RNA-seq STAR fails for inscrutable reason

jeffmengjeffmeng BroadMember, Broadie

Hi! I'm running the public method "rnaseq_bam_star_rsem_rnaseqc_v1-1_BETA_cfg". Though the first task "rnaseq_pipeline_bam_workflow.samtofastq" succeeded, the second task "rnaseq_pipeline_bam_workflow.star" failed. The stderr says:

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Error! See details below.
{"status":404,"response":{"req":{"method":"HEAD","url":"https://fc-9eebc834-cb07-4ed3-8dda-a3638ae1722a.storage.googleapis.com/d0bd5bf7-aa3d-44cf-9174-5131b97ba06d/rnaseq_pipeline_bam_workflow/04bfa6c2-0de8-485d-96d6-50f9d5ccd946/call-star/star-stderr.log","headers":{"user-agent":"node-superagent/3.8.3","authorization":"Bearer ya29.c.ElpCBhKOFirUqS7H2gMMWYWUhbXszPIsFiYifXp3X6V6HwoHwCRUkavw47Bd-JqgscqWB-OYc9QO3tY7CGeIJPX_W-Bt4WVRHP2PlHV4Gjoe3SVhaY840L0bHYs"}},"header":{"x-guploader-uploadid":"AEnB2UpTpq0guIG-uD07KIa30-eUapl_qQZVncBgeFDPlvDnVgxHYz8p4MNs-s-9JvQgI6qpmFYZ8BkY2tAJQgIPGv47v94gnYulEBGF5H8RsOPxF6DjxZI","content-type":"application/xml; charset=UTF-8","content-length":"330","date":"Fri, 26 Oct 2018 01:35:41 GMT","expires":"Fri, 26 Oct 2018 01:35:41 GMT","cache-control":"private, max-age=0","server":"UploadServer","alt-svc":"quic=\":443\"; ma=2592000; v=\"44,43,39,35\"","connection":"close"},"status":404}}
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Does anyone know what this means and how to fix the error?

Thanks,
Jeff

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Best Answer

  • jeffmengjeffmeng Broad
    Accepted Answer

    @SChaluvadi I'm good for now. I found that I failed to provide a required input to the method, and now I've fixed it. I still don't understand the AccessDenied issue above, but it appears not to be the cause of the failed run "rnaseq_bam_star_rsem_rnaseqc_v1-1_BETA_cfg". Thanks.

Answers

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @jeffmeng It looks like you do not have the permissions needed for the bucket listed in the error you posted above - therefore the task is timing out. Since you imported the public method, can you check to see that you modified the configuration to point to a bucket that you have permissions/access to?

    This link shows how to check a bucket's permissions. If you imported the method to your workspace and made the necessary modifications to your config and also have the necessary roles for the bucket please let me know and I will loop in the team to help determine what else could be happening.

  • jeffmengjeffmeng BroadMember, Broadie

    @SChaluvadi Thanks for your reply! I used gsutil iam get gs://fc-9eebc834-cb07-4ed3-8dda-a3638ae1722a and got this result:

    AccessDeniedException: 403 [email protected] does not have storage.buckets.getIamPolicy access to fc-9eebc834-cb07-4ed3-8dda-a3638ae1722a.

    This is really strange because gs://fc-9eebc834-cb07-4ed3-8dda-a3638ae1722a is the bucket I've been using all along for my workspace and I've had no access issues. Any clue what might be wrong? Thanks!

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @jeffmeng - sorry for the delay! Would you mind sharing your workspace so that we can take a closer look at the errors?

  • jeffmengjeffmeng BroadMember, Broadie
    Accepted Answer

    @SChaluvadi I'm good for now. I found that I failed to provide a required input to the method, and now I've fixed it. I still don't understand the AccessDenied issue above, but it appears not to be the cause of the failed run "rnaseq_bam_star_rsem_rnaseqc_v1-1_BETA_cfg". Thanks.

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @jeffmeng Great to hear that you were able to solve the issue! Out of curiosity, what kind of permissions do you have for the fc-9eebc834-cb07-4ed3-8dda-a3638ae1722a bucket?

  • jeffmengjeffmeng BroadMember, Broadie

    @SChaluvadi I created the workspace and I'm the workspace owner. When I open the bucket, however, I see "You don't have permission to view this bucket's metadata. Contact the bucket owner to grant you the "storage.buckets.get" and "storage.buckets.getIamPolicy" permissions."

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