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% @chr19:49138205, elapsed 0.0s, est remaining 0.3s, peak mem 66MB, user 0.0s, sys 0.1s, output queue size 393
progress 10% @chr19:50629784, elapsed 0.0s, est remaining 0.2s, peak mem 66MB, user 0.0s, sys 0.1s, output queue size 991
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.2s, peak mem 66MB, user 0.0s, sys 0.1s, output queue size 1362
progress 20% @chr19:54818315, elapsed 0.0s, est remaining 0.2s, peak mem 66MB, user 0.0s, sys 0.1s, output queue size 761
progress 25% @chr19:56221575, elapsed 0.1s, est remaining 0.2s, peak mem 66MB, user 0.0s, sys 0.1s, output queue size 1201
progress 30% @chr19:58260851, elapsed 0.1s, est remaining 0.1s, peak mem 66MB, user 0.0s, sys 0.2s, output queue size 1440
progress 35% @chr21:30348409, elapsed 0.2s, est remaining 0.3s, peak mem 96MB, user 0.7s, sys 0.2s, output queue size 118
progress 40% @chr21:36460976, elapsed 0.3s, est remaining 0.5s, peak mem 132MB, user 1.8s, sys 0.2s, output queue size 107
progress 45% @chr21:41497133, elapsed 1.2s, est remaining 1.4s, peak mem 258MB, user 9.6s, sys 0.3s, output queue size 128
progress 50% @chr21:45505838, elapsed 1.5s, est remaining 1.5s, peak mem 264MB, user 12.4s, sys 0.3s, output queue size 9
progress 55% @chr22:19394342, elapsed 1.5s, est remaining 1.2s, peak mem 264MB, user 13.0s, sys 0.3s, output queue size 10
progress 60% @chr22:22195903, elapsed 1.5s, est remaining 1.0s, peak mem 264MB, user 13.0s, sys 0.3s, output queue size 489
progress 65% @chr22:23882459, elapsed 1.5s, est remaining 0.8s, peak mem 264MB, user 13.0s, sys 0.4s, output queue size 708
progress 70% @chr22:29288004, elapsed 1.5s, est remaining 0.7s, peak mem 264MB, user 13.0s, sys 0.4s, output queue size 1220
progress 75% @chr22:31843645, elapsed 1.6s, est remaining 0.5s, peak mem 264MB, user 13.0s, sys 0.5s, output queue size 1759
progress 80% @chr22:37947281, elapsed 1.6s, est remaining 0.4s, peak mem 264MB, user 13.0s, sys 0.6s, output queue size 2318
progress 85% @chr22:41346003, elapsed 1.6s, est remaining 0.3s, peak mem 264MB, user 13.0s, sys 0.6s, output queue size 2859
progress 90% @chr22:46256561, elapsed 1.6s, est remaining 0.2s, peak mem 264MB, user 13.0s, sys 0.7s, output queue size 3452
progress 95% @chr22:50720184, elapsed 1.6s, est remaining 0.1s, peak mem 264MB, user 13.0s, sys 0.7s, output queue size 4025
progress 100% @chrY:12735612, elapsed 1.6s, est remaining 0.0s, peak mem 264MB, user 13.1s, sys 0.7s, output queue size 4602
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 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74586815
output file size: 79932
reads: 1001133
contig: 9624 intervals 1921786 bases
"assemble": 324 calls 0.736 user 0.018 sys 0.846 real
"assemble_addRead": 324 calls 0.061 user 0.000 sys 0.047 real
"assemble_buildGraph": 688 calls 0.354 user 0.006 sys 0.417 real
"assemble_computecigar": 523 calls 0.248 user 0.010 sys 0.390 real
"assemble_kg_build_calcsize": 688 calls 0.202 user 0.000 sys 0.232 real
"assemble_kg_build_clear": 826 calls 0.016 user 0.000 sys 0.020 real
"assemble_kg_build_prepare": 1376 calls 0.252 user 0.006 sys 0.212 real
"assemble_kg_build_threading": 550 calls 0.152 user 0.006 sys 0.179 real
"assemble_kg_op1": 550 calls 0.019 user 0.001 sys 0.036 real
"assemble_kg_op2": 550 calls 0.010 user 0.000 sys 0.010 real
"assemble_kg_op3": 550 calls 0.000 user 0.000 sys 0.012 real
"assemble_sg_clean": 523 calls 0.014 user 0.000 sys 0.041 real
"assemble_sg_create": 523 calls 0.053 user 0.006 sys 0.055 real
"checkGraph": 324 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 324 calls 0.272 user 0.011 sys 0.410 real
active: 19646 calls 0.018 user 0.000 sys 0.015 real
advance: 10022 calls 2.524 user 0.058 sys 3.091 real
annotate: 394 calls 0.012 user 0.000 sys 0.034 real
assemble_region: 324 calls 1.068 user 0.030 sys 1.307 real
build_variants: 322 calls 0.000 user 0.000 sys 0.002 real
calc: 19646 calls 0.171 user 0.002 sys 0.317 real
calc_region: 322 calls 5.953 user 0.021 sys 6.356 real
call_region: 322 calls 0.051 user 0.000 sys 0.065 real
clip_region: 646 calls 0.059 user 0.000 sys 0.081 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.005 user 0.003 sys 1.693 real
fetch: 19646 calls 0.137 user 0.005 sys 0.162 real
fetch_db: 322 calls 0.048 user 0.000 sys 0.086 real
fetch_ref: 19970 calls 0.012 user 0.018 sys 0.086 real
fetch_region: 324 calls 0.003 user 0.000 sys 0.017 real
idle: 39 calls 0.003 user 0.022 sys 13.314 real
init: 1 calls 0.044 user 0.006 sys 0.047 real
pairhmm: 2270 calls 10.034 user 0.010 sys 10.779 real
realign: 697 calls 0.471 user 0.001 sys 0.722 real
region: 19646 calls 9.708 user 0.058 sys 9.794 real
tracker: 19646 calls 0.025 user 0.002 sys 0.025 real
trim_region: 324 calls 0.013 user 0.000 sys 0.005 real
overall: 277000192 mem 17.016 user 1.488 sys 2.830 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory