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/01/500ff411ac93a70f78f4f5a487b4e0/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/1b/9cf16232f6308bf5e170bf35e998c6/HCC1395_BL.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/67b2f0e91ea561f47eaf645e5fc329/.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/e1/67b2f0e91ea561f47eaf645e5fc329/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/500ff411ac93a70f78f4f5a487b4e0/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% @chr1:167000001, elapsed 0.1s, est remaining 2.2s, peak mem 341MB, user 0.3s, sys 2.7s, output queue size 11
progress 10% @chr2:76000001, elapsed 0.2s, est remaining 1.9s, peak mem 503MB, user 0.5s, sys 5.2s, output queue size 41
progress 15% @chr2:234000001, elapsed 0.3s, est remaining 1.6s, peak mem 587MB, user 0.7s, sys 7.8s, output queue size 4
progress 20% @chr3:136000001, elapsed 0.4s, est remaining 1.5s, peak mem 689MB, user 0.9s, sys 10.3s, output queue size 17
progress 25% @chr4:117000001, elapsed 0.5s, est remaining 1.4s, peak mem 791MB, user 1.1s, sys 12.7s, output queue size 14
progress 30% @chr5:87000001, elapsed 0.6s, est remaining 1.3s, peak mem 845MB, user 1.3s, sys 15.1s, output queue size 13
progress 35% @chr6:68000001, elapsed 0.6s, est remaining 1.2s, peak mem 965MB, user 1.5s, sys 17.6s, output queue size 19
progress 40% @chr7:56000001, elapsed 0.7s, est remaining 1.1s, peak mem 1019MB, user 1.8s, sys 20.0s, output queue size 13
progress 45% @chr8:59000001, elapsed 0.8s, est remaining 1.0s, peak mem 1124MB, user 2.0s, sys 22.5s, output queue size 7
progress 50% @chr9:76000001, elapsed 0.9s, est remaining 0.9s, peak mem 1211MB, user 2.2s, sys 24.9s, output queue size 10
progress 55% @chr10:95000001, elapsed 1.0s, est remaining 0.8s, peak mem 1268MB, user 2.5s, sys 27.3s, output queue size 2
progress 60% @chr11:123000001, elapsed 1.1s, est remaining 0.7s, peak mem 1349MB, user 2.8s, sys 29.6s, output queue size 15
progress 65% @chr13:17000001, elapsed 1.2s, est remaining 0.6s, peak mem 1397MB, user 3.0s, sys 32.0s, output queue size 15
progress 70% @chr14:64000001, elapsed 1.2s, est remaining 0.5s, peak mem 1484MB, user 3.2s, sys 34.5s, output queue size 25
progress 75% @chr16:13000001, elapsed 1.3s, est remaining 0.4s, peak mem 1550MB, user 3.4s, sys 37.2s, output queue size 12
progress 80% @chr17:78000001, elapsed 1.5s, est remaining 0.4s, peak mem 1586MB, user 3.9s, sys 42.3s, output queue size 25
progress 85% @chr20:45000001, elapsed 1.7s, est remaining 0.3s, peak mem 1679MB, user 4.5s, sys 48.2s, output queue size 17
progress 90% @chrX:43000001, elapsed 2.1s, est remaining 0.2s, peak mem 2759MB, user 7.2s, sys 51.3s, output queue size 114
progress 95% @chrY:35000001, elapsed 2.3s, est remaining 0.1s, peak mem 2789MB, user 10.8s, sys 53.5s, output queue size 276
progress 100% @chr21:41000001, elapsed 4.3s, est remaining 0.0s, peak mem 2804MB, user 21.6s, sys 56.9s, 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: 51395347
output file size: 71692763
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 0.002 user 0.000 sys 0.025 real
ReadQualCal::init: 1 calls 0.010 user 0.000 sys 0.006 real
advance: 3219322 calls 1.532 user 6.427 sys 8.715 real
done: 1 calls 0.410 user 0.218 sys 0.632 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.004 user 0.000 sys 4.419 real
fetch: 3219322 calls 0.374 user 6.918 sys 7.207 real
fetch_reads: 3219322 calls 0.544 user 7.320 sys 7.296 real
fetch_ref: 13103 calls 0.050 user 0.010 sys 0.063 real
fetch_vcf: 13103 calls 1.256 user 0.041 sys 1.393 real
idle: 1681 calls 0.868 user 0.205 sys 104.804 real
init: 1 calls 0.005 user 0.000 sys 0.031 real
update: 13298 calls 5.706 user 1.672 sys 7.877 real
write: 3219322 calls 7.985 user 6.539 sys 14.847 real
overall: 2941222912 mem 25.553 user 58.038 sys 6.436 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 384
algo: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.020 user 0.010 sys 0.026 real
done: 1 calls 0.039 user 0.021 sys 0.055 real
idle: 61 calls 0.002 user 0.000 sys 31.261 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 81862656 mem 0.062 user 0.047 sys 1.051 real