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/53/e65673fe365c12861f62f5f603bc25/.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/98/a4798a32f5e9daf45b045790a1d26d/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/a4798a32f5e9daf45b045790a1d26d/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/e65673fe365c12861f62f5f603bc25/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/scatter/chr8_93795409-93795507.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 chr8_93795409-93795507.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr8_93795409-93795507.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr8:144254813, elapsed 0.0s, est remaining 0.8s, peak mem 84MB, user 0.0s, sys 0.1s, output queue size 2130
progress 10% @chr9:36833270, elapsed 0.1s, est remaining 0.7s, peak mem 93MB, user 0.1s, sys 0.3s, output queue size 4344
progress 15% @chr9:96641759, elapsed 0.1s, est remaining 0.6s, peak mem 100MB, user 0.1s, sys 0.4s, output queue size 6127
progress 20% @chr9:128907165, elapsed 0.1s, est remaining 0.6s, peak mem 111MB, user 0.1s, sys 0.6s, output queue size 445
progress 25% @chr10:14908408, elapsed 0.2s, est remaining 0.6s, peak mem 123MB, user 0.2s, sys 0.8s, output queue size 3199
progress 30% @chr10:69200280, elapsed 0.2s, est remaining 0.5s, peak mem 132MB, user 0.2s, sys 0.9s, output queue size 5589
progress 35% @chr10:100506040, elapsed 0.3s, est remaining 0.5s, peak mem 144MB, user 0.2s, sys 1.0s, output queue size 8243
progress 40% @chr11:308193, elapsed 0.3s, est remaining 0.5s, peak mem 156MB, user 0.3s, sys 1.2s, output queue size 10824
progress 45% @chr11:17781670, elapsed 0.3s, est remaining 0.4s, peak mem 163MB, user 0.3s, sys 1.3s, output queue size 12980
progress 50% @chr11:61419922, elapsed 0.4s, est remaining 0.4s, peak mem 174MB, user 0.3s, sys 1.5s, output queue size 15347
progress 55% @chr11:73234160, elapsed 0.4s, est remaining 0.3s, peak mem 184MB, user 0.3s, sys 1.7s, output queue size 18021
progress 60% @chr11:114445979, elapsed 0.5s, est remaining 0.3s, peak mem 196MB, user 0.4s, sys 1.9s, output queue size 20307
progress 65% @chr12:6457406, elapsed 0.5s, est remaining 0.3s, peak mem 204MB, user 0.4s, sys 2.1s, output queue size 22670
progress 70% @chr12:31697740, elapsed 0.5s, est remaining 0.2s, peak mem 213MB, user 0.4s, sys 2.2s, output queue size 24761
progress 75% @chr12:55971521, elapsed 0.6s, est remaining 0.2s, peak mem 226MB, user 0.5s, sys 2.3s, output queue size 27238
progress 80% @chr12:99984104, elapsed 0.6s, est remaining 0.2s, peak mem 235MB, user 0.5s, sys 2.6s, output queue size 29967
progress 85% @chr12:123781080, elapsed 0.7s, est remaining 0.1s, peak mem 249MB, user 0.5s, sys 2.8s, output queue size 32821
progress 90% @chr13:48429756, elapsed 0.7s, est remaining 0.1s, peak mem 256MB, user 0.6s, sys 2.9s, output queue size 35186
progress 95% @chr14:22610859, elapsed 0.7s, est remaining 0.0s, peak mem 271MB, user 0.6s, sys 3.1s, output queue size 37449
progress 100% @chr14:64120927, elapsed 0.8s, est remaining 0.0s, peak mem 279MB, user 0.7s, sys 3.2s, output queue size 39997
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: 71692772
output file size: 22307
reads: 1001089
contig: 48642 intervals 9000010 bases
active: 98785 calls 0.007 user 0.008 sys 0.018 real
advance: 50143 calls 0.001 user 0.009 sys 0.019 real
calc: 98785 calls 0.004 user 0.016 sys 0.018 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.005 user 0.001 sys 1.414 real
fetch: 98785 calls 0.010 user 0.010 sys 0.019 real
fetch_ref: 98785 calls 0.091 user 0.077 sys 0.368 real
idle: 39 calls 0.011 user 0.030 sys 19.967 real
init: 1 calls 0.040 user 0.010 sys 0.042 real
region: 98785 calls 0.000 user 0.005 sys 0.021 real
tracker: 98785 calls 0.026 user 0.007 sys 0.087 real
overall: 295948288 mem 1.260 user 4.835 sys 2.530 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory