{
  "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
197  i192  96  CF  i192-dy-all-16  96  CONFIGURING  3000M  0:37  1  alignstats-20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ
199  i192  16  CF  i192-dy-all-16  16  CONFIGURING  3000M  0:37  1  goleft-20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ
200  i192  16  CF  i192-dy-all-16  16  CONFIGURING  3000M  0:37  1  mosdepth-20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ
201  i192  16  CF  i192-dy-all-16  16  CONFIGURING  3000M  0:37  1  gen_samstats-20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ
203  i192  192  CF  i192-dy-all-17  192  CONFIGURING  200000M  0:37  1  sent_DNAscope-20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ
205  i192  16  CF  i192-dy-all-16  16  CONFIGURING  1000M  0:37  1  cyrius-20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ
207  i192  16  CF  i192-dy-all-16  16  CONFIGURING  3000M  0:37  1  calc_coverage_evenness-20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ
208  i192  32  CF  i192-dy-all-18  32  CONFIGURING  62.50G  0:37  1  legacy_cram_compat_bam-20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ
184  i192  192  CF  i192-dy-all-15  192  CONFIGURING  200000M  1:46  1  sentmm2ont_align_sort-ONT-4Coriells-chip1-NA03986-DMPK-chip1-barcode20-chip1-0021-PF-ONT-PROMETHION
168  i192  192  CF  i192-dy-all-14  24  CONFIGURING  80000M  2:02  1  gatk_contam-20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ
165  i192  192  CF  i192-dy-all-13  192  CONFIGURING  200000M  3:17  1  sentmm2ont_align_sort-ONT-4Coriells-chip1-NA03986-DMPK-chip1-barcode20-chip1-0019-PF-ONT-PROMETHION
211  i192  192  R  i192-dy-all-3  192  RUNNING  200000M  0:27  1  sentmm2ont_align_sort-ONT-4Coriells-chip2-NA03986-DMPK-chip2-barcode20-chip2-0022-PF-ONT-PROMETHION
212  i192  192  R  i192-dy-all-4  192  RUNNING  200000M  0:27  1  sentmm2ont_align_sort-ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-0001-PF-ONT-PROMETHION
187  i192  16  R  i192-dy-all-5  16  RUNNING  3000M  0:37  1  gen_samstats-20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ
188  i192  32  R  i192-dy-all-5  32  RUNNING  62.50G  0:37  1  legacy_cram_compat_bam-20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ
190  i192  16  R  i192-dy-all-10  16  RUNNING  32000M  0:37  1  expansionhunter_call-20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ
192  i192  4  R  i192-dy-all-1  4  RUNNING  3000M  0:37  1  relatedness_batch_somalier_extract-20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ
193  i192  96  R  i192-dy-all-12  96  RUNNING  3000M  0:37  1  alignstats-20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ
198  i192  16  R  i192-dy-all-10  16  RUNNING  32000M  0:37  1  expansionhunter_call-20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ
202  i192  4  R  i192-dy-all-1  4  RUNNING  3000M  0:37  1  relatedness_batch_somalier_extract-20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ
185  i192  16  R  i192-dy-all-8  16  RUNNING  3000M  0:38  1  calc_coverage_evenness-20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ
186  i192  16  R  i192-dy-all-8  16  RUNNING  3000M  0:38  1  mosdepth-20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ
183  i192  192  R  i192-dy-all-7  192  RUNNING  200000M  1:46  1  sentmm2ont_align_sort-ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-0067-PF-ONT-PROMETHION
170  i192  16  R  i192-dy-all-1  16  RUNNING  3000M  1:50  1  gen_samstats-20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ
171  i192  16  R  i192-dy-all-1  16  RUNNING  3000M  1:50  1  calc_coverage_evenness-20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ
172  i192  32  R  i192-dy-all-1  32  RUNNING  62.50G  1:50  1  legacy_cram_compat_bam-20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ
173  i192  16  R  i192-dy-all-10  16  RUNNING  32000M  1:50  1  expansionhunter_call-20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ
174  i192  16  R  i192-dy-all-10  16  RUNNING  3000M  1:50  1  mosdepth-20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ
175  i192  96  R  i192-dy-all-12  96  RUNNING  3000M  1:50  1  alignstats-20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ
182  i192  192  R  i192-dy-all-6  192  RUNNING  200000M  1:50  1  sent_DNAscope-20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ
144  i192  96  R  i192-dy-all-10  96  RUNNING  3000M  3:40  1  alignstats-20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ
161  i192  16  R  i192-dy-all-8  16  RUNNING  3000M  3:40  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  3:40  1  alignstats-20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ
160  i192  16  R  i192-dy-all-8  16  RUNNING  3000M  3:41  1  calc_coverage_evenness-20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ
147  i192  192  R  i192-dy-all-11  192  RUNNING  200000M  4:10  1  sent_DNAscope-20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ
132  i192  16  R  i192-dy-all-8  16  RUNNING  3000M  8:01  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  8:01  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  8:01  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  8:01  1  gen_samstats-20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ
130  i192  96  R  i192-dy-all-8  96  RUNNING  3000M  8:02  1  alignstats-20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ
117  i192  16  R  i192-dy-all-8  16  RUNNING  3000M  9:10  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  9:10  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  12:49  1  alignstats-20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ
94  i192  4  R  i192-dy-all-1  4  RUNNING  16000M  17:58  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  18:38  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  18:59  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  19:19  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  20:50  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  57:40  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  57:40  1  fastqc_subsampled-20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ
5  i192  32  R  i192-dy-all-1  32  RUNNING  3000M  57:40  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  57:40  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  57:40  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  57:40  1  fastqc_subsampled-20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ
189  i192mem  16  R  i192mem-dy-all-3  16  RUNNING  62.50G  0:37  1  unmapped_metagenomics_ganon2_quick-20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ
195  i192mem  16  R  i192mem-dy-all-3  16  RUNNING  62.50G  0:37  1  unmapped_metagenomics_sourmash_gather-20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ
196  i192mem  16  R  i192mem-dy-all-3  16  RUNNING  62.50G  0:37  1  unmapped_metagenomics_kraken2_quick-20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ
204  i192mem  16  R  i192mem-dy-all-3  16  RUNNING  62.50G  0:37  1  unmapped_metagenomics_kraken2_quick-20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ
206  i192mem  16  R  i192mem-dy-all-3  16  RUNNING  62.50G  0:37  1  unmapped_metagenomics_ganon2_quick-20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ
209  i192mem  16  R  i192mem-dy-all-3  16  RUNNING  62.50G  0:37  1  unmapped_metagenomics_sourmash_gather-20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ
210  i192mem  192  R  i192mem-dy-all-4  192  RUNNING  200000M  0:37  1  sent_DNAscope-20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ
176  i192mem  16  R  i192mem-dy-all-3  16  RUNNING  62.50G  1:50  1  unmapped_metagenomics_ganon2_quick-20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ
178  i192mem  16  R  i192mem-dy-all-3  16  RUNNING  62.50G  1:50  1  unmapped_metagenomics_sourmash_gather-20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ
179  i192mem  16  R  i192mem-dy-all-3  16  RUNNING  62.50G  1:50  1  unmapped_metagenomics_kraken2_quick-20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ
95  i192mem  192  R  i192mem-dy-all-2  192  RUNNING  200000M  17:58  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  18:38  1  doppelmark_dups-20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ
