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/de/84846ab8bf9332125e45b501a6c0d3/.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/37/9abee178273dcf278f97a25778bfc1/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/37/9abee178273dcf278f97a25778bfc1/germline_control_2.dv_only_sites.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/84846ab8bf9332125e45b501a6c0d3/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/8cec261d5efbf269078e42e83159b5/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/8cec261d5efbf269078e42e83159b5/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 0.1s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 111
progress 10% @chr2:214792290, elapsed 0.0s, est remaining 0.1s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 31
progress 15% @chr3:142538482, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 248
progress 20% @chr5:112827091, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 430
progress 25% @chr7:6003675, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 563
progress 30% @chr7:55176897, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 604
progress 35% @chr9:21970761, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 739
progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 885
progress 45% @chr11:64803513, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1003
progress 50% @chr12:11773199, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1184
progress 55% @chr12:11792759, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1195
progress 60% @chr12:11860606, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1213
progress 65% @chr12:132672595, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1285
progress 70% @chr14:65075125, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1454
progress 75% @chr15:89303863, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1606
progress 80% @chr17:17212802, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1845
progress 85% @chr17:39530604, elapsed 0.1s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 2021
progress 90% @chr17:61680325, elapsed 0.1s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 2123
progress 95% @chr19:52170836, elapsed 0.1s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 2307
progress 100% @chr21:34787802, elapsed 0.1s, est remaining 0.0s, peak mem 84MB, user 0.2s, sys 0.2s, output queue size 124
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 74381931
output file size: 22314
reads: 1001133
contig: 2712 intervals 851273 bases
active: 5761 calls 0.004 user 0.000 sys 0.003 real
advance: 3049 calls 0.081 user 0.035 sys 0.141 real
calc: 5761 calls 0.029 user 0.000 sys 0.037 real
clip_region: 7 calls 0.000 user 0.000 sys 0.002 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.000 user 0.004 sys 0.132 real
fetch: 5761 calls 0.010 user 0.002 sys 0.010 real
fetch_ref: 5768 calls 0.003 user 0.002 sys 0.027 real
fetch_region: 7 calls 0.000 user 0.000 sys 0.001 real
idle: 25 calls 0.005 user 0.009 sys 12.680 real
init: 1 calls 0.000 user 0.000 sys 0.002 real
region: 5761 calls 0.000 user 0.001 sys 0.005 real
tracker: 5761 calls 0.000 user 0.001 sys 0.010 real
overall: 88326144 mem 0.362 user 0.422 sys 1.194 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory