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/40/c2b0eb611467aa29ca8c1489de19bf/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/0d/c3bca81a476152bf3445d0f9b9ee75/HCC1395_BL.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/ded0dc28f0bedef0afd0b3c848896c/.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/ad/ded0dc28f0bedef0afd0b3c848896c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/c2b0eb611467aa29ca8c1489de19bf/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% @chr1:159000001, elapsed 0.2s, est remaining 3.0s, peak mem 329MB, user 0.5s, sys 3.8s, output queue size 4
progress 10% @chr2:72000001, elapsed 0.3s, est remaining 2.6s, peak mem 500MB, user 1.0s, sys 7.3s, output queue size 41
progress 15% @chr3:17000001, elapsed 0.4s, est remaining 2.4s, peak mem 608MB, user 1.3s, sys 11.0s, output queue size 6
progress 20% @chr3:149000001, elapsed 0.5s, est remaining 2.2s, peak mem 713MB, user 1.7s, sys 14.6s, output queue size 4
progress 25% @chr4:92000001, elapsed 0.7s, est remaining 2.0s, peak mem 776MB, user 2.1s, sys 18.2s, output queue size 23
progress 30% @chr5:73000001, elapsed 0.8s, est remaining 1.9s, peak mem 809MB, user 2.5s, sys 22.0s, output queue size 17
progress 35% @chr6:20000001, elapsed 1.0s, est remaining 1.9s, peak mem 905MB, user 3.0s, sys 27.6s, output queue size 45
progress 40% @chr7:4000001, elapsed 1.3s, est remaining 1.9s, peak mem 968MB, user 3.3s, sys 33.9s, output queue size 51
progress 45% @chr8:80000001, elapsed 1.5s, est remaining 1.8s, peak mem 1079MB, user 3.8s, sys 40.7s, output queue size 47
progress 50% @chr9:93000001, elapsed 1.7s, est remaining 1.7s, peak mem 1106MB, user 4.1s, sys 47.0s, output queue size 82
progress 55% @chr10:116000001, elapsed 1.9s, est remaining 1.6s, peak mem 1145MB, user 4.6s, sys 53.2s, output queue size 71
progress 60% @chr11:56000001, elapsed 2.1s, est remaining 1.4s, peak mem 1205MB, user 5.0s, sys 59.0s, output queue size 100
progress 65% @chr13:36000001, elapsed 2.3s, est remaining 1.3s, peak mem 1253MB, user 5.5s, sys 65.2s, output queue size 64
progress 70% @chr13:111000001, elapsed 2.6s, est remaining 1.1s, peak mem 1298MB, user 5.7s, sys 71.9s, output queue size 65
progress 75% @chr16:30000001, elapsed 2.8s, est remaining 0.9s, peak mem 1331MB, user 6.2s, sys 78.1s, output queue size 51
progress 80% @chr18:16000001, elapsed 3.0s, est remaining 0.7s, peak mem 1397MB, user 6.6s, sys 84.6s, output queue size 50
progress 85% @chr20:38000001, elapsed 3.2s, est remaining 0.6s, peak mem 1412MB, user 6.9s, sys 90.8s, output queue size 54
progress 90% @chrX:35000001, elapsed 3.6s, est remaining 0.4s, peak mem 2756MB, user 10.6s, sys 94.5s, output queue size 114
progress 95% @chrY:17000001, elapsed 3.9s, est remaining 0.2s, peak mem 2792MB, user 13.6s, sys 97.7s, output queue size 276
progress 100% @chr21:41000001, elapsed 5.8s, est remaining 0.0s, peak mem 2801MB, user 25.0s, sys 102.0s, 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: 51395348
output file size: 71692760
reads: 1001089
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.032 sys 0.041 real
ReadQualCal::delayed_init: 1 calls 0.001 user 0.000 sys 0.031 real
ReadQualCal::init: 1 calls 0.000 user 0.000 sys 0.006 real
advance: 3219322 calls 1.611 user 13.180 sys 15.014 real
done: 1 calls 0.370 user 0.321 sys 0.695 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.006 user 0.002 sys 5.842 real
fetch: 3219322 calls 0.322 user 12.848 sys 11.499 real
fetch_reads: 3219322 calls 0.465 user 12.826 sys 11.586 real
fetch_ref: 13103 calls 0.050 user 0.022 sys 0.073 real
fetch_vcf: 13103 calls 1.250 user 0.064 sys 1.424 real
idle: 1503 calls 0.747 user 0.265 sys 79.487 real
init: 1 calls 0.001 user 0.000 sys 0.038 real
update: 13298 calls 6.546 user 1.576 sys 8.587 real
write: 3219322 calls 8.300 user 12.907 sys 21.340 real
overall: 2937081856 mem 28.538 user 103.691 sys 7.199 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 0.028 user 0.002 sys 0.025 real
done: 1 calls 0.057 user 0.003 sys 0.055 real
idle: 61 calls 0.002 user 0.000 sys 31.475 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 81944576 mem 0.075 user 0.032 sys 1.054 real