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-rnd-pltf-dev-nextflow-scratch-01/work/de/50dd12f94eeb22331190484c74ad72/HCC1395_tumor.md.bam.bai
  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/ce/2ef7d0d76e7bbe6fa73bbdbcc429b7/.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-rnd-pltf-dev-nextflow-scratch-01/work/ce/2ef7d0d76e7bbe6fa73bbdbcc429b7/.command.run
  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/de/50dd12f94eeb22331190484c74ad72/HCC1395_tumor.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/ad2d0428b8334b69c4d0849c139fa8/HCC1395_tumor.table
  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_tumor.md.bam --read_filter QualCalFilter,table=HCC1395_tumor.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_tumor.table.post --algo ReadWriter HCC1395_tumor.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:159000001, elapsed 0.2s, est remaining 3.1s, peak mem 300MB, user 0.2s, sys 4.1s, output queue size 2
progress 10% @chr2:73000001, elapsed 0.3s, est remaining 2.6s, peak mem 459MB, user 0.5s, sys 7.9s, output queue size 1
progress 15% @chr2:234000001, elapsed 0.4s, est remaining 2.4s, peak mem 634MB, user 0.7s, sys 11.8s, output queue size 4
progress 20% @chr3:152000001, elapsed 0.6s, est remaining 2.2s, peak mem 710MB, user 0.9s, sys 15.7s, output queue size 1
progress 25% @chr4:115000001, elapsed 0.7s, est remaining 2.1s, peak mem 809MB, user 1.3s, sys 19.5s, output queue size 2
progress 30% @chr5:85000001, elapsed 0.8s, est remaining 1.9s, peak mem 859MB, user 1.5s, sys 23.4s, output queue size 1
progress 35% @chr6:63000001, elapsed 1.0s, est remaining 1.8s, peak mem 899MB, user 1.7s, sys 27.3s, output queue size 2
progress 40% @chr7:55000001, elapsed 1.1s, est remaining 1.6s, peak mem 939MB, user 2.0s, sys 31.3s, output queue size 1
progress 45% @chr8:58000001, elapsed 1.2s, est remaining 1.5s, peak mem 1071MB, user 2.2s, sys 35.2s, output queue size 12
progress 50% @chr9:73000001, elapsed 1.4s, est remaining 1.4s, peak mem 1196MB, user 2.5s, sys 39.1s, output queue size 11
progress 55% @chr10:94000001, elapsed 1.5s, est remaining 1.2s, peak mem 1246MB, user 2.9s, sys 43.0s, output queue size 1
progress 60% @chr11:112000001, elapsed 1.6s, est remaining 1.1s, peak mem 1333MB, user 3.1s, sys 46.9s, output queue size 11
progress 65% @chr13:15000001, elapsed 1.8s, est remaining 1.0s, peak mem 1397MB, user 3.3s, sys 50.8s, output queue size 1
progress 70% @chr14:60000001, elapsed 1.9s, est remaining 0.8s, peak mem 1459MB, user 3.6s, sys 54.7s, output queue size 2
progress 75% @chr16:15000001, elapsed 2.0s, est remaining 0.7s, peak mem 1528MB, user 3.9s, sys 58.6s, output queue size 13
progress 80% @chr18:2000001, elapsed 2.2s, est remaining 0.5s, peak mem 1548MB, user 4.1s, sys 62.5s, output queue size 9
progress 85% @chr20:23000001, elapsed 2.3s, est remaining 0.4s, peak mem 1633MB, user 4.3s, sys 66.4s, output queue size 25
progress 90% @chrX:44000001, elapsed 2.7s, est remaining 0.3s, peak mem 2807MB, user 8.0s, sys 68.2s, output queue size 114
progress 95% @chrY:39000001, elapsed 2.9s, est remaining 0.2s, peak mem 2829MB, user 11.2s, sys 69.4s, output queue size 276
progress 100% @chr21:41000001, elapsed 6.2s, est remaining 0.0s, peak mem 2856MB, user 28.7s, sys 71.7s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 31 max 128
algo: QualCal ReadWriter
license: sentieon:QualCal=31 sentieon:ReadWriter=31
input file size: 50811681
output file size: 81706630
reads: 1001320
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.034 real
ReadQualCal::delayed_init: 1 calls 0.007 user 0.002 sys 0.027 real
ReadQualCal::init: 1 calls 0.009 user 0.001 sys 0.008 real
advance: 3219322 calls 2.014 user 8.708 sys 10.883 real
done: 1 calls 0.324 user 0.293 sys 0.620 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.005 user 0.000 sys 6.216 real
fetch: 3219322 calls 0.385 user 8.537 sys 9.038 real
fetch_reads: 3219322 calls 0.426 user 8.603 sys 9.171 real
fetch_ref: 11263 calls 0.004 user 0.016 sys 0.049 real
fetch_vcf: 11263 calls 1.314 user 0.054 sys 1.436 real
idle: 2337 calls 1.723 user 0.351 sys 115.268 real
init: 1 calls 0.011 user 0.002 sys 0.034 real
update: 11451 calls 8.162 user 1.319 sys 10.709 real
write: 3219322 calls 11.989 user 9.182 sys 20.635 real
overall: 2995523584 mem 34.730 user 72.754 sys 7.576 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before HCC1395_tumor.table --after HCC1395_tumor.table.post HCC1395_tumor.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: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 31 max 128
algo: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.019 user 0.001 sys 0.032 real
done: 1 calls 0.068 user 0.002 sys 0.071 real
idle: 61 calls 0.003 user 0.000 sys 31.267 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 83189760 mem 0.098 user 0.032 sys 1.053 real