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,
On Mon, Mar 9, 2015 at 8:08 AM, Scott Szakonyi <Scott.B.Szakonyi.1(a)nd.edu>
I have a user who is getting the following error when analyzing a FASTQ
file using TopHat for Illumina.
[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.
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
Scott B. Szakonyi
*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
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