I still don't know what's going wrong or what the solution to the problem is, but I talked to someone in a neighboring lab, and it turns out that they had a similar issue with tpp and offered a workaround. Apparently, the problem only occurred for them when they accessed the interact file by clicking on the interact.pep.shtml link but not when they accessed it directly by clicking on the interact.pepXML link. Going directly through the pepXML file seems to be working for me too. Just fyi, they also claimed that this was not a problem when accessing the interact file on their dedicated server for peptide identification, but only when later running tpp locally on a Mac. Since I am using a PC, this issue doesn't seem to be platform specific.
On Mar 15, 4:52 pm, "[email protected]" <[email protected]> wrote: > Applying the analytical troubleshooting skills that I learned at the > bench to the problem, I have discovered that the problem starts after > I try to export the spreadsheet specifically after applying the > sorting by protein and PeptideProphet min(=0.8) options under the > summary tab of the PepXML viewer. Anyone have any ideas of what may be > going wrong? > > I think that I tried to export the spreadsheet at around 16:25:40 and > that it timed out at 16:32:43. Here is the Apache log file: > > [Thu Mar 15 16:25:17 2012] [error] [client 127.0.0.1] call to > unsupported function: rampValidateOrDeriveInputFilename(char *inbuf, > int inbuflen, char *spectrumName)\r, > referer:http://localhost/tpp-bin/PepXMLViewer.cgi?page=1&columns=&displayStat... > [Thu Mar 15 16:25:18 2012] [error] [client 127.0.0.1] , > referer:http://localhost/tpp-bin/XPressPeptideUpdateParser.cgi?LightFirstScan... > [Thu Mar 15 16:25:36 2012] [error] [client 127.0.0.1] call to > unsupported function: rampValidateOrDeriveInputFilename(char *inbuf, > int inbuflen, char *spectrumName)\r, > referer:http://localhost/tpp-bin/XPressPeptideUpdateParser.cgi?LightFirstScan... > [Thu Mar 15 16:25:40 2012] [error] [client 127.0.0.1] , > referer:http://localhost/tpp-bin/XPressPeptideUpdateParser.cgi?InteractDir=&I... > [Thu Mar 15 16:25:41 2012] [error] [client 127.0.0.1] call to > unsupported function: rampValidateOrDeriveInputFilename(char *inbuf, > int inbuflen, char *spectrumName)\r, > referer:http://localhost/tpp-bin/XPressPeptideUpdateParser.cgi?InteractDir=&I... > [Thu Mar 15 16:25:41 2012] [error] [client 127.0.0.1] , > referer:http://localhost/tpp-bin/XPressPeptideUpdateParser.cgi?InteractDir=&I... > [Thu Mar 15 16:32:43 2012] [error] [client 127.0.0.1] \r, > referer:http://localhost/tpp-bin/PepXMLViewer.cgi?page=1&columns=Pprobability... > [Thu Mar 15 16:32:43 2012] [error] [client 127.0.0.1] This application > has requested the Runtime to terminate it in an unusual way., > referer:http://localhost/tpp-bin/PepXMLViewer.cgi?page=1&columns=Pprobability... > [Thu Mar 15 16:32:43 2012] [error] [client 127.0.0.1] Please contact > the application's support team for more information.\r, > referer:http://localhost/tpp-bin/PepXMLViewer.cgi?page=1&columns=Pprobability... > > On Mar 15, 4:09 pm, "[email protected]" <[email protected]> wrote: > > > > > > > > > This is what I see in the Apache error log file when I try to open the > > interact.pep.shtml file after the problem occurs: > > > [Thu Mar 15 15:35:34 2012] [error] [client 127.0.0.1] [Thu Mar 15 > > 15:35:34 2012] tpp_gui.pl: Use of uninitialized value in pattern match > > (m//) at C:\\Inetpub\\tpp-bin\\tpp_gui.pl line 5975., > > referer:http://localhost/tpp-bin/tpp_gui.pl > > [Thu Mar 15 15:35:34 2012] [error] [client 127.0.0.1] [Thu Mar 15 > > 15:35:34 2012] tpp_gui.pl: Use of uninitialized value in pattern match > > (m//) at C:\\Inetpub\\tpp-bin\\tpp_gui.pl line 5975., > > referer:http://localhost/tpp-bin/tpp_gui.pl > > [Thu Mar 15 15:35:34 2012] [error] [client 127.0.0.1] [Thu Mar 15 > > 15:35:34 2012] tpp_gui.pl: Use of uninitialized value in pattern match > > (m//) at C:\\Inetpub\\tpp-bin\\tpp_gui.pl line 5975., > > referer:http://localhost/tpp-bin/tpp_gui.pl > > [Thu Mar 15 15:43:49 2012] [error] [client 127.0.0.1] \r, > > referer:http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=filebrowser&f... > > [Thu Mar 15 15:43:49 2012] [error] [client 127.0.0.1] This application > > has requested the Runtime to terminate it in an unusual way., > > referer:http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=filebrowser&f... > > [Thu Mar 15 15:43:49 2012] [error] [client 127.0.0.1] Please contact > > the application's support team for more information.\r, > > referer:http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=filebrowser&f... > > [Thu Mar 15 15:43:50 2012] [error] [client 127.0.0.1] File does not > > exist: C:/Program Files (x86)/Apache Software Foundation/Apache2.2/ > > htdocs/favicon.ico > > > Also, I'm using the latest version of tpp (4.5), installed from the > > msi file. One of the options I exhausted when trying to fix this was > > to upgrade from version 1 to version 2 after the first instance of the > > problem. > > > On Mar 14, 10:07 pm, "[email protected]" <[email protected]> wrote: > > > > Hi, > > > > I'm running TPP on a Windows 7 64 bit machine. I have no problem > > > analyzing peptides running xinteract, but when I try to export the > > > results as a spreadsheet, it seems to hang, displaying a waiting for > > > localhost message in my browser until it times out and loads a blank > > > page. Once this happens, it seems to corrupt some of the interact > > > files because I have the same problem when I try to reload the > > > interact.pep.shtml file (which I had no problem with before I tried to > > > export the spreadsheet). I had this happen once. When I felt like I > > > exhausted all my options, I deleted all > > ... > > read more » -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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