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/4b/77f7ae6d2659ec7c056abb9c1117b6/HCC1395_BL.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/16/a6b0b2bf8a8522a668d33f5b636022/HCC1395_BL.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/c0a67c1d98a52e016e1ee4b829f9ba/.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/e8/c0a67c1d98a52e016e1ee4b829f9ba/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/77f7ae6d2659ec7c056abb9c1117b6/HCC1395_BL.md.bam.bai
  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 HCC1395_BL.md.bam --read_filter QualCalFilter,table=HCC1395_BL.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 HCC1395_BL.table.post --algo ReadWriter HCC1395_BL.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:164000001, elapsed 0.3s, est remaining 5.2s, peak mem 387MB, user 2.3s, sys 4.9s, output queue size 10
progress 10% @chr2:65000001, elapsed 0.5s, est remaining 4.4s, peak mem 557MB, user 4.4s, sys 9.3s, output queue size 41
progress 15% @chr2:221000001, elapsed 0.7s, est remaining 4.0s, peak mem 639MB, user 6.4s, sys 13.8s, output queue size 14
progress 20% @chr3:139000001, elapsed 0.9s, est remaining 3.6s, peak mem 720MB, user 8.6s, sys 18.1s, output queue size 14
progress 25% @chr4:122000001, elapsed 1.1s, est remaining 3.3s, peak mem 820MB, user 10.6s, sys 22.2s, output queue size 8
progress 30% @chr5:76000001, elapsed 1.3s, est remaining 3.0s, peak mem 859MB, user 11.9s, sys 26.6s, output queue size 11
progress 35% @chr6:20000001, elapsed 1.5s, est remaining 2.7s, peak mem 972MB, user 13.2s, sys 30.8s, output queue size 45
progress 40% @chr7:38000001, elapsed 1.7s, est remaining 2.5s, peak mem 1024MB, user 14.5s, sys 35.1s, output queue size 17
progress 45% @chr8:67000001, elapsed 1.8s, est remaining 2.3s, peak mem 1137MB, user 16.0s, sys 39.2s, output queue size 65
progress 50% @chr9:76000001, elapsed 2.0s, est remaining 2.0s, peak mem 1230MB, user 17.2s, sys 43.8s, output queue size 8
progress 55% @chr10:105000001, elapsed 2.2s, est remaining 1.8s, peak mem 1271MB, user 18.4s, sys 48.3s, output queue size 7
progress 60% @chr11:127000001, elapsed 2.4s, est remaining 1.6s, peak mem 1347MB, user 19.5s, sys 53.0s, output queue size 11
progress 65% @chr13:1000001, elapsed 2.6s, est remaining 1.4s, peak mem 1361MB, user 20.8s, sys 57.4s, output queue size 15
progress 70% @chr14:77000001, elapsed 2.8s, est remaining 1.2s, peak mem 1396MB, user 22.2s, sys 61.2s, output queue size 16
progress 75% @chr15:98000001, elapsed 2.9s, est remaining 1.0s, peak mem 1451MB, user 23.6s, sys 65.1s, output queue size 33
progress 80% @chr18:10000001, elapsed 3.1s, est remaining 0.8s, peak mem 1530MB, user 24.7s, sys 69.1s, output queue size 17
progress 85% @chr20:24000001, elapsed 3.3s, est remaining 0.6s, peak mem 1598MB, user 26.0s, sys 72.9s, output queue size 16
progress 90% @chrX:46000001, elapsed 3.8s, est remaining 0.4s, peak mem 2816MB, user 30.9s, sys 75.2s, output queue size 114
progress 95% @chrY:39000001, elapsed 4.1s, est remaining 0.2s, peak mem 2843MB, user 37.0s, sys 76.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 5.7s, est remaining 0.0s, peak mem 2861MB, user 55.0s, sys 78.7s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 00050657
  features: 1f8bfbff fffa3203
  extended: d19f47ab 00000018
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz
threads: 31 max 64
algo: QualCal ReadWriter
license: sentieon:QualCal=31 sentieon:ReadWriter=31
input file size: 51395357
output file size: 71692772
reads: 1001089
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.002 user 0.018 sys 0.075 real
ReadQualCal::delayed_init: 1 calls 0.007 user 0.001 sys 0.032 real
ReadQualCal::init: 1 calls 0.010 user 0.000 sys 0.011 real
advance: 3219322 calls 4.919 user 9.714 sys 14.609 real
done: 1 calls 0.609 user 0.381 sys 0.997 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.002 user 0.009 sys 5.824 real
fetch: 3219322 calls 2.419 user 8.904 sys 11.701 real
fetch_reads: 3219322 calls 2.645 user 8.424 sys 11.859 real
fetch_ref: 13103 calls 0.100 user 0.032 sys 0.116 real
fetch_vcf: 13103 calls 2.277 user 0.109 sys 2.653 real
idle: 2069 calls 3.496 user 0.469 sys 96.409 real
init: 1 calls 0.009 user 0.001 sys 0.041 real
update: 13298 calls 13.080 user 2.705 sys 16.415 real
write: 3219322 calls 11.711 user 9.006 sys 20.921 real
overall: 3000303616 mem 64.338 user 80.046 sys 8.330 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before HCC1395_BL.table --after HCC1395_BL.table.post HCC1395_BL.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: 00050657
  features: 1f8bfbff fffa3203
  extended: d19f47ab 00000018
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz
threads: 31 max 64
algo: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.035 user 0.000 sys 0.043 real
done: 1 calls 0.080 user 0.025 sys 0.102 real
idle: 60 calls 0.001 user 0.000 sys 31.443 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 83386368 mem 0.111 user 0.066 sys 1.068 real