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/25/1a4064ab82825b8e5da8800eb88b8d/Sig_18_Blood.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/fd07f3bccb2b3e7b5521fe26c79365/.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/16/fd07f3bccb2b3e7b5521fe26c79365/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/4448d88d22dbf0401f991ab3b3c741/Sig_18_Blood.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/4448d88d22dbf0401f991ab3b3c741/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% @chr1:160000001, elapsed 0.2s, est remaining 3.9s, peak mem 326MB, user 0.6s, sys 5.0s, output queue size 8
progress 10% @chr2:72000001, elapsed 0.4s, est remaining 3.3s, peak mem 539MB, user 1.4s, sys 9.3s, output queue size 41
progress 15% @chr2:233000001, elapsed 0.5s, est remaining 3.0s, peak mem 605MB, user 1.9s, sys 13.9s, output queue size 22
progress 20% @chr3:132000001, elapsed 0.7s, est remaining 2.8s, peak mem 725MB, user 2.4s, sys 18.4s, output queue size 21
progress 25% @chr4:115000001, elapsed 0.9s, est remaining 2.6s, peak mem 839MB, user 3.1s, sys 22.7s, output queue size 15
progress 30% @chr5:84000001, elapsed 1.0s, est remaining 2.4s, peak mem 920MB, user 3.6s, sys 27.2s, output queue size 7
progress 35% @chr6:75000001, elapsed 1.2s, est remaining 2.2s, peak mem 953MB, user 4.2s, sys 31.4s, output queue size 8
progress 40% @chr7:65000001, elapsed 1.3s, est remaining 2.0s, peak mem 1007MB, user 4.6s, sys 35.9s, output queue size 12
progress 45% @chr8:82000001, elapsed 1.6s, est remaining 1.9s, peak mem 1091MB, user 5.0s, sys 41.7s, output queue size 65
progress 50% @chr9:72000001, elapsed 1.9s, est remaining 1.9s, peak mem 1193MB, user 5.6s, sys 50.8s, output queue size 38
progress 55% @chr10:98000001, elapsed 2.2s, est remaining 1.8s, peak mem 1253MB, user 6.2s, sys 60.6s, output queue size 31
progress 60% @chr11:120000001, elapsed 2.5s, est remaining 1.7s, peak mem 1289MB, user 6.7s, sys 70.0s, output queue size 27
progress 65% @chr13:8000001, elapsed 2.8s, est remaining 1.5s, peak mem 1331MB, user 7.3s, sys 79.3s, output queue size 25
progress 70% @chr14:57000001, elapsed 3.2s, est remaining 1.4s, peak mem 1409MB, user 7.8s, sys 88.9s, output queue size 28
progress 75% @chr16:10000001, elapsed 3.5s, est remaining 1.2s, peak mem 1457MB, user 8.4s, sys 98.3s, output queue size 13
progress 80% @chr18:10000001, elapsed 3.8s, est remaining 1.0s, peak mem 1508MB, user 8.8s, sys 107.8s, output queue size 14
progress 85% @chr20:21000001, elapsed 4.1s, est remaining 0.7s, peak mem 1547MB, user 9.2s, sys 117.2s, output queue size 10
progress 90% @chrX:38000001, elapsed 4.6s, est remaining 0.5s, peak mem 2744MB, user 13.5s, sys 122.1s, output queue size 114
progress 95% @chrY:39000001, elapsed 4.9s, est remaining 0.3s, peak mem 2762MB, user 18.2s, sys 126.9s, output queue size 276
progress 100% @chr21:41000001, elapsed 7.0s, est remaining 0.0s, peak mem 2768MB, user 29.1s, sys 133.9s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 52290615
output file size: 74586815
reads: 1001133
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.019 real
ReadQualCal::delayed_init: 1 calls 0.006 user 0.001 sys 0.021 real
ReadQualCal::init: 1 calls 0.000 user 0.000 sys 0.006 real
advance: 3219322 calls 2.101 user 16.203 sys 18.762 real
done: 1 calls 0.287 user 0.532 sys 0.822 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.005 user 0.000 sys 7.089 real
fetch: 3219322 calls 0.403 user 16.262 sys 16.909 real
fetch_reads: 3219322 calls 0.450 user 15.744 sys 17.019 real
fetch_ref: 13318 calls 0.034 user 0.070 sys 0.090 real
fetch_vcf: 13318 calls 1.152 user 0.135 sys 1.623 real
idle: 1380 calls 0.745 user 0.364 sys 109.355 real
init: 1 calls 0.008 user 0.001 sys 0.027 real
update: 13537 calls 6.475 user 2.103 sys 9.323 real
write: 3219322 calls 10.373 user 16.365 sys 26.968 real
overall: 2903117824 mem 32.378 user 135.632 sys 9.318 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 6.12.83
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 0.019 user 0.001 sys 0.027 real
done: 1 calls 0.046 user 0.004 sys 0.058 real
idle: 61 calls 0.002 user 0.000 sys 31.344 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 81895424 mem 0.068 user 0.045 sys 1.052 real