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/a3/c19f25946eb325db6b70959fc13bba/.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/a3/c19f25946eb325db6b70959fc13bba/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/b9327ccd07f95c93afdb2eed727086/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/03/b9327ccd07f95c93afdb2eed727086/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 1.2s, peak mem 84MB, user 0.0s, sys 0.2s, output queue size 2274
progress 10% @chr15:40902616, elapsed 0.1s, est remaining 1.1s, peak mem 88MB, user 0.1s, sys 0.3s, output queue size 2266
progress 15% @chr15:63911908, elapsed 0.2s, est remaining 1.1s, peak mem 93MB, user 0.1s, sys 0.6s, output queue size 4888
progress 20% @chr15:87989891, elapsed 0.2s, est remaining 1.0s, peak mem 96MB, user 0.2s, sys 0.8s, output queue size 7179
progress 25% @chr16:1967274, elapsed 0.3s, est remaining 0.9s, peak mem 100MB, user 0.2s, sys 0.9s, output queue size 8875
progress 30% @chr16:23529744, elapsed 0.3s, est remaining 0.8s, peak mem 111MB, user 0.2s, sys 1.1s, output queue size 11342
progress 35% @chr16:66566514, elapsed 0.4s, est remaining 0.7s, peak mem 118MB, user 0.3s, sys 1.2s, output queue size 13944
progress 40% @chr16:89286670, elapsed 0.4s, est remaining 0.7s, peak mem 127MB, user 0.3s, sys 1.4s, output queue size 16420
progress 45% @chr17:10315693, elapsed 0.5s, est remaining 0.6s, peak mem 136MB, user 0.4s, sys 1.7s, output queue size 19038
progress 50% @chr17:36260780, elapsed 0.6s, est remaining 0.6s, peak mem 148MB, user 0.4s, sys 1.8s, output queue size 21627
progress 55% @chr17:45117994, elapsed 0.6s, est remaining 0.5s, peak mem 151MB, user 0.4s, sys 2.0s, output queue size 23875
progress 60% @chr17:68420189, elapsed 0.7s, est remaining 0.4s, peak mem 163MB, user 0.5s, sys 2.1s, output queue size 26403
progress 65% @chr18:5890198, elapsed 0.7s, est remaining 0.4s, peak mem 177MB, user 0.5s, sys 2.2s, output queue size 29122
progress 70% @chr18:62576512, elapsed 0.8s, est remaining 0.3s, peak mem 181MB, user 0.6s, sys 2.3s, output queue size 31498
progress 75% @chr19:6753456, elapsed 0.9s, est remaining 0.3s, peak mem 198MB, user 0.6s, sys 2.5s, output queue size 484
progress 80% @chr19:15265354, elapsed 1.0s, est remaining 0.3s, peak mem 207MB, user 0.7s, sys 2.6s, output queue size 2741
progress 85% @chr19:36915796, elapsed 1.1s, est remaining 0.2s, peak mem 216MB, user 0.7s, sys 2.8s, output queue size 5054
progress 90% @chr19:46493558, elapsed 1.2s, est remaining 0.1s, peak mem 220MB, user 0.7s, sys 2.9s, output queue size 7227
progress 95% @chr20:36912423, elapsed 1.3s, est remaining 0.1s, peak mem 237MB, user 0.8s, sys 3.0s, output queue size 9865
progress 100% @chr20:63950759, elapsed 1.3s, est remaining 0.0s, peak mem 246MB, user 0.8s, sys 3.2s, output queue size 12304
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: 74586810
output file size: 22309
reads: 1001133
contig: 48152 intervals 9000028 bases
active: 97912 calls 0.000 user 0.002 sys 0.022 real
advance: 49760 calls 0.002 user 0.006 sys 0.030 real
calc: 97912 calls 0.000 user 0.003 sys 0.022 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.006 user 0.001 sys 2.470 real
fetch: 97912 calls 0.001 user 0.009 sys 0.023 real
fetch_ref: 97912 calls 0.060 user 0.018 sys 0.416 real
idle: 51 calls 0.006 user 0.007 sys 26.258 real
init: 1 calls 0.048 user 0.010 sys 0.058 real
region: 97912 calls 0.002 user 0.000 sys 0.025 real
tracker: 97912 calls 0.022 user 0.014 sys 0.122 real
overall: 258170880 mem 1.556 user 5.262 sys 3.634 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory