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/e5/97ace15b42a842a7af342ffe454d45/.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/e5/97ace15b42a842a7af342ffe454d45/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/afbce3389bf5bcfac4e357eeed7653/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/chr14_64122012-64122133.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/afbce3389bf5bcfac4e357eeed7653/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 chr14_64122012-64122133.bed.gz -i Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_2.haplotyper.chr14_64122012-64122133.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr14:100880712, elapsed 0.0s, est remaining 0.8s, peak mem 75MB, user 0.0s, sys 0.1s, output queue size 2364
progress 10% @chr15:40899144, elapsed 0.1s, est remaining 0.8s, peak mem 78MB, user 0.1s, sys 0.3s, output queue size 1046
progress 15% @chr15:63774694, elapsed 0.1s, est remaining 0.7s, peak mem 90MB, user 0.1s, sys 0.5s, output queue size 3663
progress 20% @chr15:87966131, elapsed 0.2s, est remaining 0.7s, peak mem 99MB, user 0.1s, sys 0.6s, output queue size 5949
progress 25% @chr16:1961497, elapsed 0.2s, est remaining 0.6s, peak mem 105MB, user 0.1s, sys 0.8s, output queue size 7644
progress 30% @chr16:23494303, elapsed 0.2s, est remaining 0.6s, peak mem 108MB, user 0.2s, sys 0.9s, output queue size 10115
progress 35% @chr16:66569936, elapsed 0.3s, est remaining 0.5s, peak mem 120MB, user 0.2s, sys 1.1s, output queue size 12723
progress 40% @chr16:89270813, elapsed 0.3s, est remaining 0.5s, peak mem 129MB, user 0.2s, sys 1.3s, output queue size 15197
progress 45% @chr17:10312574, elapsed 0.4s, est remaining 0.5s, peak mem 135MB, user 0.3s, sys 1.6s, output queue size 17812
progress 50% @chr17:36328061, elapsed 0.4s, est remaining 0.4s, peak mem 147MB, user 0.4s, sys 1.8s, output queue size 20404
progress 55% @chr17:45115094, elapsed 0.5s, est remaining 0.4s, peak mem 153MB, user 0.4s, sys 1.9s, output queue size 22649
progress 60% @chr17:68385064, elapsed 0.5s, est remaining 0.3s, peak mem 165MB, user 0.5s, sys 2.2s, output queue size 25180
progress 65% @chr18:5890198, elapsed 0.6s, est remaining 0.3s, peak mem 174MB, user 0.5s, sys 2.3s, output queue size 27903
progress 70% @chr18:62574057, elapsed 0.6s, est remaining 0.3s, peak mem 180MB, user 0.6s, sys 2.5s, output queue size 30277
progress 75% @chr19:6924678, elapsed 0.7s, est remaining 0.2s, peak mem 186MB, user 0.6s, sys 2.7s, output queue size 32666
progress 80% @chr19:15263420, elapsed 0.7s, est remaining 0.2s, peak mem 204MB, user 0.7s, sys 2.8s, output queue size 34921
progress 85% @chr19:36915130, elapsed 0.7s, est remaining 0.1s, peak mem 213MB, user 0.7s, sys 2.9s, output queue size 37236
progress 90% @chr19:46493558, elapsed 0.8s, est remaining 0.1s, peak mem 219MB, user 0.7s, sys 3.1s, output queue size 39411
progress 95% @chr20:36934998, elapsed 0.8s, est remaining 0.0s, peak mem 225MB, user 0.8s, sys 3.2s, output queue size 42048
progress 100% @chr20:57710460, elapsed 0.9s, est remaining 0.0s, peak mem 237MB, user 0.8s, sys 3.3s, output queue size 44485
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: 74586803
output file size: 22310
reads: 1001133
contig: 48152 intervals 9000028 bases
active: 97912 calls 0.003 user 0.014 sys 0.018 real
advance: 49760 calls 0.000 user 0.023 sys 0.022 real
calc: 97912 calls 0.010 user 0.000 sys 0.018 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.004 sys 1.957 real
fetch: 97912 calls 0.000 user 0.000 sys 0.018 real
fetch_ref: 97912 calls 0.117 user 0.053 sys 0.354 real
idle: 51 calls 0.003 user 0.018 sys 25.553 real
init: 1 calls 0.020 user 0.020 sys 0.042 real
region: 97912 calls 0.000 user 0.012 sys 0.020 real
tracker: 97912 calls 0.020 user 0.000 sys 0.088 real
overall: 251785216 mem 1.359 user 5.672 sys 3.075 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory