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% @chr4:86780402, elapsed 0.4s, est remaining 8.5s, peak mem 86MB, user 0.1s, sys 0.4s, output queue size 1928
progress 10% @chr4:152332564, elapsed 0.5s, est remaining 4.7s, peak mem 95MB, user 0.2s, sys 0.8s, output queue size 4323
progress 15% @chr5:36177185, elapsed 0.6s, est remaining 3.4s, peak mem 106MB, user 0.2s, sys 1.1s, output queue size 559
progress 20% @chr5:91163782, elapsed 0.7s, est remaining 2.7s, peak mem 113MB, user 0.3s, sys 1.5s, output queue size 3135
progress 25% @chr5:141187319, elapsed 0.8s, est remaining 2.3s, peak mem 124MB, user 0.4s, sys 1.9s, output queue size 5544
progress 30% @chr5:177293824, elapsed 0.8s, est remaining 1.9s, peak mem 133MB, user 0.4s, sys 2.4s, output queue size 7661
progress 35% @chr6:30948547, elapsed 0.9s, est remaining 1.7s, peak mem 143MB, user 0.4s, sys 2.7s, output queue size 9856
progress 40% @chr6:43624510, elapsed 1.0s, est remaining 1.5s, peak mem 152MB, user 0.5s, sys 3.1s, output queue size 12393
progress 45% @chr6:106622818, elapsed 1.1s, est remaining 1.3s, peak mem 163MB, user 0.6s, sys 3.6s, output queue size 14881
progress 50% @chr6:149474239, elapsed 1.2s, est remaining 1.2s, peak mem 171MB, user 0.6s, sys 3.8s, output queue size 16957
progress 55% @chr7:13911239, elapsed 1.3s, est remaining 1.0s, peak mem 179MB, user 0.7s, sys 4.1s, output queue size 19214
progress 60% @chr7:64219314, elapsed 1.4s, est remaining 0.9s, peak mem 187MB, user 0.8s, sys 4.3s, output queue size 21284
progress 65% @chr7:100951841, elapsed 1.5s, est remaining 0.8s, peak mem 196MB, user 0.9s, sys 4.5s, output queue size 23800
progress 70% @chr7:139345501, elapsed 1.6s, est remaining 0.7s, peak mem 200MB, user 0.9s, sys 4.8s, output queue size 26166
progress 75% @chr8:13305225, elapsed 1.6s, est remaining 0.5s, peak mem 209MB, user 1.0s, sys 5.0s, output queue size 28230
progress 80% @chr8:38831125, elapsed 1.7s, est remaining 0.4s, peak mem 215MB, user 1.0s, sys 5.1s, output queue size 29851
progress 85% @chrX:15525288, elapsed 1.8s, est remaining 0.3s, peak mem 224MB, user 1.1s, sys 5.4s, output queue size 32354
progress 90% @chrX:54924989, elapsed 1.8s, est remaining 0.2s, peak mem 233MB, user 1.2s, sys 5.6s, output queue size 34731
progress 95% @chrX:111718112, elapsed 1.9s, est remaining 0.1s, peak mem 242MB, user 1.3s, sys 5.9s, output queue size 36655
progress 100% @chrX:154532386, elapsed 2.0s, est remaining 0.0s, peak mem 251MB, user 1.3s, sys 6.2s, output queue size 38875
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050657
  features: bfebfbff 7ffefbff
  extended: d39ff7eb 00000818
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz
threads: 12 max 96
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74586806
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 0.000 user 0.000 sys 0.024 real
advance: 47638 calls 0.001 user 0.023 sys 0.041 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.002 real
calc: 93348 calls 0.000 user 0.002 sys 0.024 real
clip_region: 1 calls 0.000 user 0.000 sys 0.000 real
done: 1 calls 0.000 user 0.000 sys 0.004 real
execute: 1 calls 0.006 user 0.001 sys 3.748 real
fetch: 93348 calls 0.001 user 0.010 sys 0.026 real
fetch_ref: 93349 calls 0.200 user 0.088 sys 0.636 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 51 calls 0.005 user 0.010 sys 34.224 real
init: 1 calls 0.057 user 0.003 sys 0.067 real
region: 93348 calls 0.000 user 0.009 sys 0.029 real
tracker: 93348 calls 0.054 user 0.010 sys 0.168 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 267194368 mem 2.078 user 8.545 sys 4.929 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory