## ONT
# conda environments:
	(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.
	(day-deactivate / dy-d)   - Deactivate the current environment.
	                           Use 'dy-d reset' to hard reset the environment.
Attempting to deactivate existing environments & re-init with --project hyb-only .
Executing: snakemake --profile=/fsx/analysis_results/ubuntu/hybonly_ont_kitchensink_mounted_20260606T053415Z/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
Building DAG of jobs...
## ILMN
# conda environments:
	(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.
	(day-deactivate / dy-d)   - Deactivate the current environment.
	                           Use 'dy-d reset' to hard reset the environment.
Attempting to deactivate existing environments & re-init with --project hyb-only .
Executing: snakemake --profile=/fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/config/day_profiles/slurm 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
Building DAG of jobs...
Creating conda environment workflow/envs/somalier.yaml...
Environment for /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/rules/../envs/somalier.yaml created (location: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-81/a2363387ce455d48f02d1fd7a1643fdc_)
Creating conda environment workflow/envs/alignstats_v0.2.yaml...
Environment for /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/rules/../envs/alignstats_v0.2.yaml created (location: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-81/bc1a74e52dbef168e070adef567b9cfa_)
Creating conda environment workflow/envs/peddy_v0.1.yaml...
Environment for /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/rules/../envs/peddy_v0.1.yaml created (location: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-81/33327866ded710a14c3e73cc8116eec0_)
Creating conda environment workflow/envs/site_mix_contam_v0.1.yaml...
Environment for /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/rules/../envs/site_mix_contam_v0.1.yaml created (location: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-81/e16773008a9eb117d91285f7b1cb6ab6_)
Creating conda environment workflow/envs/haplocheck_v0.1.yaml...
Environment for /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/rules/../envs/haplocheck_v0.1.yaml created (location: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-81/cb3e084a2b91b0f9dbf54b67853eb975_)
Creating conda environment workflow/envs/fastqc_v0.1.yaml...
Environment for /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/rules/../envs/fastqc_v0.1.yaml created (location: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-81/8ad11a3ecec11ba3035b130d80e455bf_)
Creating conda environment workflow/envs/gatkcontam_v0.1.yaml...
Environment for /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/rules/../envs/gatkcontam_v0.1.yaml created (location: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-81/aeb93d5e853ec27fe200a4a0e6b1cb1b_)
Creating conda environment workflow/envs/report.yaml...
Environment for /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/rules/../envs/report.yaml created (location: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-81/78f3045fcae4980edd6182a4d4c7b898_)
Creating conda environment workflow/envs/read_haps_v0.1.yaml...
Environment for /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/rules/../envs/read_haps_v0.1.yaml created (location: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-81/b7b00565f6d6e15ef0dac3373783b014_)
Creating conda environment workflow/envs/sentD_v0.2.yaml...
Environment for /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/rules/../envs/sentD_v0.2.yaml created (location: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-81/eba8eddca110a7475a7d6f3081ca273b_)
Creating conda environment workflow/envs/doppelmark_v0.1.yaml...
Environment for /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/rules/../envs/doppelmark_v0.1.yaml created (location: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-81/3a0e4f206e093d942d8271fad4d35296_)
Creating conda environment workflow/envs/unmapped_metagenomics_sourmash_v0.1.yaml...
Environment for /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/workflow/rules/../envs/unmapped_metagenomics_sourmash_v0.1.yaml created (location: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-81/ff4326369a074729b1ce16ec028c4a31_)
Removing incomplete Conda environment workflow/envs/mosdepth_v0.1.yaml...
