DAY-EC activated.
DAY-EC activated.
=== status ===
{
  "command": "bin/day_run produce_alignstats produce_sentdont_snv_vcf produce_snv_concordances produce_relatedness produce_vep produce_multiqc_all --config 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 5 -k",
  "completed_at": "2026-05-29T22:20:25Z",
  "exit_code": 1,
  "repo_path": "/fsx/analysis_results/ubuntu/ccv20260529r6_ont_snv_alignstats_kitchensink/daylily-omics-analysis",
  "session_name": "ccv20260529r6_ont_snv_alignstats_kitchensink",
  "started_at": "2026-05-29T21:38:05Z"
}
=== repo ===
/fsx/analysis_results/ubuntu/ccv20260529r6_ont_snv_alignstats_kitchensink/daylily-omics-analysis
=== latest snakemake logs ===
1780093224.0000000000 .snakemake/log/2026-05-29T213829.368059.snakemake.log
1780093228.0000000000 .snakemake/log/2026-05-29T222025.663646.snakemake.log
=== latest log path: .snakemake/log/2026-05-29T222025.663646.snakemake.log ===
=== latest log tail ===
Unlocking working directory.
=== rule logs with errors ===
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:11:[E::hts_open_format] Failed to open file "results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1_1/tp_vcf_gz_stripped.vcf.gz" : No such file or directory
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:12:[init_data] Error: cannot write to "results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1_1/tp_vcf_gz_stripped.vcf.gz": No such file or directory
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:13:tbx_index_build3 failed: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1_1/tp_vcf_gz_stripped.vcf.gz
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:15:Traceback (most recent call last):
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:28:FileNotFoundError: [Errno 2] No such file or directory: 'results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1_1/tp_vcf_gz_stripped.vcf.gz'
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:30:During handling of the above exception, another exception occurred:
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:32:Traceback (most recent call last):
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:36:FileNotFoundError: [Errno 2] No such file or directory: 'results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1_1/tp_vcf_gz_stripped.vcf.gz.X_tv_snp.vcf'
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:44:[E::hts_open_format] Failed to open file "results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1_1/fp_vcf_gz_stripped.vcf.gz" : No such file or directory
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:45:[init_data] Error: cannot write to "results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1_1/fp_vcf_gz_stripped.vcf.gz": No such file or directory
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:46:tbx_index_build3 failed: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1_1/fp_vcf_gz_stripped.vcf.gz
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:48:Traceback (most recent call last):
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:61:FileNotFoundError: [Errno 2] No such file or directory: 'results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1_1/fp_vcf_gz_stripped.vcf.gz'
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:63:During handling of the above exception, another exception occurred:
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:65:Traceback (most recent call last):
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:69:FileNotFoundError: [Errno 2] No such file or directory: 'results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1_1/fp_vcf_gz_stripped.vcf.gz.X_tv_snp.vcf'
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:71:[E::hts_open_format] Failed to open file "results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1_1/fn_vcf_gz_stripped.vcf.gz" : No such file or directory
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:72:[init_data] Error: cannot write to "results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1_1/fn_vcf_gz_stripped.vcf.gz": No such file or directory
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:73:tbx_index_build3 failed: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1_1/fn_vcf_gz_stripped.vcf.gz
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:75:Traceback (most recent call last):
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:88:FileNotFoundError: [Errno 2] No such file or directory: 'results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1_1/fn_vcf_gz_stripped.vcf.gz'
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:90:During handling of the above exception, another exception occurred:
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:92:Traceback (most recent call last):
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.altair-v1.1.parse_vcfeval_summary.log:96:FileNotFoundError: [Errno 2] No such file or directory: 'results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/concordance/_altair-v1_1/fn_vcf_gz_stripped.vcf.gz.X_tv_snp.vcf'
results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/goleft/logs/goleft.log:2:error: missing value for --sex
logs/slurm/mosdepth/mosdepth.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.72.err:44:        test -s results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/mosdepth/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.mosdepth.summary.txt || (printf 'ERROR: mosdepth summary output is missing or empty: %s\n' results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/mosdepth/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.mosdepth.summary.txt | tee -a results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/mosdepth/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.mosdepth.log >&2; exit 1)
logs/slurm/mosdepth/mosdepth.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.72.err:45:        test -s results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/mosdepth/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.mosdepth.global.dist.txt || (printf 'ERROR: mosdepth global_dist output is missing or empty: %s\n' results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/mosdepth/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.mosdepth.global.dist.txt | tee -a results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/mosdepth/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.mosdepth.log >&2; exit 1)
logs/slurm/mosdepth/mosdepth.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.72.err:46:        test -s results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/mosdepth/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.mosdepth.region.dist.txt || (printf 'ERROR: mosdepth region_dist output is missing or empty: %s\n' results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/mosdepth/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.mosdepth.region.dist.txt | tee -a results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/mosdepth/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.mosdepth.log >&2; exit 1)
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.42.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.30.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.3.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.26.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.54.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.28.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.14.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.36.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.44.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.38.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.12.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.52.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.20.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.16.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.18.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.24.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.32.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.8.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.40.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.22.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.50.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.10.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.46.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.48.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/vep_chromosome/vep_chromosome.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.34.err:42:            echo "ERROR: VEP cache not found: /fsx/references/runtime_assets/tool_specific_resources/vep//homo_sapiens/114_GRCh38" >&2
logs/slurm/calc_coverage_evenness/calc_coverage_evenness.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.69.err:53:        rm $(dirname results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/norm_cov_eveness/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.md)/*per-base* || echo 'rm perbase failed';
logs/slurm/goleft/goleft.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.73.err:41:        rm -rf $(dirname results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/goleft/golefttwo.done ) || echo rmGOLfailed ;
logs/slurm/goleft/goleft.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.73.err:53:Error in rule goleft:
logs/slurm/goleft/goleft.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.73.err:57:    log: results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/goleft/logs/goleft.log (check log file(s) for error details)
logs/slurm/goleft/goleft.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.73.err:63:        rm -rf $(dirname results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/goleft/golefttwo.done ) || echo rmGOLfailed ;
logs/slurm/goleft/goleft.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.73.err:73:        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
logs/slurm/goleft/goleft.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.73.err:76:Exiting because a job execution failed. Look above for error message
logs/slurm/sent_snv_ont/sent_snv_ont.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.5.err:64:        ulimit -n 65536 || echo "ulimit mod failed" >> results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/log/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.snv.log 2>&1;
logs/slurm/sent_snv_ont/sent_snv_ont.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.5.err:103:            echo "ERROR: sentieon-cli dnascope-longread failed with exit code $cli_rc" >> results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/log/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.snv.log 2>&1;
logs/slurm/sent_snv_ont/sent_snv_ont.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.5.err:114:            echo "ERROR: SNV VCF not produced by sentieon-cli" >> results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/snv/sentdont/log/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.sentdont.snv.log 2>&1;
logs/slurm/vep_concat_index_chunks/vep_concat_index_chunks.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.1.err:44:            echo "ERROR: VEP annotated variant count ($ann_count) does not match input chunk count ($input_count)" >&2
logs/slurm/vep_concat_index_chunks/vep_concat_index_chunks.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.1.err:52:            echo "ERROR: final VEP VCF count ($final_count) does not match input count ($input_count)" >&2
logs/slurm/site_mix_contam/site_mix_contam.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.78.err:45:            echo "ERROR: site_mix_contam production rule uses GATK pileup tables and does not support candidate_manifest donor attribution. Use the estimator CLI BAM/CRAM mode for donor attribution." >&2
logs/slurm/site_mix_contam/site_mix_contam.TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.78.err:60:            if grep -Eq '^ERROR: Only [0-9]+ usable sites after depth filters; need at least [0-9]+' results/day/hg38_broad/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION/align/ont/na/alignqc/contam/site_mix/logs/TVBONT5X-HG003-5x-1-D0-PF-ONT-PROMETHION.ont.na.site_mix.log; then
