cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr19_47340800-47341813.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr19:49153407, elapsed 0.0s, est remaining 0.2s, peak mem 70MB, user 0.0s, sys 0.0s, output queue size 489
progress 10% @chr19:50629784, elapsed 0.0s, est remaining 0.2s, peak mem 70MB, user 0.0s, sys 0.1s, output queue size 1069
progress 15% @chr19:52613014, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 1433
progress 20% @chr19:54803891, elapsed 0.0s, est remaining 0.1s, peak mem 75MB, user 0.0s, sys 0.1s, output queue size 288
progress 25% @chr19:56422891, elapsed 0.0s, est remaining 0.1s, peak mem 76MB, user 0.0s, sys 0.2s, output queue size 751
progress 30% @chr19:58338254, elapsed 0.0s, est remaining 0.1s, peak mem 78MB, user 0.0s, sys 0.2s, output queue size 977
progress 35% @chr21:28966370, elapsed 0.1s, est remaining 0.2s, peak mem 105MB, user 0.5s, sys 0.3s, output queue size 84
progress 40% @chr21:36460976, elapsed 0.3s, est remaining 0.4s, peak mem 151MB, user 1.5s, sys 0.3s, output queue size 106
progress 45% @chr21:41501693, elapsed 0.9s, est remaining 1.1s, peak mem 278MB, user 7.6s, sys 0.4s, output queue size 105
progress 50% @chr21:45512188, elapsed 1.0s, est remaining 1.0s, peak mem 278MB, user 8.7s, sys 0.4s, output queue size 114
progress 55% @chr22:19405786, elapsed 1.1s, est remaining 0.9s, peak mem 282MB, user 9.4s, sys 0.4s, output queue size 42
progress 60% @chr22:22201834, elapsed 1.1s, est remaining 0.7s, peak mem 282MB, user 9.4s, sys 0.5s, output queue size 522
progress 65% @chr22:23882459, elapsed 1.1s, est remaining 0.6s, peak mem 282MB, user 9.4s, sys 0.5s, output queue size 739
progress 70% @chr22:29286324, elapsed 1.1s, est remaining 0.5s, peak mem 282MB, user 9.4s, sys 0.5s, output queue size 1252
progress 75% @chr22:31836972, elapsed 1.1s, est remaining 0.4s, peak mem 282MB, user 9.4s, sys 0.5s, output queue size 1789
progress 80% @chr22:37947281, elapsed 1.2s, est remaining 0.3s, peak mem 282MB, user 9.4s, sys 0.5s, output queue size 2352
progress 85% @chr22:41240874, elapsed 1.2s, est remaining 0.2s, peak mem 282MB, user 9.4s, sys 0.5s, output queue size 2872
progress 90% @chr22:46256561, elapsed 1.2s, est remaining 0.1s, peak mem 282MB, user 9.4s, sys 0.6s, output queue size 3486
progress 95% @chr22:50627556, elapsed 1.2s, est remaining 0.1s, peak mem 282MB, user 9.5s, sys 0.6s, output queue size 4054
progress 100% @chrY:24774350, elapsed 1.2s, est remaining 0.0s, peak mem 282MB, user 9.5s, sys 0.6s, output queue size 4635
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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: 71692773
output file size: 77724
reads: 1001089
contig: 9624 intervals 1921786 bases
"assemble": 315 calls 0.422 user 0.012 sys 0.679 real
"assemble_addRead": 315 calls 0.042 user 0.000 sys 0.034 real
"assemble_buildGraph": 650 calls 0.229 user 0.002 sys 0.334 real
"assemble_computecigar": 513 calls 0.339 user 0.000 sys 0.365 real
"assemble_kg_build_calcsize": 650 calls 0.106 user 0.000 sys 0.182 real
"assemble_kg_build_clear": 775 calls 0.000 user 0.000 sys 0.015 real
"assemble_kg_build_prepare": 1300 calls 0.085 user 0.004 sys 0.151 real
"assemble_kg_build_threading": 525 calls 0.123 user 0.002 sys 0.147 real
"assemble_kg_op1": 525 calls 0.025 user 0.002 sys 0.032 real
"assemble_kg_op2": 525 calls 0.010 user 0.000 sys 0.008 real
"assemble_kg_op3": 525 calls 0.012 user 0.000 sys 0.011 real
"assemble_sg_clean": 513 calls 0.003 user 0.000 sys 0.040 real
"assemble_sg_create": 513 calls 0.035 user 0.003 sys 0.052 real
"checkGraph": 315 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 315 calls 0.360 user 0.000 sys 0.383 real
active: 19646 calls 0.000 user 0.000 sys 0.013 real
advance: 10022 calls 2.106 user 0.116 sys 3.004 real
annotate: 358 calls 0.017 user 0.000 sys 0.026 real
assemble_region: 315 calls 0.825 user 0.012 sys 1.100 real
build_variants: 312 calls 0.000 user 0.000 sys 0.001 real
calc: 19646 calls 0.200 user 0.009 sys 0.292 real
calc_region: 312 calls 4.078 user 0.011 sys 4.406 real
call_region: 312 calls 0.018 user 0.000 sys 0.050 real
clip_region: 627 calls 0.049 user 0.000 sys 0.062 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.003 sys 1.249 real
fetch: 19646 calls 0.189 user 0.008 sys 0.136 real
fetch_db: 312 calls 0.018 user 0.000 sys 0.080 real
fetch_ref: 19961 calls 0.016 user 0.010 sys 0.075 real
fetch_region: 315 calls 0.026 user 0.001 sys 0.017 real
idle: 39 calls 0.004 user 0.001 sys 13.005 real
init: 1 calls 0.035 user 0.005 sys 0.041 real
pairhmm: 1803 calls 6.324 user 0.003 sys 6.897 real
realign: 598 calls 0.551 user 0.001 sys 0.516 real
region: 19646 calls 6.568 user 0.054 sys 6.474 real
tracker: 19646 calls 0.017 user 0.000 sys 0.027 real
trim_region: 315 calls 0.000 user 0.000 sys 0.004 real
overall: 295948288 mem 12.512 user 1.099 sys 2.364 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory