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/33/2aa9c9057d6aa30f9992ee3be94756/.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/33/2aa9c9057d6aa30f9992ee3be94756/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/381faa0df790cd8579fab559ff3f2b/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/cd/381faa0df790cd8579fab559ff3f2b/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 0.1s, est remaining 1.2s, peak mem 79MB, user 0.0s, sys 0.1s, output queue size 1979
progress 10% @chr15:40899144, elapsed 0.1s, est remaining 0.9s, peak mem 85MB, user 0.1s, sys 0.2s, output queue size 4222
progress 15% @chr15:63774694, elapsed 0.1s, est remaining 0.8s, peak mem 91MB, user 0.1s, sys 0.4s, output queue size 1464
progress 20% @chr15:87980531, elapsed 0.2s, est remaining 0.7s, peak mem 102MB, user 0.1s, sys 0.5s, output queue size 3752
progress 25% @chr16:1950844, elapsed 0.2s, est remaining 0.7s, peak mem 109MB, user 0.1s, sys 0.6s, output queue size 5437
progress 30% @chr16:23524371, elapsed 0.5s, est remaining 1.3s, peak mem 111MB, user 0.2s, sys 0.7s, output queue size 7917
progress 35% @chr16:66566514, elapsed 0.6s, est remaining 1.1s, peak mem 120MB, user 0.2s, sys 0.9s, output queue size 10523
progress 40% @chr16:89290624, elapsed 0.6s, est remaining 1.0s, peak mem 135MB, user 0.2s, sys 1.0s, output queue size 12998
progress 45% @chr17:10309522, elapsed 0.7s, est remaining 0.8s, peak mem 141MB, user 0.3s, sys 1.2s, output queue size 15611
progress 50% @chr17:36428927, elapsed 0.7s, est remaining 0.7s, peak mem 156MB, user 0.3s, sys 1.3s, output queue size 18228
progress 55% @chr17:45113439, elapsed 0.8s, est remaining 0.7s, peak mem 165MB, user 0.3s, sys 1.5s, output queue size 20446
progress 60% @chr17:68426075, elapsed 0.9s, est remaining 0.6s, peak mem 175MB, user 0.4s, sys 1.6s, output queue size 22983
progress 65% @chr18:5890198, elapsed 0.9s, est remaining 0.5s, peak mem 186MB, user 0.4s, sys 1.7s, output queue size 25700
progress 70% @chr18:62574057, elapsed 1.0s, est remaining 0.4s, peak mem 196MB, user 0.4s, sys 1.9s, output queue size 28076
progress 75% @chr19:6924678, elapsed 1.0s, est remaining 0.3s, peak mem 204MB, user 0.5s, sys 2.0s, output queue size 30466
progress 80% @chr19:15264404, elapsed 1.1s, est remaining 0.3s, peak mem 213MB, user 0.5s, sys 2.1s, output queue size 32723
progress 85% @chr19:36996317, elapsed 1.1s, est remaining 0.2s, peak mem 222MB, user 0.6s, sys 2.3s, output queue size 35046
progress 90% @chr19:46469733, elapsed 1.2s, est remaining 0.1s, peak mem 228MB, user 0.6s, sys 2.5s, output queue size 37209
progress 95% @chr20:36916678, elapsed 1.2s, est remaining 0.1s, peak mem 232MB, user 0.6s, sys 2.6s, output queue size 39848
progress 100% @chr20:63408413, elapsed 1.3s, est remaining 0.0s, peak mem 244MB, user 0.7s, sys 2.7s, output queue size 42286
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 12 max 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74586800
output file size: 22310
reads: 1001133
contig: 48152 intervals 9000028 bases
active: 97912 calls 0.000 user 0.001 sys 0.017 real
advance: 49760 calls 0.004 user 0.003 sys 0.023 real
calc: 97912 calls 0.003 user 0.010 sys 0.017 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.007 user 0.002 sys 2.025 real
fetch: 97912 calls 0.000 user 0.002 sys 0.017 real
fetch_ref: 97912 calls 0.074 user 0.034 sys 0.361 real
idle: 39 calls 0.007 user 0.009 sys 21.535 real
init: 1 calls 0.038 user 0.009 sys 0.043 real
region: 97912 calls 0.000 user 0.004 sys 0.020 real
tracker: 97912 calls 0.013 user 0.004 sys 0.095 real
overall: 259788800 mem 1.286 user 4.764 sys 3.147 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory