$ echo $IMAGE_NAME
gridss/gridss:2.13.0
$ docker run --rm -v $PWD/work:/data/work:rw $IMAGE_NAME gridss --steps preprocess,assemble,call --externalaligner --reference work/ref/genome.fa --blacklist work/ref/gridss/blacklist-2011-05-04-ENCFF001TDO.bed --threads 8 --labels $WT --skipsoftcliprealignment --assembly work/result/$WT.assembly.bam --output work/result/$WT.gridss.vcf.gz --workingdir work/workspace work/$WT.sample.dupmarked.bam
Using working directory "work/workspace"
Mon Dec  6 11:45:13 UTC 2021: Full log file is: work/workspace/gridss.full.20211206_114513.eede6af1f171.1.log
Mon Dec  6 11:45:13 UTC 2021: Found /usr/bin/time
Mon Dec  6 11:45:13 UTC 2021: Using GRIDSS jar /opt/gridss/gridss-2.13.0-gridss-jar-with-dependencies.jar
...
Mon Dec  6 11:45:13 UTC 2021: samtools version: 1.10+htslib-1.10.2-3
Mon Dec  6 11:45:13 UTC 2021: samtools 1.13 or later is required.
"exit $EX_CONFIG" command completed with exit code 78.
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The underlying error message can be found in work/workspace/gridss.full.20211206_114513.eede6af1f171.1.log
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