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/75/dc00e06cb6c0ba1b2e646f8d77ef31/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/dc00e06cb6c0ba1b2e646f8d77ef31/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/e4074af2c587ac87b9ca741e5cecc9/1029_0W2-N1-BDNA-1_B23KGCJLT4_1.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/f5/e4074af2c587ac87b9ca741e5cecc9/1029_0W2-N1-BDNA-1_B23KGCJLT4_1.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 1029_0W2-N1-BDNA-1_B23KGCJLT4_1.md.bam --algo AlignmentStat 1029_0W2-N1-BDNA-1_B23KGCJLT4_1.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo 1029_0W2-N1-BDNA-1_B23KGCJLT4_1.sentieon.insert_size_metrics --algo QualDistribution 1029_0W2-N1-BDNA-1_B23KGCJLT4_1.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle 1029_0W2-N1-BDNA-1_B23KGCJLT4_1.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle 1029_0W2-N1-BDNA-1_B23KGCJLT4_1.sentieon.quality_by_cycle_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:181000001, elapsed 2.2s, est remaining 41.6s, peak mem 908MB, user 51.2s, sys 0.7s, output queue size 146
progress 10% @chr2:46000001, elapsed 3.9s, est remaining 35.4s, peak mem 1179MB, user 109.3s, sys 1.2s, output queue size 117
progress 15% @chr3:18000001, elapsed 6.0s, est remaining 33.8s, peak mem 1770MB, user 166.4s, sys 1.8s, output queue size 203
progress 20% @chr3:178000001, elapsed 7.7s, est remaining 30.8s, peak mem 1845MB, user 221.6s, sys 2.5s, output queue size 174
progress 25% @chr4:98000001, elapsed 9.2s, est remaining 27.6s, peak mem 1845MB, user 269.4s, sys 2.8s, output queue size 302
progress 30% @chr5:106000001, elapsed 10.4s, est remaining 24.2s, peak mem 1877MB, user 304.6s, sys 3.0s, output queue size 464
progress 35% @chr6:79000001, elapsed 12.1s, est remaining 22.4s, peak mem 1910MB, user 351.4s, sys 3.4s, output queue size 625
progress 40% @chr7:79000001, elapsed 14.0s, est remaining 21.0s, peak mem 2032MB, user 402.7s, sys 3.7s, output queue size 786
progress 45% @chr8:74000001, elapsed 16.2s, est remaining 19.8s, peak mem 2061MB, user 478.1s, sys 4.0s, output queue size 204
progress 50% @chr9:81000001, elapsed 18.0s, est remaining 18.0s, peak mem 2061MB, user 523.8s, sys 4.2s, output queue size 366
progress 55% @chr10:73000001, elapsed 20.1s, est remaining 16.5s, peak mem 2083MB, user 589.1s, sys 4.5s, output queue size 527
progress 60% @chr11:65000001, elapsed 22.3s, est remaining 14.9s, peak mem 2090MB, user 661.6s, sys 4.9s, output queue size 510
progress 65% @chr12:106000001, elapsed 24.4s, est remaining 13.1s, peak mem 2104MB, user 719.9s, sys 5.4s, output queue size 672
progress 70% @chr14:69000001, elapsed 25.7s, est remaining 11.0s, peak mem 2109MB, user 755.6s, sys 5.6s, output queue size 833
progress 75% @chr16:41000001, elapsed 28.3s, est remaining 9.4s, peak mem 2156MB, user 822.0s, sys 6.2s, output queue size 995
progress 80% @chr18:9000001, elapsed 31.8s, est remaining 8.0s, peak mem 2177MB, user 935.4s, sys 7.3s, output queue size 623
progress 85% @chr20:23000001, elapsed 34.9s, est remaining 6.2s, peak mem 2177MB, user 1048.3s, sys 8.0s, output queue size 351
progress 90% @chrX:36000001, elapsed 36.7s, est remaining 4.1s, peak mem 2189MB, user 1102.3s, sys 8.3s, output queue size 513
progress 95% @chrY:53000001, elapsed 37.8s, est remaining 2.0s, peak mem 2213MB, user 1138.0s, sys 8.7s, output queue size 675
progress 100% @chr22:23000001, elapsed 42.1s, est remaining 0.0s, peak mem 2270MB, user 1187.7s, sys 9.0s, output queue size 3635
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 192
algo: AlignmentStat InsertSizeMetricAlgo QualDistribution BaseDistributionByCycle MeanQualityByCycle
license: sentieon:Metrics=31
input file size: 15384196355
reads: 298726454
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 245.670 user 5.803 sys 250.509 real
done: 1 calls 0.006 user 0.000 sys 0.014 real
exec_no_coor: 1 calls 0.001 user 0.000 sys 0.003 real
execute: 1 calls 0.003 user 0.003 sys 42.209 real
idle: 160 calls 0.181 user 0.001 sys 138.047 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 2380566528 mem 1189.603 user 9.119 sys 43.237 real