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/f7/1cf10506b6a6c17ee84da6ad24850a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/1cf10506b6a6c17ee84da6ad24850a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/e82a429921c26fa3f476a28aea2901/659_Lx-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/e82a429921c26fa3f476a28aea2901/659_Lx-T1-TDNA-1_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.fai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i 659_Lx-T1-TDNA-1_A23MHWWLT4_1.md.bam --algo AlignmentStat 659_Lx-T1-TDNA-1_A23MHWWLT4_1.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo 659_Lx-T1-TDNA-1_A23MHWWLT4_1.sentieon.insert_size_metrics --algo QualDistribution 659_Lx-T1-TDNA-1_A23MHWWLT4_1.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle 659_Lx-T1-TDNA-1_A23MHWWLT4_1.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle 659_Lx-T1-TDNA-1_A23MHWWLT4_1.sentieon.quality_by_cycle_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:174000001, elapsed 0.0s, est remaining 0.5s, peak mem 85MB, user 0.2s, sys 0.3s, output queue size 16
progress 10% @chr2:77000001, elapsed 0.1s, est remaining 0.5s, peak mem 87MB, user 0.5s, sys 0.7s, output queue size 41
progress 15% @chr2:234000001, elapsed 0.1s, est remaining 0.4s, peak mem 91MB, user 0.8s, sys 1.2s, output queue size 203
progress 20% @chr3:147000001, elapsed 0.1s, est remaining 0.4s, peak mem 96MB, user 1.0s, sys 1.9s, output queue size 364
progress 25% @chr4:111000001, elapsed 0.1s, est remaining 0.4s, peak mem 100MB, user 1.3s, sys 2.4s, output queue size 525
progress 30% @chr5:88000001, elapsed 0.2s, est remaining 0.4s, peak mem 100MB, user 1.4s, sys 3.0s, output queue size 687
progress 35% @chr6:56000001, elapsed 0.2s, est remaining 0.3s, peak mem 102MB, user 1.7s, sys 3.5s, output queue size 848
progress 40% @chr7:61000001, elapsed 0.2s, est remaining 0.3s, peak mem 103MB, user 2.0s, sys 4.0s, output queue size 42
progress 45% @chr8:60000001, elapsed 0.2s, est remaining 0.3s, peak mem 103MB, user 2.2s, sys 4.4s, output queue size 25
progress 50% @chr9:69000001, elapsed 0.3s, est remaining 0.3s, peak mem 103MB, user 2.4s, sys 4.8s, output queue size 8
progress 55% @chr10:107000001, elapsed 0.3s, est remaining 0.2s, peak mem 103MB, user 2.7s, sys 5.2s, output queue size 22
progress 60% @chr11:126000001, elapsed 0.3s, est remaining 0.2s, peak mem 103MB, user 2.8s, sys 5.7s, output queue size 10
progress 65% @chr12:122000001, elapsed 0.3s, est remaining 0.2s, peak mem 103MB, user 3.1s, sys 6.1s, output queue size 27
progress 70% @chr14:62000001, elapsed 0.3s, est remaining 0.1s, peak mem 103MB, user 3.3s, sys 6.5s, output queue size 12
progress 75% @chr16:16000001, elapsed 0.4s, est remaining 0.1s, peak mem 103MB, user 3.6s, sys 6.9s, output queue size 28
progress 80% @chr18:8000001, elapsed 0.4s, est remaining 0.1s, peak mem 103MB, user 3.8s, sys 7.3s, output queue size 41
progress 85% @chr20:30000001, elapsed 0.4s, est remaining 0.1s, peak mem 103MB, user 4.1s, sys 7.6s, output queue size 13
progress 90% @chrX:29000001, elapsed 0.4s, est remaining 0.0s, peak mem 103MB, user 4.5s, sys 7.8s, output queue size 49
progress 95% @chrY:26000001, elapsed 0.4s, est remaining 0.0s, peak mem 103MB, user 4.8s, sys 8.2s, output queue size 3
progress 100% @HLA-DRB1*15:01:01:02:1, elapsed 0.5s, est remaining 0.0s, peak mem 103MB, user 4.9s, sys 8.6s, output queue size 1987
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: 29954637
reads: 524817
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.308 user 4.352 sys 5.573 real
done: 1 calls 0.000 user 0.000 sys 0.001 real
exec_no_coor: 1 calls 0.000 user 0.001 sys 0.003 real
execute: 1 calls 0.003 user 0.005 sys 0.472 real
idle: 73 calls 0.001 user 0.001 sys 31.073 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 108855296 mem 5.289 user 9.061 sys 1.527 real