Zih-Hua Fang

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3. Issue with accessing the external bucket for ImportGVCFs task in GATK joint-genotyping workflow

Hi Emil, I would like understand more about the pet-service account access to the Google bucket (gs://amp-pd-genomics). I ran a test on Terra terminal to check if I have access to all the files in ...

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• Edited November 03, 2021 17:31
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3. Issue with accessing the external bucket for ImportGVCFs task in GATK joint-genotyping workflow

Hi Emil, I have checked the difference, and there was no difference for the script block of this particular task (task ImportGVCFs). Best wishes, Zih-Hua

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• November 02, 2021 18:27
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3. Issue with accessing the external bucket for ImportGVCFs task in GATK joint-genotyping workflow

Hi Emil, I want to report that when I increase the number of the samples in the sample map, the permission issue happened across all the shards.  In my previous tests (the ones that I reported the ...

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• November 02, 2021 11:23
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3. Issue with accessing the external bucket for ImportGVCFs task in GATK joint-genotyping workflow

Dear Emil, I understand your point for the temporary solution. I will continue to submit the workflow with call-caching enabled while waiting for the definite solution. I just want to point out tha...

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• October 29, 2021 08:43
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3. Issue with accessing the external bucket for ImportGVCFs task in GATK joint-genotyping workflow

Hi Emil, I have shared the workspace (name: GP2 Sequencing). Here are the relevant submission IDs (I tested the same workflow and the same input for three times): ee826f08-f778-484c-9f96-efc4fac639...

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• Edited October 26, 2021 15:39
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3. Issue with accessing the external bucket for ImportGVCFs task in GATK joint-genotyping workflow

Hi Emil, Thank you for following up on this issue. I understand that the "get" access for the Google bucket. However, the ImportGVCFs task run on the same sample map with just different intervals (...

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• October 21, 2021 07:24
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Issue with accessing the external bucket for ImportGVCFs task in GATK joint-genotyping workflow

Hi, I am running Joint-genotyping workflow on Terra. The ImportGVCFs task was performed in parallel with shards. However, not all the shards were run successfully. I got the error message for the G...

• Zih-Hua Fang
• Edited October 19, 2021 15:23
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