Question: ERROR running Realigner Target Creator (GATK intervals)
gravatar for sbernazz
9 months ago by
sbernazz0 wrote:

My workflow paused due to an error at the Realigner Target Creator (GATK intervals) step.

An error occured while running the tool This is the error it spit out:

Error: Unable to access jarfile /GenomeAnalysisTK.jar

Is there any way to ameliorate this? I have tried running it multiple times with no luck.

alignment jarfile galaxy gatk • 250 views
ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson25k • written 9 months ago by sbernazz0
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k wrote:


All GATK tools at Galaxy Main and in the Main Tool Shed are deprecated and may error. We will not be updating these tools.

Alternative variant analysis tools/workflows are in the Galaxy tutorials here:

The public Main Galaxy server at is presenting with job errors across many tools at this time. We are actively working to correct the issues. Please follow this ticket for updates:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 9 months ago by Jennifer Hillman Jackson25k
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