Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/48b8b93fb3831e505792e5a5125897/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/8467a0f89a3b28cafdce3f1ccefdce/Sig_18_tissue.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/48b8b93fb3831e505792e5a5125897/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/8467a0f89a3b28cafdce3f1ccefdce/Sig_18_tissue.md.bam
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i Sig_18_tissue.md.bam --algo AlignmentStat Sig_18_tissue.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo Sig_18_tissue.sentieon.insert_size_metrics --algo QualDistribution Sig_18_tissue.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle Sig_18_tissue.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle Sig_18_tissue.sentieon.quality_by_cycle_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:162000001, elapsed 0.0s, est remaining 0.5s, peak mem 78MB, user 0.1s, sys 0.3s, output queue size 17
progress 10% @chr2:73000001, elapsed 0.0s, est remaining 0.4s, peak mem 78MB, user 0.2s, sys 0.9s, output queue size 5
progress 15% @chr2:234000001, elapsed 0.1s, est remaining 0.4s, peak mem 78MB, user 0.3s, sys 1.5s, output queue size 10
progress 20% @chr3:154000001, elapsed 0.1s, est remaining 0.4s, peak mem 78MB, user 0.3s, sys 2.0s, output queue size 17
progress 25% @chr4:117000001, elapsed 0.1s, est remaining 0.3s, peak mem 78MB, user 0.4s, sys 2.6s, output queue size 15
progress 30% @chr5:87000001, elapsed 0.1s, est remaining 0.3s, peak mem 78MB, user 0.4s, sys 3.1s, output queue size 14
progress 35% @chr6:65000001, elapsed 0.2s, est remaining 0.3s, peak mem 78MB, user 0.6s, sys 3.7s, output queue size 3
progress 40% @chr7:57000001, elapsed 0.2s, est remaining 0.3s, peak mem 78MB, user 0.7s, sys 4.3s, output queue size 16
progress 45% @chr8:57000001, elapsed 0.2s, est remaining 0.2s, peak mem 78MB, user 0.9s, sys 4.8s, output queue size 4
progress 50% @chr9:73000001, elapsed 0.2s, est remaining 0.2s, peak mem 78MB, user 1.0s, sys 5.4s, output queue size 1
progress 55% @chr10:97000001, elapsed 0.2s, est remaining 0.2s, peak mem 78MB, user 1.1s, sys 5.9s, output queue size 8
progress 60% @chr11:123000001, elapsed 0.3s, est remaining 0.2s, peak mem 78MB, user 1.2s, sys 6.4s, output queue size 15
progress 65% @chr13:14000001, elapsed 0.3s, est remaining 0.2s, peak mem 78MB, user 1.3s, sys 6.8s, output queue size 1
progress 70% @chr14:63000001, elapsed 0.3s, est remaining 0.1s, peak mem 78MB, user 1.5s, sys 7.3s, output queue size 16
progress 75% @chr16:13000001, elapsed 0.3s, est remaining 0.1s, peak mem 78MB, user 1.5s, sys 7.9s, output queue size 11
progress 80% @chr18:1000001, elapsed 0.3s, est remaining 0.1s, peak mem 78MB, user 1.7s, sys 8.4s, output queue size 6
progress 85% @chr20:4000001, elapsed 0.4s, est remaining 0.1s, peak mem 78MB, user 1.9s, sys 9.0s, output queue size 18
progress 90% @chrX:45000001, elapsed 0.4s, est remaining 0.0s, peak mem 96MB, user 2.3s, sys 9.2s, output queue size 114
progress 95% @chrY:37000001, elapsed 0.5s, est remaining 0.0s, peak mem 108MB, user 2.9s, sys 9.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.2s, est remaining 0.0s, peak mem 120MB, user 6.0s, sys 10.3s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: AlignmentStat InsertSizeMetricAlgo QualDistribution BaseDistributionByCycle MeanQualityByCycle
license: sentieon:Metrics=31
input file size: 50047059
reads: 1001838
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.217 user 5.159 sys 6.516 real
done: 1 calls 0.000 user 0.000 sys 0.001 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.003 user 0.004 sys 1.246 real
idle: 77 calls 0.021 user 0.021 sys 52.056 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 125984768 mem 6.227 user 10.824 sys 2.293 real