FastQ detects full drive on Docker machine with volumes mounted directly in Windows

Question: FastQ detects full drive on Docker machine with volumes mounted directly in Windows

2.1 years ago by

The error

[Errno 28] No space left on device

Tried to run

FastQ

The actual command

python /shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/3fdc1a74d866/fastqc/rgFastQC.py -i "/export/galaxy-central/database/files/000/dataset_1.dat" -d "/export/galaxy-central/database/job_working_directory/000/73/dataset_79_files" -o "/export/galaxy-central/database/files/000/dataset_79.dat" -t "/export/galaxy-central/database/files/000/dataset_80.dat" -f "fastq" -j "Illumina iDEA Datasets (sub-sampled)/BT20 paired-end RNA-seq subsampled (end 1)"

Context Running Galaxy from Hyper-V on a Windows 10. The Docker image is https://github.com/bgruening/docker-galaxy-stable. Started the image from Kitematic with volumes mounted /var/lib/docker, /data, /export

While looking on the system, I noticed that all mounted drives apear as full

#df -a
Filesystem     1K-blocks     Used Available Use% Mounted on
none            57830428 11706668  43163020  22% /
tmpfs            1006672        0   1006672   0% /dev
tmpfs            1006672  1006672         0 100% /data
tmpfs            1006672  1006672         0 100% /export
/dev/sda2       57830428 11706668  43163020  22% /etc/resolv.conf
/dev/sda2       57830428 11706668  43163020  22% /etc/hostname
/dev/sda2       57830428 11706668  43163020  22% /etc/hosts
tmpfs            1006672  1006672         0 100% /var/lib/docker
tmpfs            1006672        0   1006672   0% /proc/kcore
tmpfs            1006672        0   1006672   0% /proc/timer_list
tmpfs            1006672        0   1006672   0% /proc/sched_debug

Is this a detection error because of the mounted drives? Any ideas on how to fix/trick the system?

EDIT : edited title to mentioned that my volumes are mounted into Windows (so not even in the VM)

fastq conda galaxy docker • 1.0k views

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modified 2.1 years ago • written 2.1 years ago by alexandrurepede • 20

Since you're using Kitematic, I assume you're running OS X with the hypervisor. What happens if you run Linux instead? I wonder if the inceptionesque windows->OSX->linux setup is causing the problem with limited volume sizes.

Alternatively, what sort of settings are you giving your hypervisor?

ADD REPLY • link written 2.1 years ago by Devon Ryan • 1.9k

i was using windows 10 and yes it runs ok on linux, but i made a data container for the linux machine not volumes mounted directly through kitematic. still, i was curios what would be the issue...

ADD REPLY • link written 2.1 years ago by alexandrurepede • 20

Good question, I unfortunately don't know.

ADD REPLY • link written 2.1 years ago by Devon Ryan • 1.9k

2.1 years ago by

Mo Heydarian ♦ 830

United States

Mo Heydarian ♦ 830 wrote:

Hello,

I have run into a similar situation when my Galaxy in Docker gets close to 10 Gb of data. This is not an ideal solution, but when this has happened I clear out all of the Docker volumes and start from scratch by shutting down my Galaxy in Docker and running:

$ docker volume rm $(docker volume ls -qf dangling=true)

Be aware, the above strategy WILL DELETE YOUR DATA.

Perhaps Bjorn Gruening or Devon Ryan could suggest an alternative approach?

If you've figured out a solution since posting this message, do let us know!

Cheers, Mo Heydarian

ADD COMMENT • link written 2.1 years ago by Mo Heydarian ♦ 830

Mo, please look out for a VM on your system and try to increase the space that the VM can use.

ADD REPLY • link written 2.1 years ago by Bjoern Gruening ♦ 5.1k

i was running on kitematic mounted volumes, that means there were out of the MobyLinuxVM, and into my win machine, right?

ADD REPLY • link written 2.1 years ago by alexandrurepede • 20

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