{
  "command": "bin/day_run produce_alignstats produce_sentdont_snv_vcf produce_snv_concordances produce_relatedness produce_vep produce_multiqc_all --config 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 5 -k --rerun-triggers mtime",
  "completed_at": null,
  "exit_code": null,
  "repo_path": "/fsx/analysis_results/ubuntu/hybonly_ont_kitchensink_mounted_20260606T053415Z_retry1/daylily-omics-analysis",
  "session_name": "hybonly_ont_kitchensink_mounted_20260606T053415Z_retry1",
  "started_at": "2026-06-06T06:20:47Z"
}
{
  "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"
}
DAY-EC activated.
DAY-EC activated.
JOBID  PARTITION  CPUS  ST  NODELIST  MIN_CPUS  STATE  MIN_MEMORY  TIME  NODES  NAME
165  i192  192  CF  i192-dy-all-13  192  CONFIGURING  200000M  0:45  1  sentmm2ont_align_sort-ONT-4Coriells-chip1-NA03986-DMPK-chip1-barcode20-chip1-0019-PF-ONT-PROMETHION
166  i192  192  R  i192-dy-all-3  192  RUNNING  200000M  0:16  1  sentmm2ont_align_sort-ONT-4Coriells-chip2-NA03986-DMPK-chip2-barcode20-chip2-0021-PF-ONT-PROMETHION
167  i192  192  R  i192-dy-all-4  192  RUNNING  200000M  0:16  1  sentmm2ont_align_sort-ONT-4Coriells-chip4-NA09677-SMN-chip4-barcode19-chip4-0012-PF-ONT-PROMETHION
164  i192  192  R  i192-dy-all-7  24  RUNNING  80000M  0:48  1  gatk_contam-20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ
144  i192  96  R  i192-dy-all-10  96  RUNNING  3000M  1:08  1  alignstats-20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ
161  i192  16  R  i192-dy-all-8  16  RUNNING  3000M  1:08  1  gen_samstats-20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ
162  i192  96  R  i192-dy-all-5  96  RUNNING  3000M  1:08  1  alignstats-20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ
163  i192  16  R  i192-dy-all-5  16  RUNNING  3000M  1:08  1  mosdepth-20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ
160  i192  16  R  i192-dy-all-8  16  RUNNING  3000M  1:09  1  calc_coverage_evenness-20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ
158  i192  192  R  i192-dy-all-6  192  RUNNING  200000M  1:27  1  sentmm2ont_align_sort-ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-0034-PF-ONT-PROMETHION
147  i192  192  R  i192-dy-all-11  192  RUNNING  200000M  1:38  1  sent_DNAscope-20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ
148  i192  192  R  i192-dy-all-12  192  RUNNING  200000M  1:38  1  sentmm2ont_align_sort-ONT-4Coriells-chip4-NA03986-DMPK-chip4-barcode20-chip4-0016-PF-ONT-PROMETHION
132  i192  16  R  i192-dy-all-8  16  RUNNING  3000M  5:29  1  gen_samstats-20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ
133  i192  16  R  i192-dy-all-5  16  RUNNING  3000M  5:29  1  calc_coverage_evenness-20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ
141  i192  16  R  i192-dy-all-5  16  RUNNING  3000M  5:29  1  calc_coverage_evenness-20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ
143  i192  16  R  i192-dy-all-5  16  RUNNING  3000M  5:29  1  gen_samstats-20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ
146  i192  32  R  i192-dy-all-5  32  RUNNING  62.50G  5:29  1  legacy_cram_compat_bam-20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ
130  i192  96  R  i192-dy-all-8  96  RUNNING  3000M  5:30  1  alignstats-20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ
117  i192  16  R  i192-dy-all-8  16  RUNNING  3000M  6:38  1  gen_samstats-20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ
118  i192  192  R  i192-dy-all-9  192  RUNNING  200000M  6:38  1  sent_DNAscope-20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ
108  i192  96  R  i192-dy-all-2  96  RUNNING  3000M  10:17  1  alignstats-20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ
109  i192  16  R  i192-dy-all-1  16  RUNNING  3000M  10:17  1  calc_coverage_evenness-20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ
94  i192  4  R  i192-dy-all-1  4  RUNNING  16000M  15:26  1  no_dedup-20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ
92  i192  4  R  i192-dy-all-1  4  RUNNING  16000M  16:06  1  no_dedup-20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ
89  i192  4  R  i192-dy-all-1  4  RUNNING  16000M  16:27  1  no_dedup-20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ
85  i192  4  R  i192-dy-all-1  4  RUNNING  16000M  16:47  1  no_dedup-20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ
82  i192  4  R  i192-dy-all-1  4  RUNNING  16000M  18:18  1  no_dedup-20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ
1  i192  32  R  i192-dy-all-1  32  RUNNING  3000M  55:08  1  fastqc_subsampled-20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ
2  i192  32  R  i192-dy-all-1  32  RUNNING  3000M  55:08  1  fastqc_subsampled-20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ
3  i192  32  R  i192-dy-all-1  32  RUNNING  3000M  55:08  1  fastqc_subsampled-20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ
5  i192  32  R  i192-dy-all-1  32  RUNNING  3000M  55:08  1  fastqc_subsampled-20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ
8  i192  32  R  i192-dy-all-2  32  RUNNING  3000M  55:08  1  fastqc_subsampled-20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ
12  i192  32  R  i192-dy-all-2  32  RUNNING  3000M  55:08  1  fastqc_subsampled-20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ
14  i192  32  R  i192-dy-all-2  32  RUNNING  3000M  55:08  1  fastqc_subsampled-20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ
95  i192mem  192  R  i192mem-dy-all-2  192  RUNNING  200000M  15:26  1  doppelmark_dups-20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ
93  i192mem  192  R  i192mem-dy-all-1  192  RUNNING  200000M  16:06  1  doppelmark_dups-20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ
90  i192mem  192  R  i192mem-dy-all-4  192  RUNNING  200000M  16:25  1  doppelmark_dups-20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ
84  i192mem  192  R  i192mem-dy-all-5  192  RUNNING  200000M  16:47  1  doppelmark_dups-20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ
81  i192mem  192  R  i192mem-dy-all-6  192  RUNNING  200000M  18:18  1  doppelmark_dups-20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ
