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.recal.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% @chr21:44222913, elapsed 0.0s, est remaining 0.3s, peak mem 78MB, user 0.0s, sys 0.0s, output queue size 2
progress 10% @chr21:44286007, elapsed 0.1s, est remaining 0.5s, peak mem 99MB, user 0.2s, sys 0.0s, output queue size 40
progress 15% @chr21:44391272, elapsed 0.1s, est remaining 0.4s, peak mem 112MB, user 0.5s, sys 0.0s, output queue size 70
progress 20% @chr21:44456645, elapsed 0.1s, est remaining 0.3s, peak mem 118MB, user 0.6s, sys 0.0s, output queue size 99
progress 25% @chr21:44550691, elapsed 0.1s, est remaining 0.3s, peak mem 154MB, user 0.7s, sys 0.0s, output queue size 108
progress 31% @chr21:44224713, elapsed 0.1s, est remaining 0.2s, peak mem 154MB, user 0.8s, sys 0.0s, output queue size 109
progress 35% @chr21:44681833, elapsed 0.2s, est remaining 0.4s, peak mem 207MB, user 1.2s, sys 0.1s, output queue size 7
progress 40% @chr21:44627172, elapsed 0.3s, est remaining 0.5s, peak mem 207MB, user 1.9s, sys 0.1s, output queue size 29
progress 45% @chr21:45175730, elapsed 0.4s, est remaining 0.4s, peak mem 207MB, user 2.5s, sys 0.1s, output queue size 52
progress 50% @chr21:44851367, elapsed 0.4s, est remaining 0.4s, peak mem 207MB, user 3.2s, sys 0.1s, output queue size 60
progress 55% @chr21:45505838, elapsed 0.4s, est remaining 0.3s, peak mem 207MB, user 3.4s, sys 0.1s, output queue size 94
progress 60% @chr21:45986526, elapsed 0.4s, est remaining 0.3s, peak mem 207MB, user 3.8s, sys 0.1s, output queue size 29
progress 65% @chr21:46121556, elapsed 0.4s, est remaining 0.2s, peak mem 207MB, user 4.1s, sys 0.1s, output queue size 12
progress 70% @chr21:46131954, elapsed 0.5s, est remaining 0.2s, peak mem 207MB, user 4.3s, sys 0.1s, output queue size 22
progress 75% @chr21:46261280, elapsed 0.5s, est remaining 0.2s, peak mem 207MB, user 4.4s, sys 0.1s, output queue size 54
progress 80% @chr21:46265925, elapsed 0.6s, est remaining 0.1s, peak mem 208MB, user 4.6s, sys 0.1s, output queue size 84
progress 85% @chr21:46390670, elapsed 0.6s, est remaining 0.1s, peak mem 208MB, user 5.1s, sys 0.1s, output queue size 22
progress 90% @chr21:46496988, elapsed 0.6s, est remaining 0.1s, peak mem 208MB, user 5.2s, sys 0.1s, output queue size 46
progress 95% @chr21:46366584, elapsed 0.6s, est remaining 0.0s, peak mem 208MB, user 5.4s, sys 0.1s, output queue size 55
progress 100% @chr21:46602278, elapsed 0.6s, est remaining 0.0s, peak mem 208MB, user 5.6s, sys 0.1s, output queue size 11
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: 111697681
output file size: 38952
reads: 1322929
contig: 516 intervals 92221 bases
"assemble": 95 calls 0.220 user 0.007 sys 0.326 real
"assemble_addRead": 95 calls 0.000 user 0.000 sys 0.013 real
"assemble_buildGraph": 203 calls 0.101 user 0.007 sys 0.169 real
"assemble_computecigar": 140 calls 0.123 user 0.009 sys 0.229 real
"assemble_kg_build_calcsize": 203 calls 0.052 user 0.005 sys 0.099 real
"assemble_kg_build_clear": 262 calls 0.009 user 0.000 sys 0.006 real
"assemble_kg_build_prepare": 406 calls 0.071 user 0.000 sys 0.072 real
"assemble_kg_build_threading": 144 calls 0.048 user 0.000 sys 0.068 real
"assemble_kg_op1": 144 calls 0.004 user 0.000 sys 0.014 real
"assemble_kg_op2": 144 calls 0.000 user 0.000 sys 0.004 real
"assemble_kg_op3": 144 calls 0.003 user 0.000 sys 0.004 real
"assemble_sg_clean": 140 calls 0.014 user 0.000 sys 0.018 real
"assemble_sg_create": 140 calls 0.011 user 0.000 sys 0.022 real
"checkGraph": 95 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 95 calls 0.133 user 0.009 sys 0.235 real
active: 1044 calls 0.010 user 0.000 sys 0.009 real
advance: 528 calls 1.588 user 0.025 sys 1.823 real
annotate: 106 calls 0.012 user 0.000 sys 0.013 real
assemble_region: 95 calls 0.353 user 0.016 sys 0.575 real
build_variants: 94 calls 0.000 user 0.000 sys 0.001 real
calc: 1044 calls 0.225 user 0.000 sys 0.200 real
calc_region: 94 calls 2.265 user 0.025 sys 2.361 real
call_region: 94 calls 0.012 user 0.000 sys 0.022 real
clip_region: 189 calls 0.026 user 0.001 sys 0.024 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.002 sys 0.648 real
fetch: 1044 calls 0.064 user 0.001 sys 0.064 real
fetch_db: 94 calls 0.027 user 0.000 sys 0.042 real
fetch_ref: 1139 calls 0.014 user 0.000 sys 0.007 real
fetch_region: 95 calls 0.000 user 0.000 sys 0.004 real
idle: 48 calls 0.029 user 0.000 sys 12.684 real
init: 1 calls 0.040 user 0.020 sys 0.059 real
pairhmm: 469 calls 4.084 user 0.042 sys 4.315 real
realign: 195 calls 0.230 user 0.000 sys 0.238 real
region: 1044 calls 3.643 user 0.064 sys 3.819 real
tracker: 1044 calls 0.010 user 0.000 sys 0.009 real
trim_region: 95 calls 0.000 user 0.000 sys 0.002 real
overall: 218886144 mem 7.420 user 0.179 sys 1.796 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory