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/e2/ac49834ce3228005de882431f9fbfe/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/ac49834ce3228005de882431f9fbfe/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/25dc077a00a8ba972f2936f02d2b56/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/9b/25dc077a00a8ba972f2936f02d2b56/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% @chr1:166000001, elapsed 0.0s, est remaining 0.5s, peak mem 78MB, user 0.1s, sys 0.4s, output queue size 13
progress 10% @chr2:79000001, elapsed 0.1s, est remaining 0.5s, peak mem 78MB, user 0.2s, sys 1.0s, output queue size 16
progress 15% @chr2:237000001, elapsed 0.1s, est remaining 0.4s, peak mem 78MB, user 0.3s, sys 1.6s, output queue size 9
progress 20% @chr3:152000001, elapsed 0.1s, est remaining 0.4s, peak mem 78MB, user 0.4s, sys 2.2s, output queue size 1
progress 25% @chr4:116000001, elapsed 0.1s, est remaining 0.4s, peak mem 78MB, user 0.5s, sys 2.7s, output queue size 10
progress 30% @chr5:89000001, elapsed 0.1s, est remaining 0.3s, peak mem 78MB, user 0.6s, sys 3.3s, output queue size 25
progress 35% @chr6:35000001, elapsed 0.2s, est remaining 0.3s, peak mem 78MB, user 0.6s, sys 4.0s, output queue size 30
progress 40% @chr7:60000001, elapsed 0.2s, est remaining 0.3s, peak mem 78MB, user 0.7s, sys 4.6s, output queue size 25
progress 45% @chr8:38000001, elapsed 0.2s, est remaining 0.3s, peak mem 78MB, user 0.8s, sys 5.2s, output queue size 21
progress 50% @chr9:74000001, elapsed 0.2s, est remaining 0.2s, peak mem 78MB, user 0.8s, sys 5.8s, output queue size 18
progress 55% @chr10:95000001, elapsed 0.3s, est remaining 0.2s, peak mem 78MB, user 0.9s, sys 6.5s, output queue size 5
progress 60% @chr11:122000001, elapsed 0.3s, est remaining 0.2s, peak mem 78MB, user 0.9s, sys 7.0s, output queue size 14
progress 65% @chr13:15000001, elapsed 0.3s, est remaining 0.2s, peak mem 78MB, user 1.0s, sys 7.6s, output queue size 19
progress 70% @chr14:54000001, elapsed 0.3s, est remaining 0.1s, peak mem 78MB, user 1.1s, sys 8.1s, output queue size 7
progress 75% @chr16:12000001, elapsed 0.3s, est remaining 0.1s, peak mem 78MB, user 1.2s, sys 8.9s, output queue size 1
progress 80% @chr17:82000001, elapsed 0.4s, est remaining 0.1s, peak mem 78MB, user 1.3s, sys 9.4s, output queue size 2
progress 85% @chr20:21000001, elapsed 0.4s, est remaining 0.1s, peak mem 78MB, user 1.4s, sys 9.9s, output queue size 1
progress 90% @chrX:44000001, elapsed 0.4s, est remaining 0.0s, peak mem 93MB, user 1.8s, sys 10.2s, output queue size 114
progress 95% @chrY:39000001, elapsed 0.5s, est remaining 0.0s, peak mem 108MB, user 2.5s, sys 10.5s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.2s, est remaining 0.0s, peak mem 132MB, user 5.4s, sys 10.8s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  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: 52290606
reads: 1001133
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.263 user 5.259 sys 6.912 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 0.001 user 0.001 sys 1.201 real
idle: 78 calls 0.015 user 0.020 sys 50.547 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 138502144 mem 5.765 user 11.489 sys 2.243 real