DAY-EC activated.
DAY-EC activated.
=== status ===
{
  "command": "bin/day_run produce_snv_concordances produce_sentdhiomr_sv produce_sentdhiomr_snv_vcf produce_relatedness produce_vep produce_multiqc_all --config 'dedupers=[\"dmd\"]' 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 100 -k",
  "completed_at": "2026-05-30T00:46:58Z",
  "exit_code": 1,
  "repo_path": "/fsx/analysis_results/ubuntu/ccv20260529r7_hybrid_ilmn_ont_snv_kitchensink/daylily-omics-analysis",
  "session_name": "ccv20260529r7_hybrid_ilmn_ont_snv_kitchensink",
  "started_at": "2026-05-29T23:40:40Z"
}
=== repo ===
/fsx/analysis_results/ubuntu/ccv20260529r7_hybrid_ilmn_ont_snv_kitchensink/daylily-omics-analysis
=== latest snakemake logs ===
1780102017.0000000000 .snakemake/log/2026-05-29T234104.146765.snakemake.log
1780102021.0000000000 .snakemake/log/2026-05-30T004658.536249.snakemake.log
=== latest log path: .snakemake/log/2026-05-30T004658.536249.snakemake.log ===
=== latest log tail ===
Unlocking working directory.
=== rule logs with errors ===
logs/slurm/sentdhiomr_stage3/sentdhiomr_stage3.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.146.err:76:            samtools quickcheck results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/4/tmp/hybrid_stage3.bam >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.4.stage3.log 2>&1 ||                 (echo "ERROR: empty Stage3 BAM failed integrity check" >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.4.stage3.log && exit 1)
logs/slurm/sentdhiomr_stage3/sentdhiomr_stage3.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.186.err:76:            samtools quickcheck results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/5/tmp/hybrid_stage3.bam >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.5.stage3.log 2>&1 ||                 (echo "ERROR: empty Stage3 BAM failed integrity check" >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.5.stage3.log && exit 1)
logs/slurm/sentdhiomr_stage3/sentdhiomr_stage3.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.626.err:76:            samtools quickcheck results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/16/tmp/hybrid_stage3.bam >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.16.stage3.log 2>&1 ||                 (echo "ERROR: empty Stage3 BAM failed integrity check" >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.16.stage3.log && exit 1)
logs/slurm/sentdhiomr_stage3/sentdhiomr_stage3.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.666.err:76:            samtools quickcheck results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/vcfs/17-19/tmp/hybrid_stage3.bam >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.17-19.stage3.log 2>&1 ||                 (echo "ERROR: empty Stage3 BAM failed integrity check" >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.17-19.stage3.log && exit 1)
logs/slurm/mosdepth/mosdepth.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.765.err:43:        test -s 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 || (printf 'ERROR: mosdepth summary output is missing or empty: %s\n' 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 | tee -a 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.log >&2; exit 1)
logs/slurm/mosdepth/mosdepth.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.765.err:44:        test -s 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.global.dist.txt || (printf 'ERROR: mosdepth global_dist output is missing or empty: %s\n' 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.global.dist.txt | tee -a 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.log >&2; exit 1)
logs/slurm/mosdepth/mosdepth.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.765.err:45:        test -s 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.region.dist.txt || (printf 'ERROR: mosdepth region_dist output is missing or empty: %s\n' 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.region.dist.txt | tee -a 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.log >&2; exit 1)
logs/slurm/mosdepth/mosdepth.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.764.err:43:        test -s 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 || (printf 'ERROR: mosdepth summary output is missing or empty: %s\n' 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 | tee -a 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.log >&2; exit 1)
logs/slurm/mosdepth/mosdepth.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.764.err:44:        test -s 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.global.dist.txt || (printf 'ERROR: mosdepth global_dist output is missing or empty: %s\n' 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.global.dist.txt | tee -a 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.log >&2; exit 1)
logs/slurm/mosdepth/mosdepth.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.764.err:45:        test -s 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.region.dist.txt || (printf 'ERROR: mosdepth region_dist output is missing or empty: %s\n' 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.region.dist.txt | tee -a 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.log >&2; exit 1)
logs/slurm/goleft/goleft.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.766.err:40:        rm -rf $(dirname results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/alignqc/goleft/golefttwo.done ) || echo rmGOLfailed ;
logs/slurm/goleft/goleft.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.766.err:52:Error in rule goleft:
logs/slurm/goleft/goleft.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.766.err:56:    log: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/alignqc/goleft/logs/goleft.log (check log file(s) for error details)
logs/slurm/goleft/goleft.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.766.err:62:        rm -rf $(dirname results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/alignqc/goleft/golefttwo.done ) || echo rmGOLfailed ;
logs/slurm/goleft/goleft.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.766.err:72:        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
logs/slurm/goleft/goleft.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.766.err:75:Exiting because a job execution failed. Look above for error message
logs/slurm/goleft/goleft.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.767.err:40:        rm -rf $(dirname results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/na/alignqc/goleft/golefttwo.done ) || echo rmGOLfailed ;
logs/slurm/goleft/goleft.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.767.err:52:Error in rule goleft:
logs/slurm/goleft/goleft.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.767.err:56:    log: results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/na/alignqc/goleft/logs/goleft.log (check log file(s) for error details)
logs/slurm/goleft/goleft.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.767.err:62:        rm -rf $(dirname results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/na/alignqc/goleft/golefttwo.done ) || echo rmGOLfailed ;
logs/slurm/goleft/goleft.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.767.err:72:        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
logs/slurm/goleft/goleft.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.767.err:75:Exiting because a job execution failed. Look above for error message
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.298.err:46:            echo "ERROR: Failed to create TMPDIR: $TMPDIR" >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.8.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.298.err:55:        ulimit -n 65536 || echo "ulimit mod failed" > results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.8.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.298.err:91:            echo "ERROR: ONT CRAM results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.cram is empty (0 bytes). This sample has no ONT data." >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.8.pass1.log
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.538.err:46:            echo "ERROR: Failed to create TMPDIR: $TMPDIR" >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.14.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.538.err:55:        ulimit -n 65536 || echo "ulimit mod failed" > results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.14.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.538.err:91:            echo "ERROR: ONT CRAM results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.cram is empty (0 bytes). This sample has no ONT data." >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.14.pass1.log
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.578.err:46:            echo "ERROR: Failed to create TMPDIR: $TMPDIR" >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.15.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.578.err:55:        ulimit -n 65536 || echo "ulimit mod failed" > results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.15.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.578.err:91:            echo "ERROR: ONT CRAM results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.cram is empty (0 bytes). This sample has no ONT data." >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.15.pass1.log
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.218.err:46:            echo "ERROR: Failed to create TMPDIR: $TMPDIR" >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.6.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.218.err:55:        ulimit -n 65536 || echo "ulimit mod failed" > results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.6.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.218.err:91:            echo "ERROR: ONT CRAM results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.cram is empty (0 bytes). This sample has no ONT data." >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.6.pass1.log
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.258.err:46:            echo "ERROR: Failed to create TMPDIR: $TMPDIR" >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.7.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.258.err:55:        ulimit -n 65536 || echo "ulimit mod failed" > results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.7.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.258.err:91:            echo "ERROR: ONT CRAM results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.cram is empty (0 bytes). This sample has no ONT data." >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.7.pass1.log
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.338.err:46:            echo "ERROR: Failed to create TMPDIR: $TMPDIR" >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.9.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.338.err:55:        ulimit -n 65536 || echo "ulimit mod failed" > results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.9.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.338.err:91:            echo "ERROR: ONT CRAM results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.cram is empty (0 bytes). This sample has no ONT data." >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.9.pass1.log
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.498.err:46:            echo "ERROR: Failed to create TMPDIR: $TMPDIR" >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.13.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.498.err:55:        ulimit -n 65536 || echo "ulimit mod failed" > results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.13.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.498.err:91:            echo "ERROR: ONT CRAM results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.cram is empty (0 bytes). This sample has no ONT data." >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.13.pass1.log
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.98.err:46:            echo "ERROR: Failed to create TMPDIR: $TMPDIR" >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.3.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.98.err:55:        ulimit -n 65536 || echo "ulimit mod failed" > results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.3.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.98.err:91:            echo "ERROR: ONT CRAM results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.cram is empty (0 bytes). This sample has no ONT data." >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.3.pass1.log
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.378.err:46:            echo "ERROR: Failed to create TMPDIR: $TMPDIR" >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.10.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.378.err:55:        ulimit -n 65536 || echo "ulimit mod failed" > results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.10.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.378.err:91:            echo "ERROR: ONT CRAM results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.cram is empty (0 bytes). This sample has no ONT data." >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.10.pass1.log
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.418.err:46:            echo "ERROR: Failed to create TMPDIR: $TMPDIR" >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.11.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.418.err:55:        ulimit -n 65536 || echo "ulimit mod failed" > results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.11.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.418.err:91:            echo "ERROR: ONT CRAM results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.cram is empty (0 bytes). This sample has no ONT data." >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.11.pass1.log
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.58.err:46:            echo "ERROR: Failed to create TMPDIR: $TMPDIR" >> results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.2.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.58.err:55:        ulimit -n 65536 || echo "ulimit mod failed" > results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/dmd/snv/sentdhiomr/log/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.ont.dmd.2.pass1.log 2>&1;
logs/slurm/sentdhiomr_pass1/sentdhiomr_pass1.TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.58.err:91:            echo "ERROR: ONT CRAM results/day/hg38_broad/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ/align/ont/TVBHIO5X5X-HG003-ILMN5x-ONT5x-1-D0-PF-ILMN-NOVASEQ.cram--output truncated--