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no space left on device error when using latest gatk4 release from gcr

bshifawbshifaw Member, Broadie, Moderator admin
edited June 2018 in Ask the FireCloud Team


I'm getting the following error when i try to use the gatk4.0.5.0 gcr image that was released today. (us.gcr.io/broad-gatk/gatk:

failed to register layer: Error processing tar file(exit status 1): write /root/.cache/pip/http/c/d/7/5/4/cd754ee3e1f32413f09f243232a69bc3b2d214c7d6bca9509ded9809: no space left on device

The pulling the image works fine when its done on a personnel google vm instance, but doesn't work when lunching a workflow on FC.

Post edited by bshifaw on

Best Answer

  • bshifawbshifaw admin
    Accepted Answer

    Increasing bootdisksize seems to fix this. Cromwell allows you to adjust the size by specifying bootDiskSize in the runtime block.

    runtime {
      # Yikes, we have a big OS in this docker image! ...
      bootDiskSizeGb: 12

    More info on Cromwell runtime attriubtes can be found here

    The devs are working on making the gatk image smaller, but this may not be available until a later release.


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