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/ff/f3a375b7b100b7ddc159ec42bc9e55/.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/ff/f3a375b7b100b7ddc159ec42bc9e55/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/55e68b26048fb02e6d377a2b8f5bd1/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/scatter/chr14_64122012-64122133.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/55e68b26048fb02e6d377a2b8f5bd1/Sig_18_Blood.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
==> STAGING COMPLETE (9 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr14_64122012-64122133.bed.gz -i Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_2.haplotyper.chr14_64122012-64122133.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr14:100880712, elapsed 0.0s, est remaining 0.9s, peak mem 84MB, user 0.0s, sys 0.2s, output queue size 1948
progress 10% @chr15:40899144, elapsed 0.1s, est remaining 0.8s, peak mem 94MB, user 0.0s, sys 0.3s, output queue size 4189
progress 15% @chr15:63924816, elapsed 0.1s, est remaining 0.8s, peak mem 102MB, user 0.1s, sys 0.5s, output queue size 6813
progress 20% @chr15:87989891, elapsed 0.2s, est remaining 0.7s, peak mem 111MB, user 0.1s, sys 0.6s, output queue size 1161
progress 25% @chr16:1952874, elapsed 0.2s, est remaining 0.6s, peak mem 118MB, user 0.2s, sys 0.7s, output queue size 2849
progress 30% @chr16:23524371, elapsed 0.3s, est remaining 0.6s, peak mem 127MB, user 0.2s, sys 1.0s, output queue size 5329
progress 35% @chr16:66536964, elapsed 0.3s, est remaining 0.6s, peak mem 138MB, user 0.3s, sys 1.2s, output queue size 7930
progress 40% @chr16:89270813, elapsed 0.3s, est remaining 0.5s, peak mem 147MB, user 0.4s, sys 1.4s, output queue size 10408
progress 45% @chr17:10019777, elapsed 0.4s, est remaining 0.5s, peak mem 163MB, user 0.4s, sys 1.6s, output queue size 13018
progress 50% @chr17:36260780, elapsed 0.5s, est remaining 0.5s, peak mem 171MB, user 0.4s, sys 1.9s, output queue size 15615
progress 55% @chr17:45113122, elapsed 0.5s, est remaining 0.4s, peak mem 180MB, user 0.5s, sys 2.2s, output queue size 17858
progress 60% @chr17:68347125, elapsed 0.5s, est remaining 0.4s, peak mem 193MB, user 0.5s, sys 2.4s, output queue size 20390
progress 65% @chr18:5433903, elapsed 0.6s, est remaining 0.3s, peak mem 201MB, user 0.6s, sys 2.7s, output queue size 23110
progress 70% @chr18:62978262, elapsed 0.7s, est remaining 0.3s, peak mem 213MB, user 0.6s, sys 3.0s, output queue size 25505
progress 75% @chr19:6924678, elapsed 0.7s, est remaining 0.2s, peak mem 222MB, user 0.7s, sys 3.2s, output queue size 27876
progress 80% @chr19:15263420, elapsed 0.7s, est remaining 0.2s, peak mem 228MB, user 0.7s, sys 3.4s, output queue size 30132
progress 85% @chr19:36922771, elapsed 0.8s, est remaining 0.1s, peak mem 243MB, user 0.8s, sys 3.6s, output queue size 32447
progress 90% @chr19:46493558, elapsed 0.8s, est remaining 0.1s, peak mem 247MB, user 0.8s, sys 3.8s, output queue size 34621
progress 95% @chr20:36905333, elapsed 0.9s, est remaining 0.0s, peak mem 262MB, user 0.8s, sys 4.1s, output queue size 37258
progress 100% @chr20:64273221, elapsed 0.9s, est remaining 0.0s, peak mem 270MB, user 0.9s, sys 4.3s, output queue size 39696
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 12 max 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74586807
output file size: 22310
reads: 1001133
contig: 48152 intervals 9000028 bases
active: 97912 calls 0.009 user 0.003 sys 0.021 real
advance: 49760 calls 0.009 user 0.021 sys 0.025 real
calc: 97912 calls 0.000 user 0.010 sys 0.021 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.001 user 0.010 sys 1.673 real
fetch: 97912 calls 0.011 user 0.000 sys 0.021 real
fetch_ref: 97912 calls 0.175 user 0.057 sys 0.400 real
idle: 39 calls 0.002 user 0.005 sys 21.468 real
init: 1 calls 0.027 user 0.023 sys 0.053 real
region: 97912 calls 0.000 user 0.006 sys 0.022 real
tracker: 97912 calls 0.046 user 0.012 sys 0.104 real
overall: 286576640 mem 1.380 user 6.356 sys 2.812 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory