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/7d/5d477eb26187980f9c0547a08c2486/.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/7d/5d477eb26187980f9c0547a08c2486/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/f2b19ea24476199183849c3fbd492f/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/1d/f2b19ea24476199183849c3fbd492f/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% @chr8:144240992, elapsed 0.0s, est remaining 0.8s, peak mem 75MB, user 0.0s, sys 0.1s, output queue size 1421
progress 10% @chr9:36833270, elapsed 0.1s, est remaining 0.7s, peak mem 78MB, user 0.0s, sys 0.3s, output queue size 3642
progress 15% @chr9:96645893, elapsed 0.1s, est remaining 0.6s, peak mem 84MB, user 0.1s, sys 0.4s, output queue size 5419
progress 20% @chr9:128945687, elapsed 0.1s, est remaining 0.6s, peak mem 108MB, user 0.1s, sys 0.6s, output queue size 8040
progress 25% @chr10:14908408, elapsed 0.2s, est remaining 0.6s, peak mem 111MB, user 0.1s, sys 0.7s, output queue size 10791
progress 30% @chr10:69248424, elapsed 0.2s, est remaining 0.5s, peak mem 126MB, user 0.1s, sys 0.9s, output queue size 13192
progress 35% @chr10:100499160, elapsed 0.3s, est remaining 0.5s, peak mem 138MB, user 0.2s, sys 1.0s, output queue size 15833
progress 40% @chr11:314922, elapsed 0.3s, est remaining 0.5s, peak mem 144MB, user 0.2s, sys 1.2s, output queue size 18417
progress 45% @chr11:17781670, elapsed 0.3s, est remaining 0.4s, peak mem 156MB, user 0.2s, sys 1.3s, output queue size 20569
progress 50% @chr11:61415666, elapsed 0.4s, est remaining 0.4s, peak mem 165MB, user 0.3s, sys 1.5s, output queue size 22937
progress 55% @chr11:73234160, elapsed 0.4s, est remaining 0.3s, peak mem 177MB, user 0.3s, sys 1.7s, output queue size 25611
progress 60% @chr11:114439529, elapsed 0.5s, est remaining 0.3s, peak mem 186MB, user 0.3s, sys 1.8s, output queue size 3100
progress 65% @chr12:6460855, elapsed 0.5s, est remaining 0.3s, peak mem 198MB, user 0.4s, sys 2.0s, output queue size 5462
progress 70% @chr12:31709293, elapsed 0.5s, est remaining 0.2s, peak mem 201MB, user 0.4s, sys 2.1s, output queue size 7560
progress 75% @chr12:55966831, elapsed 0.6s, est remaining 0.2s, peak mem 216MB, user 0.4s, sys 2.3s, output queue size 10028
progress 80% @chr12:100057571, elapsed 0.6s, est remaining 0.2s, peak mem 225MB, user 0.5s, sys 2.5s, output queue size 12763
progress 85% @chr12:123781080, elapsed 0.7s, est remaining 0.1s, peak mem 234MB, user 0.5s, sys 2.6s, output queue size 15617
progress 90% @chr13:48473332, elapsed 0.7s, est remaining 0.1s, peak mem 243MB, user 0.5s, sys 2.7s, output queue size 17992
progress 95% @chr14:22633768, elapsed 0.7s, est remaining 0.0s, peak mem 255MB, user 0.6s, sys 2.9s, output queue size 20241
progress 100% @chr14:61782247, elapsed 0.8s, est remaining 0.0s, peak mem 267MB, user 0.6s, sys 3.1s, output queue size 22793
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: 12 max 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74586797
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 0.003 user 0.010 sys 0.018 real
advance: 50143 calls 0.010 user 0.013 sys 0.022 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.000 real
calc: 98785 calls 0.010 user 0.012 sys 0.018 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 0.009 user 0.000 sys 1.373 real
fetch: 98785 calls 0.010 user 0.000 sys 0.019 real
fetch_ref: 98786 calls 0.134 user 0.069 sys 0.393 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.002 user 0.006 sys 19.669 real
init: 1 calls 0.039 user 0.001 sys 0.043 real
region: 98785 calls 0.004 user 0.000 sys 0.021 real
tracker: 98785 calls 0.031 user 0.005 sys 0.087 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 280109056 mem 1.243 user 4.995 sys 2.493 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory