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-rnd-pltf-dev-nextflow-scratch-01/work/ee/7136949d40d953659fd7a38775cd98/HCC1395_BL.md.bam
  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/7a/e0b429ae1a44bb4a39dd96b7aacc63/HCC1395_BL.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/a4798a32f5e9daf45b045790a1d26d/.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/98/a4798a32f5e9daf45b045790a1d26d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/7136949d40d953659fd7a38775cd98/HCC1395_BL.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 HCC1395_BL.md.bam --read_filter QualCalFilter,table=HCC1395_BL.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_BL.table.post --algo ReadWriter HCC1395_BL.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:159000001, elapsed 0.1s, est remaining 2.8s, peak mem 351MB, user 0.4s, sys 3.5s, output queue size 11
progress 10% @chr2:62000001, elapsed 0.3s, est remaining 2.4s, peak mem 552MB, user 0.7s, sys 6.7s, output queue size 41
progress 15% @chr2:239000001, elapsed 0.4s, est remaining 2.2s, peak mem 634MB, user 0.9s, sys 10.1s, output queue size 10
progress 20% @chr3:152000001, elapsed 0.5s, est remaining 2.0s, peak mem 741MB, user 1.2s, sys 13.5s, output queue size 1
progress 25% @chr4:117000001, elapsed 0.6s, est remaining 1.8s, peak mem 835MB, user 1.4s, sys 16.7s, output queue size 14
progress 30% @chr5:85000001, elapsed 0.7s, est remaining 1.7s, peak mem 865MB, user 1.6s, sys 19.9s, output queue size 2
progress 35% @chr6:67000001, elapsed 0.8s, est remaining 1.5s, peak mem 927MB, user 1.9s, sys 23.2s, output queue size 17
progress 40% @chr7:53000001, elapsed 0.9s, est remaining 1.4s, peak mem 994MB, user 2.1s, sys 26.4s, output queue size 2
progress 45% @chr8:57000001, elapsed 1.1s, est remaining 1.3s, peak mem 1128MB, user 2.3s, sys 29.6s, output queue size 65
progress 50% @chr9:75000001, elapsed 1.2s, est remaining 1.2s, peak mem 1216MB, user 2.7s, sys 32.9s, output queue size 10
progress 55% @chr10:98000001, elapsed 1.3s, est remaining 1.1s, peak mem 1266MB, user 3.0s, sys 36.0s, output queue size 20
progress 60% @chr11:110000001, elapsed 1.4s, est remaining 0.9s, peak mem 1344MB, user 3.3s, sys 39.2s, output queue size 14
progress 65% @chr13:14000001, elapsed 1.5s, est remaining 0.8s, peak mem 1387MB, user 3.5s, sys 42.4s, output queue size 2
progress 70% @chr14:58000001, elapsed 1.6s, est remaining 0.7s, peak mem 1470MB, user 3.8s, sys 45.6s, output queue size 3
progress 75% @chr16:14000001, elapsed 1.7s, est remaining 0.6s, peak mem 1518MB, user 4.1s, sys 48.9s, output queue size 1
progress 80% @chr17:82000001, elapsed 1.8s, est remaining 0.5s, peak mem 1563MB, user 4.3s, sys 52.1s, output queue size 2
progress 85% @chr20:21000001, elapsed 2.0s, est remaining 0.3s, peak mem 1675MB, user 4.5s, sys 55.6s, output queue size 8
progress 90% @chrX:42000001, elapsed 2.3s, est remaining 0.3s, peak mem 2782MB, user 7.1s, sys 57.2s, output queue size 114
progress 95% @chrY:42000001, elapsed 2.4s, est remaining 0.1s, peak mem 2809MB, user 8.8s, sys 58.2s, output queue size 276
progress 100% @chr21:41000001, elapsed 4.4s, est remaining 0.0s, peak mem 2830MB, user 20.9s, sys 59.8s, 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 192
algo: QualCal ReadWriter
license: sentieon:QualCal=31 sentieon:ReadWriter=31
input file size: 51395357
output file size: 71692772
reads: 1001089
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.022 real
ReadQualCal::delayed_init: 1 calls 0.000 user 0.000 sys 0.025 real
ReadQualCal::init: 1 calls 0.000 user 0.000 sys 0.006 real
advance: 3219322 calls 1.643 user 7.122 sys 8.867 real
done: 1 calls 0.288 user 0.406 sys 0.699 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.002 user 0.000 sys 4.478 real
fetch: 3219322 calls 0.313 user 7.380 sys 7.720 real
fetch_reads: 3219322 calls 0.408 user 6.984 sys 7.799 real
fetch_ref: 13103 calls 0.036 user 0.007 sys 0.055 real
fetch_vcf: 13103 calls 1.158 user 0.079 sys 1.391 real
idle: 2010 calls 1.110 user 0.230 sys 105.216 real
init: 1 calls 0.006 user 0.000 sys 0.031 real
update: 13298 calls 5.644 user 0.997 sys 7.406 real
write: 3219322 calls 7.229 user 7.157 sys 14.389 real
overall: 2968305664 mem 25.011 user 61.003 sys 6.529 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before HCC1395_BL.table --after HCC1395_BL.table.post HCC1395_BL.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 192
algo: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.020 user 0.000 sys 0.025 real
done: 1 calls 0.050 user 0.000 sys 0.055 real
idle: 61 calls 0.002 user 0.000 sys 31.242 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 82067456 mem 0.073 user 0.031 sys 1.051 real