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/93/9f6f7dc873db92282fd597fb3d7695/.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/93/9f6f7dc873db92282fd597fb3d7695/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/scatter/chr1_69091-70008.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/8cec261d5efbf269078e42e83159b5/Sig_18_Blood.recalibrated.bam.bai
  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 chr1_69091-70008.bed.gz -i Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_2.haplotyper.chr1_69091-70008.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:18365223, elapsed 0.0s, est remaining 0.9s, peak mem 85MB, user 0.0s, sys 0.1s, output queue size 2286
progress 10% @chr1:37761367, elapsed 0.1s, est remaining 0.9s, peak mem 100MB, user 0.0s, sys 0.3s, output queue size 4933
progress 15% @chr1:65394898, elapsed 0.1s, est remaining 0.8s, peak mem 108MB, user 0.1s, sys 0.4s, output queue size 2163
progress 20% @chr1:113837590, elapsed 0.2s, est remaining 0.8s, peak mem 118MB, user 0.1s, sys 0.7s, output queue size 4922
progress 25% @chr1:155247782, elapsed 0.2s, est remaining 0.7s, peak mem 130MB, user 0.1s, sys 0.8s, output queue size 7268
progress 30% @chr1:179102287, elapsed 0.3s, est remaining 0.7s, peak mem 142MB, user 0.2s, sys 1.0s, output queue size 9748
progress 35% @chr1:209796348, elapsed 0.3s, est remaining 0.6s, peak mem 148MB, user 0.2s, sys 1.2s, output queue size 12169
progress 40% @chr1:246986967, elapsed 0.4s, est remaining 0.6s, peak mem 162MB, user 0.2s, sys 1.4s, output queue size 14575
progress 45% @chr2:32812504, elapsed 0.4s, est remaining 0.5s, peak mem 171MB, user 0.2s, sys 1.6s, output queue size 16890
progress 50% @chr2:74461275, elapsed 0.5s, est remaining 0.5s, peak mem 180MB, user 0.3s, sys 1.7s, output queue size 19351
progress 55% @chr2:113499257, elapsed 0.5s, est remaining 0.4s, peak mem 193MB, user 0.3s, sys 1.9s, output queue size 21882
progress 60% @chr2:170997712, elapsed 0.6s, est remaining 0.4s, peak mem 204MB, user 0.3s, sys 2.1s, output queue size 24580
progress 65% @chr2:202814702, elapsed 0.6s, est remaining 0.3s, peak mem 216MB, user 0.3s, sys 2.3s, output queue size 26856
progress 70% @chr2:233772261, elapsed 0.6s, est remaining 0.3s, peak mem 225MB, user 0.4s, sys 2.4s, output queue size 29329
progress 75% @chr3:25623515, elapsed 0.7s, est remaining 0.2s, peak mem 231MB, user 0.4s, sys 2.6s, output queue size 31552
progress 80% @chr3:49805308, elapsed 0.7s, est remaining 0.2s, peak mem 246MB, user 0.5s, sys 2.8s, output queue size 34025
progress 85% @chr3:101664964, elapsed 0.8s, est remaining 0.1s, peak mem 256MB, user 0.5s, sys 3.0s, output queue size 36663
progress 90% @chr3:139561010, elapsed 0.8s, est remaining 0.1s, peak mem 267MB, user 0.5s, sys 3.2s, output queue size 39258
progress 95% @chr3:188240450, elapsed 0.9s, est remaining 0.0s, peak mem 277MB, user 0.5s, sys 3.4s, output queue size 41668
progress 100% @chr4:25312810, elapsed 0.9s, est remaining 0.0s, peak mem 285MB, user 0.6s, sys 3.5s, output queue size 43903
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 74381931
output file size: 22307
reads: 1001133
contig: 49651 intervals 9000373 bases
active: 100735 calls 0.017 user 0.002 sys 0.017 real
advance: 51084 calls 0.000 user 0.005 sys 0.021 real
calc: 100735 calls 0.000 user 0.009 sys 0.017 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.005 user 0.002 sys 1.543 real
fetch: 100735 calls 0.000 user 0.005 sys 0.017 real
fetch_ref: 100735 calls 0.089 user 0.066 sys 0.375 real
idle: 39 calls 0.004 user 0.006 sys 20.240 real
init: 1 calls 0.038 user 0.011 sys 0.041 real
region: 100735 calls 0.010 user 0.010 sys 0.020 real
tracker: 100735 calls 0.020 user 0.005 sys 0.089 real
overall: 302231552 mem 1.229 user 5.762 sys 2.659 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory