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The problem with running xinteract on OMSSA pepxml
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Subject: The problem with running xinteract on OMSSA pepxml
From: Ping <yanpp...@gmail.com>
To: spctools-discuss <spctools-discuss@googlegroups.com>
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Hi,
I am trying to run the xinteract on the omssa pep.xml output files. my
omssa's version is 2.1.4, my TPP version is 4.2.1. But I couldn't get
it through. I search the old post, there is a similar post, but the
problem was solved by specifying enzyme to xinteract.
I tried it, but is still not working. InteractParse went through, but
PeptideProphetParser got stuck by a segmentation fault.
Any help would be greatly appreciated!
Many Thanks,
Ping
***** output for interactParser and PeptideProphetParser
InteractParser 'interact.pep.xml' 'omssa.pep.xml' -L'7' -E'trypsin' -C
-P
file 1: ParoSaliv_SHAM_03.pep.xml
processed altogether 2623 results
PeptideProphetParser 'interact.pep.xml' DECOY=DECOY MINPROB=0
NONPARAM
Using Decoy Label "DECOY".
Using non-parametric distributions
(OMSSA) (minprob 0)
WARNING!! The discriminant function for OMSSA is not yet complete. It
is presented here to help facilitate trial and discussion. Reliance
on this code for publishable scientific results is not recommended.
init with OMSSA Trypsin
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization:
UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
PeptideProphet (TPP v4.2 JETSTREAM rev 1, Build 200905131510
(linux)) AKeller@ISB
read in 75 1+, 1790 2+, 749 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
Initialising statistical models ...
WARNING: No decoys with label DECOY were found in this dataset.
reverting to fully unsupervised method.
Iterations: .........10.........20
Segmentation fault
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