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% @chr4:86782201, elapsed 0.0s, est remaining 0.8s, peak mem 85MB, user 0.0s, sys 0.1s, output queue size 2217
progress 10% @chr4:152332564, elapsed 0.1s, est remaining 0.7s, peak mem 91MB, user 0.1s, sys 0.2s, output queue size 4614
progress 15% @chr5:36171603, elapsed 0.1s, est remaining 0.7s, peak mem 102MB, user 0.1s, sys 0.3s, output queue size 731
progress 20% @chr5:91375511, elapsed 0.2s, est remaining 0.7s, peak mem 112MB, user 0.1s, sys 0.5s, output queue size 3312
progress 25% @chr5:141192553, elapsed 0.2s, est remaining 0.6s, peak mem 124MB, user 0.2s, sys 0.6s, output queue size 5717
progress 30% @chr5:177293824, elapsed 0.2s, est remaining 0.6s, peak mem 132MB, user 0.2s, sys 0.8s, output queue size 7831
progress 35% @chr6:30948547, elapsed 0.3s, est remaining 0.5s, peak mem 141MB, user 0.2s, sys 0.9s, output queue size 10024
progress 40% @chr6:43625363, elapsed 0.3s, est remaining 0.5s, peak mem 153MB, user 0.2s, sys 1.1s, output queue size 12567
progress 45% @chr6:106519131, elapsed 0.4s, est remaining 0.4s, peak mem 162MB, user 0.2s, sys 1.3s, output queue size 15030
progress 50% @chr6:149474239, elapsed 0.4s, est remaining 0.4s, peak mem 174MB, user 0.3s, sys 1.5s, output queue size 17131
progress 55% @chr7:13914223, elapsed 0.4s, est remaining 0.4s, peak mem 183MB, user 0.3s, sys 1.6s, output queue size 19390
progress 60% @chr7:64219314, elapsed 0.5s, est remaining 0.3s, peak mem 189MB, user 0.3s, sys 1.8s, output queue size 21458
progress 65% @chr7:100951841, elapsed 0.5s, est remaining 0.3s, peak mem 202MB, user 0.4s, sys 1.9s, output queue size 23976
progress 70% @chr7:139345501, elapsed 0.5s, est remaining 0.2s, peak mem 208MB, user 0.4s, sys 2.1s, output queue size 26341
progress 75% @chr8:13099347, elapsed 0.6s, est remaining 0.2s, peak mem 222MB, user 0.5s, sys 2.2s, output queue size 28405
progress 80% @chr8:38819522, elapsed 0.6s, est remaining 0.2s, peak mem 226MB, user 0.5s, sys 2.3s, output queue size 30024
progress 85% @chrX:15537134, elapsed 0.6s, est remaining 0.1s, peak mem 238MB, user 0.5s, sys 2.5s, output queue size 32535
progress 90% @chrX:54963257, elapsed 0.7s, est remaining 0.1s, peak mem 250MB, user 0.5s, sys 2.6s, output queue size 34895
progress 95% @chrX:111724934, elapsed 0.7s, est remaining 0.0s, peak mem 256MB, user 0.6s, sys 2.7s, output queue size 36833
progress 100% @chrX:153592506, elapsed 0.8s, est remaining 0.0s, peak mem 262MB, user 0.6s, sys 2.9s, output queue size 39049
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: 71699821
output file size: 22309
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 0.000 user 0.000 sys 0.017 real
advance: 47638 calls 0.000 user 0.006 sys 0.024 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.000 real
calc: 93348 calls 0.005 user 0.019 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 0.008 user 0.001 sys 1.344 real
fetch: 93348 calls 0.019 user 0.001 sys 0.018 real
fetch_ref: 93349 calls 0.132 user 0.062 sys 0.385 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.002 user 0.016 sys 19.542 real
init: 1 calls 0.040 user 0.000 sys 0.044 real
region: 93348 calls 0.003 user 0.008 sys 0.021 real
tracker: 93348 calls 0.024 user 0.001 sys 0.084 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 278663168 mem 1.154 user 4.881 sys 2.467 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory