DAY-EC activated.
DAY-EC activated.
session=hybonly_ilmn_final_multiqc_file_20260606T100052Z
tmux=present
0: bash* (1 panes) [80x24] [layout 5964,80x24,0,0,15] @15 (active)
0: [80x24] [history 267/2000, 86912 bytes] %15 (active)
capture_tail:
        (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-10-0-0-81:/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 results/day/hg38/reports/DAY_final_multiq
c.html results/day/hg38/reports/dayoa_evidence_manifest.json --config 'aligners=
["sent"]' 'dedupers=["dmd"]' 'snv_callers=["sentd"]' 'htd_callers=["cyrius"]' 'm
ultiqc_qc={"enable_tools":["vep","metagenomics","contam_identity"]}' -j 200 -p -
k --rerun-triggers mtime
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 results/day/hg38/reports/DAY_final_multiqc.html results/day/h
g38/reports/dayoa_evidence_manifest.json --config aligners=["sent"] dedupers=["d
md"] snv_callers=["sentd"] htd_callers=["cyrius"] multiqc_qc={"enable_tools":["v
ep","metagenomics","contam_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

tmux_log=/home/ubuntu/daylily-runs/hybonly_ilmn_final_multiqc_file_20260606T100052Z/tmux.log
tmux_log_tail:
[31m??[m pipeline_workflow_checkpoint_20260606T095538Z.pdf
[31m??[m pipeline_workflow_final_success.mmd
[31m??[m pipeline_workflow_final_success.pdf
[31m??[m pipeline_workflow_planned.mmd
[31m??[m pipeline_workflow_planned.pdf
[31m??[m sbatch_errs.log
[?2004h(DAY-EC) ubuntu@ip-10-0-0-81:/fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis$ git rev-parse HEAD
[?2004l
d02a1bd825c8c13bac3751d26854b9834c5c3a53
[?2004h(DAY-EC) ubuntu@ip-10-0-0-81:/fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis$ source dyoainit
[?2004l
Notice: --project not set. Using default project name: hyb-only
Notice: Cluster config sets aws-parallelcluster-enforce-budget=skip; skipping project validation.
Project: hyb-only
Skip Project Check: true
Skipping project validation as --skip-project-check was passed.

________________________________________________________
AWS Budget lookup skipped for project 'hyb-only' in region 'us-west-2'.
  Total: NA
  Used: NA
  Percent Used: NA
________________________________________________________
Using configured Sentieon license file: /fsx/references/runtime_assets/cached_envs/Life_Sciences_Manufacturing_Corporation_eval.lic

# conda environments:
#
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/29f97eda4256feaf020134a890479ff1_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/33327866ded710a14c3e73cc8116eec0_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/35fb4175790f4023c274462ba7075854_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3a0e4f206e093d942d8271fad4d35296_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/3d0893252281fa51ad1d8a1c220b797a_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/4c31f8647962b8e3834ad37fb4a58585_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/65b1d6df12278175b9f30fb65980f024_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/78f3045fcae4980edd6182a4d4c7b898_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/7c29ee1ebe032a24169825719f2e1a4d_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/8ad11a3ecec11ba3035b130d80e455bf_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/8d1cfbb0e385ff40e65802642a116261_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/a2363387ce455d48f02d1fd7a1643fdc_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/adc26e8656bed67f886fa90365098b54_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/aeb93d5e853ec27fe200a4a0e6b1cb1b_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/b63d181b1412fcb12187b3f526fa0fb7_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/b7b00565f6d6e15ef0dac3373783b014_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/bc1a74e52dbef168e070adef567b9cfa_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/be5f834cbbdb5fa84aa89d321fd38c36_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/cb3e084a2b91b0f9dbf54b67853eb975_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/cbbbc9232aca1ecab85b8cd15aaa8927_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/e16773008a9eb117d91285f7b1cb6ab6_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/eba8eddca110a7475a7d6f3081ca273b_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/ece8bf2dfb9a32ee5a36d91fa49a722b_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/fb5136439b50c216431e912fdab988a8_
                       /fsx/resources/environments/conda/ubuntu/ip-10-0-0-81/ff4326369a074729b1ce16ec028c4a31_
base                   /home/ubuntu/miniconda3
DAY-EC               * /home/ubuntu/miniconda3/envs/DAY-EC
DAYOA                  /home/ubuntu/miniconda3/envs/DAYOA

Day CLI initialized for project 'hyb-only' 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 build for the current environment.
	                           
	(day-run / dy-r)          - Run a command in the current environment.
	                           <tab> for exposed targets, -<tab> for all command line flags.
	                           
	(day-monitor / dy-m)      - Monitor workflow status (Snakemake, SLURM, logs).
	                           Use --block-and-poll to wait for completion.
	                           
	(day-deactivate / dy-d)   - Deactivate the current environment.
	                           Use 'dy-d reset' to hard reset the environment.
	                           
	                           
	                           
	                           
	. 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/samples.tsv

		cp .test_data/data/0.01xwgs_HG002_hg38.units.tsv config/units.tsv



		# 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 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)

[?2004h(DAYOA) ubuntu@ip-10-0-0-81:/fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis$ dy-a slurm hg38
[?2004l
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_mounted_20260606T053415Z/daylily-omics-analysis/config/day_profiles/slurm are newer than the templates. clear 2 go.
yq is already installed.
Using sentieon license file: /fsx/references/runtime_assets/cached_envs/Life_Sciences_Manufacturing_Corporation_eval.lic from ~/.config/daylily/daylily_cli_global.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 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 _______       
[?2004h[36;1m[Dslu][0m(DAYOA) dy-r produce_multiqc_all results/day/hg38/reports/DAY_final_multiqc.html results/day/hg38/reports/dayoa_evidence_manifest.json --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
[?2004l
[1m[48;5;88m[38;5;79mYour config files in /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/config/day_profiles/slurm are newer than the templates. clear 2 go.[0m
[1m[40m[38;5;118mExecuting: snakemake --profile=/fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/config/day_profiles/slurm produce_multiqc_all results/day/hg38/reports/DAY_final_multiqc.html results/day/hg38/reports/dayoa_evidence_manifest.json --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[0m
[33mConfig file config/global.yaml is extended by additional config specified via the command line.[0m
loading global: /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/config/global_AWSPC.yaml
[33mConfig file config/global_AWSPC.yaml is extended by additional config specified via the command line.[0m
loading profile rule_config: /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/config/day_profiles/slurm/rule_config.yaml
[33mConfig file config/day_profiles/slurm/rule_config.yaml is extended by additional config specified via the command line.[0m
INFO::: The genome build hg38 is supported.  The genome build prefix is 'chr''.
[1m[38;5;79maligners: [sent][0m
[1m[38;5;79maligners (final): [sent][0m
[1m[38;5;79mdeduper (final): [dmd][0m
[1m[38;5;79mSNV Callers:[sentd][0m
[1m[38;5;79mSNV Callers (final): [sentd][0m
[1m[38;5;79mSomatic SNV Callers:[senttn][0m
[1m[48;5;166m[38;5;79m... WARNING: No sv_callers set in the config.[0m
[1m[38;5;79mSV Callers (final): [][0m
A    N   A   L  Y S I S    SAMPLE TABLE DETECTED ::: /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/config/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
reports:
MISSING /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/results/day/hg38/reports/DAY_final_multiqc.html
MISSING /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/results/day/hg38/reports/DAY_final_multiqc_data/multiqc_data.json
MISSING /fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/results/day/hg38/logs/produce_multiqc_all.log
controllers:
ubuntu    498749  498258  1 10:01 pts/12   00:00:00 bash bin/day_run produce_multiqc_all results/day/hg38/reports/DAY_final_multiqc.html results/day/hg38/reports/dayoa_evidence_manifest.json --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
ubuntu    498965  498749  0 10:01 pts/12   00:00:00 bash bin/day_run produce_multiqc_all results/day/hg38/reports/DAY_final_multiqc.html results/day/hg38/reports/dayoa_evidence_manifest.json --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
ubuntu    498966  498965 99 10:01 pts/12   00:00:04 /home/ubuntu/miniconda3/envs/DAYOA/bin/python /home/ubuntu/miniconda3/envs/DAYOA/bin/snakemake --profile=/fsx/analysis_results/ubuntu/hybonly_ilmn_kitchensink_mounted_20260606T053415Z/daylily-omics-analysis/config/day_profiles/slurm produce_multiqc_all results/day/hg38/reports/DAY_final_multiqc.html results/day/hg38/reports/dayoa_evidence_manifest.json --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
ubuntu    498967  498965  0 10:01 pts/12   00:00:00 bash bin/day_run produce_multiqc_all results/day/hg38/reports/DAY_final_multiqc.html results/day/hg38/reports/dayoa_evidence_manifest.json --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
