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/c0/27a7120bbd056aabaf825da99c116d/Sig_18_Blood.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/8fc7f5716dfc4a815738382b6d56eb/.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/f1/8fc7f5716dfc4a815738382b6d56eb/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/bbd12b88b5b205c4c95cb8bf8866c9/Sig_18_Blood.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/bbd12b88b5b205c4c95cb8bf8866c9/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% @chr1:164000001, elapsed 0.1s, est remaining 2.5s, peak mem 308MB, user 0.3s, sys 3.2s, output queue size 11
progress 10% @chr2:73000001, elapsed 0.2s, est remaining 2.1s, peak mem 512MB, user 0.5s, sys 6.0s, output queue size 41
progress 15% @chr2:234000001, elapsed 0.3s, est remaining 1.8s, peak mem 614MB, user 0.8s, sys 8.6s, output queue size 10
progress 20% @chr3:156000001, elapsed 0.4s, est remaining 1.7s, peak mem 764MB, user 1.0s, sys 11.2s, output queue size 5
progress 25% @chr4:117000001, elapsed 0.5s, est remaining 1.5s, peak mem 860MB, user 1.2s, sys 13.9s, output queue size 18
progress 30% @chr5:89000001, elapsed 0.6s, est remaining 1.4s, peak mem 941MB, user 1.5s, sys 16.4s, output queue size 27
progress 35% @chr6:66000001, elapsed 0.7s, est remaining 1.3s, peak mem 977MB, user 1.8s, sys 18.9s, output queue size 23
progress 40% @chr7:49000001, elapsed 0.9s, est remaining 1.3s, peak mem 1019MB, user 2.2s, sys 23.4s, output queue size 14
progress 45% @chr8:82000001, elapsed 1.0s, est remaining 1.3s, peak mem 1079MB, user 2.6s, sys 28.5s, output queue size 10
progress 50% @chr9:69000001, elapsed 1.2s, est remaining 1.2s, peak mem 1157MB, user 3.1s, sys 33.4s, output queue size 11
progress 55% @chr10:85000001, elapsed 1.4s, est remaining 1.2s, peak mem 1220MB, user 3.3s, sys 40.3s, output queue size 18
progress 60% @chr11:121000001, elapsed 1.7s, est remaining 1.1s, peak mem 1277MB, user 3.6s, sys 47.5s, output queue size 14
progress 65% @chr13:11000001, elapsed 1.9s, est remaining 1.0s, peak mem 1343MB, user 4.0s, sys 54.6s, output queue size 26
progress 70% @chr14:72000001, elapsed 2.2s, est remaining 0.9s, peak mem 1409MB, user 4.3s, sys 61.8s, output queue size 13
progress 75% @chr16:21000001, elapsed 2.4s, est remaining 0.8s, peak mem 1457MB, user 4.7s, sys 69.0s, output queue size 4
progress 80% @chr17:79000001, elapsed 2.7s, est remaining 0.7s, peak mem 1457MB, user 5.0s, sys 76.5s, output queue size 9
progress 85% @chr20:18000001, elapsed 2.9s, est remaining 0.5s, peak mem 1505MB, user 5.4s, sys 84.0s, output queue size 12
progress 90% @chrX:41000001, elapsed 3.4s, est remaining 0.4s, peak mem 2756MB, user 9.9s, sys 88.0s, output queue size 114
progress 95% @chrY:36000001, elapsed 3.7s, est remaining 0.2s, peak mem 2777MB, user 13.2s, sys 91.9s, output queue size 276
progress 100% @chr21:41000001, elapsed 5.8s, est remaining 0.0s, peak mem 2786MB, user 25.4s, sys 97.6s, 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: 52290598
output file size: 74586805
reads: 1001133
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.018 real
ReadQualCal::delayed_init: 1 calls 0.005 user 0.001 sys 0.018 real
ReadQualCal::init: 1 calls 0.000 user 0.000 sys 0.006 real
advance: 3219322 calls 1.744 user 12.981 sys 14.272 real
done: 1 calls 0.319 user 0.844 sys 1.164 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.006 user 0.001 sys 5.878 real
fetch: 3219322 calls 0.298 user 12.432 sys 10.411 real
fetch_reads: 3219322 calls 0.460 user 11.588 sys 10.544 real
fetch_ref: 13318 calls 0.038 user 0.132 sys 0.095 real
fetch_vcf: 13318 calls 1.253 user 0.151 sys 1.642 real
idle: 1500 calls 0.837 user 0.295 sys 115.672 real
init: 1 calls 0.005 user 0.001 sys 0.024 real
update: 13537 calls 6.518 user 2.230 sys 9.304 real
write: 3219322 calls 9.542 user 12.844 sys 22.189 real
overall: 2921398272 mem 28.564 user 99.594 sys 8.235 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: 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 0.027 user 0.003 sys 0.027 real
done: 1 calls 0.055 user 0.005 sys 0.059 real
idle: 61 calls 0.002 user 0.000 sys 31.330 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 81887232 mem 0.079 user 0.036 sys 1.051 real