Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/32a5ed1750e61a116a0e2c4769877c/germline_control_1.dv_only_sites.vcf.gz
  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/94/4f9bb8cea9fd3d5d282c86766b2c15/.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/8f/8ee7221cb00667c7914a883215e2de/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/8ee7221cb00667c7914a883215e2de/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/94/4f9bb8cea9fd3d5d282c86766b2c15/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/32a5ed1750e61a116a0e2c4769877c/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% @chr2:29531915, elapsed 0.0s, est remaining 0.1s, peak mem 52MB, user 0.0s, sys 0.0s, output queue size 25
progress 10% @chr2:214725647, elapsed 0.0s, est remaining 0.1s, peak mem 52MB, user 0.0s, sys 0.0s, output queue size 150
progress 15% @chr3:142536108, elapsed 0.0s, est remaining 0.1s, peak mem 52MB, user 0.0s, sys 0.0s, output queue size 379
progress 20% @chr5:112829994, elapsed 0.0s, est remaining 0.1s, peak mem 53MB, user 0.0s, sys 0.0s, output queue size 561
progress 25% @chr7:6002447, elapsed 0.0s, est remaining 0.1s, peak mem 54MB, user 0.0s, sys 0.0s, output queue size 693
progress 30% @chr7:55204953, elapsed 0.0s, est remaining 0.1s, peak mem 55MB, user 0.0s, sys 0.0s, output queue size 743
progress 35% @chr9:21970761, elapsed 0.0s, est remaining 0.1s, peak mem 55MB, user 0.0s, sys 0.0s, output queue size 640
progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 55MB, user 0.1s, sys 0.0s, output queue size 787
progress 45% @chr11:61445932, elapsed 0.0s, est remaining 0.0s, peak mem 55MB, user 0.1s, sys 0.0s, output queue size 902
progress 50% @chr12:11770919, elapsed 0.0s, est remaining 0.0s, peak mem 56MB, user 0.1s, sys 0.0s, output queue size 1083
progress 55% @chr12:11792759, elapsed 0.0s, est remaining 0.0s, peak mem 56MB, user 0.1s, sys 0.0s, output queue size 1096
progress 60% @chr12:11855326, elapsed 0.0s, est remaining 0.0s, peak mem 56MB, user 0.1s, sys 0.0s, output queue size 1111
progress 65% @chr12:132665290, elapsed 0.0s, est remaining 0.0s, peak mem 56MB, user 0.1s, sys 0.0s, output queue size 1177
progress 70% @chr14:65075125, elapsed 0.0s, est remaining 0.0s, peak mem 58MB, user 0.1s, sys 0.1s, output queue size 1349
progress 75% @chr10:86921507, elapsed 0.0s, est remaining 0.0s, peak mem 60MB, user 0.1s, sys 0.1s, output queue size 1505
progress 80% @chr17:7679199, elapsed 0.1s, est remaining 0.0s, peak mem 61MB, user 0.1s, sys 0.1s, output queue size 1739
progress 85% @chr17:39530604, elapsed 0.1s, est remaining 0.0s, peak mem 61MB, user 0.1s, sys 0.1s, output queue size 1919
progress 90% @chr17:61679140, elapsed 0.1s, est remaining 0.0s, peak mem 61MB, user 0.1s, sys 0.1s, output queue size 2022
progress 95% @chr19:52211260, elapsed 0.1s, est remaining 0.0s, peak mem 62MB, user 0.1s, sys 0.1s, output queue size 2217
progress 100% @chr21:34787802, elapsed 0.1s, est remaining 0.0s, peak mem 91MB, user 0.1s, sys 0.2s, output queue size 124
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 128
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 0.003 real
advance: 3049 calls 0.035 user 0.061 sys 0.120 real
calc: 5761 calls 0.014 user 0.000 sys 0.030 real
clip_region: 7 calls 0.000 user 0.000 sys 0.002 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.006 user 0.003 sys 0.120 real
fetch: 5761 calls 0.001 user 0.002 sys 0.009 real
fetch_ref: 5768 calls 0.000 user 0.002 sys 0.026 real
fetch_region: 7 calls 0.000 user 0.000 sys 0.001 real
idle: 24 calls 0.004 user 0.008 sys 12.491 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 0.002 user 0.006 sys 0.009 real
overall: 95944704 mem 0.285 user 0.456 sys 1.181 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory