DAY-EC activated.
DAY-EC activated.

        if [[ 'na' != 'na' ]]; then
            echo 'downsampling to na' >> results/day/hg38_broad/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-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_20260425T014942Z/602220-20260417-2047_S15-A-Z0298-CAAGACTGATATGAT-ULTIMA-PF-gdna-prod-cram_CAAGACTGATATGAT_0/602220-S15_A-Z0298-CAAGACTGATATGAT.cram -o results/day/hg38_broad/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA.cram >> results/day/hg38_broad/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA.cram.log 2>&1;

            sleep 5;
            samtools index results/day/hg38_broad/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA.cram >> results/day/hg38_broad/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA.cram.log 2>&1;

        else
            echo 'not downsampling: na' >> results/day/hg38_broad/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA.cram.log 2>&1;
             ln -s   /fsx/data/staged_sample_data/remote_stage_20260425T014942Z/602220-20260417-2047_S15-A-Z0298-CAAGACTGATATGAT-ULTIMA-PF-gdna-prod-cram_CAAGACTGATATGAT_0/602220-S15_A-Z0298-CAAGACTGATATGAT.cram results/day/hg38_broad/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA.cram >> results/day/hg38_broad/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA.cram.log 2>&1;
            sleep 5;
             ln -s   /fsx/data/staged_sample_data/remote_stage_20260425T014942Z/602220-20260417-2047_S15-A-Z0298-CAAGACTGATATGAT-ULTIMA-PF-gdna-prod-cram_CAAGACTGATATGAT_0/602220-S15_A-Z0298-CAAGACTGATATGAT.cram.crai results/day/hg38_broad/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA.cram.crai >> results/day/hg38_broad/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S15-A-Z0298-CAAGACTGATATGAT-prod-cram-6-CAAGACTGATATGAT-PF-UG-ULTIMA.cram.log 2>&1;
        fi
        
Submitted job 26 with external jobid '1790'.

[Sat Apr 25 09:01:26 2026]
rule pre_prep_ultima_cram:
    input: /fsx/data/staged_sample_data/remote_stage_20260425T014942Z/602220-20260417-2047_S21-A-Z0301-CAAGAGAGAGCTGAT-ULTIMA-PF-gdna-prod-cram_CAAGAGAGAGCTGAT_0/602220-S21_A-Z0301-CAAGAGAGAGCTGAT.cram, /fsx/data/staged_sample_data/remote_stage_20260425T014942Z/602220-20260417-2047_S21-A-Z0301-CAAGAGAGAGCTGAT-ULTIMA-PF-gdna-prod-cram_CAAGAGAGAGCTGAT_0/602220-S21_A-Z0301-CAAGAGAGAGCTGAT.cram.crai
    output: results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram, results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram.crai
    log: results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram.log
    jobid: 46
    reason: Missing output files: results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram, results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram.crai
    wildcards: sample=602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA, sample_lane=602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-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 $(dirname results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram.log) || echo results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram.log dir exists) >> results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram.log 2>&1;
        export TMPDIR=$(dirname results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram.log)/tmpdir;
        mkdir -p $TMPDIR || echo results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram.log dir exists >> results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram.log 2>&1;

        if [[ 'na' != 'na' ]]; then
            echo 'downsampling to na' >> results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-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_20260425T014942Z/602220-20260417-2047_S21-A-Z0301-CAAGAGAGAGCTGAT-ULTIMA-PF-gdna-prod-cram_CAAGAGAGAGCTGAT_0/602220-S21_A-Z0301-CAAGAGAGAGCTGAT.cram -o results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram >> results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram.log 2>&1;

            sleep 5;
            samtools index results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram >> results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram.log 2>&1;

        else
            echo 'not downsampling: na' >> results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram.log 2>&1;
             ln -s   /fsx/data/staged_sample_data/remote_stage_20260425T014942Z/602220-20260417-2047_S21-A-Z0301-CAAGAGAGAGCTGAT-ULTIMA-PF-gdna-prod-cram_CAAGAGAGAGCTGAT_0/602220-S21_A-Z0301-CAAGAGAGAGCTGAT.cram results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram >> results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram.log 2>&1;
            sleep 5;
             ln -s   /fsx/data/staged_sample_data/remote_stage_20260425T014942Z/602220-20260417-2047_S21-A-Z0301-CAAGAGAGAGCTGAT-ULTIMA-PF-gdna-prod-cram_CAAGAGAGAGCTGAT_0/602220-S21_A-Z0301-CAAGAGAGAGCTGAT.cram.crai results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram.crai >> results/day/hg38_broad/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S21-A-Z0301-CAAGAGAGAGCTGAT-prod-cram-11-CAAGAGAGAGCTGAT-PF-UG-ULTIMA.cram.log 2>&1;
        fi
        
Submitted job 46 with external jobid '1791'.

[Sat Apr 25 09:01:26 2026]
rule pre_prep_ultima_cram:
    input: /fsx/data/staged_sample_data/remote_stage_20260425T014942Z/602220-20260417-2047_S12a-A-Z0295-CATGCAATACATGAGAT-ULTIMA-PF-gdna-prod-cram_CATGCAATACATGAGAT_0/602220-S12a_A-Z0295-CATGCAATACATGAGAT.cram, /fsx/data/staged_sample_data/remote_stage_20260425T014942Z/602220-20260417-2047_S12a-A-Z0295-CATGCAATACATGAGAT-ULTIMA-PF-gdna-prod-cram_CATGCAATACATGAGAT_0/602220-S12a_A-Z0295-CATGCAATACATGAGAT.cram.crai
    output: results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram, results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram.crai
    log: results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram.log
    jobid: 10
    reason: Missing output files: results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram, results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram.crai
    wildcards: sample=602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA, sample_lane=602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-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 $(dirname results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram.log) || echo results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram.log dir exists) >> results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram.log 2>&1;
        export TMPDIR=$(dirname results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram.log)/tmpdir;
        mkdir -p $TMPDIR || echo results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram.log dir exists >> results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram.log 2>&1;

        if [[ 'na' != 'na' ]]; then
            echo 'downsampling to na' >> results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-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_20260425T014942Z/602220-20260417-2047_S12a-A-Z0295-CATGCAATACATGAGAT-ULTIMA-PF-gdna-prod-cram_CATGCAATACATGAGAT_0/602220-S12a_A-Z0295-CATGCAATACATGAGAT.cram -o results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram >> results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram.log 2>&1;

            sleep 5;
            samtools index results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram >> results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram.log 2>&1;

        else
            echo 'not downsampling: na' >> results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram.log 2>&1;
             ln -s   /fsx/data/staged_sample_data/remote_stage_20260425T014942Z/602220-20260417-2047_S12a-A-Z0295-CATGCAATACATGAGAT-ULTIMA-PF-gdna-prod-cram_CATGCAATACATGAGAT_0/602220-S12a_A-Z0295-CATGCAATACATGAGAT.cram results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram >> results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram.log 2>&1;
            sleep 5;
             ln -s   /fsx/data/staged_sample_data/remote_stage_20260425T014942Z/602220-20260417-2047_S12a-A-Z0295-CATGCAATACATGAGAT-ULTIMA-PF-gdna-prod-cram_CATGCAATACATGAGAT_0/602220-S12a_A-Z0295-CATGCAATACATGAGAT.cram.crai results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram.crai >> results/day/hg38_broad/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA/align/ug/logs/602220-20260417-2047-S12a-A-Z0295-CATGCAATACATGAGAT-prod-cram-2-CATGCAATACATGAGAT-PF-UG-ULTIMA.cram.log 2>&1;
        fi
        
Submitted job 10 with external jobid '1792'.
