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/13/0837493c0d08d538b780f1d4f40b73/1029_D5N-N1-BDNA-1_B23KGCJLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/dd698cf81ea94d2d27dbee844f4b94/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/dd698cf81ea94d2d27dbee844f4b94/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/0837493c0d08d538b780f1d4f40b73/1029_D5N-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i 1029_D5N-N1-BDNA-1_B23KGCJLT4_1.md.bam --algo AlignmentStat 1029_D5N-N1-BDNA-1_B23KGCJLT4_1.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo 1029_D5N-N1-BDNA-1_B23KGCJLT4_1.sentieon.insert_size_metrics --algo QualDistribution 1029_D5N-N1-BDNA-1_B23KGCJLT4_1.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle 1029_D5N-N1-BDNA-1_B23KGCJLT4_1.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle 1029_D5N-N1-BDNA-1_B23KGCJLT4_1.sentieon.quality_by_cycle_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:188000001, elapsed 2.1s, est remaining 39.0s, peak mem 862MB, user 48.0s, sys 0.6s, output queue size 146
progress 10% @chr2:70000001, elapsed 3.8s, est remaining 34.2s, peak mem 1196MB, user 102.0s, sys 1.1s, output queue size 117
progress 15% @chr3:16000001, elapsed 5.7s, est remaining 32.4s, peak mem 1519MB, user 161.0s, sys 1.7s, output queue size 122
progress 20% @chr3:175000001, elapsed 7.6s, est remaining 30.3s, peak mem 1567MB, user 215.7s, sys 2.0s, output queue size 174
progress 25% @chr4:133000001, elapsed 9.3s, est remaining 27.8s, peak mem 1567MB, user 269.8s, sys 2.4s, output queue size 302
progress 30% @chr5:79000001, elapsed 10.7s, est remaining 24.9s, peak mem 1589MB, user 310.1s, sys 2.7s, output queue size 464
progress 35% @chr6:44000001, elapsed 12.6s, est remaining 23.4s, peak mem 1612MB, user 367.5s, sys 3.1s, output queue size 625
progress 40% @chr7:65000001, elapsed 14.9s, est remaining 22.3s, peak mem 1656MB, user 423.2s, sys 3.3s, output queue size 786
progress 45% @chr8:82000001, elapsed 17.5s, est remaining 21.4s, peak mem 1671MB, user 513.5s, sys 3.8s, output queue size 261
progress 50% @chr9:42000001, elapsed 19.9s, est remaining 19.9s, peak mem 1713MB, user 575.7s, sys 4.1s, output queue size 366
progress 55% @chr10:118000001, elapsed 22.7s, est remaining 18.6s, peak mem 1754MB, user 659.4s, sys 4.5s, output queue size 527
progress 60% @chr11:117000001, elapsed 25.5s, est remaining 17.0s, peak mem 1757MB, user 741.9s, sys 4.8s, output queue size 689
progress 65% @chr13:23000001, elapsed 28.3s, est remaining 15.2s, peak mem 1757MB, user 830.1s, sys 5.2s, output queue size 672
progress 70% @chr14:85000001, elapsed 29.9s, est remaining 12.8s, peak mem 1757MB, user 877.1s, sys 5.4s, output queue size 833
progress 75% @chr16:41000001, elapsed 32.6s, est remaining 10.9s, peak mem 1779MB, user 959.0s, sys 5.7s, output queue size 995
progress 80% @chr18:25000001, elapsed 36.7s, est remaining 9.2s, peak mem 1812MB, user 1077.5s, sys 6.2s, output queue size 623
progress 85% @chr20:9000001, elapsed 40.2s, est remaining 7.1s, peak mem 1812MB, user 1207.7s, sys 6.6s, output queue size 351
progress 90% @chrX:36000001, elapsed 42.1s, est remaining 4.7s, peak mem 1819MB, user 1271.5s, sys 6.8s, output queue size 513
progress 95% @chrY:52000001, elapsed 43.3s, est remaining 2.3s, peak mem 1819MB, user 1304.6s, sys 7.1s, output queue size 675
progress 100% @chr22:23000001, elapsed 47.8s, est remaining 0.0s, peak mem 1821MB, user 1359.9s, sys 7.3s, output queue size 3635
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: 13575943775
reads: 276873939
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 260.009 user 5.283 sys 264.168 real
done: 1 calls 0.006 user 0.000 sys 0.010 real
exec_no_coor: 1 calls 0.001 user 0.000 sys 0.004 real
execute: 1 calls 0.001 user 0.002 sys 47.882 real
idle: 176 calls 0.157 user 0.001 sys 143.228 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 1910259712 mem 1361.387 user 7.756 sys 48.886 real