Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/1d9ed6f0824dc17258d49b90e70733/.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-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/scatter/chr4_30730753-30730788.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/1d9ed6f0824dc17258d49b90e70733/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/55e68b26048fb02e6d377a2b8f5bd1/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/55e68b26048fb02e6d377a2b8f5bd1/Sig_18_Blood.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
==> STAGING COMPLETE (9 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr4_30730753-30730788.bed.gz -i Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_2.haplotyper.chr4_30730753-30730788.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr4:86809769, elapsed 0.0s, est remaining 0.9s, peak mem 85MB, user 0.1s, sys 0.2s, output queue size 149
progress 10% @chr4:152337759, elapsed 0.1s, est remaining 0.9s, peak mem 90MB, user 0.1s, sys 0.3s, output queue size 2541
progress 15% @chr5:36181818, elapsed 0.2s, est remaining 1.0s, peak mem 91MB, user 0.1s, sys 0.5s, output queue size 5015
progress 20% @chr5:93587917, elapsed 0.3s, est remaining 1.1s, peak mem 105MB, user 0.2s, sys 0.7s, output queue size 7599
progress 25% @chr5:141192553, elapsed 0.4s, est remaining 1.1s, peak mem 111MB, user 0.2s, sys 0.9s, output queue size 9992
progress 30% @chr5:177304625, elapsed 0.4s, est remaining 1.0s, peak mem 115MB, user 0.2s, sys 1.1s, output queue size 12115
progress 35% @chr6:30948547, elapsed 0.5s, est remaining 1.0s, peak mem 121MB, user 0.2s, sys 1.2s, output queue size 14302
progress 40% @chr6:43640021, elapsed 0.6s, est remaining 0.9s, peak mem 127MB, user 0.3s, sys 1.5s, output queue size 16849
progress 45% @chr6:106544788, elapsed 0.7s, est remaining 0.8s, peak mem 139MB, user 0.3s, sys 1.6s, output queue size 19318
progress 50% @chr6:149450683, elapsed 0.8s, est remaining 0.8s, peak mem 147MB, user 0.4s, sys 1.8s, output queue size 21413
progress 55% @chr7:13914223, elapsed 0.8s, est remaining 0.7s, peak mem 156MB, user 0.4s, sys 2.0s, output queue size 1212
progress 60% @chr7:64219314, elapsed 0.9s, est remaining 0.6s, peak mem 163MB, user 0.5s, sys 2.1s, output queue size 3280
progress 65% @chr7:100951841, elapsed 1.1s, est remaining 0.6s, peak mem 169MB, user 0.5s, sys 2.3s, output queue size 5799
progress 70% @chr7:139297787, elapsed 1.1s, est remaining 0.5s, peak mem 181MB, user 0.5s, sys 2.5s, output queue size 8163
progress 75% @chr8:13393553, elapsed 1.2s, est remaining 0.4s, peak mem 189MB, user 0.6s, sys 2.6s, output queue size 10228
progress 80% @chr8:39221610, elapsed 1.2s, est remaining 0.3s, peak mem 195MB, user 0.6s, sys 2.8s, output queue size 11914
progress 85% @chrX:15541982, elapsed 1.3s, est remaining 0.2s, peak mem 202MB, user 0.6s, sys 2.9s, output queue size 14358
progress 90% @chrX:54960824, elapsed 1.4s, est remaining 0.2s, peak mem 213MB, user 0.7s, sys 3.0s, output queue size 16720
progress 95% @chrX:111726809, elapsed 1.4s, est remaining 0.1s, peak mem 219MB, user 0.7s, sys 3.2s, output queue size 18659
progress 100% @chrX:153959331, elapsed 1.5s, est remaining 0.0s, peak mem 223MB, user 0.8s, sys 3.4s, output queue size 20874
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 12 max 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74586807
output file size: 22310
reads: 1001133
contig: 45710 intervals 9000068 bases
"assemble": 1 calls 0.000 user 0.000 sys 0.001 real
"assemble_addRead": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_buildGraph": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_computecigar": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_calcsize": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_clear": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_prepare": 4 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_threading": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op1": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op2": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op3": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_sg_clean": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_sg_create": 2 calls 0.000 user 0.000 sys 0.000 real
"checkGraph": 1 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 1 calls 0.000 user 0.000 sys 0.000 real
active: 93348 calls 0.000 user 0.000 sys 0.020 real
advance: 47638 calls 0.005 user 0.004 sys 0.029 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.001 real
calc: 93348 calls 0.000 user 0.007 sys 0.020 real
clip_region: 1 calls 0.000 user 0.000 sys 0.000 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.002 user 0.001 sys 2.510 real
fetch: 93348 calls 0.000 user 0.003 sys 0.021 real
fetch_ref: 93349 calls 0.031 user 0.021 sys 0.414 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 51 calls 0.003 user 0.024 sys 25.088 real
init: 1 calls 0.050 user 0.000 sys 0.053 real
region: 93348 calls 0.000 user 0.003 sys 0.023 real
tracker: 93348 calls 0.025 user 0.003 sys 0.107 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 234590208 mem 1.288 user 5.069 sys 3.653 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory