DAY-EC activated.
DAY-EC activated.
Cloning into '/fsx/analysis_results/ubuntu/ccv20260529r26_illumina_hg002_kitchensink_multiqc/daylily-omics-analysis'...
Note: switching to '3d5e86c38f1a03a2a47cbad570d4ace5386bbec6'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

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Cloning repository...

Great success! Daylily repository cloned.
Repository: https://github.com/Daylily-Informatics/daylily-omics-analysis.git
Reference : 2.0.23
Location  : /fsx/analysis_results/ubuntu/ccv20260529r26_illumina_hg002_kitchensink_multiqc/daylily-omics-analysis

To get started:
  cd /fsx/analysis_results/ubuntu/ccv20260529r26_illumina_hg002_kitchensink_multiqc/daylily-omics-analysis
  # initialize and run the analysis repository per its documentation
Notice: --project not set. Using default project name: dyec-test
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-10-0-0-88/0c86add3b549fcc28843f5872250be8c_
                       /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-10-0-0-88/268f6065d6f69417fea15776392afaf9_
                       /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/d42215c34ab8867d1a29ad0dad583781_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-88/e28353b323f26af0747eb0fc4db2c579_
                       /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
Attempting to deactivate existing environments & re-init with --project dyec-test .
Remote call detected. Activating conda hack
 > >> >>>
ACTIVE CONFIG FILES NOT FOUND IN /fsx/analysis_results/ubuntu/ccv20260529r26_illumina_hg002_kitchensink_multiqc/daylily-omics-analysis/config/day_profiles/slurm ... copying
Copying template yaml files to active config files /fsx/analysis_results/ubuntu/ccv20260529r26_illumina_hg002_kitchensink_multiqc/daylily-omics-analysis/config/day_profiles/slurm
Copying template bash files to active config files /fsx/analysis_results/ubuntu/ccv20260529r26_illumina_hg002_kitchensink_multiqc/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 _______
Remote call detected. Activating conda hack
Your config files in /fsx/analysis_results/ubuntu/ccv20260529r26_illumina_hg002_kitchensink_multiqc/daylily-omics-analysis/config/day_profiles/slurm are newer than the templates. clear 2 go.
Executing: snakemake --profile=/fsx/analysis_results/ubuntu/ccv20260529r26_illumina_hg002_kitchensink_multiqc/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
Config file config/global.yaml is extended by additional config specified via the command line.
loading global: /fsx/analysis_results/ubuntu/ccv20260529r26_illumina_hg002_kitchensink_multiqc/daylily-omics-analysis/config/global_AWSPC.yaml
Config file config/global_AWSPC.yaml is extended by additional config specified via the command line.
loading profile rule_config: /fsx/analysis_results/ubuntu/ccv20260529r26_illumina_hg002_kitchensink_multiqc/daylily-omics-analysis/config/day_profiles/slurm/rule_config.yaml
Config file config/day_profiles/slurm/rule_config.yaml is extended by additional config specified via the command line.
INFO::: The genome build hg38 is supported.  The genome build prefix is 'chr''.
aligners: [sent]
aligners (final): [sent]
...INFO: Auto-detected dedupers. DDUP updated to: ['dmd']
deduper (final): [dmd]
SNV Callers:[sentd]
SNV Callers (final): [sentd]
Somatic SNV Callers:[senttn]
... WARNING: No sv_callers set in the config.
SV Callers (final): []
A    N   A   L  Y S I S    SAMPLE TABLE DETECTED ::: /fsx/analysis_results/ubuntu/ccv20260529r26_illumina_hg002_kitchensink_multiqc/daylily-omics-analysis/config/samples.tsv
A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/ubuntu/ccv20260529r26_illumina_hg002_kitchensink_multiqc/daylily-omics-analysis/config/units.tsv
Building DAG of jobs...
All Wildcards:    all snv_CALLERS:  ['sentd']  all ALIGNERS:  ['sent']  all CRAM_ALIGNERS:  []  all samples:  {'JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ': ['JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ']}  all concordance samples:  dict_keys(['JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ'])
Creating conda environment workflow/envs/unmapped_metagenomics_ganon2_v0.1.yaml...
Downloading and installing remote packages.
Environment for /fsx/analysis_results/ubuntu/ccv20260529r26_illumina_hg002_kitchensink_multiqc/daylily-omics-analysis/workflow/rules/../envs/unmapped_metagenomics_ganon2_v0.1.yaml created (location: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-88/1993fd6aa5cfbaeeadfc7774cd7f8c2c_)
Creating conda environment workflow/envs/unmapped_metagenomics_sourmash_v0.1.yaml...
Downloading and installing remote packages.
