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