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storage.objects.list access error for freecredit project

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.

Best Answer


  • myceciliamycecilia Member

    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.


  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    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!

  • myceciliamycecilia Member

    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.

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