Re: [Bio-bwa-help] BWA error

[Nakhoul, H. N <hna...@tu...>]

Dear all,

I'm getting the same error while trying to run bwa mem on paired-end reads against a combined human-virus index. This virus's DNA is expected to integrate at random sites in the human genome, so could it be that my problem is similar to what Won experienced with circular DNA? Here's the command:

bwa mem -t 24 $combined_index $fq_1 $fq_2 > output.sam

Assertion failed: (*beg <= mid && mid < *end), function bns_fetch_seq, file bntseq.c, line 394.
Abort trap: 6

Indices built from the human or viral genomes individually work fine, however. I've tried both bwa 0.7.9a and 0.7.10 on Mac OS X 10.7.5. I'd be grateful for any help you can provide.

Thanks,
Hani Nakhoul





This should be a bug. Is your data publicly available? Or could you send me part of the input files that may trigger the issue? I promise to only use the data for the debugging purpose.

Thanks a lot,

Heng

On May 19, 2014, at 3:53 PM, Won C Yim <wyim@...> wrote:

> Dear All,
> 
> 
> I am using bwa mem to align paired end reads to repeat sequence (circular; chloroplast). 
> 
> The command is like:
> bwa mem -t 14 -M index_assembly read1.fastq.gz read2.fastq.gz 2> bwalog 1>
> output.sam
> 
> this run encounter the error message: 
> 
> Assertion failed: (*beg <= mid && mid < *end), function bns_fetch_seq, file bntseq.c, line 394.
> Abort trap: 6
> 
> I know this repeat region of circular genome is dirty job.
> 
> But is it normal? and is there anyway to get SAM file?
> 
> Thank you.
> 
> Won
> 
> 
> __
> Yim, Won Cheol
> 
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> 
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