jvarkit docker container memory error #251
Description
Subject of the issue
The docker container for the jvarkit software (https://hub.docker.com/r/lindenb/jvarkit) is throwing a memory error:
"There is insufficient memory for the Java Runtime Environment to continue.
Cannot create worker GC thread. Out of system resources."
Your environment
Running jvarkit through the docker container so the environment is the docker container.
Steps to reproduce
I ran the docker container interactively with:
docker run --rm -it -v $PWD:/my_data -u $(id -u):$(id -g) lindenb/jvarkit:1b2aedf24
and then ran this code from within the container:
java -jar /opt/jvarkit/dist/jvarkit.jar biostar84452 --samoutputformat BAM --output sample_name_clipped.bam sample_name_trimmed.sorted.bam
I am running the docker container on a virtual machine. I was able to run the command without issues locally on my machine but not through the docker container. I also tried increasing the memory of my VM to 30GB, but got the same error when trying to use the docker container.
I did not try to run the docker container with other commands as I am unfamiliar with those.
Expected behaviour
proceed with no error and create a bam file with hard clipped bases from reads.
Actual behaviour
Throws a memory error: "There is insufficient memory for the Java Runtime Environment to continue.
Cannot create worker GC thread. Out of system resources."