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% @chr21:14373617, elapsed 0.0s, est remaining 0.7s, peak mem 102MB, user 0.3s, sys 0.0s, output queue size 47
progress 10% @chr21:21418473, elapsed 0.1s, est remaining 0.6s, peak mem 112MB, user 0.5s, sys 0.0s, output queue size 85
progress 15% @chr21:28935109, elapsed 0.1s, est remaining 0.5s, peak mem 114MB, user 0.7s, sys 0.0s, output queue size 14
progress 20% @chr21:29591112, elapsed 0.1s, est remaining 0.4s, peak mem 118MB, user 0.9s, sys 0.0s, output queue size 64
progress 25% @chr21:31135933, elapsed 0.1s, est remaining 0.4s, peak mem 126MB, user 1.1s, sys 0.1s, output queue size 22
progress 30% @chr21:32341466, elapsed 0.2s, est remaining 0.4s, peak mem 130MB, user 1.4s, sys 0.1s, output queue size 20
progress 35% @chr21:32771326, elapsed 0.2s, est remaining 0.3s, peak mem 133MB, user 1.6s, sys 0.1s, output queue size 56
progress 40% @chr21:33578307, elapsed 0.2s, est remaining 0.3s, peak mem 133MB, user 1.8s, sys 0.1s, output queue size 25
progress 45% @chr21:34716321, elapsed 0.2s, est remaining 0.3s, peak mem 141MB, user 2.0s, sys 0.1s, output queue size 100
progress 51% @chr21:33549476, elapsed 0.3s, est remaining 0.3s, peak mem 193MB, user 2.3s, sys 0.1s, output queue size 165
progress 55% @chr21:36756542, elapsed 0.4s, est remaining 0.3s, peak mem 208MB, user 2.8s, sys 0.1s, output queue size 118
progress 60% @chr21:37165550, elapsed 0.4s, est remaining 0.3s, peak mem 208MB, user 3.1s, sys 0.1s, output queue size 15
progress 65% @chr21:39264891, elapsed 0.4s, est remaining 0.2s, peak mem 217MB, user 3.3s, sys 0.1s, output queue size 58
progress 70% @chr21:41243376, elapsed 0.5s, est remaining 0.2s, peak mem 232MB, user 3.5s, sys 0.1s, output queue size 148
progress 75% @chr21:41488133, elapsed 1.0s, est remaining 0.3s, peak mem 334MB, user 5.9s, sys 0.1s, output queue size 4
progress 80% @chr21:41859031, elapsed 1.3s, est remaining 0.3s, peak mem 396MB, user 10.9s, sys 0.2s, output queue size 35
progress 85% @chr21:42219972, elapsed 1.6s, est remaining 0.3s, peak mem 402MB, user 13.3s, sys 0.2s, output queue size 87
progress 90% @chr21:41990895, elapsed 1.7s, est remaining 0.2s, peak mem 406MB, user 14.3s, sys 0.2s, output queue size 66
progress 95% @chr21:43101366, elapsed 1.7s, est remaining 0.1s, peak mem 406MB, user 14.9s, sys 0.2s, output queue size 7
progress 100% @chr21:44120348, elapsed 1.8s, est remaining 0.0s, peak mem 406MB, user 15.1s, sys 0.2s, output queue size 0
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
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 0.631 user 0.001 sys 0.850 real
"assemble_addRead": 223 calls 0.030 user 0.000 sys 0.045 real
"assemble_buildGraph": 457 calls 0.335 user 0.000 sys 0.439 real
"assemble_computecigar": 366 calls 0.346 user 0.018 sys 0.416 real
"assemble_kg_build_calcsize": 457 calls 0.189 user 0.000 sys 0.249 real
"assemble_kg_build_clear": 525 calls 0.000 user 0.000 sys 0.025 real
"assemble_kg_build_prepare": 914 calls 0.174 user 0.001 sys 0.209 real
"assemble_kg_build_threading": 389 calls 0.146 user 0.000 sys 0.186 real
"assemble_kg_op1": 389 calls 0.011 user 0.000 sys 0.033 real
"assemble_kg_op2": 389 calls 0.015 user 0.000 sys 0.011 real
"assemble_kg_op3": 389 calls 0.012 user 0.000 sys 0.010 real
"assemble_sg_clean": 366 calls 0.047 user 0.000 sys 0.041 real
"assemble_sg_create": 366 calls 0.013 user 0.000 sys 0.041 real
"checkGraph": 223 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 223 calls 0.394 user 0.018 sys 0.446 real
active: 3201 calls 0.009 user 0.000 sys 0.009 real
advance: 1625 calls 3.115 user 0.135 sys 3.832 real
annotate: 248 calls 0.037 user 0.000 sys 0.032 real
assemble_region: 223 calls 1.063 user 0.019 sys 1.344 real
build_variants: 219 calls 0.000 user 0.000 sys 0.002 real
calc: 3201 calls 0.296 user 0.001 sys 0.406 real
calc_region: 219 calls 7.044 user 0.023 sys 7.258 real
call_region: 219 calls 0.072 user 0.000 sys 0.084 real
clip_region: 442 calls 0.063 user 0.000 sys 0.088 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.006 user 0.001 sys 1.762 real
fetch: 3201 calls 0.305 user 0.001 sys 0.243 real
fetch_db: 219 calls 0.020 user 0.000 sys 0.053 real
fetch_ref: 3424 calls 0.010 user 0.000 sys 0.015 real
fetch_region: 223 calls 0.062 user 0.002 sys 0.030 real
idle: 39 calls 0.045 user 0.000 sys 12.435 real
init: 1 calls 0.039 user 0.000 sys 0.043 real
pairhmm: 3494 calls 12.973 user 0.030 sys 13.480 real
realign: 789 calls 0.721 user 0.000 sys 0.905 real
region: 3201 calls 11.190 user 0.065 sys 11.188 real
tracker: 3201 calls 0.010 user 0.000 sys 0.011 real
trim_region: 223 calls 0.000 user 0.000 sys 0.005 real
overall: 425885696 mem 20.530 user 0.279 sys 2.878 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory