cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr21_5117103-5117231.bed.gz -i HCC1395_BL.recal.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant HCC1395_BL.haplotyper.chr21_5117103-5117231.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:14373617, elapsed 0.0s, est remaining 0.8s, peak mem 96MB, user 0.3s, sys 0.0s, output queue size 50
progress 10% @chr21:21466606, elapsed 0.1s, est remaining 0.7s, peak mem 102MB, user 0.6s, sys 0.0s, output queue size 85
progress 15% @chr21:28879870, elapsed 0.1s, est remaining 0.6s, peak mem 105MB, user 0.8s, sys 0.0s, output queue size 11
progress 20% @chr21:29587366, elapsed 0.1s, est remaining 0.5s, peak mem 112MB, user 1.0s, sys 0.1s, output queue size 103
progress 25% @chr21:31141325, elapsed 0.2s, est remaining 0.5s, peak mem 124MB, user 1.3s, sys 0.1s, output queue size 30
progress 30% @chr21:32344570, elapsed 0.2s, est remaining 0.4s, peak mem 127MB, user 1.5s, sys 0.1s, output queue size 20
progress 35% @chr21:32764348, elapsed 0.2s, est remaining 0.4s, peak mem 129MB, user 1.9s, sys 0.1s, output queue size 57
progress 40% @chr21:33509783, elapsed 0.3s, est remaining 0.4s, peak mem 129MB, user 2.1s, sys 0.1s, output queue size 26
progress 45% @chr21:34834409, elapsed 0.3s, est remaining 0.4s, peak mem 136MB, user 2.4s, sys 0.1s, output queue size 101
progress 50% @chr21:33549476, elapsed 0.3s, est remaining 0.3s, peak mem 178MB, user 2.7s, sys 0.1s, output queue size 155
progress 55% @chr21:36756542, elapsed 0.5s, est remaining 0.4s, peak mem 207MB, user 3.7s, sys 0.1s, output queue size 120
progress 60% @chr21:37165550, elapsed 0.5s, est remaining 0.3s, peak mem 207MB, user 4.0s, sys 0.1s, output queue size 15
progress 65% @chr21:39293811, elapsed 0.5s, est remaining 0.3s, peak mem 213MB, user 4.3s, sys 0.1s, output queue size 60
progress 70% @chr21:41245962, elapsed 0.6s, est remaining 0.2s, peak mem 226MB, user 4.5s, sys 0.2s, output queue size 150
progress 75% @chr21:41482133, elapsed 1.6s, est remaining 0.5s, peak mem 393MB, user 9.1s, sys 0.2s, output queue size 14
progress 80% @chr21:41836113, elapsed 2.2s, est remaining 0.5s, peak mem 411MB, user 17.4s, sys 0.3s, output queue size 40
progress 85% @chr21:41990895, elapsed 2.5s, est remaining 0.4s, peak mem 411MB, user 20.2s, sys 0.3s, output queue size 99
progress 90% @chr21:42363255, elapsed 2.5s, est remaining 0.3s, peak mem 415MB, user 23.1s, sys 0.4s, output queue size 52
progress 95% @chr21:43419021, elapsed 2.6s, est remaining 0.1s, peak mem 415MB, user 23.6s, sys 0.4s, output queue size 19
progress 100% @chr21:44120348, elapsed 2.6s, est remaining 0.0s, peak mem 415MB, user 23.9s, sys 0.4s, output queue size 0
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 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 111697681
output file size: 61481
reads: 1322929
contig: 1576 intervals 300011 bases
"assemble": 223 calls 0.812 user 0.092 sys 1.191 real
"assemble_addRead": 223 calls 0.124 user 0.008 sys 0.074 real
"assemble_buildGraph": 457 calls 0.384 user 0.030 sys 0.617 real
"assemble_computecigar": 365 calls 0.584 user 0.054 sys 0.656 real
"assemble_kg_build_calcsize": 457 calls 0.241 user 0.000 sys 0.350 real
"assemble_kg_build_clear": 526 calls 0.018 user 0.000 sys 0.034 real
"assemble_kg_build_prepare": 914 calls 0.180 user 0.041 sys 0.303 real
"assemble_kg_build_threading": 388 calls 0.143 user 0.029 sys 0.260 real
"assemble_kg_op1": 388 calls 0.024 user 0.021 sys 0.047 real
"assemble_kg_op2": 388 calls 0.010 user 0.000 sys 0.014 real
"assemble_kg_op3": 388 calls 0.040 user 0.000 sys 0.012 real
"assemble_sg_clean": 365 calls 0.063 user 0.000 sys 0.059 real
"assemble_sg_create": 365 calls 0.062 user 0.000 sys 0.057 real
"checkGraph": 223 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 223 calls 0.609 user 0.054 sys 0.698 real
active: 3201 calls 0.023 user 0.000 sys 0.026 real
advance: 1625 calls 4.087 user 0.052 sys 4.420 real
annotate: 248 calls 0.066 user 0.000 sys 0.053 real
assemble_region: 223 calls 1.547 user 0.154 sys 1.967 real
build_variants: 219 calls 0.000 user 0.000 sys 0.003 real
calc: 3201 calls 0.550 user 0.000 sys 0.631 real
calc_region: 219 calls 12.386 user 0.105 sys 12.788 real
call_region: 219 calls 0.137 user 0.000 sys 0.131 real
clip_region: 442 calls 0.090 user 0.000 sys 0.121 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.002 user 0.002 sys 2.602 real
fetch: 3201 calls 0.365 user 0.039 sys 0.297 real
fetch_db: 219 calls 0.025 user 0.000 sys 0.073 real
fetch_ref: 3424 calls 0.016 user 0.001 sys 0.020 real
fetch_region: 223 calls 0.040 user 0.000 sys 0.025 real
idle: 39 calls 0.027 user 0.000 sys 12.498 real
init: 1 calls 0.030 user 0.020 sys 0.045 real
pairhmm: 3815 calls 20.721 user 0.027 sys 21.424 real
realign: 797 calls 0.965 user 0.000 sys 1.268 real
region: 3201 calls 18.730 user 0.210 sys 19.210 real
tracker: 3201 calls 0.020 user 0.000 sys 0.020 real
trim_region: 223 calls 0.017 user 0.000 sys 0.007 real
overall: 435965952 mem 30.408 user 0.469 sys 3.743 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory