trna_pick_and_transform_to_gff.py has error in JAWS

When running the workflow in JAWS with jaws run submit annotation_full.wdl bfoster-inputs-short3.json out jgi where the input file is the large (550M) Ga0438891_contigs.fna, I get an error:

ValueError: invalid literal for int() with base 10: 'Setting'
The script trna_pick_and_transform_to_gff.py failed! Aborting!

The command is from this WDL.
trnascan.wdl => task: call-trnascan_ba

Running the script commands seems to work fine outside of JAWS. For example (on lrcs):

set -xeuo pipefail

base=$(basename /global/scratch/jaws/jaws-prod/cromwell-executions/annotation/83fee83b-c806-4ea5-88f8-e1b744318c23/call-s_annotate/shard-50/sa.s_annotate/1ca96042-a66f-44cc-a060-2849557b8501/call-trnascan/trnascan.trnascan/8c56d4b6-8b45-494e-a870-0039a0619a70/call-trnascan_ba/inputs/-1311688498/51_Ga0438891_contigs.fna)

cp /global/scratch/jaws/jaws-prod/cromwell-executions/annotation/83fee83b-c806-4ea5-88f8-e1b744318c23/call-s_annotate/shard-50/sa.s_annotate/1ca96042-a66f-44cc-a060-2849557b8501/call-trnascan/trnascan.trnascan/8c56d4b6-8b45-494e-a870-0039a0619a70/call-trnascan_ba/inputs/-1311688498/51_Ga0438891_contigs.fna ./Ga0438891_contigs.fna_contigs.fna

singularity exec docker://bfoster1/img-omics:0.1.8 /global/scratch/jfroula/JAWS/Marcel-test/bin/trnascan-se_trnas.sh Ga0438891_contigs.fna_contigs.fna metagenome 16