{
  "command": "bin/day_run produce_sentmm2ont_align produce_alignstats produce_na_dedup_cram -p -j 5 -k --rerun-triggers mtime",
  "completed_at": null,
  "exit_code": null,
  "repo_path": "/fsx/analysis_results/ubuntu/hybonly_ont_chipbarcode_limited_live_20260606T090222Z/daylily-omics-analysis",
  "session_name": "hybonly_ont_chipbarcode_limited_live_20260606T090222Z",
  "started_at": "2026-06-06T09:02:51Z"
}
DAY-EC activated.
DAY-EC activated.
        echo "INSTANCE TYPE: $itype" > results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont_sort.log;
        start_time=$(date +%s);
        ulimit -n 65536 || echo "ulimit mod failed";

        timestamp=$(date +%Y%m%d%H%M%S);
        export TMPDIR="/dev/shm/sentmm2ont_tmp_${timestamp}_$$";
        export SENTIEON_TMPDIR="$TMPDIR";
        mkdir -p "$TMPDIR";
        if [ ! -d "$TMPDIR" ]; then
            echo "ERROR: Failed to create TMPDIR: $TMPDIR" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;
            exit 5;
        fi
        echo "TMPDIR created: $TMPDIR" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;
        ls -ld "$TMPDIR" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;
        df -h /dev/shm >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;
        export APPTAINER_HOME="$TMPDIR";
        trap 'rm -rf "$TMPDIR" 2>/dev/null || true' EXIT;

        tdir="$TMPDIR";
        epocsec=$(date +'%s');

        # Find the jemalloc library in the active conda environment
        jemalloc_path="";
        for _dir in "$CONDA_PREFIX/lib" "$CONDA_PREFIX/lib64" "$CONDA_PREFIX/lib/x86_64-linux-gnu"; do
            if [[ -d "$_dir" ]]; then
                for _ext in so dylib; do
                    _candidate=$(find "$_dir" -maxdepth 1 -name "libjemalloc*.$_ext*" 2>/dev/null | head -n 1);
                    if [[ -n "$_candidate" && -r "$_candidate" ]]; then
                        jemalloc_path="$_candidate";
                        break 2;
                    fi
                done
            fi
        done

        # Check if jemalloc was found and set LD_PRELOAD accordingly
        if [[ -n "$jemalloc_path" ]]; then
            export LD_PRELOAD="$jemalloc_path";
            export MALLOC_CONF=background_thread:true,metadata_thp:auto,dirty_decay_ms:5000,muzzy_decay_ms:5000;
            echo "LD_PRELOAD set to: $LD_PRELOAD" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont_sort.log;
            echo "MALLOC_CONF set to: $MALLOC_CONF" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont_sort.log;
        else
            echo "libjemalloc not found in CONDA_PREFIX=$CONDA_PREFIX (searched lib, lib64, lib/x86_64-linux-gnu)." >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont_sort.log;
            echo "libjemalloc not found in CONDA_PREFIX=$CONDA_PREFIX (searched lib, lib64, lib/x86_64-linux-gnu).";
            exit 3;
        fi

        # Verify TMPDIR still exists before pipeline
        if [ ! -d "$tdir" ]; then
            echo "ERROR: TMPDIR disappeared before pipeline start: $tdir" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;
            exit 6;
        fi

        (
            if [[ "fastq" == "fastq" ]]; then
                for read_path in /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_0.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_1.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_10.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_11.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_12.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_13.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_14.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_15.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_16.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_17.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_18.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_19.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_2.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_20.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_21.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_22.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_23.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_24.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_25.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_26.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_27.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_28.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_29.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_3.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_30.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_31.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_32.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_33.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_34.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_35.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_36.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_37.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_38.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_39.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_4.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_40.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_41.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_42.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_43.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_44.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_45.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_46.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_47.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_48.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_49.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_5.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_50.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_51.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_52.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_53.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_54.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_55.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_56.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_57.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_58.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_59.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_6.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_60.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_61.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_62.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_63.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_64.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_65.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_66.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_67.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_68.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_69.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_7.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_70.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_71.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_72.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_8.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_9.fastq.gz; do
                    if [[ "$read_path" == *.gz || "$read_path" == *.bgz ]]; then
                        gzip -dc -- "$read_path";
                    else
                        cat -- "$read_path";
                    fi
                done;
            elif [[ "fastq" == "ubam" ]]; then
                samtools fastq -@ 4 -T MM,ML /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_0.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_1.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_10.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_11.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_12.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_13.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_14.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_15.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_16.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_17.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_18.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_19.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_2.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_20.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_21.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_22.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_23.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_24.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_25.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_26.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_27.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_28.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_29.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_3.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_30.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_31.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_32.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_33.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_34.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_35.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_36.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_37.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_38.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_39.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_4.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_40.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_41.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_42.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_43.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_44.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_45.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_46.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_47.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_48.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_49.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_5.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_50.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_51.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_52.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_53.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_54.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_55.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_56.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_57.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_58.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_59.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_6.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_60.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_61.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_62.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_63.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_64.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_65.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_66.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_67.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_68.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_69.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_7.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_70.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_71.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_72.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_8.fastq.gz /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode19/PBM13545_pass_barcode19_f3392d36_eb9b0a06_9.fastq.gz;
            else
                echo "ERROR: unsupported sentmm2ont input kind: fastq" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;
                exit 8;
            fi
        )           | LD_PRELOAD=$LD_PRELOAD /fsx/references/runtime_assets/cached_envs/sentieon-genomics-202503.02/bin/minimap2          -ax map-ont          -R '@RG\tID:ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION-$epocsec\tSM:ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION\tLB:ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION-LB-1\tPL:ONT\tPU:presumedCombinedLanes\tCN:CenterName\tPG:minimap2'         -t 160         /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.fasta         -  | mbuffer -m 32G -q -s 2M          | samtools sort         -l 1         -m 3G         -@ 32         -T "$tdir/srt"         -O CRAM         --reference /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.fasta         --write-index         -o results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.cram##idx##results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.cram.crai >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;

        end_time=$(date +%s);
        elapsed_time=$((($end_time - $start_time) / 60));
        echo "Elapsed-Time-min:	$itype	$elapsed_time" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/logs/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont_sort.log 2>&1;

        
Submitted job 18 with external jobid '855'.

[Sat Jun  6 09:03:15 2026]
rule sentmm2ont_align_sort:
    input: /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode20/PBM13545_pass_barcode20_f3392d36_eb9b0a06_0.fastq.gz, /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode20/PBM13545_pass_barcode20_f3392d36_eb9b0a06_1.fastq.gz, /fsx/run_dir_mounts/ont-4coriells-chip1/fastq_pass/barcode20/PBM13545_pass_barcode20_f3392d3--output truncated--
DAY-EC activated.
DAY-EC activated.
JOBID  PARTITION  CPUS  ST  NODELIST  MIN_CPUS  STATE  MIN_MEMORY  TIME  NODES  NAME
855  i192  192  CF  i192-dy-all-16  192  CONFIGURING  200000M  0:14  1  sentmm2ont_align_sort-ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION
856  i192  192  CF  i192-dy-all-17  192  CONFIGURING  200000M  0:14  1  sentmm2ont_align_sort-ONT-4Coriells-chip1-NA03986-DMPK-chip1-barcode20-chip1-PF-ONT-PROMETHION
852  i192  192  CF  i192-dy-all-2  192  CONFIGURING  200000M  0:15  1  sentmm2ont_align_sort-ONT-4Coriells-chip4-NA03986-DMPK-chip4-barcode20-chip4-PF-ONT-PROMETHION
853  i192  192  CF  i192-dy-all-4  192  CONFIGURING  200000M  0:15  1  sentmm2ont_align_sort-ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION
854  i192  192  CF  i192-dy-all-15  192  CONFIGURING  200000M  0:15  1  sentmm2ont_align_sort-ONT-4Coriells-chip2-NA03986-DMPK-chip2-barcode20-chip2-PF-ONT-PROMETHION
694  i192  8  R  i192-dy-all-3  8  RUNNING  16000M  1:33:56  1  haplocheck_vcf_contam_identity-20260526-LH01121-0004-B23WW2NLT4-NA00232-SMN-all-S46-PF-ILMN-NOVASEQ
620  i192  8  R  i192-dy-all-1  8  RUNNING  16000M  1:35:15  1  haplocheck_vcf_contam_identity-20260526-LH01121-0004-B23WW2NLT4-HG003-c-GIAB-all-S9-PF-ILMN-NOVASEQ
561  i192  8  R  i192-dy-all-5  8  RUNNING  16000M  1:36:15  1  haplocheck_vcf_contam_identity-20260526-LH01121-0004-B23WW2NLT4-HG003-a-GIAB-all-S7-PF-ILMN-NOVASEQ
487  i192  8  R  i192-dy-all-14  8  RUNNING  16000M  1:37:39  1  haplocheck_vcf_contam_identity-20260526-LH01121-0004-B23WW2NLT4-HG003-b-GIAB-all-S8-PF-ILMN-NOVASEQ
417  i192  8  R  i192-dy-all-1  8  RUNNING  16000M  1:39:49  1  haplocheck_vcf_contam_identity-20260526-LH01121-0004-B23WW2NLT4-NA09677-SMN-all-S47-PF-ILMN-NOVASEQ
351  i192  8  R  i192-dy-all-1  8  RUNNING  16000M  1:42:34  1  haplocheck_vcf_contam_identity-20260526-LH01121-0004-B23WW2NLT4-NA03986-DMPK-all-S48-PF-ILMN-NOVASEQ
256  i192  8  R  i192-dy-all-1  8  RUNNING  16000M  1:47:02  1  haplocheck_vcf_contam_identity-20260526-LH01121-0004-B23WW2NLT4-NA05164-DMPK-all-S49-PF-ILMN-NOVASEQ
