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/e5/5e14d3c54516fce231a15f3d7307d2/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/7f/f5e082a230a78092275a6a1565f0e7/HCC1395_BL.table
  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/e7/493cf948b1d450f8051fba2ea0097a/.command.sh
  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/e7/493cf948b1d450f8051fba2ea0097a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/5e14d3c54516fce231a15f3d7307d2/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% @chr1:142000001, elapsed 0.1s, est remaining 2.8s, peak mem 332MB, user 0.3s, sys 3.7s, output queue size 29
progress 10% @chr2:52000001, elapsed 0.3s, est remaining 2.5s, peak mem 467MB, user 0.7s, sys 7.0s, output queue size 41
progress 15% @chr2:218000001, elapsed 0.4s, est remaining 2.2s, peak mem 626MB, user 1.0s, sys 10.5s, output queue size 18
progress 20% @chr3:155000001, elapsed 0.6s, est remaining 2.3s, peak mem 731MB, user 1.3s, sys 15.4s, output queue size 27
progress 25% @chr4:113000001, elapsed 0.8s, est remaining 2.4s, peak mem 794MB, user 1.7s, sys 21.6s, output queue size 29
progress 30% @chr5:80000001, elapsed 1.0s, est remaining 2.3s, peak mem 845MB, user 2.1s, sys 28.1s, output queue size 34
progress 35% @chr6:48000001, elapsed 1.2s, est remaining 2.3s, peak mem 926MB, user 2.5s, sys 34.3s, output queue size 21
progress 40% @chr7:80000001, elapsed 1.5s, est remaining 2.2s, peak mem 992MB, user 2.9s, sys 40.8s, output queue size 39
progress 45% @chr8:77000001, elapsed 1.7s, est remaining 2.1s, peak mem 1109MB, user 3.2s, sys 49.0s, output queue size 70
progress 50% @chr9:57000001, elapsed 2.0s, est remaining 2.0s, peak mem 1178MB, user 3.6s, sys 57.7s, output queue size 30
progress 55% @chr10:78000001, elapsed 2.3s, est remaining 1.9s, peak mem 1223MB, user 4.0s, sys 66.0s, output queue size 24
progress 60% @chr11:115000001, elapsed 2.6s, est remaining 1.7s, peak mem 1307MB, user 4.3s, sys 74.2s, output queue size 17
progress 65% @chr13:3000001, elapsed 2.8s, est remaining 1.5s, peak mem 1352MB, user 4.7s, sys 82.2s, output queue size 20
progress 70% @chr14:50000001, elapsed 3.1s, est remaining 1.3s, peak mem 1421MB, user 5.0s, sys 90.3s, output queue size 18
progress 75% @chr16:12000001, elapsed 3.4s, est remaining 1.1s, peak mem 1496MB, user 5.3s, sys 98.6s, output queue size 11
progress 80% @chr17:75000001, elapsed 3.7s, est remaining 0.9s, peak mem 1520MB, user 5.7s, sys 106.9s, output queue size 16
progress 85% @chr20:16000001, elapsed 4.0s, est remaining 0.7s, peak mem 1586MB, user 5.9s, sys 115.5s, output queue size 8
progress 90% @chrX:40000001, elapsed 4.4s, est remaining 0.5s, peak mem 2774MB, user 9.8s, sys 120.1s, output queue size 114
progress 95% @chrY:39000001, elapsed 4.7s, est remaining 0.2s, peak mem 2792MB, user 13.0s, sys 124.2s, output queue size 276
progress 100% @chr21:41000001, elapsed 6.6s, est remaining 0.0s, peak mem 2810MB, user 23.9s, sys 130.1s, output queue size 3664
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 384
algo: QualCal ReadWriter
license: sentieon:QualCal=31 sentieon:ReadWriter=31
input file size: 51395354
output file size: 71692765
reads: 1001089
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.023 real
ReadQualCal::delayed_init: 1 calls 0.005 user 0.001 sys 0.018 real
ReadQualCal::init: 1 calls 0.009 user 0.001 sys 0.006 real
advance: 3219322 calls 1.666 user 16.654 sys 18.067 real
done: 1 calls 0.353 user 0.317 sys 0.674 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.002 user 0.000 sys 6.635 real
fetch: 3219322 calls 0.352 user 16.675 sys 14.464 real
fetch_reads: 3219322 calls 0.383 user 16.695 sys 14.569 real
fetch_ref: 13103 calls 0.041 user 0.016 sys 0.077 real
fetch_vcf: 13103 calls 1.289 user 0.098 sys 1.464 real
idle: 1346 calls 0.670 user 0.217 sys 76.890 real
init: 1 calls 0.012 user 0.001 sys 0.025 real
update: 13298 calls 6.654 user 1.396 sys 8.531 real
write: 3219322 calls 8.648 user 16.892 sys 24.696 real
overall: 2946551808 mem 27.259 user 131.726 sys 7.969 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 6.12.88
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 384
algo: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.029 user 0.001 sys 0.026 real
done: 1 calls 0.060 user 0.002 sys 0.056 real
idle: 61 calls 0.002 user 0.000 sys 31.313 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 81944576 mem 0.071 user 0.040 sys 1.050 real