1.0 > -nC,9.0" > > WARNING: Found more than one variable mod on 'C'. > > XPRESS error - cannot open file from basename > c:/Inetpub/wwwroot/ISB/data/SSM411/F030382, will try to derive from scan names > > scan-derived scan file c:/Inetpub/wwwroot/ISB/data/SSM411/.mzXML (from ) not > found, cannot proceed... > > > > command "C:/Inetpub/tpp-bin/XPressPeptideParser "SSM411.pep.xml" -m1.0 > -nC,9.0" failed: Operation not permitted > > > > command "C:/Inetpub/tpp-bin/XPressPeptideParser "SSM411.pep.xml" -m1.0 > -nC,9.0" exited with non-zero exit code: 1 > > QUIT - the job is incomplete > > > > command "c:\Inetpub\tpp-bin\xinteract -NSSM411.pep.xml -p0.05 -l1 -Oi > -X-m1.0-nC,9.0 -A-lC-r0.5-mC9.0 > c:/Inetpub/wwwroot/ISB/data/SSM411/F030382.pep.xml" failed: Operation not > permitted > > END OUTPUT > > RETURN CODE:256 > > ###### End Command Execution ###### > > # All finished at Mon Jun 28 16:24:39 2010 > > # END COMMAND BLOCK > > > > Any suggestion for fixing this? > > Thanks in advance > > Jing > > > > On Thu, Jun 24, 2010 at 8:06 AM, Brian Pratt <[email protected]>wrote: > >> Not everyone has read access to the ISB's FTP server (including me), which >> is why I said "upload your new mascot result file to the files area at >> http://groups.google.com/group/spctools-discuss?hl=en. " >> >> Anyway, there are two problems: >> 1) 'error: enzyme in search constraint "Trypsin/P" is not recognized' >> 2) the above message doesn't appear by default and the program fails >> silently >> >> I'll check in a fix for the second problem. >> > > -- > 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]<spctools-discuss%[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.
