User

tmajarian

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Total activity 42
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Posts

Recent activity by tmajarian

  • Job scheduling at 4 days, total submission time limit of 7 days

    Hi-   I have some very long running jobs (~5 days) that I have been trying to run for a few weeks now. I am seeing some odd behavior in Terra where there is a delay of 3+ days from submission to st...

    • 3 followers
    • 2 comments
    • 0 votes

  • Deleting entire data tables

    Hi- I have multiple workspaces with 5+ data tables in each. I would like to delete each table in its entirety in each workspace -- to remove all data tables but keep the workspaces themselves. I am...

    • 2 followers
    • 7 comments
    • 0 votes

  • Cloud environment provisions a 2 CPU main node regardless of configuration

    Hi- I have been trying to start a cluster through Terra running the default Hail docker image. I customized my environment when creating, selecting an 8 CPU machine as the spark master and 5 worker...

    • 2 followers
    • 1 comment
    • 0 votes

  • VEP with Hail

    Hi- I'd like to run the variant effect predictor through Hail from within a Terra notebook. Instructions for setting up a dataproc cluster that would be able to do this are provided by the hail tea...

    • 6 followers
    • 5 comments
    • 19 votes

  • Updating Hail

    Hi- I'm writing some notebooks for Terra that utilize Hail but noticed that the version currently used is 0.2.11. This seems to be >1 year old with the current version being 0.2.26. There have been...

    • 2 followers
    • 1 comment
    • 1 vote

  • Job manager unavailable to specific user

    Hi- A user in my group is having some issues with the job manager page. He has been unable to view the status of jobs in multiple workspaces. I have verified that, using my account, I can view both...

    • 3 followers
    • 5 comments
    • 0 votes

  • Notebook runtime creation failed -- not enough memory

    Hi- I am attempting to start a very small runtime environment for notebook development but am getting the following error (with the configuration below):   Is this error due to the kernel that I h...

    • 2 followers
    • 4 comments
    • 0 votes

  • Workflow outputs not copied to data model

    Hi-  I seem to have an issue similar to: https://support.terra.bio/hc/en-us/community/posts/360043439671-Successful-workflows-not-copying-to-data-model I have a workflow that completes successfully...

    • 2 followers
    • 7 comments
    • 1 vote

  • Allow full access to notebook VMs

    One fundamentally awesome aspect of notebooks (at least for me) is not having to handle permissions, auth tokens, or anything of the sort. It allows our group to keep data secure while still gettin...

    • 2 followers
    • 1 comment
    • 3 votes
    • Planned

  • Python version mismatch in notebook cluster

    Hi- I have written a jupyter notebook for a demo workspace in Terra, utilizing Hail. This notebook runs without error locally but fails in Terra. Below is the script being used and the error output...

    • 2 followers
    • 2 comments
    • 0 votes