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Question: GATK workflow error
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gravatar for scherra
4.0 years ago by
scherra • 0
United States
scherra • 0 wrote:

Hi,

I have been using a workflow to analyze sequencing data has previously worked well, but recently the workflow has failed at steps using GATK tools. The GATK tools work fine when used individually, but when compiled into a workflow the 'false' settings are changed to 'true', which then causes an error.

For example in the Unified Genotyper tool, I set the "Disable experimental low-memory sharding functionality" to 'false'. When run as part of the workflow, this option is switched to 'true' and leads to an error "ERROR MESSAGE: Argument with name 'disable_experimental_low_memory_sharding' isn't defined." I can fix this issue by running each tool individually and unchecking the boxes, but that defeats the purpose of the workflow. Does anyone know what would be causing this problem? Is it a Galaxy issue or a GATK issue?

Thanks

 

 

 
workflow software error galaxy gatk • 1.2k views
ADD COMMENT • link •
modified 4.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.0 years ago by scherra • 0
0
gravatar for Jennifer Hillman Jackson
4.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This was most likely caused by a specific issue with the Workflow processing itself that has now been resolved. Please try your workflow again and let us know if the problem persists.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 4.0 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jen! Everything works now.

ADD REPLY • link written 4.0 years ago by scherra • 0
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