On Tue, Apr 24, 2012 at 10:03 AM, Ciara Ledero <lederoc@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