Re: [spctools-discuss] xtandem search didn't run through Petunia
Furthermore, I also did: C:\Inetpub\wwwroot\ISB\data\17mixc:\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\tandemc:\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 -L7 command C:/Inetpub/tpp-bin/InteractParser interact.pep.xml c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tande m.pep.xml -L7 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 -L7 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 l...@systemsbiology.orgwrote: 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 brian.pr...@insilicos.comwrote: 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 l...@systemsbiology.orgwrote: 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 spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.comspctools-discuss%2bunsubscr...@googlegroups.com . 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 spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.comspctools-discuss%2bunsubscr...@googlegroups.com . 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
Re: [spctools-discuss] xtandem search didn't run through Petunia
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 l...@systemsbiology.org wrote: Furthermore, I also did: C:\Inetpub\wwwroot\ISB\data\17mixc:\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\tandemc:\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 -L7 command C:/Inetpub/tpp-bin/InteractParser interact.pep.xml c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tande m.pep.xml -L7 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 -L7 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 l...@systemsbiology.org 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 brian.pr...@insilicos.com 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 l...@systemsbiology.org 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 spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. 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 spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com.
Re: [spctools-discuss] xtandem search didn't run through Petunia
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 jke...@gmail.com 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 l...@systemsbiology.org wrote: Furthermore, I also did: C:\Inetpub\wwwroot\ISB\data\17mixc:\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\tandemc:\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 -L7 command C:/Inetpub/tpp-bin/InteractParser interact.pep.xml c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tande m.pep.xml -L7 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 -L7 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 l...@systemsbiology.org 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 brian.pr...@insilicos.com 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 l...@systemsbiology.org 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
Re: [spctools-discuss] xtandem search didn't run through Petunia
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 l...@systemsbiology.orgwrote: 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 jke...@gmail.com 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 l...@systemsbiology.org wrote: Furthermore, I also did: C:\Inetpub\wwwroot\ISB\data\17mixc:\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\tandemc:\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 -L7 command C:/Inetpub/tpp-bin/InteractParser interact.pep.xml c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tande m.pep.xml -L7 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 -L7 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 l...@systemsbiology.org 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 brian.pr...@insilicos.com 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 l...@systemsbiology.org 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
Re: [spctools-discuss] xtandem search didn't run through Petunia
Hi Brian, On Wed, Mar 10, 2010 at 3:34 PM, Brian Pratt brian.pr...@insilicos.comwrote: 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? I still get command dir failed: Unknown error What do you see when you type this into your browser address bar? http://localhost/tpp-bin/check_env.pl SCRIPT_NAME = /tpp-bin/check_env.pl SERVER_NAME = localhost HTTP_ACCEPT_ENCODING = gzip,deflate HTTP_CONNECTION = keep-alive REQUEST_METHOD = GET SYSTEMROOT = C:\WINDOWS HTTP_ACCEPT = text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8 SCRIPT_FILENAME = C:/Inetpub/tpp-bin/check_env.pl COMSPEC = C:\WINDOWS\system32\cmd.exe SERVER_SOFTWARE = Apache/2.2.8 (Win32) HTTP_ACCEPT_CHARSET = ISO-8859-1,utf-8;q=0.7,*;q=0.7 WINDIR = C:\WINDOWS QUERY_STRING = REMOTE_PORT = 3227 PATHEXT = .COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH HTTP_USER_AGENT = Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.9.0.18) Gecko/2010020220 Firefox/3.0.18 (.NET CLR 3.5.30729) SERVER_PORT = 80 SERVER_SIGNATURE = HTTP_ACCEPT_LANGUAGE = en-us,en;q=0.5 HTTP_COOKIE = TPPSession=TYBEEDEHS:guest:249069786675ffea98006f8c1b444fa1 REMOTE_ADDR = 127.0.0.1 WEBSERVER_ROOT = c:\Inetpub\wwwroot;c:\Inetpub\wwwroot HTTP_KEEP_ALIVE = 300 SERVER_PROTOCOL = HTTP/1.1 PATH = C:\Inetpub\tpp-bin;C:\Xcalibur\system\programs;C:\Program Files\Thermo\Foundation;C:\Perl\site\bin;C:\Perl\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\Common Files\Adaptec Shared\System;C:\Program Files\Analyst\bin REQUEST_URI = /tpp-bin/check_env.pl GATEWAY_INTERFACE = CGI/1.1 SERVER_ADDR = 127.0.0.1 DOCUMENT_ROOT = C:/Program Files/Apache Software Foundation/Apache2.2/htdocs HTTP_HOST = localhost Thanks for your help, Lik Wee 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 l...@systemsbiology.orgwrote: 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 jke...@gmail.com 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 l...@systemsbiology.org wrote: Furthermore, I also did: C:\Inetpub\wwwroot\ISB\data\17mixc:\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\tandemc:\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 -L7 command C:/Inetpub/tpp-bin/InteractParser interact.pep.xml c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tande m.pep.xml -L7 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 -L7 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 l...@systemsbiology.org 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 brian.pr...@insilicos.com wrote: run_in is just a little program that runs one or more commands in the indicated directory. For example
Re: [spctools-discuss] xtandem search didn't run through Petunia
Did you have a working TPP installation before? On Wed, Mar 10, 2010 at 3:54 PM, Lik Wee Lee l...@systemsbiology.orgwrote: Hi Brian, On Wed, Mar 10, 2010 at 3:34 PM, Brian Pratt brian.pr...@insilicos.comwrote: 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? I still get command dir failed: Unknown error What do you see when you type this into your browser address bar? http://localhost/tpp-bin/check_env.pl SCRIPT_NAME = /tpp-bin/check_env.pl SERVER_NAME = localhost HTTP_ACCEPT_ENCODING = gzip,deflate HTTP_CONNECTION = keep-alive REQUEST_METHOD = GET SYSTEMROOT = C:\WINDOWS HTTP_ACCEPT = text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8 SCRIPT_FILENAME = C:/Inetpub/tpp-bin/check_env.pl COMSPEC = C:\WINDOWS\system32\cmd.exe SERVER_SOFTWARE = Apache/2.2.8 (Win32) HTTP_ACCEPT_CHARSET = ISO-8859-1,utf-8;q=0.7,*;q=0.7 WINDIR = C:\WINDOWS QUERY_STRING = REMOTE_PORT = 3227 PATHEXT = .COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH HTTP_USER_AGENT = Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.9.0.18) Gecko/2010020220 Firefox/3.0.18 (.NET CLR 3.5.30729) SERVER_PORT = 80 SERVER_SIGNATURE = HTTP_ACCEPT_LANGUAGE = en-us,en;q=0.5 HTTP_COOKIE = TPPSession=TYBEEDEHS:guest:249069786675ffea98006f8c1b444fa1 REMOTE_ADDR = 127.0.0.1 WEBSERVER_ROOT = c:\Inetpub\wwwroot;c:\Inetpub\wwwroot HTTP_KEEP_ALIVE = 300 SERVER_PROTOCOL = HTTP/1.1 PATH = C:\Inetpub\tpp-bin;C:\Xcalibur\system\programs;C:\Program Files\Thermo\Foundation;C:\Perl\site\bin;C:\Perl\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\Common Files\Adaptec Shared\System;C:\Program Files\Analyst\bin REQUEST_URI = /tpp-bin/check_env.pl GATEWAY_INTERFACE = CGI/1.1 SERVER_ADDR = 127.0.0.1 DOCUMENT_ROOT = C:/Program Files/Apache Software Foundation/Apache2.2/htdocs HTTP_HOST = localhost Thanks for your help, Lik Wee 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 l...@systemsbiology.orgwrote: 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 jke...@gmail.com 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 l...@systemsbiology.org wrote: Furthermore, I also did: C:\Inetpub\wwwroot\ISB\data\17mixc:\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\tandemc:\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 -L7 command C:/Inetpub/tpp-bin/InteractParser interact.pep.xml c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tande m.pep.xml -L7 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 -L7 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 l...@systemsbiology.org 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,
Re: [spctools-discuss] xtandem search didn't run through Petunia
ah, wait, I do see one weird thing: WEBSERVER_ROOT = c:\Inetpub\wwwroot;c:\Inetpub\wwwroot change that environment variable to WEBSERVER_ROOT = c:\Inetpub\wwwroot and see how it goes. On Wed, Mar 10, 2010 at 4:18 PM, Lik Wee Lee l...@systemsbiology.orgwrote: Nope. I installed it recently and it complained about missing perl so I downloaded 5.10 and installed it successfully. But when I ran into problems, I thought it might be due to the perl version, so I uninstall Perl 5.10.1 and TPP and then reinstall Perl 5.8.9 and TPP. Lik Wee On Wed, Mar 10, 2010 at 4:08 PM, Brian Pratt brian.pr...@insilicos.comwrote: Did you have a working TPP installation before? On Wed, Mar 10, 2010 at 3:54 PM, Lik Wee Lee l...@systemsbiology.orgwrote: Hi Brian, On Wed, Mar 10, 2010 at 3:34 PM, Brian Pratt brian.pr...@insilicos.com wrote: 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? I still get command dir failed: Unknown error What do you see when you type this into your browser address bar? http://localhost/tpp-bin/check_env.pl SCRIPT_NAME = /tpp-bin/check_env.pl SERVER_NAME = localhost HTTP_ACCEPT_ENCODING = gzip,deflate HTTP_CONNECTION = keep-alive REQUEST_METHOD = GET SYSTEMROOT = C:\WINDOWS HTTP_ACCEPT = text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8 SCRIPT_FILENAME = C:/Inetpub/tpp-bin/check_env.pl COMSPEC = C:\WINDOWS\system32\cmd.exe SERVER_SOFTWARE = Apache/2.2.8 (Win32) HTTP_ACCEPT_CHARSET = ISO-8859-1,utf-8;q=0.7,*;q=0.7 WINDIR = C:\WINDOWS QUERY_STRING = REMOTE_PORT = 3227 PATHEXT = .COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH HTTP_USER_AGENT = Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.9.0.18) Gecko/2010020220 Firefox/3.0.18 (.NET CLR 3.5.30729) SERVER_PORT = 80 SERVER_SIGNATURE = HTTP_ACCEPT_LANGUAGE = en-us,en;q=0.5 HTTP_COOKIE = TPPSession=TYBEEDEHS:guest:249069786675ffea98006f8c1b444fa1 REMOTE_ADDR = 127.0.0.1 WEBSERVER_ROOT = c:\Inetpub\wwwroot;c:\Inetpub\wwwroot HTTP_KEEP_ALIVE = 300 SERVER_PROTOCOL = HTTP/1.1 PATH = C:\Inetpub\tpp-bin;C:\Xcalibur\system\programs;C:\Program Files\Thermo\Foundation;C:\Perl\site\bin;C:\Perl\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\Common Files\Adaptec Shared\System;C:\Program Files\Analyst\bin REQUEST_URI = /tpp-bin/check_env.pl GATEWAY_INTERFACE = CGI/1.1 SERVER_ADDR = 127.0.0.1 DOCUMENT_ROOT = C:/Program Files/Apache Software Foundation/Apache2.2/htdocs HTTP_HOST = localhost Thanks for your help, Lik Wee 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 l...@systemsbiology.org 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 jke...@gmail.com 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 l...@systemsbiology.org wrote: Furthermore, I also did: C:\Inetpub\wwwroot\ISB\data\17mixc:\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\tandemc:\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 -L7 command C:/Inetpub/tpp-bin/InteractParser interact.pep.xml c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tande m.pep.xml -L7 failed: Unknown error command C:/Inetpub/tpp-bin/InteractParser interact.pep.xml
Re: [spctools-discuss] xtandem search didn't run through Petunia
Thanks!!. It is working normally now...phew. Lik Wee On Wed, Mar 10, 2010 at 4:46 PM, Brian Pratt brian.pr...@insilicos.comwrote: It's a windows thing: ControlPanel|System|Advanced|EnvironmentVariables Good luck! Brian On Wed, Mar 10, 2010 at 4:33 PM, Lik Wee Lee l...@systemsbiology.orgwrote: I am not sure how to do this. There is a section in the apache httpd.conf that shows: Should I just delete either one of the PassEnv WEBSERVER_ROOT? Thanks. # # Begin settings for the Trans Proteomic Pipeline # # Add 5-hour timeout Timeout 18000 Alias /tpp-bin C:/Inetpub/tpp-bin Directory C:/Inetpub/tpp-bin Options Indexes MultiViews ExecCGI AllowOverride None Order allow,deny Allow from all AddHandler cgi-script .cgi .pl ScriptInterpreterSource Registry PassEnv WEBSERVER_ROOT PassEnv WEBSERVER_TMP /Directory Alias /ISB C:/Inetpub/wwwroot/ISB Alias /schema C:/Inetpub/wwwroot/schema Directory C:/Inetpub/wwwroot Options Indexes MultiViews Includes AllowOverride None Order allow,deny Allow from all AddType text/html .shtml AddHandler server-parsed .shtml PassEnv WEBSERVER_ROOT PassEnv WEBSERVER_TMP /Directory # # End settings for the Trans Proteomic Pipeline # On Wed, Mar 10, 2010 at 4:21 PM, Brian Pratt brian.pr...@insilicos.com wrote: ah, wait, I do see one weird thing: WEBSERVER_ROOT = c:\Inetpub\wwwroot;c:\Inetpub\wwwroot change that environment variable to WEBSERVER_ROOT = c:\Inetpub\wwwroot and see how it goes. On Wed, Mar 10, 2010 at 4:18 PM, Lik Wee Lee l...@systemsbiology.orgwrote: Nope. I installed it recently and it complained about missing perl so I downloaded 5.10 and installed it successfully. But when I ran into problems, I thought it might be due to the perl version, so I uninstall Perl 5.10.1 and TPP and then reinstall Perl 5.8.9 and TPP. Lik Wee On Wed, Mar 10, 2010 at 4:08 PM, Brian Pratt brian.pr...@insilicos.com wrote: Did you have a working TPP installation before? On Wed, Mar 10, 2010 at 3:54 PM, Lik Wee Lee l...@systemsbiology.org wrote: Hi Brian, On Wed, Mar 10, 2010 at 3:34 PM, Brian Pratt brian.pr...@insilicos.com wrote: 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? I still get command dir failed: Unknown error What do you see when you type this into your browser address bar? http://localhost/tpp-bin/check_env.pl SCRIPT_NAME = /tpp-bin/check_env.pl SERVER_NAME = localhost HTTP_ACCEPT_ENCODING = gzip,deflate HTTP_CONNECTION = keep-alive REQUEST_METHOD = GET SYSTEMROOT = C:\WINDOWS HTTP_ACCEPT = text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8 SCRIPT_FILENAME = C:/Inetpub/tpp-bin/check_env.pl COMSPEC = C:\WINDOWS\system32\cmd.exe SERVER_SOFTWARE = Apache/2.2.8 (Win32) HTTP_ACCEPT_CHARSET = ISO-8859-1,utf-8;q=0.7,*;q=0.7 WINDIR = C:\WINDOWS QUERY_STRING = REMOTE_PORT = 3227 PATHEXT = .COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH HTTP_USER_AGENT = Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.9.0.18) Gecko/2010020220 Firefox/3.0.18 (.NET CLR 3.5.30729) SERVER_PORT = 80 SERVER_SIGNATURE = HTTP_ACCEPT_LANGUAGE = en-us,en;q=0.5 HTTP_COOKIE = TPPSession=TYBEEDEHS:guest:249069786675ffea98006f8c1b444fa1 REMOTE_ADDR = 127.0.0.1 WEBSERVER_ROOT = c:\Inetpub\wwwroot;c:\Inetpub\wwwroot HTTP_KEEP_ALIVE = 300 SERVER_PROTOCOL = HTTP/1.1 PATH = C:\Inetpub\tpp-bin;C:\Xcalibur\system\programs;C:\Program Files\Thermo\Foundation;C:\Perl\site\bin;C:\Perl\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\Common Files\Adaptec Shared\System;C:\Program Files\Analyst\bin REQUEST_URI = /tpp-bin/check_env.pl GATEWAY_INTERFACE = CGI/1.1 SERVER_ADDR = 127.0.0.1 DOCUMENT_ROOT = C:/Program Files/Apache Software Foundation/Apache2.2/htdocs HTTP_HOST = localhost Thanks for your help, Lik Wee 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 l...@systemsbiology.org 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 jke...@gmail.comwrote: 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,
