DAY-EC activated.
DAY-EC activated.


        set -euo pipefail
        mkdir -p $(dirname results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.vep.vcf.gz) $(dirname results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.vep.concat.log)
        input_count=$(awk '{s+=$1} END {print s+0}' results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr1/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr1.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr2/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr2.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr3/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr3.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr4/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr4.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr5/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr5.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr6/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr6.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr7/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr7.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr8/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr8.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr9/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr9.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr10/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr10.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr11/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr11.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr12/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr12.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr13/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr13.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr14/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr14.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr15/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr15.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr16/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr16.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr17/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr17.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr18/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr18.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr19/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr19.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr20/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr20.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr21/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr21.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr22/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr22.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chrX/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chrX.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chrY/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chrY.input.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chrM/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chrM.input.vcf.gz.record_count)
        ann_count=$(awk '{s+=$1} END {print s+0}' results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr1/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr1.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr2/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr2.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr3/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr3.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr4/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr4.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr5/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr5.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr6/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr6.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr7/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr7.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr8/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr8.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr9/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr9.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr10/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr10.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr11/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr11.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr12/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr12.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr13/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr13.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr14/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr14.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr15/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr15.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr16/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr16.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr17/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr17.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr18/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr18.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr19/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr19.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr20/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr20.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr21/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr21.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chr22/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chr22.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chrX/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chrX.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chrY/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chrY.vep.vcf.gz.record_count results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/chunks/chrM/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.chrM.vep.vcf.gz.record_count)
        if [ "$input_count" -ne "$ann_count" ]; then
            echo "ERROR: VEP annotated variant count ($ann_count) does not match input chunk count ($input_count)" >&2
            exit 2
        fi
        bcftools concat -a -d all --threads 16 -f results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.vep.concat.vcf.gz.fofn -O z -o results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.vep.temp.vcf.gz >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.vep.concat.log 2>&1
        mv results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.vep.temp.vcf.gz results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.vep.vcf.gz
        tabix -f -p vcf results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.vep.vcf.gz >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.vep.concat.log 2>&1
        final_count=$(bcftools view -H results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.vep.vcf.gz | wc -l | awk '{print $1}')
        if [ "$final_count" -ne "$input_count" ]; then
            echo "ERROR: final VEP VCF count ($final_count) does not match input count ($input_count)" >&2
            exit 2
        fi
        test -s results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.vep.vcf.gz
        test -s results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.vep.vcf.gz.tbi
        

[Fri May 29 23:38:15 2026]
localrule vep_annotation_gather:
    input: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.vep.vcf.gz.tbi
    output: results/day/hg38_broad/other_reports/vep_annotation_mqc.tsv
    jobid: 785
    reason: Missing output files: results/day/hg38_broad/other_reports/vep_annotation_mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.vep.vcf.gz.tbi
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/dev/shm, threads=1, time=5440, partition=i192,i128,i192mem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=

[Fri May 29 23:38:15 2026]
localrule produce_vep:
    input: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.vep.vcf.gz.tbi, results/day/hg38_broad/other_reports/vep_annotation_mqc.tsv
    output: logs/vep_gathered.done
    jobid: 3
    reason: Missing output files: logs/vep_gathered.done; Input files updated by another job: results/day/hg38_broad/other_reports/vep_annotation_mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vep/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.vep.vcf.gz.tbi
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/dev/shm, threads=1, time=5440, partition=i192,i128,i192mem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=

touch logs/vep_gathered.done;

[Fri May 29 23:38:15 2026]
localrule aggregate_report_components:
    input: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/seqqc/fastqc/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.fastqc.done, results/day/hg38_broad/other_reports/seqfu_mqc.tsv, results/day/hg38_broad/other_reports/input_sample_libraries_mqc.tsv, results/day/hg38_broad/other_reports/sequence_qc_outputs_mqc.tsv, results/day/hg38_broad/other_reports/alignstats_combo_mqc.tsv, results/day/hg38_broad/other_reports/norm_cov_evenness_combo_mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/alignqc/samtmetrics/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.complete, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/na/alignqc/samtmetrics/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.na.complete, results/day/hg38_broad/other_reports/samtools_metrics_gather.done, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/alignqc/mosdepth/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.mosdepth.summary.txt, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/na/alignqc/mosdepth/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.na.mosdepth.summary.txt, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/alignqc/goleft.done, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/na/alignqc/goleft.done, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/alignqc/norm_cov_eveness/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.md, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/na/alignqc/norm_cov_eveness/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.na.md, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/alignqc/contam/gatk/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.gatk.tsv, results/day/hg38_broad/other_reports/alignment_qc_outputs_mqc.tsv, results/day/hg38_broad/other_reports/contamination_mqc.tsv, results/day/hg38_broad/other_reports/site_mix_contam_mqc.tsv, results/day/hg38_broad/other_reports/site_mix_donor_mqc.tsv, results/day/hg38_broad/other_reports/relatedness_mqc.tsv, results/day/hg38_broad/other_reports/relatedness/ont/dmd/somalier/cohort.samples.tsv, results/day/hg38_broad/other_reports/relatedness/ont/dmd/somalier/cohort.pairs.tsv, results/day/hg38_broad/other_reports/bcftools_variant_stats_mqc.tsv, results/day/hg38_broad/other_reports/rtg_vcfstats_mqc.tsv, logs/peddy_gathered.done, results/day/hg38_broad/other_reports/peddy_sample_qc_mqc.tsv, results/day/hg38_broad/other_reports/vep_annotation_mqc.tsv, results/day/hg38_broad/other_reports/giab_concordance_mqc.tsv
    output: results/day/hg38_broad/logs/report_components_aggregated.done
    jobid: 809
    reason: Missing output files: results/day/hg38_broad/logs/report_components_aggregated.done; Input files updated by another job: results/day/hg38_broad/other_reports/giab_concordance_mqc.tsv, results/day/hg38_broad/other_reports/alignstats_combo_mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/alignqc/goleft.done, results/day/hg38_broad/other_reports/contamination_mqc.tsv, results/day/hg38_broad/other_reports/bcftools_variant_stats_mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/seqqc/fastqc/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.fastqc.done, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/na/alignqc/goleft.done, results/day/hg38_broad/other_reports/rtg_vcfstats_mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/alignqc/contam/gatk/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.gatk.tsv, results/day/hg38_broad/other_reports/vep_annotation_mqc.tsv, results/day/hg38_broad/other_reports/relatedness_mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/na/alignqc/mosdepth/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.na.mosdepth.summary.txt, results/day/hg38_broad/other_reports/input_sample_libraries_mqc.tsv, results/day/hg38_broad/other_reports/relatedness/ont/dmd/somalier/cohort.samples.tsv, results/day/hg38_broad/other_reports/sequence_qc_outputs_mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/na/alignqc/samtmetrics/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.na.complete, results/day/hg38_broad/other_reports/site_mix_contam_mqc.tsv, results/day/hg38_broad/other_reports/site_mix_donor_mqc.tsv, results/day/hg38_broad/other_reports/seqfu_mqc.tsv, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/alignqc/norm_cov_eveness/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.md, results/day/hg38_broad/other_reports/samtools_metrics_gather.done, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/na/alignqc/norm_cov_eveness/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.na.md, results/day/hg38_broad/other_reports/alignment_qc_outputs_mqc.tsv, results/day/hg38_broad/other_reports/norm_cov_evenness_combo_mqc.tsv, results/day/hg38_broad/other_reports/relatedness/ont/dmd/somalier/cohort.pairs.tsv, results/day/hg38_broad/other_reports/peddy_sample_qc_mqc.tsv, logs/peddy_gathered.done, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/alignqc/samtmetrics/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.complete, results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/alignqc/mosdepth/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.mosdepth.summary.txt
    threads: 2
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/dev/shm, threads=1, time=5440, partition=i192,i128,i192mem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=

mkdir -p $(dirname results/day/hg38_broad/logs/report_components_aggregated.done); touch results/day/hg38_broad/logs/report_components_aggregated.done;

[Fri May 29 23:38:15 2026]
localrule collect_rules_benchmark_data:
    input: results/day/hg38_broad/logs/report_components_aggregated.done
    output: results/day/hg38_broad/other_reports/rules_benchmark_data_mqc.tsv
    log: results/day/hg38_broad/other_reports/logs/rules_benchmarks_summary.log
    jobid: 844
    reason: Missing output files: results/day/hg38_broad/other_reports/rules_benchmark_data_mqc.tsv; Input files updated by another job: results/day/hg38_broad/logs/report_components_aggregated.done
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/dev/shm, threads=1, time=5440, partition=i192,i128,i192mem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=

bin/util/benchmarks/collect_day_benchmark_data.sh hg38_broad > results/day/hg38_broad/other_reports/logs/rules_benchmarks_summary.log;python bin/util/benchmarks/split_bench_rule_col.py results/day/hg38_broad/reports/benchmarks_summary.tsv results/day/hg38_broad/other_reports/rules_benchmark_data_mqc.tsv > results/day/hg38_broad/other_reports/logs/rules_benchmarks_summary.log;sed -i -E 's/	$/	NA/' results/day/hg38_broad/other_reports/rules_benchmark_data_mqc.tsv;

[Fri May 29 23:38:15 2026]
localrule stage_multiqc_inputs:
    input: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/seqqc/fastqc/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.fastqc.done, results/day/hg38_broad/other_reports/seqfu_mqc.tsv, results/day/hg38_broad/other_reports/input_sample_libraries_mqc.tsv, results/day/hg38_broad/other_reports/sequence_qc_outputs_mqc.tsv, results/day/hg38_broad/other_reports/alignstats_combo_mqc.tsv, results/day/hg38_broad/other_reports--output truncated--
