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/4b/3ec33c3a133b92d7a0f056fc61ed88/.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/1a/a95586b1b08a697566ea24e2f6d852/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/a95586b1b08a697566ea24e2f6d852/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/3ec33c3a133b92d7a0f056fc61ed88/.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% @chr8:144250212, elapsed 0.0s, est remaining 0.9s, peak mem 75MB, user 0.1s, sys 0.1s, output queue size 2283
progress 10% @chr9:36923323, elapsed 0.1s, est remaining 0.8s, peak mem 78MB, user 0.1s, sys 0.2s, output queue size 1735
progress 15% @chr9:96758778, elapsed 0.1s, est remaining 0.7s, peak mem 84MB, user 0.1s, sys 0.3s, output queue size 3518
progress 20% @chr9:128941668, elapsed 0.2s, est remaining 0.7s, peak mem 96MB, user 0.1s, sys 0.5s, output queue size 6139
progress 25% @chr10:15103315, elapsed 0.2s, est remaining 0.7s, peak mem 108MB, user 0.1s, sys 0.8s, output queue size 8917
progress 30% @chr10:69202439, elapsed 0.3s, est remaining 0.7s, peak mem 117MB, user 0.2s, sys 1.0s, output queue size 11279
progress 35% @chr10:100507425, elapsed 0.3s, est remaining 0.6s, peak mem 126MB, user 0.2s, sys 1.2s, output queue size 13934
progress 40% @chr11:308193, elapsed 0.4s, est remaining 0.6s, peak mem 132MB, user 0.2s, sys 1.4s, output queue size 16513
progress 45% @chr11:17959470, elapsed 0.5s, est remaining 0.6s, peak mem 144MB, user 0.3s, sys 1.5s, output queue size 18671
progress 50% @chr11:48216810, elapsed 0.5s, est remaining 0.5s, peak mem 153MB, user 0.3s, sys 1.7s, output queue size 21048
progress 55% @chr11:73234160, elapsed 0.6s, est remaining 0.5s, peak mem 159MB, user 0.4s, sys 1.9s, output queue size 23709
progress 60% @chr11:114444541, elapsed 0.6s, est remaining 0.4s, peak mem 171MB, user 0.4s, sys 2.0s, output queue size 25996
progress 65% @chr12:6541512, elapsed 0.7s, est remaining 0.4s, peak mem 177MB, user 0.4s, sys 2.2s, output queue size 28405
progress 70% @chr12:31672304, elapsed 0.7s, est remaining 0.3s, peak mem 186MB, user 0.5s, sys 2.4s, output queue size 30447
progress 75% @chr12:55961622, elapsed 0.8s, est remaining 0.3s, peak mem 195MB, user 0.5s, sys 2.5s, output queue size 32925
progress 80% @chr12:100050168, elapsed 0.8s, est remaining 0.2s, peak mem 204MB, user 0.5s, sys 2.7s, output queue size 35654
progress 85% @chr12:123787804, elapsed 0.9s, est remaining 0.2s, peak mem 213MB, user 0.6s, sys 3.0s, output queue size 38511
progress 90% @chr13:48473332, elapsed 0.9s, est remaining 0.1s, peak mem 222MB, user 0.6s, sys 3.1s, output queue size 40884
progress 95% @chr14:22633768, elapsed 1.0s, est remaining 0.1s, peak mem 228MB, user 0.7s, sys 3.3s, output queue size 43132
progress 100% @chr14:63998219, elapsed 1.0s, est remaining 0.0s, peak mem 243MB, user 0.7s, sys 3.4s, output queue size 45687
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692772
output file size: 22308
reads: 1001089
contig: 48642 intervals 9000010 bases
active: 98785 calls 0.002 user 0.000 sys 0.018 real
advance: 50143 calls 0.005 user 0.003 sys 0.020 real
calc: 98785 calls 0.000 user 0.000 sys 0.018 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.002 user 0.000 sys 2.569 real
fetch: 98785 calls 0.004 user 0.008 sys 0.018 real
fetch_ref: 98785 calls 0.035 user 0.038 sys 0.361 real
idle: 51 calls 0.003 user 0.004 sys 30.789 real
init: 1 calls 0.035 user 0.011 sys 0.044 real
region: 98785 calls 0.007 user 0.004 sys 0.021 real
tracker: 98785 calls 0.012 user 0.008 sys 0.089 real
overall: 258084864 mem 1.154 user 5.236 sys 3.690 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory