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 0.2s, peak mem 70MB, user 0.0s, sys 0.0s, output queue size 452
progress 10% @chr19:50629294, elapsed 0.0s, est remaining 0.3s, peak mem 70MB, user 0.1s, sys 0.0s, output queue size 208
progress 15% @chr19:52613014, elapsed 0.1s, est remaining 0.5s, peak mem 70MB, user 0.1s, sys 0.0s, output queue size 574
progress 20% @chr19:54818315, elapsed 0.1s, est remaining 0.4s, peak mem 70MB, user 0.1s, sys 0.0s, output queue size 963
progress 25% @chr19:56221575, elapsed 0.1s, est remaining 0.3s, peak mem 72MB, user 0.1s, sys 0.1s, output queue size 1398
progress 30% @chr19:57701635, elapsed 0.1s, est remaining 0.3s, peak mem 73MB, user 0.1s, sys 0.1s, output queue size 1646
progress 35% @chr21:30319403, elapsed 0.2s, est remaining 0.4s, peak mem 109MB, user 0.8s, sys 0.2s, output queue size 117
progress 40% @chr21:36460976, elapsed 0.4s, est remaining 0.6s, peak mem 147MB, user 1.9s, sys 0.3s, output queue size 106
progress 45% @chr21:42383970, elapsed 1.3s, est remaining 1.6s, peak mem 270MB, user 9.7s, sys 0.3s, output queue size 112
progress 50% @chr21:44224713, elapsed 1.6s, est remaining 1.6s, peak mem 275MB, user 12.4s, sys 0.4s, output queue size 253
progress 55% @chr22:19447378, elapsed 1.6s, est remaining 1.3s, peak mem 278MB, user 12.9s, sys 0.5s, output queue size 383
progress 60% @chr22:22201834, elapsed 1.6s, est remaining 1.1s, peak mem 278MB, user 12.9s, sys 0.5s, output queue size 600
progress 65% @chr22:23883772, elapsed 1.6s, est remaining 0.9s, peak mem 278MB, user 12.9s, sys 0.5s, output queue size 818
progress 70% @chr22:29286684, elapsed 1.6s, est remaining 0.7s, peak mem 278MB, user 12.9s, sys 0.5s, output queue size 1329
progress 75% @chr22:31814992, elapsed 1.6s, est remaining 0.5s, peak mem 278MB, user 12.9s, sys 0.6s, output queue size 1867
progress 80% @chr22:37951460, elapsed 1.7s, est remaining 0.4s, peak mem 278MB, user 12.9s, sys 0.6s, output queue size 2431
progress 85% @chr22:41256711, elapsed 1.7s, est remaining 0.3s, peak mem 278MB, user 13.0s, sys 0.6s, output queue size 2950
progress 90% @chr22:46256561, elapsed 1.7s, est remaining 0.2s, peak mem 278MB, user 13.0s, sys 0.6s, output queue size 3567
progress 95% @chr22:50720184, elapsed 1.7s, est remaining 0.1s, peak mem 278MB, user 13.0s, sys 0.7s, output queue size 4139
progress 100% @chrY:23280013, elapsed 1.7s, est remaining 0.0s, peak mem 278MB, user 13.0s, sys 0.7s, output queue size 4712
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 74732894
output file size: 79936
reads: 1001133
contig: 9624 intervals 1921786 bases
"assemble": 324 calls 0.661 user 0.016 sys 0.850 real
"assemble_addRead": 324 calls 0.030 user 0.000 sys 0.057 real
"assemble_buildGraph": 688 calls 0.281 user 0.004 sys 0.426 real
"assemble_computecigar": 523 calls 0.324 user 0.005 sys 0.387 real
"assemble_kg_build_calcsize": 688 calls 0.144 user 0.000 sys 0.238 real
"assemble_kg_build_clear": 826 calls 0.024 user 0.001 sys 0.022 real
"assemble_kg_build_prepare": 1376 calls 0.183 user 0.011 sys 0.202 real
"assemble_kg_build_threading": 550 calls 0.137 user 0.004 sys 0.182 real
"assemble_kg_op1": 550 calls 0.036 user 0.000 sys 0.037 real
"assemble_kg_op2": 550 calls 0.010 user 0.000 sys 0.010 real
"assemble_kg_op3": 550 calls 0.001 user 0.000 sys 0.012 real
"assemble_sg_clean": 523 calls 0.031 user 0.000 sys 0.042 real
"assemble_sg_create": 523 calls 0.073 user 0.001 sys 0.056 real
"checkGraph": 324 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 324 calls 0.334 user 0.005 sys 0.406 real
active: 19646 calls 0.013 user 0.001 sys 0.016 real
advance: 10022 calls 2.255 user 0.084 sys 3.133 real
annotate: 394 calls 0.016 user 0.000 sys 0.040 real
assemble_region: 324 calls 1.025 user 0.021 sys 1.317 real
build_variants: 322 calls 0.008 user 0.000 sys 0.002 real
calc: 19646 calls 0.250 user 0.009 sys 0.328 real
calc_region: 322 calls 5.904 user 0.028 sys 6.231 real
call_region: 322 calls 0.018 user 0.000 sys 0.074 real
clip_region: 646 calls 0.058 user 0.000 sys 0.098 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.000 user 0.002 sys 1.767 real
fetch: 19646 calls 0.233 user 0.025 sys 0.224 real
fetch_db: 322 calls 0.046 user 0.009 sys 0.089 real
fetch_ref: 19970 calls 0.009 user 0.010 sys 0.079 real
fetch_region: 324 calls 0.035 user 0.000 sys 0.032 real
idle: 39 calls 0.003 user 0.007 sys 13.326 real
init: 1 calls 0.046 user 0.003 sys 0.042 real
pairhmm: 2270 calls 10.163 user 0.036 sys 10.814 real
realign: 697 calls 0.488 user 0.005 sys 0.724 real
region: 19646 calls 9.442 user 0.083 sys 9.562 real
tracker: 19646 calls 0.011 user 0.000 sys 0.026 real
trim_region: 324 calls 0.000 user 0.000 sys 0.005 real
overall: 292442112 mem 17.090 user 1.182 sys 2.887 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory