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/ae/a1aa68bbf0d79397d84344154f097b/.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/ae/a1aa68bbf0d79397d84344154f097b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/8fc7f5716dfc4a815738382b6d56eb/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/f1/8fc7f5716dfc4a815738382b6d56eb/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% @chr14:101760685, elapsed 0.0s, est remaining 0.8s, peak mem 85MB, user 0.1s, sys 0.1s, output queue size 2190
progress 10% @chr15:40902616, elapsed 0.1s, est remaining 0.7s, peak mem 91MB, user 0.1s, sys 0.2s, output queue size 4425
progress 15% @chr15:63774694, elapsed 0.1s, est remaining 0.7s, peak mem 105MB, user 0.2s, sys 0.3s, output queue size 7052
progress 20% @chr15:87989891, elapsed 0.2s, est remaining 0.6s, peak mem 114MB, user 0.2s, sys 0.5s, output queue size 2257
progress 25% @chr16:1950844, elapsed 0.2s, est remaining 0.6s, peak mem 123MB, user 0.2s, sys 0.6s, output queue size 3940
progress 30% @chr16:23525127, elapsed 0.2s, est remaining 0.5s, peak mem 130MB, user 0.2s, sys 0.8s, output queue size 6421
progress 35% @chr16:66548978, elapsed 0.3s, est remaining 0.5s, peak mem 139MB, user 0.2s, sys 1.0s, output queue size 9024
progress 40% @chr16:89286670, elapsed 0.3s, est remaining 0.5s, peak mem 153MB, user 0.3s, sys 1.1s, output queue size 11500
progress 45% @chr17:10306459, elapsed 0.4s, est remaining 0.4s, peak mem 163MB, user 0.3s, sys 1.3s, output queue size 14110
progress 50% @chr17:36328498, elapsed 0.4s, est remaining 0.4s, peak mem 172MB, user 0.4s, sys 1.4s, output queue size 16709
progress 55% @chr17:45115094, elapsed 0.4s, est remaining 0.4s, peak mem 181MB, user 0.4s, sys 1.5s, output queue size 18953
progress 60% @chr17:68420189, elapsed 0.5s, est remaining 0.3s, peak mem 193MB, user 0.4s, sys 1.7s, output queue size 21484
progress 65% @chr18:5890198, elapsed 0.5s, est remaining 0.3s, peak mem 207MB, user 0.5s, sys 1.8s, output queue size 24205
progress 70% @chr18:62570103, elapsed 0.6s, est remaining 0.2s, peak mem 217MB, user 0.5s, sys 1.9s, output queue size 26580
progress 75% @chr19:6921713, elapsed 0.6s, est remaining 0.2s, peak mem 228MB, user 0.5s, sys 2.0s, output queue size 28969
progress 80% @chr19:15267416, elapsed 0.7s, est remaining 0.2s, peak mem 235MB, user 0.6s, sys 2.1s, output queue size 31228
progress 85% @chr19:36922771, elapsed 0.7s, est remaining 0.1s, peak mem 246MB, user 0.6s, sys 2.3s, output queue size 33540
progress 90% @chr19:46493558, elapsed 0.7s, est remaining 0.1s, peak mem 258MB, user 0.6s, sys 2.4s, output queue size 35714
progress 95% @chr20:36916678, elapsed 0.8s, est remaining 0.0s, peak mem 267MB, user 0.6s, sys 2.5s, output queue size 38350
progress 100% @chr20:62351909, elapsed 0.8s, est remaining 0.0s, peak mem 279MB, user 0.7s, sys 2.7s, output queue size 40789
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: 74586805
output file size: 22310
reads: 1001133
contig: 48152 intervals 9000028 bases
active: 97912 calls 0.002 user 0.015 sys 0.016 real
advance: 49760 calls 0.013 user 0.010 sys 0.024 real
calc: 97912 calls 0.000 user 0.000 sys 0.015 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.002 user 0.001 sys 1.492 real
fetch: 97912 calls 0.003 user 0.005 sys 0.016 real
fetch_ref: 97912 calls 0.106 user 0.047 sys 0.326 real
idle: 39 calls 0.011 user 0.018 sys 20.495 real
init: 1 calls 0.040 user 0.000 sys 0.043 real
region: 97912 calls 0.007 user 0.001 sys 0.016 real
tracker: 97912 calls 0.030 user 0.006 sys 0.086 real
overall: 296013824 mem 1.214 user 4.294 sys 2.613 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory