DAY-EC activated.
DAY-EC activated.
            # Log
            echo "Concordance sentinel complete. footprints=altair-v1.1,clinvar_genes,giabHC,giabHC_x_clinvar_genes,giabHC_x_ultima,giabHC_x_ultima_x_clinvar,giabHCv5q,hg38,hg38_m_giabHC,ultima mqcs=10" >> results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/logs/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.concordance.log;

Submitted job 130 with external jobid '4621'.
[Sat May 30 18:47:30 2026]
Finished job 130.
154 of 161 steps (96%) done
Select jobs to execute...

[Sat May 30 18:47:30 2026]
localrule produce_snv_concordances:
    input: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/concordance.done, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_altair-v1.1/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_clinvar_genes/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_clinvar_genes_concordance.mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_giabHC_concordance.mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC_x_clinvar_genes/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC_x_ultima/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_ultima_concordance.mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC_x_ultima_x_clinvar/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_ultima_x_clinvar_concordance.mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHCv5q/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_giabHCv5q_concordance.mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38_m_giabHC/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_concordance.mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_ultima/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_ultima_concordance.mqc.tsv
    output: results/day/hg38/other_reports/giab_concordance_mqc.tsv
    jobid: 129
    reason: Missing output files: results/day/hg38/other_reports/giab_concordance_mqc.tsv; Input files updated by another job: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_giabHC_concordance.mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_altair-v1.1/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_altair-v1.1_concordance.mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC_x_ultima_x_clinvar/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_ultima_x_clinvar_concordance.mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_clinvar_genes/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_clinvar_genes_concordance.mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/concordance.done, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_hg38_concordance.mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC_x_ultima/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_ultima_concordance.mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHCv5q/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_giabHCv5q_concordance.mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC_x_clinvar_genes/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_giabHC_x_clinvar_genes_concordance.mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_hg38_m_giabHC/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_hg38_m_giabHC_concordance.mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_ultima/snv_JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ_ultima_concordance.mqc.tsv
    priority: 48
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/dev/shm, threads=1, time=5440, partition=i192,i128,i192mem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=

Config file config/global.yaml is extended by additional config specified via the command line.
loading global: /fsx/analysis_results/ubuntu/ccv20260530r50_illumina_hg002_kitchensink_multiqc/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/ccv20260530r50_illumina_hg002_kitchensink_multiqc/daylily-omics-analysis/config/day_profiles/slurm/rule_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/ubuntu/ccv20260530r50_illumina_hg002_kitchensink_multiqc/daylily-omics-analysis/config/samples.tsv
A    N   A   L  Y S I S    UNIT TABLE DETECTED ::: /fsx/analysis_results/ubuntu/ccv20260530r50_illumina_hg002_kitchensink_multiqc/daylily-omics-analysis/config/units.tsv
Building DAG of jobs...
All Wildcards:    all snv_CALLERS:  ['sentd']  all ALIGNERS:  ['sent']  all CRAM_ALIGNERS:  []  all samples:  {'JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ': ['JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ']}  all concordance samples:  dict_keys(['JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ'])
Using shell: /home/ubuntu/miniconda3/envs/DAY-EC/bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, threads=1, time=5440, vcpu=1
Select jobs to execute...
All Wildcards:    all snv_CALLERS:  ['sentd']  all ALIGNERS:  ['sent']  all CRAM_ALIGNERS:  []  all samples:  {'JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ': ['JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ']}  all concordance samples:  dict_keys(['JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ'])
All Wildcards:    all snv_CALLERS:  ['sentd']  all ALIGNERS:  ['sent']  all CRAM_ALIGNERS:  []  all samples:  {'JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ': ['JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ']}  all concordance samples:  dict_keys(['JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ'])
[Sat May 30 18:47:33 2026]
Finished job 129.
155 of 161 steps (96%) done
Select jobs to execute...

[Sat May 30 18:47:33 2026]
localrule aggregate_report_components:
    input: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/seqqc/fastqc/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.fastqc.done, results/day/hg38/other_reports/seqfu_mqc.tsv, results/day/hg38/other_reports/input_sample_libraries_mqc.tsv, results/day/hg38/other_reports/sequence_qc_outputs_mqc.tsv, results/day/hg38/other_reports/alignstats_combo_mqc.tsv, results/day/hg38/other_reports/norm_cov_evenness_combo_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/samtmetrics/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.complete, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/na/alignqc/samtmetrics/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.na.complete, results/day/hg38/other_reports/samtools_metrics_gather.done, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/mosdepth/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.mosdepth.summary.txt, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/na/alignqc/mosdepth/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.na.mosdepth.summary.txt, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/goleft.done, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/na/alignqc/goleft.done, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/norm_cov_eveness/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.md, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/na/alignqc/norm_cov_eveness/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.na.md, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/contam/gatk/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.gatk.tsv, results/day/hg38/other_reports/unmapped_metagenomics_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/unmapped_metagenomics/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.kraken2.quick.report.txt, results/day/hg38/other_reports/unmapped_metagenomics_ganon2_mqc.tsv, results/day/hg38/other_reports/unmapped_metagenomics_sourmash_mqc.tsv, results/day/hg38/other_reports/alignment_qc_outputs_mqc.tsv, results/day/hg38/other_reports/contamination_mqc.tsv, results/day/hg38/other_reports/site_mix_contam_mqc.tsv, results/day/hg38/other_reports/site_mix_donor_mqc.tsv, results/day/hg38/other_reports/relatedness_mqc.tsv, results/day/hg38/other_reports/relatedness/sent/dmd/somalier/cohort.samples.tsv, results/day/hg38/other_reports/relatedness/sent/dmd/somalier/cohort.pairs.tsv, results/day/hg38/other_reports/contam_identity_mqc.tsv, results/day/hg38/other_reports/haplocheck_mtdna_mqc.tsv, results/day/hg38/other_reports/read_haps_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.contamination.txt, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.contamination.raw.txt, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.report.html, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/read_haps/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.read_haps.txt, results/day/hg38/other_reports/bcftools_variant_stats_mqc.tsv, results/day/hg38/other_reports/rtg_vcfstats_mqc.tsv, logs/peddy_gathered.done, results/day/hg38/other_reports/peddy_sample_qc_mqc.tsv, results/day/hg38/other_reports/expansionhunter_mqc.tsv, results/day/hg38/other_reports/vep_annotation_mqc.tsv, results/day/hg38/other_reports/htd_calls_mqc.tsv, results/day/hg38/other_reports/giab_concordance_mqc.tsv
    output: results/day/hg38/logs/report_components_aggregated.done
    jobid: 97
    reason: Missing output files: results/day/hg38/logs/report_components_aggregated.done; Input files updated by another job: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/na/alignqc/mosdepth/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.na.mosdepth.summary.txt, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.contamination.raw.txt, results/day/hg38/other_reports/contamination_mqc.tsv, results/day/hg38/other_reports/vep_annotation_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/na/alignqc/samtmetrics/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.na.complete, results/day/hg38/other_reports/haplocheck_mtdna_mqc.tsv, results/day/hg38/other_reports/relatedness/sent/dmd/somalier/cohort.pairs.tsv, results/day/hg38/other_reports/bcftools_variant_stats_mqc.tsv, results/day/hg38/other_reports/unmapped_metagenomics_sourmash_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/goleft.done, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/samtmetrics/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.complete, results/day/hg38/other_reports/site_mix_donor_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/na/alignqc/norm_cov_eveness/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.na.md, results/day/hg38/other_reports/relatedness/sent/dmd/somalier/cohort.samples.tsv, results/day/hg38/other_reports/htd_calls_mqc.tsv, results/day/hg38/other_reports/giab_concordance_mqc.tsv, logs/peddy_gathered.done, results/day/hg38/other_reports/sequence_qc_outputs_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/unmapped_metagenomics/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.kraken2.quick.report.txt, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/norm_cov_eveness/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.md, results/day/hg38/other_reports/site_mix_contam_mqc.tsv, results/day/hg38/other_reports/peddy_sample_qc_mqc.tsv, results/day/hg38/other_reports/unmapped_metagenomics_mqc.tsv, results/day/hg38/other_reports/rtg_vcfstats_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/seqqc/fastqc/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.fastqc.done, results/day/hg38/other_reports/unmapped_metagenomics_ganon2_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.contamination.txt, results/day/hg38/other_reports/alignment_qc_outputs_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/read_haps/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.read_haps.txt, results/day/hg38/other_reports/read_haps_mqc.tsv, results/day/hg38/other_reports/relatedness_mqc.tsv, results/day/hg38/other_reports/input_sample_libraries_mqc.tsv, results/day/hg38/other_reports/samtools_metrics_gather.done, results/day/hg38/other_reports/contam_identity_mqc.tsv, results/day/hg38/other_reports/expansionhunter_mqc.tsv, results/day/hg38/other_reports/norm_cov_evenness_combo_mqc.tsv, results/day/hg38/other_reports/alignstats_combo_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/na/alignqc/goleft.done, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/contam/gatk/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.gatk.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.report.html, results/day/hg38/other_reports/seqfu_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/mosdepth/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.mosdepth.summary.txt
    threads: 2
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/dev/shm, threads=1, time=5440, partition=i192,i128,i192mem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=

mkdir -p $(dirname results/day/hg38/logs/report_components_aggregated.done); touch results/day/hg38/logs/report_components_aggregated.done;
[Sat May 30 18:47:33 2026]
Finished job 97.
156 of 161 steps (97%) done
Select jobs to execute...

[Sat May 30 18:47:33 2026]
localrule collect_rules_benchmark_data:
    input: results/day/hg38/logs/report_components_aggregated.done
    output: results/day/hg38/other_reports/rules_benchmark_data_mqc.tsv
    log: results/day/hg38/other_reports/logs/rules_benchmarks_summary.log
    jobid: 151
    reason: Missing output files: results/day/hg38/other_reports/rules_benchmark_data_mqc.tsv; Input files updated by another job: results/day/hg38/logs/report_components_aggregated.done
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=/dev/shm, threads=1, time=5440, partition=i192,i128,i192mem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=

bin/util/benchmarks/collect_day_benchmark_data.sh hg38 > results/day/hg38/other_reports/logs/rules_benchmarks_summary.log;python bin/util/benchmarks/split_bench_rule_col.py results/day/hg38/reports/benchmarks_summary.tsv results/day/hg38/other_reports/rules_benchmark_data_mqc.tsv > results/day/hg38/other_reports/logs/rules_benchmarks_summary.log;sed -i -E 's/	$/	NA/' results/day/hg38/other_reports/rules_benchmark_data_mqc.tsv;
[Sat May 30 18:47:34 2026]
Finished job 151.
157 of 161 steps (98%) done
Select jobs to execute...

[Sat May 30 18:47:34 2026]
localrule stage_multiqc_inputs:
    input: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/seqqc/fastqc/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.fastqc.done, results/day/hg38/other_reports/seqfu_mqc.tsv, results/day/hg38/other_reports/input_sample_libraries_mqc.tsv, results/day/hg38/other_reports/sequence_qc_outputs_mqc.tsv, results/day/hg38/other_reports/alignstats_combo_mqc.tsv, results/day/hg38/other_reports/norm_cov_evenness_combo_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/samtmetrics/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.complete, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/na/alignqc/samtmetrics/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.na.complete, results/day/hg38/other_reports/samtools_metrics_gather.done, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/mosdepth/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.mosdepth.summary.txt, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/na/alignqc/mosdepth/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.na.mosdepth.summary.txt, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/goleft.done, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/na/alignqc/goleft.done, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/norm_cov_eveness/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.md, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/na/alignqc/norm_cov_eveness/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.na.md, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/contam/gatk/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.gatk.tsv, results/day/hg38/other_reports/unmapped_metagenomics_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/unmapped_metagenomics/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.kraken2.quick.report.txt, results/day/hg38/other_reports/unmapped_metagenomics_ganon2_mqc.tsv, results/day/hg38/other_reports/unmapped_metagenomics_sourmash_mqc.tsv, results/day/hg38/other_reports/alignment_qc_outputs_mqc.tsv, results/day/hg38/other_reports/contamination_mqc.tsv, results/day/hg38/other_reports/site_mix_contam_mqc.tsv, results/day/hg38/other_reports/site_mix_donor_mqc.tsv, results/day/hg38/other_reports/relatedness_mqc.tsv, results/day/hg38/other_reports/relatedness/sent/dmd/somalier/cohort.samples.tsv, results/day/hg38/other_reports/relatedness/sent/dmd/somalier/cohort.pairs.tsv, results/day/hg38/other_reports/contam_identity_mqc.tsv, results/day/hg38/other_reports/haplocheck_mtdna_mqc.tsv, results/day/hg38/other_reports/read_haps_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.contamination.txt, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.contamination.raw.txt, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.report.html, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/read_haps/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.read_haps.txt, results/day/hg38/other_reports/bcftools_variant_stats_mqc.tsv, results/day/hg38/other_reports/rtg_vcfstats_mqc.tsv, logs/peddy_gathered.done, results/day/hg38/other_reports/peddy_sample_qc_mqc.tsv, results/day/hg38/other_reports/expansionhunter_mqc.tsv, results/day/hg38/other_reports/vep_annotation_mqc.tsv, results/day/hg38/other_reports/htd_calls_mqc.tsv, results/day/hg38/other_reports/giab_concordance_mqc.tsv, results/day/hg38/other_reports/rules_benchmark_data_mqc.tsv
    output: results/day/hg38/reports/multiqc_inputs/final/.stage.done, results/day/hg38/reports/multiqc_inputs/final/manifest.tsv
    log: results/day/hg38/reports/logs/final_multiqc_input_staging.log
    jobid: 152
    reason: Missing output files: results/day/hg38/reports/multiqc_inputs/final/manifest.tsv, results/day/hg38/reports/multiqc_inputs/final/.stage.done; Input files updated by another job: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/na/alignqc/mosdepth/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.na.mosdepth.summary.txt, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/haplocheck/vcf/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.haplocheck.contamination.raw.txt, results/day/hg38/other_reports/contamination_mqc.tsv, results/day/hg38/other_reports/vep_annotation_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/na/alignqc/samtmetrics/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.na.complete, results/day/hg38/other_reports/haplocheck_mtdna_mqc.tsv, results/day/hg38/other_reports/relatedness/sent/dmd/somalier/cohort.pairs.tsv, results/day/hg38/other_reports/bcftools_variant_stats_mqc.tsv, results/day/hg38/other_reports/unmapped_metagenomics_sourmash_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/goleft.done, results/day/hg38/other_reports/rules_benchmark_data_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/samtmetrics/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.complete, results/day/hg38/other_reports/site_mix_donor_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/na/alignqc/norm_cov_eveness/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.na.md, results/day/hg38/other_reports/relatedness/sent/dmd/somalier/cohort.samples.tsv, results/day/hg38/other_reports/htd_calls_mqc.tsv, results/day/hg38/other_reports/giab_concordance_mqc.tsv, logs/peddy_gathered.done, results/day/hg38/other_reports/seq--output truncated--
