I am attempting to use the GATK-SV pipeline to call structural variants, including mobile element insertions, in Illumina WGS data. Due to MELT's restrictive license, the pipeline authors cannot provide a public docker image. Instead, they provide great instructions for the user to agree to the license, download the software, build the image, and upload it us.gcr.io. I did this with MELT version 2.2.2, while making some edits to the dockerfile and image's scripts to account for this version upgrade from MELT 2.0.5 patch (see my fork and branch here).
Then, upon testing the image with the gatk-sv-single-sample workflow and the NA12878 sample data, I receive an error in the RunMELT task. I have shared my workspace "libr-wgs/LIBR-WGS-Pipeline" with support, linked to the full RunMELT log file, and copied the relevant lines below.
2022/05/02 06:02:04 Running user action: docker run -v /mnt/local-disk:/cromwell_root -v /mnt/d-1b2e5749db4b0a6439c4895809508e1e:/mnt/af7b5955462dc70f18fa6a82eae18e22:ro --entrypoint=/bin/bash us.gcr.io/gage-wgs-pipeline/melt@sha256:471540294890c1775fecf30e5658530e050b536c6c82d2995d35738cdb74c8e4 /cromwell_root/script
exec /bin/bash: exec format error
grep: /cromwell_root/stderr: No such file or directory