Need Help?

Search our documentation and community forum

Terra is a cloud-native platform for biomedical researchers to access data, run analysis tools, and collaborate.
Terra powers important scientific projects like FireCloud, AnVIL, and BioData Catalyst. Learn more.

TCGA data path error

Follow
Avatar
palash pandey

Hello!

I am working with TCGA_READ_hg38_ControlledAccess data and running SigprofilerSBS workflow on it. I am getting this error:

Failed to evaluate 'SigprofilerSBS.diskGB' (reason 1 of 1): Evaluating ceil((size(maf, "GB") * 2) + 20) failed: java.lang.IllegalArgumentException: Could not build the path "438904c4-5618-4159-a16c-8789f7209386/TCGA.READ.varscan.438904c4-5618-4159-a16c-8789f7209386.DR-10.0.protected.maf.gz". It may refer to a filesystem not supported by this instance of Cromwell. Supported filesystems are: HTTP, Google Cloud Storage, DRS. Failures: HTTP: 438904c4-5618-4159-a16c-8789f7209386/TCGA.READ.varscan.438904c4-5618-4159-a16c-8789f7209386.DR-10.0.protected.maf.gz does not have an http or https scheme (IllegalArgumentException) Google Cloud Storage: Path "438904c4-5618-4159-a16c-8789f7209386/TCGA.READ.varscan.438904c4-5618-4159-a16c-8789f7209386.DR-10.0.protected.maf.gz" does not have a gcs scheme (IllegalArgumentException) DRS: 438904c4-5618-4159-a16c-8789f7209386/TCGA.READ.varscan.438904c4-5618-4159-a16c-8789f7209386.DR-10.0.protected.maf.gz does not have a drs scheme. (IllegalArgumentException) Please refer to the documentation for more information on how to configure filesystems: http://cromwell.readthedocs.io/en/develop/backends/HPC/#filesystems

I think the error is saying that my file paths are not correct but I just imported the data from TCGA and have not tampered with it at all. A sample file path from my data looks like: c5ed2903-cbaf-446f-870d-167eed6e0bba/TCGA.READ.mutect.c5ed2903-cbaf-446f-870d-167eed6e0bba.DR-10.0.protected.maf.gz. I believe the file path should have a prefix like gs/ http etc. but I am not sure if I need to add that here as well.

Any help is greatly appreciated!

-Palash

0

Comments

3 comments

Sort by Date Votes
  • Avatar
    Samantha Velasquez

    Hi palash pandey,

     

    Thanks for writing in. Can you share the workspace where you are seeing this issue with GROUP_FireCloud-Support@firecloud.org by clicking the Share button in your workspace? The Share option is in the three-dots menu at the top-right.

    1. Add GROUP_FireCloud-Support@firecloud.org to the User email field and press enter on your keyboard.
    2. Click Save.

     

    Let us know the workspace name, as well as the relevant submission and workflow IDs. We’ll be happy to take a closer look as soon as we can.

     

    Best,

    Samantha

    0
    Comment actions Permalink
  • Avatar
    palash pandey

    Hey Samantha!

    Thanks so much for the quick response. I have shared the workspace with you, it is called "palash-gcp/TCGA_READ_hg38_ControlledAccess_GDCDR-12-0_DATA copy", one of the workflows that failed is called SigprofilerSBS and has the id  714febf9-7ca5-466d-8be5-f3cc0df36880.

    Please let me know if I can provide any more details.

    -Palash

    0
    Comment actions Permalink
  • Avatar
    Samantha Velasquez

    Hi palash pandey,

     

    The hg38 workspaces require users to run a workflow in order to retrieve the data before you can to run any analyses on the referenced data files. The workflows for this purpose can be found in the 'Workflows' tab of the workspace. Once you have retrieved the data and copied it into your own workspace's bucket, you will able to run your own workflows on the data.

     

    Best,

    Samantha

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk