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Error:

2015-03-22 17:29:25 ERROR Executor:96 - Exception in task 0.0 in stage 1.0 (TID 16)
java.lang.OutOfMemoryError: GC overhead limit exceeded

Step to reproduce:

docker run -ti --rm --name client-genomics -v /data:/data gelog/avocado /bin/bash avocado-submit /data/SRR062634.adam /data/chr1.fa /data/SRR062634.avr /usr/local/avocado/avocado-sample-configs/basic.properties

You can get the files by following the step from :

• snap
• adam

We need to validate that the image is OK to rule out that the problem is only related to missing memory on my old laptop.

Steps to reproduce:

1. Build the image: docker build --rm=true -t avocado .
2. Run the container: docker run --rm=true avocado

Error:

Java HotSpot(TM) 64-Bit Server VM warning: INFO: os::commit_memory(0x00000006fff80000, 2863661056, 0) failed; error='Cannot allocate memory' (errno=12)
#
# There is insufficient memory for the Java Runtime Environment to continue.
# Native memory allocation (malloc) failed to allocate 2863661056 bytes for committing reserved memory.
# An error report file with more information is saved as:
# //hs_err_pid40.log