cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr4_30730753-30730788.bed.gz -i Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_2.haplotyper.chr4_30730753-30730788.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr4:86803709, elapsed 0.1s, est remaining 1.0s, peak mem 75MB, user 0.0s, sys 0.1s, output queue size 1770
progress 10% @chr4:152328169, elapsed 0.1s, est remaining 1.0s, peak mem 75MB, user 0.1s, sys 0.3s, output queue size 4162
progress 15% @chr5:36168313, elapsed 0.2s, est remaining 1.0s, peak mem 87MB, user 0.1s, sys 0.6s, output queue size 6633
progress 20% @chr5:91376621, elapsed 0.2s, est remaining 0.9s, peak mem 102MB, user 0.1s, sys 0.8s, output queue size 9217
progress 25% @chr5:141302960, elapsed 0.3s, est remaining 0.9s, peak mem 105MB, user 0.1s, sys 0.9s, output queue size 2043
progress 30% @chr5:177302752, elapsed 0.3s, est remaining 0.8s, peak mem 108MB, user 0.2s, sys 1.0s, output queue size 4159
progress 35% @chr6:30948547, elapsed 0.4s, est remaining 0.7s, peak mem 114MB, user 0.2s, sys 1.2s, output queue size 6349
progress 40% @chr6:43636381, elapsed 0.4s, est remaining 0.6s, peak mem 123MB, user 0.2s, sys 1.3s, output queue size 8894
progress 45% @chr6:106527305, elapsed 0.5s, est remaining 0.6s, peak mem 129MB, user 0.3s, sys 1.5s, output queue size 11360
progress 50% @chr6:149450683, elapsed 0.5s, est remaining 0.5s, peak mem 138MB, user 0.3s, sys 1.6s, output queue size 13455
progress 55% @chr7:13903840, elapsed 0.6s, est remaining 0.5s, peak mem 144MB, user 0.4s, sys 1.7s, output queue size 15715
progress 60% @chr7:64336887, elapsed 0.6s, est remaining 0.4s, peak mem 159MB, user 0.4s, sys 1.8s, output queue size 17788
progress 65% @chr7:100951841, elapsed 0.7s, est remaining 0.4s, peak mem 168MB, user 0.4s, sys 2.0s, output queue size 20306
progress 70% @chr7:139345501, elapsed 0.7s, est remaining 0.3s, peak mem 177MB, user 0.5s, sys 2.1s, output queue size 22667
progress 75% @chr8:13099347, elapsed 0.8s, est remaining 0.3s, peak mem 183MB, user 0.5s, sys 2.2s, output queue size 24731
progress 80% @chr8:38836162, elapsed 0.8s, est remaining 0.2s, peak mem 189MB, user 0.5s, sys 2.3s, output queue size 26353
progress 85% @chrX:15573367, elapsed 0.9s, est remaining 0.2s, peak mem 204MB, user 0.6s, sys 2.4s, output queue size 28873
progress 90% @chrX:54993911, elapsed 0.9s, est remaining 0.1s, peak mem 210MB, user 0.6s, sys 2.5s, output queue size 31223
progress 95% @chrX:111723798, elapsed 1.0s, est remaining 0.1s, peak mem 219MB, user 0.6s, sys 2.7s, output queue size 33159
progress 100% @chrX:154953892, elapsed 1.0s, est remaining 0.0s, peak mem 222MB, user 0.6s, sys 2.9s, output queue size 35376
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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: 74586812
output file size: 22310
reads: 1001133
contig: 45710 intervals 9000068 bases
"assemble": 1 calls 0.000 user 0.000 sys 0.001 real
"assemble_addRead": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_buildGraph": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_computecigar": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_calcsize": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_clear": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_prepare": 4 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_threading": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op1": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op2": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op3": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_sg_clean": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_sg_create": 2 calls 0.000 user 0.000 sys 0.000 real
"checkGraph": 1 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 1 calls 0.000 user 0.000 sys 0.000 real
active: 93348 calls 0.008 user 0.005 sys 0.019 real
advance: 47638 calls 0.005 user 0.002 sys 0.028 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.001 real
calc: 93348 calls 0.005 user 0.000 sys 0.018 real
clip_region: 1 calls 0.000 user 0.000 sys 0.000 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.003 sys 1.829 real
fetch: 93348 calls 0.000 user 0.001 sys 0.020 real
fetch_ref: 93349 calls 0.068 user 0.041 sys 0.404 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.004 user 0.004 sys 22.245 real
init: 1 calls 0.037 user 0.013 sys 0.043 real
region: 93348 calls 0.000 user 0.002 sys 0.021 real
tracker: 93348 calls 0.032 user 0.003 sys 0.092 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 232919040 mem 1.307 user 5.218 sys 2.946 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory