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/ef/3f0f828b6d851080910468fd105025/.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/ef/3f0f828b6d851080910468fd105025/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/b9327ccd07f95c93afdb2eed727086/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/03/b9327ccd07f95c93afdb2eed727086/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% @chr8:144260186, elapsed 0.1s, est remaining 1.4s, peak mem 75MB, user 0.0s, sys 0.4s, output queue size 1260
progress 10% @chr9:37014958, elapsed 0.1s, est remaining 1.3s, peak mem 78MB, user 0.0s, sys 0.6s, output queue size 3482
progress 15% @chr9:96758778, elapsed 0.2s, est remaining 1.1s, peak mem 87MB, user 0.1s, sys 0.8s, output queue size 5252
progress 20% @chr9:128941445, elapsed 0.4s, est remaining 1.5s, peak mem 87MB, user 0.1s, sys 1.2s, output queue size 7871
progress 25% @chr10:14908408, elapsed 0.5s, est remaining 1.4s, peak mem 90MB, user 0.1s, sys 1.4s, output queue size 10628
progress 30% @chr10:69208600, elapsed 0.5s, est remaining 1.2s, peak mem 90MB, user 0.2s, sys 1.7s, output queue size 13016
progress 35% @chr10:100516096, elapsed 0.6s, est remaining 1.1s, peak mem 90MB, user 0.2s, sys 1.9s, output queue size 15675
progress 40% @chr11:314171, elapsed 0.7s, est remaining 1.1s, peak mem 93MB, user 0.3s, sys 2.1s, output queue size 18248
progress 45% @chr11:17771665, elapsed 0.8s, est remaining 1.0s, peak mem 96MB, user 0.3s, sys 2.4s, output queue size 1782
progress 50% @chr11:61416105, elapsed 0.9s, est remaining 0.9s, peak mem 102MB, user 0.3s, sys 2.7s, output queue size 4144
progress 55% @chr11:73234160, elapsed 0.9s, est remaining 0.8s, peak mem 105MB, user 0.4s, sys 3.1s, output queue size 6819
progress 60% @chr11:114530175, elapsed 1.0s, est remaining 0.7s, peak mem 111MB, user 0.4s, sys 3.4s, output queue size 9113
progress 65% @chr12:6462034, elapsed 1.1s, est remaining 0.6s, peak mem 126MB, user 0.4s, sys 3.7s, output queue size 11466
progress 70% @chr12:31697740, elapsed 1.1s, est remaining 0.5s, peak mem 126MB, user 0.4s, sys 4.0s, output queue size 13558
progress 75% @chr12:55968049, elapsed 1.3s, est remaining 0.4s, peak mem 141MB, user 0.5s, sys 4.3s, output queue size 16034
progress 80% @chr12:100058029, elapsed 1.3s, est remaining 0.3s, peak mem 147MB, user 0.5s, sys 4.6s, output queue size 18767
progress 85% @chr12:123785746, elapsed 1.4s, est remaining 0.3s, peak mem 153MB, user 0.5s, sys 4.9s, output queue size 21622
progress 90% @chr13:48456200, elapsed 1.5s, est remaining 0.2s, peak mem 165MB, user 0.6s, sys 5.1s, output queue size 23987
progress 95% @chr14:22766522, elapsed 1.6s, est remaining 0.1s, peak mem 168MB, user 0.6s, sys 5.3s, output queue size 26242
progress 100% @chr14:60808325, elapsed 1.7s, est remaining 0.0s, peak mem 168MB, user 0.7s, sys 5.6s, output queue size 28797
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: 74586810
output file size: 22310
reads: 1001133
contig: 48642 intervals 9000010 bases
"assemble": 1 calls 0.007 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 0.007 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 0.000 sys 0.016 real
advance: 50143 calls 0.005 user 0.016 sys 0.024 real
assemble_region: 1 calls 0.007 user 0.000 sys 0.000 real
calc: 98785 calls 0.001 user 0.000 sys 0.016 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 3.153 real
fetch: 98785 calls 0.000 user 0.005 sys 0.017 real
fetch_ref: 98786 calls 0.062 user 0.091 sys 0.429 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 51 calls 0.002 user 0.014 sys 30.034 real
init: 1 calls 0.031 user 0.019 sys 0.042 real
region: 98785 calls 0.000 user 0.012 sys 0.020 real
tracker: 98785 calls 0.054 user 0.010 sys 0.095 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 176279552 mem 1.287 user 9.140 sys 4.284 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory