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% @chr19:49139961, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 452
progress 10% @chr19:50666192, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 564
progress 15% @chr19:52582202, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.1s, sys 0.0s, output queue size 923
progress 20% @chr19:54816501, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.1s, sys 0.0s, output queue size 1310
progress 25% @chr19:56383863, elapsed 0.0s, est remaining 0.1s, peak mem 75MB, user 0.1s, sys 0.1s, output queue size 1767
progress 30% @chr19:58212161, elapsed 0.1s, est remaining 0.1s, peak mem 79MB, user 0.1s, sys 0.1s, output queue size 1986
progress 35% @chr21:29342399, elapsed 0.2s, est remaining 0.3s, peak mem 118MB, user 0.7s, sys 0.2s, output queue size 21
progress 40% @chr21:36460976, elapsed 0.3s, est remaining 0.4s, peak mem 151MB, user 1.7s, sys 0.3s, output queue size 107
progress 45% @chr21:41492213, elapsed 1.2s, est remaining 1.5s, peak mem 287MB, user 9.2s, sys 0.3s, output queue size 119
progress 50% @chr21:45505134, elapsed 1.4s, est remaining 1.4s, peak mem 294MB, user 11.9s, sys 0.4s, output queue size 101
progress 55% @chr22:19405786, elapsed 1.5s, est remaining 1.2s, peak mem 294MB, user 12.5s, sys 0.5s, output queue size 107
progress 60% @chr22:22195903, elapsed 1.5s, est remaining 1.0s, peak mem 294MB, user 12.5s, sys 0.5s, output queue size 587
progress 65% @chr22:23882759, elapsed 1.5s, est remaining 0.8s, peak mem 294MB, user 12.5s, sys 0.5s, output queue size 805
progress 70% @chr22:29287524, elapsed 1.5s, est remaining 0.7s, peak mem 294MB, user 12.5s, sys 0.5s, output queue size 1316
progress 75% @chr22:31843645, elapsed 1.5s, est remaining 0.5s, peak mem 294MB, user 12.6s, sys 0.5s, output queue size 1858
progress 80% @chr22:37933039, elapsed 1.6s, est remaining 0.4s, peak mem 294MB, user 12.6s, sys 0.5s, output queue size 2417
progress 85% @chr22:41346003, elapsed 1.6s, est remaining 0.3s, peak mem 294MB, user 12.6s, sys 0.5s, output queue size 2958
progress 90% @chr22:46281599, elapsed 1.6s, est remaining 0.2s, peak mem 294MB, user 12.6s, sys 0.5s, output queue size 3553
progress 95% @chr22:50738236, elapsed 1.6s, est remaining 0.1s, peak mem 294MB, user 12.6s, sys 0.6s, output queue size 4122
progress 100% @chr22:50488275, elapsed 1.6s, est remaining 0.0s, peak mem 294MB, user 12.6s, sys 0.6s, output queue size 4700
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: 74559500
output file size: 79936
reads: 1001133
contig: 9624 intervals 1921786 bases
"assemble": 324 calls 0.531 user 0.033 sys 0.822 real
"assemble_addRead": 324 calls 0.050 user 0.000 sys 0.038 real
"assemble_buildGraph": 688 calls 0.199 user 0.002 sys 0.415 real
"assemble_computecigar": 523 calls 0.327 user 0.012 sys 0.390 real
"assemble_kg_build_calcsize": 688 calls 0.138 user 0.000 sys 0.233 real
"assemble_kg_build_clear": 826 calls 0.014 user 0.000 sys 0.020 real
"assemble_kg_build_prepare": 1376 calls 0.230 user 0.026 sys 0.193 real
"assemble_kg_build_threading": 550 calls 0.061 user 0.002 sys 0.176 real
"assemble_kg_op1": 550 calls 0.024 user 0.001 sys 0.035 real
"assemble_kg_op2": 550 calls 0.010 user 0.000 sys 0.009 real
"assemble_kg_op3": 550 calls 0.011 user 0.000 sys 0.012 real
"assemble_sg_clean": 523 calls 0.011 user 0.000 sys 0.041 real
"assemble_sg_create": 523 calls 0.012 user 0.004 sys 0.054 real
"checkGraph": 324 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 324 calls 0.342 user 0.013 sys 0.409 real
active: 19646 calls 0.000 user 0.000 sys 0.015 real
advance: 10022 calls 2.363 user 0.116 sys 3.100 real
annotate: 394 calls 0.018 user 0.000 sys 0.031 real
assemble_region: 324 calls 0.923 user 0.046 sys 1.273 real
build_variants: 322 calls 0.010 user 0.000 sys 0.002 real
calc: 19646 calls 0.268 user 0.001 sys 0.320 real
calc_region: 322 calls 5.532 user 0.023 sys 5.741 real
call_region: 322 calls 0.056 user 0.000 sys 0.059 real
clip_region: 646 calls 0.055 user 0.000 sys 0.077 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.002 user 0.000 sys 1.644 real
fetch: 19646 calls 0.161 user 0.006 sys 0.146 real
fetch_db: 322 calls 0.031 user 0.000 sys 0.085 real
fetch_ref: 19970 calls 0.024 user 0.007 sys 0.075 real
fetch_region: 324 calls 0.004 user 0.010 sys 0.020 real
idle: 39 calls 0.003 user 0.009 sys 13.099 real
init: 1 calls 0.049 user 0.001 sys 0.042 real
pairhmm: 2270 calls 10.002 user 0.039 sys 10.747 real
realign: 697 calls 0.565 user 0.001 sys 0.711 real
region: 19646 calls 9.185 user 0.109 sys 9.236 real
tracker: 19646 calls 0.003 user 0.000 sys 0.024 real
trim_region: 324 calls 0.000 user 0.000 sys 0.004 real
overall: 309018624 mem 16.841 user 0.981 sys 2.760 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory