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/ab/7d97b7f40f77793db9e7e110b30dbc/.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-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/Sig_18_Blood/Sig_18_Blood.recal.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/1c0c5394a86f5f28fa34c19d226bca/Sig_18_Blood.dv_only_sites.vcf.gz.tbi
  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/ab/7d97b7f40f77793db9e7e110b30dbc/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/Sig_18_Blood/Sig_18_Blood.recal.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/1c0c5394a86f5f28fa34c19d226bca/Sig_18_Blood.dv_only_sites.vcf.gz
==> 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.recal.bam --algo Haplotyper --given Sig_18_Blood.dv_only_sites.vcf.gz --emit_mode variant Sig_18_Blood.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 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 51
progress 15% @chr3:142522728, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 273
progress 20% @chr5:112818952, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 455
progress 25% @chr7:6002447, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 587
progress 30% @chr7:55176897, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 626
progress 35% @chr9:21970761, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 289
progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 431
progress 45% @chr11:61445932, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 553
progress 50% @chr12:11770919, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 734
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progress 60% @chr12:11855326, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.0s, output queue size 765
progress 65% @chr12:132659281, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 825
progress 70% @chr14:65075125, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 999
progress 75% @chr15:89314597, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 1159
progress 80% @chr17:7679679, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 1391
progress 85% @chr17:39532155, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 1569
progress 90% @chr17:61681285, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 1674
progress 95% @chr19:52190411, elapsed 0.0s, est remaining 0.0s, peak mem 55MB, user 0.0s, sys 0.1s, output queue size 1860
progress 100% @chr21:34787802, elapsed 0.2s, est remaining 0.0s, peak mem 132MB, user 0.3s, 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: 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: 138653580
output file size: 22295
reads: 1685487
contig: 2712 intervals 851273 bases
active: 5761 calls 0.000 user 0.000 sys 0.003 real
advance: 3049 calls 0.186 user 0.055 sys 0.246 real
calc: 5761 calls 0.000 user 0.000 sys 0.043 real
clip_region: 7 calls 0.010 user 0.001 sys 0.004 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.001 user 0.000 sys 0.163 real
fetch: 5761 calls 0.022 user 0.003 sys 0.016 real
fetch_ref: 5768 calls 0.005 user 0.000 sys 0.022 real
fetch_region: 7 calls 0.000 user 0.000 sys 0.002 real
idle: 24 calls 0.012 user 0.007 sys 13.068 real
init: 1 calls 0.004 user 0.000 sys 0.002 real
region: 5761 calls 0.011 user 0.001 sys 0.008 real
tracker: 5761 calls 0.000 user 0.001 sys 0.007 real
overall: 140251136 mem 0.356 user 0.356 sys 1.218 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory