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/6c/e55d0dd973077eff45f84c6b9fbecb/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/17/ba2bf8801862cc2a867a5124cc7c7b/HCC1395_BL.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/984ada276a39686e53532178f7d533/.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/46/984ada276a39686e53532178f7d533/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/e55d0dd973077eff45f84c6b9fbecb/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 0.2s, est remaining 3.8s, peak mem 332MB, user 0.5s, sys 5.0s, output queue size 30
progress 10% @chr2:70000001, elapsed 0.4s, est remaining 3.4s, peak mem 506MB, user 0.9s, sys 10.0s, output queue size 41
progress 15% @chr3:18000001, elapsed 0.5s, est remaining 3.1s, peak mem 593MB, user 1.3s, sys 14.7s, output queue size 25
progress 20% @chr3:177000001, elapsed 0.7s, est remaining 2.9s, peak mem 710MB, user 1.6s, sys 19.8s, output queue size 15
progress 25% @chr4:110000001, elapsed 0.9s, est remaining 2.7s, peak mem 776MB, user 1.9s, sys 25.0s, output queue size 6
progress 30% @chr5:78000001, elapsed 1.1s, est remaining 2.5s, peak mem 818MB, user 2.1s, sys 30.1s, output queue size 8
progress 35% @chr6:39000001, elapsed 1.3s, est remaining 2.4s, peak mem 923MB, user 2.5s, sys 36.0s, output queue size 26
progress 40% @chr7:75000001, elapsed 1.5s, est remaining 2.2s, peak mem 968MB, user 2.9s, sys 42.4s, output queue size 8
progress 45% @chr8:51000001, elapsed 1.7s, est remaining 2.1s, peak mem 1106MB, user 3.2s, sys 49.0s, output queue size 65
progress 50% @chr9:66000001, elapsed 1.9s, est remaining 1.9s, peak mem 1187MB, user 3.5s, sys 55.8s, output queue size 7
progress 55% @chr10:103000001, elapsed 2.2s, est remaining 1.8s, peak mem 1223MB, user 3.8s, sys 62.4s, output queue size 7
progress 60% @chr11:123000001, elapsed 2.4s, est remaining 1.6s, peak mem 1304MB, user 4.0s, sys 69.2s, output queue size 24
progress 65% @chr13:12000001, elapsed 2.6s, est remaining 1.4s, peak mem 1352MB, user 4.2s, sys 76.1s, output queue size 3
progress 70% @chr14:60000001, elapsed 2.9s, est remaining 1.2s, peak mem 1388MB, user 4.5s, sys 82.9s, output queue size 33
progress 75% @chr16:13000001, elapsed 3.1s, est remaining 1.0s, peak mem 1457MB, user 4.8s, sys 90.2s, output queue size 10
progress 80% @chr17:74000001, elapsed 3.4s, est remaining 0.8s, peak mem 1514MB, user 5.2s, sys 97.7s, output queue size 18
progress 85% @chr20:24000001, elapsed 3.6s, est remaining 0.6s, peak mem 1577MB, user 5.4s, sys 105.1s, output queue size 1
progress 90% @chrX:39000001, elapsed 4.0s, est remaining 0.4s, peak mem 2729MB, user 9.0s, sys 108.4s, output queue size 114
progress 95% @chrY:35000001, elapsed 4.3s, est remaining 0.2s, peak mem 2753MB, user 11.8s, sys 112.1s, output queue size 276
progress 100% @chr21:41000001, elapsed 6.2s, est remaining 0.0s, peak mem 2771MB, user 23.4s, sys 116.9s, 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 384
algo: QualCal ReadWriter
license: sentieon:QualCal=31 sentieon:ReadWriter=31
input file size: 51395352
output file size: 71692764
reads: 1001089
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.004 sys 0.029 real
ReadQualCal::delayed_init: 1 calls 0.004 user 0.000 sys 0.017 real
ReadQualCal::init: 1 calls 0.010 user 0.000 sys 0.006 real
advance: 3219322 calls 1.950 user 14.744 sys 16.441 real
done: 1 calls 0.227 user 0.730 sys 0.965 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.007 user 0.001 sys 6.246 real
fetch: 3219322 calls 0.340 user 14.372 sys 14.128 real
fetch_reads: 3219322 calls 0.412 user 14.355 sys 14.213 real
fetch_ref: 13103 calls 0.012 user 0.060 sys 0.087 real
fetch_vcf: 13103 calls 1.237 user 0.176 sys 1.676 real
idle: 1572 calls 0.789 user 0.320 sys 109.797 real
init: 1 calls 0.004 user 0.000 sys 0.023 real
update: 13298 calls 6.284 user 1.740 sys 8.749 real
write: 3219322 calls 8.244 user 13.997 sys 22.819 real
overall: 2906542080 mem 26.531 user 118.784 sys 8.594 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 384
algo: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.019 user 0.011 sys 0.026 real
done: 1 calls 0.048 user 0.012 sys 0.056 real
idle: 61 calls 0.003 user 0.000 sys 31.294 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 81944576 mem 0.057 user 0.057 sys 1.047 real