[Bio-bwa-help] "the maximum barcode length is 15" error with bwa samse

[Jaaved M. <jm...@co...>]

Hi 

I am trying to align some Sanger sequencing reads to the D. simulans
assembly with BWA and I'm getting the error "the maximum barcode length is
15" when converting from BWA output format to SAM. Does anyone know how to
fix or workaround this error. Actually, I'm trying to align the same reads
from when this genome was first assembled back unto the droSim1 reference
assembly (downloadable from UCSC Genome Browser).

Here are the commands I've used to align the reads and convert to SAM
format:
bwa bwasw -t 16 -f c1674_clean.sam droSim1bwaidx c1674_clean.fq
bwa samse -f c1674_clean.sam droSim1bwaidx c1674_clean.sai c1674_clean.fq


It is the last command that outputs 
 [bwa_read_seq] the maximum barcode length is 15

It happens almost immediately once the command is executed. I don't think it
is an out-of-memory issue like other Seqanswers.com posts seem to suggest.


I'm using BWA version 0.5.9-r16 on RHEL5.5 machine with 8 processors and
16GB of RAM. As far as I can tell no barcoding was done with Sanger
sequencing, so these sequences I’m trying to align are bona fide genomic
DNA. 

The input files are large (659MB) and can be obtained temporarily
from http://compgen.bscb.cornell.edu/~jm889/perm/c1674.zip

Any help is greatly appreciated.
Thanks,
Jaaved