DAY-EC activated.
DAY-EC activated.
tmux_sessions:
hybonly_ilmn_haplo96_dryrun_20260606T092653Z: 1 windows (created Sat Jun  6 09:27:05 2026)
hybonly_ilmn_haplocheck96_dryrun_20260606T091748Z: 1 windows (created Sat Jun  6 09:25:55 2026)
hybonly_ilmn_kitchensink_mounted_20260606T053415Z_dryrun: 1 windows (created Sat Jun  6 05:40:45 2026)
hybonly_ont_alignsort_alignstats_dedupna_dryrun2_20260606T074609Z: 1 windows (created Sat Jun  6 07:46:32 2026)
hybonly_ont_alignsort_alignstats_dedupna_dryrun_20260606T074315Z: 1 windows (created Sat Jun  6 07:43:39 2026)
hybonly_ont_chipbarcode_limited_dryrun2_20260606T090029Z: 1 windows (created Sat Jun  6 09:00:56 2026)
hybonly_ont_chipbarcode_limited_dryrun_20260606T085229Z: 1 windows (created Sat Jun  6 08:55:27 2026)
hybonly_ont_chipbarcode_limited_live_20260606T090222Z: 1 windows (created Sat Jun  6 09:02:49 2026)
hybonly_ont_kitchensink_mounted_20260606T053415Z: 1 windows (created Sat Jun  6 05:59:00 2026)
hybonly_ont_kitchensink_mounted_20260606T053415Z_dryrun: 1 windows (created Sat Jun  6 05:52:28 2026)
SESSION=hybonly_ilmn_haplo96_dryrun_20260606T092653Z
0: bash* (1 panes) [80x24] [layout 5961,80x24,0,0,12] @12 (active)
0: [80x24] [history 256/2000, 81860 bytes] %12 (active)
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-10-0-0-81:/fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensin
k_mounted_20260606T053415Z/daylily-omics-analysis$ dy-a slurm hg38
Requesting profile: slurm
Attempting to deactivate existing environments & re-init with --project hyb-only
 .

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  =================||>  WARNING  <||=================
  One+ of the template config files in :
/fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/d
aylily-omics-analysis/config/day_profiles/slurm/templates
     is newer than your active config files (or missing and is expected).

  You hace 2 options. 1) remove the active files  :
(1) rm /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T05
3415Z/daylily-omics-analysis/config/day_profiles/slurm/*
    so the new template files can be copied there. Or
    2) Keep the active local copies.  You may touch
    them to avoid this error:
(2) touch /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606
T053415Z/daylily-omics-analysis/config/day_profiles/slurm/*
     will keep the files and avoid this warning/block.


Please select:
1) Remove the active config files.
2) Touch the active config files.
3) Exit.
Enter your choice (1, 2, or 3): Invalid choice. Please choose 1, 2, or 3.

ERROR: source bin/util/profile_freshness_warn.bash
(DAYOA)
SESSION=hybonly_ilmn_haplocheck96_dryrun_20260606T091748Z
0: bash* (1 panes) [80x24] [layout 5960,80x24,0,0,11] @11 (active)
0: [80x24] [history 0/2000, 1668 bytes] %11 (active)
To run a command as administrator (user "root"), use "sudo <command>".
See "man sudo_root" for details.

DAY-EC activated.
(DAY-EC) ubuntu@ip-10-0-0-81:~$



















SESSION=hybonly_ilmn_kitchensink_mounted_20260606T053415Z_dryrun
0: bash* (1 panes) [80x24] [layout b25d,80x24,0,0,0] @0 (active)
0: [80x24] [history 0/2000, 868 bytes] %0 (active)
DAY-EC activated.























