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Question: ERROR running Realigner Target Creator (GATK intervals)
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gravatar for sbernazz
9 months ago by
sbernazz • 0
sbernazz • 0 wrote:

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

An error occured while running the tool toolshed.g2.bx.psu.edu/repos/devteam/realigner_target_creator/gatk_realigner_target_creator/0.0.4 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
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modified 9 months ago by Jennifer Hillman Jackson ♦ 25k • written 9 months ago by sbernazz • 0
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gravatar for Jennifer Hillman Jackson
9 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

All GATK tools at Galaxy Main https://usegalaxy.org and in the Main Tool Shed https://usegalaxy.org.toolshed are deprecated and may error. We will not be updating these tools.

Alternative variant analysis tools/workflows are in the Galaxy tutorials here: https://galaxyproject.org/learn/

The public Main Galaxy server at https://usegalaxy.org 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: https://biostar.usegalaxy.org/p/26580/.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 9 months ago by Jennifer Hillman Jackson ♦ 25k
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