User

Seunghun Han

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Total activity 40
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Recent activity by Seunghun Han

  • Not being able to access the google bucket of my own workspace

    Hi, I was trying to access the google storage of one of my own workspaces (https://firecloud.terra.bio/#workspaces/vanallen-firecloud-nih/Seunghun_CHECKMATE_RCC)by clicking Open bucket in browser o...

    • 3 followers
    • 12 comments
    • 0 votes

  • Is there a way to incorporate "gsutil -m" for the localization of the input files for a Terra method?

    Hi, I was reviewing a log from a method I ran which takes in array file input, and I saw a following message in the log - NOTE: You are performing a sequence of gsutil operations that may run signi...

    • 3 followers
    • 2 comments
    • 0 votes

  • Keep getting the "Notebook changed" error

    Hi,  Recently when I'm using Jupyter notebook on Terra, I'm repeatedly getting this "Notebook changed" erroralong with -error while saving file. Clicking Overwrite several times sometimes fix the i...

    • 3 followers
    • 4 comments
    • 1 vote

  • Issue with Array Input

    Hi, A Terra method I'm using takes Array[File]+ input "gcnv_model_tars" in the screenshot,and the method has been working without problem.  However, when I used the same method this morning, the a...

    • 3 followers
    • 3 comments
    • 0 votes

  • Internal Server Error updating sample set table

    Hello, I am trying to update and add a new sample set to my existing sample_set table by uploading sample_set_entity.tsv and sample_set_membershipt.tsv.  I first downloaded sample_set.zip and decom...

    • 2 followers
    • 3 comments
    • 0 votes

  • Job stuck at aborting and possibly affecting call-caching

    Hi, I submitted a job (d730c1c3-4d60-44a6-9ba2-4f0a626f5070) on 10/23 and it failed at 15th tasksI fixed the problem of the method, re-submitted the job using call caching along with two other work...

    • 5 followers
    • 12 comments
    • 0 votes

  • Unable to copy an output to a google bucket

    Hi,  I'm using Hail package on Terra Notebook, and when I make a VCF output using following line, hl.export_vcf(filtered_mt,'1106_RCC_filtered_variants.vcf.bgz')  2019-11-06 20:07:49 Hail: INFO: wh...

    • 3 followers
    • 5 comments
    • 0 votes

  • PAPI error code 4

    Hi, One of the jobs I was running on Terra failed after about 168hrs (this job is expected to take long time) with following error "Task PC.PCAir:NA:1 failed. The job was stopped before the command...

    • 5 followers
    • 3 comments
    • 0 votes

  • Update R version in notebook

    It looks like the Jupyter Notebook on Terra uses R 3.5.2. Is there a way to update R version in the notebook?   

    • 2 followers
    • 2 comments
    • 0 votes