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.Szakonyi.1@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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