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/75/4310446b279f62a10c7d0a65f84c3b/.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/75/4310446b279f62a10c7d0a65f84c3b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/8cec261d5efbf269078e42e83159b5/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/d9/8cec261d5efbf269078e42e83159b5/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 0.0s, est remaining 0.8s, peak mem 81MB, user 0.0s, sys 0.2s, output queue size 1097
progress 10% @chr15:40902616, elapsed 0.1s, est remaining 0.7s, peak mem 93MB, user 0.0s, sys 0.3s, output queue size 3337
progress 15% @chr15:63774694, elapsed 0.1s, est remaining 0.7s, peak mem 105MB, user 0.1s, sys 0.5s, output queue size 5961
progress 20% @chr15:87966131, elapsed 0.2s, est remaining 0.6s, peak mem 111MB, user 0.1s, sys 0.6s, output queue size 8244
progress 25% @chr16:1947194, elapsed 0.2s, est remaining 0.6s, peak mem 124MB, user 0.2s, sys 0.7s, output queue size 9929
progress 30% @chr16:23495694, elapsed 0.2s, est remaining 0.5s, peak mem 132MB, user 0.2s, sys 1.0s, output queue size 12409
progress 35% @chr16:66569936, elapsed 0.3s, est remaining 0.5s, peak mem 141MB, user 0.3s, sys 1.1s, output queue size 15016
progress 40% @chr16:89286670, elapsed 0.3s, est remaining 0.5s, peak mem 153MB, user 0.3s, sys 1.3s, output queue size 17493
progress 45% @chr17:10309522, elapsed 0.4s, est remaining 0.5s, peak mem 163MB, user 0.3s, sys 1.5s, output queue size 20100
progress 50% @chr17:36333876, elapsed 0.4s, est remaining 0.4s, peak mem 178MB, user 0.4s, sys 1.8s, output queue size 22705
progress 55% @chr17:45102951, elapsed 0.5s, est remaining 0.4s, peak mem 184MB, user 0.4s, sys 1.9s, output queue size 24938
progress 60% @chr17:68450728, elapsed 0.5s, est remaining 0.3s, peak mem 195MB, user 0.4s, sys 2.1s, output queue size 27483
progress 65% @chr18:5956220, elapsed 0.5s, est remaining 0.3s, peak mem 205MB, user 0.5s, sys 2.3s, output queue size 30192
progress 70% @chr18:62563009, elapsed 0.6s, est remaining 0.3s, peak mem 214MB, user 0.5s, sys 2.4s, output queue size 32569
progress 75% @chr19:6919548, elapsed 0.6s, est remaining 0.2s, peak mem 228MB, user 0.5s, sys 2.6s, output queue size 34957
progress 80% @chr19:15256964, elapsed 0.7s, est remaining 0.2s, peak mem 238MB, user 0.6s, sys 2.7s, output queue size 2167
progress 85% @chr19:36936746, elapsed 0.7s, est remaining 0.1s, peak mem 249MB, user 0.6s, sys 2.9s, output queue size 4484
progress 90% @chr19:46469733, elapsed 0.8s, est remaining 0.1s, peak mem 258MB, user 0.7s, sys 3.1s, output queue size 6660
progress 95% @chr20:36927133, elapsed 0.8s, est remaining 0.0s, peak mem 270MB, user 0.7s, sys 3.3s, output queue size 9294
progress 100% @chr20:63472168, elapsed 0.8s, est remaining 0.0s, peak mem 276MB, user 0.7s, sys 3.5s, output queue size 11731
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: 74381931
output file size: 22311
reads: 1001133
contig: 48152 intervals 9000028 bases
active: 97912 calls 0.000 user 0.004 sys 0.018 real
advance: 49760 calls 0.009 user 0.011 sys 0.022 real
calc: 97912 calls 0.000 user 0.002 sys 0.018 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.006 user 0.003 sys 1.428 real
fetch: 97912 calls 0.000 user 0.000 sys 0.018 real
fetch_ref: 97912 calls 0.148 user 0.067 sys 0.364 real
idle: 39 calls 0.008 user 0.019 sys 19.456 real
init: 1 calls 0.030 user 0.010 sys 0.043 real
region: 97912 calls 0.001 user 0.002 sys 0.020 real
tracker: 97912 calls 0.023 user 0.000 sys 0.087 real
overall: 289632256 mem 1.361 user 5.262 sys 2.547 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory