On Tue, Apr 24, 2012 at 10:03 AM, Ciara Ledero <lede...@gmail.com> wrote:
> Hi there,
>
> I know  Galaxy already has a SAM-to-BAM converter, but part of my
> exercise/task is to incorporate a script that uses samtools' view command. I
> get this error:
>
> [samopen] SAM header is present: 66338 sequences.
>
> according to Galaxy. But this might not be an error at all. Is  there any
> way that I could tell Galaxy to ignore this and just continue with the
> script?
>
> Thanks in advance! Any help would be greatly appreciated.
>
> CL

As you have probably guessed, that is not an error. Rather it is
a progress/diagnostic message from samtools printed to stderr.

There is a long standing bug with Galaxy assuming that any
output on stderr indicates a failure, despite typical usage on
Unix/Linux for progress, diagnostics or warning messages:
https://bitbucket.org/galaxy/galaxy-central/issue/325/

In this situation Galaxy tools use a wrapper script to cope
with these non-error messages. That should be happening
already with sam_to_bam.py - but I am unclear if you are
having a problem with the provided SAM to BAM tool, or
your own tool which uses samtools internally.

Peter

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