cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr19_47340800-47341813.bed.gz -i Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_2.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr19:49142804, elapsed 0.0s, est remaining 0.3s, peak mem 71MB, user 0.0s, sys 0.0s, output queue size 441
progress 10% @chr19:50629294, elapsed 0.0s, est remaining 0.3s, peak mem 73MB, user 0.0s, sys 0.1s, output queue size 615
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.2s, peak mem 74MB, user 0.0s, sys 0.1s, output queue size 988
progress 20% @chr19:54813690, elapsed 0.0s, est remaining 0.2s, peak mem 77MB, user 0.0s, sys 0.1s, output queue size 1367
progress 25% @chr19:56221575, elapsed 0.1s, est remaining 0.2s, peak mem 79MB, user 0.0s, sys 0.2s, output queue size 1811
progress 30% @chr19:58246711, elapsed 0.1s, est remaining 0.2s, peak mem 79MB, user 0.0s, sys 0.2s, output queue size 2055
progress 35% @chr21:30425394, elapsed 0.2s, est remaining 0.3s, peak mem 118MB, user 0.9s, sys 0.3s, output queue size 118
progress 40% @chr21:36460976, elapsed 0.4s, est remaining 0.6s, peak mem 161MB, user 2.0s, sys 0.3s, output queue size 105
progress 45% @chr21:41497133, elapsed 1.5s, est remaining 1.9s, peak mem 290MB, user 11.8s, sys 0.5s, output queue size 134
progress 50% @chr21:45514976, elapsed 2.0s, est remaining 2.0s, peak mem 301MB, user 16.6s, sys 0.5s, output queue size 7
progress 55% @chr22:19432555, elapsed 2.0s, est remaining 1.7s, peak mem 301MB, user 17.2s, sys 0.5s, output queue size 383
progress 60% @chr22:22318898, elapsed 2.1s, est remaining 1.4s, peak mem 301MB, user 17.2s, sys 0.5s, output queue size 408
progress 65% @chr22:23957723, elapsed 2.1s, est remaining 1.1s, peak mem 301MB, user 17.2s, sys 0.6s, output queue size 631
progress 70% @chr22:29286684, elapsed 2.1s, est remaining 0.9s, peak mem 301MB, user 17.2s, sys 0.6s, output queue size 1136
progress 75% @chr22:31870590, elapsed 2.1s, est remaining 0.7s, peak mem 301MB, user 17.2s, sys 0.7s, output queue size 1679
progress 80% @chr22:37940709, elapsed 2.1s, est remaining 0.5s, peak mem 301MB, user 17.2s, sys 0.7s, output queue size 2236
progress 85% @chr22:41280933, elapsed 2.1s, est remaining 0.4s, peak mem 301MB, user 17.3s, sys 0.8s, output queue size 2764
progress 90% @chr22:46256561, elapsed 2.1s, est remaining 0.2s, peak mem 301MB, user 17.3s, sys 0.9s, output queue size 3375
progress 95% @chr22:50739271, elapsed 2.1s, est remaining 0.1s, peak mem 301MB, user 17.3s, sys 0.9s, output queue size 3941
progress 100% @chrY:23192052, elapsed 2.2s, est remaining 0.0s, peak mem 301MB, user 17.3s, sys 1.0s, output queue size 4519
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: 74586807
output file size: 79931
reads: 1001133
contig: 9624 intervals 1921786 bases
"assemble": 324 calls 0.834 user 0.022 sys 1.093 real
"assemble_addRead": 324 calls 0.086 user 0.000 sys 0.056 real
"assemble_buildGraph": 688 calls 0.399 user 0.004 sys 0.537 real
"assemble_computecigar": 523 calls 0.422 user 0.001 sys 0.547 real
"assemble_kg_build_calcsize": 688 calls 0.233 user 0.002 sys 0.292 real
"assemble_kg_build_clear": 826 calls 0.012 user 0.000 sys 0.029 real
"assemble_kg_build_prepare": 1376 calls 0.201 user 0.018 sys 0.270 real
"assemble_kg_build_threading": 550 calls 0.165 user 0.002 sys 0.237 real
"assemble_kg_op1": 550 calls 0.022 user 0.000 sys 0.049 real
"assemble_kg_op2": 550 calls 0.000 user 0.000 sys 0.011 real
"assemble_kg_op3": 550 calls 0.002 user 0.000 sys 0.013 real
"assemble_sg_clean": 523 calls 0.029 user 0.000 sys 0.054 real
"assemble_sg_create": 523 calls 0.087 user 0.001 sys 0.073 real
"checkGraph": 324 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 324 calls 0.484 user 0.001 sys 0.574 real
active: 19646 calls 0.022 user 0.001 sys 0.023 real
advance: 10022 calls 2.953 user 0.073 sys 3.491 real
annotate: 394 calls 0.015 user 0.000 sys 0.046 real
assemble_region: 324 calls 1.403 user 0.023 sys 1.727 real
build_variants: 322 calls 0.000 user 0.000 sys 0.003 real
calc: 19646 calls 0.458 user 0.000 sys 0.470 real
calc_region: 322 calls 6.959 user 0.020 sys 7.409 real
call_region: 322 calls 0.019 user 0.000 sys 0.085 real
clip_region: 646 calls 0.062 user 0.002 sys 0.112 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.007 user 0.001 sys 2.242 real
fetch: 19646 calls 0.236 user 0.045 sys 0.250 real
fetch_db: 322 calls 0.057 user 0.005 sys 0.099 real
fetch_ref: 19970 calls 0.031 user 0.027 sys 0.089 real
fetch_region: 324 calls 0.008 user 0.000 sys 0.032 real
idle: 39 calls 0.015 user 0.004 sys 13.541 real
init: 1 calls 0.040 user 0.010 sys 0.048 real
pairhmm: 2270 calls 14.858 user 0.018 sys 15.603 real
realign: 697 calls 0.811 user 0.004 sys 0.964 real
region: 19646 calls 13.235 user 0.077 sys 13.481 real
tracker: 19646 calls 0.009 user 0.001 sys 0.033 real
trim_region: 324 calls 0.030 user 0.000 sys 0.006 real
overall: 315645952 mem 23.341 user 1.638 sys 3.369 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory