DAY-EC activated.
DAY-EC activated.
pane_capture
cd '/fsx/analysis_results/BigB-4-mk/M-RGX-9WR2/daylily-omics-analysis'
export PUPPETEER_EXECUTABLE_PATH='/home/ubuntu/.cache/puppeteer/chrome-headless-
shell/linux-148.0.7778.97/chrome-headless-shell-linux64/chrome-headless-shell'
To run a command as administrator (user "root"), use "sudo <command>".
See "man sudo_root" for details.

source dyoainit 2>&1 | tee -a '/home/ubuntu/daylily-runs/dayhoff_runqc_RUN001_MR
GX9WR2_retry1_20260603/manual_relaunch.log'
DAY-EC activated.
(DAY-EC) ubuntu@ip-10-0-0-251:~$ cd '/fsx/analysis_results/BigB-4-mk/M-RGX-9WR2/
daylily-omics-analysis'
(DAY-EC) ubuntu@ip-10-0-0-251:/fsx/analysis_results/BigB-4-mk/M-RGX-9WR2/daylily
-omics-analysis$ export PUPPETEER_EXECUTABLE_PATH='/home/ubuntu/.cache/puppeteer
/chrome-headless-shell/linux-148.0.7778.97/chrome-headless-shell-linux64/chrome-
headless-shell'
(DAY-EC) ubuntu@ip-10-0-0-251:/fsx/analysis_results/BigB-4-mk/M-RGX-9WR2/daylily
-omics-analysis$ source dyoainit 2>&1 | tee -a '/home/ubuntu/daylily-runs/dayhof
f_runqc_RUN001_MRGX9WR2_retry1_20260603/manual_relaunch.log'
Notice: --project not set. Using default project name: BigB-4-mk
Notice: Cluster config sets aws-parallelcluster-enforce-budget=skip; skipping pr
oject validation.
Project: BigB-4-mk
Skip Project Check: true
Skipping project validation as --skip-project-check was passed.

________________________________________________________
AWS Budget lookup skipped for project 'BigB-4-mk' in region 'us-west-2'.
  Total: NA
  Used: NA
  Percent Used: NA
________________________________________________________
Using configured Sentieon license file: /fsx/references/runtime_assets/cached_en
vs/Life_Sciences_Manufacturing_Corporation_eval.lic

# conda environments:
#
base                   /home/ubuntu/miniconda3
DAY-EC               * /home/ubuntu/miniconda3/envs/DAY-EC
DAYOA                  /home/ubuntu/miniconda3/envs/DAYOA

Day CLI initialized for project 'BigB-4-mk' 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 bui
ld for the current environment.

        (day-run / dy-r)          - Run a command in the current environment.
                                   <tab> for exposed targets, -<tab> for all com
mand line flags.

        (day-monitor / dy-m)      - Monitor workflow status (Snakemake, SLURM, l
ogs).
                                   Use --block-and-poll to wait for completion.

        (day-deactivate / dy-d)   - Deactivate the current environment.
                                   Use 'dy-d reset' to hard reset the environmen
t.




        . 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/sample
s.tsv

                cp .test_data/data/0.01xwgs_HG002_hg38.units.tsv config/units.ts
v



                # 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 stati
stics



                # 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 call
ing

                dy-r produce_sentdug_vcf -p -k -j 20 -n        # Ultima SNV call
ing (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+O
NT 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+O
NT Modular (use hg38_broad)



                # Remove -n to execute (not dry-run)

(DAY-EC) ubuntu@ip-10-0-0-251:/fsx/analysis_results/BigB-4-mk/M-RGX-9WR2/daylily
-omics-analysis$ dy-a slurm hg38_broad 2>&1 | tee -a '/home/ubuntu/daylily-runs/
dayhoff_runqc_RUN001_MRGX9WR2_retry1_20260603/manual_relaunch.log'
dy-a: command not found
(DAY-EC) ubuntu@ip-10-0-0-251:/fsx/analysis_results/BigB-4-mk/M-RGX-9WR2/daylily
-omics-analysis$ dy-r produce_illumina_run_qc_and_bclconvert -p -j 20 -k --confi
g run_context_file=config/runs.tsv bootstrap_bclconvert=true --rerun-triggers mt
ime 2>&1 | tee -a '/home/ubuntu/daylily-runs/dayhoff_runqc_RUN001_MRGX9WR2_retry
1_20260603/manual_relaunch.log'
dy-r: command not found
(DAY-EC) ubuntu@ip-10-0-0-251:/fsx/analysis_results/BigB-4-mk/M-RGX-9WR2/daylily
-omics-analysis$
log_tail
Notice: --project not set. Using default project name: BigB-4-mk
Notice: Cluster config sets aws-parallelcluster-enforce-budget=skip; skipping project validation.
Project: BigB-4-mk
Skip Project Check: true
Skipping project validation as --skip-project-check was passed.

________________________________________________________
AWS Budget lookup skipped for project 'BigB-4-mk' in region 'us-west-2'.
  Total: NA
  Used: NA
  Percent Used: NA
________________________________________________________
Using configured Sentieon license file: /fsx/references/runtime_assets/cached_envs/Life_Sciences_Manufacturing_Corporation_eval.lic

# conda environments:
#
base                   /home/ubuntu/miniconda3
DAY-EC               * /home/ubuntu/miniconda3/envs/DAY-EC
DAYOA                  /home/ubuntu/miniconda3/envs/DAYOA

Day CLI initialized for project 'BigB-4-mk' 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)

dy-a: command not found
dy-r: command not found

