DAY-EC activated.
DAY-EC activated.
session=hybonly_ont_kitchensink_rest_20260606T102845Z
tmux=present
0: bash* (1 panes) [80x24] [layout 5965,80x24,0,0,16] @16 (active)
0: [80x24] [history 1599/2000, 562193 bytes] %16 (active)
capture_tail:
        fi

        # --- bin/dayoa_sentieon_cli dnascope-longread (ONT) ---
        # The CLI runs the full two-pass phased pipeline internally.
        # Outputs: <basename>.vcf.gz (SNV/indel) and <basename>.sv.vcf.gz (SV)
        cli_out="$TMPDIR/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-P
F-ONT-PROMETHION.sentmm2ont.sentdont";

        echo "bin/dayoa_sentieon_cli dnascope-longread starting: model=/fsx/refe
rences/runtime_assets/cached_envs/sentieon-genomics-202503.02/bundles/DNAscopeON
T2.2.bundle/DNAscopeONT2.2.bundle tech=ONT" >> results/day/hg38_broad/ONT-4Corie
lls-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/n
a/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-
PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
        echo "bin/dayoa_sentieon_cli dnascope-longread retain_tmpdir enabled; TM
PDIR=$TMPDIR" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-ba
rcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriel
ls-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentd
ont.snv.log 2>&1;
        set +e;
        bin/dayoa_sentieon_cli dnascope-longread             -r /fsx/references/
genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.fa
sta             -i results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-
barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/ONT-4Coriells-chip1-NA0967
7-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.cram             -m
"/fsx/references/runtime_assets/cached_envs/sentieon-genomics-202503.02/bundles/
DNAscopeONT2.2.bundle/DNAscopeONT2.2.bundle"             -d "/fsx/references/gen
omic_data/organism_references/H_sapiens/panhg38/pop-v20g41-20251216.vcf.gz"
        -t 191             --tech ONT             --retain_tmpdir              -
b /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/hg38_dip
loid_male.bed   --haploid_bed /fsx/references/genomic_data/organism_references/H
_sapiens/hg38_broad/hg38_haploid_male.bed              "${cli_out}.vcf.gz" >> re
sults/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ON
T-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SM
N-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;

        cli_rc=$?;
        set -e;
        echo "sentieon-cli exit code: $cli_rc" >> results/day/hg38_broad/ONT-4Co
riells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2on
t/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-O
NT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
        if [ $cli_rc -ne 0 ]; then
            echo "ERROR: bin/dayoa_sentieon_cli dnascope-longread failed with ex
it code $cli_rc" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1
-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Cor
iells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.se
ntdont.snv.log 2>&1;
            exit $cli_rc;
        fi

        # --- Reheader SNV VCF: rename sample to cluster_sample ---
        if [ -f "${cli_out}.vcf.gz" ]; then
            oldname=$(bcftools query -l "${cli_out}.vcf.gz" | head -n1);
            echo -e "${oldname} ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-
chip1-PF-ONT-PROMETHION" > "$TMPDIR/rename.txt";
            bcftools reheader -s "$TMPDIR/rename.txt" -o results/day/hg38_broad/
ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/se
ntmm2ont/na/snv/sentdont/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-P
F-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.sort.vcf.gz "${cli_out}.vcf.gz" >> r
esults/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-O
NT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-S
MN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
            bcftools index -f -t --threads 191 -o results/day/hg38_broad/ONT-4Co
riells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2on
t/na/snv/sentdont/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-P
ROMETHION.sentmm2ont.na.sentdont.snv.sort.vcf.gz.tbi results/day/hg38_broad/ONT-
4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm
2ont/na/snv/sentdont/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ON
T-PROMETHION.sentmm2ont.na.sentdont.snv.sort.vcf.gz >> results/day/hg38_broad/ON
T-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sent
mm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1
-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
        else
            echo "ERROR: SNV VCF not produced by sentieon-cli" >> results/day/hg
38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION
/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barc
ode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
            exit 20;
        fi

        # --- Reheader SV VCF ---
        if [ -f "${cli_out}.sv.vcf.gz" ]; then
            bcftools reheader -s "$TMPDIR/rename.txt" -o results/day/hg38_broad/
ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/se
ntmm2ont/na/snv/sentdont/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-P
F-ONT-PROMETHION.sentmm2ont.na.sentdont.sv.vcf.gz "${cli_out}.sv.vcf.gz" >> resu
lts/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-
PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-
chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
            bcftools index -f -t --threads 191 -o results/day/hg38_broad/ONT-4Co
riells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2on
t/na/snv/sentdont/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-P
ROMETHION.sentmm2ont.na.sentdont.sv.vcf.gz.tbi results/day/hg38_broad/ONT-4Corie
lls-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/n
a/snv/sentdont/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROM
ETHION.sentmm2ont.na.sentdont.sv.vcf.gz >> results/day/hg38_broad/ONT-4Coriells-
chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/sn
v/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROM
ETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
        else
            echo "WARNING: SV VCF not produced; creating empty placeholder" >> r
esults/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-O
NT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-S
MN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
            touch results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-b
arcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/ONT-4Coriells-
chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont
.sv.vcf.gz results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode1
9-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/ONT-4Coriells-chip1-N
A09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.sv.vcf
.gz.tbi;
        fi

        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/s
entmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-ch
ip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;


Submitted job 164 with external jobid '896'.

tmux_log=/home/ubuntu/daylily-runs/hybonly_ont_kitchensink_rest_20260606T102845Z/tmux.log
tmux_log_tail:
        echo "sentieon-cli exit code: $cli_rc" >> results/day/hg38_broad/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
        if [ $cli_rc -ne 0 ]; then
            echo "ERROR: bin/dayoa_sentieon_cli dnascope-longread failed with exit code $cli_rc" >> results/day/hg38_broad/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
            exit $cli_rc;
        fi

        # --- Reheader SNV VCF: rename sample to cluster_sample ---
        if [ -f "${cli_out}.vcf.gz" ]; then
            oldname=$(bcftools query -l "${cli_out}.vcf.gz" | head -n1);
            echo -e "${oldname}	ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION" > "$TMPDIR/rename.txt";
            bcftools reheader -s "$TMPDIR/rename.txt" -o results/day/hg38_broad/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.sort.vcf.gz "${cli_out}.vcf.gz" >> results/day/hg38_broad/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
            bcftools index -f -t --threads 191 -o results/day/hg38_broad/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.sort.vcf.gz.tbi results/day/hg38_broad/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.sort.vcf.gz >> results/day/hg38_broad/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
        else
            echo "ERROR: SNV VCF not produced by sentieon-cli" >> results/day/hg38_broad/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
            exit 20;
        fi

        # --- Reheader SV VCF ---
        if [ -f "${cli_out}.sv.vcf.gz" ]; then
            bcftools reheader -s "$TMPDIR/rename.txt" -o results/day/hg38_broad/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.sv.vcf.gz "${cli_out}.sv.vcf.gz" >> results/day/hg38_broad/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
            bcftools index -f -t --threads 191 -o results/day/hg38_broad/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.sv.vcf.gz.tbi results/day/hg38_broad/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.sv.vcf.gz >> results/day/hg38_broad/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
        else
            echo "WARNING: SV VCF not produced; creating empty placeholder" >> results/day/hg38_broad/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
            touch results/day/hg38_broad/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.sv.vcf.gz results/day/hg38_broad/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.sv.vcf.gz.tbi;
        fi

        end_time=$(date +%s);
        elapsed_time=$((($end_time - $start_time) / 60));
        echo "Elapsed-Time-min:	$itype	$elapsed_time" >> results/day/hg38_broad/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip2-NA09677-SMN-chip2-barcode19-chip2-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;

        [0m
[33mSubmitted job 172 with external jobid '895'.[0m
[32m[0m
[32m[Sat Jun  6 10:29:17 2026][0m
[32mrule sent_snv_ont:
    input: results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.cram, results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.cram.crai
    output: results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.sort.vcf.gz, results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.sort.vcf.gz.tbi, results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.sv.vcf.gz, results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.sv.vcf.gz.tbi
    log: results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log
    jobid: 164
    benchmark: results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/benchmarks/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.bench.tsv
    reason: Missing output files: results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.sort.vcf.gz, results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.sort.vcf.gz.tbi
    wildcards: sample=ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION, alnr=sentmm2ont, ddup=na
    priority: 45
    threads: 191
    resources: mem_mb=300000, mem_mib=286103, disk_mb=1000, disk_mib=954, tmpdir=<TBD>, threads=191, time=5440, partition=i192mem,i192bigmem, vcpu=191, distribution=block, exclusive=, constraint=, exclude=, include=, attempt_n=1[0m
[32m[0m
[33m
        export PATH=$PATH:/fsx/references/runtime_assets/cached_envs/sentieon-genomics-202503.02/bin/
        timestamp=$(date +%Y%m%d%H%M%S)_$$;

        export TMPDIR=/dev/shm/sentdont_tmp_$timestamp;
        export SENTIEON_TMPDIR=$TMPDIR;
        mkdir -p $TMPDIR;
        export APPTAINER_HOME=$TMPDIR;
        trap 'status=$?; keep_tmp="False"; if [ "$keep_tmp" = "True" ] || [ "$keep_tmp" = "true" ] || [ "$keep_tmp" = "1" ]; then echo "Retaining sentdont TMPDIR because sentdont.keep_tmp_dirs=true: $TMPDIR" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1; df -h /dev/shm >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1 || true; else rm -rf "$TMPDIR" 2>/dev/null || true; fi; trap - EXIT; exit "$status"' EXIT;

        if [ -z "$SENTIEON_LICENSE" ]; then
            echo "SENTIEON_LICENSE not set." >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
            exit 3;
        fi

        if [ ! -f "$SENTIEON_LICENSE" ]; then
            echo "SENTIEON_LICENSE file not found: '$SENTIEON_LICENSE'" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.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 "INSTANCE TYPE: $itype" > results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log;
        start_time=$(date +%s);

        ulimit -n 65536 || echo "ulimit mod failed" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;

        # Find jemalloc 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

        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/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log;
            echo "MALLOC_CONF set to: $MALLOC_CONF" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log;
        else
            echo "WARNING: libjemalloc not found in CONDA_PREFIX=$CONDA_PREFIX" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log;
        fi

        # --- bin/dayoa_sentieon_cli dnascope-longread (ONT) ---
        # The CLI runs the full two-pass phased pipeline internally.
        # Outputs: <basename>.vcf.gz (SNV/indel) and <basename>.sv.vcf.gz (SV)
        cli_out="$TMPDIR/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.sentdont";

        echo "bin/dayoa_sentieon_cli dnascope-longread starting: model=/fsx/references/runtime_assets/cached_envs/sentieon-genomics-202503.02/bundles/DNAscopeONT2.2.bundle/DNAscopeONT2.2.bundle tech=ONT" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
        echo "bin/dayoa_sentieon_cli dnascope-longread retain_tmpdir enabled; TMPDIR=$TMPDIR" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
        set +e;
        bin/dayoa_sentieon_cli dnascope-longread             -r /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/Homo_sapiens_assembly38.fasta             -i results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.cram             -m "/fsx/references/runtime_assets/cached_envs/sentieon-genomics-202503.02/bundles/DNAscopeONT2.2.bundle/DNAscopeONT2.2.bundle"             -d "/fsx/references/genomic_data/organism_references/H_sapiens/panhg38/pop-v20g41-20251216.vcf.gz"             -t 191             --tech ONT             --retain_tmpdir              -b /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/hg38_diploid_male.bed   --haploid_bed /fsx/references/genomic_data/organism_references/H_sapiens/hg38_broad/hg38_haploid_male.bed              "${cli_out}.vcf.gz" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;

        cli_rc=$?;
        set -e;
        echo "sentieon-cli exit code: $cli_rc" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION.sentmm2ont.na.sentdont.snv.log 2>&1;
        if [ $cli_rc -ne 0 ]; then
            echo "ERROR: bin/dayoa_sentieon_cli dnascope-longread failed with exit code $cli_rc" >> results/day/hg38_broad/ONT-4Coriells-chip1-NA09677-SMN-chip1-barcode19-chip1-PF-ONT-PROMETHION/align/sentmm2ont/na/snv/sentdont/log/ONT-4Coriells-chip1-NA09677-SMN-chip1-barco--output truncated--