DAY-EC activated.
DAY-EC activated.
## session ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun
## repo /fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis
## run_dir /home/ubuntu/daylily-runs/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun
## sentinel files
1780127720.0000000000 1323 /fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/unlock_fails.log
1780127718.0000000000 444 /fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/logs/about.log
1780127712.0000000000 833 /fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/day_cmd.log
## command wrapper logs
### /home/ubuntu/daylily-runs/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/status.json
{
  "command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_alignstats produce_snv_concordances produce_relatedness produce_gatk_contam_estimate produce_site_mix_contam_estimate produce_global_contam_check produce_vep produce_expansionhunter produce_htd_calls produce_metagenomics produce_multiqc_all --config 'aligners=[\"sent\"]' 'dedupers=[\"dmd\"]' 'snv_callers=[\"sentd\"]' 'ht
  "completed_at": "2026-05-30T07:55:17Z",
  "exit_code": 1,
  "repo_path": "/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis",
  "session_name": "ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun",
  "started_at": "2026-05-30T07:52:26Z"
}
### /fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/day_cmd.log
SMK> D:2026-05-30T07:55:12+00:00 / U:ubuntu / PWD:/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis / CMD: (snakemake --profile=/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/config/day_profiles/slurm produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_alignstats produce_snv_con
### /fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/unlock_fails.log
loading global: /fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/config/global_AWSPC.yaml
loading profile rule_config: /fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/config/day_profiles/slurm/rule_config.yaml
INFO::: The genome build hg38 is supported.  The genome build prefix is 'chr''.
[1m[48;5;166m[38;5;79m...WARNING: No aligners set in the config.[0m
[1m[38;5;79maligners (final): [][0m
[1m[48;5;166m[38;5;79m...INFO: No dedupers set in config. Defaulting to na (no dedup).[0m
[1m[38;5;79mdeduper (final): [na][0m
[1m[48;5;166m[38;5;79m...WARNING: No snv_callers set in the config.[0m
[1m[38;5;79mSNV Callers (final): [][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/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/config/samples.tsv
A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/config/units.tsv
Unlocking working directory.
### /fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/logs/about.log
THETIMEIS:2026-05-30 07:55:13
GitTag:2.0.23
GitHash:3d5e86c
SUBuser:ubuntu
SUBhost:None
SUBroot:/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis
CallingCLI:None

THETIMEIS:2026-05-30 07:55:18
GitTag:2.0.23
GitHash:3d5e86c
SUBuser:ubuntu
SUBhost:None
SUBroot:/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis
CallingCLI:None

## snakemake logs
1780127720.0000000000 29 /fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/.snakemake/log/2026-05-30T075517.855112.snakemake.log
## focused errors
### /fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/.snakemake/log/2026-05-30T075517.855112.snakemake.log
--- tail /fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/.snakemake/log/2026-05-30T075517.855112.snakemake.log
Unlocking working directory.
## runtime repair strings
/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/workflow/rules/vep.smk:178:    vep_concat_fofn,
/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/workflow/rules/vep.smk:181:rule vep_concat_fofn:
/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/workflow/rules/contam_identity.smk:12:    "produce_read_haps_contam_identity",
/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/workflow/rules/contam_identity.smk:239:    produce_read_haps_contam_identity,
/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/workflow/rules/contam_identity.smk:293:rule haplocheck_vcf_contam_identity:
/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/workflow/rules/contam_identity.smk:348:%s	NO_VARIANTS	0		0		
/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/workflow/rules/contam_identity.smk:351:%s	NO_VARIANTS	0		0		
/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/workflow/rules/contam_identity.smk:353:            printf '<html><body>NO_VARIANTS</body></html>
/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/workflow/rules/contam_identity.smk:355:            printf 'NO_VARIANTS: haplocheck skipped because the input VCF has no variant records.
/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/workflow/rules/contam_identity.smk:361:rule read_haps_contam_identity:
/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/workflow/rules/contam_identity.smk:407:0 0 0 0 0 0 NO_DATA NO_VARIANTS
/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/workflow/rules/contam_identity.smk:409:            printf 'NO_VARIANTS: read_haps skipped because the input VCF has no variant records.
/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/workflow/rules/contam_identity.smk:452:rule produce_read_haps_contam_identity:  # TARGET: run read_haps haplotype contamination evidence
/fsx/analysis_results/ubuntu/ccv20260529r31_illumina_hg002_kitchensink_multiqc_dryrun/daylily-omics-analysis/workflow/rules/go_left.smk:40:        goleft indexcov --directory $gl --fai {params.huref}.fai {input.crai} >> {log} 2>&1;
