Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/3c009dcd7aaa5257601448761dc42f/.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/c7/4fbf3267803fb7ec7138daae3aad39/germline_control_2.dv_only_sites.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/germline_rescue_targets.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/4fbf3267803fb7ec7138daae3aad39/germline_control_2.dv_only_sites.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/3c009dcd7aaa5257601448761dc42f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/afbce3389bf5bcfac4e357eeed7653/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/afbce3389bf5bcfac4e357eeed7653/Sig_18_Blood.recalibrated.bam
==> STAGING COMPLETE (9 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval germline_rescue_targets.bed -i Sig_18_Blood.recalibrated.bam --algo Haplotyper --given germline_control_2.dv_only_sites.vcf.gz --emit_mode variant germline_control_2.forcecall.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr2:29531915, elapsed 0.0s, est remaining 0.2s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 0
progress 10% @chr2:214725647, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 69
progress 15% @chr3:142523851, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 293
progress 20% @chr5:112818952, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 474
progress 25% @chr7:5993472, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 35
progress 30% @chr7:55176897, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 78
progress 35% @chr9:35073840, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 223
progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 359
progress 45% @chr11:64805617, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 481
progress 50% @chr12:11752419, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 660
progress 55% @chr12:11796959, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 671
progress 60% @chr12:11865286, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 687
progress 65% @chr12:132675715, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 765
progress 70% @chr14:65075125, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 926
progress 75% @chr15:89314597, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1086
progress 80% @chr17:7679679, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1318
progress 85% @chr17:43049007, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1500
progress 90% @chr17:61679140, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1602
progress 95% @chr19:52190411, elapsed 0.1s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1781
progress 100% @chr21:34787802, elapsed 0.1s, est remaining 0.0s, peak mem 85MB, user 0.1s, sys 0.2s, output queue size 124
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 12 max 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74586803
output file size: 22313
reads: 1001133
contig: 2712 intervals 851273 bases
active: 5761 calls 0.000 user 0.001 sys 0.002 real
advance: 3049 calls 0.055 user 0.028 sys 0.098 real
calc: 5761 calls 0.002 user 0.000 sys 0.019 real
clip_region: 7 calls 0.000 user 0.000 sys 0.002 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.003 sys 0.102 real
fetch: 5761 calls 0.003 user 0.005 sys 0.008 real
fetch_ref: 5768 calls 0.003 user 0.000 sys 0.024 real
fetch_region: 7 calls 0.000 user 0.000 sys 0.001 real
idle: 24 calls 0.009 user 0.001 sys 12.457 real
init: 1 calls 0.000 user 0.000 sys 0.002 real
region: 5761 calls 0.000 user 0.000 sys 0.004 real
tracker: 5761 calls 0.000 user 0.003 sys 0.006 real
overall: 89894912 mem 0.180 user 0.424 sys 1.153 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory