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/e0/cec0c2c41d4e9cfa578ef0dc354424/.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/ee/4b609b82c34dc281cc5bcfb7534fcf/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/ee/4b609b82c34dc281cc5bcfb7534fcf/germline_control_2.dv_only_sites.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/cec0c2c41d4e9cfa578ef0dc354424/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/9b9bdd2e3a62b63766fd1bff60945d/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/9b9bdd2e3a62b63766fd1bff60945d/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 52MB, user 0.0s, sys 0.0s, output queue size 37
progress 10% @chr2:214725647, elapsed 0.0s, est remaining 0.1s, peak mem 52MB, user 0.0s, sys 0.0s, output queue size 167
progress 15% @chr3:142535080, elapsed 0.0s, est remaining 0.1s, peak mem 52MB, user 0.0s, sys 0.0s, output queue size 388
progress 20% @chr5:112823307, elapsed 0.0s, est remaining 0.1s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 570
progress 25% @chr7:6002447, elapsed 0.0s, est remaining 0.1s, peak mem 52MB, user 0.0s, sys 0.1s, output queue size 703
progress 30% @chr7:55176897, elapsed 0.0s, est remaining 0.1s, peak mem 55MB, user 0.0s, sys 0.1s, output queue size 748
progress 35% @chr9:21970761, elapsed 0.0s, est remaining 0.0s, peak mem 56MB, user 0.0s, sys 0.1s, output queue size 879
progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 56MB, user 0.0s, sys 0.1s, output queue size 1031
progress 45% @chr11:61437994, elapsed 0.0s, est remaining 0.0s, peak mem 56MB, user 0.0s, sys 0.1s, output queue size 1143
progress 50% @chr12:11770919, elapsed 0.0s, est remaining 0.0s, peak mem 56MB, user 0.0s, sys 0.1s, output queue size 1323
progress 55% @chr12:11809199, elapsed 0.0s, est remaining 0.0s, peak mem 56MB, user 0.0s, sys 0.1s, output queue size 1336
progress 60% @chr12:11855326, elapsed 0.0s, est remaining 0.0s, peak mem 56MB, user 0.0s, sys 0.1s, output queue size 1352
progress 65% @chr12:132660824, elapsed 0.0s, est remaining 0.0s, peak mem 56MB, user 0.0s, sys 0.1s, output queue size 1414
progress 70% @chr14:65075125, elapsed 0.0s, est remaining 0.0s, peak mem 58MB, user 0.0s, sys 0.1s, output queue size 438
progress 75% @chr15:89316396, elapsed 0.1s, est remaining 0.0s, peak mem 59MB, user 0.0s, sys 0.2s, output queue size 594
progress 80% @chr17:7679679, elapsed 0.1s, est remaining 0.0s, peak mem 59MB, user 0.0s, sys 0.2s, output queue size 822
progress 85% @chr17:39532155, elapsed 0.1s, est remaining 0.0s, peak mem 60MB, user 0.0s, sys 0.2s, output queue size 1004
progress 90% @chr17:61683205, elapsed 0.1s, est remaining 0.0s, peak mem 60MB, user 0.1s, sys 0.2s, output queue size 1106
progress 95% @chr19:50416760, elapsed 0.1s, est remaining 0.0s, peak mem 60MB, user 0.1s, sys 0.2s, output queue size 1290
progress 100% @chr21:34787802, elapsed 0.1s, est remaining 0.0s, peak mem 93MB, user 0.2s, sys 0.3s, output queue size 124
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050657
  features: bfebfbff 7ffefbff
  extended: d39ff7eb 00000818
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz
threads: 12 max 96
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74586803
output file size: 22313
reads: 1001133
contig: 2712 intervals 851273 bases
active: 5761 calls 0.000 user 0.000 sys 0.003 real
advance: 3049 calls 0.080 user 0.048 sys 0.144 real
calc: 5761 calls 0.039 user 0.003 sys 0.040 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 0.000 sys 0.153 real
fetch: 5761 calls 0.010 user 0.006 sys 0.012 real
fetch_ref: 5768 calls 0.005 user 0.001 sys 0.040 real
fetch_region: 7 calls 0.010 user 0.000 sys 0.001 real
idle: 25 calls 0.018 user 0.011 sys 12.734 real
init: 1 calls 0.010 user 0.000 sys 0.003 real
region: 5761 calls 0.010 user 0.003 sys 0.006 real
tracker: 5761 calls 0.000 user 0.000 sys 0.011 real
overall: 98766848 mem 0.369 user 0.578 sys 1.225 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory