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/8a/65c3a895f3cf1f1d8a74bf73c8312b/659_cVw-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/5f02bece1213dfde74e6a3da5e1d3b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/65c3a895f3cf1f1d8a74bf73c8312b/659_cVw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/5f02bece1213dfde74e6a3da5e1d3b/.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 659_cVw-T1-TDNA-1_A23MHWWLT4_1.md.bam --algo AlignmentStat 659_cVw-T1-TDNA-1_A23MHWWLT4_1.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo 659_cVw-T1-TDNA-1_A23MHWWLT4_1.sentieon.insert_size_metrics --algo QualDistribution 659_cVw-T1-TDNA-1_A23MHWWLT4_1.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle 659_cVw-T1-TDNA-1_A23MHWWLT4_1.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle 659_cVw-T1-TDNA-1_A23MHWWLT4_1.sentieon.quality_by_cycle_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:181000001, elapsed 13.0s, est remaining 246.1s, peak mem 4434MB, user 297.2s, sys 3.3s, output queue size 146
progress 10% @chr2:84000001, elapsed 24.5s, est remaining 220.6s, peak mem 7314MB, user 660.7s, sys 6.5s, output queue size 79
progress 15% @chr3:18000001, elapsed 38.6s, est remaining 218.7s, peak mem 9463MB, user 1056.3s, sys 9.0s, output queue size 203
progress 20% @chr3:175000001, elapsed 49.1s, est remaining 196.2s, peak mem 9700MB, user 1378.6s, sys 11.6s, output queue size 283
progress 25% @chr4:137000001, elapsed 58.9s, est remaining 176.6s, peak mem 9986MB, user 1688.5s, sys 12.5s, output queue size 335
progress 30% @chr5:107000001, elapsed 66.5s, est remaining 155.1s, peak mem 10135MB, user 1946.9s, sys 13.3s, output queue size 464
progress 35% @chr6:86000001, elapsed 76.9s, est remaining 142.8s, peak mem 10181MB, user 2239.0s, sys 14.1s, output queue size 625
progress 40% @chr7:79000001, elapsed 89.7s, est remaining 134.5s, peak mem 10602MB, user 2575.5s, sys 15.2s, output queue size 786
progress 45% @chr8:79000001, elapsed 105.6s, est remaining 129.1s, peak mem 11010MB, user 3016.0s, sys 16.6s, output queue size 948
progress 50% @chr9:102000001, elapsed 118.7s, est remaining 118.7s, peak mem 11250MB, user 3368.5s, sys 17.4s, output queue size 1110
progress 55% @chr10:117000001, elapsed 133.5s, est remaining 109.2s, peak mem 11287MB, user 3904.7s, sys 18.7s, output queue size 527
progress 60% @chr11:130000001, elapsed 147.0s, est remaining 98.0s, peak mem 11287MB, user 4333.4s, sys 19.7s, output queue size 689
progress 65% @chr11:108000001, elapsed 163.3s, est remaining 87.9s, peak mem 11287MB, user 4748.1s, sys 20.6s, output queue size 851
progress 70% @chr14:76000001, elapsed 172.3s, est remaining 73.8s, peak mem 11287MB, user 5061.9s, sys 21.4s, output queue size 833
progress 75% @chr16:42000001, elapsed 188.3s, est remaining 62.8s, peak mem 11287MB, user 5556.1s, sys 22.4s, output queue size 995
progress 80% @chr17:50000001, elapsed 210.7s, est remaining 52.7s, peak mem 11292MB, user 6135.6s, sys 23.7s, output queue size 1157
progress 85% @chr19:47000001, elapsed 232.1s, est remaining 41.0s, peak mem 11310MB, user 6817.1s, sys 25.1s, output queue size 785
progress 90% @chrX:43000001, elapsed 244.6s, est remaining 27.2s, peak mem 11428MB, user 7301.8s, sys 26.5s, output queue size 947
progress 95% @chrY:55000001, elapsed 251.2s, est remaining 13.2s, peak mem 11428MB, user 7576.4s, sys 27.3s, output queue size 675
progress 100% @chr15:88000001, elapsed 283.9s, est remaining 0.0s, peak mem 11537MB, user 7929.5s, sys 28.4s, 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: 79716908892
reads: 1583694629
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1297.763 user 24.074 sys 1315.404 real
done: 1 calls 0.049 user 0.001 sys 0.058 real
exec_no_coor: 1 calls 0.016 user 0.008 sys 0.036 real
execute: 1 calls 0.009 user 0.000 sys 284.282 real
idle: 914 calls 0.195 user 0.002 sys 879.296 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 12098281472 mem 7931.715 user 28.827 sys 285.502 real