DAY-EC activated.
DAY-EC activated.
time=2026-05-30T16:16:43Z
Project: dyec-test
Skip Project Check: true
Skipping project validation as --skip-project-check was passed.

________________________________________________________
AWS Budget lookup skipped for project 'dyec-test' in region 'us-west-2'.
  Total: NA
  Used: NA
  Percent Used: NA
________________________________________________________
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

# conda environments:
#
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/051b9c93eaf518b5ddebc4344275e8a4_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/0b72e739b2cf77bd2e79394c1e549c63_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/0c86add3b549fcc28843f5872250be8c_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/100507f8e13d5e1848ac45d4d452691c_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/1142d6cbdb634d9e332e99dc4820c6a0_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/160617592874011bcee6aad07c00c9ad_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/1993fd6aa5cfbaeeadfc7774cd7f8c2c_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/268f6065d6f69417fea15776392afaf9_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/29eea103be50f20bc3f27f94244bbb15_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/2bc06e7aeab5345bc658146f339d6cd8_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/2dc9c608977f6d7c6253f8d381138ed4_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/634a8f3a2dffe15027f8cca0913f9426_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/70729e66ede5758449affc0303f52937_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/738f2ef5db9d8ccc1d2e2f995b734454_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/73dbbd9209dde9d5b560eca76639c2a0_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/7a5c7c62c589298e8e834f93fb618415_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/829d8a014f8720620c5866151c8f0779_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/86ad48bef57edc0a5a866843ec8f3737_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/9a86ccf495a30ab366c2e3a27d6ba5ef_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/a876128b7711b7b3576ee89d4b896694_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/a99ea18d415639f67a6e85afdbe2fe1b_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/b364badf61d8e9d2d9321a0a7c8fd0c6_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/d39c2ff7abeb07947030e9839a43fd4f_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/d42215c34ab8867d1a29ad0dad583781_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/da4dc21134176da342ba1bdf1057d36f_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/dff38df99218384139a313055699ea0e_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/e28353b323f26af0747eb0fc4db2c579_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/efba687ed98dc6d0ecc827ba5c267513_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/f02f4b1dcb4977fd9602b074e7c885b9_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/fb0da2b0be44b336d1294fa52fffc58e_
base                   /home/ubuntu/miniconda3
DAY-EC               * /home/ubuntu/miniconda3/envs/DAY-EC
DAYOA                  /home/ubuntu/miniconda3/envs/DAYOA

Day CLI initialized for project 'dyec-test' 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)

dyoainit_rc=0
Requesting profile: slurm
Attempting to deactivate existing environments & re-init with --project dyec-test .
Remote call detected. Activating conda hack
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 .
!!!!
       _______ GREAT SUCCESS _______
day_activate_slurm_hg38_remote_rc=0
Requesting profile: slurm
Attempting to deactivate existing environments & re-init with --project dyec-test .
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 .
!!!!
       _______ GREAT SUCCESS _______
day_activate_slurm_hg38_rc=0
env_summary:
PATH=/home/ubuntu/miniconda3/envs/DAYOA/bin:/home/ubuntu/miniconda3/envs/DAY-EC/bin:/home/ubuntu/.local/bin:/home/ubuntu/miniconda3/envs/DAY-EC/bin:/home/ubuntu/miniconda3/condabin:/opt/amazon/openmpi/bin:/opt/amazon/efa/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/opt/aws/bin:/opt/parallelcluster/pyenv/versions/3.12.8/envs/awsbatch_virtualenv/bin:/opt/slurm/bin:/fsx/references/runtime_assets/cached_envs/sentieon-genomics-202503.02/bin:/fsx/references/runtime_assets/cached_envs/sentieon-genomics-202503.02/bin:/fsx/analysis_results/ubuntu/ccv20260530r42_illumina_bclconvert/daylily-omics-analysis/bin:/fsx/references/runtime_assets/cached_envs/sentieon-genomics-202503.01.rc1//bin/:/opt/slurm/bin
