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/ff/465fdcddc07f8526bc79356a49e073/.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/38/6364050760c5582cbdad0b85841682/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/6364050760c5582cbdad0b85841682/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/465fdcddc07f8526bc79356a49e073/.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 0.0s, est remaining 0.8s, peak mem 82MB, user 0.1s, sys 0.2s, output queue size 2246
progress 10% @chr15:40899144, elapsed 0.1s, est remaining 0.7s, peak mem 94MB, user 0.1s, sys 0.3s, output queue size 4477
progress 15% @chr15:63774694, elapsed 0.1s, est remaining 0.8s, peak mem 105MB, user 0.1s, sys 0.5s, output queue size 2629
progress 20% @chr15:87989891, elapsed 0.2s, est remaining 0.9s, peak mem 109MB, user 0.1s, sys 0.7s, output queue size 4915
progress 25% @chr16:1959625, elapsed 0.3s, est remaining 0.8s, peak mem 115MB, user 0.1s, sys 0.8s, output queue size 6600
progress 30% @chr16:23525127, elapsed 0.3s, est remaining 0.7s, peak mem 126MB, user 0.1s, sys 0.9s, output queue size 9077
progress 35% @chr16:66566514, elapsed 0.4s, est remaining 0.8s, peak mem 136MB, user 0.2s, sys 1.0s, output queue size 11679
progress 40% @chr16:89286670, elapsed 0.5s, est remaining 0.7s, peak mem 147MB, user 0.2s, sys 1.1s, output queue size 14153
progress 45% @chr17:10311911, elapsed 0.5s, est remaining 0.6s, peak mem 156MB, user 0.3s, sys 1.2s, output queue size 16767
progress 50% @chr17:36333876, elapsed 0.6s, est remaining 0.6s, peak mem 169MB, user 0.3s, sys 1.3s, output queue size 19369
progress 55% @chr17:45114250, elapsed 0.6s, est remaining 0.5s, peak mem 177MB, user 0.3s, sys 1.4s, output queue size 21604
progress 60% @chr17:68420189, elapsed 0.7s, est remaining 0.4s, peak mem 186MB, user 0.4s, sys 1.5s, output queue size 24139
progress 65% @chr18:5890198, elapsed 0.7s, est remaining 0.4s, peak mem 198MB, user 0.4s, sys 1.6s, output queue size 26856
progress 70% @chr18:62574057, elapsed 0.8s, est remaining 0.3s, peak mem 207MB, user 0.4s, sys 1.8s, output queue size 29235
progress 75% @chr19:6924678, elapsed 0.8s, est remaining 0.3s, peak mem 216MB, user 0.5s, sys 1.9s, output queue size 31624
progress 80% @chr19:15256964, elapsed 0.9s, est remaining 0.2s, peak mem 223MB, user 0.5s, sys 2.0s, output queue size 33879
progress 85% @chr19:36991176, elapsed 0.9s, est remaining 0.2s, peak mem 234MB, user 0.5s, sys 2.1s, output queue size 36201
progress 90% @chr19:46525663, elapsed 1.0s, est remaining 0.1s, peak mem 243MB, user 0.5s, sys 2.2s, output queue size 38367
progress 95% @chr20:33606956, elapsed 1.0s, est remaining 0.1s, peak mem 250MB, user 0.6s, sys 2.3s, output queue size 41007
progress 100% @chr20:64219713, elapsed 1.1s, est remaining 0.0s, peak mem 261MB, user 0.6s, sys 2.4s, output queue size 43444
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 12 max 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692767
output file size: 22307
reads: 1001089
contig: 48152 intervals 9000028 bases
active: 97912 calls 0.000 user 0.007 sys 0.015 real
advance: 49760 calls 0.009 user 0.004 sys 0.020 real
calc: 97912 calls 0.000 user 0.001 sys 0.015 real
done: 1 calls 0.001 user 0.000 sys 0.027 real
execute: 1 calls 0.003 user 0.001 sys 2.079 real
fetch: 97912 calls 0.000 user 0.001 sys 0.015 real
fetch_ref: 97912 calls 0.057 user 0.025 sys 0.319 real
idle: 51 calls 0.002 user 0.002 sys 24.660 real
init: 1 calls 0.030 user 0.010 sys 0.043 real
region: 97912 calls 0.000 user 0.005 sys 0.016 real
tracker: 97912 calls 0.003 user 0.002 sys 0.085 real
overall: 275566592 mem 1.022 user 3.538 sys 3.204 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory