DAY-EC activated.
DAY-EC activated.
=== rule source markers ===
366:%s	NO_VARIANTS	0		0
369:%s	NO_VARIANTS	0		0
371:            printf '<html><body>NO_VARIANTS</body></html>
373:            printf 'NO_VARIANTS: haplocheck skipped because the input VCF has no variant records.
379:rule read_haps_contam_identity:
424:            read_haps_rc=$?
426:            if [[ "$read_haps_rc" != "0" ]] || [[ ! -s {output.txt:q} ]] || ! grep -q 'PASS_FAIL' {output.txt:q} || ! grep -q 'REASON' {output.txt:q}; then
428:0 0 0 0 0 0 NO_DATA READ_HAPS_FAILED
430:                printf 'READ_HAPS_FAILED: read_haps exited with status %s or wrote no usable QC table.
431:' "$read_haps_rc" >> {log:q}
435:0 0 0 0 0 0 NO_DATA NO_VARIANTS
437:            printf 'NO_VARIANTS: read_haps skipped because the input VCF has no variant records.
=== rule source excerpt ===
rule read_haps_contam_identity:
    input:
        bam=rules.legacy_cram_compat_bam.output.bam,
        bai=rules.legacy_cram_compat_bam.output.bai,
        vcf=_contam_identity_primary_snv_vcf,
        tbi=_contam_identity_primary_snv_tbi,
    output:
        txt=MDIR + "{sample}/align/{alnr}/{ddup}/snv/{snv}/contam_identity/read_haps/{sample}.{alnr}.{ddup}.{snv}.read_haps.txt",
    log:
        MDIR + "{sample}/align/{alnr}/{ddup}/snv/{snv}/contam_identity/read_haps/logs/{sample}.{alnr}.{ddup}.{snv}.read_haps.log",
    benchmark:
        MDIR + "{sample}/benchmarks/{sample}.{alnr}.{ddup}.{snv}.read_haps.bench.tsv"
    conda:
        config["read_haps"]["env_yaml"]
    threads: config["read_haps"]["threads"]
    resources:
        vcpu=config["read_haps"]["threads"],
        mem_mb=config["read_haps"]["mem_mb"],
        partition=config["read_haps"]["partition"],
    params:
        command=config["read_haps"]["read_haps_command"],
        reliable_snp_file=config["read_haps"]["reliable_snp_file"],
        extra_args=config["read_haps"]["extra_args"],
        ref=config["supporting_files"]["files"]["huref"]["fasta"]["name"],
        sample_ok=lambda wildcards: require_qc_eligible_sample(
            wildcards, "read_haps"
        ),
        cluster_sample=ret_sample,
    shell:
        r"""
        set -euo pipefail
        test {params.sample_ok:q} = ok
        mkdir -p "$(dirname {output.txt:q})" "$(dirname {log:q})"
        set +o pipefail
        if gzip -cd {input.vcf:q} | grep -m 1 -q -v '^#'; then
            has_variants=true
        else
            has_variants=false
        fi
        set -o pipefail
        if [[ "$has_variants" == "true" ]]; then
            command -v {params.command:q} > /dev/null
            test -s {params.reliable_snp_file:q}
            set +e
            {params.command:q} {params.extra_args} -fa {params.ref:q} {input.bam:q} {params.reliable_snp_file:q} {input.vcf:q} > {output.txt:q} 2> {log:q}
            read_haps_rc=$?
            set -e
            if [[ "$read_haps_rc" != "0" ]] || [[ ! -s {output.txt:q} ]] || ! grep -q 'PASS_FAIL' {output.txt:q} || ! grep -q 'REASON' {output.txt:q}; then
                printf 'SNP_PAIRS ERROR_PAIRS DOUBLE_ERROR_PAIR_COUNT DOUBLE_ERROR_FRACTION REL_ERROR_FRACTION NONSENSE_FRACTION PASS_FAIL REASON
0 0 0 0 0 0 NO_DATA READ_HAPS_FAILED
' > {output.txt:q}
                printf 'READ_HAPS_FAILED: read_haps exited with status %s or wrote no usable QC table.
' "$read_haps_rc" >> {log:q}
            fi
        else
            printf 'SNP_PAIRS ERROR_PAIRS DOUBLE_ERROR_PAIR_COUNT DOUBLE_ERROR_FRACTION REL_ERROR_FRACTION NONSENSE_FRACTION PASS_FAIL REASON
0 0 0 0 0 0 NO_DATA NO_VARIANTS
' > {output.txt:q}
            printf 'NO_VARIANTS: read_haps skipped because the input VCF has no variant records.
' > {log:q}
        fi
        test -s {output.txt:q}
        grep -q 'PASS_FAIL' {output.txt:q}
        grep -q 'REASON' {output.txt:q}
        """


rule contam_identity_mqc_gather:
    input:
        contamination=MDIR + "other_reports/contamination_mqc.tsv",
        haplocheck=lambda wildcards: _haplocheck_outputs("contamination.txt"),
        read_haps=lambda wildcards: _read_haps_outputs("read_haps.txt"),
    output:
        identity=MDIR + "other_reports/contam_identity_mqc.tsv",
        haplocheck=MDIR + "other_reports/haplocheck_mtdna_mqc.tsv",
        read_haps=MDIR + "other_reports/read_haps_mqc.tsv",
    params:
        sample_map=_sample_external_ids_json,
    log:
        MDIR + "other_reports/logs/contam_identity_custom_data.log",
    shell:
        r"""
        set -euo pipefail
        mkdir -p "$(dirname {output.identity:q})" "$(dirname {log:q})"
        python workflow/scripts/compile_contam_identity_mqc.py \
          --sample-map-json {params.sample_map:q} \
          --contam-identity-output {output.identity:q} \
          --haplocheck-output {output.haplocheck:q} \
          --read-haps-output {output.read_haps:q} \
          --contamination {input.contamination:q} \
          --haplocheck {input.haplocheck:q} \
=== read_haps outputs ===
0 2026-05-30T17:39:57.0000000000 results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/read_haps/logs/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.read_haps.log
=== read_haps log tails ===
--- results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/read_haps/logs/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.read_haps.log
=== read_haps text outputs ===
=== snakemake read_haps error context ===
--- .snakemake/log/2026-05-30T172758.676659.snakemake.log
43-prep_for_concordance_check                    1              8              8
44-prep_results_dirs                             1              1              1
45-prep_sentD_chunkdirs                          1              1              1
46-produce_alignstats                            1              1              1
47-produce_cov_uniformity                        1              8              8
48-produce_dmd_dedup_cram                        1              1              1
49-produce_expansionhunter                       1              1              1
50-produce_gatk_contam_estimate                  1              1              1
51-produce_global_contam_check                   1              1              1
52-produce_htd_calls                             1              1              1
53-produce_metagenomics                          1              1              1
54-produce_multiqc_all                           1              1              1
55-produce_peddy                                 1              1              1
56-produce_relatedness                           1              1              1
57-produce_samtools_metrics                      1              1              1
58-produce_sent_align                            1              1              1
59-produce_sentd_snv_vcf                         1              1              1
60-produce_site_mix_contam_estimate              1              1              1
61-produce_snv_concordances                      1              1              1
62-produce_vep                                   1              1              1
63:read_haps_contam_identity                     1              8              8
64-relatedness_batch_gather                      1              1              1
65-relatedness_batch_manifest                    1              1              1
66-relatedness_batch_report                      1              1              1
67-relatedness_batch_somalier_extract            1              4              4
68-relatedness_batch_somalier_relate             1              4              4
69-rtg_vcfeval_roi                              10             16             16
70-rtg_vcfstats                                  1             24             24
71-rtg_vcfstats_gather                           1              1              1
72-sentD_concat_fofn                             1              1              1
73-sentD_concat_index_chunks                     1              4              4
74-sentD_sort_index_chunk_vcf                    1              1              1
75-sent_DNAscope                                 1            192            192
76-sentieon_bwa_sort                             1            192            192
77-seqfu                                         1             16             16
78-sequence_qc_outputs_custom_data               1              1              1
79-site_mix_contam                               1              1              1
80-stage_multiqc_inputs                          1              1              1
81-stage_supporting_data                         1              1              1
82-unmapped_metagenomics_ganon2_multiqc          1              4              4
83-unmapped_metagenomics_ganon2_quick            1             16             16
84-unmapped_metagenomics_ganon2_summary          1              1              1
85-unmapped_metagenomics_kraken2_quick           1             16             16
86-unmapped_metagenomics_multiqc                 1              4              4
87-unmapped_metagenomics_sourmash_gather         1             16             16
88-unmapped_metagenomics_sourmash_multiqc        1              4              4
89-unmapped_metagenomics_sourmash_summary        1              1              1
90-unmapped_metagenomics_summary                 1              1              1
91-vep_annotation_gather                         1              1              1
92-vep_chromosome                               25             16             16
93-vep_chromosome_input                         25              1              1
94-vep_concat_fofn                               1              1              1
95-vep_concat_index_chunks                       1             16             16
96-vep_validate_input_contigs                    1              1              1
97-workflow_staging                              1              1              1
98-write_dayoa_evidence_manifest                 1              1              1
99-total                                       161              1            192
100-
101-Select jobs to execute...
102-
103-[Sat May 30 17:28:03 2026]
104-localrule input_sample_libraries_custom_data:
105-    input: /fsx/analysis_results/ubuntu/ccv20260530r48_illumina_hg002_kitchensink_multiqc/daylily-omics-analysis/config/samples.tsv, /fsx/analysis_results/ubuntu/ccv20260530r48_illumina_hg002_kitchensink_multiqc/daylily-omics-analysis/config/units.tsv
106-    output: results/day/hg38/other_reports/input_sample_libraries_mqc.tsv
107-    log: results/day/hg38/other_reports/logs/input_sample_libraries_custom_data.log
108-    jobid: 76
109-    reason: Missing output files: results/day/hg38/other_reports/input_sample_libraries_mqc.tsv
110-    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=
111-
112-[Sat May 30 17:28:03 2026]
113-localrule stage_supporting_data:
114-    output: logs/supporting_data_staging.done
115-    log: logs/staging_supporting_data.log
116-    jobid: 10
117-    reason: Missing output files: logs/supporting_data_staging.done
118-    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=
119-
120-touch logs/supporting_data_staging.done;
121-Activating conda environment: ../../../../resources/environments/conda/ubuntu/ip-10-0-0-88/f02f4b1dcb4977fd9602b074e7c885b9_
122-
123-[Sat May 30 17:28:03 2026]
124-localrule pre_prep_raw_fq:
125-    input: /fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG002_0.1x_R1.fastq.gz, /fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG002_0.1x_R2.fastq.gz
126-    output: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.R1.fastq.gz, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.R2.fastq.gz
127-    jobid: 11
128-    reason: Missing output files: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.R1.fastq.gz, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.R2.fastq.gz
129-    wildcards: sample=JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ, sample_lane=JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ
130-    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=
131-
132- ln -s   /fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG002_0.1x_R1.fastq.gz results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.R1.fastq.gz; ln -s   /fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG002_0.1x_R2.fastq.gz results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.R2.fastq.gz;
133-
134-[Sat May 30 17:28:03 2026]
135-localrule produce_samtools_metrics:
136-    output: results/day/hg38/other_reports/samtools_metrics_gather.done
137-    jobid: 89
138-    reason: Missing output files: results/day/hg38/other_reports/samtools_metrics_gather.done
139-    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=
140-
141-[Sat May 30 17:28:03 2026]
142-rule seqfu:
143-    input: /fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG002_0.1x_R1.fastq.gz, /fsx/control_data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/downsampled/HG002_0.1x_R2.fastq.gz
--
2093-            set -euo pipefail
2094-            export TMPDIR="/fsx/scratch/"
2095-            outdir="$(dirname results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/concordance/_giabHC_x_ultima/summary.txt)"
2096-            rm -rf "$outdir"
2097-
2098-            rtg vcfeval \
2099-              --decompose \
2100-              --squash-ploidy \
2101-              --ref-overlap \
2102-              -e /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_ultima/HG002.bed \
2103-              -b /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/giabHC_x_ultima/HG002.vcf.gz \
2104-              -c results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz \
2105-              -o "$outdir" \
2106-              -t /fsx/references/genomic_data/organism_references/H_sapiens/hg38/fasta_fai_minalt/GRCh38_no_alt_analysis_set.fasta.sdf \
2107-              --threads 16 \
2108-              > 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.giabHC_x_ultima.rtg_vcfeval.log 2>&1
2109-
2110-Submitted job 22 with external jobid '3612'.
2111-
2112-[Sat May 30 17:39:28 2026]
2113:rule read_haps_contam_identity:
2114-    input: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/compat_bam/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.legacy_compat.bam, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/compat_bam/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.legacy_compat.bam.bai, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz.tbi
2115-    output: 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
2116-    log: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/read_haps/logs/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.read_haps.log
2117-    jobid: 47
2118-    benchmark: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/benchmarks/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.read_haps.bench.tsv
2119-    reason: Missing output files: 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; Input files updated by another job: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz.tbi, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/compat_bam/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.legacy_compat.bam.bai, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/compat_bam/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.legacy_compat.bam
2120-    wildcards: sample=JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ, alnr=sent, ddup=dmd, snv=sentd
2121-    threads: 8
2122-    resources: mem_mb=32000, mem_mib=30518, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=1, time=5440, partition=i192,i192mem,i128, vcpu=8, distribution=block, exclusive=, constraint=, exclude=, include=
2123-
2124-
2125-        set -euo pipefail
2126-        test ok = ok
2127-        mkdir -p "$(dirname 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)" "$(dirname results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/read_haps/logs/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.read_haps.log)"
2128-        set +o pipefail
2129-        if gzip -cd results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz | grep -m 1 -q -v '^#'; then
2130-            has_variants=true
2131-        else
2132-            has_variants=false
2133-        fi
2134-        set -o pipefail
2135-        if [[ "$has_variants" == "true" ]]; then
2136-            command -v /fsx/references/runtime_assets/tool_specific_resources/read_haps/read_haps > /dev/null
2137-            test -s /fsx/references/runtime_assets/tool_specific_resources/read_haps/high_quality_markers_deCODE_2015.txt.gz
2138-            set +e
2139-            /fsx/references/runtime_assets/tool_specific_resources/read_haps/read_haps  -fa /fsx/references/genomic_data/organism_references/H_sapiens/hg38/fasta_fai_minalt/GRCh38_no_alt_analysis_set.fasta results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/compat_bam/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.legacy_compat.bam /fsx/references/runtime_assets/tool_specific_resources/read_haps/high_quality_markers_deCODE_2015.txt.gz results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz > 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 2> results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/read_haps/logs/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.read_haps.log
2140-            read_haps_rc=$?
2141-            set -e
2142-            if [[ "$read_haps_rc" != "0" ]] || [[ ! -s 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 ]] || ! grep -q 'PASS_FAIL' 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 || ! grep -q 'REASON' 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; then
2143-                printf 'SNP_PAIRS ERROR_PAIRS DOUBLE_ERROR_PAIR_COUNT DOUBLE_ERROR_FRACTION REL_ERROR_FRACTION NONSENSE_FRACTION PASS_FAIL REASON
2144-0 0 0 0 0 0 NO_DATA READ_HAPS_FAILED
2145-' > 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
2146-                printf 'READ_HAPS_FAILED: read_haps exited with status %s or wrote no usable QC table.
2147-' "$read_haps_rc" >> results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/read_haps/logs/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.read_haps.log
2148-            fi
2149-        else
2150-            printf 'SNP_PAIRS ERROR_PAIRS DOUBLE_ERROR_PAIR_COUNT DOUBLE_ERROR_FRACTION REL_ERROR_FRACTION NONSENSE_FRACTION PASS_FAIL REASON
2151-0 0 0 0 0 0 NO_DATA NO_VARIANTS
2152-' > 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
2153-            printf 'NO_VARIANTS: read_haps skipped because the input VCF has no variant records.
2154-' > results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/contam_identity/read_haps/logs/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.read_haps.log
2155-        fi
2156-        test -s 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
2157-        grep -q 'PASS_FAIL' 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
2158-        grep -q 'REASON' 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
2159-
2160-Submitted job 47 with external jobid '3613'.
2161-
2162-[Sat May 30 17:39:28 2026]
2163-rule rtg_vcfeval_roi:
2164-    input: results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz, results/day/hg38/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ/align/sent/dmd/snv/sentd/JEMILMN0P1-HG002-0p1x-1-D0-PF-ILMN-NOVASEQ.sent.dmd.sentd.snv.sort.vcf.gz.tbi, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/hg38_m_giabHC/HG002.vcf.gz, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/hg38_m_giabHC/HG002.vcf.gz.tbi, /fsx/references/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/hg38_m_giabH--output truncated--