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-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/c8/38465d89f33b34309f11cd6f1cff58/Sig_18_Blood.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/afbce3389bf5bcfac4e357eeed7653/.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/22/afbce3389bf5bcfac4e357eeed7653/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/d2f581f0b34a6613ec7cf9c4a975c8/Sig_18_Blood.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/d2f581f0b34a6613ec7cf9c4a975c8/Sig_18_Blood.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 Sig_18_Blood.md.bam --read_filter QualCalFilter,table=Sig_18_Blood.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 Sig_18_Blood.table.post --algo ReadWriter Sig_18_Blood.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:163000001, elapsed 0.1s, est remaining 2.5s, peak mem 308MB, user 0.3s, sys 3.2s, output queue size 13
progress 10% @chr2:75000001, elapsed 0.2s, est remaining 2.2s, peak mem 542MB, user 0.7s, sys 6.3s, output queue size 41
progress 15% @chr2:236000001, elapsed 0.4s, est remaining 2.0s, peak mem 620MB, user 1.0s, sys 9.4s, output queue size 18
progress 20% @chr3:154000001, elapsed 0.5s, est remaining 1.8s, peak mem 719MB, user 1.3s, sys 12.4s, output queue size 5
progress 25% @chr4:114000001, elapsed 0.6s, est remaining 1.7s, peak mem 806MB, user 1.5s, sys 15.4s, output queue size 1
progress 30% @chr5:80000001, elapsed 0.7s, est remaining 1.6s, peak mem 866MB, user 1.9s, sys 18.4s, output queue size 9
progress 35% @chr6:65000001, elapsed 0.8s, est remaining 1.5s, peak mem 920MB, user 2.2s, sys 21.4s, output queue size 13
progress 40% @chr7:55000001, elapsed 0.9s, est remaining 1.3s, peak mem 971MB, user 2.5s, sys 24.4s, output queue size 2
progress 45% @chr8:56000001, elapsed 1.0s, est remaining 1.2s, peak mem 1061MB, user 2.8s, sys 27.5s, output queue size 1
progress 50% @chr9:72000001, elapsed 1.1s, est remaining 1.1s, peak mem 1145MB, user 3.0s, sys 30.6s, output queue size 11
progress 55% @chr10:92000001, elapsed 1.3s, est remaining 1.0s, peak mem 1232MB, user 3.4s, sys 34.6s, output queue size 16
progress 60% @chr11:119000001, elapsed 1.5s, est remaining 1.0s, peak mem 1298MB, user 3.7s, sys 40.5s, output queue size 20
progress 65% @chr13:2000001, elapsed 1.7s, est remaining 0.9s, peak mem 1382MB, user 4.1s, sys 47.0s, output queue size 13
progress 70% @chr14:56000001, elapsed 2.0s, est remaining 0.9s, peak mem 1448MB, user 4.5s, sys 55.9s, output queue size 8
progress 75% @chr16:11000001, elapsed 2.3s, est remaining 0.8s, peak mem 1508MB, user 4.9s, sys 64.4s, output queue size 17
progress 80% @chr18:8000001, elapsed 2.6s, est remaining 0.6s, peak mem 1541MB, user 5.3s, sys 73.0s, output queue size 8
progress 85% @chr20:32000001, elapsed 2.9s, est remaining 0.5s, peak mem 1568MB, user 5.7s, sys 81.2s, output queue size 9
progress 90% @chrX:41000001, elapsed 3.4s, est remaining 0.4s, peak mem 2747MB, user 9.7s, sys 85.4s, output queue size 114
progress 95% @chrY:43000001, elapsed 3.6s, est remaining 0.2s, peak mem 2768MB, user 13.9s, sys 89.7s, output queue size 276
progress 100% @chr21:41000001, elapsed 5.8s, est remaining 0.0s, peak mem 2774MB, user 25.3s, sys 95.3s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  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: 52290599
output file size: 74586803
reads: 1001133
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.016 real
ReadQualCal::delayed_init: 1 calls 0.001 user 0.000 sys 0.018 real
ReadQualCal::init: 1 calls 0.009 user 0.001 sys 0.006 real
advance: 3219322 calls 1.900 user 12.096 sys 13.849 real
done: 1 calls 0.410 user 0.406 sys 0.820 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.007 user 0.000 sys 5.883 real
fetch: 3219322 calls 0.221 user 11.609 sys 11.620 real
fetch_reads: 3219322 calls 0.337 user 11.527 sys 11.714 real
fetch_ref: 13318 calls 0.041 user 0.090 sys 0.104 real
fetch_vcf: 13318 calls 1.250 user 0.130 sys 1.871 real
idle: 1452 calls 1.082 user 0.153 sys 112.893 real
init: 1 calls 0.002 user 0.000 sys 0.024 real
update: 13537 calls 6.436 user 1.327 sys 8.582 real
write: 3219322 calls 9.697 user 11.513 sys 21.680 real
overall: 2908811264 mem 29.519 user 96.479 sys 8.087 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before Sig_18_Blood.table --after Sig_18_Blood.table.post Sig_18_Blood.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: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  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 0.023 user 0.002 sys 0.027 real
done: 1 calls 0.045 user 0.010 sys 0.057 real
idle: 61 calls 0.002 user 0.000 sys 31.287 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 81936384 mem 0.070 user 0.040 sys 1.054 real