Hello I am running TPP 4.5.2 on Ubuntu 10.10. After using the GUI to run a tandem search on an mzxml file followed by tandem2xml I then run xinteract. When trying to view the results of that the browser window shows nothing. I presume something went wrong during xinteract but can 't figure out what. The below is the output.
Any help greatly appreciated. Thanks in advance. Brian Hampton THE BELOW FILES DO EXIST BUT DON'T DISPLAY CLICKING ON ANY OF THE FOLLOWING RESULTS ON A BLANK PAGE: /usr/local/apps/tpp/data/s1782/frac3.interact.pep.shtml [ View ] /usr/local/apps/tpp/data/s1782/frac3.interact.iproph.pep.shtml [ View ] /usr/local/apps/tpp/data/s1782/frac3.interact.iproph.prot.shtml [ View ] THIS IS THE HEAD SECTION OF ONE OF THE THE PAGES WHICH IS BLANK: <!--#include virtual="/tpp/cgi-bin/PepXMLViewer.cgi xmlFileName=/usr/ local/apps/tpp/data/s1782/frac3.interact.pep.xml.gz" --> THIS IS THE OUTPUT FROM XINTERACT ###### BEGIN Command Execution ###### [Fri Mar 2 14:22:58 2012] EXECUTING: cd /usr/local/apps/tpp/data/ s1782; /usr/local/apps/tpp/bin/xinteract -Nfrac3.interact.pep.xml.gz - p0.05 -l6 -O -ip 120223_S1782-SDS_eHILLIC-frac-3.tandem.pep.xml.gz OUTPUT: /usr/local/apps/tpp/bin/xinteract (TPP v4.5 RAPTURE rev 2, Build 201202291129 (linux)) running: "/usr/local/apps/tpp/bin/InteractParser 'frac3.interact.pep.xml.gz' '120223_S1782-SDS_eHILLIC- frac-3.tandem.pep.xml.gz' -L'6'" file 1: 120223_S1782-SDS_eHILLIC-frac-3.tandem.pep.xml.gz processed altogether 3946 results results written to file /usr/local/apps/tpp/data/s1782/ frac3.interact.pep.shtml command completed in 1 sec running: "/usr/local/apps/tpp/bin/DatabaseParser 'frac3.interact.pep.xml.gz'" command completed in 1 sec running: "/usr/local/apps/tpp/bin/RefreshParser 'frac3.interact.pep.xml.gz' '/usr/local/apps/tpp/data/dbase/ mouse.fasta'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 2 sec running: "/usr/local/apps/tpp/bin/PeptideProphetParser 'frac3.interact.pep.xml.gz' MINPROB=0.05" (X! Tandem (k-score)) init with X! Tandem (k-score) trypsin MS Instrument info: Manufacturer: Thermo Finnigan, Model: LCQ Advantage, Ionization: nanoelectrospray, Analyzer: quadrupole ion trap, Detector: electron multiplier PeptideProphet (TPP v4.5 RAPTURE rev 2, Build 201202291129 (linux)) AKeller@ISB read in 218 1+, 1854 2+, 1862 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... negmean = -0.0683082 negmean = 0.581145 negmean = -0.204067 negmean = -0.2 negmean = -0.2 negmean = -0.2 negmean = -0.2 Iterations: .........10.........20.........30. model complete after 32 iterations command completed in 1 sec running: "/usr/local/apps/tpp/bin/ProphetModels.pl -i frac3.interact.pep.xml.gz" Analyzing frac3.interact.pep.xml.gz ... plot "frac3.interact.pep_PPPROB.tsv" using 2:1 title "PeptideProphet" with line lt 1 lc 3 , x notitle with line lt 0 lc -1 ^ "frac3.interact.pep_PPPROB.gp", line 17: warning: Skipping data file with no valid points plot "frac3.interact.pep_IPPROB.tsv" using 2:1 title "iProphet" with line lt 1 lc 3 , "frac3.interact.pep_PPPROB.tsv" using 2:1 title "PeptideProphet" with line lt 1 lc 1 , x notitle with line lt 0 lc -1 ^ "frac3.interact.pep_IPPROB.gp", line 17: warning: Skipping data file with no valid points plot "frac3.interact.pep_IPPROB.tsv" using 2:1 title "iProphet" with line lt 1 lc 3 , "frac3.interact.pep_PPPROB.tsv" using 2:1 title "PeptideProphet" with line lt 1 lc 1 , x notitle with line lt 0 lc -1 ^ "frac3.interact.pep_IPPROB.gp", line 17: warning: Skipping data file with no valid points command completed in 0 sec running: "/usr/local/apps/tpp/cgi-bin/PepXMLViewer.cgi -I /usr/local/ apps/tpp/data/s1782/frac3.interact.pep.xml.gz" command completed in 1 sec running: "/usr/local/apps/tpp/bin/InterProphetParser frac3.interact.pep.xml.gz frac3.interact.iproph.pep.xml.gz" Running NSS NRS NSE NSI NSM Model EM: Computing NSS values ... Computing NRS values ... Computing NSE values ... Computing NSI values ... Computing NSM values ... Iterations: .......done results written to file /usr/local/apps/tpp/data/s1782/ frac3.interact.iproph.pep.shtml command completed in 1 sec running: "/usr/local/apps/tpp/bin/ProphetModels.pl -i frac3.interact.iproph.pep.xml.gz" Analyzing frac3.interact.iproph.pep.xml.gz ... plot "frac3.interact.iproph.pep_PPPROB.tsv" using 2:1 title "PeptideProphet" with line lt 1 lc 3 , x notitle with line lt 0 lc -1 ^ "frac3.interact.iproph.pep_PPPROB.gp", line 17: warning: Skipping data file with no valid points plot "frac3.interact.iproph.pep_IPPROB.tsv" using 2:1 title "iProphet" with line lt 1 lc 3 , "frac3.interact.iproph.pep_PPPROB.tsv" using 2:1 title "PeptideProphet" with line lt 1 lc 1 , x notitle with line lt 0 lc -1 ^ "frac3.interact.iproph.pep_IPPROB.gp", line 17: warning: Skipping data file with no valid points plot "frac3.interact.iproph.pep_IPPROB.tsv" using 2:1 title "iProphet" with line lt 1 lc 3 , "frac3.interact.iproph.pep_PPPROB.tsv" using 2:1 title "PeptideProphet" with line lt 1 lc 1 , x notitle with line lt 0 lc -1 ^ "frac3.interact.iproph.pep_IPPROB.gp", line 17: warning: Skipping data file with no valid points command completed in 0 sec running: "/usr/local/apps/tpp/cgi-bin/PepXMLViewer.cgi -I /usr/local/ apps/tpp/data/s1782/frac3.interact.iproph.pep.xml.gz" command completed in 0 sec running: "/usr/local/apps/tpp/bin/ProteinProphet 'frac3.interact.iproph.pep.xml.gz' 'frac3.interact.iproph.prot.xml.gz' XML IPROPHET" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v4.5 RAPTURE rev 2, Build 201202291129 (linux)) (xml input) (report Protein Length) (using degen pep info) . . . reading in /usr/local/apps/tpp/data/s1782/ frac3.interact.iproph.pep.xml.gz. . . . . . read in 39 1+, 608 2+, 113 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 INFO: mu=8.8089e-06, db_size=53065155 protein probabilities written to file /usr/local/apps/tpp/data/s1782/ frac3.interact.iproph.prot.xml.gz direct your browser to http://tpp.cvid.som.umaryland.edu//usr/local/apps/tpp/data/s1782/frac3.interact.iproph.prot.shtml command completed in 1 sec running: "/usr/local/apps/tpp/bin/ProtProphModels.pl -i frac3.interact.iproph.prot.xml.gz" Analyzing frac3.interact.iproph.prot.xml.gz ... command completed in 0 sec /usr/local/apps/tpp/bin/InteractParser 'frac3.interact.pep.xml.gz' '120223_S1782-SDS_eHILLIC-frac-3.tandem.pep.xml.gz' -L'6' 1 sec /usr/local/apps/tpp/bin/DatabaseParser 'frac3.interact.pep.xml.gz' /usr/local/apps/tpp/bin/RefreshParser 'frac3.interact.pep.xml.gz' '/ usr/local/apps/tpp/data/dbase/mouse.fasta' 2 sec /usr/local/apps/tpp/bin/PeptideProphetParser 'frac3.interact.pep.xml.gz' MINPROB=0.05 1 sec /usr/local/apps/tpp/bin/ProphetModels.pl -i frac3.interact.pep.xml.gz 0 sec /usr/local/apps/tpp/cgi-bin/PepXMLViewer.cgi -I /usr/local/apps/tpp/ data/s1782/frac3.interact.pep.xml.gz 1 sec /usr/local/apps/tpp/bin/InterProphetParser frac3.interact.pep.xml.gz frac3.interact.iproph.pep.xml.gz 1 sec /usr/local/apps/tpp/bin/ProphetModels.pl -i frac3.interact.iproph.pep.xml.gz 0 sec /usr/local/apps/tpp/cgi-bin/PepXMLViewer.cgi -I /usr/local/apps/tpp/ data/s1782/frac3.interact.iproph.pep.xml.gz 0 sec /usr/local/apps/tpp/bin/ProteinProphet 'frac3.interact.iproph.pep.xml.gz' 'frac3.interact.iproph.prot.xml.gz' XML IPROPHET 1 sec /usr/local/apps/tpp/bin/ProtProphModels.pl -i frac3.interact.iproph.prot.xml.gz 0 sec job completed in 8 sec END OUTPUT RETURN CODE:0 ###### End Command Execution ###### # All finished at Fri Mar 2 14:23:06 2012 # END COMMAND BLOCK -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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