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/35/97e37b1c619f2c369e709c06c53ed4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/97e37b1c619f2c369e709c06c53ed4/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/bbf3839dfd2c68f28e02f3d64e69ad/Sig_18_Blood.md.bam
  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/5b/bbf3839dfd2c68f28e02f3d64e69ad/Sig_18_Blood.md.bam.bai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i Sig_18_Blood.md.bam --algo AlignmentStat Sig_18_Blood.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo Sig_18_Blood.sentieon.insert_size_metrics --algo QualDistribution Sig_18_Blood.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle Sig_18_Blood.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle Sig_18_Blood.sentieon.quality_by_cycle_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:164000001, elapsed 0.0s, est remaining 0.4s, peak mem 81MB, user 0.1s, sys 0.3s, output queue size 30
progress 10% @chr2:72000001, elapsed 0.0s, est remaining 0.4s, peak mem 81MB, user 0.1s, sys 0.9s, output queue size 1
progress 15% @chr2:235000001, elapsed 0.1s, est remaining 0.3s, peak mem 81MB, user 0.2s, sys 1.4s, output queue size 43
progress 20% @chr3:154000001, elapsed 0.1s, est remaining 0.3s, peak mem 81MB, user 0.3s, sys 1.8s, output queue size 1
progress 25% @chr4:114000001, elapsed 0.1s, est remaining 0.3s, peak mem 81MB, user 0.3s, sys 2.3s, output queue size 3
progress 30% @chr5:87000001, elapsed 0.1s, est remaining 0.3s, peak mem 81MB, user 0.4s, sys 2.7s, output queue size 28
progress 35% @chr6:64000001, elapsed 0.1s, est remaining 0.3s, peak mem 81MB, user 0.5s, sys 3.2s, output queue size 1
progress 40% @chr7:56000001, elapsed 0.2s, est remaining 0.2s, peak mem 81MB, user 0.5s, sys 3.8s, output queue size 3
progress 45% @chr8:38000001, elapsed 0.2s, est remaining 0.2s, peak mem 81MB, user 0.6s, sys 4.3s, output queue size 19
progress 50% @chr9:71000001, elapsed 0.2s, est remaining 0.2s, peak mem 81MB, user 0.7s, sys 4.7s, output queue size 3
progress 55% @chr10:99000001, elapsed 0.2s, est remaining 0.2s, peak mem 81MB, user 0.8s, sys 5.2s, output queue size 6
progress 60% @chr11:119000001, elapsed 0.2s, est remaining 0.2s, peak mem 81MB, user 0.9s, sys 5.8s, output queue size 16
progress 65% @chr13:20000001, elapsed 0.3s, est remaining 0.1s, peak mem 81MB, user 1.0s, sys 6.3s, output queue size 4
progress 70% @chr14:62000001, elapsed 0.3s, est remaining 0.1s, peak mem 81MB, user 1.0s, sys 6.8s, output queue size 6
progress 75% @chr16:15000001, elapsed 0.3s, est remaining 0.1s, peak mem 81MB, user 1.1s, sys 7.3s, output queue size 11
progress 80% @chr18:1, elapsed 0.3s, est remaining 0.1s, peak mem 81MB, user 1.2s, sys 7.8s, output queue size 11
progress 85% @chr20:19000001, elapsed 0.3s, est remaining 0.1s, peak mem 81MB, user 1.3s, sys 8.3s, output queue size 13
progress 90% @chrX:45000001, elapsed 0.4s, est remaining 0.0s, peak mem 103MB, user 1.9s, sys 8.6s, output queue size 114
progress 95% @chrY:44000001, elapsed 0.4s, est remaining 0.0s, peak mem 115MB, user 2.3s, sys 8.8s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.3s, est remaining 0.0s, peak mem 154MB, user 6.5s, sys 8.9s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31 max 192
algo: AlignmentStat InsertSizeMetricAlgo QualDistribution BaseDistributionByCycle MeanQualityByCycle
license: sentieon:Metrics=31
input file size: 52290603
reads: 1001133
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.733 user 4.349 sys 6.267 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 0.001 sys 1.307 real
idle: 82 calls 0.038 user 0.040 sys 54.850 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 162291712 mem 6.818 user 9.507 sys 2.357 real