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Local and AWS dbGaP key not found using docker image #168

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BrenKenna opened this issue Apr 23, 2020 · 1 comment
Open

Local and AWS dbGaP key not found using docker image #168

BrenKenna opened this issue Apr 23, 2020 · 1 comment

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@BrenKenna
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Hi,

I'm trying use your docker within a aws-batch job, but I keep getting key not found error (the key does exist). Below is what I'm running and snippet from the error.

Pull image

sudo docker pull fusera/fusera:alpine

Setup mounting directory and list samples to mount

mkdir -p ~/TOPMed_test/
echo -e "SRR6769030\nSRR6769027\nSRR6769028\nSRR6769029" > ~/testing.txt

Mount data

key=$(ls ~/*ngc)
sudo docker run b22c00f65c8b fusera mount -d -n ${key} -a ~/testing.txt ~/TOPMed_test/ > ~/TOPMed-Test-Mounting.log 2>&1 &

Print log file

cat ~/TOPMed-Test-Mounting.log
DEBUG 2020/04/23 10:58:19 errors.go:48: couldn't open ngc file at: /home/ec2-user/prj_XXXXX.ngc: open /home/ec2-user/prj_XXXX.ngc: no such file or directory

@BrenKenna
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Just to extend this, if I add my local directory I get a "try running modprobe fuse" error. This is the same message I get when I try to install & run fusera mount within an AWS-batch job.

I know there is a dbGaP AMI image, but for whatever reason my jobs never move past the "RUNNABLE" state even though the instances are spun up. The OS's are the same if I use "amazon:linux" and my jobs move through the states fine, but always crash with the "modprobe fuse" error even after installing it and running it.

Run fusera mount

sudo docker run -v /home/ec2-user/:/home/ec2-user/ b22c00f65c8b fusera mount -n ${key} -a ~/testing.txt ~/TOPMed_test/ > ~/TOPMed-Test-Mounting.log 2>&1 &
[2] 19086

Print log

cat ~/TOPMed-Test-Mounting.log
stderr:
fusermount: fuse device not found, try 'modprobe fuse' first

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