Hi Jimmy, Yes, I also checked the .tandem file there were peptides with low expect score. I also looked at the .pep.xml file and checked that the scans, hyperscore, nextscore, bscore, ... matched the .tandem file.
I am puzzled why the run_in doesn't work and wondering if this is affecting the xinteract command as well. any ideas? Lik Wee On Wed, Mar 10, 2010 at 2:20 PM, Jimmy Eng <[email protected]> wrote: > I suggest you start debugging the problem one step at a time. > First confirm that your Tandem search actually ran by looking at > contents of the .tandem file. > Next, check contents of tandem.pep.xml. > Do both of these files look like they have peptide IDs in them? > > > > On Wed, Mar 10, 2010 at 2:04 PM, Lik Wee Lee <[email protected]> > wrote: > > Furthermore, I also did: > > C:\Inetpub\wwwroot\ISB\data\17mix>c:\Inetpub\tpp-bin\Tandem2XML > > c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem > > > c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem.pep.xml > > > > but if I tried to browse file in petunia and click on [PepXML], > > it opens a new window: > > > http://localhost/tpp-bin/PepXMLViewer.cgi?xmlFileName=c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem.pep.xml > > > > but with the message: > > > > error: > > can't open html > > templatec:/Inetpub/wwwroot;c:/Inetpub/wwwroot/ISB/html/PepXMLViewer.html > > > > I also had problem with xinteract: > > > > C:\Inetpub\wwwroot\ISB\data\17mix\tandem>c:\Inetpub\tpp-bin\xinteract > > -Ninteract.pep.xml -p0.05 -l7 -O > > > c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem.pep.xml > > > > c:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build > 200909091257 > > (MinGW)) > > > > running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" > > "c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tand > > em.pep.xml" -L"7"" > > > > command "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" > > "c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tande > > m.pep.xml" -L"7"" failed: Unknown error > > > > command "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" > > "c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tande > > m.pep.xml" -L"7"" exited with non-zero exit code: -1 > > QUIT - the job is incomplete > > > > > > > > Is this an installation issue? Any ideas? > > > > Thanks, > > Lik Wee > > > > On Wed, Mar 10, 2010 at 1:53 PM, Lik Wee Lee <[email protected]> > > wrote: > >> > >> Hi Brian, > >> > >> The full path still gives command "..." failed: unknown error. > >> > >> I tried "run_in c:" and didn't get any output. > >> > >> But if I try "run_in c:\; dir", I get: > >> command "dir" failed: Unknown error. > >> > >> Could it be I previously had installed Perl 5.10? I uninstalled it > >> and then installed Perl 5.8.9 followed by tpp 4.3.1. > >> > >> Lik Wee > >> > >> On Wed, Mar 10, 2010 at 1:34 PM, Brian Pratt <[email protected] > > > >> wrote: > >>> > >>> "run_in" is just a little program that runs one or more commands in the > >>> indicated directory. For example "run_in c:\foo; bar.exe; baz.exe" > performs > >>> "cd c:\foo" then runs "bar.exe" then "baz.exe". It exists to help with > >>> linux-oriented multipart command lines in the GUI, statements like "cd > >>> c:foo; bar.exe; baz.exe" (we just swap "run_in" for "cd" on the windows > >>> installation). > >>> > >>> Anyway, that's what it's for - why it doesn't work for you is a > mystery. > >>> Perhaps it's a path issue: how does the command line > >>> c:\Inetpub\tpp-bin\run_in c:/Inetpub/wwwroot/ISB/data/17mix/tandem; > >>> c:\Inetpub\tpp-bin\tandem > >>> > c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem.params > >>> > >>> work for you (that is, with full path to run_in specified)? > >>> > >>> On Wed, Mar 10, 2010 at 1:21 PM, Lik Wee Lee <[email protected]> > >>> wrote: > >>>> > >>>> Hi, > >>>> > >>>> When I tried to do a xtandem search in the TPP petunia interface, > >>>> I encountered the problem: > >>>> > >>>> # Commands for session TYBEEDEHS on Wed Mar 10 13:13:38 2010 > >>>> # BEGIN COMMAND BLOCK > >>>> ###### BEGIN Command Execution ###### > >>>> > >>>> [Wed Mar 10 13:13:38 2010] EXECUTING: run_in > >>>> c:/Inetpub/wwwroot/ISB/data/17mix/tandem; c:\Inetpub\tpp-bin\tandem > >>>> > c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem.params > >>>> OUTPUT: > >>>> > >>>> command "c:\Inetpub\tpp-bin\tandem > >>>> > c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem.params" > >>>> failed: Unknown error > >>>> > >>>> > >>>> > >>>> > >>>> END OUTPUT > >>>> RETURN CODE:65280 > >>>> ###### End Command Execution ###### > >>>> # All finished at Wed Mar 10 13:13:38 2010 > >>>> # END COMMAND BLOCK > >>>> > >>>> Does anyone have any ideas why this occur? > >>>> However, the search was performed successfully if I did it by command > >>>> line: > >>>> > >>>> c:\Inetpub\tpp-bin\tandem > >>>> > c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem.params > >>>> > >>>> If I try > >>>> > >>>> run_in c:/Inetpub/wwwroot/ISB/data/17mix/tandem; > >>>> c:\Inetpub\tpp-bin\tandem > >>>> > c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem.params > >>>> > >>>> it says command failed: Unknown error. > >>>> > >>>> I have ActivePerl 5.8.9 build 827 and TPP version 4.3.1 installed on > >>>> Windows XP SP3. > >>>> > >>>> Thanks, > >>>> Lik Wee > >>>> > >>>> -- > >>>> 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]<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]<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]<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. 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