{
  "command": "bin/day_run sentmm2ont_align_sort produce_alignstats dedup_na -p -j 5 -k --rerun-triggers mtime -n",
  "completed_at": "2026-06-06T07:44:56Z",
  "exit_code": 1,
  "repo_path": "/fsx/analysis_results/ubuntu/hybonly_ont_alignsort_alignstats_dedupna_dryrun_20260606T074315Z/daylily-omics-analysis",
  "session_name": "hybonly_ont_alignsort_alignstats_dedupna_dryrun_20260606T074315Z",
  "started_at": "2026-06-06T07:43:41Z"
}
DAY-EC activated.
DAY-EC activated.
		# Use target names directly (tab-complete available):

		dy-r produce_snv_concordances -p -k -j 20 -n   # Illumina short-read SNV concordance

		dy-r produce_alignstats -p -k -j 20 -n         # Alignment statistics



		# Platform-specific targets:

		dy-r produce_sentdont_vcf -p -k -j 20 -n       # ONT SNV calling

		dy-r produce_sentdpb_vcf -p -k -j 20 -n        # PacBio SNV calling

		dy-r produce_sentdug_vcf -p -k -j 20 -n        # Ultima SNV calling (use hg38_broad)



		# Hybrid workflow targets:

		dy-r produce_sentdhio_vcf -p -k -j 20 -n       # Hybrid Illumina+ONT CLI

		dy-r produce_sentdhuo_vcf -p -k -j 20 -n       # Hybrid Ultima+ONT CLI (use hg38_broad)

		dy-r produce_sentdhiom_vcf -p -k -j 20 -n      # Hybrid Illumina+ONT Modular

		dy-r produce_sentdhuom_vcf -p -k -j 20 -n      # Hybrid Ultima+ONT Modular (use hg38_broad)



		# Remove -n to execute (not dry-run)

Requesting profile: slurm
Attempting to deactivate existing environments & re-init with --project hyb-only .
Remote call detected. Activating conda hack
 > >> >>> 
ACTIVE CONFIG FILES NOT FOUND IN /fsx/analysis_results/ubuntu/hybonly_ont_alignsort_alignstats_dedupna_dryrun_20260606T074315Z/daylily-omics-analysis/config/day_profiles/slurm ... copying
Copying template yaml files to active config files /fsx/analysis_results/ubuntu/hybonly_ont_alignsort_alignstats_dedupna_dryrun_20260606T074315Z/daylily-omics-analysis/config/day_profiles/slurm
Copying template bash files to active config files /fsx/analysis_results/ubuntu/hybonly_ont_alignsort_alignstats_dedupna_dryrun_20260606T074315Z/daylily-omics-analysis/config/day_profiles/slurm
yq is already installed.
Using sentieon license file: /fsx/references/runtime_assets/cached_envs/Life_Sciences_Manufacturing_Corporation_eval.lic from ~/.config/daylily/daylily_cli_global.yaml

!!!!
!!!!
    WARNING: gittag:null not found touched in  ~/.config/daylily/null 
     This might be fine if you have cloned a more recent release of daylily compared to the tagged version used to create this ephemeral cluster.
     ... however, this is not expected. If you are running an ephemeral cluster headnode for days+, this is not the intended use of daylily, a fresh build might be called for.
     This is checked by testing if ~/.config/daylily/null exists .
!!!!
 > >> >>>   genome build set to ::: hg38_broad  
       _______ GREAT SUCCESS _______       
[INFO] Patched goleft empty-sex/no-usable-chromosomes repair: workflow/rules/go_left.smk
[INFO] Patched mosdepth empty-output repair: workflow/rules/mosdepth.smk
Remote call detected. Activating conda hack
Your config files in /fsx/analysis_results/ubuntu/hybonly_ont_alignsort_alignstats_dedupna_dryrun_20260606T074315Z/daylily-omics-analysis/config/day_profiles/slurm are newer than the templates. clear 2 go.
Executing: snakemake --profile=/fsx/analysis_results/ubuntu/hybonly_ont_alignsort_alignstats_dedupna_dryrun_20260606T074315Z/daylily-omics-analysis/config/day_profiles/slurm sentmm2ont_align_sort produce_alignstats dedup_na -p -j 5 -k --rerun-triggers mtime -n
loading global: /fsx/analysis_results/ubuntu/hybonly_ont_alignsort_alignstats_dedupna_dryrun_20260606T074315Z/daylily-omics-analysis/config/global_AWSPC.yaml
loading profile rule_config: /fsx/analysis_results/ubuntu/hybonly_ont_alignsort_alignstats_dedupna_dryrun_20260606T074315Z/daylily-omics-analysis/config/day_profiles/slurm/rule_config.yaml
INFO::: The genome build hg38_broad is supported.  The genome build prefix is 'chr''.
...WARNING: No aligners set in the config.
aligners (final): []
...INFO: No dedupers set in config. Defaulting to na (no dedup).
deduper (final): [na]
...WARNING: No snv_callers set in the config.
SNV Callers (final): []
Somatic SNV Callers:[senttn]
... WARNING: No sv_callers set in the config.
SV Callers (final): []
A    N   A   L  Y S I S    SAMPLE TABLE DETECTED ::: /fsx/analysis_results/ubuntu/hybonly_ont_alignsort_alignstats_dedupna_dryrun_20260606T074315Z/daylily-omics-analysis/config/samples.tsv
A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/ubuntu/hybonly_ont_alignsort_alignstats_dedupna_dryrun_20260606T074315Z/daylily-omics-analysis/config/units.tsv
Building DAG of jobs...
WorkflowError:
Target rules may not contain wildcards. Please specify concrete files or a rule without wildcards at the command line, or have a rule without wildcards at the very top of your workflow (e.g. the typical "rule all" which just collects all results you want to generate in the end).
RETURN CODE: 1
[INFO] Workflow exited with status 1
To run a command as administrator (user "root"), use "sudo <command>".
See "man sudo_root" for details.

DAY-EC activated.
(DAY-EC) ubuntu@ip-10-0-0-81:/fsx/analysis_results/ubuntu/hybonly_ont_alignsort_alignstats_dedupna_dryrun_20260606T074315Z/daylily-omics-analysis$
