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/dc/59ea044396d08f5257a4e6da413e86/.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-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/dc/59ea044396d08f5257a4e6da413e86/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/fd07f3bccb2b3e7b5521fe26c79365/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/fd07f3bccb2b3e7b5521fe26c79365/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% @chr1:18634302, elapsed 0.1s, est remaining 1.3s, peak mem 88MB, user 0.0s, sys 0.3s, output queue size 1458
progress 10% @chr1:37799567, elapsed 0.1s, est remaining 1.3s, peak mem 100MB, user 0.1s, sys 0.7s, output queue size 4113
progress 15% @chr1:65392431, elapsed 0.2s, est remaining 1.3s, peak mem 112MB, user 0.1s, sys 1.2s, output queue size 6837
progress 20% @chr1:113881773, elapsed 0.3s, est remaining 1.2s, peak mem 124MB, user 0.2s, sys 1.6s, output queue size 9610
progress 25% @chr1:155250276, elapsed 0.4s, est remaining 1.1s, peak mem 133MB, user 0.3s, sys 1.9s, output queue size 11938
progress 30% @chr1:179229241, elapsed 0.5s, est remaining 1.1s, peak mem 142MB, user 0.4s, sys 2.2s, output queue size 14419
progress 35% @chr1:209789667, elapsed 0.5s, est remaining 1.0s, peak mem 154MB, user 0.4s, sys 2.5s, output queue size 16844
progress 40% @chr1:246907551, elapsed 0.6s, est remaining 0.9s, peak mem 166MB, user 0.5s, sys 2.8s, output queue size 2081
progress 45% @chr2:32664303, elapsed 0.7s, est remaining 0.8s, peak mem 175MB, user 0.5s, sys 3.2s, output queue size 4382
progress 50% @chr2:74460221, elapsed 0.7s, est remaining 0.7s, peak mem 185MB, user 0.6s, sys 3.5s, output queue size 6855
progress 55% @chr2:113499257, elapsed 0.8s, est remaining 0.7s, peak mem 195MB, user 0.7s, sys 3.8s, output queue size 9393
progress 60% @chr2:170997712, elapsed 0.9s, est remaining 0.6s, peak mem 205MB, user 0.8s, sys 4.2s, output queue size 12083
progress 65% @chr2:202779533, elapsed 1.0s, est remaining 0.5s, peak mem 214MB, user 0.9s, sys 4.5s, output queue size 14356
progress 70% @chr2:233772261, elapsed 1.0s, est remaining 0.4s, peak mem 226MB, user 1.0s, sys 4.8s, output queue size 16834
progress 75% @chr3:25623515, elapsed 1.1s, est remaining 0.4s, peak mem 235MB, user 1.0s, sys 5.3s, output queue size 19057
progress 80% @chr3:49804181, elapsed 1.2s, est remaining 0.3s, peak mem 246MB, user 1.1s, sys 5.7s, output queue size 21535
progress 85% @chr3:101859272, elapsed 1.3s, est remaining 0.2s, peak mem 258MB, user 1.2s, sys 6.2s, output queue size 24167
progress 90% @chr3:139538781, elapsed 1.4s, est remaining 0.2s, peak mem 265MB, user 1.3s, sys 6.7s, output queue size 26767
progress 95% @chr3:187741772, elapsed 1.4s, est remaining 0.1s, peak mem 277MB, user 1.4s, sys 7.0s, output queue size 29172
progress 100% @chr4:30721423, elapsed 1.5s, est remaining 0.0s, peak mem 286MB, user 1.4s, sys 7.3s, output queue size 31408
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 00050657
  features: bfebfbff 7ffefbff
  extended: d39ff7eb 00000818
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz
threads: 12 max 96
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74586815
output file size: 22307
reads: 1001133
contig: 49651 intervals 9000373 bases
active: 100735 calls 0.000 user 0.000 sys 0.024 real
advance: 51084 calls 0.029 user 0.033 sys 0.035 real
calc: 100735 calls 0.000 user 0.014 sys 0.024 real
done: 1 calls 0.001 user 0.000 sys 0.003 real
execute: 1 calls 0.003 user 0.001 sys 2.677 real
fetch: 100735 calls 0.000 user 0.027 sys 0.027 real
fetch_ref: 100735 calls 0.308 user 0.122 sys 0.655 real
idle: 51 calls 0.009 user 0.028 sys 26.882 real
init: 1 calls 0.058 user 0.002 sys 0.064 real
region: 100735 calls 0.009 user 0.031 sys 0.027 real
tracker: 100735 calls 0.068 user 0.011 sys 0.165 real
overall: 300023808 mem 2.189 user 9.752 sys 3.854 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory