command_id=b551ffae-7bad-46f1-ae69-f341d66cf34d
DAY-EC activated.
DAY-EC activated.
__DATE__=2026-06-03T06:23:41+00:00
session already exists: dayoa_bcl_l003_6shard_argfix_20260603
0: bash* (1 panes) [80x24] [layout b261,80x24,0,0,4] @4 (active)
0: [80x24] [history 133/2000, 40424 bytes] %4 (active)
__PANE__
2bcl/bcl_l003_6shard_i192bigmem_devshm_argfix_20260603T0620Z/daylily-omics-analy
sis/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_Scie
nces_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 comp
ared 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 _______
[Dslu](DAYOA) cd /fsx/analysis_results/dyec0602bcl/bcl_l003_6shard_i192bigmem_de
vshm_argfix_20260603T0620Z/daylily-omics-analysis
[Dslu](DAYOA) source dyoainit
Notice: Cluster config sets aws-parallelcluster-enforce-budget=skip; skipping pr
oject validation.
Project: dyec0602bcl
Skip Project Check: true
Skipping project validation as --skip-project-check was passed.

________________________________________________________
AWS Budget lookup skipped for project 'dyec0602bcl' in region 'us-west-2'.
  Total: NA
  Used: NA
  Percent Used: NA
________________________________________________________
Using explicit SENTIEON_LICENSE: /fsx/references/runtime_assets/cached_envs/Life
_Sciences_Manufacturing_Corporation_eval.lic

# conda environments:
#
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-235/9d
47d7d0d1fd2da30ac182cf088a614c_
base                   /home/ubuntu/miniconda3
DAY-EC                 /home/ubuntu/miniconda3/envs/DAY-EC
DAYOA                * /home/ubuntu/miniconda3/envs/DAYOA

dy-a slurm hg38
Day CLI initialized for project 'dyec0602bcl' 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)

(DAYOA) [Dslu]dy-a slurm hg38
Requesting profile: slurm
dy-r produce_bclconvert_fastqs -p -k -j 10 --rerun-triggers mtime --configfile c
onfig/bclconvert_l003_6shard_i192bigmem_devshm_argfix.yaml -n; printf "__DRYRUN_
ARGFIX_EXIT__=%s\n" "$?"
Attempting to deactivate existing environments & re-init with --project dyec0602
bcl .


