DAY-EC activated.
DAY-EC activated.
94 of 133 steps (71%) done
[Fri May 29 21:19:43 2026]
Finished job 73.
95 of 133 steps (71%) done
[Fri May 29 21:19:53 2026]
Finished job 23.
96 of 133 steps (72%) done
[Fri May 29 21:20:04 2026]
Finished job 63.
97 of 133 steps (73%) done
[Fri May 29 21:20:04 2026]
Finished job 65.
98 of 133 steps (74%) done
[Fri May 29 21:20:04 2026]
Finished job 67.
99 of 133 steps (74%) done
[Fri May 29 21:20:15 2026]
Finished job 17.
100 of 133 steps (75%) done
[Fri May 29 21:20:25 2026]
Finished job 21.
101 of 133 steps (76%) done
Select jobs to execute...

[Fri May 29 21:20:25 2026]
rule prep_for_concordance_check:
    input: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_altair-v1.1/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC_x_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38_m_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_concordance.mqc.tsv
    output: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/concordance.done, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/concordance.fofn, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/concordance.fin.cmds
    log: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/logs/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.concordance.log
    jobid: 1
    benchmark: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/benchmarks/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.concordance.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/concordance.done; Input files updated by another job: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_altair-v1.1/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38_m_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC_x_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz.tbi
    wildcards: sample=TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ, alnr=sent, ddup=dmd, snv=sentd
    priority: 48
    threads: 8
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=16, time=5440, partition=i192mem,i192bigmem, vcpu=16, distribution=block, exclusive=, constraint=, exclude=, include=


            set +euo pipefail;

            mkdir -p $(dirname results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/concordance.done);
            mkdir -p $(dirname results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/logs/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.concordance.log);

            utc_ts=$(date -u +%Y-%m-%dT%H:%M:%SZ);

            # Write informational fofn
            {
                echo "# Refactor: per-ROI jobs are scheduled by Snakemake; this file is informational.";
                echo "# generated_at_utc=$utc_ts";
                echo "# truth_dir=/fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/";
                echo "# footprints=altair-v1.1,clinvar_genes,giabHC,giabHC_x_clinvar_genes,hg38,hg38_m_giabHC";
                for mqc in results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_altair-v1.1/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_clinvar_genes_concordance.mqc.tsv results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_concordance.mqc.tsv results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC_x_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_clinvar_genes_concordance.mqc.tsv results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38_m_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_concordance.mqc.tsv; do
                    echo "$mqc";
                done;
            } > results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/concordance.fofn;

            # Write informational fin.cmds
            {
                echo "# Refactor: see Snakemake DAG for exact commands.";
                echo "# generated_at_utc=$utc_ts";
            } > results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/concordance.fin.cmds;

            # SKIPPED sentinel if no mqcs
            if [ "6" -eq 0 ]; then
                echo "No truthset ROI directories found; concordance skipped." > results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/concordance.done.SKIPPED;
            fi;

            # Log
            echo "Concordance sentinel complete. footprints=altair-v1.1,clinvar_genes,giabHC,giabHC_x_clinvar_genes,hg38,hg38_m_giabHC mqcs=6" >> results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/logs/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.concordance.log;
            
Submitted job 1 with external jobid '115'.
[Fri May 29 21:20:25 2026]
Finished job 57.
102 of 133 steps (77%) done
[Fri May 29 21:20:25 2026]
Finished job 59.
103 of 133 steps (77%) done
[Fri May 29 21:20:25 2026]
Finished job 61.
104 of 133 steps (78%) done
[Fri May 29 21:20:26 2026]
Finished job 53.
105 of 133 steps (79%) done
[Fri May 29 21:20:36 2026]
Finished job 1.
106 of 133 steps (80%) done
Select jobs to execute...

[Fri May 29 21:20:36 2026]
localrule produce_snv_concordances:
    input: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/concordance.done, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_altair-v1.1/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC_x_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38_m_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_concordance.mqc.tsv
    output: results/day/hg38_broad/other_reports/giab_concordance_mqc.tsv
    jobid: 0
    reason: Missing output files: results/day/hg38_broad/other_reports/giab_concordance_mqc.tsv; Input files updated by another job: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_altair-v1.1/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38_m_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC_x_clinvar_genes/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC/snv_TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ_giabHC_concordance.mqc.tsv, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/concordance.done
    priority: 48
    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 21:20:36 2026]
Finished job 55.
107 of 133 steps (80%) done
Config file config/global.yaml is extended by additional config specified via the command line.
loading global: /fsx/analysis_results/ubuntu/ccv20260529r5_illumina_snv_alignstats_relatedness_vep_multiqc/daylily-omics-analysis/config/global_AWSPC.yaml
Config file config/global_AWSPC.yaml is extended by additional config specified via the command line.
loading profile rule_config: /fsx/analysis_results/ubuntu/ccv20260529r5_illumina_snv_alignstats_relatedness_vep_multiqc/daylily-omics-analysis/config/day_profiles/slurm/rule_config.yaml
Config file config/day_profiles/slurm/rule_config.yaml is extended by additional config specified via the command line.
INFO::: The genome build hg38_broad is supported.  The genome build prefix is 'chr''.
...WARNING: No aligners set in the config.
...INFO: Auto-detected aligners from env: ['sent']
aligners (final): [sent]
...INFO: No dedupers set in config. Defaulting to na (no dedup).
...INFO: Auto-detected dedupers. DDUP updated to: ['dmd']
deduper (final): [dmd]
...WARNING: No snv_callers set in the config.
...INFO: Auto-detected SNV callers from env: ['sentd']
SNV Callers (final): [sentd]
Somatic SNV Callers:[senttn]
... WARNING: No sv_callers set in the config.
SV Callers (final): []
A    N   A   L  Y S I S    SAMPLE TABLE DETECTED ::: /fsx/analysis_results/ubuntu/ccv20260529r5_illumina_snv_alignstats_relatedness_vep_multiqc/daylily-omics-analysis/config/samples.tsv
A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/ubuntu/ccv20260529r5_illumina_snv_alignstats_relatedness_vep_multiqc/daylily-omics-analysis/config/units.tsv
Building DAG of jobs...
All Wildcards:    all snv_CALLERS:  ['sentd']  all ALIGNERS:  ['sent']  all CRAM_ALIGNERS:  []  all samples:  {'TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ': ['TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ']}  all concordance samples:  dict_keys(['TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ'])
Using shell: /home/ubuntu/miniconda3/envs/DAY-EC/bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, threads=1, time=5440, vcpu=1
Select jobs to execute...
All Wildcards:    all snv_CALLERS:  ['sentd']  all ALIGNERS:  ['sent']  all CRAM_ALIGNERS:  []  all samples:  {'TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ': ['TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ']}  all concordance samples:  dict_keys(['TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ'])
All Wildcards:    all snv_CALLERS:  ['sentd']  all ALIGNERS:  ['sent']  all CRAM_ALIGNERS:  []  all samples:  {'TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ': ['TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ']}  all concordance samples:  dict_keys(['TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ'])
[Fri May 29 21:20:39 2026]
Finished job 0.
108 of 133 steps (81%) done
[Fri May 29 21:21:36 2026]
Finished job 51.
109 of 133 steps (82%) done
[Fri May 29 21:21:36 2026]
Finished job 49.
110 of 133 steps (83%) done
[Fri May 29 21:21:36 2026]
Finished job 45.
111 of 133 steps (83%) done
[Fri May 29 21:21:56 2026]
Finished job 47.
112 of 133 steps (84%) done
[Fri May 29 21:22:07 2026]
Finished job 37.
113 of 133 steps (85%) done
[Fri May 29 21:22:07 2026]
Finished job 43.
114 of 133 steps (86%) done
[Fri May 29 21:22:07 2026]
Finished job 39.
115 of 133 steps (86%) done
[Fri May 29 21:22:27 2026]
Finished job 41.
116 of 133 steps (87%) done
[Fri May 29 21:22:47 2026]
Finished job 33.
117 of 133 steps (88%) done
[Fri May 29 21:23:07 2026]
Finished job 35.
118 of 133 steps (89%) done
[Fri May 29 21:24:07 2026]
Finished job 28.
119 of 133 steps (89%) done
[Fri May 29 21:24:27 2026]
Finished job 31.
120 of 133 steps (90%) done
Select jobs to execute...

[Fri May 29 21:24:27 2026]
localrule vep_concat_fofn:
    input: results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr1/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr1.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr3/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr3.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr4/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr4.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr5/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr5.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr6/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr6.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr8/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr8.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr9/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr9.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr10/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr10.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr12/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr12.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr13/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr13.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr14/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr14.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr15/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr15.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr16/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr16.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr17/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr17.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr18/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr18.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr20/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr20.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr21/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr21.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr22/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr22.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chrX/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chrX.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chrY/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chrY.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chrM/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chrM.vep.vcf.gz.tbi, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr1/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr1.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr2/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr2.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr3/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr3.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr4/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr4.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr5/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr5.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr6/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr6.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr7/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr7.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr8/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr8.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr9/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr9.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr10/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr10.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr11/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr11.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr12/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr12.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr13/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr13.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr14/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr14.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr15/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr15.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr16/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr16.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr17/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr17.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr18/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr18.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr19/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.chr19.vep.vcf.gz.record_count, results/day/hg38_broad/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/chunks/chr20/TVBILMN5X-HG003-5x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.--output truncated--
