Re: [Samtools-help] Can't manage to convert SAM to BAM

[Thomas W. B. <tb...@um...>]

Marine  -

The command lines look good.  Could this be a local file system 
problem -- "no space left on device", or something like that ? 
Or a typing error in one of the file names ?  I'm just guessing, 
but that's what I would look for.

Oh, just remembered:  a favorite error of mine used to be making 
<out.prefix> the same as the name of the unsorted input .bam file. 
When I do that, the unsorted .bam file gets deleted from the file 
system before it is ever read.  The two file names have to be 
different.

 	 	 	 	 	-  tom blackwell  -

On Wed, 4 Jun 2014, Marine Rohmer wrote:

> Hello Samtools team,
>
> I try to convert some SAM files to BAM files following the FAQ method :
> First indexing my reference fasta file (I have no header in my SAM file)
> :
> samtools faidx ref.fa
> Then converting my SAM file to BAM file :
> samtools view -bt ref.fa.fai aln.sam > aln.bam
>
> Until here, everything seems fine, but...
>
> When trying to sort my BAM file :
> samtools sort aln.bam aln-sorted
> I instantly get :
> [bam_header_read] invalid BAM binary header (this is not a BAM file).
> [bam_sort_core] truncated file. Continue anyway.
> Seegmentation fault (core dumped)
>
> I really don't understand what is happening. My SAM file seems OK.
> Several weeks ago I've already done that on another data and everything
> went fine... Could someone tell me what is wrong ?
> I'd be very grateful if someone could help me !!! :)
>
> Hoping I'm writing to good mailing list
>
> Best regards,
>
> Marine
>
>
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