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/c242640440ac643f310ec017c4c7ac/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/c242640440ac643f310ec017c4c7ac/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/bbd12b88b5b205c4c95cb8bf8866c9/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/e4/bbd12b88b5b205c4c95cb8bf8866c9/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% @chr1:161000001, elapsed 0.0s, est remaining 0.5s, peak mem 81MB, user 0.0s, sys 0.3s, output queue size 14
progress 10% @chr2:75000001, elapsed 0.0s, est remaining 0.4s, peak mem 81MB, user 0.1s, sys 0.8s, output queue size 12
progress 15% @chr2:234000001, elapsed 0.1s, est remaining 0.4s, peak mem 81MB, user 0.2s, sys 1.4s, output queue size 2
progress 20% @chr3:155000001, elapsed 0.1s, est remaining 0.4s, peak mem 81MB, user 0.2s, sys 2.0s, output queue size 8
progress 25% @chr4:96000001, elapsed 0.1s, est remaining 0.3s, peak mem 81MB, user 0.3s, sys 2.6s, output queue size 19
progress 30% @chr5:67000001, elapsed 0.1s, est remaining 0.3s, peak mem 81MB, user 0.3s, sys 3.3s, output queue size 19
progress 35% @chr6:65000001, elapsed 0.2s, est remaining 0.3s, peak mem 81MB, user 0.4s, sys 3.8s, output queue size 14
progress 40% @chr7:55000001, elapsed 0.2s, est remaining 0.3s, peak mem 81MB, user 0.5s, sys 4.4s, output queue size 7
progress 45% @chr8:58000001, elapsed 0.2s, est remaining 0.2s, peak mem 81MB, user 0.5s, sys 5.0s, output queue size 22
progress 50% @chr9:75000001, elapsed 0.2s, est remaining 0.2s, peak mem 81MB, user 0.5s, sys 5.6s, output queue size 16
progress 55% @chr10:97000001, elapsed 0.2s, est remaining 0.2s, peak mem 81MB, user 0.6s, sys 6.2s, output queue size 10
progress 60% @chr11:123000001, elapsed 0.3s, est remaining 0.2s, peak mem 81MB, user 0.6s, sys 6.7s, output queue size 18
progress 65% @chr13:15000001, elapsed 0.3s, est remaining 0.1s, peak mem 81MB, user 0.7s, sys 7.3s, output queue size 14
progress 70% @chr14:61000001, elapsed 0.3s, est remaining 0.1s, peak mem 81MB, user 0.8s, sys 7.8s, output queue size 11
progress 75% @chr16:13000001, elapsed 0.3s, est remaining 0.1s, peak mem 81MB, user 0.9s, sys 8.3s, output queue size 20
progress 80% @chr17:60000001, elapsed 0.3s, est remaining 0.1s, peak mem 81MB, user 0.9s, sys 8.9s, output queue size 24
progress 85% @chr20:24000001, elapsed 0.4s, est remaining 0.1s, peak mem 81MB, user 0.9s, sys 9.4s, output queue size 15
progress 90% @chrX:39000001, elapsed 0.4s, est remaining 0.0s, peak mem 106MB, user 1.3s, sys 9.8s, output queue size 114
progress 95% @chrY:41000001, elapsed 0.4s, est remaining 0.0s, peak mem 124MB, user 1.9s, sys 10.1s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.1s, est remaining 0.0s, peak mem 160MB, user 4.9s, sys 10.4s, 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 192
algo: AlignmentStat InsertSizeMetricAlgo QualDistribution BaseDistributionByCycle MeanQualityByCycle
license: sentieon:Metrics=31
input file size: 52290598
reads: 1001133
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.220 user 5.169 sys 6.600 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 0.003 sys 1.160 real
idle: 75 calls 0.026 user 0.043 sys 50.495 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 168529920 mem 5.082 user 11.011 sys 2.212 real