The output from the "xinteract" command of the analysis stage will tell you more about your problem than the Apache logs will. The pepXMLViewer error is probably just a result of some previous failure.
Brian On Thu, Jan 13, 2011 at 10:03 PM, Furuki Eiko <efur...@etc.a-star.edu.sg> wrote: > Hi, > > I've been trying to set up TPP for quite some time. I have successfully > converted my .raw (Waters QTof) into .mxXML, did a database search with > Tandem and converted the results to .pep.xml. I can even view the pepxml on > the web interface. However, every time I try to proceed to the analysis > stage, the command will fail with an "Unknown error". On top of that, a > system error with PepXMLViewer.cgi pops out and states it has encountered an > error and needs to be closed. > > I have scoured the discussion page and none of the pepXMLViewer error seems > to be the same as the problem I'm facing. Also, even though the pepxml files > were successfully generated, I suspect that there is an error that I don't > know or am unable to spot. This is because, when I open the pepxml file in > Crimson editor, there is a portion just below the header that was very > "messy" as compared to an older file generated by an ex-colleague (who > successfully ran everything through to the analysis stage). > > At the apache error log, I found this: > > [Tue Jan 11 16:01:13 2011] [error] [client 127.0.0.1] [Tue Jan 11 16:01:13 > 2011] tpp_gui.pl: Use of uninitialized value $files_dir in concatenation (.) > or string at C:/Inetpub/tpp-bin/tpp_gui.pl line 1314., referer: > http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=home > [Tue Jan 11 16:03:32 2011] [error] [client 127.0.0.1] [Tue Jan 11 16:03:32 > 2011] tpp_gui.pl: Use of uninitialized value $files_dir in concatenation (.) > or string at C:/Inetpub/tpp-bin/tpp_gui.pl line 1314., referer: > http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=home > [Tue Jan 11 16:20:29 2011] [error] [client 127.0.0.1] [Tue Jan 11 16:20:29 > 2011] tpp_gui.pl: Use of uninitialized value $files_dir in concatenation (.) > or string at C:/Inetpub/tpp-bin/tpp_gui.pl line 1314., referer: > http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=home > [Tue Jan 11 16:20:40 2011] [error] [client 127.0.0.1] [Tue Jan 11 16:20:40 > 2011] tpp_gui.pl: Use of uninitialized value $files_dir in concatenation (.) > or string at C:/Inetpub/tpp-bin/tpp_gui.pl line 1314., referer: > http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=mzxml > [Tue Jan 11 16:20:47 2011] [error] [client 127.0.0.1] [Tue Jan 11 16:20:47 > 2011] tpp_gui.pl: Use of uninitialized value $files_dir in concatenation (.) > or string at C:/Inetpub/tpp-bin/tpp_gui.pl line 1314., referer: > http://localhost/tpp-bin/tpp_gui.pl > [Tue Jan 11 16:20:52 2011] [error] [client 127.0.0.1] [Tue Jan 11 16:20:52 > 2011] tpp_gui.pl: Use of uninitialized value $files_dir in concatenation (.) > or string at C:/Inetpub/tpp-bin/tpp_gui.pl line 1314., referer: > http://localhost/tpp-bin/tpp_gui.pl > [Tue Jan 11 16:37:59 2011] [error] [client 127.0.0.1] The system cannot find > the path specified.\r, referer: > http://localhost/ISB/html/post_to_spectrast.html?fasta=ipi.HUMAN.v3.62mod.fasta&tppcgi=/tpp-bin/&Dta=c:/Inetpub/wwwroot/ISB/data/Test/PHHUP00416G00336GL03B01Mix/PHHUP00416G00336GL03B01Mix.00340.00340.2.dta > [Tue Jan 11 16:52:36 2011] [error] [client 127.0.0.1] The system cannot find > the path specified.\r, referer: > http://localhost/tpp-bin/PepXMLViewer.cgi?xmlFileName=c:/Inetpub/wwwroot/ISB/data/Test/PHHUP00416G00336GL03B01Mix.tandem.pep.xml > [Tue Jan 11 16:52:46 2011] [error] [client 127.0.0.1] 'pwd' is not recognized > as an internal or external command,\r, referer: > http://localhost/tpp-bin/PepXMLViewer.cgi?xmlFileName=c:/Inetpub/wwwroot/ISB/data/Test/PHHUP00416G00336GL03B01Mix.tandem.pep.xml > [Tue Jan 11 16:52:46 2011] [error] [client 127.0.0.1] operable program or > batch file.\r, referer: > http://localhost/tpp-bin/PepXMLViewer.cgi?xmlFileName=c:/Inetpub/wwwroot/ISB/data/Test/PHHUP00416G00336GL03B01Mix.tandem.pep.xml > [Tue Jan 11 16:52:46 2011] [error] [client 127.0.0.1] Use of uninitialized > value $actual_FDR_thresh in numeric ne (!=) at > C:/Inetpub/tpp-bin/calctppstat.pl line 572, <INFILE> line 18876., referer: > http://localhost/tpp-bin/PepXMLViewer.cgi?xmlFileName=c:/Inetpub/wwwroot/ISB/data/Test/PHHUP00416G00336GL03B01Mix.tandem.pep.xml > [Tue Jan 11 16:52:46 2011] [error] [client 127.0.0.1] Use of uninitialized > value $actual_FDR_thresh in concatenation (.) or string at > C:/Inetpub/tpp-bin/calctppstat.pl line 574, <INFILE> line 18876., referer: > http://localhost/tpp-bin/PepXMLViewer.cgi?xmlFileName=c:/Inetpub/wwwroot/ISB/data/Test/PHHUP00416G00336GL03B01Mix.tandem.pep.xml > [Tue Jan 11 16:52:46 2011] [error] [client 127.0.0.1] Illegal division by > zero at C:/Inetpub/tpp-bin/calctppstat.pl line 773., referer: > http://localhost/tpp-bin/PepXMLViewer.cgi?xmlFileName=c:/Inetpub/wwwroot/ISB/data/Test/PHHUP00416G00336GL03B01Mix.tandem.pep.xml > [Wed Jan 12 14:08:39 2011] [error] [client 127.0.0.1] [Wed Jan 12 14:08:39 > 2011] tpp_gui.pl: Use of uninitialized value $files_dir in concatenation (.) > or string at C:/Inetpub/tpp-bin/tpp_gui.pl line 1314., referer: > http://localhost/tpp-bin/tpp_gui.pl > [Wed Jan 12 14:13:25 2011] [error] [client 127.0.0.1] [Wed Jan 12 14:13:25 > 2011] tpp_gui.pl: Use of uninitialized value $files_dir in concatenation (.) > or string at C:/Inetpub/tpp-bin/tpp_gui.pl line 1314., referer: > http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=mzxml > [Wed Jan 12 15:14:32 2011] [error] [client 127.0.0.1] [Wed Jan 12 15:14:32 > 2011] tpp_gui.pl: Use of uninitialized value $files_dir in concatenation (.) > or string at C:/Inetpub/tpp-bin/tpp_gui.pl line 1314., referer: > http://localhost/tpp-bin/tpp_gui.pl > > As I am not a developer or trained in any computer languages, I am unable to > solve this problem. Could somebody point out where it went wrong? Am I > missing some files or computer programs? > > Thank you! > > -Eiko > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-discuss@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-discuss@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.
