{
  "command": "bin/day_run produce_sentmm2ont_align produce_alignstats produce_na_dedup_cram -p -j 5 -k --rerun-triggers mtime -n",
  "completed_at": "2026-06-06T07:47:19Z",
  "exit_code": 0,
  "repo_path": "/fsx/analysis_results/ubuntu/hybonly_ont_alignsort_alignstats_dedupna_dryrun2_20260606T074609Z/daylily-omics-analysis",
  "session_name": "hybonly_ont_alignsort_alignstats_dedupna_dryrun2_20260606T074609Z",
  "started_at": "2026-06-06T07:46:34Z"
}
DAY-EC activated.
DAY-EC activated.
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/dev/shm, threads=1, time=5440, partition=i192,i128,i192mem,bcl2fq-i384-nvme-test, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=

[Sat Jun  6 07:47:16 2026]
localrule finish_align_stats:
    input: results/day/hg38_broad/ONT-4Coriells-chip2-NA00232-SMN-chip2-barcode18-chip2-0042-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip2-NA00232-SMN-chip2-barcode18-chip2-0042-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.json
    output: results/day/hg38_broad/ONT-4Coriells-chip2-NA00232-SMN-chip2-barcode18-chip2-0042-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip2-NA00232-SMN-chip2-barcode18-chip2-0042-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv
    log: results/day/hg38_broad/ONT-4Coriells-chip2-NA00232-SMN-chip2-barcode18-chip2-0042-PF-ONT-PROMETHION/logs/ONT-4Coriells-chip2-NA00232-SMN-chip2-barcode18-chip2-0042-PF-ONT-PROMETHION.sentmm2ont.na.finish_align_stats.log
    jobid: 2442
    reason: Missing output files: results/day/hg38_broad/ONT-4Coriells-chip2-NA00232-SMN-chip2-barcode18-chip2-0042-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip2-NA00232-SMN-chip2-barcode18-chip2-0042-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv; Input files updated by another job: results/day/hg38_broad/ONT-4Coriells-chip2-NA00232-SMN-chip2-barcode18-chip2-0042-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip2-NA00232-SMN-chip2-barcode18-chip2-0042-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.json
    wildcards: sample=ONT-4Coriells-chip2-NA00232-SMN-chip2-barcode18-chip2-0042-PF-ONT-PROMETHION, alnr=sentmm2ont, ddup=na
    threads: 2
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/dev/shm, threads=1, time=5440, partition=i192,i128,i192mem,bcl2fq-i384-nvme-test, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=

[Sat Jun  6 07:47:16 2026]
localrule alignstats_gather:
    input: results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0000-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0000-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0001-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0001-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0002-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0002-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0003-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0003-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0004-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0004-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0005-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0005-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0006-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0006-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0007-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0007-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0008-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0008-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0009-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0009-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0010-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0010-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0011-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0011-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0012-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0012-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0013-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0013-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0014-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0014-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0015-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0015-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0016-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0016-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0017-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0017-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0018-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0018-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0019-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0019-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0020-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0020-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0021-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0021-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0022-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0022-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0023-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0023-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0024-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0024-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0025-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0025-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0026-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0026-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0027-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0027-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0028-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0028-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0029-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0029-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0030-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0030-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0031-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0031-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0032-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0032-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0033-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0033-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0034-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0034-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0035-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0035-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0036-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0036-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0037-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0037-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0038-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0038-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0039-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0039-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0040-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0040-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0041-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0041-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0042-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0042-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0043-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0043-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, 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results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0048-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0048-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0049-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0049-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0050-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0050-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, results/day/hg38_broad/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0051-PF-ONT-PROMETHION/align/sentmm2ont/na/alignqc/alignstats/ONT-4Coriells-chip1-NA00232-SMN-chip1-barcode18-chip1-0051-PF-ONT-PROMETHION.sentmm2ont.na.alignstats.tsv, 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