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Successfully installed ansi2html-1.9.2 appdirs-1.4.4 argparse-dataclass-2.0.0 attrs-26.1.0 boto3-1.43.18 botocore-1.43.18 chromedriver-binary-auto-0.3.1 colr-0.9.1 configargparse-1.7.5 connection_pool-0.0.3 datrie-0.8.3 docopt-0.6.2 docutils-0.23 dpath-2.2.0 fastjsonschema-2.21.2 gitdb-4.0.12 gitpython-3.1.50 html2image-2.0.7 humanfriendly-10.0 jmespath-1.1.0 jsonschema-4.26.0 jsonschema-specifications-2025.9.1 jupyter-core-5.9.1 nbformat-5.10.4 pulp-3.3.2 referencing-0.37.0 rgbw-colorspace-converter-0.1.4 rpds-py-2026.5.1 ruamel.yaml-0.19.1 s3transfer-0.18.0 smart_open-7.6.1 smmap-5.0.3 snakemake-7.25.0+14.g903efe44 stopit-1.1.2 tabulate-0.10.0 throttler-1.2.3 toposort-1.10 websocket-client-1.9.0 yte-1.9.4

done
#
# To activate this environment, use
#
#     $ conda activate DAYOA
#
# To deactivate an active environment, use
#
#     $ conda deactivate

DAYOA environment created successfully.
Installing Mermaid CLI for DAYOA pipeline diagram rendering: @mermaid-js/mermaid-cli@11.15.0

added 355 packages in 13s

43 packages are looking for funding
  run `npm fund` for details
npm notice
npm notice New minor version of npm available! 11.13.0 -> 11.16.0
npm notice Changelog: https://github.com/npm/cli/releases/tag/v11.16.0
npm notice To update run: npm install -g npm@11.16.0
npm notice

Try the following commands to get started:
  source dyinit --project <PROJECT>
  dy-a local
  dy-r help

Installation complete.
Please log out and log back in, then run:
  source dyinit --project <PROJECT>
  dy-a local
  dy-r help
DAYOA install success
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)

/home/ubuntu/daylily-runs/ccv20260529_simple-test_dryrun/launch.sh: line 94: dy-a: command not found
/home/ubuntu/daylily-runs/ccv20260529_simple-test_dryrun/launch.sh: line 94: dy-r: command not found
[INFO] Workflow exited with status 127
To run a command as administrator (user "root"), use "sudo <command>".
See "man sudo_root" for details.

DAY-EC activated.
(DAY-EC) ubuntu@ip-10-0-0-88:/fsx/analysis_results/ubuntu/ccv20260529_simple-test_dryrun/daylily-omics-analysis$
