User

Sabrina Camp

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Total activity 68
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Posts

Votes on activity by Sabrina Camp

  • Workflows failing with GCSBatchFlow errors

    Hi, I have 3 different workflows in two workspaces that have been giving me GCSBatchFlow related errors since 10 pm last night. I have ran these workflows successfully before with the same configur...

    • 3 followers
    • 3 comments
    • 3 votes
  • TCGA MC3 BAMs failing workflows

    Hi, I have been working with HG19 TCGA data held in various TCGA_{cancercode}_ControlledAccess_V1-0_DATA workspaces. There are 209 MC3 bams that fail every workflow I run on them with an error code...

    • 4 followers
    • 4 comments
    • 2 votes
  • Display preempted jobs differently than errors that cause job failure

    Hi! When I am running workflows that involve scatter jobs on preemptible machines, I have noticed it is difficult to find the error that caused my workflow to fail. Each time a scattered job is pre...

    • 2 followers
    • 2 comments
    • 1 vote
    • Completed
  • Issue copying Jupyter notebook to new workspace

    Hi! I am trying to copy a jupyter notebook to a different workspace that I have owner access to. However, when I search for that workspace after selecting "copy to new workspace" it does not appear.

    • 2 followers
    • 6 comments
    • 1 vote
    • Answered
  • Error modifying cloud environment - Terra notebook not able to be used

    Hi, I was trying to start a python 3 kernel jupyter notebook with the "Python" application configuration (us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.0.4), and the kernel would never star...

    • Edited
    • 2 followers
    • 2 comments
    • 0 votes
  • Terra notebooks fail to autosave

    Hi, I am receiving an error while using Terra notebooks that the notebook failed to autosave. When I try to manually save and checkpoint using the File dropdown menu, it also does not save. This is...

    • Edited
    • 1 follower
    • 2 comments
    • 0 votes
  • Increasing disk size on attached persistent disk does not increase space on /home/jupyter/notebooks

    Hi, I am using a jupyter notebook on Terra, and I am trying to increase the amount of disk space available from 100 GB to 200 GB on /home/jupyter/notebooks where I am storing various files.  I am s...

    • 2 followers
    • 3 comments
    • 0 votes
  • Many different errors today

    Hi! On different workflows, and in different workspaces, I have been getting an assortment of errors on jobs. These are the errors where the only solution (that I know of) is to rerun the workflow,...

    • 2 followers
    • 3 comments
    • 0 votes
  • hg19 and hg38 TCGA workspaces

    Hi! I was wondering if there is any documentation on the curation of the hg19 and hg38 controlled-access TCGA workspaces. I have found some samples in the GDC legacy archive that aren't listed in t...

    • 4 followers
    • 13 comments
    • 0 votes
  • error updating sample set table

    Hi,   I am trying to upload a tsv to update paths in my sample set table. However, I keep getting this error pop up. Do you have more information about this error or what I should try next?    Best...

    • 2 followers
    • 6 comments
    • 0 votes