Singularity container - deepvariant binding directories to $PATH? - containers

Question

I am trying to use a deepvariant singularity container on my HPC.
However there is something wrong with the way that I am using the container and where it is binding.
This is my code:
#!/bin/bash --login
#SBATCH -J AmyHouseman_deepvariant
#SBATCH -o %x.stdout.%J.%N
#SBATCH -e %x.stderr.%J.%N
#SBATCH --ntasks=1
#SBATCH --ntasks-per-node=1
#SBATCH -p c_compute_wgp
#SBATCH --account=scw1581
#SBATCH --mail-type=ALL # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=HousemanA#cardiff.ac.uk # Where to send mail
#SBATCH --array=1-33
#SBATCH --time=02:00:00
#SBATCH --time=072:00:00
#SBATCH --mem-per-cpu=32GB
module purge
module load singularity
module load parallel
# Set bash error trapping to exit on first error.
set -eu
WDPATH=/scratch/$USER/$SLURM_ARRAY_JOB_ID
CONTAINER_FILE=deepvariant_1.3.0.sif
MY_CONTAINER_PATH=/scratch/$USER/containers
CONTAINER=$MY_CONTAINER_PATH/$CONTAINER_FILE
if [ "$SLURM_ARRAY_TASK_ID" == "1" ]
then
mkdir -p $MY_CONTAINER_PATH
[ -f "$CONTAINER" ] || ssh cl1 wget -O $CONTAINER https://wotan.cardiff.ac.uk/containers/$CONTAINER_FILE
mkdir $WDPATH
fi
while [ ! -d $WDPATH ]
do
sleep 10
done
cd /scratch/c.c21087028/
sed -n "${SLURM_ARRAY_TASK_ID}p" Polyposis_Exome_Analysis/fastp/All_fastp_input/List_of_33_exome_IDs | parallel -j 1 "singularity run $CONTAINER --model_type=WES \
-ref=Polyposis_Exome_Analysis/bwa/index/HumanRefSeq/GRCh38_latest_genomic.fna \
--reads=Polyposis_Exome_Analysis/samtools/index/indexed_picardbamfiles/{}PE_markedduplicates.bam \
--output_vcf=Polyposis_Exome_Analysis/deepvariant/vcf/{}PE_output.vcf.gz \
--output_gvcf=Polyposis_Exome_Analysis/deepvariant/gvcf/{}PE_output.vcf.gz \
--intermediate_results_dir=Polyposis_Exome_Analysis/deepvariant/intermediateresults/{}PE_output_intermediate"
The error message I get is set:
invalid option: "--"
FATAL: "--model_type": executable file not found in $PATH
I find it a bit strange because I haven't had a problem with any of the other singularity containers I've used before, so not really sure how to go ahead - I've tried adding in the bit in their manual singularity run -B /usr/lib/locale/:/usr/lib/locale/
but I'm still unsure as to why I would need to do this step when I haven't previously on my other tools like bwa, and samtools.
I also know I can get rid of parallel bits as its not actually running in parallel, so I am aware of that.
I hope this makes sense!
Thank you!
Amy