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 389
progress 10% @chr19:50629294, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 985
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.1s, peak mem 73MB, user 0.0s, sys 0.1s, output queue size 1351
progress 20% @chr19:54775165, elapsed 0.0s, est remaining 0.1s, peak mem 79MB, user 0.0s, sys 0.1s, output queue size 1738
progress 25% @chr19:56383863, elapsed 0.0s, est remaining 0.1s, peak mem 81MB, user 0.0s, sys 0.1s, output queue size 2194
progress 30% @chr19:58260851, elapsed 0.0s, est remaining 0.1s, peak mem 81MB, user 0.0s, sys 0.1s, output queue size 628
progress 35% @chr21:26844225, elapsed 0.1s, est remaining 0.2s, peak mem 115MB, user 0.7s, sys 0.2s, output queue size 118
progress 40% @chr21:36460976, elapsed 0.3s, est remaining 0.4s, peak mem 163MB, user 1.5s, sys 0.2s, output queue size 107
progress 45% @chr21:42110880, elapsed 1.1s, est remaining 1.4s, peak mem 294MB, user 8.5s, sys 0.3s, output queue size 133
progress 50% @chr21:45531389, elapsed 1.4s, est remaining 1.4s, peak mem 303MB, user 11.3s, sys 0.3s, output queue size 113
progress 55% @chr22:19392101, elapsed 1.5s, est remaining 1.2s, peak mem 303MB, user 12.0s, sys 0.3s, output queue size 10
progress 60% @chr22:22201834, elapsed 1.5s, est remaining 1.0s, peak mem 303MB, user 12.0s, sys 0.4s, output queue size 489
progress 65% @chr22:23883772, elapsed 1.5s, est remaining 0.8s, peak mem 303MB, user 12.0s, sys 0.4s, output queue size 707
progress 70% @chr22:29294124, elapsed 1.5s, est remaining 0.6s, peak mem 303MB, user 12.0s, sys 0.4s, output queue size 1215
progress 75% @chr22:31814992, elapsed 1.5s, est remaining 0.5s, peak mem 303MB, user 12.0s, sys 0.4s, output queue size 1756
progress 80% @chr22:37933039, elapsed 1.5s, est remaining 0.4s, peak mem 303MB, user 12.0s, sys 0.5s, output queue size 2318
progress 85% @chr22:41254308, elapsed 1.5s, est remaining 0.3s, peak mem 303MB, user 12.0s, sys 0.6s, output queue size 2836
progress 90% @chr22:46256561, elapsed 1.5s, est remaining 0.2s, peak mem 303MB, user 12.0s, sys 0.6s, output queue size 3449
progress 95% @chr22:40826538, elapsed 1.5s, est remaining 0.1s, peak mem 303MB, user 12.0s, sys 0.6s, output queue size 4024
progress 100% @chrY:12918043, elapsed 1.5s, est remaining 0.0s, peak mem 303MB, user 12.0s, sys 0.7s, output queue size 4601
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: 74318159
output file size: 79935
reads: 1001133
contig: 9624 intervals 1921786 bases
"assemble": 324 calls 0.757 user 0.011 sys 0.803 real
"assemble_addRead": 324 calls 0.015 user 0.000 sys 0.037 real
"assemble_buildGraph": 688 calls 0.370 user 0.004 sys 0.406 real
"assemble_computecigar": 523 calls 0.355 user 0.009 sys 0.378 real
"assemble_kg_build_calcsize": 688 calls 0.251 user 0.000 sys 0.229 real
"assemble_kg_build_clear": 826 calls 0.011 user 0.000 sys 0.019 real
"assemble_kg_build_prepare": 1376 calls 0.234 user 0.004 sys 0.185 real
"assemble_kg_build_threading": 550 calls 0.119 user 0.004 sys 0.172 real
"assemble_kg_op1": 550 calls 0.033 user 0.001 sys 0.035 real
"assemble_kg_op2": 550 calls 0.010 user 0.000 sys 0.010 real
"assemble_kg_op3": 550 calls 0.020 user 0.000 sys 0.012 real
"assemble_sg_clean": 523 calls 0.019 user 0.000 sys 0.041 real
"assemble_sg_create": 523 calls 0.030 user 0.002 sys 0.054 real
"checkGraph": 324 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 324 calls 0.371 user 0.009 sys 0.397 real
active: 19646 calls 0.031 user 0.014 sys 0.014 real
advance: 10022 calls 2.541 user 0.053 sys 3.025 real
annotate: 394 calls 0.017 user 0.000 sys 0.030 real
assemble_region: 324 calls 1.143 user 0.020 sys 1.241 real
build_variants: 322 calls 0.000 user 0.000 sys 0.002 real
calc: 19646 calls 0.167 user 0.000 sys 0.304 real
calc_region: 322 calls 5.148 user 0.009 sys 5.423 real
call_region: 322 calls 0.032 user 0.000 sys 0.058 real
clip_region: 646 calls 0.047 user 0.000 sys 0.074 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.006 user 0.002 sys 1.579 real
fetch: 19646 calls 0.117 user 0.015 sys 0.142 real
fetch_db: 322 calls 0.006 user 0.000 sys 0.083 real
fetch_ref: 19970 calls 0.009 user 0.012 sys 0.076 real
fetch_region: 324 calls 0.020 user 0.005 sys 0.016 real
idle: 40 calls 0.002 user 0.002 sys 13.079 real
init: 1 calls 0.030 user 0.010 sys 0.041 real
pairhmm: 2270 calls 9.751 user 0.025 sys 10.687 real
realign: 697 calls 0.620 user 0.001 sys 0.708 real
region: 19646 calls 8.917 user 0.080 sys 8.921 real
tracker: 19646 calls 0.013 user 0.011 sys 0.023 real
trim_region: 324 calls 0.004 user 0.000 sys 0.005 real
overall: 317865984 mem 16.498 user 1.194 sys 2.690 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory