please update the the docker run parameter,
the docker executable: plasmidID.sh not plasmidID
docker run -v $PWD:$PWD -w $PWD buisciii/plasmidid plasmidID.sh
-1 test/KPN_TEST_R1.fastq.gz
-2 test/KPN_TEST_R2.fastq.gz
-d test/plasmids_TEST_database.fasta
-c test/contigs_KPN_TEST.fasta
--no-trim
-s KPN