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/a1/b9e8f6a23125f68e8e78703115a44a/.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/46/984ada276a39686e53532178f7d533/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/984ada276a39686e53532178f7d533/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/b9e8f6a23125f68e8e78703115a44a/.command.run
  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-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 HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr14_64122012-64122133.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr14:101760685, elapsed 0.1s, est remaining 1.0s, peak mem 75MB, user 0.0s, sys 0.1s, output queue size 1939
progress 10% @chr15:40899144, elapsed 0.1s, est remaining 0.9s, peak mem 84MB, user 0.0s, sys 0.3s, output queue size 4173
progress 15% @chr15:63912108, elapsed 0.2s, est remaining 0.9s, peak mem 93MB, user 0.1s, sys 0.6s, output queue size 6796
progress 20% @chr15:87966131, elapsed 0.2s, est remaining 0.9s, peak mem 99MB, user 0.1s, sys 0.8s, output queue size 9080
progress 25% @chr16:1941257, elapsed 0.3s, est remaining 0.8s, peak mem 105MB, user 0.1s, sys 1.0s, output queue size 10767
progress 30% @chr16:23482923, elapsed 0.3s, est remaining 0.7s, peak mem 120MB, user 0.1s, sys 1.2s, output queue size 13246
progress 35% @chr16:66558190, elapsed 0.4s, est remaining 0.7s, peak mem 135MB, user 0.2s, sys 1.5s, output queue size 1694
progress 40% @chr16:89299556, elapsed 0.5s, est remaining 0.7s, peak mem 144MB, user 0.2s, sys 1.9s, output queue size 4178
progress 45% @chr17:10311103, elapsed 0.5s, est remaining 0.6s, peak mem 150MB, user 0.3s, sys 2.2s, output queue size 6786
progress 50% @chr17:36260780, elapsed 0.6s, est remaining 0.6s, peak mem 162MB, user 0.3s, sys 2.6s, output queue size 9379
progress 55% @chr17:45102951, elapsed 0.6s, est remaining 0.5s, peak mem 168MB, user 0.4s, sys 2.9s, output queue size 11623
progress 60% @chr17:68420189, elapsed 0.7s, est remaining 0.5s, peak mem 186MB, user 0.4s, sys 3.2s, output queue size 14156
progress 65% @chr18:5890198, elapsed 0.8s, est remaining 0.4s, peak mem 189MB, user 0.4s, sys 3.6s, output queue size 16875
progress 70% @chr18:62574057, elapsed 0.9s, est remaining 0.4s, peak mem 201MB, user 0.5s, sys 3.9s, output queue size 19252
progress 75% @chr19:6924678, elapsed 0.9s, est remaining 0.3s, peak mem 210MB, user 0.5s, sys 4.2s, output queue size 21640
progress 80% @chr19:15264404, elapsed 1.0s, est remaining 0.2s, peak mem 222MB, user 0.5s, sys 4.3s, output queue size 23899
progress 85% @chr19:36936746, elapsed 1.0s, est remaining 0.2s, peak mem 228MB, user 0.6s, sys 4.6s, output queue size 26213
progress 90% @chr19:46469733, elapsed 1.1s, est remaining 0.1s, peak mem 228MB, user 0.6s, sys 4.8s, output queue size 28387
progress 95% @chr20:37035242, elapsed 1.1s, est remaining 0.1s, peak mem 243MB, user 0.7s, sys 5.2s, output queue size 31036
progress 100% @chr20:63940150, elapsed 1.2s, est remaining 0.0s, peak mem 255MB, user 0.7s, sys 5.5s, output queue size 33461
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: 71692764
output file size: 22307
reads: 1001089
contig: 48152 intervals 9000028 bases
active: 97912 calls 0.007 user 0.009 sys 0.018 real
advance: 49760 calls 0.010 user 0.002 sys 0.022 real
calc: 97912 calls 0.000 user 0.011 sys 0.017 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.001 sys 2.357 real
fetch: 97912 calls 0.012 user 0.004 sys 0.018 real
fetch_ref: 97912 calls 0.115 user 0.084 sys 0.385 real
idle: 51 calls 0.003 user 0.010 sys 26.284 real
init: 1 calls 0.040 user 0.010 sys 0.042 real
region: 97912 calls 0.006 user 0.002 sys 0.021 real
tracker: 97912 calls 0.023 user 0.022 sys 0.088 real
overall: 267538432 mem 1.241 user 8.128 sys 3.488 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory