I was running xinteract on a number of MS runs with a command-line of:
xinteract -x20 -p0 -OlAp *.xml. The data were collected on a QTrap
and searched with X!Tandem (kscore).
PeptideProphet itself seemed to run OK, although I got this warning
"WARNING: Found unanticipated cleavage in refinement mode. Turning
off NTT model."
When running this command:
running: "/tools/bin/TPP/tpp-trunk-4635/bin/ProphetModels.pl -i
interact.pep.xml"
hit a die statement with the output shown at the bottom. In my
version of the script line 628 is this conditional:
if ($fdr_pp*(1-$fdr_pp)/$num_pos_pp > 0){
$PP_uncert = sqrt($fdr_pp*(1-$fdr_pp)/$num_pos_pp);
}
So $num_pos_pp appears to be zero. It may be that one file simply has
no data, but wanted to report the error.
-Dave
Parsing search results "../YKB_OnlyCys_CAM_04Aug09-
dp_ykb2_only_cyscam_2ndrun (X! Tandem (k-score))"...
=> Total of 916 hits.
Warning: empty y range [0:0], adjusting to [0:1]
Warning: empty y range [0:0], adjusting to [0:1]
Illegal division by zero at /tools/bin/TPP/tpp-trunk-4635/bin/
ProphetModels.pl line 628.
Using decoy ratio of 0.520158182401739 for PeptideProphet.
command "/tools/bin/TPP/tpp-trunk-4635/bin/ProphetModels.pl -i
interact.pep.xml" exited with non-zero exit code: 6400
QUIT - the job is incomplete
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