DAY-EC activated.
DAY-EC activated.
=== status.json ===
{
  "command": "bin/day_run produce_sentcg_align produce_dmd_dedup_cram produce_cgt7p_snv_vcf produce_alignstats produce_snv_concordances -p -j 20 -k -T 1 --retries 0 --rerun-incomplete --keep-incomplete -n",
  "completed_at": "2026-05-30T18:29:22Z",
  "exit_code": 1,
  "repo_path": "/fsx/analysis_results/ubuntu/ccv20260530r53_complete_genomics_mgi_snv_concordance_dryrun/daylily-omics-analysis",
  "session_name": "ccv20260530r53_complete_genomics_mgi_snv_concordance_dryrun",
  "started_at": "2026-05-30T18:28:58Z"
}
=== tmux.log size ===
75840 /home/ubuntu/daylily-runs/ccv20260530r53_complete_genomics_mgi_snv_concordance_dryrun/tmux.log
726 /home/ubuntu/daylily-runs/ccv20260530r53_complete_genomics_mgi_snv_concordance_dryrun/tmux.log
=== tmux.log last 220 lines ===

[Sat May 30 18:29:22 2026]
localrule finish_align_stats:
    input: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/na/alignqc/alignstats/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.na.alignstats.json
    output: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/na/alignqc/alignstats/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.na.alignstats.tsv
    jobid: 12
    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/na/alignqc/alignstats/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.na.alignstats.tsv; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/na/alignqc/alignstats/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.na.alignstats.json
    wildcards: sample=TVBCG5X-HG003-5x-1-D0-PF-CG-MGI, alnr=sentcg, ddup=na
    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=

[Sat May 30 18:29:22 2026]
rule cgt7p_DNAscope:
    input: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cram, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cram.crai, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.ready
    output: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.vcf, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.vcf.tmp
    log: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/vcfs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.log
    jobid: 21
    benchmark: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/benchmarks/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.vcf; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cram, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.ready, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cram.crai
    wildcards: sample=TVBCG5X-HG003-5x-1-D0-PF-CG-MGI, alnr=sentcg, ddup=dmd, dchrm=1-24
    priority: 45
    threads: 192
    resources: mem_mb=200000, mem_mib=190735, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=192, time=5440, partition=i192,i192mem,i192bigmem, vcpu=192, distribution=block, exclusive=, constraint=, exclude=, include=, attempt_n=1


        export bwt_max_mem=100G;
        timestamp=$(date +%Y%m%d%H%M%S)_$$;
        main_bashpid=${BASHPID:-};
        tmp_root=$(dirname results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/vcfs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.log)/../tmp;
        mkdir -p "$tmp_root";
        export TMPDIR="$tmp_root";
        meta_tmp=$TMPDIR/cgt7p_meta_$timestamp;
        export SENTIEON_TMPDIR=$TMPDIR/cgt7p_driver_$timestamp;
        export APPTAINER_HOME=$meta_tmp/apptainer_home;
        mkdir -p "$SENTIEON_TMPDIR" "$APPTAINER_HOME";

        trap 'status=$?; if [ "${BASHPID:-}" != "$main_bashpid" ]; then exit "$status"; fi; if [ "$status" -eq 0 ]; then rm -rf "$meta_tmp" "$SENTIEON_TMPDIR" 2>/dev/null || true; else echo "Preserving scratch after failure under $TMPDIR" >> results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/vcfs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.log 2>&1; fi; trap - EXIT; exit "$status"' EXIT;
        ulimit -n 65536 || echo "ulimit mod failed" > results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/vcfs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.log 2>&1;

        if [ -z "${SENTIEON_LICENSE:-}" ]; then
            echo "SENTIEON_LICENSE not set. Please set the SENTIEON_LICENSE environment variable to the license file path & make this update to your dyinit file as well." >> results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/vcfs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.log 2>&1;
            exit 3;
        fi

        if [[ ! "$SENTIEON_LICENSE" =~ : ]] && [ ! -f "$SENTIEON_LICENSE" ]; then
            echo "The file referenced by SENTIEON_LICENSE ('$SENTIEON_LICENSE') does not exist. Please provide a valid file path." >> results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/vcfs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.log 2>&1;
            exit 4;
        fi

        TOKEN=$(curl -s -X PUT 'http://169.254.169.254/latest/api/token' -H 'X-aws-ec2-metadata-token-ttl-seconds: 21600');
        itype=$(curl -s -H "X-aws-ec2-metadata-token: $TOKEN" http://169.254.169.254/latest/meta-data/instance-type || echo "unknown");
        echo "INSTANCE TYPE: $itype" > results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/vcfs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.log;
        echo "INSTANCE TYPE: $itype";
        start_time=$(date +%s);

        /fsx/references/runtime_assets/cached_envs/sentieon-genomics-202503.02/bin/sentieon driver --thread_count 192         --interval chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY --reference /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.fasta --input results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cram         --algo DNAscope -d /fsx/references/genomic_data/organism_references/H_sapiens/panhg38/pop-v20g41-20251216.vcf.gz --pcr_indel_model none --emit_mode variant         --model /fsx/references/runtime_assets/cached_envs/sentieon-genomics-202503.02/bundles/DNAscopeMGIWGS2.1.bundle/dnascope.model results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.vcf.tmp >> results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/vcfs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.log 2>&1;

        /fsx/references/runtime_assets/cached_envs/sentieon-genomics-202503.02/bin/sentieon driver -t 192         -r /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.fasta --algo DNAModelApply --model /fsx/references/runtime_assets/cached_envs/sentieon-genomics-202503.02/bundles/DNAscopeMGIWGS2.1.bundle/dnascope.model -v results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.vcf.tmp results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.vcf >> results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/vcfs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.log 2>&1;

        end_time=$(date +%s);
        elapsed_time=$((($end_time - $start_time) / 60));
        echo "Elapsed-Time-min:	$itype	$elapsed_time";
        echo "Elapsed-Time-min:	$itype	$elapsed_time" >> results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/vcfs/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.log 2>&1;

        touch results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.vcf;

Would remove temporary output results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.vcf.tmp

[Sat May 30 18:29:22 2026]
localrule alignstats_gather:
    input: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/alignqc/alignstats/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.alignstats.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/na/alignqc/alignstats/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.na.alignstats.tsv
    output: results/day/hg38_broad/other_reports/alignstats_summary_gather.done, results/day/hg38_broad/benchmarks/all.alignstats_summary.bench.tsv
    log: results/day/hg38_broad/logs/alignstats_summary_gather.log
    jobid: 8
    benchmark: results/day/hg38_broad/benchmarks/all.alignstats_summary.bench.tsv
    reason: Missing output files: results/day/hg38_broad/other_reports/alignstats_summary_gather.done; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/alignqc/alignstats/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.alignstats.tsv, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/na/alignqc/alignstats/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.na.alignstats.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 results/day/hg38_broad/other_reports/alignstats_summary_gather.done; touch results/day/hg38_broad/benchmarks/all.alignstats_summary.bench.tsv

[Sat May 30 18:29:22 2026]
rule cgt7p_sort_index_chunk_vcf:
    input: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.vcf
    output: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.sort.vcf, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.sort.vcf.gz, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.sort.vcf.gz.tbi
    log: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/log/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.sort.vcf.gz.log
    jobid: 20
    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.sort.vcf.gz.tbi; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.vcf
    wildcards: sample=TVBCG5X-HG003-5x-1-D0-PF-CG-MGI, alnr=sentcg, ddup=dmd, dchrm=1-24
    priority: 46
    resources: mem_mb=3000, mem_mib=2862, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=1, time=5440, partition=i192,i192mem,i192bigmem, vcpu=1, distribution=block, exclusive=, constraint=, exclude=, include=


        bedtools sort -header -i results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.vcf > results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.sort.vcf 2> results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/log/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.sort.vcf.gz.log;
        bgzip -f -c results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.sort.vcf > results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.sort.vcf.gz 2>> results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/log/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.sort.vcf.gz.log;
        tabix -f -p vcf results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.sort.vcf.gz >> results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/log/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.sort.vcf.gz.log 2>&1;

Would remove temporary output results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.vcf
Would remove temporary output results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.sort.vcf

[Sat May 30 18:29:22 2026]
localrule alignstats_compile:
    input: results/day/hg38_broad/other_reports/alignstats_summary_gather.done
    output: results/day/hg38_broad/other_reports/alignstats_bsummary.tsv, results/day/hg38_broad/other_reports/alignstats_csummary.tsv, results/day/hg38_broad/other_reports/alignstats_combo_mqc.tsv, results/day/hg38_broad/other_reports/alignstats_gs_mqc.tsv
    log: results/day/hg38_broad/logs/alignstats_summary_compile.log
    jobid: 7
    benchmark: results/day/hg38_broad/benchmarks/all.alignstats_smmary_compile.bench.tsv
    reason: Missing output files: results/day/hg38_broad/other_reports/alignstats_bsummary.tsv; Input files updated by another job: results/day/hg38_broad/other_reports/alignstats_summary_gather.done
    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=


        set -euo pipefail
        python workflow/scripts/compile_alignstats.py           --mdir results/day/hg38_broad/           --log results/day/hg38_broad/logs/alignstats_summary_compile.log           --bsummary results/day/hg38_broad/other_reports/alignstats_bsummary.tsv           --csummary results/day/hg38_broad/other_reports/alignstats_csummary.tsv           --combo results/day/hg38_broad/other_reports/alignstats_combo_mqc.tsv           --generalstats results/day/hg38_broad/other_reports/alignstats_gs_mqc.tsv


[Sat May 30 18:29:22 2026]
localrule cgt7p_concat_fofn:
    input: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.sort.vcf.gz.tbi
    output: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.concat.vcf.gz.fofn, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.concat.vcf.gz.fofn.tmp
    log: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.concat.fofn.log
    jobid: 19
    benchmark: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/benchmarks/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.concat.fofn.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.concat.vcf.gz.fofn; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.sort.vcf.gz.tbi
    wildcards: sample=TVBCG5X-HG003-5x-1-D0-PF-CG-MGI, alnr=sentcg, ddup=dmd
    priority: 44
    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=


        rm -f results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.concat.vcf.gz.fofn.tmp;
        for i in results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/vcfs/1-24/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.1-24.snv.sort.vcf.gz.tbi; do
            ii=$(echo "$i" | perl -pe 's/\.tbi$//g');
            echo "$ii" >> results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.concat.vcf.gz.fofn.tmp;
        done;
        workflow/scripts/sort_concat_chrm_list.py results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.concat.vcf.gz.fofn.tmp TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p. results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.concat.vcf.gz.fofn >> results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.concat.fofn.log 2>&1;

Would remove temporary output results/day/hg38_broad/other_reports/alignstats_csummary.tsv

[Sat May 30 18:29:22 2026]
localrule produce_alignstats:
    input: results/day/hg38_broad/other_reports/alignstats_bsummary.tsv
    jobid: 6
    reason: Input files updated by another job: results/day/hg38_broad/other_reports/alignstats_bsummary.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=

[Sat May 30 18:29:22 2026]
rule cgt7p_concat_index_chunks:
    input: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.concat.vcf.gz.fofn
    output: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.vcf.gz, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.temp.vcf.gz, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.vcf.gz.tbi
    log: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.merge.sort.gathered.log
    jobid: 18
    benchmark: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/benchmarks/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.merge.bench.tsv
    reason: Missing output files: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.vcf.gz, results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.vcf.gz.tbi; Input files updated by another job: results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.concat.vcf.gz.fofn
    wildcards: sample=TVBCG5X-HG003-5x-1-D0-PF-CG-MGI, alnr=sentcg, ddup=dmd
    priority: 47
    threads: 16
    resources: mem_mb=50000, mem_mib=47684, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=16, time=5440, partition=i192,i192mem,i192bigmem, vcpu=16, distribution=block, exclusive=, constraint=, exclude=, include=, attempt_n=1


        touch results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.merge.sort.gathered.log;
        mkdir -p $(dirname results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.merge.sort.gathered.log);

        bcftools concat -a -d all --threads 16 -f results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.concat.vcf.gz.fofn -O z -o results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.temp.vcf.gz >> results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.merge.sort.gathered.log 2>&1;

        oldname=$(bcftools query -l results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.temp.vcf.gz | head -n1) >> results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.merge.sort.gathered.log 2>&1;
        echo -e "${oldname}	TVBCG5X-HG003-5x-1-D0-PF-CG-MGI" > results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.vcf.gz.rename.txt;
        bcftools reheader -s results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.vcf.gz.rename.txt -o results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.vcf.gz results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.temp.vcf.gz >> results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.merge.sort.gathered.log 2>&1;
        bcftools index -f -t --threads 16 -o results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.vcf.gz.tbi results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.vcf.gz >> results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.merge.sort.gathered.log 2>&1;

        rm -rf $(dirname results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.sort.vcf.gz)/vcfs >> results/day/hg38_broad/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI/align/sentcg/dmd/snv/cgt7p/log/TVBCG5X-HG003-5x-1-D0-PF-CG-MGI.sentcg.dmd.cgt7p.snv.merge.sort.gathered.log 2>&1;

Would remove temporary output results/day/hg38_broad/other_reports/alignstats_bsummary.tsv
W--output truncated--