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]. >>>> 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. >> > > -- > 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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