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/0a/33b1c3ef876f67c1658eae3a9e8968/1047_JG-T1-TDNA-1_A23MHWWLT4_1.md.bam
  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.tbi
  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/c7/830a34aef9dfc8188652c861204b99/.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-rnd-pltf-dev-nextflow-scratch-01/work/0a/33b1c3ef876f67c1658eae3a9e8968/1047_JG-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  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/d8/2e271f016111516bea060eecb5da0f/1047_JG-T1-TDNA-1_A23MHWWLT4_1.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/830a34aef9dfc8188652c861204b99/.command.run
  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 1047_JG-T1-TDNA-1_A23MHWWLT4_1.md.bam --read_filter QualCalFilter,table=1047_JG-T1-TDNA-1_A23MHWWLT4_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 1047_JG-T1-TDNA-1_A23MHWWLT4_1.table.post --algo ReadWriter 1047_JG-T1-TDNA-1_A23MHWWLT4_1.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:178000001, elapsed 62.1s, est remaining 1179.3s, peak mem 10320MB, user 1532.7s, sys 12.8s, output queue size 58
progress 10% @chr2:55000001, elapsed 110.3s, est remaining 992.3s, peak mem 14033MB, user 3089.5s, sys 20.4s, output queue size 48
progress 15% @chr2:201000001, elapsed 168.1s, est remaining 952.7s, peak mem 16340MB, user 4741.3s, sys 29.1s, output queue size 122
progress 20% @chr3:154000001, elapsed 216.6s, est remaining 866.3s, peak mem 16562MB, user 6279.7s, sys 35.1s, output queue size 141
progress 25% @chr4:83000001, elapsed 263.0s, est remaining 788.9s, peak mem 16683MB, user 7688.0s, sys 40.0s, output queue size 302
progress 30% @chr4:105000001, elapsed 299.2s, est remaining 698.1s, peak mem 17069MB, user 8812.9s, sys 44.2s, output queue size 464
progress 35% @chr6:41000001, elapsed 348.3s, est remaining 646.9s, peak mem 17249MB, user 10134.7s, sys 48.9s, output queue size 625
progress 40% @chr7:56000001, elapsed 401.7s, est remaining 602.5s, peak mem 17723MB, user 11817.6s, sys 55.3s, output queue size 194
progress 45% @chr8:78000001, elapsed 458.7s, est remaining 560.6s, peak mem 17875MB, user 13525.2s, sys 63.0s, output queue size 204
progress 50% @chr9:88000001, elapsed 506.3s, est remaining 506.3s, peak mem 18477MB, user 14879.9s, sys 69.6s, output queue size 366
progress 55% @chr10:94000001, elapsed 562.8s, est remaining 460.5s, peak mem 18682MB, user 16677.6s, sys 78.1s, output queue size 348
progress 60% @chr12:1000001, elapsed 620.3s, est remaining 413.6s, peak mem 18682MB, user 18264.0s, sys 85.1s, output queue size 510
progress 65% @chr12:102000001, elapsed 678.4s, est remaining 365.3s, peak mem 18682MB, user 20014.8s, sys 92.8s, output queue size 672
progress 70% @chr14:79000001, elapsed 714.5s, est remaining 306.2s, peak mem 18759MB, user 21118.5s, sys 97.9s, output queue size 833
progress 75% @chr16:42000001, elapsed 773.4s, est remaining 257.8s, peak mem 18837MB, user 22899.6s, sys 105.5s, output queue size 461
progress 80% @chr18:11000001, elapsed 854.8s, est remaining 213.7s, peak mem 19016MB, user 25101.9s, sys 115.4s, output queue size 623
progress 85% @chr19:45000001, elapsed 925.5s, est remaining 163.3s, peak mem 19048MB, user 27614.4s, sys 126.5s, output queue size 351
progress 90% @chrX:18000001, elapsed 975.0s, est remaining 108.3s, peak mem 19506MB, user 29107.8s, sys 133.2s, output queue size 513
progress 95% @chrY:54000001, elapsed 1010.6s, est remaining 53.2s, peak mem 19506MB, user 30315.2s, sys 138.4s, output queue size 211
progress 100% @chrX:67000001, elapsed 1075.3s, est remaining 0.0s, peak mem 19515MB, user 31340.4s, sys 143.9s, output queue size 3540
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: QualCal ReadWriter
license: sentieon:QualCal=31 sentieon:ReadWriter=31
input file size: 140423331250
output file size: 201975097872
reads: 3098808471
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.011 real
ReadQualCal::delayed_init: 1 calls 0.005 user 0.002 sys 0.026 real
ReadQualCal::init: 1 calls 0.000 user 0.000 sys 0.006 real
advance: 3219322 calls 3372.975 user 42.719 sys 3504.925 real
done: 1 calls 0.608 user 0.261 sys 0.875 real
exec_no_coor: 1 calls 0.280 user 0.077 sys 0.403 real
execute: 1 calls 0.000 user 0.001 sys 1078.541 real
fetch: 3219323 calls 255.737 user 0.503 sys 358.129 real
fetch_reads: 3219322 calls 741.599 user 1.748 sys 758.591 real
fetch_ref: 2389991 calls 13.683 user 1.447 sys 10.516 real
fetch_vcf: 2389991 calls 88.612 user 2.128 sys 90.893 real
idle: 92878 calls 19.491 user 0.458 sys 1489.760 real
init: 1 calls 0.005 user 0.002 sys 0.033 real
update: 3077070 calls 5844.510 user 3.936 sys 6170.328 real
write: 3219323 calls 23729.025 user 85.796 sys 24010.235 real
overall: 20463185920 mem 31375.435 user 248.190 sys 1081.542 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before 1047_JG-T1-TDNA-1_A23MHWWLT4_1.table --after 1047_JG-T1-TDNA-1_A23MHWWLT4_1.table.post 1047_JG-T1-TDNA-1_A23MHWWLT4_1.csv
This software is licensed to bgold@natera.com by Sentieon Inc.
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.029 user 0.002 sys 0.041 real
done: 1 calls 0.058 user 0.012 sys 0.079 real
idle: 61 calls 0.002 user 0.000 sys 31.323 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 86794240 mem 0.087 user 0.043 sys 1.057 real