Question: Cloudman instance: Tophat error
gravatar for karmella.haynes
2.3 years ago by
United States
karmella.haynes40 wrote:

Hello community,

I am encountering the following error when I try to run Tophat Galaxy Version 0.9 within my Cloudman instance:

[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. Fatal error: Tool execution

My inputs are fastq.gz files that I trimmed (outside of Galaxy) with Trimmomatic, then uploaded as fastqsanger (Human hg19).

Am I using the wrong type of input?

Thank you for your help.

ADD COMMENTlink modified 2.3 years ago by Jennifer Hillman Jackson25k • written 2.3 years ago by karmella.haynes40
gravatar for Jennifer Hillman Jackson
2.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The first pass solution is to allocate more memory for the analysis.

This is how to scale up the head/worker nodes on a cloudman instance (see item 5):

Best, Jen, Galaxy team

ADD COMMENTlink written 2.3 years ago by Jennifer Hillman Jackson25k
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