Hello,

I would start by confirming the SAMTools indexes and tool installs. Confirm
that you can execute SAMTools tool's successfully within Galaxy. If there
are problems, check to see if there is a PATH issue. Make sure the "galaxy
user" is accessing the correct version (and indexes for reference genomes
used). If you are using a cluster, then confirm the tools/indexes are
configured correctly there, too.

Hopefully this helps,
Jen
Galaxy team

On Mon, Mar 9, 2015 at 8:08 AM, Scott Szakonyi <scott.b.szakony...@nd.edu>
wrote:

> Hello all,
>
> I have a user who is getting the following error when analyzing a FASTQ
> file using TopHat for Illumina.
>
> TopHat v2.0.10
> [bam_header_read] EOF marker is absent. The input is probably truncated.
> [bam_header_read] invalid BAM binary header (this is not a BAM file).
> [bam_index_core] Invalid BAM header.
> [bam_index_build2] fail to index the BAM file.
> Error indexin
>
>
> I've tried reloading the tool and all it's dependencies, to no avail.
> We've been able to run the same FASTQ file successfully on another Galaxy
> server with identical tool configuration. I'm out of ideas, being
> relatively new to Galaxy. Has anyone seen a similar error? Can you offer an
> possible solutions?
>
> Thanks!
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
>
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-- 
Jennifer Hillman-Jackson
http://galaxyproject.org
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