cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr21_44120631-44120778.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant HCC1395_BL.haplotyper.chr21_44120631-44120778.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:44254617, elapsed 0.0s, est remaining 0.3s, peak mem 86MB, user 0.1s, sys 0.0s, output queue size 2
progress 10% @chr21:44318470, elapsed 0.1s, est remaining 0.5s, peak mem 111MB, user 0.2s, sys 0.0s, output queue size 37
progress 15% @chr21:44401681, elapsed 0.1s, est remaining 0.4s, peak mem 123MB, user 0.5s, sys 0.0s, output queue size 70
progress 20% @chr21:44456645, elapsed 0.1s, est remaining 0.3s, peak mem 130MB, user 0.6s, sys 0.0s, output queue size 97
progress 30% @chr21:44224713, elapsed 0.1s, est remaining 0.2s, peak mem 160MB, user 0.7s, sys 0.0s, output queue size 108
progress 35% @chr21:44773547, elapsed 0.2s, est remaining 0.4s, peak mem 208MB, user 0.9s, sys 0.0s, output queue size 9
progress 40% @chr21:44865395, elapsed 0.3s, est remaining 0.5s, peak mem 208MB, user 2.2s, sys 0.1s, output queue size 26
progress 45% @chr21:45175730, elapsed 0.3s, est remaining 0.4s, peak mem 208MB, user 2.4s, sys 0.1s, output queue size 51
progress 50% @chr21:45405379, elapsed 0.3s, est remaining 0.3s, peak mem 208MB, user 3.0s, sys 0.1s, output queue size 69
progress 55% @chr21:45455531, elapsed 0.4s, est remaining 0.3s, peak mem 208MB, user 3.5s, sys 0.1s, output queue size 23
progress 60% @chr21:45986526, elapsed 0.4s, est remaining 0.2s, peak mem 208MB, user 3.6s, sys 0.1s, output queue size 29
progress 65% @chr21:46115872, elapsed 0.4s, est remaining 0.2s, peak mem 208MB, user 3.9s, sys 0.1s, output queue size 12
progress 70% @chr21:46131954, elapsed 0.4s, est remaining 0.2s, peak mem 208MB, user 4.1s, sys 0.1s, output queue size 22
progress 75% @chr21:46254392, elapsed 0.5s, est remaining 0.2s, peak mem 208MB, user 4.2s, sys 0.1s, output queue size 53
progress 80% @chr21:46326377, elapsed 0.5s, est remaining 0.1s, peak mem 208MB, user 4.6s, sys 0.1s, output queue size 20
progress 85% @chr21:46401551, elapsed 0.6s, est remaining 0.1s, peak mem 208MB, user 4.7s, sys 0.1s, output queue size 32
progress 90% @chr21:46353104, elapsed 0.6s, est remaining 0.1s, peak mem 208MB, user 5.0s, sys 0.1s, output queue size 30
progress 95% @chr21:46554822, elapsed 0.6s, est remaining 0.0s, peak mem 208MB, user 5.1s, sys 0.1s, output queue size 57
progress 100% @chr21:46602278, elapsed 0.6s, est remaining 0.0s, peak mem 208MB, user 5.3s, sys 0.1s, output queue size 11
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 128
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 163002590
output file size: 38711
reads: 1955548
contig: 516 intervals 92221 bases
"assemble": 96 calls 0.175 user 0.007 sys 0.290 real
"assemble_addRead": 96 calls 0.000 user 0.000 sys 0.013 real
"assemble_buildGraph": 205 calls 0.072 user 0.000 sys 0.144 real
"assemble_computecigar": 140 calls 0.112 user 0.012 sys 0.181 real
"assemble_kg_build_calcsize": 205 calls 0.022 user 0.000 sys 0.083 real
"assemble_kg_build_clear": 265 calls 0.003 user 0.000 sys 0.006 real
"assemble_kg_build_prepare": 410 calls 0.042 user 0.001 sys 0.068 real
"assemble_kg_build_threading": 145 calls 0.050 user 0.000 sys 0.059 real
"assemble_kg_op1": 145 calls 0.010 user 0.006 sys 0.014 real
"assemble_kg_op2": 145 calls 0.000 user 0.000 sys 0.003 real
"assemble_kg_op3": 145 calls 0.000 user 0.000 sys 0.004 real
"assemble_sg_clean": 140 calls 0.026 user 0.000 sys 0.015 real
"assemble_sg_create": 140 calls 0.002 user 0.000 sys 0.020 real
"checkGraph": 96 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 96 calls 0.122 user 0.013 sys 0.186 real
active: 1044 calls 0.030 user 0.000 sys 0.005 real
advance: 528 calls 1.445 user 0.031 sys 1.689 real
annotate: 105 calls 0.010 user 0.000 sys 0.012 real
assemble_region: 96 calls 0.297 user 0.019 sys 0.491 real
build_variants: 95 calls 0.000 user 0.000 sys 0.001 real
calc: 1044 calls 0.173 user 0.008 sys 0.205 real
calc_region: 95 calls 1.916 user 0.001 sys 2.069 real
call_region: 95 calls 0.020 user 0.000 sys 0.020 real
clip_region: 191 calls 0.010 user 0.000 sys 0.024 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.001 user 0.000 sys 0.603 real
fetch: 1044 calls 0.101 user 0.001 sys 0.089 real
fetch_db: 95 calls 0.024 user 0.002 sys 0.035 real
fetch_ref: 1140 calls 0.003 user 0.010 sys 0.011 real
fetch_region: 96 calls 0.000 user 0.000 sys 0.005 real
idle: 53 calls 0.067 user 0.000 sys 12.638 real
init: 1 calls 0.045 user 0.011 sys 0.049 real
pairhmm: 430 calls 3.783 user 0.016 sys 4.039 real
realign: 197 calls 0.154 user 0.000 sys 0.224 real
region: 1044 calls 3.474 user 0.043 sys 3.580 real
tracker: 1044 calls 0.000 user 0.000 sys 0.004 real
trim_region: 96 calls 0.000 user 0.000 sys 0.002 real
overall: 218992640 mem 6.886 user 0.158 sys 1.730 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory