DAY-EC activated.
DAY-EC activated.
tmux_sessions:
hybonly_ilmn_final_multiqc_20260606T095442Z: 1 windows (created Sat Jun  6 09:55:26 2026)
hybonly_ilmn_haplo96_dryrun_20260606T092653Z: 1 windows (created Sat Jun  6 09:27:05 2026)
hybonly_ilmn_haplo96_dryrun_20260606T092935Z: 1 windows (created Sat Jun  6 09:29:47 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_final_multiqc_20260606T095442Z
0: bash* (1 panes) [80x24] [layout 5963,80x24,0,0,14] @14 (active)
0: [80x24] [history 279/2000, 92296 bytes] %14 (active)


                # 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
 .
Your config files in /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mount
ed_20260606T053415Z/daylily-omics-analysis/config/day_profiles/slurm are newer t
han the templates. clear 2 go.
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
       _______ GREAT SUCCESS _______
[Dslu](DAYOA) dy-r produce_multiqc_all --config 'aligners=["sent"]' 'dedupers=["
dmd"]' 'snv_callers=["sentd"]' 'htd_callers=["cyrius"]' 'multiqc_qc={"enable_too
ls":["vep","metagenomics","contam_identity"]}' -j 200 -p -k --rerun-triggers mti
me
Your config files in /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mount
ed_20260606T053415Z/daylily-omics-analysis/config/day_profiles/slurm are newer t
han the templates. clear 2 go.
Executing: snakemake --profile=/fsx/analysis_results/ubuntu/hybonly_ilmn_kitchen
sink_mounted_20260606T053415Z/daylily-omics-analysis/config/day_profiles/slurm p
roduce_multiqc_all --config aligners=["sent"] dedupers=["dmd"] snv_callers=["sen
td"] htd_callers=["cyrius"] multiqc_qc={"enable_tools":["vep","metagenomics","co
ntam_identity"]} -j 200 -p -k --rerun-triggers mtime
Config file config/global.yaml is extended by additional config specified via th
e command line.
loading global: /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20
260606T053415Z/daylily-omics-analysis/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/ubuntu/hybonly_ilmn_kitchensi
nk_mounted_20260606T053415Z/daylily-omics-analysis/config/day_profiles/slurm/rul
e_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 is supported.  The genome build prefix is 'chr''.
aligners: [sent]
aligners (final): [sent]
deduper (final): [dmd]
SNV Callers:[sentd]
SNV Callers (final): [sentd]
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/ubunt
u/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/confi
g/samples.tsv
A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/ubuntu/
hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/config/
units.tsv
Building DAG of jobs...
All Wildcards:    all snv_CALLERS:  ['sentd']  all ALIGNERS:  ['sent']  all CRAM
_ALIGNERS:  []  all samples:  {'20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-al
l-S7-PF-ILMN-NOVASEQ': ['20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF
-ILMN-NOVASEQ'], '20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-N
OVASEQ': ['20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ'
], '20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ': ['202
60526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ'], '20260526-L
H01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ': ['20260526-LH01121-
0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ'], '20260526-LH01121-0004-B2
3WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ': ['20260526-LH01121-0004-B23WW2NL
T4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ'], '20260526-LH01121-0004-B23WW2NLT4-NA0
5164-DMPK-all-S49-PF-ILMN-NOVASEQ': ['20260526-LH01121-0004-B23WW2NLT4-NA05164-D
MPK-all-S49-PF-ILMN-NOVASEQ'], '20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all
-S47-PF-ILMN-NOVASEQ': ['20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF
-ILMN-NOVASEQ']}  all concordance samples:  dict_keys(['20260526-LH01121-0004-B2
3WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ', '20260526-LH01121-0004-B23WW2NLT4
-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ', '20260526-LH01121-0004-B23WW2NLT4-HG003-c
-GIAB-all-S9-PF-ILMN-NOVASEQ'])
Nothing to be done (all requested files are present and up to date).

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_haplo96_dryrun_20260606T092935Z
0: bash* (1 panes) [80x24] [layout 5962,80x24,0,0,13] @13 (active)
0: [80x24] [history 293/2000, 98244 bytes] %13 (active)
                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
 .
Your config files in /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mount
ed_20260606T053415Z/daylily-omics-analysis/config/day_profiles/slurm are newer t
han the templates. clear 2 go.
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
       _______ GREAT SUCCESS _______
[Dslu](DAYOA) dy-r produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_v
cf produce_alignstats produce_snv_concordances produce_relatedness produce_gatk_
contam_estimate produce_site_mix_contam_estimate produce_global_contam_check pro
duce_vep produce_expansionhunter produce_htd_calls produce_metagenomics produce_
multiqc_all --config 'aligners=["sent"]' 'dedupers=["dmd"]' 'snv_callers=["sentd
"]' 'htd_callers=["cyrius"]' 'multiqc_qc={"enable_tools":["vep","metagenomics","
contam_identity"]}' -j 200 -p -k --rerun-triggers mtime -n
Your config files in /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mount
ed_20260606T053415Z/daylily-omics-analysis/config/day_profiles/slurm are newer t
han the templates. clear 2 go.
Executing: snakemake --profile=/fsx/analysis_results/ubuntu/hybonly_ilmn_kitchen
sink_mounted_20260606T053415Z/daylily-omics-analysis/config/day_profiles/slurm p
roduce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_alignstat
s produce_snv_concordances produce_relatedness produce_gatk_contam_estimate prod
uce_site_mix_contam_estimate produce_global_contam_check produce_vep produce_exp
ansionhunter produce_htd_calls produce_metagenomics produce_multiqc_all --config
 aligners=["sent"] dedupers=["dmd"] snv_callers=["sentd"] htd_callers=["cyrius"]
 multiqc_qc={"enable_tools":["vep","metagenomics","contam_identity"]} -j 200 -p
-k --rerun-triggers mtime -n
Config file config/global.yaml is extended by additional config specified via th
e command line.
loading global: /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20
260606T053415Z/daylily-omics-analysis/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/ubuntu/hybonly_ilmn_kitchensi
nk_mounted_20260606T053415Z/daylily-omics-analysis/config/day_profiles/slurm/rul
e_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 is supported.  The genome build prefix is 'chr''.
aligners: [sent]
aligners (final): [sent]
...INFO: Auto-detected dedupers. DDUP updated to: ['dmd']
deduper (final): [dmd]
SNV Callers:[sentd]
SNV Callers (final): [sentd]
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/ubunt
u/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/confi
g/samples.tsv
A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/ubuntu/
hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/config/
units.tsv
Building DAG of jobs...
All Wildcards:    all snv_CALLERS:  ['sentd']  all ALIGNERS:  ['sent']  all CRAM
_ALIGNERS:  []  all samples:  {'20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-al
l-S7-PF-ILMN-NOVASEQ': ['20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF
-ILMN-NOVASEQ'], '20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-N
OVASEQ': ['20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ'
], '20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ': ['202
60526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ'], '20260526-L
H01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ': ['20260526-LH01121-
0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ'], '20260526-LH01121-0004-B2
3WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ': ['20260526-LH01121-0004-B23WW2NL
T4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ'], '20260526-LH01121-0004-B23WW2NLT4-NA0
5164-DMPK-all-S49-PF-ILMN-NOVASEQ': ['20260526-LH01121-0004-B23WW2NLT4-NA05164-D
MPK-all-S49-PF-ILMN-NOVASEQ'], '20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all
-S47-PF-ILMN-NOVASEQ': ['20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF
-ILMN-NOVASEQ']}  all concordance samples:  dict_keys(['20260526-LH01121-0004-B2
3WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ', '20260526-LH01121-0004-B23WW2NLT4
-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ', '20260526-LH01121-0004-B23WW2NLT4-HG003-c
-GIAB-all-S9-PF-ILMN-NOVASEQ'])
Singularity image docker://ensemblorg/ensembl-vep:release_114.2 will be pulled.
Nothing to be done (all requested files are present and up to date).
RETURN CODE: 0
[Dslu](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.























