Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/4e72016856e6b8ecccb46678a6653e/1029_HJ2-N1-BDNA-1_B23KFG5LT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/4e72016856e6b8ecccb46678a6653e/1029_HJ2-N1-BDNA-1_B23KFG5LT4_1.md.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/beta/Homo_sapiens_assembly38.known_indels.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/e97f9e45d58d2b530751bf057dc3ad/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/beta/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/e97f9e45d58d2b530751bf057dc3ad/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/7c8374af1d910e9805f0888721a64a/1029_HJ2-N1-BDNA-1_B23KFG5LT4_1.table
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
==> STAGING COMPLETE (13 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i 1029_HJ2-N1-BDNA-1_B23KFG5LT4_1.md.bam --read_filter QualCalFilter,table=1029_HJ2-N1-BDNA-1_B23KFG5LT4_1.table,indel=false --algo QualCal -k dbsnp_146.hg38.vcf.gz -k Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -k Homo_sapiens_assembly38.known_indels.vcf.gz 1029_HJ2-N1-BDNA-1_B23KFG5LT4_1.table.post --algo ReadWriter 1029_HJ2-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:175000001, elapsed 13.5s, est remaining 256.7s, peak mem 3708MB, user 319.6s, sys 5.0s, output queue size 145
progress 10% @chr1:226000001, elapsed 24.3s, est remaining 218.5s, peak mem 4382MB, user 675.9s, sys 7.0s, output queue size 96
progress 15% @chr3:4000001, elapsed 36.5s, est remaining 206.8s, peak mem 4560MB, user 1024.2s, sys 9.3s, output queue size 122
progress 20% @chr3:174000001, elapsed 46.6s, est remaining 186.3s, peak mem 4570MB, user 1344.7s, sys 11.8s, output queue size 141
progress 25% @chr4:133000001, elapsed 56.6s, est remaining 169.8s, peak mem 4627MB, user 1643.4s, sys 13.0s, output queue size 302
progress 30% @chr5:107000001, elapsed 64.7s, est remaining 150.9s, peak mem 4664MB, user 1875.7s, sys 14.2s, output queue size 464
progress 35% @chr6:81000001, elapsed 75.8s, est remaining 140.9s, peak mem 4680MB, user 2179.6s, sys 16.0s, output queue size 625
progress 40% @chr7:47000001, elapsed 88.1s, est remaining 132.1s, peak mem 4738MB, user 2520.1s, sys 17.1s, output queue size 786
progress 45% @chr8:82000001, elapsed 101.5s, est remaining 124.1s, peak mem 4741MB, user 2964.4s, sys 18.7s, output queue size 204
progress 50% @chr9:89000001, elapsed 112.3s, est remaining 112.3s, peak mem 4780MB, user 3280.5s, sys 19.8s, output queue size 366
progress 55% @chr10:62000001, elapsed 125.8s, est remaining 103.0s, peak mem 4827MB, user 3682.5s, sys 21.2s, output queue size 348
progress 60% @chr11:130000001, elapsed 139.3s, est remaining 92.9s, peak mem 4831MB, user 4087.9s, sys 22.8s, output queue size 510
progress 65% @chr13:23000001, elapsed 152.1s, est remaining 81.9s, peak mem 4837MB, user 4446.5s, sys 24.2s, output queue size 672
progress 70% @chr14:85000001, elapsed 160.2s, est remaining 68.6s, peak mem 4837MB, user 4688.9s, sys 25.3s, output queue size 833
progress 75% @chr16:42000001, elapsed 174.5s, est remaining 58.2s, peak mem 4871MB, user 5073.5s, sys 26.9s, output queue size 995
progress 80% @chr18:25000001, elapsed 195.3s, est remaining 48.8s, peak mem 4903MB, user 5687.0s, sys 28.8s, output queue size 623
progress 85% @chr19:15000001, elapsed 213.1s, est remaining 37.6s, peak mem 4903MB, user 6331.6s, sys 30.8s, output queue size 351
progress 90% @chr22:46000001, elapsed 224.3s, est remaining 24.9s, peak mem 4981MB, user 6680.3s, sys 32.2s, output queue size 513
progress 95% @chrY:54000001, elapsed 230.8s, est remaining 12.1s, peak mem 5003MB, user 6857.6s, sys 33.2s, output queue size 675
progress 100% @chr22:23000001, elapsed 245.1s, est remaining 0.0s, peak mem 5003MB, user 7136.6s, sys 34.4s, output queue size 3635
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 31 max 128
algo: QualCal ReadWriter
license: sentieon:QualCal=31 sentieon:ReadWriter=31
input file size: 14249713899
output file size: 26971898491
reads: 317573315
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.001 user 0.010 sys 0.051 real
ReadQualCal::delayed_init: 1 calls 0.006 user 0.001 sys 0.019 real
ReadQualCal::init: 1 calls 0.009 user 0.001 sys 0.008 real
advance: 3219322 calls 481.938 user 8.216 sys 492.715 real
done: 1 calls 0.585 user 0.340 sys 0.929 real
exec_no_coor: 1 calls 0.007 user 0.001 sys 0.015 real
execute: 1 calls 0.004 user 0.000 sys 245.452 real
fetch: 3219323 calls 18.872 user 0.565 sys 27.758 real
fetch_reads: 3219322 calls 84.810 user 0.632 sys 87.454 real
fetch_ref: 1456573 calls 5.402 user 1.293 sys 6.543 real
fetch_vcf: 1456573 calls 122.449 user 1.975 sys 124.979 real
idle: 10676 calls 5.857 user 0.171 sys 372.131 real
init: 1 calls 0.011 user 0.001 sys 0.026 real
update: 1543928 calls 1695.081 user 2.983 sys 1718.024 real
write: 3219323 calls 5182.071 user 14.273 sys 5232.658 real
overall: 5246246912 mem 7155.444 user 43.925 sys 247.825 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before 1029_HJ2-N1-BDNA-1_B23KFG5LT4_1.table --after 1029_HJ2-N1-BDNA-1_B23KFG5LT4_1.table.post 1029_HJ2-N1-BDNA-1_B23KFG5LT4_1.csv
This software is licensed to bgold@natera.com by Sentieon Inc.
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 31 max 128
algo: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.058 user 0.002 sys 0.059 real
done: 1 calls 0.098 user 0.012 sys 0.106 real
idle: 61 calls 0.002 user 0.000 sys 31.265 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 88367104 mem 0.119 user 0.043 sys 1.051 real