DAY-EC activated.
DAY-EC activated.
	                           
	(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 dyec5117 .
Remote call detected. Activating conda hack
 > >> >>> 
ACTIVE CONFIG FILES NOT FOUND IN /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260601T234556Z/daylily-omics-analysis/config/day_profiles/slurm ... copying
Copying template yaml files to active config files /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260601T234556Z/daylily-omics-analysis/config/day_profiles/slurm
Copying template bash files to active config files /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260601T234556Z/daylily-omics-analysis/config/day_profiles/slurm
yq is already installed.
WARNING: sentieon lic file /fsx/references/runtime_assets/cached_envs/x.lic not found.
WARNING: SENTIEON_LICENSE was not configured with a valid file; auto assigning a detected Sentieon license: /fsx/references/runtime_assets/cached_envs/Life_Sciences_Manufacturing_Corporation_eval.lic

!!!!
!!!!
    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  
       _______ GREAT SUCCESS _______       
[INFO] Patched /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260601T234556Z/daylily-omics-analysis/config/day_profiles/slurm/rule_config.yaml bclconvert direct mounted-input mode for 20260514_LH01106_0009_B23TVLGLT4: /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260601T234556Z/daylily-omics-analysis/config/run_dir_links/20260514_LH01106_0009_B23TVLGLT4
[ERROR] DayOA BCL Convert rules do not expose native lane-split support; use a DayOA release with native mounted-run BCL Convert. Missing markers: workflow/scripts/prepare_bclconvert_lane_samplesheet.py
