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/3d/26f5e5140ddc81856991db8b56563d/.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/3d/26f5e5140ddc81856991db8b56563d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/8cec261d5efbf269078e42e83159b5/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/d9/8cec261d5efbf269078e42e83159b5/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% @chr8:144243863, elapsed 0.1s, est remaining 1.2s, peak mem 82MB, user 0.0s, sys 0.3s, output queue size 274
progress 10% @chr9:36833270, elapsed 0.1s, est remaining 1.1s, peak mem 92MB, user 0.1s, sys 0.5s, output queue size 2490
progress 15% @chr9:96641759, elapsed 0.2s, est remaining 1.0s, peak mem 99MB, user 0.1s, sys 0.7s, output queue size 4271
progress 20% @chr9:128941445, elapsed 0.2s, est remaining 0.9s, peak mem 111MB, user 0.2s, sys 1.0s, output queue size 6891
progress 25% @chr10:14899250, elapsed 0.3s, est remaining 1.0s, peak mem 121MB, user 0.2s, sys 1.3s, output queue size 9646
progress 30% @chr10:69198372, elapsed 0.4s, est remaining 0.9s, peak mem 128MB, user 0.2s, sys 1.6s, output queue size 12032
progress 35% @chr10:100497667, elapsed 0.5s, est remaining 0.9s, peak mem 137MB, user 0.3s, sys 1.9s, output queue size 14687
progress 40% @chr11:298501, elapsed 0.5s, est remaining 0.8s, peak mem 147MB, user 0.4s, sys 2.3s, output queue size 17270
progress 45% @chr11:18007941, elapsed 0.6s, est remaining 0.7s, peak mem 155MB, user 0.4s, sys 2.6s, output queue size 19433
progress 50% @chr11:61420470, elapsed 0.7s, est remaining 0.7s, peak mem 166MB, user 0.5s, sys 2.9s, output queue size 21789
progress 55% @chr11:73140031, elapsed 0.7s, est remaining 0.6s, peak mem 177MB, user 0.5s, sys 3.3s, output queue size 24461
progress 60% @chr11:114443856, elapsed 0.8s, est remaining 0.5s, peak mem 185MB, user 0.5s, sys 3.5s, output queue size 26748
progress 65% @chr12:6457406, elapsed 0.9s, est remaining 0.5s, peak mem 193MB, user 0.6s, sys 3.8s, output queue size 29113
progress 70% @chr12:31697740, elapsed 1.0s, est remaining 0.4s, peak mem 206MB, user 0.6s, sys 4.1s, output queue size 854
progress 75% @chr12:55958473, elapsed 1.0s, est remaining 0.3s, peak mem 217MB, user 0.7s, sys 4.4s, output queue size 3329
progress 80% @chr12:100047943, elapsed 1.1s, est remaining 0.3s, peak mem 227MB, user 0.7s, sys 4.8s, output queue size 6059
progress 85% @chr12:123781080, elapsed 1.2s, est remaining 0.2s, peak mem 236MB, user 0.8s, sys 5.1s, output queue size 8915
progress 90% @chr13:48490111, elapsed 1.2s, est remaining 0.1s, peak mem 246MB, user 0.8s, sys 5.4s, output queue size 11292
progress 95% @chr14:22609724, elapsed 1.3s, est remaining 0.1s, peak mem 255MB, user 0.9s, sys 5.6s, output queue size 13543
progress 100% @chr14:64007043, elapsed 1.4s, est remaining 0.0s, peak mem 265MB, user 1.0s, sys 5.9s, output queue size 16091
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 128
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74381931
output file size: 22311
reads: 1001133
contig: 48642 intervals 9000010 bases
"assemble": 1 calls 0.000 user 0.000 sys 0.001 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 0.040 sys 0.028 real
advance: 50143 calls 0.015 user 0.036 sys 0.036 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.001 real
calc: 98785 calls 0.008 user 0.018 sys 0.028 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 0.004 user 0.002 sys 2.294 real
fetch: 98785 calls 0.002 user 0.031 sys 0.030 real
fetch_ref: 98786 calls 0.163 user 0.090 sys 0.443 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.003 user 0.007 sys 23.723 real
init: 1 calls 0.031 user 0.020 sys 0.049 real
region: 98785 calls 0.000 user 0.004 sys 0.035 real
tracker: 98785 calls 0.123 user 0.005 sys 0.179 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 278319104 mem 1.721 user 9.563 sys 3.456 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory