Unable to access gs://firecloud-tcga-open-access/tutorial

calbachcalbach Member
edited December 2016 in Ask the FireCloud Team

Attempted to follow tutorial here:
http://gatkforums.broadinstitute.org/firecloud/discussion/6863/broad-mini-mutation-calling-workflow

After creating a billing enabled project and cloning the workspace, my workflow run is failing because it cannot access these files. My understanding is that this data is not controlled access and so I shouldn't need to do any additional account linking, as described here:
"""
How do I access controlled access TCGA data in FireCloud? To access workspaces in FireCloud containing controlled access data, you must have an eRA Commons or NIH account with dbGaP authorization; and link your FireCloud account to that eRA Commons or NIH account.
"""

My workspace is called "billing-trial-test/MiniMutationCalling_V1_Tutorial".

Answers

  • jneffjneff BostonMember, Broadie, Moderator admin

    You shouldn't need to do any additional linking. I'm looking into this internally to see if there's a known bug. We'll get back to you soon.

  • jneffjneff BostonMember, Broadie, Moderator admin

    There's a known issue where users experience a lag in receiving access to a Google bucket for a newly created workspace. Please try to re-run your workflows now and see if you can click on the Google bucket in the workspace summary tab.

    Let us know if you continue to experience issues.

    Thanks,
    Jason

  • calbachcalbach Member

    Hi Jason,

    Thanks. I'm able to click through to the Google bucket associated with my workspace. However, the workflow still fails with an inability to stage the TCGA data:

    From the JES logs:
    """
    2016/12/15 18:55:04 I: Running command: sudo gsutil -q -m cp gs://firecloud-tcga-open-access/tutorial/reference/dbsnp_134_b37.leftAligned.vcf /mnt/local-disk/firecloud-tcga-open-access/tutorial/reference/dbsnp_134_b37.leftAligned.vcf
    2016/12/15 18:55:06 E: command failed: AccessDeniedException: 403 Forbidden
    CommandException: 1 file/object could not be transferred.
    (exit status 1)
    ...
    """

    Thanks,
    CH

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