Question: GATK workflow error
gravatar for scherra
4.0 years ago by
United States
scherra0 wrote:


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?





ADD COMMENTlink modified 4.0 years ago by Jennifer Hillman Jackson25k • written 4.0 years ago by scherra0
gravatar for Jennifer Hillman Jackson
4.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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 COMMENTlink written 4.0 years ago by Jennifer Hillman Jackson25k

Thanks Jen! Everything works now.

ADD REPLYlink written 4.0 years ago by scherra0
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