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/5b/08ca36877099402a09ab55585f19fe/.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/0e/a2ccef1525a551970c21f9713564f9/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/08ca36877099402a09ab55585f19fe/.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-rnd-pltf-dev-nextflow-scratch-01/work/0e/a2ccef1525a551970c21f9713564f9/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 0.1s, output queue size 2190
progress 10% @chr15:40931503, elapsed 0.1s, est remaining 0.7s, peak mem 91MB, user 0.0s, sys 0.2s, output queue size 4428
progress 15% @chr15:63983533, elapsed 0.1s, est remaining 0.7s, peak mem 103MB, user 0.1s, sys 0.4s, output queue size 1227
progress 20% @chr15:87989891, elapsed 0.2s, est remaining 0.6s, peak mem 112MB, user 0.1s, sys 0.5s, output queue size 3511
progress 25% @chr16:1944837, elapsed 0.2s, est remaining 0.5s, peak mem 117MB, user 0.1s, sys 0.6s, output queue size 5193
progress 30% @chr16:23482923, elapsed 0.2s, est remaining 0.5s, peak mem 127MB, user 0.1s, sys 0.8s, output queue size 7671
progress 35% @chr16:66566514, elapsed 0.3s, est remaining 0.5s, peak mem 139MB, user 0.2s, sys 0.9s, output queue size 10278
progress 40% @chr16:89286670, elapsed 0.3s, est remaining 0.4s, peak mem 148MB, user 0.2s, sys 1.1s, output queue size 12756
progress 45% @chr17:10019777, elapsed 0.3s, est remaining 0.4s, peak mem 160MB, user 0.2s, sys 1.3s, output queue size 15363
progress 50% @chr17:36262666, elapsed 0.4s, est remaining 0.4s, peak mem 169MB, user 0.2s, sys 1.5s, output queue size 17961
progress 55% @chr17:45103709, elapsed 0.4s, est remaining 0.3s, peak mem 180MB, user 0.2s, sys 1.7s, output queue size 20202
progress 60% @chr17:61982198, elapsed 0.5s, est remaining 0.3s, peak mem 187MB, user 0.2s, sys 1.9s, output queue size 22738
progress 65% @chr18:5433903, elapsed 0.5s, est remaining 0.3s, peak mem 202MB, user 0.3s, sys 2.1s, output queue size 25455
progress 70% @chr18:62574057, elapsed 0.5s, est remaining 0.2s, peak mem 213MB, user 0.3s, sys 2.3s, output queue size 27836
progress 75% @chr19:6924678, elapsed 0.6s, est remaining 0.2s, peak mem 219MB, user 0.3s, sys 2.4s, output queue size 30222
progress 80% @chr19:15256964, elapsed 0.6s, est remaining 0.2s, peak mem 232MB, user 0.4s, sys 2.5s, output queue size 32476
progress 85% @chr19:36914965, elapsed 0.6s, est remaining 0.1s, peak mem 243MB, user 0.4s, sys 2.7s, output queue size 34791
progress 90% @chr19:46469733, elapsed 0.7s, est remaining 0.1s, peak mem 252MB, user 0.4s, sys 2.8s, output queue size 36971
progress 95% @chr20:36904118, elapsed 0.7s, est remaining 0.0s, peak mem 265MB, user 0.4s, sys 2.9s, output queue size 39605
progress 100% @chr20:59968967, elapsed 0.8s, est remaining 0.0s, peak mem 273MB, user 0.5s, sys 3.1s, output queue size 42041
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: 74586807
output file size: 22311
reads: 1001133
contig: 48152 intervals 9000028 bases
active: 97912 calls 0.000 user 0.020 sys 0.019 real
advance: 49760 calls 0.000 user 0.026 sys 0.027 real
calc: 97912 calls 0.004 user 0.006 sys 0.019 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.000 sys 1.371 real
fetch: 97912 calls 0.005 user 0.000 sys 0.020 real
fetch_ref: 97912 calls 0.083 user 0.052 sys 0.345 real
idle: 39 calls 0.009 user 0.019 sys 19.749 real
init: 1 calls 0.031 user 0.009 sys 0.042 real
region: 97912 calls 0.000 user 0.001 sys 0.022 real
tracker: 97912 calls 0.005 user 0.011 sys 0.089 real
overall: 288100352 mem 1.050 user 5.180 sys 2.487 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory