Hi, I frequently get the following error when using BWA 0.4.6 to do alignments:
[bns_coor_pac2real] bug! Coordinate is longer than sequence (4294967295>=98936). Abort!
I've tracked down some cases that seem to trigger this, and it seems to occur when a read is mapped by BWA 'aln' (slightly) off of the end of a reference sequence.
A subsequent call to BWA 'samse' will then produce this error, presumably because the read has a negative (wraparound) coordinate relative to the beginning of the reference sequence. Some kind of sign/underflow error related to this case.
To replicate: Choose some relatively short sequence (1000-2000nt will do.) Generate some simulated reads from this sequence (e.g. use Maq 'simulate', I've been working with 35-50nt reads). Create enough reads that all start points in the ref sequence will be covered with good quality reads.
Now, trim the front end off of this ref sequence (say 100nt) and build a BWA index (-a is) with this new trimmed ref sequence. Use BWA to Align your reads from above to the index. (aln -c -t 8 -n 4) Now run bwa samse. You should eventually get the error I get above.
I have been doing alignments in color space, and I run samse with the -n INT option, and I have not tested for this error outside of those settings, so you *may* need to do the same to replicate.
The error seems to occur when a read is placed by bwa aln like this: (R= read, S= ref sequence)
The n bases of the read dangling off the front end of the reference sequence cause the samse to abort.
Thanks for any help. Other than this, BWA is turning out to be a very useful tool, so I hope this is easy to fix!
Cheers, Vaughn (vsi at u.washington.edu)
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