DAY-EC activated.
DAY-EC activated.
time=2026-05-30T16:15:55Z
tmux:
absent
status:
{
  "command": "bin/day_run produce_bclconvert_fastqs_and_metrics -p -j 20 -k --config run_context_file=config/runs.tsv bootstrap_bclconvert=true",
  "completed_at": "",
  "exit_code": null,
  "repo_path": "/fsx/analysis_results/ubuntu/ccv20260530r42_illumina_bclconvert/daylily-omics-analysis",
  "session_name": "ccv20260530r42_bclconvert_rc0_recheck",
  "started_at": "2026-05-30T16:15:27Z"
}

squeue:
log_tail:
DAY-EC activated.
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)

Requesting profile: slurm
