DAY-EC activated.
DAY-EC activated.
        (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$ dy-a slurm hg38_broad
Requesting profile: slurm
Attempting to deactivate existing environments & re-init with --project BigB-4-m
k .
 > >> >>>
ACTIVE CONFIG FILES NOT FOUND IN /fsx/analysis_results/BigB-4-mk/M-RGX-9WR2/dayl
ily-omics-analysis/config/day_profiles/slurm ... copying
Copying template yaml files to active config files /fsx/analysis_results/BigB-4-
mk/M-RGX-9WR2/daylily-omics-analysis/config/day_profiles/slurm
Copying template bash files to active config files /fsx/analysis_results/BigB-4-
mk/M-RGX-9WR2/daylily-omics-analysis/config/day_profiles/slurm
yq is already installed.
Using sentieon license file: /fsx/references/runtime_assets/cached_envs/Life_Sci
ences_Manufacturing_Corporation_eval.lic from ~/.config/daylily/daylily_cli_glob
al.yaml

!!!!
!!!!
    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_broad
       _______ GREAT SUCCESS _______
[Dslu](DAYOA) dy-r produce_illumina_run_qc_and_bclconvert -p -j 20 -k --config r
un_context_file=config/runs.tsv bootstrap_bclconvert=true --rerun-triggers mtime
Your config files in /fsx/analysis_results/BigB-4-mk/M-RGX-9WR2/daylily-omics-an
alysis/config/day_profiles/slurm are newer than the templates. clear 2 go.
Executing: snakemake --profile=/fsx/analysis_results/BigB-4-mk/M-RGX-9WR2/daylil
y-omics-analysis/config/day_profiles/slurm produce_illumina_run_qc_and_bclconver
t -p -j 20 -k --config run_context_file=config/runs.tsv bootstrap_bclconvert=tru
e --rerun-triggers mtime
Config file config/global.yaml is extended by additional config specified via th
e command line.
loading global: /fsx/analysis_results/BigB-4-mk/M-RGX-9WR2/daylily-omics-analysi
s/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/BigB-4-mk/M-RGX-9WR2/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_broad is supported.  The genome build prefix is 'c
hr''.
...WARNING: No aligners set in the config.
aligners (final): []
...INFO: No dedupers set in config. Defaulting to na (no dedup).
deduper (final): [na]
...WARNING: No snv_callers set in the config.
SNV Callers (final): []
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/BigB-
4-mk/M-RGX-9WR2/daylily-omics-analysis/config/samples.tsv
A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/BigB-4-
mk/M-RGX-9WR2/daylily-omics-analysis/config/units.tsv
Building DAG of jobs...
Creating conda environment workflow/envs/run_qc_reports_v0.1.yaml...
Downloading and installing remote packages.


