Hi: I install TPP 4-3-1(along with ActivePerl 5.10.1.1007) and TPP4-4-1(along with ActivePerl 5.12.2.1202) on my Windows system separately, but both environments would face the same problems in analyzing X!tandem results via Xinteract.
I start from transforming raw data, and TPP works fine in mzXML conversion, database search, along with generating pepXML. When I start to analyze the pep.xml result, however, the system pops with the message window "PepXMLViewer.cgi must be closed" (I translate it from Chinese, but it just terminate and asks for reporting problems). While there are still 7 png files showing some probability distribution, the interact.pep.xml contains only the following two lines and cannot be open: <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 3.0//EN"> <!--#include virtual="/tpp-bin/PepXMLViewer.cgi?xmlFileName=c:/Inetpub/ wwwroot/ISB/data/Phospho/interact.pep.xml" --> I wonder if I configure something wrong so that the situation happens, and I would appreciate if someone could point it out. Below is some information on my setting: (1) The environment is Microsoft XP professional SP3 in Chinese Traditional. (2) I install ActivePerl and Apache 2.2 before running TPP. (3) I add WEBSERVER_ROOT to the system variable. (4) I also attach the system message of running Xinteract here: # THE MESSAGE BEGINS# run_in c:/Inetpub/wwwroot/ISB/data/Phospho; c:\Inetpub\tpp-bin \xinteract -Ninteract.pep.xml -p0.05 -l7 -O c:/Inetpub/wwwroot/ISB/ data/Phospho/site1.2010_11_29_10_03_30.t.tandem.pep.xml # Commands for session H9Q1Q2IUS on Mon Nov 29 10:05:43 2010 # BEGIN COMMAND BLOCK ###### BEGIN Command Execution ###### [Mon Nov 29 10:05:44 2010] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/ data/Phospho; c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 - l7 -O c:/Inetpub/wwwroot/ISB/data/Phospho/ site1.2010_11_29_10_03_30.t.tandem.pep.xml OUTPUT: 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/Phospho/ site1.2010_11_29_10_03_30.t.tandem.pep.xml" -L"7"" file 1: c:/Inetpub/wwwroot/ISB/data/Phospho/ site1.2010_11_29_10_03_30.t.tandem.pep.xml processed altogether 13 results results written to file c:/Inetpub/wwwroot/ISB/data/Phospho/ interact.pep.xml direct your browser to http://localhost/ISB/data/Phospho/interact.pep.shtml command completed in 1 sec running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" MINPROB=0.05" (X! Tandem) WARNING: Found unanticipated cleavage in refinement mode. Turning off NTT model. init with X! Tandem trypsin MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ, Ionization: NSI, Analyzer: ITMS, Detector: unknown PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 200909091257 (MinGW)) akel...@isb read in 0 1+, 10 2+, 3 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Iterations: .........10.........20 model complete after 21 iterations command completed in 0 sec running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i interact.pep.xml" Analyzing interact.pep.xml ... Parsing search results "c:/Inetpub/wwwroot/ISB/data/Phospho/site1 (X! Tandem)"... => Total of 0 hits. command completed in 1 sec running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml"" command completed in 0 sec running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" "c:/ Inetpub/wwwroot/ISB/data/Phospho/ipi.HUMAN.v3.77.fasta"" - Searching the tree... - Linking duplicate entries... - Printing results... - Building Commentz-Walter keyword tree...command completed in 5 sec running: "c:/inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/ wwwroot/ISB/data/Phospho/interact.pep.xml" command "c:/inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/ wwwroot/ISB/data/Phospho/interact.pep.xml" failed: Unknown error command "c:/inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/ wwwroot/ISB/data/Phospho/interact.pep.xml" exited with non-zero exit code: -1073741819 QUIT - the job is incomplete command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -O c:/Inetpub/wwwroot/ISB/data/Phospho/ site1.2010_11_29_10_03_30.t.tandem.pep.xml" failed: Unknown error END OUTPUT RETURN CODE:1280 # THE MESSAGE ENDS HERE# Please inform me once the above information is insufficient. Thanks! Yen-Yi -- 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.
