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/4e/a9e9080646b0a19ec368c51fb45704/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/2ebbced2538083c56e3a578610caa7/1029_BAE3-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/a9e9080646b0a19ec368c51fb45704/.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/f7/2ebbced2538083c56e3a578610caa7/1029_BAE3-N1-BDNA-1_B23KGCJLT4_1.md.bam
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i 1029_BAE3-N1-BDNA-1_B23KGCJLT4_1.md.bam --algo AlignmentStat 1029_BAE3-N1-BDNA-1_B23KGCJLT4_1.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo 1029_BAE3-N1-BDNA-1_B23KGCJLT4_1.sentieon.insert_size_metrics --algo QualDistribution 1029_BAE3-N1-BDNA-1_B23KGCJLT4_1.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle 1029_BAE3-N1-BDNA-1_B23KGCJLT4_1.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle 1029_BAE3-N1-BDNA-1_B23KGCJLT4_1.sentieon.quality_by_cycle_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:187000001, elapsed 2.7s, est remaining 50.5s, peak mem 1099MB, user 63.6s, sys 1.1s, output queue size 146
progress 10% @chr1:226000001, elapsed 4.9s, est remaining 43.7s, peak mem 1447MB, user 132.5s, sys 2.3s, output queue size 117
progress 15% @chr3:8000001, elapsed 7.3s, est remaining 41.1s, peak mem 1759MB, user 206.0s, sys 3.3s, output queue size 122
progress 20% @chr3:155000001, elapsed 9.4s, est remaining 37.8s, peak mem 1800MB, user 266.7s, sys 3.6s, output queue size 283
progress 25% @chr4:134000001, elapsed 11.4s, est remaining 34.3s, peak mem 1828MB, user 333.8s, sys 4.0s, output queue size 302
progress 30% @chr5:83000001, elapsed 13.0s, est remaining 30.4s, peak mem 1898MB, user 383.4s, sys 4.3s, output queue size 464
progress 35% @chr5:141000001, elapsed 15.4s, est remaining 28.6s, peak mem 1941MB, user 445.7s, sys 4.8s, output queue size 625
progress 40% @chr7:63000001, elapsed 18.0s, est remaining 27.1s, peak mem 2028MB, user 514.2s, sys 5.1s, output queue size 786
progress 45% @chr7:102000001, elapsed 21.3s, est remaining 26.0s, peak mem 2035MB, user 615.6s, sys 5.4s, output queue size 948
progress 50% @chr9:39000001, elapsed 24.0s, est remaining 24.0s, peak mem 2084MB, user 691.7s, sys 5.7s, output queue size 366
progress 55% @chr10:118000001, elapsed 27.3s, est remaining 22.3s, peak mem 2114MB, user 795.5s, sys 6.2s, output queue size 527
progress 60% @chr11:117000001, elapsed 30.8s, est remaining 20.5s, peak mem 2114MB, user 899.4s, sys 6.6s, output queue size 510
progress 65% @chr12:102000001, elapsed 33.8s, est remaining 18.2s, peak mem 2130MB, user 993.5s, sys 7.0s, output queue size 672
progress 70% @chr14:71000001, elapsed 35.7s, est remaining 15.3s, peak mem 2132MB, user 1056.1s, sys 7.3s, output queue size 833
progress 75% @chr16:42000001, elapsed 39.2s, est remaining 13.1s, peak mem 2209MB, user 1151.7s, sys 7.8s, output queue size 995
progress 80% @chr18:29000001, elapsed 44.0s, est remaining 11.0s, peak mem 2277MB, user 1266.6s, sys 8.3s, output queue size 1157
progress 85% @chr20:23000001, elapsed 48.5s, est remaining 8.6s, peak mem 2278MB, user 1429.6s, sys 8.9s, output queue size 1319
progress 90% @chrX:43000001, elapsed 51.5s, est remaining 5.7s, peak mem 2329MB, user 1543.6s, sys 9.3s, output queue size 513
progress 95% @chrY:54000001, elapsed 53.6s, est remaining 2.8s, peak mem 2352MB, user 1601.3s, sys 9.5s, output queue size 675
progress 100% @chrX:67000001, elapsed 62.1s, est remaining 0.0s, peak mem 2367MB, user 1696.6s, sys 9.9s, output queue size 3540
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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 192
algo: AlignmentStat InsertSizeMetricAlgo QualDistribution BaseDistributionByCycle MeanQualityByCycle
license: sentieon:Metrics=31
input file size: 16852621513
reads: 355692431
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 307.340 user 6.732 sys 312.268 real
done: 1 calls 0.013 user 0.000 sys 0.014 real
exec_no_coor: 1 calls 0.000 user 0.002 sys 0.006 real
execute: 1 calls 0.006 user 0.002 sys 62.250 real
idle: 277 calls 0.139 user 0.001 sys 252.548 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 2482343936 mem 1698.654 user 9.988 sys 63.366 real