Error at scorer.cpp

[Taejoon Kwon]

Hi,

I've got an error as below:

crux: scorer.cpp:1769: void add_intensity(FLOAT_T*, int, FLOAT_T):
Assertion `add_idx >= 0' failed.

I tested (1) crux-1,36-binary (linux x86), (2) crux-1.36 after compile
(ubuntu 10.10, kernel 2.6.32, libstdc++6-4.4), and (3)
crux-1.35-binary (linux x86), but all runs were terminated with the
same error. I also tested both 'sequest-search' and
'search-for-matches', so it may somewhat related to fundamental code
in crux.

Just in case, I posted ms2 & DB fasta file that I used for this test
on my website (I converted Thermo RAW file to mzXML first (32bit
encoding) with msconvert, then convert it again to ms2 with msconvert
included in crux+tide package).

http://www.marcottelab.org/users/taejoon/test.ms2
http://www.marcottelab.org/users/taejoon/XENLA_prot_v4.combined.fasta

Could you let me know how I can resolve this error?

Thanks,

Taejoon

--
-=-=-=-=-
Marcotte Lab http://www.marcottelab.org
Institute for Cellular and Molecular Biology
University of Texas at Austin

[Sean McIlwain]

Taejoon Kwon,

Looking at your fasta file, I see that there are some protein sequences that contain the amino acid J.  I believe that this amino acid letter is supposed to mean that the residue is either I or L.  The next release of crux will handle sequences that contain the amino acid J, but as a temporary fix you can replace all of the J amino acids within your fasta file with either I or L.

Thanks,
Sean

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Sean J. McIlwain, Ph. D.
Post-doctoral Fellow, Noble Lab,
Dept. of Genome Sciences,
University of Washington
http://noble.gs.washington.edu/~mcilwain