DAY-EC activated.
DAY-EC activated.
        bcftools concat -a -d all --threads 16 -f results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.concat.vcf.gz.fofn -O z -o results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.temp.vcf.gz >> results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/log/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.concat.log 2>&1
        mv results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.temp.vcf.gz results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.vcf.gz
        tabix -f -p vcf results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.vcf.gz >> results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/log/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.concat.log 2>&1
        final_count=$(bcftools view -H results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.vcf.gz | wc -l | awk '{print $1}')
        if [ "$final_count" -ne "$input_count" ]; then
            echo "ERROR: final VEP VCF count ($final_count) does not match input count ($input_count)" >&2
            exit 2
        fi
        test -s results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.vcf.gz
        test -s results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.vcf.gz.tbi
        

[Sat May 30 10:28:35 2026]
localrule vep_annotation_gather:
    input: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.vcf.gz.tbi
    output: results/day/hg38/other_reports/vep_annotation_mqc.tsv
    jobid: 99
    reason: Missing output files: results/day/hg38/other_reports/vep_annotation_mqc.tsv; Input files updated by another job: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.vcf.gz.tbi
    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=

[Sat May 30 10:28:35 2026]
localrule produce_vep:
    input: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.vcf.gz.tbi, results/day/hg38/other_reports/vep_annotation_mqc.tsv
    output: logs/vep_gathered.done
    jobid: 45
    reason: Missing output files: logs/vep_gathered.done; Input files updated by another job: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/vep/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.vep.vcf.gz.tbi, results/day/hg38/other_reports/vep_annotation_mqc.tsv
    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=

touch logs/vep_gathered.done;

[Sat May 30 10:28:35 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: 103
    reason: Missing output files: results/day/hg38/logs/report_components_aggregated.done; Input files updated by another job: results/day/hg38/other_reports/expansionhunter_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/na/alignqc/samtmetrics/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.na.complete, results/day/hg38/other_reports/rtg_vcfstats_mqc.tsv, 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/site_mix_contam_mqc.tsv, results/day/hg38/other_reports/contamination_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, results/day/hg38/other_reports/site_mix_donor_mqc.tsv, results/day/hg38/other_reports/unmapped_metagenomics_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.report.html, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/na/alignqc/goleft.done, results/day/hg38/other_reports/vep_annotation_mqc.tsv, results/day/hg38/other_reports/contam_identity_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/unmapped_metagenomics_ganon2_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/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/alignqc/norm_cov_eveness/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.md, results/day/hg38/other_reports/relatedness/sent/dmd/somalier/cohort.pairs.tsv, results/day/hg38/other_reports/relatedness_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/goleft.done, results/day/hg38/other_reports/seqfu_mqc.tsv, results/day/hg38/other_reports/giab_concordance_mqc.tsv, results/day/hg38/other_reports/alignstats_combo_mqc.tsv, results/day/hg38/other_reports/unmapped_metagenomics_sourmash_mqc.tsv, results/day/hg38/other_reports/haplocheck_mtdna_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/samtools_metrics_gather.done, 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/other_reports/alignment_qc_outputs_mqc.tsv, results/day/hg38/other_reports/peddy_sample_qc_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/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/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/sequence_qc_outputs_mqc.tsv, logs/peddy_gathered.done, 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/bcftools_variant_stats_mqc.tsv, results/day/hg38/other_reports/relatedness/sent/dmd/somalier/cohort.samples.tsv, results/day/hg38/other_reports/input_sample_libraries_mqc.tsv, results/day/hg38/other_reports/htd_calls_mqc.tsv
    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 10:28:35 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: 154
    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 10:28:35 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: 155
    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/other_reports/expansionhunter_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/na/alignqc/samtmetrics/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.na.complete, results/day/hg38/other_reports/rtg_vcfstats_mqc.tsv, 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/site_mix_contam_mqc.tsv, results/day/hg38/other_reports/contamination_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, results/day/hg38/other_reports/site_mix_donor_mqc.tsv, results/day/hg38/other_reports/unmapped_metagenomics_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.report.html, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/na/alignqc/goleft.done, results/day/hg38/other_reports/vep_annotation_mqc.tsv, results/day/hg38/other_reports/contam_identity_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/unmapped_metagenomics_ganon2_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/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/alignqc/norm_cov_eveness/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.md, results/day/hg38/other_reports/relatedness/sent/dmd/somalier/cohort.pairs.tsv, results/day/hg38/other_reports/relatedness_mqc.tsv, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/alignqc/goleft.done, results/day/hg38/other_reports/seqfu_mqc.tsv, results/day/hg38/other_reports/giab_concordance_mqc.tsv, results/day/hg38/other_reports/alignstats_combo_mqc.tsv, results/day/hg38/other_reports/unmapped_metagenomics_sourmash_mqc.tsv, results/day/hg38/other_reports/haplocheck_mtdna_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/samtools_metrics_gather.done, 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/other_reports/rules_benchmark_data_mqc.tsv, results/day/hg38/other_reports/alignment_qc_outputs_mqc.tsv, results/day/hg38/other_reports/peddy_sample_qc_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/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/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/sequence_qc_outputs_mqc.tsv, logs/peddy_gathered.done, 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/bcftools_variant_stats_mqc.tsv, results/day/hg38/other_reports/relatedness/sent/dmd/somalier/cohort.samples.tsv, results/day/hg38/other_reports/input_sample_libraries_mqc.tsv, results/day/hg38/other_reports/htd_calls_mqc.tsv
    wildcards: report_stage=final
    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=


        set -euo pipefail
        mkdir -p $(dirname results/day/hg38/reports/logs/final_multiqc_input_staging.log)
        python workflow/scripts/stage_multiqc_inputs.py           --input-root results/day/hg38/           --output-dir results/day/hg38/reports/multiqc_inputs/final           --manifest results/day/hg38/reports/multiqc_inputs/final/manifest.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/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--output truncated--
