DAY-EC activated.
DAY-EC activated.

        touch results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.merge.sort.gathered.log;
        mkdir -p $(dirname results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.merge.sort.gathered.log);

        bcftools concat -a -d all --threads 8 -f results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.concat.vcf.gz.fofn -O z -o results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.temp.vcf.gz >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.merge.sort.gathered.log 2>&1;

        export oldname=$(bcftools query -l results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.temp.vcf.gz | head -n1) >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.merge.sort.gathered.log 2>&1;
        echo -e "${oldname}\tHYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ" > results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz.rename.txt
        bcftools reheader --threads 8 -s results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz.rename.txt -o results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.temp.vcf.gz >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.merge.sort.gathered.log 2>&1;
        bcftools index -f -t --threads 8 -o results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz.tbi results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.merge.sort.gathered.log 2>&1;

        # Conditional cleanup of per-chunk tmp dirs (controlled by keep_tmp_dirs config flag)
        KEEP_TMP="False"
        if [ "$KEEP_TMP" = "False" ] || [ "$KEEP_TMP" = "false" ]; then
            echo "Cleaning up chunk tmp dirs under $(dirname results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz)/vcfs/" >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.merge.sort.gathered.log 2>&1;
            rm -rf $(dirname results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz)/vcfs/*/tmp >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.merge.sort.gathered.log 2>&1 || true;
        else
            echo "Retaining chunk tmp dirs (keep_tmp_dirs=true)" >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.merge.sort.gathered.log 2>&1;
        fi
        

[Sat Jun  6 12:09:33 2026]
rule sentdhiomr_concat_index_chunks:
    input: results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.concat.vcf.gz.fofn
    output: results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.temp.vcf.gz, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz.tbi
    log: results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.merge.sort.gathered.log
    jobid: 730
    benchmark: results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/benchmarks/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.merge.bench.tsv
    reason: Missing output files: results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz.tbi; Input files updated by another job: results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.concat.vcf.gz.fofn
    wildcards: sample=HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ, alnr=ont, ddup=dmd
    priority: 47
    threads: 8
    resources: mem_mb=16000, mem_mib=15259, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=8, time=5440, partition=i192mem,i192bigmem, vcpu=8, distribution=block, exclusive=, constraint=, exclude=, include=


        touch results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.merge.sort.gathered.log;
        mkdir -p $(dirname results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.merge.sort.gathered.log);

        bcftools concat -a -d all --threads 8 -f results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.concat.vcf.gz.fofn -O z -o results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.temp.vcf.gz >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.merge.sort.gathered.log 2>&1;

        export oldname=$(bcftools query -l results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.temp.vcf.gz | head -n1) >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.merge.sort.gathered.log 2>&1;
        echo -e "${oldname}\tHYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ" > results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz.rename.txt
        bcftools reheader --threads 8 -s results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz.rename.txt -o results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.temp.vcf.gz >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.merge.sort.gathered.log 2>&1;
        bcftools index -f -t --threads 8 -o results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz.tbi results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.merge.sort.gathered.log 2>&1;

        # Conditional cleanup of per-chunk tmp dirs (controlled by keep_tmp_dirs config flag)
        KEEP_TMP="False"
        if [ "$KEEP_TMP" = "False" ] || [ "$KEEP_TMP" = "false" ]; then
            echo "Cleaning up chunk tmp dirs under $(dirname results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz)/vcfs/" >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.merge.sort.gathered.log 2>&1;
            rm -rf $(dirname results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.sort.vcf.gz)/vcfs/*/tmp >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.merge.sort.gathered.log 2>&1 || true;
        else
            echo "Retaining chunk tmp dirs (keep_tmp_dirs=true)" >> results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.ont.dmd.sentdhiomr.snv.merge.sort.gathered.log 2>&1;
        fi
        

[Sat Jun  6 12:09:33 2026]
rule multiqc_final_wgs:
    input: results/day/hg38_broad/logs/report_components_aggregated.done, results/day/hg38_broad/other_reports/rules_benchmark_data_mqc.tsv, results/day/hg38_broad/reports/multiqc_inputs/final/.stage.done, results/day/hg38_broad/reports/multiqc_inputs/final/manifest.tsv, config/multiqc_module_exclude.txt
    output: results/day/hg38_broad/reports/DAY_final_multiqc.html, results/day/hg38_broad/reports/DAY_final_multiqc.original.html, results/day/hg38_broad/reports/multiqc_header.yaml, results/day/hg38_broad/reports/DAY_final_multiqc_data/multiqc_data.json, results/day/hg38_broad/reports/DAY_final_multiqc_data/multiqc_general_stats.txt, results/day/hg38_broad/reports/DAY_final_multiqc_data/multiqc_sources.txt, results/day/hg38_broad/reports/DAY_final_multiqc_data/multiqc.log
    log: results/day/hg38_broad/reports/logs/all__mqc_fin_a.log
    jobid: 1648
    benchmark: results/day/hg38_broad/benchmarks/DAY_all.final_multiqc.bench.tsv
    reason: Missing output files: results/day/hg38_broad/reports/DAY_final_multiqc_data/multiqc_general_stats.txt, results/day/hg38_broad/reports/DAY_final_multiqc.html, results/day/hg38_broad/reports/DAY_final_multiqc_data/multiqc.log, results/day/hg38_broad/reports/DAY_final_multiqc_data/multiqc_sources.txt, results/day/hg38_broad/reports/DAY_final_multiqc_data/multiqc_data.json; Input files updated by another job: results/day/hg38_broad/reports/multiqc_inputs/final/.stage.done, results/day/hg38_broad/reports/multiqc_inputs/final/manifest.tsv, results/day/hg38_broad/other_reports/rules_benchmark_data_mqc.tsv, results/day/hg38_broad/logs/report_components_aggregated.done
    priority: 50
    threads: 4
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=4, time=5440, partition=i192,i192mem,i128, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=


        dbill='$';
        mkdir -p $(dirname results/day/hg38_broad/reports/DAY_final_multiqc.html) $(dirname results/day/hg38_broad/reports/logs/all__mqc_fin_a.log)
        python workflow/scripts/multiqc_log_guard.py --log-dir results/day/hg38_broad/other_reports/logs > results/day/hg38_broad/reports/logs/all__mqc_fin_a.log 2>&1
        multiqc --version >> results/day/hg38_broad/reports/logs/all__mqc_fin_a.log 2>&1 || true
        echo '''
report_header_info:
  - Project/Budget: "REGSUB_PROJECT"
  - Budget @ Runtime: "REGSUB_BUDGET"
  - Spot Instances: "REGSUB_SPOTINSTANCES"
  - Spot Costs per hr: "REGSUB_SPOTCOST"
  - FQ->BAM.sort avg Costs: "REGSUB_TOTALCOST"
  - BAM mrkdup avg Cost: "REGSUB_MRKDUPCOST"
  - Results Dir (GB): "REGSUB_TOTALSIZE"
  ''' > results/day/hg38_broad/reports/multiqc_header.yaml 2>> results/day/hg38_broad/reports/logs/all__mqc_fin_a.log;

        perl -pi -e "s/REGSUB_PROJECT/$DAY_PROJECT/g;"  results/day/hg38_broad/reports/multiqc_header.yaml >> results/day/hg38_broad/reports/logs/all__mqc_fin_a.log 2>&1;
        perl -pi -e "s/REGSUB_BUDGET/\\$dbill$USED_BUDGET of \\$dbill$TOTAL_BUDGET spent ( $PERCENT_USED\%)/g;" results/day/hg38_broad/reports/multiqc_header.yaml >> results/day/hg38_broad/reports/logs/all__mqc_fin_a.log 2>&1;

        size=$(du -hs results | cut -f1) >> results/day/hg38_broad/reports/logs/all__mqc_fin_a.log 2>&1;
        perl -pi -e "s/REGSUB_TOTALSIZE/$size/g;" results/day/hg38_broad/reports/multiqc_header.yaml >> results/day/hg38_broad/reports/logs/all__mqc_fin_a.log 2>&1;

        source bin/proc_spot_price_logs.sh >> results/day/hg38_broad/reports/logs/all__mqc_fin_a.log 2>&1;
        perl -pi -e "s/REGSUB_SPOTCOST/median: \\$dbill$MEDIAN_SPOT_PRICE  mean: \\$dbill$AVERAGE_SPOT_PRICE ( avg cost per vcpu,per min: \\$dbill$VCPU_COST_PER_MIN ) /g;"  results/day/hg38_broad/reports/multiqc_header.yaml >> results/day/hg38_broad/reports/logs/all__mqc_fin_a.log 2>&1;
        perl -pi -e "s/REGSUB_SPOTINSTANCES/ $INSTANCE_TYPES_LINE /g;" results/day/hg38_broad/reports/multiqc_header.yaml >> results/day/hg38_broad/reports/logs/all__mqc_fin_a.log 2>&1;

        source bin/proc_aligner_costs.sh results/day/hg38_broad/other_reports/rules_benchmark_data_mqc.tsv $VCPU_COST_PER_MIN >> results/day/hg38_broad/reports/logs/all__mqc_fin_a.log 2>&1;
        perl -pi -e "s/REGSUB_TOTALCOST/$ALNR_SUMMARY_COST/g;" results/day/hg38_broad/reports/multiqc_header.yaml >> results/day/hg38_broad/reports/logs/all__mqc_fin_a.log 2>&1;

        source bin/proc_mrkdup_costs.sh results/day/hg38_broad/other_reports/rules_benchmark_data_mqc.tsv $VCPU_COST_PER_MIN  >> results/day/hg38_broad/reports/logs/all__mqc_fin_a.log 2>&1;
        perl -pi -e "s/REGSUB_MRKDUPCOST/$MRKDUP_AVG_MINUTES min, costing \\$dbill$MRKDUP_AVG_COST/g;" results/day/hg38_broad/reports/multiqc_header.yaml >> results/day/hg38_broad/reports/logs/all__mqc_fin_a.log 2>&1;

        module_excludes="$(python workflow/scripts/multiqc_module_exclude_args.py config/multiqc_module_exclude.txt)"
        multiqc -f          $module_excludes         --config results/day/hg38_broad/reports/multiqc_header.yaml         --config ./config/external_tools/multiqc_config.yaml          --custom-css-file ./config/external_tools/multiqc.css         --ignore "*/other_reports/logs/*"         --ignore "other_reports/logs/*"         --ignore "*_mqc.log"         --template default         --filename results/day/hg38_broad/reports/DAY_final_multiqc.html         -i 'Final Multiqc Report '         -b 'https://github.com/lsmc-bio/daylily-omics-analysis (BRANCH:* jem-dev) (TAG:5.0.2) (HASH:9af2dd1) '         results/day/hg38_broad/reports/multiqc_inputs/final >> results/day/hg38_broad/reports/logs/all__mqc_fin_a.log 2>&1;
        python workflow/scripts/force_multiqc_dark_mode.py           --html results/day/hg38_broad/reports/DAY_final_multiqc.html           --backup results/day/hg38_broad/reports/DAY_final_multiqc.original.html >> results/day/hg38_broad/reports/logs/all__mqc_fin_a.log 2>&1;
        python workflow/scripts/validate_multiqc_sample_ids.py           --manifest results/day/hg38_broad/reports/multiqc_inputs/final/manifest.tsv           --multiqc-data results/day/hg38_broad/reports/DAY_final_multiqc_data/multiqc_data.json >> results/day/hg38_broad/reports/logs/all__mqc_fin_a.log 2>&1;
        ls -lt results/day/hg38_broad/reports/DAY_final_multiqc.html results/day/hg38_broad/reports/DAY_final_multiqc.original.html results/day/hg38_broad/reports/multiqc_header.yaml >> results/day/hg38_broad/reports/logs/all__mqc_fin_a.log 2>&1;
        

[Sat Jun  6 12:09:33 2026]
localrule write_dayoa_evidence_manifest:
    input: results/day/hg38_broad/reports/DAY_final_multiqc.html, results/day/hg38_broad/reports/DAY_final_multiqc_data/multiqc_data.json, results/day/hg38_broad/reports/DAY_final_multiqc_data/multiqc_general_stats.txt, results/day/hg38_broad/reports/DAY_final_multiqc_data/multiqc_sources.txt, results/day/hg38_broad/reports/DAY_final_multiqc_data/multiqc.log, results/day/hg38_broad/reports/multiqc_inputs/final/manifest.tsv, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/seqqc/fastqc/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.fastqc.done, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/seqqc/fastqc/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-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/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/samtmetrics/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.sent.dmd.complete, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ/align/sent/na/alignqc/samtmetrics/HYB-4Coriells-chip1-chip2-NA00232-SMN-chip1-chip2-barcode18-chip1-chip2-PF-ILMN-NOVASEQ.sent.na.complete, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/samtmetrics/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ.sent.dmd.complete, results/day/hg38_broad/HYB-4Coriells-chip1-chip2-NA09677-SMN-chip1-chip2-barcode19-chip1-chip2-PF-ILMN-NOVASEQ/align/sent/na/alignq--output truncated--
