## ILMN_STATUS
{
  "command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_alignstats produce_snv_concordances produce_relatedness produce_gatk_contam_estimate produce_site_mix_contam_estimate produce_global_contam_check produce_vep produce_expansionhunter produce_htd_calls produce_metagenomics produce_multiqc_all --config 'aligners=[\"sent\"]' 'dedupers=[\"dmd\"]' 'snv_callers=[\"sentd\"]' 'htd_callers=[\"cyrius\"]' 'multiqc_qc={\"enable_tools\":[\"vep\",\"metagenomics\",\"contam_identity\"]}' -j 200 -p -k --rerun-triggers mtime",
  "completed_at": null,
  "exit_code": null,
  "repo_path": "/fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis",
  "session_name": "hybonly_ilmn_kitchensink_mounted_20260606T053415Z",
  "started_at": "2026-06-06T05:59:22Z"
}
## ONT_LIMITED_STATUS
{
  "command": "bin/day_run produce_sentmm2ont_align produce_alignstats produce_na_dedup_cram -p -j 5 -k --rerun-triggers mtime",
  "completed_at": "2026-06-06T08:30:49Z",
  "exit_code": 130,
  "repo_path": "/fsx/analysis_results/ubuntu/hybonly_ont_alignsort_alignstats_dedupna_live_20260606T074825Z/daylily-omics-analysis",
  "session_name": "hybonly_ont_alignsort_alignstats_dedupna_live_20260606T074825Z",
  "started_at": "2026-06-06T07:48:50Z",
  "stop_cancelled_slurm_job_ids": [
    "850",
    "851",
    "848",
    "849",
    "847"
  ],
  "stop_reason": "dyec workflow stop",
  "stopped": true
}
## ILMN_PROGRESS
524 of 729 steps (72%) done
525 of 729 steps (72%) done
526 of 729 steps (72%) done
527 of 729 steps (72%) done
528 of 729 steps (72%) done
529 of 729 steps (73%) done
530 of 729 steps (73%) done
531 of 729 steps (73%) done
532 of 729 steps (73%) done
533 of 729 steps (73%) done
## QUEUE_FILTERED
DAY-EC activated.
694  i192  8  R  i192-dy-all-3  8  RUNNING  16000M  1:18:30  1  haplocheck_vcf_contam_identity-20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ
620  i192  8  R  i192-dy-all-1  8  RUNNING  16000M  1:19:49  1  haplocheck_vcf_contam_identity-20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ
561  i192  8  R  i192-dy-all-5  8  RUNNING  16000M  1:20:49  1  haplocheck_vcf_contam_identity-20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ
487  i192  8  R  i192-dy-all-14  8  RUNNING  16000M  1:22:13  1  haplocheck_vcf_contam_identity-20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ
417  i192  8  R  i192-dy-all-1  8  RUNNING  16000M  1:24:23  1  haplocheck_vcf_contam_identity-20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ
351  i192  8  R  i192-dy-all-1  8  RUNNING  16000M  1:27:08  1  haplocheck_vcf_contam_identity-20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ
256  i192  8  R  i192-dy-all-1  8  RUNNING  16000M  1:31:36  1  haplocheck_vcf_contam_identity-20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ
