Permission issues on internal file in workspace

Post author
Sara Balch

Hi Terra Crew,

I'm trying to run a workflow and it keeps failing when it tries to access a file I uploaded to a workspace I created. The file is just a list of other file locations that the workflow will use. Every file in that list was manually uploaded into the workspace as well and I can access all of them. When I run the specific workflow that needs to read in these files, I'm receiving a PAPI error code 9 when it tries to access this file.

2022/02/28 17:55:17 Localizing input gs://fc-08250b31-6e35-47ef-baee-31d9c4edf973/star_genome_list/chrNameLength.txt -> /cromwell_root/fc-08250b31-6e35-47ef-baee-31d9c4edf973/star_genome_list/chrNameLength.txt Error attempting to localize file with command: 'mkdir -p '/cromwell_root/fc-08250b31-6e35-47ef-baee-31d9c4edf973/star_genome_list/' && rm -f /root/.config/gcloud/gce && gsutil -o 'GSUtil:parallel_thread_count=1' -o 'GSUtil:sliced_object_download_max_components=8' cp 'gs://fc-08250b31-6e35-47ef-baee-31d9c4edf973/star_genome_list/chrNameLength.txt ' '/cromwell_root/fc-08250b31-6e35-47ef-baee-31d9c4edf973/star_genome_list/'' CommandException: No URLs matched: gs://fc-08250b31-6e35-47ef-baee-31d9c4edf973/star_genome_list/chrNameLength.txt grep: /cromwell_root/stderr: No such file or directory

I've added to the workspace sbalch_er_loss_rna. The workflow is AB_star2pass_rsem_singlesample_copy_SB and the submission ID is 47220545-cd8e-4dc1-9991-bcdc6495afe2.

All of the files are in the workspace bucket and I can access all of them so any help on understanding why the workflow can't find them would be awesome. 

Thanks in advance for your help!




  • Comment author
    Anika Das

    Hi Sara, 

    Thank you for reaching out and sharing your workspace! We will look into this and get back to you as soon as we can!

    Kind Regards, 


  • Comment author
    Jason Cerrato

    Hey Sara,

    We recently changed our support address to Can you share the workspace with this address instead?

    Many thanks,



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