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. 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
I happens almost immediately as well once the command is executed. I don't think it is an out-of-memory issue like other posts seem to suggest.
I'm using BWA version 0.5.9-r16 on RHEL5.5 machine with 16 processors and 48GB of RAM. As far as I can tell no barcoding was done with Sanger sequencing.
The input files are large (659MB), but I can put it up somewhere for download temporarily.
Any help is greatly appreciated.
Thanks,
David
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. 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
I happens almost immediately as well once the command is executed. I don't think it is an out-of-memory issue like other posts seem to suggest.
I'm using BWA version 0.5.9-r16 on RHEL5.5 machine with 16 processors and 48GB of RAM. As far as I can tell no barcoding was done with Sanger sequencing.
The input files are large (659MB), but I can put it up somewhere for download temporarily.
Any help is greatly appreciated.
Thanks,
David
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