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/3c/05f80ecb4bdae6b39b61214c403343/1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/8bb8cb457af127d516ed3894578c81/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/8bb8cb457af127d516ed3894578c81/.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/3c/05f80ecb4bdae6b39b61214c403343/1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam --algo AlignmentStat 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.sentieon.insert_size_metrics --algo QualDistribution 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.sentieon.quality_by_cycle_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:188000001, elapsed 18.8s, est remaining 357.9s, peak mem 5464MB, user 414.0s, sys 4.4s, output queue size 146
progress 10% @chr2:70000001, elapsed 36.4s, est remaining 327.9s, peak mem 8457MB, user 952.1s, sys 7.3s, output queue size 166
progress 15% @chr2:214000001, elapsed 51.1s, est remaining 289.8s, peak mem 8912MB, user 1487.0s, sys 10.6s, output queue size 122
progress 20% @chr3:158000001, elapsed 63.9s, est remaining 255.4s, peak mem 8912MB, user 1841.5s, sys 11.7s, output queue size 283
progress 25% @chr4:134000001, elapsed 75.3s, est remaining 225.9s, peak mem 8912MB, user 2220.9s, sys 12.6s, output queue size 302
progress 30% @chr5:107000001, elapsed 84.9s, est remaining 198.0s, peak mem 8912MB, user 2503.7s, sys 13.3s, output queue size 464
progress 35% @chr6:91000001, elapsed 100.3s, est remaining 186.3s, peak mem 9213MB, user 2916.5s, sys 14.7s, output queue size 625
progress 40% @chr7:47000001, elapsed 116.3s, est remaining 174.4s, peak mem 9549MB, user 3361.8s, sys 15.9s, output queue size 786
progress 45% @chr8:70000001, elapsed 132.5s, est remaining 162.0s, peak mem 9653MB, user 3957.0s, sys 17.6s, output queue size 204
progress 50% @chr9:81000001, elapsed 146.9s, est remaining 146.9s, peak mem 9927MB, user 4319.2s, sys 18.6s, output queue size 366
progress 55% @chr10:73000001, elapsed 164.4s, est remaining 134.5s, peak mem 10534MB, user 4837.9s, sys 20.1s, output queue size 485
progress 60% @chr11:134000001, elapsed 181.1s, est remaining 120.7s, peak mem 10534MB, user 5360.6s, sys 21.6s, output queue size 510
progress 65% @chr12:123000001, elapsed 197.5s, est remaining 106.4s, peak mem 10534MB, user 5803.8s, sys 22.6s, output queue size 672
progress 70% @chr14:72000001, elapsed 207.7s, est remaining 89.0s, peak mem 10534MB, user 6152.1s, sys 23.4s, output queue size 833
progress 75% @chr16:42000001, elapsed 226.3s, est remaining 75.4s, peak mem 10534MB, user 6783.1s, sys 25.0s, output queue size 461
progress 80% @chr18:29000001, elapsed 253.6s, est remaining 63.4s, peak mem 10776MB, user 7536.3s, sys 27.0s, output queue size 623
progress 85% @chr19:55000001, elapsed 278.7s, est remaining 49.2s, peak mem 10776MB, user 8347.0s, sys 28.7s, output queue size 785
progress 90% @chrX:24000001, elapsed 294.3s, est remaining 32.7s, peak mem 10867MB, user 8784.2s, sys 29.8s, output queue size 947
progress 95% @chrY:54000001, elapsed 302.9s, est remaining 15.9s, peak mem 11087MB, user 9140.5s, sys 30.6s, output queue size 675
progress 100% @chr15:88000001, elapsed 344.9s, est remaining 0.0s, peak mem 11145MB, user 9584.4s, sys 31.9s, output queue size 4099
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: 89084754634
reads: 1834997666
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1472.380 user 27.235 sys 1500.603 real
done: 1 calls 0.053 user 0.008 sys 0.070 real
exec_no_coor: 1 calls 0.032 user 0.021 sys 0.063 real
execute: 1 calls 0.005 user 0.002 sys 345.313 real
idle: 1148 calls 0.195 user 0.002 sys 1118.516 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 11686678528 mem 9586.913 user 32.428 sys 346.755 real