getting Cromwell error

[shinlin77]

On scg, I'm running

module load caper
module load java

caper run atac.wdl -i https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ_subsampled.json

But I get this error

2022-03-26 09:25:04,049|caper.nb_subproc_thread|ERROR| Cromwell failed. returncode=1
2022-03-26 09:25:04,049|caper.cli|ERROR| Check stdout in /oak/stanford/scg/lab_mpsnyder/shinlin/chrombpnet/atac-seq-pipeline/cromwell.out

within cromwell.out I see these types of errors

2022-03-26 09:56:42,566 cromwell-system-akka.dispatchers.backend-dispatcher-130 WARN - slurm [UUID(fca199cf)]: Key/s [conda, disks] is/are
not supported by backend. Unsupported attributes will not be part of job executions.

the error file has these errors

There is insufficient memory for the Java Runtime Environment to continue.

Native memory allocation (malloc) failed to allocate 16 bytes for AllocateHeap

Possible reasons:

The system is out of physical RAM or swap space

The process is running with CompressedOops enabled, and the Java Heap may be blocking the growth of the native heap

Possible solutions:

Any suggestions on how to deal with this?

[leepc12]

Please don't module load caper.
You need to pip install it. Please take a closer look at SCG instruction on README.
You first need to run caper init scg first and then edit ~/.caper/default.conf.
And then run with sbatch.