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/49/36ea9ad3a59dc4769086629d8cc0aa/.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/cf/6fd23e85f78a8fbdafb08660cd0e69/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/cf/6fd23e85f78a8fbdafb08660cd0e69/germline_control_2.dv_only_sites.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/36ea9ad3a59dc4769086629d8cc0aa/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/381faa0df790cd8579fab559ff3f2b/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/381faa0df790cd8579fab559ff3f2b/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% @chr2:29768270, elapsed 0.0s, est remaining 0.5s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 107
progress 10% @chr3:10046579, elapsed 0.0s, est remaining 0.3s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 174
progress 15% @chr4:54235562, elapsed 0.0s, est remaining 0.2s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 388
progress 20% @chr5:132556931, elapsed 0.0s, est remaining 0.2s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 553
progress 25% @chr7:55155528, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 698
progress 30% @chr7:116764469, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 733
progress 35% @chr9:21992256, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 860
progress 40% @chr10:43111197, elapsed 0.1s, est remaining 0.1s, peak mem 51MB, user 0.1s, sys 0.0s, output queue size 995
progress 45% @chr11:61437994, elapsed 0.1s, est remaining 0.1s, peak mem 51MB, user 0.1s, sys 0.0s, output queue size 258
progress 50% @chr12:11776559, elapsed 0.1s, est remaining 0.1s, peak mem 51MB, user 0.1s, sys 0.0s, output queue size 440
progress 55% @chr12:11818559, elapsed 0.1s, est remaining 0.1s, peak mem 51MB, user 0.1s, sys 0.0s, output queue size 454
progress 60% @chr12:11860606, elapsed 0.1s, est remaining 0.0s, peak mem 51MB, user 0.1s, sys 0.0s, output queue size 470
progress 65% @chr13:32317216, elapsed 0.1s, est remaining 0.0s, peak mem 51MB, user 0.1s, sys 0.0s, output queue size 561
progress 70% @chr14:65075125, elapsed 0.1s, est remaining 0.0s, peak mem 51MB, user 0.1s, sys 0.0s, output queue size 708
progress 75% @chr15:90727893, elapsed 0.1s, est remaining 0.0s, peak mem 51MB, user 0.1s, sys 0.0s, output queue size 871
progress 80% @chr17:7685679, elapsed 0.1s, est remaining 0.0s, peak mem 52MB, user 0.1s, sys 0.0s, output queue size 1101
progress 85% @chr17:39532155, elapsed 0.1s, est remaining 0.0s, peak mem 52MB, user 0.1s, sys 0.0s, output queue size 1278
progress 90% @chr17:61742992, elapsed 0.1s, est remaining 0.0s, peak mem 52MB, user 0.1s, sys 0.1s, output queue size 1389
progress 95% @chr19:52170836, elapsed 0.1s, est remaining 0.0s, peak mem 52MB, user 0.1s, sys 0.1s, output queue size 1565
progress 100% @chr21:34787802, elapsed 0.1s, est remaining 0.0s, peak mem 88MB, user 0.2s, sys 0.1s, 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: 74586800
output file size: 22313
reads: 1001133
contig: 2712 intervals 851273 bases
active: 5761 calls 0.000 user 0.000 sys 0.002 real
advance: 3049 calls 0.048 user 0.035 sys 0.098 real
calc: 5761 calls 0.007 user 0.001 sys 0.019 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 0.005 user 0.002 sys 0.152 real
fetch: 5761 calls 0.000 user 0.001 sys 0.008 real
fetch_ref: 5768 calls 0.001 user 0.002 sys 0.022 real
fetch_region: 7 calls 0.009 user 0.000 sys 0.001 real
idle: 24 calls 0.018 user 0.004 sys 12.610 real
init: 1 calls 0.000 user 0.000 sys 0.001 real
region: 5761 calls 0.009 user 0.000 sys 0.004 real
tracker: 5761 calls 0.000 user 0.000 sys 0.006 real
overall: 93065216 mem 0.245 user 0.242 sys 1.205 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory