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/69/24ada015d15bb604adf91710f2a6b4/germline_control_1.dv_only_sites.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/071ef23c5bb915778959fe01917b2f/.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/38/6364050760c5582cbdad0b85841682/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/6364050760c5582cbdad0b85841682/HCC1395_BL.recalibrated.bam.bai
  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/f7/071ef23c5bb915778959fe01917b2f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/24ada015d15bb604adf91710f2a6b4/germline_control_1.dv_only_sites.vcf.gz.tbi
==> 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 HCC1395_BL.recalibrated.bam --algo Haplotyper --given germline_control_1.dv_only_sites.vcf.gz --emit_mode variant germline_control_1.forcecall.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr2:29768270, elapsed 0.0s, est remaining 0.2s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 6
progress 10% @chr2:214725647, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 125
progress 15% @chr3:142523851, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 351
progress 20% @chr5:112821885, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 528
progress 25% @chr7:55019018, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 669
progress 30% @chr7:55176897, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 125
progress 35% @chr9:21968576, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 255
progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 407
progress 45% @chr11:64803513, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 516
progress 50% @chr12:11770919, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 698
progress 55% @chr12:11796959, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 710
progress 60% @chr12:11855326, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 728
progress 65% @chr12:132668794, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 799
progress 70% @chr14:65075125, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 970
progress 75% @chr10:102617280, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1130
progress 80% @chr17:7679679, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 1352
progress 85% @chr17:39530604, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.0s, output queue size 1536
progress 90% @chr17:61679140, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 1637
progress 95% @chr19:52170836, elapsed 0.0s, est remaining 0.0s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 1821
progress 100% @chr21:34787802, elapsed 0.1s, est remaining 0.0s, peak mem 85MB, user 0.1s, 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: 71692767
output file size: 22310
reads: 1001089
contig: 2712 intervals 851273 bases
active: 5761 calls 0.000 user 0.000 sys 0.002 real
advance: 3049 calls 0.040 user 0.057 sys 0.103 real
calc: 5761 calls 0.000 user 0.000 sys 0.017 real
clip_region: 7 calls 0.001 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 0.002 sys 0.094 real
fetch: 5761 calls 0.003 user 0.006 sys 0.008 real
fetch_ref: 5768 calls 0.002 user 0.000 sys 0.022 real
fetch_region: 7 calls 0.000 user 0.000 sys 0.001 real
idle: 24 calls 0.003 user 0.003 sys 12.405 real
init: 1 calls 0.000 user 0.000 sys 0.002 real
region: 5761 calls 0.001 user 0.000 sys 0.004 real
tracker: 5761 calls 0.003 user 0.000 sys 0.007 real
overall: 89919488 mem 0.186 user 0.359 sys 1.146 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory