Samuel Terkper Ahuno

Do you want to abort this job? Y/N

Dear Terra Support,   please could you make `Abort` a two step process and the option of checking `don't ask me again?` i think i mistakenly aborted some jobs.   thanks S

• Samuel Terkper Ahuno
• Edited August 07, 2020 11:21
• 2 followers
• 1 comment
• 1 vote

1. Community
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3. cnv-somatic workflow not compatible with gatk latest versions (4.1.7.0 above)

Hi Samantha (she/her)    i confirm cnv-somatic-pair workflow version 4.1.7.0 works with corresonponding gatk docker 4.1.7.0   thanks S

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• July 29, 2020 00:52
• 0 votes

1. Community
2. General Discussion
3. cnv-somatic workflow not compatible with gatk latest versions (4.1.7.0 above)

Hi Samantha (she/her) just to be sure we not missing anything I repeated cnv-somatic-wokflow with same parameters;    Repeated subissions with "us.gcr.io/broad-gatk/gatk:4.1.8.0" ; Submission ID- 1...

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• July 28, 2020 17:41
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1. Community
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3. cnv-somatic workflow not compatible with gatk latest versions (4.1.7.0 above)

Hi Samantha (she/her) I have shared workspace with GROUP_FireCloud-Support@firecloud.org email;    - failed - gatk 4.1.7.0; submission-id: b5b9e7a1-bbd6-4fda-a356-96ae196c0370 - failed - gatk:4.1.8...

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• July 28, 2020 15:09
• 0 votes

cnv-somatic workflow not compatible with gatk latest versions (4.1.7.0 above)

Hi, Has anyone had success running cnv-somatic workflow with latest versions of gatk? fails at `PlotDenoisedCopyRatiosNormal` Task when run with docker gatk 4.1.8.1 , 4.1.8.0 & 4.1.7.0 Error; CNVSo...

• Samuel Terkper Ahuno
• July 28, 2020 11:08
• 2 followers
• 7 comments
• 0 votes

1. Platform-wide (security, status and updates)
2. Service Notifications
3. Service Incident - July 7, 2020

I think it's now resolved, I run workflows paired-fastq-to-ubam, preprocessing for variant discovery and haplotype-caller on WES 216 samples yesterday evening without any errors (except user input ...

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• July 09, 2020 12:55
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3. GenotypeGVCFs error; A USER ERROR has occurred: use-new-qual-calculator is not a recognized option

i spotted where the error is coming from; it appears the work JointCalling workflow is not compliant with latest versions of gatk (4.1.6.0) and 4.1.5.0. and throws the error A USER ERROR has occurr...

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• April 03, 2020 14:34
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GenotypeGVCFs error; A USER ERROR has occurred: use-new-qual-calculator is not a recognized option

Hello Terra,  I am running JointCalling on Whole Exome samples using clone of this workflow  however the GenotypeGVCFs tasks keeps failing with this error in all the shards; `A USER ERROR has occur...

• Samuel Terkper Ahuno
• April 03, 2020 03:41
• 2 followers
• 2 comments
• 0 votes

1. Community
2. General Discussion
3. are there Alternatives for JointCalling (Germline variant calling) for <50 samples?

Hi Jason Cerrato is there a particular reason why jointGenotyping has been capped at >= 50 samples? although, gatk best practices recommends a joint-calling for larger cohort  i still need to perfo...

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• April 03, 2020 03:15
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