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/16/705d0cac758131a030918985683919/.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/1a/a95586b1b08a697566ea24e2f6d852/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/a95586b1b08a697566ea24e2f6d852/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/705d0cac758131a030918985683919/.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% @chr14:100880712, elapsed 0.1s, est remaining 1.0s, peak mem 75MB, user 0.0s, sys 0.2s, output queue size 2274
progress 10% @chr15:40902616, elapsed 0.1s, est remaining 0.9s, peak mem 81MB, user 0.1s, sys 0.3s, output queue size 1851
progress 15% @chr15:63925941, elapsed 0.2s, est remaining 0.9s, peak mem 93MB, user 0.1s, sys 0.5s, output queue size 4475
progress 20% @chr15:87966131, elapsed 0.2s, est remaining 0.8s, peak mem 102MB, user 0.2s, sys 0.6s, output queue size 6756
progress 25% @chr16:1953956, elapsed 0.2s, est remaining 0.7s, peak mem 108MB, user 0.2s, sys 0.7s, output queue size 8445
progress 30% @chr16:22150695, elapsed 0.3s, est remaining 0.7s, peak mem 117MB, user 0.2s, sys 0.9s, output queue size 10923
progress 35% @chr16:66565886, elapsed 0.4s, est remaining 0.7s, peak mem 132MB, user 0.2s, sys 1.0s, output queue size 13528
progress 40% @chr16:89274812, elapsed 0.4s, est remaining 0.6s, peak mem 141MB, user 0.3s, sys 1.2s, output queue size 16003
progress 45% @chr17:10309522, elapsed 0.5s, est remaining 0.6s, peak mem 153MB, user 0.3s, sys 1.3s, output queue size 18617
progress 50% @chr17:36383701, elapsed 0.5s, est remaining 0.5s, peak mem 162MB, user 0.4s, sys 1.6s, output queue size 21227
progress 55% @chr17:45115094, elapsed 0.6s, est remaining 0.5s, peak mem 171MB, user 0.4s, sys 1.8s, output queue size 23454
progress 60% @chr17:66877333, elapsed 0.7s, est remaining 0.4s, peak mem 180MB, user 0.4s, sys 2.1s, output queue size 25994
progress 65% @chr18:5890198, elapsed 0.7s, est remaining 0.4s, peak mem 183MB, user 0.5s, sys 2.3s, output queue size 28704
progress 70% @chr18:62715684, elapsed 0.8s, est remaining 0.3s, peak mem 186MB, user 0.5s, sys 2.5s, output queue size 31082
progress 75% @chr19:6919548, elapsed 0.9s, est remaining 0.3s, peak mem 201MB, user 0.5s, sys 2.7s, output queue size 33471
progress 80% @chr19:15272815, elapsed 0.9s, est remaining 0.2s, peak mem 210MB, user 0.6s, sys 2.9s, output queue size 35731
progress 85% @chr19:36949512, elapsed 1.0s, est remaining 0.2s, peak mem 216MB, user 0.6s, sys 3.1s, output queue size 38044
progress 90% @chr19:46493558, elapsed 1.0s, est remaining 0.1s, peak mem 225MB, user 0.7s, sys 3.2s, output queue size 40216
progress 95% @chr20:36916678, elapsed 1.1s, est remaining 0.1s, peak mem 237MB, user 0.7s, sys 3.4s, output queue size 42854
progress 100% @chr20:62811462, elapsed 1.2s, est remaining 0.0s, peak mem 246MB, user 0.7s, sys 3.7s, output queue size 45292
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: 71692772
output file size: 22307
reads: 1001089
contig: 48152 intervals 9000028 bases
active: 97912 calls 0.000 user 0.006 sys 0.017 real
advance: 49760 calls 0.002 user 0.007 sys 0.022 real
calc: 97912 calls 0.005 user 0.000 sys 0.017 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.002 sys 2.738 real
fetch: 97912 calls 0.000 user 0.000 sys 0.018 real
fetch_ref: 97912 calls 0.078 user 0.035 sys 0.391 real
idle: 51 calls 0.003 user 0.005 sys 31.485 real
init: 1 calls 0.030 user 0.010 sys 0.043 real
region: 97912 calls 0.001 user 0.000 sys 0.019 real
tracker: 97912 calls 0.026 user 0.001 sys 0.087 real
overall: 261230592 mem 1.283 user 5.245 sys 3.855 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory