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/8b/c941a753a8d429230748ece94e1f1c/.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/f3/c85943de6834ceed0afb9c1aa1e7e1/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/f3/c85943de6834ceed0afb9c1aa1e7e1/germline_control_2.dv_only_sites.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/c941a753a8d429230748ece94e1f1c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/39fc4609d5b3bb227efea5d5dd4332/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/39fc4609d5b3bb227efea5d5dd4332/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 107
progress 10% @chr2:214725647, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 236
progress 15% @chr3:142550131, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 175
progress 20% @chr5:112834929, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 356
progress 25% @chr7:6003969, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 487
progress 30% @chr7:55176897, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 541
progress 35% @chr9:21967753, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 665
progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 806
progress 45% @chr11:64803513, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 925
progress 50% @chr12:11770919, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1106
progress 55% @chr12:11796959, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1119
progress 60% @chr12:11860606, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1135
progress 65% @chr12:132665290, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1202
progress 70% @chr14:65075125, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1373
progress 75% @chr15:89306007, elapsed 0.1s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1531
progress 80% @chr17:7683519, elapsed 0.1s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.2s, output queue size 1766
progress 85% @chr17:43049007, elapsed 0.1s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.2s, output queue size 1947
progress 90% @chr17:61681285, elapsed 0.1s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.2s, output queue size 2047
progress 95% @chr19:50416391, elapsed 0.1s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.3s, output queue size 2228
progress 100% @chr21:34787802, elapsed 0.1s, est remaining 0.0s, peak mem 72MB, user 0.1s, sys 0.3s, output queue size 124
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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: 74586810
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 0.053 user 0.056 sys 0.133 real
calc: 5761 calls 0.006 user 0.002 sys 0.021 real
clip_region: 7 calls 0.000 user 0.002 sys 0.002 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.000 sys 0.137 real
fetch: 5761 calls 0.005 user 0.002 sys 0.011 real
fetch_ref: 5768 calls 0.001 user 0.000 sys 0.031 real
fetch_region: 7 calls 0.000 user 0.000 sys 0.001 real
idle: 33 calls 0.009 user 0.003 sys 12.518 real
init: 1 calls 0.001 user 0.000 sys 0.002 real
region: 5761 calls 0.000 user 0.002 sys 0.005 real
tracker: 5761 calls 0.002 user 0.002 sys 0.009 real
overall: 75632640 mem 0.251 user 0.669 sys 1.190 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory