Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/500ff411ac93a70f78f4f5a487b4e0/HCC1395_BL.md.bam
  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/a2/1c3f4effdf288073f10c3bac7d426d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/1c3f4effdf288073f10c3bac7d426d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/500ff411ac93a70f78f4f5a487b4e0/HCC1395_BL.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 HCC1395_BL.md.bam --algo AlignmentStat HCC1395_BL.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo HCC1395_BL.sentieon.insert_size_metrics --algo QualDistribution HCC1395_BL.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle HCC1395_BL.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle HCC1395_BL.sentieon.quality_by_cycle_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:167000001, elapsed 0.1s, est remaining 1.5s, peak mem 78MB, user 0.1s, sys 1.8s, output queue size 30
progress 10% @chr2:69000001, elapsed 0.2s, est remaining 1.4s, peak mem 78MB, user 0.2s, sys 3.9s, output queue size 4
progress 15% @chr2:202000001, elapsed 0.2s, est remaining 1.2s, peak mem 78MB, user 0.3s, sys 6.1s, output queue size 33
progress 20% @chr3:154000001, elapsed 0.3s, est remaining 1.2s, peak mem 78MB, user 0.3s, sys 8.2s, output queue size 7
progress 25% @chr4:115000001, elapsed 0.4s, est remaining 1.1s, peak mem 78MB, user 0.4s, sys 10.3s, output queue size 2
progress 30% @chr5:83000001, elapsed 0.4s, est remaining 1.0s, peak mem 78MB, user 0.5s, sys 12.4s, output queue size 3
progress 35% @chr6:66000001, elapsed 0.5s, est remaining 0.9s, peak mem 78MB, user 0.6s, sys 14.5s, output queue size 3
progress 40% @chr7:62000001, elapsed 0.6s, est remaining 0.9s, peak mem 78MB, user 0.7s, sys 16.5s, output queue size 7
progress 45% @chr8:56000001, elapsed 0.6s, est remaining 0.8s, peak mem 78MB, user 0.8s, sys 18.7s, output queue size 3
progress 50% @chr9:70000001, elapsed 0.7s, est remaining 0.7s, peak mem 78MB, user 0.8s, sys 20.9s, output queue size 3
progress 55% @chr10:92000001, elapsed 0.8s, est remaining 0.6s, peak mem 78MB, user 0.9s, sys 23.0s, output queue size 6
progress 60% @chr11:122000001, elapsed 0.9s, est remaining 0.6s, peak mem 78MB, user 1.0s, sys 25.0s, output queue size 16
progress 65% @chr13:17000001, elapsed 0.9s, est remaining 0.5s, peak mem 78MB, user 1.1s, sys 27.1s, output queue size 5
progress 70% @chr14:63000001, elapsed 1.0s, est remaining 0.4s, peak mem 78MB, user 1.2s, sys 29.2s, output queue size 4
progress 75% @chr16:4000001, elapsed 1.1s, est remaining 0.4s, peak mem 78MB, user 1.2s, sys 31.3s, output queue size 11
progress 80% @chr17:76000001, elapsed 1.1s, est remaining 0.3s, peak mem 78MB, user 1.3s, sys 33.3s, output queue size 8
progress 85% @chr20:16000001, elapsed 1.2s, est remaining 0.2s, peak mem 78MB, user 1.4s, sys 35.3s, output queue size 6
progress 90% @chrX:37000001, elapsed 1.3s, est remaining 0.1s, peak mem 93MB, user 2.4s, sys 36.5s, output queue size 114
progress 95% @chrY:35000001, elapsed 1.4s, est remaining 0.1s, peak mem 111MB, user 3.0s, sys 38.0s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.2s, est remaining 0.0s, peak mem 132MB, user 5.6s, sys 40.4s, output queue size 3664
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 384
algo: AlignmentStat InsertSizeMetricAlgo QualDistribution BaseDistributionByCycle MeanQualityByCycle
license: sentieon:Metrics=31
input file size: 51395347
reads: 1001089
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.253 user 20.929 sys 22.163 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 0.002 user 0.003 sys 2.179 real
idle: 77 calls 0.004 user 0.016 sys 50.985 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 138518528 mem 5.789 user 41.146 sys 3.235 real