MosaikAlign: ERROR: Found a gap in both the reference sequence and query sequence.

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What steps will reproduce the problem?
1. create ref library using MosaikBuild
2. convert FASTQ file derived from 454 reads using MosaikBuild
3. Run the MosaikAlign command below

What is the expected output? What do you see instead?

I get the following error with certain input FASTQ files, but not all:

fedora@fedora ~]$ /usr/bin/mosaik-aligner/bin/MosaikAligner -bw 51 -rur
/mnt/hgfs/Experiments/8357/library/Binned/GCDLV3C01.MID03/SBT/GCDLV3C01.MID03.mo
saik.unaligned.fastq
-out
/mnt/hgfs/Experiments/8357/library/Binned/GCDLV3C01.MID03/SBT/GCDLV3C01.MID03.mo
saik
-in
/mnt/hgfs/Experiments/8357/library/Binned/GCDLV3C01.MID03/SBT/GCDLV3C01.MID03.bo
wtie.unaligned.dat
-ia /mnt/hgfs/Experiments/8357/library/Shared/mosaik.dat
------------------------------------------------------------------------------
MosaikAligner 1.0.1388                                              2010-02-01
Michael Stromberg & Wan-Ping Lee  Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- Using the following alignment algorithm: all positions
- Using the following alignment mode: aligning reads to all possible locations
- Using a maximum mismatch threshold of 4
- Using a Smith-Waterman bandwidth of 51
- Reporting all unaligned reads to
/mnt/hgfs/Experiments/8357/library/Binned/GCDLV3C01.MID03/SBT/GCDLV3C01.MID03.mo
saik.unaligned.fastq.
- Using a homo-polymer gap open penalty of 4

Hashing reference sequence:
100%[==================================================================]
3,920,035 ref bases/s        in  1 s  

- loading reference sequence... finished.

Aligning read library (2207):
 0% [                                                                     
]    0.9970 reads/s      ETA 36:52 \ERROR: Found a gap in both the
reference sequence and query sequence.

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

Fedora 12.  mosaik 1.0.1388

Please provide any additional information below.

This error occurs sporadically from certain FASTQ files.  I have used this
approach successfully with many comparable fastq files.  please let me know
if i can provide other information to help.

Original issue reported on code.google.com by bbimber@gmail.com on 1 Jun 2010 at 11:48