cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr4_30730753-30730788.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr4_30730753-30730788.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr4:86799101, elapsed 0.0s, est remaining 0.7s, peak mem 84MB, user 0.1s, sys 0.0s, output queue size 2422
progress 10% @chr4:152329639, elapsed 0.1s, est remaining 0.7s, peak mem 94MB, user 0.1s, sys 0.2s, output queue size 2339
progress 15% @chr5:36171603, elapsed 0.1s, est remaining 0.6s, peak mem 103MB, user 0.1s, sys 0.4s, output queue size 4813
progress 20% @chr5:91163782, elapsed 0.1s, est remaining 0.6s, peak mem 115MB, user 0.1s, sys 0.5s, output queue size 7392
progress 25% @chr5:141192553, elapsed 0.2s, est remaining 0.6s, peak mem 124MB, user 0.1s, sys 0.7s, output queue size 9795
progress 30% @chr5:177293824, elapsed 0.2s, est remaining 0.5s, peak mem 133MB, user 0.2s, sys 0.8s, output queue size 11918
progress 35% @chr6:30948547, elapsed 0.2s, est remaining 0.5s, peak mem 144MB, user 0.2s, sys 0.9s, output queue size 14112
progress 40% @chr6:43636381, elapsed 0.3s, est remaining 0.4s, peak mem 154MB, user 0.2s, sys 1.1s, output queue size 16649
progress 45% @chr6:107705200, elapsed 0.3s, est remaining 0.4s, peak mem 165MB, user 0.2s, sys 1.3s, output queue size 19173
progress 50% @chr6:149450683, elapsed 0.4s, est remaining 0.4s, peak mem 171MB, user 0.3s, sys 1.4s, output queue size 21210
progress 55% @chr7:13911239, elapsed 0.4s, est remaining 0.3s, peak mem 183MB, user 0.3s, sys 1.5s, output queue size 23470
progress 60% @chr7:64219314, elapsed 0.4s, est remaining 0.3s, peak mem 190MB, user 0.3s, sys 1.6s, output queue size 25540
progress 65% @chr7:100951841, elapsed 0.5s, est remaining 0.3s, peak mem 201MB, user 0.4s, sys 1.8s, output queue size 28064
progress 70% @chr7:139293232, elapsed 0.5s, est remaining 0.2s, peak mem 211MB, user 0.4s, sys 1.9s, output queue size 30421
progress 75% @chr8:13099347, elapsed 0.5s, est remaining 0.2s, peak mem 222MB, user 0.4s, sys 2.1s, output queue size 32487
progress 80% @chr8:38819522, elapsed 0.6s, est remaining 0.1s, peak mem 228MB, user 0.5s, sys 2.2s, output queue size 34104
progress 85% @chrX:15556073, elapsed 0.6s, est remaining 0.1s, peak mem 238MB, user 0.5s, sys 2.4s, output queue size 36622
progress 90% @chrX:54951905, elapsed 0.6s, est remaining 0.1s, peak mem 249MB, user 0.5s, sys 2.5s, output queue size 38977
progress 95% @chrX:111718112, elapsed 0.7s, est remaining 0.0s, peak mem 255MB, user 0.6s, sys 2.6s, output queue size 40912
progress 100% @chrX:154380234, elapsed 0.7s, est remaining 0.0s, peak mem 267MB, user 0.6s, sys 2.8s, output queue size 43131
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 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692773
output file size: 22308
reads: 1001089
contig: 45710 intervals 9000068 bases
"assemble": 1 calls 0.000 user 0.000 sys 0.000 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 0.007 user 0.006 sys 0.017 real
advance: 47638 calls 0.006 user 0.008 sys 0.024 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.000 real
calc: 93348 calls 0.000 user 0.007 sys 0.017 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 0.001 user 0.001 sys 1.283 real
fetch: 93348 calls 0.000 user 0.008 sys 0.017 real
fetch_ref: 93349 calls 0.089 user 0.059 sys 0.355 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.002 user 0.007 sys 19.465 real
init: 1 calls 0.030 user 0.010 sys 0.041 real
region: 93348 calls 0.005 user 0.002 sys 0.019 real
tracker: 93348 calls 0.021 user 0.005 sys 0.082 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 283348992 mem 1.134 user 4.419 sys 2.396 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory