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/32/80400a96cb7dabd96ddd514cfcc172/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/115b64305d060833379ba5675af81f/Sig_18_tissue.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/80400a96cb7dabd96ddd514cfcc172/.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/ab/115b64305d060833379ba5675af81f/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 0.1s, est remaining 1.0s, peak mem 78MB, user 0.1s, sys 1.2s, output queue size 6
progress 10% @chr2:76000001, elapsed 0.1s, est remaining 0.9s, peak mem 78MB, user 0.2s, sys 2.5s, output queue size 13
progress 15% @chr2:234000001, elapsed 0.1s, est remaining 0.8s, peak mem 78MB, user 0.3s, sys 3.8s, output queue size 22
progress 20% @chr3:155000001, elapsed 0.2s, est remaining 0.8s, peak mem 78MB, user 0.4s, sys 5.1s, output queue size 14
progress 25% @chr4:107000001, elapsed 0.3s, est remaining 0.8s, peak mem 78MB, user 0.5s, sys 6.7s, output queue size 15
progress 30% @chr5:81000001, elapsed 0.3s, est remaining 0.7s, peak mem 78MB, user 0.6s, sys 8.6s, output queue size 15
progress 35% @chr6:59000001, elapsed 0.4s, est remaining 0.7s, peak mem 78MB, user 0.7s, sys 10.3s, output queue size 37
progress 40% @chr7:54000001, elapsed 0.4s, est remaining 0.6s, peak mem 78MB, user 0.8s, sys 12.1s, output queue size 6
progress 45% @chr8:60000001, elapsed 0.5s, est remaining 0.6s, peak mem 78MB, user 0.9s, sys 13.2s, output queue size 1
progress 50% @chr9:59000001, elapsed 0.5s, est remaining 0.5s, peak mem 78MB, user 1.0s, sys 14.4s, output queue size 28
progress 55% @chr10:96000001, elapsed 0.6s, est remaining 0.5s, peak mem 78MB, user 1.1s, sys 15.6s, output queue size 12
progress 60% @chr11:123000001, elapsed 0.6s, est remaining 0.4s, peak mem 78MB, user 1.2s, sys 16.8s, output queue size 5
progress 65% @chr13:13000001, elapsed 0.6s, est remaining 0.3s, peak mem 78MB, user 1.3s, sys 18.0s, output queue size 2
progress 70% @chr14:63000001, elapsed 0.7s, est remaining 0.3s, peak mem 78MB, user 1.4s, sys 19.3s, output queue size 7
progress 75% @chr16:12000001, elapsed 0.7s, est remaining 0.2s, peak mem 78MB, user 1.4s, sys 20.6s, output queue size 5
progress 80% @chr17:82000001, elapsed 0.8s, est remaining 0.2s, peak mem 78MB, user 1.5s, sys 21.9s, output queue size 2
progress 85% @chr20:21000001, elapsed 0.8s, est remaining 0.1s, peak mem 78MB, user 1.5s, sys 23.2s, output queue size 3
progress 90% @chrX:43000001, elapsed 0.9s, est remaining 0.1s, peak mem 96MB, user 2.1s, sys 23.7s, output queue size 114
progress 95% @chrY:40000001, elapsed 0.9s, est remaining 0.0s, peak mem 108MB, user 2.9s, sys 24.3s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.7s, est remaining 0.0s, peak mem 120MB, user 5.8s, sys 25.2s, 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: 50047057
reads: 1001838
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.125 user 12.426 sys 14.338 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 0.005 user 0.005 sys 1.713 real
idle: 79 calls 0.014 user 0.014 sys 51.918 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 125927424 mem 6.050 user 25.767 sys 2.760 real