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.recalibrated.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% @chr21:10454134, elapsed 0.0s, est remaining 0.9s, peak mem 100MB, user 0.4s, sys 0.0s, output queue size 47
progress 10% @chr21:15878303, elapsed 0.1s, est remaining 0.7s, peak mem 105MB, user 0.7s, sys 0.0s, output queue size 85
progress 15% @chr21:26934466, elapsed 0.1s, est remaining 0.6s, peak mem 111MB, user 0.9s, sys 0.0s, output queue size 11
progress 20% @chr21:29555052, elapsed 0.1s, est remaining 0.5s, peak mem 114MB, user 1.2s, sys 0.1s, output queue size 64
progress 25% @chr21:31135933, elapsed 0.2s, est remaining 0.5s, peak mem 124MB, user 1.5s, sys 0.1s, output queue size 27
progress 30% @chr21:32324491, elapsed 0.2s, est remaining 0.4s, peak mem 129MB, user 1.7s, sys 0.1s, output queue size 20
progress 35% @chr21:32764348, elapsed 0.2s, est remaining 0.4s, peak mem 132MB, user 2.1s, sys 0.1s, output queue size 57
progress 40% @chr21:33509783, elapsed 0.2s, est remaining 0.4s, peak mem 132MB, user 2.4s, sys 0.1s, output queue size 26
progress 45% @chr21:33888152, elapsed 0.3s, est remaining 0.3s, peak mem 135MB, user 2.6s, sys 0.1s, output queue size 100
progress 50% @chr21:36230450, elapsed 0.3s, est remaining 0.3s, peak mem 172MB, user 2.9s, sys 0.1s, output queue size 49
progress 55% @chr21:36744728, elapsed 0.5s, est remaining 0.4s, peak mem 199MB, user 3.7s, sys 0.1s, output queue size 120
progress 60% @chr21:37233362, elapsed 0.5s, est remaining 0.3s, peak mem 199MB, user 4.0s, sys 0.1s, output queue size 27
progress 65% @chr21:39278743, elapsed 0.5s, est remaining 0.3s, peak mem 208MB, user 4.2s, sys 0.1s, output queue size 59
progress 70% @chr21:41168264, elapsed 0.6s, est remaining 0.2s, peak mem 220MB, user 4.5s, sys 0.2s, output queue size 149
progress 75% @chr21:41495693, elapsed 1.3s, est remaining 0.4s, peak mem 358MB, user 8.0s, sys 0.2s, output queue size 15
progress 80% @chr21:41490173, elapsed 1.8s, est remaining 0.4s, peak mem 408MB, user 13.9s, sys 0.3s, output queue size 43
progress 85% @chr21:42287889, elapsed 2.0s, est remaining 0.4s, peak mem 409MB, user 16.6s, sys 0.3s, output queue size 88
progress 91% @chr21:41501693, elapsed 2.2s, est remaining 0.2s, peak mem 409MB, user 19.0s, sys 0.3s, output queue size 172
progress 95% @chr21:43419021, elapsed 2.2s, est remaining 0.1s, peak mem 409MB, user 19.2s, sys 0.3s, output queue size 55
progress 100% @chr21:44120348, elapsed 2.2s, est remaining 0.0s, peak mem 409MB, user 19.6s, sys 0.3s, output queue size 0
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 163002590
output file size: 61539
reads: 1955548
contig: 1576 intervals 300011 bases
"assemble": 223 calls 0.820 user 0.019 sys 1.056 real
"assemble_addRead": 223 calls 0.014 user 0.000 sys 0.048 real
"assemble_buildGraph": 457 calls 0.396 user 0.003 sys 0.552 real
"assemble_computecigar": 366 calls 0.433 user 0.018 sys 0.474 real
"assemble_kg_build_calcsize": 457 calls 0.173 user 0.000 sys 0.314 real
"assemble_kg_build_clear": 525 calls 0.021 user 0.000 sys 0.030 real
"assemble_kg_build_prepare": 914 calls 0.187 user 0.015 sys 0.261 real
"assemble_kg_build_threading": 389 calls 0.223 user 0.003 sys 0.232 real
"assemble_kg_op1": 389 calls 0.035 user 0.000 sys 0.042 real
"assemble_kg_op2": 389 calls 0.020 user 0.000 sys 0.013 real
"assemble_kg_op3": 389 calls 0.001 user 0.000 sys 0.012 real
"assemble_sg_clean": 366 calls 0.030 user 0.000 sys 0.051 real
"assemble_sg_create": 366 calls 0.085 user 0.000 sys 0.051 real
"checkGraph": 223 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 223 calls 0.449 user 0.024 sys 0.511 real
active: 3201 calls 0.030 user 0.000 sys 0.012 real
advance: 1625 calls 4.427 user 0.159 sys 4.825 real
annotate: 248 calls 0.021 user 0.000 sys 0.038 real
assemble_region: 223 calls 1.284 user 0.043 sys 1.619 real
build_variants: 219 calls 0.000 user 0.000 sys 0.002 real
calc: 3201 calls 0.514 user 0.000 sys 0.599 real
calc_region: 219 calls 9.248 user 0.084 sys 9.512 real
call_region: 219 calls 0.064 user 0.000 sys 0.100 real
clip_region: 442 calls 0.104 user 0.010 sys 0.108 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.002 user 0.001 sys 2.215 real
fetch: 3201 calls 0.267 user 0.020 sys 0.286 real
fetch_db: 219 calls 0.014 user 0.001 sys 0.064 real
fetch_ref: 3424 calls 0.010 user 0.000 sys 0.018 real
fetch_region: 223 calls 0.015 user 0.000 sys 0.027 real
idle: 39 calls 0.036 user 0.000 sys 12.609 real
init: 1 calls 0.040 user 0.020 sys 0.053 real
pairhmm: 3494 calls 16.585 user 0.029 sys 17.222 real
realign: 789 calls 1.020 user 0.008 sys 1.097 real
region: 3201 calls 14.204 user 0.097 sys 14.400 real
tracker: 3201 calls 0.002 user 0.000 sys 0.010 real
trim_region: 223 calls 0.000 user 0.000 sys 0.006 real
overall: 429621248 mem 25.945 user 0.420 sys 3.348 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory