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/b0/c010c4afca5106694ec3cf776055b0/.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/b0/c010c4afca5106694ec3cf776055b0/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/8fc7f5716dfc4a815738382b6d56eb/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/8fc7f5716dfc4a815738382b6d56eb/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% @chr4:86785231, elapsed 0.0s, est remaining 0.8s, peak mem 82MB, user 0.1s, sys 0.1s, output queue size 1953
progress 10% @chr4:152329639, elapsed 0.1s, est remaining 0.7s, peak mem 90MB, user 0.1s, sys 0.2s, output queue size 4347
progress 15% @chr5:36171603, elapsed 0.1s, est remaining 0.7s, peak mem 106MB, user 0.1s, sys 0.4s, output queue size 6821
progress 20% @chr5:91374922, elapsed 0.2s, est remaining 0.6s, peak mem 114MB, user 0.1s, sys 0.6s, output queue size 9400
progress 25% @chr5:141192553, elapsed 0.2s, est remaining 0.6s, peak mem 124MB, user 0.2s, sys 0.7s, output queue size 1177
progress 30% @chr5:177303986, elapsed 0.2s, est remaining 0.5s, peak mem 132MB, user 0.2s, sys 0.9s, output queue size 3299
progress 35% @chr6:30986237, elapsed 0.3s, est remaining 0.5s, peak mem 139MB, user 0.2s, sys 1.1s, output queue size 5490
progress 40% @chr6:43636381, elapsed 0.3s, est remaining 0.5s, peak mem 150MB, user 0.2s, sys 1.3s, output queue size 8032
progress 45% @chr6:106527305, elapsed 0.4s, est remaining 0.4s, peak mem 162MB, user 0.3s, sys 1.5s, output queue size 10498
progress 50% @chr6:149517354, elapsed 0.4s, est remaining 0.4s, peak mem 172MB, user 0.3s, sys 1.7s, output queue size 12600
progress 55% @chr7:13914223, elapsed 0.4s, est remaining 0.4s, peak mem 177MB, user 0.3s, sys 1.8s, output queue size 14856
progress 60% @chr7:64219314, elapsed 0.5s, est remaining 0.3s, peak mem 189MB, user 0.3s, sys 2.0s, output queue size 16923
progress 65% @chr7:100951841, elapsed 0.5s, est remaining 0.3s, peak mem 198MB, user 0.3s, sys 2.3s, output queue size 19443
progress 70% @chr7:139283024, elapsed 0.6s, est remaining 0.2s, peak mem 205MB, user 0.3s, sys 2.4s, output queue size 21807
progress 75% @chr8:13099347, elapsed 0.6s, est remaining 0.2s, peak mem 216MB, user 0.4s, sys 2.5s, output queue size 23865
progress 80% @chr8:38827168, elapsed 0.6s, est remaining 0.2s, peak mem 220MB, user 0.4s, sys 2.6s, output queue size 25490
progress 85% @chrX:15531328, elapsed 0.7s, est remaining 0.1s, peak mem 232MB, user 0.5s, sys 2.8s, output queue size 27996
progress 90% @chrX:54951905, elapsed 0.7s, est remaining 0.1s, peak mem 243MB, user 0.5s, sys 2.9s, output queue size 30360
progress 95% @chrX:111721603, elapsed 0.7s, est remaining 0.0s, peak mem 249MB, user 0.6s, sys 3.0s, output queue size 32296
progress 100% @chrX:153786801, elapsed 0.8s, est remaining 0.0s, peak mem 259MB, user 0.6s, sys 3.2s, output queue size 34514
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: 74586805
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 0.010 sys 0.020 real
advance: 47638 calls 0.016 user 0.000 sys 0.028 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.001 real
calc: 93348 calls 0.017 user 0.008 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 0.009 sys 1.438 real
fetch: 93348 calls 0.000 user 0.004 sys 0.021 real
fetch_ref: 93349 calls 0.088 user 0.088 sys 0.383 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.002 user 0.016 sys 20.716 real
init: 1 calls 0.040 user 0.010 sys 0.052 real
region: 93348 calls 0.007 user 0.011 sys 0.022 real
tracker: 93348 calls 0.017 user 0.014 sys 0.100 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 273891328 mem 1.183 user 5.361 sys 2.575 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory