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/b9/c6da0997bf6ac83bf14df3e120a080/.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/be/b16da18d4681325da6218d44c5ecf9/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/be/b16da18d4681325da6218d44c5ecf9/germline_control_2.dv_only_sites.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/c6da0997bf6ac83bf14df3e120a080/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/b8328367b22c15bd3300ec483b8d21/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/b8328367b22c15bd3300ec483b8d21/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% @chr2:29717578, elapsed 0.0s, est remaining 0.1s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 14
progress 10% @chr2:214725647, elapsed 0.0s, est remaining 0.1s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 4
progress 15% @chr3:142542665, elapsed 0.0s, est remaining 0.1s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 225
progress 20% @chr5:112828853, elapsed 0.0s, est remaining 0.1s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 407
progress 25% @chr7:6000358, elapsed 0.0s, est remaining 0.1s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 539
progress 30% @chr7:55176897, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 578
progress 35% @chr9:21970761, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 718
progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 861
progress 45% @chr11:61445932, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 979
progress 50% @chr12:11770919, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.0s, sys 0.1s, output queue size 1161
progress 55% @chr12:11792759, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.0s, sys 0.1s, output queue size 1173
progress 60% @chr12:11855326, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.0s, sys 0.1s, output queue size 1189
progress 65% @chr12:132660824, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.0s, sys 0.1s, output queue size 1251
progress 70% @chr14:65075125, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1426
progress 75% @chr15:89305605, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 1580
progress 80% @chr17:7677279, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 1815
progress 85% @chr17:39530604, elapsed 0.0s, est remaining 0.0s, peak mem 54MB, user 0.0s, sys 0.1s, output queue size 2000
progress 90% @chr17:61679140, elapsed 0.0s, est remaining 0.0s, peak mem 54MB, user 0.0s, sys 0.1s, output queue size 2102
progress 95% @chr19:50416760, elapsed 0.0s, est remaining 0.0s, peak mem 54MB, user 0.0s, sys 0.1s, output queue size 2284
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 6.12.83
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 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74732894
output file size: 22314
reads: 1001133
contig: 2712 intervals 851273 bases
active: 5761 calls 0.000 user 0.000 sys 0.002 real
advance: 3049 calls 0.057 user 0.025 sys 0.100 real
calc: 5761 calls 0.009 user 0.000 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 0.000 user 0.008 sys 0.096 real
fetch: 5761 calls 0.003 user 0.001 sys 0.009 real
fetch_ref: 5768 calls 0.001 user 0.000 sys 0.024 real
fetch_region: 7 calls 0.000 user 0.000 sys 0.001 real
idle: 25 calls 0.018 user 0.006 sys 12.452 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 0.001 user 0.000 sys 0.007 real
overall: 89919488 mem 0.252 user 0.337 sys 1.148 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory