DAY-EC activated.
DAY-EC activated.
DAY-EC               * /home/ubuntu/miniconda3/envs/DAY-EC
DAYOA                  /home/ubuntu/miniconda3/envs/DAYOA

Day CLI initialized for project 'hyb-only' in region 'us-west-2'.
The Daylily CLI is now available.
Available commands (tab completion is enabled for all):
 
	(day-activate / dy-a) [slurm|local] ([hg38|hg38_broad|b37])- Activate a Slurm or local environment.
	                           
	{day-set-genome-build / dy-g) [b37|hg38|hg38_broad] - Set the genome build for the current environment.
	                           
	(day-run / dy-r)          - Run a command in the current environment.
	                           <tab> for exposed targets, -<tab> for all command line flags.
	                           
	(day-monitor / dy-m)      - Monitor workflow status (Snakemake, SLURM, logs).
	                           Use --block-and-poll to wait for completion.
	                           
	(day-deactivate / dy-d)   - Deactivate the current environment.
	                           Use 'dy-d reset' to hard reset the environment.
	                           
	                           
	                           
	                           
	. To Stage Sample Data, see daylily-ephemeral-cluster docs for running ~/projects/daylily-ephemeral-cluster/bin/daylily-stage-analysis-samples-headnode 
	  ... which once run, you will copy the samples.tsv and units.tsv files to config/ in this directory.
	                           
	(example): ACTIVATE AN ANALYSIS ENV





		dy-a slurm hg38 # or hg38_broad or b37

	(example): RUN ANALYSES

		cp .test_data/data/0.01xwgs_HG002_hg38.samples.tsv config/samples.tsv

		cp .test_data/data/0.01xwgs_HG002_hg38.units.tsv config/units.tsv



		# 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_kitchensink_mounted_20260606T053415Z_dryrun/daylily-omics-analysis/config/day_profiles/slurm ... copying
Copying template yaml files to active config files /fsx/analysis_results/ubuntu/hybonly_ont_kitchensink_mounted_20260606T053415Z_dryrun/daylily-omics-analysis/config/day_profiles/slurm
Copying template bash files to active config files /fsx/analysis_results/ubuntu/hybonly_ont_kitchensink_mounted_20260606T053415Z_dryrun/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
[INFO] Patched RTG vcfeval parse/JVM-memory repair: workflow/rules/rtg_vcfeval.smk
[INFO] Patched VEP zero-variant concat repair: workflow/rules/vep.smk
Remote call detected. Activating conda hack
Your config files in /fsx/analysis_results/ubuntu/hybonly_ont_kitchensink_mounted_20260606T053415Z_dryrun/daylily-omics-analysis/config/day_profiles/slurm are newer than the templates. clear 2 go.
...AUTO-CONFIG: snv_callers=sentdont (from target rules → env)
Executing: snakemake --profile=/fsx/analysis_results/ubuntu/hybonly_ont_kitchensink_mounted_20260606T053415Z_dryrun/daylily-omics-analysis/config/day_profiles/slurm 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 -n
Config file config/global.yaml is extended by additional config specified via the command line.
loading global: /fsx/analysis_results/ubuntu/hybonly_ont_kitchensink_mounted_20260606T053415Z_dryrun/daylily-omics-analysis/config/global_AWSPC.yaml
Config file config/global_AWSPC.yaml is extended by additional config specified via the command line.
loading profile rule_config: /fsx/analysis_results/ubuntu/hybonly_ont_kitchensink_mounted_20260606T053415Z_dryrun/daylily-omics-analysis/config/day_profiles/slurm/rule_config.yaml
Config file config/day_profiles/slurm/rule_config.yaml is extended by additional config specified via the command line.
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.
...INFO: Auto-detected SNV callers from env: ['sentdont']
SNV Callers (final): [sentdont]
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_kitchensink_mounted_20260606T053415Z_dryrun/daylily-omics-analysis/config/samples.tsv
A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/ubuntu/hybonly_ont_kitchensink_mounted_20260606T053415Z_dryrun/daylily-omics-analysis/config/units.tsv
Building DAG of jobs...
DAY-EC activated.
DAY-EC activated.
    reason: Missing output files: results/day/hg38/reports/dayoa_evidence_manifest.json; Input files updated by another job: results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/norm_cov_eveness/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ.sent.dmd.md, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/contam/gatk/20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ.sent.dmd.gatk.tsv, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ/align/sent/na/alignqc/norm_cov_eveness/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ.sent.na.md, results/day/hg38/other_reports/relatedness/sent/dmd/somalier/cohort.pairs.tsv, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.contamination.raw.txt, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/contam/gatk/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ.sent.dmd.gatk.tsv, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.contamination.txt, results/day/hg38/reports/multiqc_inputs/final/manifest.tsv, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ/align/sent/na/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ.sent.na.complete, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.report.html, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ/align/sent/na/alignqc/goleft.done, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/goleft.done, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ/align/sent/na/alignqc/goleft.done, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.contamination.txt, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.contamination.txt, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/unmapped_metagenomics/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ.sent.dmd.kraken2.quick.report.txt, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.contamination.txt, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/unmapped_metagenomics/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ.sent.dmd.kraken2.quick.report.txt, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ/align/sent/na/alignqc/mosdepth/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ.sent.na.mosdepth.summary.txt, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ/align/sent/na/alignqc/mosdepth/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ.sent.na.mosdepth.summary.txt, results/day/hg38/other_reports/unmapped_metagenomics_mqc.tsv, logs/peddy_gathered.done, results/day/hg38/other_reports/peddy_sample_qc_mqc.tsv, results/day/hg38/other_reports/expansionhunter_mqc.tsv, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ/align/sent/na/alignqc/goleft.done, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/read_haps/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ.sent.dmd.sentd.read_haps.txt, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/mosdepth/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ.sent.dmd.mosdepth.summary.txt, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/contam/gatk/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ.sent.dmd.gatk.tsv, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ/align/sent/na/alignqc/mosdepth/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ.sent.na.mosdepth.summary.txt, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ.sent.dmd.complete, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ/align/sent/na/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ.sent.na.complete, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ/align/sent/na/alignqc/norm_cov_eveness/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ.sent.na.md, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.report.html, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ/align/sent/na/alignqc/goleft.done, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/norm_cov_eveness/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ.sent.dmd.md, results/day/hg38/reports/DAY_final_multiqc.html, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/read_haps/20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ.sent.dmd.sentd.read_haps.txt, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ/seqqc/fastqc/20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ.fastqc.done, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ/align/sent/na/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ.sent.na.complete, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ/align/sent/na/alignqc/norm_cov_eveness/20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ.sent.na.md, results/day/hg38/other_reports/unmapped_metagenomics_ganon2_mqc.tsv, results/day/hg38/reports/DAY_final_multiqc_data/multiqc_general_stats.txt, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ/seqqc/fastqc/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ.fastqc.done, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.contamination.txt, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.contamination.raw.txt, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/contam/gatk/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ.sent.dmd.gatk.tsv, results/day/hg38/other_reports/norm_cov_evenness_combo_mqc.tsv, results/day/hg38/other_reports/rtg_vcfstats_mqc.tsv, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ/seqqc/fastqc/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ.fastqc.done, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/unmapped_metagenomics/20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ.sent.dmd.kraken2.quick.report.txt, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ.sent.dmd.complete, results/day/hg38/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ/align/sent/na/alignqc/samtmetrics/20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ.sent.na.complete, 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