storage.objects.list access error for freecredit project

mycecilia

Hi,
I ran a modified method 3-Joint-Discovery from workspace help-gatk/Germline-SNPs-Indels-GATK4-hg38. The GVCF input files failed to import. Because it's a trial account, I couldn't modify the IAM settings of the data bucket. I've searched on storage.objects.list error topics, and found the ACL setting tricks but I'm not sure which part I should modify in the workflow.

2019/03/25 05:17:02 I: Running command: sudo gsutil -q -m cp gs://fc-12f21f92-dfe5-451e-bca8-95552bd85f03/4665e834-aac7-40b7-b28f-8d574cf5be00/HaplotypeCallerGvcf_GATK4/f206209b-af79-482b-8f5b-77839edb52fb/call-MergeGVCFs/Sample_100.SpinachV2pseudo.aligned.duplicate_marked.sorted.g.vcf.gz /mnt/local-disk/fc-12f21f92-dfe5-451e-bca8-95552bd85f03/4665e834-aac7-40b7-b28f-8d574cf5be00/HaplotypeCallerGvcf_GATK4/f206209b-af79-482b-8f5b-77839edb52fb/call-MergeGVCFs/Sample_100.SpinachV2pseudo.aligned.duplicate_marked.sorted.g.vcf.gz
2019/03/25 05:17:05 E: command failed: AccessDeniedException: 403 [email protected]eaccount.com does not have storage.objects.list access to fc-12f21f92-dfe5-451e-bca8-95552bd85f03.
CommandException: 1 file/object could not be transferred.

SChaluvadi

@mycecilia
Can you confirm if the workspace bucket fc-12f21f92-dfe5-451e-bca8-95552bd85f03 (listed above in the error) is the bucket that is one that is associated with a workspace that you are an owner of? Or, is the bucket an external bucket that you are trying to import GVCF files from?

SChaluvadi

@mycecilia
Can you confirm if the workspace bucket fc-12f21f92-dfe5-451e-bca8-95552bd85f03 (listed above in the error) is the bucket that is one that is associated with a workspace that you are an owner of? Or, is the bucket an external bucket that you are trying to import GVCF files from?

mycecilia

Hi @SChaluvadi,

Thank you for the reply.

I'm the owner of the workspace, bucket fc-6caf19cb-f3dc-4cac-a72d-8c66a935f273 is the one associated with the workspace. Bucket fc-12f21f92-dfe5-451e-bca8-95552bd85f03 is associated with another workspace that's not owned by me but was cloned into my current workspace. I double checked with the lab mate who owned Bucket fc-12f21f92-dfe5-451e-bca8-95552bd85f03. That bucket is not active anymore.

I don't understand where the method read the false file path from, because the GVCF file input was defined as this.samples.output_vcf in the method configuration. And, in my metadata for Sample_100, the output_vcf column actually has value of gs://fc-6caf19cb-f3dc-4cac-a72d-8c66a935f273/05a8d79c-c02c-4de8-9cbf-9289a736ec12/HaplotypeCallerGvcf_GATK4/508dc43c-5ee2-43f9-ae21-29aa4c3b65cb/call-MergeGVCFs/Sample_100.SpinachV2pseudo.aligned.duplicate_marked.sorted.g.vcf.gz. The other samples in the sample set got assigned the right file path except for Sample_100.

Cecilia

SChaluvadi

@mycecilia
Can you ask your lab mate what they mean by "inactivated"? Does this mean that the bucket has been deleted permanently? If you could, sharing your workspace with [email protected] along with the name of the workspace and Method will make trouble-shooting much easier!

mycecilia

The problem was caused by me ignoring to configure the output for the previous step so that the records in metadata didn't update correctly. After I correct the configuration of HaplotypeCaller and rerun it, the wrong path doesn't come up in JointGenotyping step anymore.