I think the fact that run_in doesn't work indicates some kind of system level problem that's going to make everything else flaky. Perl shouldn't be an issue, at least at this point.
So "c:\inetpub\tpp-bin\run_in c:\; dir" doesn't work for you? What do you see when you type this into your browser address bar? http://localhost/tpp-bin/check_env.pl It should give you a bunch of info including the PATH setting for your webserver. On Wed, Mar 10, 2010 at 2:47 PM, Lik Wee Lee <[email protected]>wrote: > 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. > 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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