Re: [Bio-bwa-help] bwa mem error with failure: [bns_restore_core] Parse error reading ref.fa.amb

[Heng Li <lh...@me...>]

Is your reference genome public? Could you share it with me? It is strange that aln works but bwa-mem not. They use the same code to read ref.fa.amb. For now, I have no clue about where goes wrong.

Thanks,

Heng

On Jan 5, 2015, at 12:41, Steve Salipante <stevesal@u.washington.edu> wrote:

> Hi:
> 
> I am experiencing a problem using bwa mem to align illumina PE reads to a custom reference genome.  The custom reference genome is a multi-fasta composed of a number of individual gene sequences (one per fasta) parsed from various bacterial genomes. 
> 
> Notably, I am able to successfuly align my reads to this reference genome using "bwa aln" -- I only get the failure when I invoke "bwa mem".
> 
> Here's the commands I used to format the reference genome and analyze:
> 
> #format ref genome
> bwa index -a bwtsw ref.fa
> samtools faidx ref.fa
> 
> #this command works fine
> bwa aln ref.fa Read1.fastq.gz Read2.fastq.gz > aln.pe
> 
> #this command fails
> bwa mem ref.fa Read1.fastq.gz Read2.fastq.gz > mem.pe
> #with the error
> [bns_restore_core] Parse error reading ref.fa.amb
> 
> I have tried using bwa v0.7.10 and v0.7.12, and get the same error.  I have tried samtools v1.1 and v0.19, and similarly get the same error with both versions of bwa.  I am not sure if this is a bug or if I am doing something wrong. 
> 
> I think the error is similar to those in prior reports, but these prior reports do not have posted solutions and do not appear to be addressed:
> http://sourceforge.net/p/bio-bwa/mailman/message/31605571/
> http://sourceforge.net/p/bio-bwa/mailman/message/32423730/
> 
> Any help you can provide would be very much appreciated.
> 
> Best,
> 
> Steve
> 
> 
> 
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