Jason Cerrato
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Activity overview
Latest activity by Jason Cerrato-
Jason Cerrato commented,
Genevieve-Brandt-she-her I'm seeing the WDL for the script in the Workflow Dashboard here. This is the relevant part of the WDL: Combined with the input for the task command_mem_gb_sort = 550comm...
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Jason Cerrato created a post,
Fatal error detected by the Java Runtime Environment when running MarkDuplicates
This issue is being filed on behalf of Eduardo Maury. Description of issue Eduardo Maury wrote to Terra Support to get assistance with running this featured workflow processing-for-variant-discover...
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Jason Cerrato commented,
Hi joy bordini, My name is Jason and I'm one of the Terra Support Specialist. I'm not very familiar with the requirements for snakemake, but I may have some ideas for how you can leverage Terra for...
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Jason Cerrato commented,
Hi Wang Ziwei, Apologies for the delay on this issue. Did you happen to isolate the root cause of the discrepancy you were experiencing between running on command line and running in the docker? Ki...
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Jason Cerrato commented,
Hi Priyanka Sebastian, Thanks for writing in. Based on your message, I believe you are running these workflows on your own Cromwell instance rather than on Terra, is that correct? Even if you are n...
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Jason Cerrato commented,
Hi Mia, I'm glad to hear you were able to get it working after removing the two variants. The Github issues section will be the best place to go to keep track of work done toward solving these bugs...
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Jason Cerrato commented,
Hi Mia, I'm seeing this in your .log file: 23:37:25.124 INFO Funcotator - Shutting down engine[August 28, 2020 11:37:25 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elaps...
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Jason Cerrato commented,
Hi Mia, Here's what I've heard back from the author. Short answer to all 3: It should accept a vcf.gz.tbi, and everything should "just work" With respect to #3 - Yes - I think it sho...
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Jason Cerrato commented,
Hi Maira, You can share the information here if you are comfortable doing so. No one will be able to access the workspace or job details unless you give them permission. If you are not comfortable ...
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Jason Cerrato commented,
Hi Mia, I've heard back from the author. They were able to reproduce the error with the variant you provided. They're digging deeper into the issue, but they think it's looking like a bug. In the ...