DAY-EC activated.
DAY-EC activated.

        if [[ 'na' != 'na' ]]; then
            echo 'downsampling to na' >> results/day/hg38_broad/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA.cram.log 2>&1;
            samtools view -@ 48 -T /fsx/data/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.fasta -C -s 33.na /fsx/data/staged_sample_data/remote_stage_20260424T222834Z/504970-20260331-1722_L11092-Z0869-CAAGCATCTCAGTGAT-ULTIMA-PF-gdna-prod-cram_CAAGCATCTCAGTGAT_0/504970-L11092-Z0869-CAAGCATCTCAGTGAT.cram -o results/day/hg38_broad/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA.cram >> results/day/hg38_broad/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA.cram.log 2>&1;

            sleep 5;
            samtools index results/day/hg38_broad/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA.cram >> results/day/hg38_broad/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA.cram.log 2>&1;

        else
            echo 'not downsampling: na' >> results/day/hg38_broad/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA.cram.log 2>&1;
             ln -s   /fsx/data/staged_sample_data/remote_stage_20260424T222834Z/504970-20260331-1722_L11092-Z0869-CAAGCATCTCAGTGAT-ULTIMA-PF-gdna-prod-cram_CAAGCATCTCAGTGAT_0/504970-L11092-Z0869-CAAGCATCTCAGTGAT.cram results/day/hg38_broad/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA.cram >> results/day/hg38_broad/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA.cram.log 2>&1;
            sleep 5;
             ln -s   /fsx/data/staged_sample_data/remote_stage_20260424T222834Z/504970-20260331-1722_L11092-Z0869-CAAGCATCTCAGTGAT-ULTIMA-PF-gdna-prod-cram_CAAGCATCTCAGTGAT_0/504970-L11092-Z0869-CAAGCATCTCAGTGAT.cram.crai results/day/hg38_broad/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA.cram.crai >> results/day/hg38_broad/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11092-Z0869-CAAGCATCTCAGTGAT-prod-cram-5-CAAGCATCTCAGTGAT-PF-UG-ULTIMA.cram.log 2>&1;
        fi
        
Submitted job 22 with external jobid '1774'.

[Sat Apr 25 09:00:50 2026]
rule pre_prep_ultima_cram:
    input: /fsx/data/staged_sample_data/remote_stage_20260424T222834Z/504970-20260331-1722_L11100-Z0877-CGATCTCATCATTGAT-ULTIMA-PF-gdna-prod-cram_CGATCTCATCATTGAT_0/504970-L11100-Z0877-CGATCTCATCATTGAT.cram, /fsx/data/staged_sample_data/remote_stage_20260424T222834Z/504970-20260331-1722_L11100-Z0877-CGATCTCATCATTGAT-ULTIMA-PF-gdna-prod-cram_CGATCTCATCATTGAT_0/504970-L11100-Z0877-CGATCTCATCATTGAT.cram.crai
    output: results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram, results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram.crai
    log: results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram.log
    jobid: 54
    reason: Missing output files: results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram, results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram.crai
    wildcards: sample=504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA, sample_lane=504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA
    threads: 48
    resources: mem_mb=20000, mem_mib=19074, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=48, time=5440, partition=i192,i192mem,i128, vcpu=48, distribution=block, exclusive=, constraint=, exclude=, include=


        (mkdir -p $(dirname results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram.log) || echo results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram.log dir exists) >> results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram.log 2>&1;
        export TMPDIR=$(dirname results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram.log)/tmpdir;
        mkdir -p $TMPDIR || echo results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram.log dir exists >> results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram.log 2>&1;

        if [[ 'na' != 'na' ]]; then
            echo 'downsampling to na' >> results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram.log 2>&1;
            samtools view -@ 48 -T /fsx/data/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.fasta -C -s 33.na /fsx/data/staged_sample_data/remote_stage_20260424T222834Z/504970-20260331-1722_L11100-Z0877-CGATCTCATCATTGAT-ULTIMA-PF-gdna-prod-cram_CGATCTCATCATTGAT_0/504970-L11100-Z0877-CGATCTCATCATTGAT.cram -o results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram >> results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram.log 2>&1;

            sleep 5;
            samtools index results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram >> results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram.log 2>&1;

        else
            echo 'not downsampling: na' >> results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram.log 2>&1;
             ln -s   /fsx/data/staged_sample_data/remote_stage_20260424T222834Z/504970-20260331-1722_L11100-Z0877-CGATCTCATCATTGAT-ULTIMA-PF-gdna-prod-cram_CGATCTCATCATTGAT_0/504970-L11100-Z0877-CGATCTCATCATTGAT.cram results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram >> results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram.log 2>&1;
            sleep 5;
             ln -s   /fsx/data/staged_sample_data/remote_stage_20260424T222834Z/504970-20260331-1722_L11100-Z0877-CGATCTCATCATTGAT-ULTIMA-PF-gdna-prod-cram_CGATCTCATCATTGAT_0/504970-L11100-Z0877-CGATCTCATCATTGAT.cram.crai results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram.crai >> results/day/hg38_broad/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11100-Z0877-CGATCTCATCATTGAT-prod-cram-13-CGATCTCATCATTGAT-PF-UG-ULTIMA.cram.log 2>&1;
        fi
        
Submitted job 54 with external jobid '1775'.

[Sat Apr 25 09:00:50 2026]
rule pre_prep_ultima_cram:
    input: /fsx/data/staged_sample_data/remote_stage_20260424T222834Z/504970-20260331-1722_L11097-Z0874-CTTACATGTGCGAT-ULTIMA-PF-gdna-prod-cram_CTTACATGTGCGAT_0/504970-L11097-Z0874-CTTACATGTGCGAT.cram, /fsx/data/staged_sample_data/remote_stage_20260424T222834Z/504970-20260331-1722_L11097-Z0874-CTTACATGTGCGAT-ULTIMA-PF-gdna-prod-cram_CTTACATGTGCGAT_0/504970-L11097-Z0874-CTTACATGTGCGAT.cram.crai
    output: results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram, results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram.crai
    log: results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram.log
    jobid: 42
    reason: Missing output files: results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram, results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram.crai
    wildcards: sample=504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA, sample_lane=504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA
    threads: 48
    resources: mem_mb=20000, mem_mib=19074, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=48, time=5440, partition=i192,i192mem,i128, vcpu=48, distribution=block, exclusive=, constraint=, exclude=, include=


        (mkdir -p $(dirname results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram.log) || echo results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram.log dir exists) >> results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram.log 2>&1;
        export TMPDIR=$(dirname results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram.log)/tmpdir;
        mkdir -p $TMPDIR || echo results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram.log dir exists >> results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram.log 2>&1;

        if [[ 'na' != 'na' ]]; then
            echo 'downsampling to na' >> results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram.log 2>&1;
            samtools view -@ 48 -T /fsx/data/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.fasta -C -s 33.na /fsx/data/staged_sample_data/remote_stage_20260424T222834Z/504970-20260331-1722_L11097-Z0874-CTTACATGTGCGAT-ULTIMA-PF-gdna-prod-cram_CTTACATGTGCGAT_0/504970-L11097-Z0874-CTTACATGTGCGAT.cram -o results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram >> results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram.log 2>&1;

            sleep 5;
            samtools index results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram >> results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram.log 2>&1;

        else
            echo 'not downsampling: na' >> results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram.log 2>&1;
             ln -s   /fsx/data/staged_sample_data/remote_stage_20260424T222834Z/504970-20260331-1722_L11097-Z0874-CTTACATGTGCGAT-ULTIMA-PF-gdna-prod-cram_CTTACATGTGCGAT_0/504970-L11097-Z0874-CTTACATGTGCGAT.cram results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram >> results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram.log 2>&1;
            sleep 5;
             ln -s   /fsx/data/staged_sample_data/remote_stage_20260424T222834Z/504970-20260331-1722_L11097-Z0874-CTTACATGTGCGAT-ULTIMA-PF-gdna-prod-cram_CTTACATGTGCGAT_0/504970-L11097-Z0874-CTTACATGTGCGAT.cram.crai results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram.crai >> results/day/hg38_broad/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA/align/ug/logs/504970-20260331-1722-L11097-Z0874-CTTACATGTGCGAT-prod-cram-10-CTTACATGTGCGAT-PF-UG-ULTIMA.cram.log 2>&1;
        fi
        
Submitted job 42 with external jobid '1776'.
