Hi,
I have run the xtandem with k-score enabled and then I was able to
produce pepXML file without any issues.
At this stage I am able to view the results using pepXMLViewer and
then I run the pipeline as follows, the pipeline ended with exit code
at the last. On a separate execution, I am not able to view the
interact-padulaxtandemjagan-J2597_interact.pep.xml' immediately after
running PeptideProphetParser.
I wonder anyone give some advice on it please.
Here is the complete pipeline execution ....
========================================================================
[r...@apcf-hn3 Tutorial]# /var/www/tpp/bin/xinteract -
Npadulaxtandemjagan-J2597_interact -p0.05 -l7 -O -X-m1.0 -A-lC-r0.5
padulaxtandemjagan-J2597_pep.xml
/var/www/tpp/bin/xinteract (TPP v4.3 JETSTREAM rev 1, Build
200911041458 (linux))
naming output file interact-padulaxtandemjagan-J2597_interact.pep.xml
running: "/var/www/tpp431/bin/InteractParser 'interact-
padulaxtandemjagan-J2597_interact.pep.xml' 'padulaxtandemjagan-
J2597_pep.xml' -L'7'"
file 1: padulaxtandemjagan-J2597_pep.xml
processed altogether 4 results
results written to file /mnt/sanfs/APCF/TPP/Tutorial/interact-
padulaxtandemjagan-J2597_interact.pep.shtml
command completed in 0 sec
running: "/var/www/tpp431/bin/PeptideProphetParser 'interact-
padulaxtandemjagan-J2597_interact.pep.xml' MINPROB=0.05"
(X! Tandem (k-score))
init with X! Tandem (k-score) trypsin
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization:
UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 200911041458
(linux)) akel...@isb
read in 0 1+, 4 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
Initialising statistical models ...
negmean = 0.0533258
negmean = 1
negmean = -0.2
negmean = -0.2
negmean = -0.2
negmean = -0.2
negmean = -0.2
Iterations: .........10.........20
model complete after 21 iterations
command completed in 1 sec
running: "/var/www/tpp431/bin/ProphetModels.pl -i interact-
padulaxtandemjagan-J2597_interact.pep.xml"
Analyzing interact-padulaxtandemjagan-J2597_interact.pep.xml ...
Parsing search results "padulaxtandemjagan-J2597 (X! Tandem (k-
score))"...
=> Total of 0 hits.
"interact-padulaxtandemjagan-J2597_interact.pep_FVAL.gp",
line 4: undefined variable: out
"interact-padulaxtandemjagan-J2597_interact.pep_PPPROB.gp",
line 5: undefined variable: out
"interact-padulaxtandemjagan-J2597_interact.pep_IPPROB.gp",
line 5: undefined variable: out
command completed in 0 sec
running: "/var/www/tpp431/bin/XPressPeptideParser 'interact-
padulaxtandemjagan-J2597_interact.pep.xml' -m1.0"
command completed in 0 sec
running: "/var/www/tpp431/bin/ASAPRatioPeptideParser 'interact-
padulaxtandemjagan-J2597_interact.pep.xml' -lC -r0.5"
command completed in 0 sec
running: "/var/www/tpp431/bin/DatabaseParser 'interact-
padulaxtandemjagan-J2597_interact.pep.xml'"
command completed in 0 sec
running: "/var/www/tpp431/bin/RefreshParser 'interact-
padulaxtandemjagan-J2597_interact.pep.xml' '/home/APCF/databases/
Ludwig/LudwigNR_generic_forward.fasta.pro'"
- Building Commentz-Walter keyword tree... - Searching the tree...
- Linking duplicate entries... - Printing results...
command completed in 55 sec
running: "/var/www/tpp431/cgi-bin/PepXMLViewer.cgi -I /mnt/sanfs/APCF/
TPP/Tutorial/interact-padulaxtandemjagan-J2597_interact.pep.xml"
command "/var/www/tpp431/cgi-bin/PepXMLViewer.cgi -I /mnt/sanfs/APCF/
TPP/Tutorial/interact-padulaxtandemjagan-J2597_interact.pep.xml"
exited with non-zero exit code: 11
QUIT - the job is incomplete
[r...@apcf-hn3 Tutorial]#
=========================================================================
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