DAY-EC activated.
DAY-EC activated.

		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: local
Attempting to deactivate existing environments & re-init with --project dyec-test .
 > >> >>>
ACTIVE CONFIG FILES NOT FOUND IN /fsx/analysis_results/ubuntu/ccv20260529r7_simple-test_dryrun/daylily-omics-analysis/config/day_profiles/local ... copying
Copying template yaml files to active config files /fsx/analysis_results/ubuntu/ccv20260529r7_simple-test_dryrun/daylily-omics-analysis/config/day_profiles/local
Copying template bash files to active config files /fsx/analysis_results/ubuntu/ccv20260529r7_simple-test_dryrun/daylily-omics-analysis/config/day_profiles/local
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 _______
Your config files in /fsx/analysis_results/ubuntu/ccv20260529r7_simple-test_dryrun/daylily-omics-analysis/config/day_profiles/local are newer than the templates. clear 2 go.
Executing: snakemake --profile=/fsx/analysis_results/ubuntu/ccv20260529r7_simple-test_dryrun/daylily-omics-analysis/config/day_profiles/local -p -k -j 1 help
loading global: /fsx/analysis_results/ubuntu/ccv20260529r7_simple-test_dryrun/daylily-omics-analysis/config/global_AWSPC.yaml
loading profile rule_config: /fsx/analysis_results/ubuntu/ccv20260529r7_simple-test_dryrun/daylily-omics-analysis/config/day_profiles/local/rule_config.yaml
INFO::: The genome build hg38 is supported.  The genome build prefix is 'chr''.
...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/ubuntu/ccv20260529r7_simple-test_dryrun/daylily-omics-analysis/config/samples.tsv
A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/ubuntu/ccv20260529r7_simple-test_dryrun/daylily-omics-analysis/config/units.tsv
Building DAG of jobs...
Using shell: /home/ubuntu/miniconda3/envs/DAY-EC/bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Job stats:
job      count    min threads    max threads
-----  -------  -------------  -------------
help         1              1              1
total        1              1              1

Select jobs to execute...

[Fri May 29 23:47:16 2026]
rule help:
    jobid: 0
    reason: Rules with neither input nor output files are always executed.
    resources: tmpdir=/dev/shm, vcpu=1, threads=1, partition=i8,i192,i192mem



        colr '##### DY-CLI HELP                                                    ' "$DY_IT2" "$DY_IB2" "$DY_IS2" 1>&2;
        colr '/-----------------------------------------------------------------------------' "$DY_IT1" "$DY_IB1" "$DY_IS1" 1>&2;
        colr 'Welcome to daylily.

        Complete docs can be found here:
              https://github.com/Daylily-Informatics/daylily-omics-analysis and  https://github.com/Daylily-Informatics/daylily-ephemeral-cluster


        ========================================================================
        The dy- cli , first source it:

        . dyinit
        . dyinit -h


        Day CLI initialized for project $PROJECT in region $region.
        The Daylily CLI is now available.
        The following commands are available:
	**TAB COMPLETION(single and double tabbing) IS ENABLED FOR ALL CLI COMMANDS AND FLAGS, tab following a space or following a - to see completions**

          (day-help / dy-h)         - Display this help message.
          (day-activate / dy-a) (slurm | local) - Activate a Slurm or local environment.
          (day-run / dy-r)           - Run a command in the current environment.
          (day-deactivate / dy-d)    - Deactivate the current environment.
                             Use dy-d reset to hard reset the environment (may kill your terminal!).
          (day-build / dy-b)         - Build a new environment. **Only needs to be run once per head node user.**


        ========================================================================
        For use with dy-r [rules, try produce_<tab><tab>] [flags, try --con<tab><tab>]
        + Important snakemake arguments (all optional):
          `-n` == dryrun, generates an execution plan, but runs no commands.
              Good practice to run with -n before pulling the trigger.
          `-p` == print shell commands, pretty much always include this one
          `--rerun-triggers mtime` == this will calculate an execution plan
              only re-running rules which have parent files timestamps are
              newer than children.  w/out this, snakemake cohsiders not only
              timestamps, but edits to config files, source data changes, code
              changes, environment changes... and will re-run agressively.
              ! Always run with -n before you attempt to re-run, or add,
              analysis to an existing results directory.  You can easily
              erase a lot of work if not careful.
          `-h` == snakemake help... `--help` == snakemake exhaustive help
          `--rerun-incomplete` == if rerunning a workflow which failed
              ungracefully, snakemake will not proceed unless this flag is
              set so it can cleanup  the incomplete results subdirs.
          `--jobs n` == limit the snakemake scheduler to only running
              `n` jobs at once.
          `--report FILENAME.html` == produce a summary report of the workflow
          `--dag|--rulegraph|--filegraph` == use as follows to produce
              various graph visualizations of the TARGET being asked for:
              `dy-r produce_deduplicated_bams --rulegraph | dot -Tpng > rg.png`
         ========================================================================
                + TARGETS (which are snakemake rules that are a terminal point
                      in the larger DAG of rules). A few common ones:
                   - produce_deduplicated_bams == will run the specified
                      aligner(s) and the specified dup marker (only one ddup
                      presently can run at a time). aligners, ddupers,
                      SNV&SV(multiple of each of these allowed) callers are
                      all configured in the:
                       config/day_profles/{local,slurm}/rule_config.yaml
                   - produce_snv_concordances == runs all specified
                      aligners/SV callers and produces a concordance report
                      for each aligner+SVcaller+sample (in the other_reports
                      dir)
                   - produce_final_multiqc_wgs == runs everything and produces
                      the big final MQC report in the `reports` dir. ' ;

       colr '/-----------------------------------------------------------------------------' "$DY_IT2" "$DY_IB2" "$DY_IS2"  1>&2;


##### DY-CLI HELP
/-----------------------------------------------------------------------------
Welcome to daylily.

        Complete docs can be found here:
              https://github.com/Daylily-Informatics/daylily-omics-analysis and  https://github.com/Daylily-Informatics/daylily-ephemeral-cluster


        ========================================================================
        The dy- cli , first source it:

        . dyinit
        . dyinit -h


        Day CLI initialized for project $PROJECT in region $region.
        The Daylily CLI is now available.
        The following commands are available:
	**TAB COMPLETION(single and double tabbing) IS ENABLED FOR ALL CLI COMMANDS AND FLAGS, tab following a space or following a - to see completions**

          (day-help / dy-h)         - Display this help message.
          (day-activate / dy-a) (slurm | local) - Activate a Slurm or local environment.
          (day-run / dy-r)           - Run a command in the current environment.
          (day-deactivate / dy-d)    - Deactivate the current environment.
                             Use dy-d reset to hard reset the environment (may kill your terminal!).
          (day-build / dy-b)         - Build a new environment. **Only needs to be run once per head node user.**


        ========================================================================
        For use with dy-r [rules, try produce_<tab><tab>] [flags, try --con<tab><tab>]
        + Important snakemake arguments (all optional):
          `-n` == dryrun, generates an execution plan, but runs no commands.
              Good practice to run with -n before pulling the trigger.
          `-p` == print shell commands, pretty much always include this one
          `--rerun-triggers mtime` == this will calculate an execution plan
              only re-running rules which have parent files timestamps are
              newer than children.  w/out this, snakemake cohsiders not only
              timestamps, but edits to config files, source data changes, code
              changes, environment changes... and will re-run agressively.
              ! Always run with -n before you attempt to re-run, or add,
              analysis to an existing results directory.  You can easily
              erase a lot of work if not careful.
          `-h` == snakemake help... `--help` == snakemake exhaustive help
          `--rerun-incomplete` == if rerunning a workflow which failed
              ungracefully, snakemake will not proceed unless this flag is
              set so it can cleanup  the incomplete results subdirs.
          `--jobs n` == limit the snakemake scheduler to only running
              `n` jobs at once.
          `--report FILENAME.html` == produce a summary report of the workflow
          `--dag|--rulegraph|--filegraph` == use as follows to produce
              various graph visualizations of the TARGET being asked for:
              `dy-r produce_deduplicated_bams --rulegraph | dot -Tpng > rg.png`
         ========================================================================
                + TARGETS (which are snakemake rules that are a terminal point
                      in the larger DAG of rules). A few common ones:
                   - produce_deduplicated_bams == will run the specified
                      aligner(s) and the specified dup marker (only one ddup
                      presently can run at a time). aligners, ddupers,
                      SNV&SV(multiple of each of these allowed) callers are
                      all configured in the:
                       config/day_profles/{local,slurm}/rule_config.yaml
                   - produce_snv_concordances == runs all specified
                      aligners/SV callers and produces a concordance report
                      for each aligner+SVcaller+sample (in the other_reports
                      dir)
                   - produce_final_multiqc_wgs == runs everything and produces
                      the big final MQC report in the `reports` dir.
/-----------------------------------------------------------------------------
[Fri May 29 23:47:17 2026]
Finished job 0.
1 of 1 steps (100%) done
Complete log: .snakemake/log/2026-05-29T234713.259378.snakemake.log


	WARNING!!!! ALL Directories Are Remaining Unlocked. To have directories lock automatically upon successful completion, set --lock-analysis-dirs when calling day-run.



]]]]--------WORKFLOW SUCCESS====================]]]]]--
RETURN CODE: 0
[INFO] Workflow exited with status 0
DAY-EC activated.
(DAY-EC) ubuntu@ip-10-0-0-88:/fsx/analysis_results/ubuntu/ccv20260529r7_simple-test_dryrun/daylily-omics-analysis$
