I'm trying to integrate tpp 4.4 with cpas.
I did the build with XML_ONLY=1 but it appears that it is still trying operate in web mode. I also posted this question to spctools-discuss but maybe you've seen this before.
Thanks,
Bill
Log out put below:
20 May 2009 13:44:32,691 INFO : /usr/local/labkey/bin/bin/xinteract
(TPP v4.2 JETSTREAM rev 1, Build 200905191640 (linux)) 20 May 2009 13:44:32,691 INFO :
20 May 2009 13:44:32,691 INFO : running: "InteractParser 'UPS1-01.pep.xml' '../UPS1-01_raw.pep.xml' -L'7'"
20 May 2009 13:44:32,736 INFO : file 1: ../UPS1-01_raw.pep.xml 20 May 2009 13:44:32,806 INFO : processed altogether 694 results 20 May 2009 13:44:32,856 INFO : command completed in 0 sec 20 May 2009 13:44:32,857 INFO :
20 May 2009 13:44:32,857 INFO : running: "PeptideProphetParser 'UPS1-01.pep.xml' EXTRAITRS=20"
20 May 2009 13:44:32,883 INFO : (X! Tandem) 20 May 2009 13:44:32,892 INFO : init with X! Tandem trypsin 20 May 2009 13:44:32,924 INFO : MS Instrument info: Manufacturer:
ThermoFinnigan, Model: LTQ, Ionization: ESI, Analyzer: Ion Trap,
Detector: EMT
20 May 2009 13:44:32,925 INFO :
20 May 2009 13:44:32,925 INFO : PeptideProphet (TPP v4.2 JETSTREAM rev 1, Build 200905191640 (linux)) AKeller@ISB 20 May 2009 13:44:32,926 INFO : read in 13 1+, 314 2+, 348 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
20 May 2009 13:44:32,926 INFO : Initialising statistical models ...
20 May 2009 13:44:32,926 INFO : negmean = -0.973112 20 May 2009 13:44:32,926 INFO : negmean = -0.111325 20 May 2009 13:44:32,926 INFO : negmean = -0.194256 20 May 2009 13:44:32,927 INFO : negmean = -0.2 20 May 2009 13:44:32,927 INFO : negmean = -0.2 20 May 2009 13:44:32,927 INFO : negmean = -0.2 20 May 2009 13:44:32,927 INFO : negmean = -0.2 20 May 2009 13:44:32,959 INFO : Iterations: .........
10.........20......
20 May 2009 13:44:32,960 INFO : model complete after 27 iterations 20 May 2009 13:44:33,017 INFO : command completed in 1 sec 20 May 2009 13:44:33,018 INFO :
20 May 2009 13:44:33,018 INFO : running: "ProphetModels.pl -i UPS1-01.pep.xml"
20 May 2009 13:44:33,305 INFO : Analyzing UPS1-01.pep.xml ...
20 May 2009 13:44:33,306 INFO : Parsing search results "/raid/labkey/ Test/Human Standard/UPS1-01 (X! Tandem)"...
20 May 2009 13:44:33,306 INFO : => Total of 110 hits.
20 May 2009 13:44:33,692 INFO : Warning: empty y range [0:0], adjusting to [0:1] 20 May 2009 13:44:33,701 INFO : Warning: empty y range [0:0], adjusting to [0:1] 20 May 2009 13:44:33,809 INFO :
20 May 2009 13:44:33,809 INFO : plot "UPS1-01.pep_IPPROB.tsv" using
2:1 title "iProphet" with line lc 2 , x notitle with line lt 0 lc -1 20 May 2009 13:44:33,811 INFO :
^
20 May 2009 13:44:33,811 INFO : "UPS1-01.pep_IPPROB.gp", line 16:
warning: Skipping data file with no valid points 20 May 2009 13:44:33,845 INFO : command completed in 0 sec 20 May 2009 13:44:33,846 INFO :
20 May 2009 13:44:33,846 INFO : running: "/usr/local/labkey/bin/cgi- bin/PepXMLViewer.cgi -I /raid/labkey/Test/Human Standard/xtandem/test8/ UPS1-01.work/UPS1-01.pep.xml"
20 May 2009 13:44:33,849 INFO : sh: /usr/local/labkey/bin/cgi-bin/
PepXMLViewer.cgi: No such file or directory 20 May 2009 13:44:33,852 INFO :
20 May 2009 13:44:33,852 INFO : command "/usr/local/labkey/bin/cgi-bin/ PepXMLViewer.cgi -I /raid/labkey/Test/Human Standard/xtandem/test8/ UPS1-01.work/UPS1-01.pep.xml" exited with non-zero exit code: 32512 20 May 2009 13:44:33,853 INFO : QUIT - the job is incomplete 20 May 2009 13:44:33,854 ERROR: Failed to remove work directory /raid/ labkey/Test/Human Standard/xtandem/test8/UPS1-01.work unexpected files
found:
UPS1-01.pep.xml
UPS1-01.pep_FVAL_1.png
UPS1-01.pep_FVAL_2.png
UPS1-01.pep_FVAL_3.png
UPS1-01.pep_FVAL_4.png
UPS1-01.pep_FVAL_5.png
UPS1-01.pep_PPPROB.png
UPS1-01.pep_IPPROB.png |