Just to keep the list in the loop, this was posted over on seqanswers too
and the cause ended up being that "-Sbt" was needed rather than just "-bt".
Version 0.1.18 was being used, but even there -t looks like it forces -S in
the code, so it's still unclear why this happened (perhaps a transient
filesystem error caused a malformed BAM file and all that was needed was
rerunning the conversion). But in any case, Marine was able to get the file
converted.
Devon
--
Devon Ryan, Ph.D.
Email: [email protected]
Laboratory for Molecular and Cellular Cognition
German Centre for Neurodegenerative Diseases (DZNE)
Ludwig-Erhard-Allee 2
53175 Bonn
Germany
<[email protected]>
On Wed, Jun 4, 2014 at 2:49 PM, Thomas W. Blackwell <[email protected]>
wrote:
> 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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