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Failure during junction identification #50

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?

1. I will run it again from scratch with the same files although restarting it 
at the Identifying Junction Candidates causes the problem to reoccur.

What version of the product are you using? On what operating system?

Breseq 0.19 on OSX 10.7.4, compiled with default settings, using Bowtie2 beta 7 
and R 2.15.1 beta

Please provide any additional information below.

I am running Breseq 0.19 on osx 10.7.4 with the B. subtilis 000964.3 refseq 
genome and some 50bp paired end Illumina fastq files from CASAVA 1.8. It worked 
properly with at least one sample from the same run, but with another it fails 
during Identifying junction candidates with

!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR <!!!!!!!!!!!!!!!!!!!!!!!
Incorrect junction sequence length for 
NC_000964__16__-1__NC_000964__283706__-1__19____-3__101__0__0
-----many many lines of nucleotide sequence-----
FILE: candidate_junctions.cpp   LINE: 1406
!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR <!!!!!!!!!!!!!!!!!!!!!!!
Assertion failed: (false), function my_assertion_handler, file 
libbreseq/common.h, line 92.
Abort trap: 6

Original issue reported on code.google.com by jonat...@allthestairs.com on 5 Sep 2012 at 10:06

GoogleCodeExporter commented 8 years ago 
Due to overlap extending past the end of a sequence in a rare junction case. 
Will be fixed in 0.20 release.

Original comment by jeffrey....@gmail.com on 14 Sep 2012 at 6:27