User

Sabrina Camp

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Total activity 71
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Posts

Recent activity by Sabrina Camp

  • 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
    • 7 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

  • Unable to create cloud environment for jupyter notebook

    Hi! This morning I have been unable to create a new cloud environment to use for a Terra jupyter notebook. The environment shows it is being created for 10 minutes, and then it times out. I have tr...

    • 3 followers
    • 7 comments
    • -1 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

  • 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

  • Updated hg19 TCGA BAM links causing error in multiple workflows

    Hi, I have been attempting to work with the tcga hg19 aligned BAMs that have updated paths and have been receiving an error in two different workflows. One workflow uses samtools to get the statist...

    • 3 followers
    • 5 comments
    • 0 votes