Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/1804dd3d879d62f8f7ec0f415fcf73/NTC_0002_0015_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/1804dd3d879d62f8f7ec0f415fcf73/NTC_0002_0015_A23MHWWLT4_1.md.bam.bai
  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/6b/16d2fbb2ff9e3c3f7a99e59012edcf/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/16d2fbb2ff9e3c3f7a99e59012edcf/.command.run
  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 NTC_0002_0015_A23MHWWLT4_1.md.bam --algo AlignmentStat NTC_0002_0015_A23MHWWLT4_1.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo NTC_0002_0015_A23MHWWLT4_1.sentieon.insert_size_metrics --algo QualDistribution NTC_0002_0015_A23MHWWLT4_1.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle NTC_0002_0015_A23MHWWLT4_1.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle NTC_0002_0015_A23MHWWLT4_1.sentieon.quality_by_cycle_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:162000001, elapsed 0.0s, est remaining 0.4s, peak mem 81MB, user 0.1s, sys 0.3s, output queue size 7
progress 10% @chr2:69000001, elapsed 0.0s, est remaining 0.4s, peak mem 81MB, user 0.1s, sys 0.8s, output queue size 41
progress 15% @chr2:235000001, elapsed 0.1s, est remaining 0.4s, peak mem 87MB, user 0.3s, sys 1.6s, output queue size 203
progress 20% @chr3:156000001, elapsed 0.1s, est remaining 0.4s, peak mem 91MB, user 0.3s, sys 2.2s, output queue size 364
progress 25% @chr4:113000001, elapsed 0.1s, est remaining 0.4s, peak mem 96MB, user 0.4s, sys 2.9s, output queue size 525
progress 30% @chr5:86000001, elapsed 0.1s, est remaining 0.3s, peak mem 100MB, user 0.5s, sys 3.6s, output queue size 687
progress 35% @chr6:64000001, elapsed 0.2s, est remaining 0.3s, peak mem 105MB, user 0.6s, sys 4.2s, output queue size 848
progress 40% @chr7:54000001, elapsed 0.2s, est remaining 0.3s, peak mem 109MB, user 0.7s, sys 4.9s, output queue size 1009
progress 45% @chr8:58000001, elapsed 0.2s, est remaining 0.3s, peak mem 114MB, user 0.7s, sys 5.5s, output queue size 1171
progress 50% @chr9:75000001, elapsed 0.2s, est remaining 0.2s, peak mem 115MB, user 0.9s, sys 6.1s, output queue size 1333
progress 55% @chr10:97000001, elapsed 0.3s, est remaining 0.2s, peak mem 115MB, user 1.0s, sys 6.6s, output queue size 1494
progress 60% @chr11:123000001, elapsed 0.3s, est remaining 0.2s, peak mem 115MB, user 1.0s, sys 7.2s, output queue size 1656
progress 65% @chr13:1, elapsed 0.3s, est remaining 0.2s, peak mem 115MB, user 1.1s, sys 7.7s, output queue size 1818
progress 70% @chr14:61000001, elapsed 0.3s, est remaining 0.1s, peak mem 115MB, user 1.4s, sys 8.3s, output queue size 5
progress 75% @chr16:14000001, elapsed 0.4s, est remaining 0.1s, peak mem 115MB, user 1.5s, sys 8.8s, output queue size 10
progress 80% @chr18:2000001, elapsed 0.4s, est remaining 0.1s, peak mem 115MB, user 1.6s, sys 9.2s, output queue size 8
progress 85% @chr20:24000001, elapsed 0.4s, est remaining 0.1s, peak mem 115MB, user 1.7s, sys 9.8s, output queue size 17
progress 90% @chrX:17000001, elapsed 0.4s, est remaining 0.0s, peak mem 115MB, user 1.8s, sys 10.3s, output queue size 17
progress 95% @chrY:27000001, elapsed 0.4s, est remaining 0.0s, peak mem 115MB, user 1.8s, sys 10.9s, output queue size 24
progress 100% @HLA-DRB1*15:03:01:01:1, elapsed 0.5s, est remaining 0.0s, peak mem 115MB, user 1.9s, sys 11.2s, output queue size 2393
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: 2828557
reads: 42902
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 0.444 user 5.638 sys 6.381 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 0.463 real
idle: 74 calls 0.001 user 0.002 sys 31.085 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 121335808 mem 2.041 user 11.960 sys 1.518 real