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/52/79554f24242ec9e970d29b5e8a7a95/.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/52/79554f24242ec9e970d29b5e8a7a95/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/43822faf2c2779416cb601556825c7/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/chr8_93795409-93795507.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/43822faf2c2779416cb601556825c7/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 chr8_93795409-93795507.bed.gz -i Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_2.haplotyper.chr8_93795409-93795507.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr8:144247301, elapsed 0.0s, est remaining 0.8s, peak mem 75MB, user 0.0s, sys 0.1s, output queue size 2389
progress 10% @chr9:36903627, elapsed 0.1s, est remaining 0.7s, peak mem 81MB, user 0.1s, sys 0.3s, output queue size 2892
progress 15% @chr9:96655090, elapsed 0.1s, est remaining 0.6s, peak mem 87MB, user 0.1s, sys 0.5s, output queue size 4673
progress 20% @chr9:128941445, elapsed 0.1s, est remaining 0.6s, peak mem 105MB, user 0.1s, sys 0.6s, output queue size 7293
progress 25% @chr10:14908408, elapsed 0.2s, est remaining 0.6s, peak mem 114MB, user 0.2s, sys 0.8s, output queue size 10045
progress 30% @chr10:69199104, elapsed 0.2s, est remaining 0.5s, peak mem 120MB, user 0.2s, sys 1.0s, output queue size 12433
progress 35% @chr10:100506040, elapsed 0.3s, est remaining 0.5s, peak mem 135MB, user 0.3s, sys 1.2s, output queue size 15088
progress 40% @chr11:294556, elapsed 0.3s, est remaining 0.5s, peak mem 150MB, user 0.3s, sys 1.4s, output queue size 17672
progress 45% @chr11:17995796, elapsed 0.4s, est remaining 0.4s, peak mem 156MB, user 0.3s, sys 1.6s, output queue size 19829
progress 50% @chr11:61419922, elapsed 0.4s, est remaining 0.4s, peak mem 162MB, user 0.3s, sys 1.7s, output queue size 22190
progress 55% @chr11:73234160, elapsed 0.4s, est remaining 0.4s, peak mem 180MB, user 0.4s, sys 2.0s, output queue size 24864
progress 60% @chr11:114440656, elapsed 0.5s, est remaining 0.3s, peak mem 186MB, user 0.4s, sys 2.1s, output queue size 27150
progress 65% @chr12:6514773, elapsed 0.5s, est remaining 0.3s, peak mem 192MB, user 0.4s, sys 2.3s, output queue size 29529
progress 70% @chr12:31701863, elapsed 0.6s, est remaining 0.2s, peak mem 207MB, user 0.4s, sys 2.5s, output queue size 31606
progress 75% @chr12:55969475, elapsed 0.6s, est remaining 0.2s, peak mem 213MB, user 0.5s, sys 2.6s, output queue size 34080
progress 80% @chr12:100051079, elapsed 0.7s, est remaining 0.2s, peak mem 225MB, user 0.5s, sys 2.9s, output queue size 36810
progress 85% @chr12:123774149, elapsed 0.7s, est remaining 0.1s, peak mem 237MB, user 0.6s, sys 3.2s, output queue size 39668
progress 90% @chr13:48411389, elapsed 0.7s, est remaining 0.1s, peak mem 249MB, user 0.6s, sys 3.3s, output queue size 42036
progress 95% @chr14:22633768, elapsed 0.8s, est remaining 0.0s, peak mem 258MB, user 0.6s, sys 3.5s, output queue size 44288
progress 100% @chr14:64120927, elapsed 0.8s, est remaining 0.0s, peak mem 267MB, user 0.6s, sys 3.7s, output queue size 1365
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 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74586799
output file size: 22310
reads: 1001133
contig: 48642 intervals 9000010 bases
"assemble": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_addRead": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_buildGraph": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_computecigar": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_calcsize": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_clear": 3 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_prepare": 4 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_threading": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op1": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op2": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op3": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_sg_clean": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_sg_create": 1 calls 0.000 user 0.000 sys 0.000 real
"checkGraph": 1 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 1 calls 0.000 user 0.000 sys 0.000 real
active: 98785 calls 0.000 user 0.007 sys 0.016 real
advance: 50143 calls 0.001 user 0.014 sys 0.019 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.000 real
calc: 98785 calls 0.011 user 0.000 sys 0.015 real
clip_region: 1 calls 0.000 user 0.000 sys 0.000 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.005 user 0.002 sys 1.531 real
fetch: 98785 calls 0.000 user 0.002 sys 0.016 real
fetch_ref: 98786 calls 0.142 user 0.068 sys 0.390 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.003 user 0.020 sys 20.799 real
init: 1 calls 0.039 user 0.001 sys 0.042 real
region: 98785 calls 0.000 user 0.000 sys 0.018 real
tracker: 98785 calls 0.048 user 0.018 sys 0.085 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 280104960 mem 1.036 user 5.365 sys 2.648 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory