DAY-EC activated.
DAY-EC activated.
		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 dyec5117 .
Remote call detected. Activating conda hack
 > >> >>> 
ACTIVE CONFIG FILES NOT FOUND IN /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260602T000418Z/daylily-omics-analysis/config/day_profiles/slurm ... copying
Copying template yaml files to active config files /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260602T000418Z/daylily-omics-analysis/config/day_profiles/slurm
Copying template bash files to active config files /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260602T000418Z/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 _______       
[INFO] Patched /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260602T000418Z/daylily-omics-analysis/config/day_profiles/slurm/rule_config.yaml bclconvert direct mounted-input mode for 20260514_LH01106_0009_B23TVLGLT4: /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260602T000418Z/daylily-omics-analysis/config/run_dir_links/20260514_LH01106_0009_B23TVLGLT4
[INFO] DayOA native BCL Convert lane-split rules detected; no DYEC runtime rule patch applied.
Remote call detected. Activating conda hack
Your config files in /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260602T000418Z/daylily-omics-analysis/config/day_profiles/slurm are newer than the templates. clear 2 go.
Executing: snakemake --profile=/fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260602T000418Z/daylily-omics-analysis/config/day_profiles/slurm produce_bclconvert_fastqs -p -j 192 -k --config run_context_file=config/runs.tsv bootstrap_bclconvert=true bclconvert={"barcode_mismatches_index1":"0","barcode_mismatches_index2":"0","compression_threads":"64","conversion_threads":"4","decompression_threads":"32","fastq_gzip_compression_level":"1","force":"true","merge_lane_fastqs":"false","num_unknown_barcodes_reported":"1000","output_legacy_stats":"true","parallel_tiles":"24","partition":"i192mem","sample_sheet_settings":"{}","sample_sheet_settings_by_lane":"{}","shared_thread_odirect_output":"true","threads":"192","tile_compression_threads":"24","tile_conversion_threads":"2","tile_decompression_threads":"8","tile_parallel_tiles":"8","tile_shard_lanes":"L003","tile_shard_level":"lane","tile_shard_mem_mb":"180000","tile_shard_threads":"48","tmpdir":"/dev/shm"}
ERROR: Mermaid PDF rendering failed for /fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260602T000418Z/daylily-omics-analysis/pipeline_workflow_planned.mmd: Generating single mermaid chart

Error: Could not find Chrome (ver. 148.0.7778.97). This can occur if either
 1. you did not perform an installation before running the script (e.g. `npx puppeteer browsers install chrome-headless-shell`) or
 2. your cache path is incorrectly configured (which is: /home/ubuntu/.cache/puppeteer).
For (2), check out our guide on configuring puppeteer at https://pptr.dev/guides/configuration.
    at ChromeLauncher.resolveExecutablePath (file:///home/ubuntu/miniconda3/envs/DAYOA/lib/node_modules/@mermaid-js/mermaid-cli/node_modules/puppeteer-core/lib/esm/puppeteer/node/BrowserLauncher.js:307:27)
    at ChromeLauncher.computeLaunchArguments (file:///home/ubuntu/miniconda3/envs/DAYOA/lib/node_modules/@mermaid-js/mermaid-cli/node_modules/puppeteer-core/lib/esm/puppeteer/node/ChromeLauncher.js:86:24)
    at async ChromeLauncher.launch (file:///home/ubuntu/miniconda3/envs/DAYOA/lib/node_modules/@mermaid-js/mermaid-cli/node_modules/puppeteer-core/lib/esm/puppeteer/node/BrowserLauncher.js:55:28)
    at async run (file:///home/ubuntu/miniconda3/envs/DAYOA/lib/node_modules/@mermaid-js/mermaid-cli/src/index.js:623:19)
    at async cli (file:///home/ubuntu/miniconda3/envs/DAYOA/lib/node_modules/@mermaid-js/mermaid-cli/src/index.js:260:3)
[INFO] Workflow exited with status 2
To run a command as administrator (user "root"), use "sudo <command>".
See "man sudo_root" for details.

DAY-EC activated.
(DAY-EC) ubuntu@ip-10-0-0-225:/fsx/analysis_results/ubuntu/bcl25b_l003_whole_lane_20260602T000418Z/daylily-omics-analysis$
