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/54/67e80fd959906794093fa1156b5149/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/ca/b758ef17618f14fc6d3195b06dd458/HCC1395_BL.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/8ee7221cb00667c7914a883215e2de/.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/8f/8ee7221cb00667c7914a883215e2de/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/67e80fd959906794093fa1156b5149/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% @chr1:164000001, elapsed 0.2s, est remaining 2.9s, peak mem 360MB, user 0.2s, sys 3.9s, output queue size 10
progress 10% @chr2:76000001, elapsed 0.3s, est remaining 2.4s, peak mem 531MB, user 0.6s, sys 7.1s, output queue size 41
progress 15% @chr2:235000001, elapsed 0.4s, est remaining 2.1s, peak mem 629MB, user 0.8s, sys 10.1s, output queue size 8
progress 20% @chr3:153000001, elapsed 0.5s, est remaining 1.9s, peak mem 720MB, user 1.0s, sys 13.0s, output queue size 1
progress 25% @chr4:118000001, elapsed 0.6s, est remaining 1.7s, peak mem 818MB, user 1.3s, sys 15.9s, output queue size 15
progress 30% @chr5:86000001, elapsed 0.7s, est remaining 1.6s, peak mem 849MB, user 1.5s, sys 18.8s, output queue size 8
progress 35% @chr6:69000001, elapsed 0.8s, est remaining 1.4s, peak mem 959MB, user 1.7s, sys 21.6s, output queue size 6
progress 40% @chr7:55000001, elapsed 0.9s, est remaining 1.3s, peak mem 1019MB, user 2.0s, sys 24.6s, output queue size 10
progress 45% @chr8:58000001, elapsed 1.0s, est remaining 1.2s, peak mem 1148MB, user 2.2s, sys 27.7s, output queue size 8
progress 50% @chr9:74000001, elapsed 1.1s, est remaining 1.1s, peak mem 1239MB, user 2.4s, sys 30.6s, output queue size 21
progress 55% @chr10:90000001, elapsed 1.2s, est remaining 1.0s, peak mem 1272MB, user 2.7s, sys 33.4s, output queue size 5
progress 60% @chr11:123000001, elapsed 1.3s, est remaining 0.9s, peak mem 1337MB, user 2.9s, sys 36.3s, output queue size 3
progress 65% @chr13:16000001, elapsed 1.4s, est remaining 0.7s, peak mem 1358MB, user 3.1s, sys 39.1s, output queue size 5
progress 70% @chr14:55000001, elapsed 1.5s, est remaining 0.6s, peak mem 1425MB, user 3.4s, sys 42.0s, output queue size 6
progress 75% @chr16:14000001, elapsed 1.6s, est remaining 0.5s, peak mem 1473MB, user 3.7s, sys 44.7s, output queue size 6
progress 80% @chr18:2000001, elapsed 1.7s, est remaining 0.4s, peak mem 1508MB, user 3.9s, sys 47.6s, output queue size 18
progress 85% @chr20:22000001, elapsed 1.8s, est remaining 0.3s, peak mem 1599MB, user 4.1s, sys 50.5s, output queue size 2
progress 90% @chrX:45000001, elapsed 2.1s, est remaining 0.2s, peak mem 2793MB, user 6.6s, sys 52.2s, output queue size 114
progress 95% @chrY:43000001, elapsed 2.2s, est remaining 0.1s, peak mem 2816MB, user 8.7s, sys 53.0s, output queue size 276
progress 100% @chr21:41000001, elapsed 4.2s, est remaining 0.0s, peak mem 2838MB, user 20.5s, sys 54.6s, 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 192
algo: QualCal ReadWriter
license: sentieon:QualCal=31 sentieon:ReadWriter=31
input file size: 51395352
output file size: 71692767
reads: 1001089
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.027 real
ReadQualCal::delayed_init: 1 calls 0.001 user 0.000 sys 0.028 real
ReadQualCal::init: 1 calls 0.000 user 0.000 sys 0.006 real
advance: 3219322 calls 1.434 user 7.089 sys 8.269 real
done: 1 calls 0.374 user 0.349 sys 0.727 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.000 user 0.006 sys 4.262 real
fetch: 3219322 calls 0.264 user 6.224 sys 6.886 real
fetch_reads: 3219322 calls 0.358 user 6.600 sys 6.985 real
fetch_ref: 13103 calls 0.040 user 0.016 sys 0.053 real
fetch_vcf: 13103 calls 1.175 user 0.064 sys 1.386 real
idle: 2011 calls 1.223 user 0.305 sys 82.062 real
init: 1 calls 0.001 user 0.003 sys 0.034 real
update: 13298 calls 5.817 user 1.440 sys 7.862 real
write: 3219322 calls 7.274 user 6.218 sys 13.808 real
overall: 2976784384 mem 24.766 user 55.749 sys 5.610 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 6.12.88
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 192
algo: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.030 user 0.000 sys 0.026 real
done: 1 calls 0.050 user 0.010 sys 0.056 real
idle: 60 calls 0.002 user 0.000 sys 31.376 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 83648512 mem 0.082 user 0.023 sys 1.058 real