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/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/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
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/9224b114c369a1a447550d5fcd91e5/Sig_18_Blood.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/9b9bdd2e3a62b63766fd1bff60945d/.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/cc/9b9bdd2e3a62b63766fd1bff60945d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/f84457a21aa906d2a86c8a3c95aa99/Sig_18_Blood.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/f84457a21aa906d2a86c8a3c95aa99/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% @chr1:152000001, elapsed 0.1s, est remaining 2.2s, peak mem 296MB, user 0.4s, sys 2.5s, output queue size 26
progress 10% @chr2:76000001, elapsed 0.2s, est remaining 1.9s, peak mem 533MB, user 0.7s, sys 5.2s, output queue size 17
progress 15% @chr2:238000001, elapsed 0.3s, est remaining 1.7s, peak mem 608MB, user 1.0s, sys 7.7s, output queue size 20
progress 20% @chr3:158000001, elapsed 0.4s, est remaining 1.6s, peak mem 749MB, user 1.4s, sys 10.2s, output queue size 14
progress 25% @chr4:115000001, elapsed 0.5s, est remaining 1.5s, peak mem 860MB, user 1.8s, sys 12.7s, output queue size 15
progress 30% @chr5:90000001, elapsed 0.6s, est remaining 1.4s, peak mem 935MB, user 2.1s, sys 15.3s, output queue size 13
progress 35% @chr6:47000001, elapsed 0.7s, est remaining 1.3s, peak mem 959MB, user 2.4s, sys 17.7s, output queue size 18
progress 40% @chr7:48000001, elapsed 0.8s, est remaining 1.2s, peak mem 1001MB, user 2.8s, sys 21.2s, output queue size 23
progress 45% @chr8:83000001, elapsed 1.0s, est remaining 1.2s, peak mem 1100MB, user 3.4s, sys 25.7s, output queue size 22
progress 50% @chr9:80000001, elapsed 1.1s, est remaining 1.1s, peak mem 1211MB, user 3.9s, sys 30.2s, output queue size 39
progress 55% @chr10:102000001, elapsed 1.3s, est remaining 1.1s, peak mem 1283MB, user 4.6s, sys 35.0s, output queue size 18
progress 60% @chr12:13000001, elapsed 1.5s, est remaining 1.0s, peak mem 1313MB, user 4.9s, sys 39.7s, output queue size 25
progress 65% @chr13:38000001, elapsed 1.7s, est remaining 0.9s, peak mem 1391MB, user 5.5s, sys 44.5s, output queue size 30
progress 70% @chr14:85000001, elapsed 1.8s, est remaining 0.8s, peak mem 1445MB, user 5.9s, sys 49.3s, output queue size 25
progress 75% @chr15:80000001, elapsed 2.1s, est remaining 0.7s, peak mem 1508MB, user 6.6s, sys 55.8s, output queue size 37
progress 80% @chr18:3000001, elapsed 2.3s, est remaining 0.6s, peak mem 1589MB, user 7.1s, sys 62.4s, output queue size 28
progress 85% @chr20:20000001, elapsed 2.5s, est remaining 0.4s, peak mem 1619MB, user 7.5s, sys 68.9s, output queue size 45
progress 90% @chrX:39000001, elapsed 2.9s, est remaining 0.3s, peak mem 2744MB, user 11.2s, sys 71.7s, output queue size 114
progress 95% @chrY:39000001, elapsed 3.1s, est remaining 0.2s, peak mem 2768MB, user 13.9s, sys 73.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 5.6s, est remaining 0.0s, peak mem 2789MB, user 28.1s, sys 76.2s, 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: 52290600
output file size: 74586803
reads: 1001133
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.013 real
ReadQualCal::delayed_init: 1 calls 0.001 user 0.000 sys 0.034 real
ReadQualCal::init: 1 calls 0.009 user 0.001 sys 0.006 real
advance: 3219322 calls 2.110 user 8.874 sys 12.132 real
done: 1 calls 0.328 user 0.265 sys 0.595 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.002 user 0.000 sys 5.686 real
fetch: 3219322 calls 0.243 user 8.755 sys 9.829 real
fetch_reads: 3219322 calls 0.345 user 9.232 sys 9.925 real
fetch_ref: 13318 calls 0.048 user 0.046 sys 0.081 real
fetch_vcf: 13318 calls 1.443 user 0.109 sys 1.759 real
idle: 1959 calls 1.328 user 0.240 sys 95.676 real
init: 1 calls 0.007 user 0.000 sys 0.040 real
update: 13537 calls 6.656 user 1.289 sys 9.248 real
write: 3219322 calls 10.379 user 9.197 sys 19.440 real
overall: 2925461504 mem 32.980 user 77.264 sys 7.035 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 0.029 user 0.001 sys 0.027 real
done: 1 calls 0.058 user 0.002 sys 0.058 real
idle: 61 calls 0.002 user 0.000 sys 31.373 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 81944576 mem 0.088 user 0.022 sys 1.057 real