DAY-EC activated.
DAY-EC activated.
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)

(DAYOA) ubuntu@ip-10-0-0-251:/fsx/analysis_results/BigB-4-mk/M-RGX-9WR2/daylily-
omics-analysis$

