Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/d48431c7b5765fd6f4f76ac5db2eba/1136_6G2-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
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/d608d389d00847ed9bc183677b58a4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/d608d389d00847ed9bc183677b58a4/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/d48431c7b5765fd6f4f76ac5db2eba/1136_6G2-T1-TDNA-1_A23MHWWLT4_1.md.bam
  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 1136_6G2-T1-TDNA-1_A23MHWWLT4_1.md.bam --algo AlignmentStat 1136_6G2-T1-TDNA-1_A23MHWWLT4_1.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo 1136_6G2-T1-TDNA-1_A23MHWWLT4_1.sentieon.insert_size_metrics --algo QualDistribution 1136_6G2-T1-TDNA-1_A23MHWWLT4_1.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle 1136_6G2-T1-TDNA-1_A23MHWWLT4_1.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle 1136_6G2-T1-TDNA-1_A23MHWWLT4_1.sentieon.quality_by_cycle_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:173000001, elapsed 11.2s, est remaining 212.4s, peak mem 3058MB, user 261.4s, sys 2.6s, output queue size 146
progress 10% @chr2:71000001, elapsed 19.6s, est remaining 176.7s, peak mem 4404MB, user 539.2s, sys 4.6s, output queue size 166
progress 15% @chr3:8000001, elapsed 28.9s, est remaining 163.8s, peak mem 4896MB, user 823.0s, sys 6.3s, output queue size 210
progress 20% @chr3:176000001, elapsed 37.3s, est remaining 149.1s, peak mem 5027MB, user 1076.8s, sys 7.3s, output queue size 283
progress 25% @chr4:129000001, elapsed 44.2s, est remaining 132.7s, peak mem 5179MB, user 1297.1s, sys 8.1s, output queue size 302
progress 30% @chr5:94000001, elapsed 49.4s, est remaining 115.3s, peak mem 5254MB, user 1444.1s, sys 8.5s, output queue size 464
progress 35% @chr6:91000001, elapsed 58.1s, est remaining 107.9s, peak mem 5569MB, user 1671.0s, sys 9.5s, output queue size 625
progress 40% @chr7:65000001, elapsed 67.3s, est remaining 101.0s, peak mem 5589MB, user 1983.7s, sys 10.5s, output queue size 195
progress 45% @chr8:67000001, elapsed 77.7s, est remaining 95.0s, peak mem 5711MB, user 2279.0s, sys 11.4s, output queue size 356
progress 50% @chr9:81000001, elapsed 85.6s, est remaining 85.6s, peak mem 5890MB, user 2518.4s, sys 12.0s, output queue size 366
progress 55% @chr10:104000001, elapsed 96.6s, est remaining 79.0s, peak mem 6299MB, user 2861.0s, sys 12.9s, output queue size 348
progress 60% @chr12:1000001, elapsed 108.3s, est remaining 72.2s, peak mem 6303MB, user 3182.1s, sys 13.8s, output queue size 510
progress 65% @chr13:26000001, elapsed 118.2s, est remaining 63.7s, peak mem 6412MB, user 3547.1s, sys 14.5s, output queue size 167
progress 70% @chr14:72000001, elapsed 123.7s, est remaining 53.0s, peak mem 6412MB, user 3729.8s, sys 15.0s, output queue size 299
progress 75% @chr16:42000001, elapsed 135.7s, est remaining 45.2s, peak mem 6603MB, user 4046.8s, sys 15.9s, output queue size 461
progress 80% @chr17:74000001, elapsed 155.2s, est remaining 38.8s, peak mem 6890MB, user 4519.9s, sys 17.2s, output queue size 623
progress 85% @chr20:43000001, elapsed 174.2s, est remaining 30.7s, peak mem 7054MB, user 5199.1s, sys 19.0s, output queue size 351
progress 90% @chrX:36000001, elapsed 184.1s, est remaining 20.5s, peak mem 7054MB, user 5553.7s, sys 19.8s, output queue size 513
progress 95% @chrY:55000001, elapsed 189.5s, est remaining 10.0s, peak mem 7092MB, user 5754.7s, sys 20.2s, output queue size 240
progress 100% @chr22:23000001, elapsed 217.6s, est remaining 0.0s, peak mem 7092MB, user 5964.7s, sys 20.8s, output queue size 3635
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31 max 192
algo: AlignmentStat InsertSizeMetricAlgo QualDistribution BaseDistributionByCycle MeanQualityByCycle
license: sentieon:Metrics=31
input file size: 56390667151
reads: 1090474054
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1122.256 user 17.875 sys 1141.490 real
done: 1 calls 0.055 user 0.000 sys 0.062 real
exec_no_coor: 1 calls 0.008 user 0.016 sys 0.029 real
execute: 1 calls 0.002 user 0.004 sys 217.830 real
idle: 837 calls 0.156 user 0.000 sys 795.630 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 7436943360 mem 5967.025 user 21.498 sys 219.117 real