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-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-rnd-pltf-dev-nextflow-scratch-01/work/68/11d7483211e7265d69dc99e5dab5c5/1029_G9Q-N1-BDNA-1_B23KFG5LT4_1.table
  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/ed/9b9a6fde2c6c9fd2444f269ba7ba81/1029_G9Q-N1-BDNA-1_B23KFG5LT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/eefc8abdd8cae5e739056371bed369/.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/ed/9b9a6fde2c6c9fd2444f269ba7ba81/1029_G9Q-N1-BDNA-1_B23KFG5LT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/eefc8abdd8cae5e739056371bed369/.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 1029_G9Q-N1-BDNA-1_B23KFG5LT4_1.md.bam --read_filter QualCalFilter,table=1029_G9Q-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_G9Q-N1-BDNA-1_B23KFG5LT4_1.table.post --algo ReadWriter 1029_G9Q-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:178000001, elapsed 10.5s, est remaining 199.6s, peak mem 3617MB, user 252.5s, sys 5.1s, output queue size 145
progress 10% @chr2:17000001, elapsed 19.0s, est remaining 171.4s, peak mem 4284MB, user 530.0s, sys 6.7s, output queue size 56
progress 15% @chr3:18000001, elapsed 28.8s, est remaining 163.4s, peak mem 4512MB, user 811.0s, sys 8.4s, output queue size 122
progress 20% @chr3:176000001, elapsed 36.8s, est remaining 147.3s, peak mem 4523MB, user 1065.7s, sys 9.8s, output queue size 141
progress 25% @chr4:129000001, elapsed 44.0s, est remaining 132.1s, peak mem 4556MB, user 1281.8s, sys 10.8s, output queue size 302
progress 30% @chr5:107000001, elapsed 49.7s, est remaining 115.9s, peak mem 4585MB, user 1452.5s, sys 11.5s, output queue size 464
progress 35% @chr6:91000001, elapsed 57.5s, est remaining 106.9s, peak mem 4585MB, user 1663.8s, sys 12.4s, output queue size 625
progress 40% @chr7:47000001, elapsed 66.3s, est remaining 99.5s, peak mem 4641MB, user 1904.4s, sys 13.6s, output queue size 786
progress 45% @chr8:79000001, elapsed 75.8s, est remaining 92.7s, peak mem 4663MB, user 2226.3s, sys 15.0s, output queue size 204
progress 50% @chr9:88000001, elapsed 83.4s, est remaining 83.4s, peak mem 4723MB, user 2451.0s, sys 16.2s, output queue size 366
progress 55% @chr10:62000001, elapsed 93.0s, est remaining 76.1s, peak mem 4771MB, user 2715.9s, sys 17.6s, output queue size 527
progress 60% @chr11:130000001, elapsed 102.8s, est remaining 68.5s, peak mem 4771MB, user 3032.1s, sys 18.9s, output queue size 510
progress 65% @chr13:18000001, elapsed 112.3s, est remaining 60.5s, peak mem 4771MB, user 3298.2s, sys 20.1s, output queue size 672
progress 70% @chr14:72000001, elapsed 118.2s, est remaining 50.7s, peak mem 4771MB, user 3485.3s, sys 20.9s, output queue size 833
progress 75% @chr16:41000001, elapsed 128.8s, est remaining 42.9s, peak mem 4781MB, user 3819.0s, sys 22.3s, output queue size 461
progress 80% @chr18:13000001, elapsed 143.6s, est remaining 35.9s, peak mem 4796MB, user 4207.6s, sys 23.8s, output queue size 623
progress 85% @chr18:47000001, elapsed 156.7s, est remaining 27.7s, peak mem 4813MB, user 4687.4s, sys 25.9s, output queue size 351
progress 90% @chrX:42000001, elapsed 165.6s, est remaining 18.4s, peak mem 4923MB, user 4944.3s, sys 27.2s, output queue size 513
progress 95% @chrY:53000001, elapsed 172.2s, est remaining 9.1s, peak mem 4929MB, user 5111.3s, sys 28.1s, output queue size 675
progress 100% @chrX:67000001, elapsed 184.1s, est remaining 0.0s, peak mem 4934MB, user 5367.8s, sys 29.5s, output queue size 3540
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: QualCal ReadWriter
license: sentieon:QualCal=31 sentieon:ReadWriter=31
input file size: 14356714391
output file size: 25969177318
reads: 313764322
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.003 user 0.020 sys 0.034 real
ReadQualCal::delayed_init: 1 calls 0.005 user 0.002 sys 0.025 real
ReadQualCal::init: 1 calls 0.000 user 0.010 sys 0.006 real
advance: 3219322 calls 348.931 user 7.294 sys 365.809 real
done: 1 calls 0.474 user 0.459 sys 0.933 real
exec_no_coor: 1 calls 0.000 user 0.005 sys 0.012 real
execute: 1 calls 0.000 user 0.009 sys 184.389 real
fetch: 3219323 calls 13.805 user 0.392 sys 20.903 real
fetch_reads: 3219322 calls 65.713 user 0.586 sys 66.985 real
fetch_ref: 1474731 calls 4.968 user 1.055 sys 6.005 real
fetch_vcf: 1474731 calls 103.258 user 1.821 sys 106.712 real
idle: 13365 calls 6.843 user 0.187 sys 302.409 real
init: 1 calls 0.005 user 0.002 sys 0.032 real
update: 1560379 calls 1135.803 user 3.299 sys 1174.861 real
write: 3219323 calls 3957.023 user 11.485 sys 3985.299 real
overall: 5174104064 mem 5384.813 user 38.028 sys 186.627 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before 1029_G9Q-N1-BDNA-1_B23KFG5LT4_1.table --after 1029_G9Q-N1-BDNA-1_B23KFG5LT4_1.table.post 1029_G9Q-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: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 192
algo: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.050 user 0.000 sys 0.044 real
done: 1 calls 0.080 user 0.010 sys 0.082 real
idle: 61 calls 0.002 user 0.000 sys 31.355 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 88293376 mem 0.110 user 0.020 sys 1.056 real