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 441
progress 10% @chr19:50629784, elapsed 0.0s, est remaining 0.2s, peak mem 70MB, user 0.0s, sys 0.0s, output queue size 1033
progress 15% @chr19:51643779, elapsed 0.0s, est remaining 0.2s, peak mem 70MB, user 0.0s, sys 0.0s, output queue size 369
progress 20% @chr19:54818315, elapsed 0.0s, est remaining 0.2s, peak mem 70MB, user 0.1s, sys 0.0s, output queue size 756
progress 25% @chr19:56223631, elapsed 0.1s, est remaining 0.2s, peak mem 73MB, user 0.1s, sys 0.1s, output queue size 1195
progress 30% @chr19:58260851, elapsed 0.1s, est remaining 0.1s, peak mem 73MB, user 0.1s, sys 0.1s, output queue size 1436
progress 35% @chr21:30425394, elapsed 0.1s, est remaining 0.3s, peak mem 115MB, user 0.8s, sys 0.1s, output queue size 118
progress 40% @chr21:36460976, elapsed 0.3s, est remaining 0.5s, peak mem 162MB, user 1.7s, sys 0.2s, output queue size 106
progress 45% @chr21:42383970, elapsed 1.2s, est remaining 1.5s, peak mem 289MB, user 9.8s, sys 0.3s, output queue size 112
progress 50% @chr21:45510064, elapsed 1.4s, est remaining 1.4s, peak mem 298MB, user 12.3s, sys 0.3s, output queue size 105
progress 55% @chr22:19444265, elapsed 1.5s, est remaining 1.2s, peak mem 298MB, user 12.9s, sys 0.4s, output queue size 383
progress 60% @chr22:22195903, elapsed 1.5s, est remaining 1.0s, peak mem 298MB, user 13.0s, sys 0.4s, output queue size 860
progress 65% @chr22:23882459, elapsed 1.5s, est remaining 0.8s, peak mem 298MB, user 13.0s, sys 0.4s, output queue size 1077
progress 70% @chr22:29293284, elapsed 1.5s, est remaining 0.7s, peak mem 298MB, user 13.0s, sys 0.4s, output queue size 1587
progress 75% @chr22:31845018, elapsed 1.5s, est remaining 0.5s, peak mem 298MB, user 13.0s, sys 0.4s, output queue size 582
progress 80% @chr22:37970687, elapsed 1.5s, est remaining 0.4s, peak mem 298MB, user 13.0s, sys 0.4s, output queue size 1149
progress 85% @chr22:41280933, elapsed 1.6s, est remaining 0.3s, peak mem 298MB, user 13.0s, sys 0.5s, output queue size 1667
progress 90% @chr22:46256561, elapsed 1.6s, est remaining 0.2s, peak mem 298MB, user 13.0s, sys 0.5s, output queue size 2276
progress 95% @chr22:50720184, elapsed 1.6s, est remaining 0.1s, peak mem 298MB, user 13.0s, sys 0.5s, output queue size 2845
progress 100% @chr22:50316025, elapsed 1.6s, est remaining 0.0s, peak mem 298MB, user 13.1s, sys 0.5s, output queue size 3424
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: 74586797
output file size: 79931
reads: 1001133
contig: 9624 intervals 1921786 bases
"assemble": 324 calls 0.555 user 0.028 sys 0.812 real
"assemble_addRead": 324 calls 0.010 user 0.000 sys 0.039 real
"assemble_buildGraph": 688 calls 0.300 user 0.012 sys 0.409 real
"assemble_computecigar": 523 calls 0.334 user 0.029 sys 0.378 real
"assemble_kg_build_calcsize": 688 calls 0.111 user 0.000 sys 0.228 real
"assemble_kg_build_clear": 826 calls 0.003 user 0.000 sys 0.020 real
"assemble_kg_build_prepare": 1376 calls 0.130 user 0.021 sys 0.190 real
"assemble_kg_build_threading": 550 calls 0.185 user 0.003 sys 0.175 real
"assemble_kg_op1": 550 calls 0.012 user 0.000 sys 0.035 real
"assemble_kg_op2": 550 calls 0.000 user 0.000 sys 0.010 real
"assemble_kg_op3": 550 calls 0.016 user 0.000 sys 0.012 real
"assemble_sg_clean": 523 calls 0.021 user 0.000 sys 0.042 real
"assemble_sg_create": 523 calls 0.060 user 0.004 sys 0.054 real
"checkGraph": 324 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 324 calls 0.349 user 0.029 sys 0.398 real
active: 19646 calls 0.010 user 0.000 sys 0.015 real
advance: 10022 calls 2.396 user 0.106 sys 3.028 real
annotate: 394 calls 0.032 user 0.000 sys 0.031 real
assemble_region: 324 calls 0.914 user 0.057 sys 1.252 real
build_variants: 322 calls 0.000 user 0.000 sys 0.002 real
calc: 19646 calls 0.152 user 0.000 sys 0.306 real
calc_region: 322 calls 6.278 user 0.025 sys 6.677 real
call_region: 322 calls 0.045 user 0.000 sys 0.060 real
clip_region: 646 calls 0.043 user 0.010 sys 0.077 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.005 user 0.002 sys 1.634 real
fetch: 19646 calls 0.108 user 0.032 sys 0.160 real
fetch_db: 322 calls 0.018 user 0.000 sys 0.083 real
fetch_ref: 19970 calls 0.023 user 0.000 sys 0.073 real
fetch_region: 324 calls 0.000 user 0.000 sys 0.023 real
idle: 39 calls 0.012 user 0.019 sys 13.038 real
init: 1 calls 0.040 user 0.000 sys 0.041 real
pairhmm: 2270 calls 10.325 user 0.014 sys 10.684 real
realign: 697 calls 0.376 user 0.000 sys 0.708 real
region: 19646 calls 9.760 user 0.070 sys 9.829 real
tracker: 19646 calls 0.010 user 0.000 sys 0.024 real
trim_region: 324 calls 0.000 user 0.000 sys 0.004 real
overall: 312602624 mem 16.680 user 0.878 sys 2.745 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory