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/8d/715d94e7b803327d6eeb03a723c140/.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/15/2756d90861e8e5a0c2d42b8a8e1daf/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/15/2756d90861e8e5a0c2d42b8a8e1daf/germline_control_2.dv_only_sites.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/715d94e7b803327d6eeb03a723c140/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/fd07f3bccb2b3e7b5521fe26c79365/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/fd07f3bccb2b3e7b5521fe26c79365/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 51MB, user 0.0s, sys 0.0s, output queue size 19
progress 10% @chr2:214725647, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 143
progress 15% @chr3:142523851, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 369
progress 20% @chr5:112818952, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 550
progress 25% @chr7:6000358, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 685
progress 30% @chr7:55176897, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 728
progress 35% @chr9:21968576, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 864
progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 32
progress 45% @chr11:64803513, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 144
progress 50% @chr12:11770919, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 329
progress 55% @chr12:11792759, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 340
progress 60% @chr12:11853394, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 357
progress 65% @chr12:132660824, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 420
progress 70% @chr14:65075125, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 597
progress 75% @chr15:89307601, elapsed 0.1s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 755
progress 80% @chr17:7675962, elapsed 0.1s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 989
progress 85% @chr17:39530604, elapsed 0.1s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1169
progress 90% @chr17:61681285, elapsed 0.1s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1272
progress 95% @chr19:52185532, elapsed 0.1s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.2s, output queue size 1455
progress 100% @chr21:34787802, elapsed 0.1s, est remaining 0.0s, peak mem 75MB, user 0.1s, 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: 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: 74586815
output file size: 22314
reads: 1001133
contig: 2712 intervals 851273 bases
active: 5761 calls 0.000 user 0.000 sys 0.003 real
advance: 3049 calls 0.056 user 0.046 sys 0.127 real
calc: 5761 calls 0.001 user 0.000 sys 0.021 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 0.003 user 0.004 sys 0.128 real
fetch: 5761 calls 0.003 user 0.006 sys 0.011 real
fetch_ref: 5768 calls 0.005 user 0.000 sys 0.029 real
fetch_region: 7 calls 0.010 user 0.000 sys 0.001 real
idle: 25 calls 0.007 user 0.014 sys 12.500 real
init: 1 calls 0.000 user 0.000 sys 0.002 real
region: 5761 calls 0.019 user 0.001 sys 0.005 real
tracker: 5761 calls 0.001 user 0.003 sys 0.008 real
overall: 78778368 mem 0.258 user 0.624 sys 1.179 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory