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/7d/4070f0e968e11dbf50efa48b1303e7/.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/5d/3cfabeb790a6f016a7b8ea9337df7f/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/3cfabeb790a6f016a7b8ea9337df7f/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/4070f0e968e11dbf50efa48b1303e7/.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 0.9s, peak mem 84MB, user 0.1s, sys 0.1s, output queue size 2355
progress 10% @chr15:40902616, elapsed 0.1s, est remaining 0.8s, peak mem 91MB, user 0.1s, sys 0.2s, output queue size 1924
progress 15% @chr15:63971423, elapsed 0.1s, est remaining 0.8s, peak mem 102MB, user 0.1s, sys 0.5s, output queue size 4552
progress 20% @chr15:87989891, elapsed 0.2s, est remaining 0.7s, peak mem 114MB, user 0.1s, sys 0.6s, output queue size 6831
progress 25% @chr16:1950844, elapsed 0.2s, est remaining 0.6s, peak mem 118MB, user 0.1s, sys 0.7s, output queue size 8517
progress 30% @chr16:23493360, elapsed 0.3s, est remaining 0.6s, peak mem 126MB, user 0.2s, sys 0.9s, output queue size 10995
progress 35% @chr16:66566514, elapsed 0.3s, est remaining 0.6s, peak mem 141MB, user 0.2s, sys 1.1s, output queue size 13600
progress 40% @chr16:89270813, elapsed 0.3s, est remaining 0.5s, peak mem 153MB, user 0.2s, sys 1.3s, output queue size 16077
progress 45% @chr17:10309234, elapsed 0.4s, est remaining 0.5s, peak mem 165MB, user 0.2s, sys 1.6s, output queue size 18689
progress 50% @chr17:36379396, elapsed 0.4s, est remaining 0.4s, peak mem 172MB, user 0.3s, sys 1.8s, output queue size 21299
progress 55% @chr17:45104859, elapsed 0.5s, est remaining 0.4s, peak mem 181MB, user 0.3s, sys 2.1s, output queue size 23526
progress 60% @chr17:68395073, elapsed 0.5s, est remaining 0.4s, peak mem 193MB, user 0.4s, sys 2.2s, output queue size 26059
progress 65% @chr18:5489001, elapsed 0.6s, est remaining 0.3s, peak mem 205MB, user 0.4s, sys 2.5s, output queue size 28780
progress 70% @chr18:62574057, elapsed 0.6s, est remaining 0.3s, peak mem 216MB, user 0.4s, sys 2.7s, output queue size 31157
progress 75% @chr19:7019161, elapsed 0.7s, est remaining 0.2s, peak mem 225MB, user 0.4s, sys 2.9s, output queue size 33553
progress 80% @chr19:15264404, elapsed 0.7s, est remaining 0.2s, peak mem 235MB, user 0.5s, sys 3.0s, output queue size 35802
progress 85% @chr19:34341422, elapsed 0.8s, est remaining 0.1s, peak mem 241MB, user 0.5s, sys 3.3s, output queue size 38123
progress 90% @chr19:46469733, elapsed 0.8s, est remaining 0.1s, peak mem 252MB, user 0.6s, sys 3.4s, output queue size 40294
progress 95% @chr20:36919328, elapsed 0.9s, est remaining 0.0s, peak mem 262MB, user 0.6s, sys 3.7s, output queue size 42927
progress 100% @chr20:59882095, elapsed 0.9s, est remaining 0.0s, peak mem 274MB, user 0.6s, sys 3.8s, output queue size 45365
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71699821
output file size: 22308
reads: 1001089
contig: 48152 intervals 9000028 bases
active: 97912 calls 0.000 user 0.002 sys 0.019 real
advance: 49760 calls 0.007 user 0.009 sys 0.024 real
calc: 97912 calls 0.000 user 0.003 sys 0.019 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.001 user 0.010 sys 1.544 real
fetch: 97912 calls 0.000 user 0.000 sys 0.020 real
fetch_ref: 97912 calls 0.061 user 0.050 sys 0.358 real
idle: 39 calls 0.005 user 0.034 sys 20.114 real
init: 1 calls 0.030 user 0.010 sys 0.042 real
region: 97912 calls 0.001 user 0.003 sys 0.023 real
tracker: 97912 calls 0.034 user 0.011 sys 0.092 real
overall: 291229696 mem 1.195 user 5.989 sys 2.663 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory