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/e2/c43c8806fc987f868a85c04756a207/.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/ad/ded0dc28f0bedef0afd0b3c848896c/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/ded0dc28f0bedef0afd0b3c848896c/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/c43c8806fc987f868a85c04756a207/.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% @chr14:101561497, elapsed 0.1s, est remaining 1.0s, peak mem 79MB, user 0.0s, sys 0.2s, output queue size 2016
progress 10% @chr15:40895938, elapsed 0.1s, est remaining 0.9s, peak mem 91MB, user 0.1s, sys 0.4s, output queue size 4255
progress 15% @chr15:63911908, elapsed 0.2s, est remaining 0.9s, peak mem 103MB, user 0.1s, sys 0.7s, output queue size 942
progress 20% @chr15:87989891, elapsed 0.2s, est remaining 0.9s, peak mem 112MB, user 0.2s, sys 0.9s, output queue size 3233
progress 25% @chr16:1941257, elapsed 0.3s, est remaining 0.8s, peak mem 118MB, user 0.2s, sys 1.0s, output queue size 4913
progress 30% @chr16:23596123, elapsed 0.3s, est remaining 0.7s, peak mem 127MB, user 0.2s, sys 1.4s, output queue size 7413
progress 35% @chr16:66566514, elapsed 0.4s, est remaining 0.7s, peak mem 136MB, user 0.3s, sys 1.6s, output queue size 10002
progress 40% @chr16:89270813, elapsed 0.4s, est remaining 0.6s, peak mem 148MB, user 0.3s, sys 1.9s, output queue size 12474
progress 45% @chr17:10306459, elapsed 0.5s, est remaining 0.6s, peak mem 159MB, user 0.4s, sys 2.2s, output queue size 15084
progress 50% @chr17:36260780, elapsed 0.5s, est remaining 0.5s, peak mem 168MB, user 0.4s, sys 2.5s, output queue size 17681
progress 55% @chr17:45102951, elapsed 0.6s, est remaining 0.5s, peak mem 178MB, user 0.5s, sys 2.7s, output queue size 19924
progress 60% @chr17:68370444, elapsed 0.6s, est remaining 0.4s, peak mem 190MB, user 0.5s, sys 3.1s, output queue size 22454
progress 65% @chr18:5890198, elapsed 0.7s, est remaining 0.4s, peak mem 199MB, user 0.6s, sys 3.3s, output queue size 25176
progress 70% @chr18:62574057, elapsed 0.8s, est remaining 0.3s, peak mem 210MB, user 0.6s, sys 3.6s, output queue size 27552
progress 75% @chr19:6919548, elapsed 0.8s, est remaining 0.3s, peak mem 217MB, user 0.7s, sys 3.9s, output queue size 29941
progress 80% @chr19:15360848, elapsed 0.9s, est remaining 0.2s, peak mem 229MB, user 0.7s, sys 4.1s, output queue size 32207
progress 85% @chr19:36718948, elapsed 1.0s, est remaining 0.2s, peak mem 238MB, user 0.8s, sys 4.3s, output queue size 34517
progress 90% @chr19:46493558, elapsed 1.0s, est remaining 0.1s, peak mem 247MB, user 0.8s, sys 4.4s, output queue size 36686
progress 95% @chr20:36930728, elapsed 1.1s, est remaining 0.1s, peak mem 255MB, user 0.8s, sys 4.7s, output queue size 39324
progress 100% @chr20:64016723, elapsed 1.2s, est remaining 0.0s, peak mem 267MB, user 0.9s, sys 4.9s, output queue size 41762
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 12 max 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692760
output file size: 22307
reads: 1001089
contig: 48152 intervals 9000028 bases
active: 97912 calls 0.005 user 0.008 sys 0.022 real
advance: 49760 calls 0.010 user 0.007 sys 0.029 real
calc: 97912 calls 0.000 user 0.013 sys 0.022 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.007 user 0.002 sys 2.610 real
fetch: 97912 calls 0.000 user 0.000 sys 0.022 real
fetch_ref: 97912 calls 0.146 user 0.087 sys 0.410 real
idle: 51 calls 0.002 user 0.007 sys 28.963 real
init: 1 calls 0.037 user 0.019 sys 0.053 real
region: 97912 calls 0.001 user 0.005 sys 0.026 real
tracker: 97912 calls 0.024 user 0.002 sys 0.110 real
overall: 283332608 mem 1.510 user 7.073 sys 3.754 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory