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% @chr19:49133796, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 466
progress 10% @chr19:50629784, elapsed 0.0s, est remaining 0.2s, peak mem 75MB, user 0.1s, sys 0.0s, output queue size 1062
progress 15% @chr19:52613014, elapsed 0.0s, est remaining 0.2s, peak mem 76MB, user 0.1s, sys 0.0s, output queue size 935
progress 20% @chr19:54851998, elapsed 0.0s, est remaining 0.1s, peak mem 78MB, user 0.1s, sys 0.0s, output queue size 1339
progress 25% @chr19:56383863, elapsed 0.0s, est remaining 0.1s, peak mem 81MB, user 0.1s, sys 0.0s, output queue size 1779
progress 30% @chr19:58212161, elapsed 0.0s, est remaining 0.1s, peak mem 82MB, user 0.1s, sys 0.0s, output queue size 2005
progress 35% @chr21:30282168, elapsed 0.1s, est remaining 0.2s, peak mem 120MB, user 0.7s, sys 0.2s, output queue size 82
progress 40% @chr21:36460976, elapsed 0.3s, est remaining 0.4s, peak mem 160MB, user 1.6s, sys 0.2s, output queue size 106
progress 45% @chr21:42388929, elapsed 1.1s, est remaining 1.3s, peak mem 285MB, user 8.8s, sys 0.3s, output queue size 113
progress 50% @chr21:45505838, elapsed 1.4s, est remaining 1.4s, peak mem 292MB, user 11.4s, sys 0.3s, output queue size 34
progress 55% @chr22:19432555, elapsed 1.4s, est remaining 1.2s, peak mem 292MB, user 12.0s, sys 0.3s, output queue size 383
progress 60% @chr22:22201834, elapsed 1.5s, est remaining 1.0s, peak mem 292MB, user 12.0s, sys 0.3s, output queue size 420
progress 65% @chr22:23883772, elapsed 1.5s, est remaining 0.8s, peak mem 292MB, user 12.0s, sys 0.3s, output queue size 639
progress 70% @chr22:29294124, elapsed 1.5s, est remaining 0.6s, peak mem 292MB, user 12.0s, sys 0.4s, output queue size 1147
progress 75% @chr22:31814992, elapsed 1.5s, est remaining 0.5s, peak mem 292MB, user 12.0s, sys 0.4s, output queue size 1688
progress 80% @chr22:37956773, elapsed 1.5s, est remaining 0.4s, peak mem 292MB, user 12.0s, sys 0.4s, output queue size 2254
progress 85% @chr22:41224967, elapsed 1.5s, est remaining 0.3s, peak mem 292MB, user 12.1s, sys 0.5s, output queue size 2771
progress 90% @chr22:46256561, elapsed 1.5s, est remaining 0.2s, peak mem 292MB, user 12.1s, sys 0.5s, output queue size 3384
progress 95% @chr22:50720184, elapsed 1.5s, est remaining 0.1s, peak mem 292MB, user 12.1s, sys 0.5s, output queue size 3955
progress 100% @chrY:21904606, elapsed 1.5s, est remaining 0.0s, peak mem 292MB, user 12.1s, sys 0.5s, output queue size 4533
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: 74586805
output file size: 79931
reads: 1001133
contig: 9624 intervals 1921786 bases
"assemble": 324 calls 0.647 user 0.013 sys 0.808 real
"assemble_addRead": 324 calls 0.022 user 0.000 sys 0.039 real
"assemble_buildGraph": 688 calls 0.328 user 0.004 sys 0.404 real
"assemble_computecigar": 523 calls 0.262 user 0.011 sys 0.376 real
"assemble_kg_build_calcsize": 688 calls 0.161 user 0.000 sys 0.227 real
"assemble_kg_build_clear": 826 calls 0.027 user 0.000 sys 0.018 real
"assemble_kg_build_prepare": 1376 calls 0.150 user 0.002 sys 0.193 real
"assemble_kg_build_threading": 550 calls 0.167 user 0.004 sys 0.172 real
"assemble_kg_op1": 550 calls 0.018 user 0.000 sys 0.035 real
"assemble_kg_op2": 550 calls 0.008 user 0.000 sys 0.009 real
"assemble_kg_op3": 550 calls 0.001 user 0.000 sys 0.012 real
"assemble_sg_clean": 523 calls 0.054 user 0.000 sys 0.041 real
"assemble_sg_create": 523 calls 0.015 user 0.001 sys 0.053 real
"checkGraph": 324 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 324 calls 0.296 user 0.011 sys 0.395 real
active: 19646 calls 0.012 user 0.000 sys 0.014 real
advance: 10022 calls 2.345 user 0.096 sys 2.968 real
annotate: 394 calls 0.030 user 0.000 sys 0.032 real
assemble_region: 324 calls 0.965 user 0.024 sys 1.245 real
build_variants: 322 calls 0.000 user 0.000 sys 0.002 real
calc: 19646 calls 0.121 user 0.000 sys 0.305 real
calc_region: 322 calls 5.574 user 0.010 sys 5.987 real
call_region: 322 calls 0.040 user 0.000 sys 0.061 real
clip_region: 646 calls 0.027 user 0.000 sys 0.074 real
done: 1 calls 0.000 user 0.002 sys 0.002 real
execute: 1 calls 0.009 user 0.001 sys 1.569 real
fetch: 19646 calls 0.131 user 0.012 sys 0.131 real
fetch_db: 322 calls 0.021 user 0.002 sys 0.083 real
fetch_ref: 19970 calls 0.004 user 0.000 sys 0.076 real
fetch_region: 324 calls 0.014 user 0.000 sys 0.018 real
idle: 39 calls 0.003 user 0.006 sys 12.991 real
init: 1 calls 0.031 user 0.009 sys 0.041 real
pairhmm: 2270 calls 10.059 user 0.037 sys 10.570 real
realign: 697 calls 0.462 user 0.002 sys 0.706 real
region: 19646 calls 8.988 user 0.109 sys 9.123 real
tracker: 19646 calls 0.018 user 0.000 sys 0.023 real
trim_region: 324 calls 0.010 user 0.000 sys 0.005 real
overall: 306864128 mem 16.574 user 0.922 sys 2.680 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory