Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/a12e5b75158f326754e94b8e274a99/.command.sh
  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/08/a12e5b75158f326754e94b8e274a99/.command.run
  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/63/3deb87201b3dbfb093e36f83dee947/1029_T05-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/3deb87201b3dbfb093e36f83dee947/1029_T05-T1-TDNA-1_A23MHWWLT4_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_T05-T1-TDNA-1_A23MHWWLT4_1.md.bam --algo AlignmentStat 1029_T05-T1-TDNA-1_A23MHWWLT4_1.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo 1029_T05-T1-TDNA-1_A23MHWWLT4_1.sentieon.insert_size_metrics --algo QualDistribution 1029_T05-T1-TDNA-1_A23MHWWLT4_1.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle 1029_T05-T1-TDNA-1_A23MHWWLT4_1.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle 1029_T05-T1-TDNA-1_A23MHWWLT4_1.sentieon.quality_by_cycle_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:15000001, elapsed 13.2s, est remaining 250.6s, peak mem 4044MB, user 311.6s, sys 3.3s, output queue size 150
progress 10% @chr2:38000001, elapsed 25.9s, est remaining 233.5s, peak mem 6855MB, user 681.1s, sys 5.2s, output queue size 166
progress 15% @chr2:237000001, elapsed 37.9s, est remaining 214.8s, peak mem 8127MB, user 1084.1s, sys 8.5s, output queue size 161
progress 20% @chr3:158000001, elapsed 48.6s, est remaining 194.4s, peak mem 8412MB, user 1402.2s, sys 10.0s, output queue size 283
progress 25% @chr4:129000001, elapsed 57.4s, est remaining 172.1s, peak mem 8552MB, user 1689.6s, sys 11.2s, output queue size 302
progress 30% @chr5:100000001, elapsed 64.7s, est remaining 150.9s, peak mem 8798MB, user 1903.5s, sys 11.9s, output queue size 464
progress 35% @chr6:91000001, elapsed 75.6s, est remaining 140.5s, peak mem 9200MB, user 2193.5s, sys 13.0s, output queue size 625
progress 40% @chr7:64000001, elapsed 88.2s, est remaining 132.3s, peak mem 9403MB, user 2557.7s, sys 14.0s, output queue size 786
progress 45% @chr8:23000001, elapsed 102.3s, est remaining 125.1s, peak mem 9625MB, user 3016.6s, sys 15.2s, output queue size 204
progress 50% @chr9:102000001, elapsed 113.4s, est remaining 113.4s, peak mem 9625MB, user 3304.2s, sys 16.2s, output queue size 366
progress 55% @chr10:99000001, elapsed 128.6s, est remaining 105.3s, peak mem 10140MB, user 3811.0s, sys 17.6s, output queue size 348
progress 60% @chr11:121000001, elapsed 141.7s, est remaining 94.5s, peak mem 10140MB, user 4232.2s, sys 18.8s, output queue size 510
progress 65% @chr13:39000001, elapsed 154.3s, est remaining 83.1s, peak mem 10221MB, user 4538.3s, sys 19.9s, output queue size 672
progress 70% @chr14:71000001, elapsed 162.8s, est remaining 69.8s, peak mem 10238MB, user 4761.5s, sys 20.7s, output queue size 833
progress 75% @chr16:42000001, elapsed 176.4s, est remaining 58.8s, peak mem 10238MB, user 5234.5s, sys 22.0s, output queue size 797
progress 80% @chr18:25000001, elapsed 197.9s, est remaining 49.5s, peak mem 10277MB, user 5854.2s, sys 23.9s, output queue size 623
progress 85% @chr20:9000001, elapsed 219.6s, est remaining 38.8s, peak mem 10330MB, user 6546.8s, sys 25.3s, output queue size 785
progress 90% @chrX:36000001, elapsed 233.9s, est remaining 26.0s, peak mem 10577MB, user 6918.5s, sys 26.5s, output queue size 947
progress 95% @chrY:54000001, elapsed 244.7s, est remaining 12.9s, peak mem 10635MB, user 7214.4s, sys 27.3s, output queue size 1109
progress 100% @chrX:67000001, elapsed 280.3s, est remaining 0.0s, peak mem 10650MB, user 7772.4s, sys 28.6s, output queue size 3540
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: 80063761426
reads: 1549027000
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1298.713 user 24.623 sys 1322.463 real
done: 1 calls 0.082 user 0.000 sys 0.085 real
exec_no_coor: 1 calls 0.018 user 0.000 sys 0.030 real
execute: 1 calls 0.001 user 0.001 sys 280.501 real
idle: 953 calls 0.201 user 0.001 sys 924.519 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 11167543296 mem 7774.797 user 29.167 sys 281.911 real