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/f8/4c3f1760ae87377a7d034892bb0a95/.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/f8/4c3f1760ae87377a7d034892bb0a95/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/913060702caf09fcfc1e4e7b484246/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/ae/913060702caf09fcfc1e4e7b484246/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% @chr14:100880712, elapsed 0.1s, est remaining 1.0s, peak mem 81MB, user 0.0s, sys 0.2s, output queue size 2154
progress 10% @chr15:40902616, elapsed 0.1s, est remaining 0.8s, peak mem 88MB, user 0.0s, sys 0.3s, output queue size 4397
progress 15% @chr15:63774694, elapsed 0.1s, est remaining 0.8s, peak mem 96MB, user 0.1s, sys 0.6s, output queue size 1245
progress 20% @chr15:87989891, elapsed 0.2s, est remaining 0.8s, peak mem 106MB, user 0.1s, sys 0.7s, output queue size 3532
progress 25% @chr16:1953956, elapsed 0.2s, est remaining 0.7s, peak mem 111MB, user 0.1s, sys 0.8s, output queue size 5221
progress 30% @chr16:23486710, elapsed 0.3s, est remaining 0.7s, peak mem 124MB, user 0.2s, sys 0.9s, output queue size 7697
progress 35% @chr16:66566514, elapsed 0.3s, est remaining 0.6s, peak mem 133MB, user 0.2s, sys 1.1s, output queue size 10304
progress 40% @chr16:89286670, elapsed 0.4s, est remaining 0.6s, peak mem 145MB, user 0.3s, sys 1.3s, output queue size 12778
progress 45% @chr17:10306459, elapsed 0.4s, est remaining 0.5s, peak mem 156MB, user 0.3s, sys 1.5s, output queue size 15392
progress 50% @chr17:36260780, elapsed 0.5s, est remaining 0.5s, peak mem 171MB, user 0.4s, sys 1.6s, output queue size 17987
progress 55% @chr17:45114250, elapsed 0.5s, est remaining 0.4s, peak mem 177MB, user 0.4s, sys 1.9s, output queue size 20230
progress 60% @chr17:68420189, elapsed 0.6s, est remaining 0.4s, peak mem 184MB, user 0.5s, sys 2.0s, output queue size 22763
progress 65% @chr18:5956220, elapsed 0.7s, est remaining 0.4s, peak mem 198MB, user 0.5s, sys 2.2s, output queue size 25481
progress 70% @chr18:62574057, elapsed 0.7s, est remaining 0.3s, peak mem 210MB, user 0.6s, sys 2.4s, output queue size 27859
progress 75% @chr19:6919548, elapsed 0.8s, est remaining 0.3s, peak mem 220MB, user 0.6s, sys 2.5s, output queue size 30247
progress 80% @chr19:15268905, elapsed 0.8s, est remaining 0.2s, peak mem 228MB, user 0.6s, sys 2.7s, output queue size 32508
progress 85% @chr19:36937147, elapsed 0.8s, est remaining 0.1s, peak mem 235MB, user 0.6s, sys 2.8s, output queue size 34822
progress 90% @chr19:46493558, elapsed 0.9s, est remaining 0.1s, peak mem 246MB, user 0.7s, sys 2.9s, output queue size 36991
progress 95% @chr20:36919328, elapsed 1.0s, est remaining 0.1s, peak mem 256MB, user 0.7s, sys 3.1s, output queue size 39630
progress 100% @chr20:59886707, elapsed 1.0s, est remaining 0.0s, peak mem 264MB, user 0.8s, sys 3.2s, output queue size 42068
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: 74559500
output file size: 22311
reads: 1001133
contig: 48152 intervals 9000028 bases
active: 97912 calls 0.001 user 0.000 sys 0.018 real
advance: 49760 calls 0.002 user 0.004 sys 0.023 real
calc: 97912 calls 0.004 user 0.004 sys 0.018 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.002 sys 2.006 real
fetch: 97912 calls 0.005 user 0.008 sys 0.019 real
fetch_ref: 97912 calls 0.066 user 0.052 sys 0.350 real
idle: 51 calls 0.004 user 0.019 sys 24.564 real
init: 1 calls 0.030 user 0.010 sys 0.043 real
region: 97912 calls 0.012 user 0.000 sys 0.020 real
tracker: 97912 calls 0.025 user 0.001 sys 0.093 real
overall: 280236032 mem 1.317 user 5.051 sys 3.142 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory