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DAY-EC activated.
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Cloning repository...

Great success! Daylily repository cloned.
Repository: https://github.com/lsmc-bio/daylily-omics-analysis.git
Reference : jem-dev
Location  : /fsx/analysis_results/ubuntu/pg_ilmn_sentpg_dryrun_20260609T104016Z/daylily-omics-analysis

To get started:
  cd /fsx/analysis_results/ubuntu/pg_ilmn_sentpg_dryrun_20260609T104016Z/daylily-omics-analysis
  # initialize and run the analysis repository per its documentation
Notice: --project not set. Using default project name: dyecX4
Project: dyecX4
Skip Project Check: true
Skipping project validation as --skip-project-check was passed.

________________________________________________________
AWS Budget lookup skipped for project 'dyecX4' 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:
#
base                   /home/ubuntu/miniconda3
DAY-EC               * /home/ubuntu/miniconda3/envs/DAY-EC
DAYOA                  /home/ubuntu/miniconda3/envs/DAYOA

Day CLI initialized for project 'dyecX4' 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)

Requesting profile: slurm
Attempting to deactivate existing environments & re-init with --project dyecX4 .
Remote call detected. Activating conda hack
 > >> >>> 
ACTIVE CONFIG FILES NOT FOUND IN /fsx/analysis_results/ubuntu/pg_ilmn_sentpg_dryrun_20260609T104016Z/daylily-omics-analysis/config/day_profiles/slurm ... copying
Copying template yaml files to active config files /fsx/analysis_results/ubuntu/pg_ilmn_sentpg_dryrun_20260609T104016Z/daylily-omics-analysis/config/day_profiles/slurm
Copying template bash files to active config files /fsx/analysis_results/ubuntu/pg_ilmn_sentpg_dryrun_20260609T104016Z/daylily-omics-analysis/config/day_profiles/slurm
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 _______       
Remote call detected. Activating conda hack
bwa_mem2a_aln_sort.partition=i192nvme,i384nvme
i192nvme: avg=2.970233 min=2.235800 c8id.48xlarge=3.293200,c8id.metal-48xl=2.235800,m8id.48xlarge=2.775000,m8id.metal-48xl=3.639000,r8id.48xlarge=3.568300,r8id.metal-48xl=2.310100
i384nvme: avg=4.633083 min=3.296800 c8id.96xlarge=3.689700,c8id.metal-96xl=3.296800,m8id.96xlarge=7.116200,m8id.metal-96xl=4.617100,r8id.96xlarge=4.835800,r8id.metal-96xl=4.242900
Your config files in /fsx/analysis_results/ubuntu/pg_ilmn_sentpg_dryrun_20260609T104016Z/daylily-omics-analysis/config/day_profiles/slurm are newer than the templates. clear 2 go.
...AUTO-CONFIG: snv_callers=sentpg (from target rules → env)
Executing: snakemake --profile=/fsx/analysis_results/ubuntu/pg_ilmn_sentpg_dryrun_20260609T104016Z/daylily-omics-analysis/config/day_profiles/slurm produce_sentpg_snv_vcf -p -j 150 -k -T 0 --rerun-triggers mtime -n --default-resources time=100
loading global: /fsx/analysis_results/ubuntu/pg_ilmn_sentpg_dryrun_20260609T104016Z/daylily-omics-analysis/config/global_AWSPC.yaml
loading profile rule_config: /fsx/analysis_results/ubuntu/pg_ilmn_sentpg_dryrun_20260609T104016Z/daylily-omics-analysis/config/day_profiles/slurm/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.
...INFO: Auto-detected SNV callers from env: ['sentpg']
SNV Callers (final): [sentpg]
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/pg_ilmn_sentpg_dryrun_20260609T104016Z/daylily-omics-analysis/config/samples.tsv
A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/ubuntu/pg_ilmn_sentpg_dryrun_20260609T104016Z/daylily-omics-analysis/config/units.tsv
[Errno 2] No such file or directory: '/fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG003_1x_R1.fastq.gz'
[Errno 2] No such file or directory: '/fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG003_5x_R1.fastq.gz'
[Errno 2] No such file or directory: '/fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG003_15x_R1.fastq.gz'
[Errno 2] No such file or directory: '/fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG003_40x_R1.fastq.gz'
Building DAG of jobs...
MissingInputException in rule pre_prep_raw_fq in file /fsx/analysis_results/ubuntu/pg_ilmn_sentpg_dryrun_20260609T104016Z/daylily-omics-analysis/workflow/rules/prep_input_sample_files.smk, line 361:
Missing input files for rule pre_prep_raw_fq:
    output: results/day/hg38/R15x-HG003-D0-0-D0-PCR-FREE-ILMN-NOVASEQ/R15x-HG003-D0-0-D0-PCR-FREE-ILMN-NOVASEQ.R1.fastq.gz, results/day/hg38/R15x-HG003-D0-0-D0-PCR-FREE-ILMN-NOVASEQ/R15x-HG003-D0-0-D0-PCR-FREE-ILMN-NOVASEQ.R2.fastq.gz
    wildcards: sample=R15x-HG003-D0-0-D0-PCR-FREE-ILMN-NOVASEQ, sample_lane=R15x-HG003-D0-0-D0-PCR-FREE-ILMN-NOVASEQ
    affected files:
        /fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG003_15x_R2.fastq.gz
        /fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG003_15x_R1.fastq.gz
RETURN CODE: 1
[INFO] Workflow exited with status 1
To run a command as administrator (user "root"), use "sudo <command>".
See "man sudo_root" for details.

DAY-EC activated.
(DAY-EC) ubuntu@ip-10-0-0-45:/fsx/analysis_results/ubuntu/pg_ilmn_sentpg_dryrun_20260609T104016Z/daylily-omics-analysis$
