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% @chr4:86803709, elapsed 0.0s, est remaining 0.9s, peak mem 75MB, user 0.0s, sys 0.2s, output queue size 2349
progress 10% @chr4:152330694, elapsed 0.1s, est remaining 0.8s, peak mem 75MB, user 0.0s, sys 0.2s, output queue size 987
progress 15% @chr5:36170344, elapsed 0.1s, est remaining 0.8s, peak mem 90MB, user 0.1s, sys 0.4s, output queue size 3458
progress 20% @chr5:91374114, elapsed 0.2s, est remaining 0.7s, peak mem 96MB, user 0.1s, sys 0.5s, output queue size 6037
progress 25% @chr5:141192553, elapsed 0.2s, est remaining 0.7s, peak mem 105MB, user 0.1s, sys 0.7s, output queue size 8441
progress 30% @chr5:177303009, elapsed 0.3s, est remaining 0.6s, peak mem 120MB, user 0.2s, sys 0.8s, output queue size 10560
progress 35% @chr6:30948547, elapsed 0.3s, est remaining 0.6s, peak mem 129MB, user 0.2s, sys 0.9s, output queue size 12752
progress 40% @chr6:43640021, elapsed 0.4s, est remaining 0.5s, peak mem 132MB, user 0.2s, sys 1.1s, output queue size 15296
progress 45% @chr6:106519131, elapsed 0.4s, est remaining 0.5s, peak mem 147MB, user 0.2s, sys 1.3s, output queue size 17759
progress 50% @chr6:149450683, elapsed 0.4s, est remaining 0.4s, peak mem 159MB, user 0.3s, sys 1.4s, output queue size 19856
progress 55% @chr7:13914223, elapsed 0.5s, est remaining 0.4s, peak mem 168MB, user 0.3s, sys 1.5s, output queue size 22116
progress 60% @chr7:64219314, elapsed 0.5s, est remaining 0.3s, peak mem 171MB, user 0.3s, sys 1.7s, output queue size 24186
progress 65% @chr7:100951841, elapsed 0.6s, est remaining 0.3s, peak mem 183MB, user 0.4s, sys 1.9s, output queue size 26713
progress 70% @chr7:139283024, elapsed 0.6s, est remaining 0.3s, peak mem 198MB, user 0.4s, sys 2.0s, output queue size 29070
progress 75% @chr8:13099347, elapsed 0.6s, est remaining 0.2s, peak mem 204MB, user 0.4s, sys 2.2s, output queue size 31127
progress 80% @chr8:38819522, elapsed 0.7s, est remaining 0.2s, peak mem 210MB, user 0.5s, sys 2.3s, output queue size 32751
progress 85% @chrX:15573367, elapsed 0.7s, est remaining 0.1s, peak mem 225MB, user 0.5s, sys 2.4s, output queue size 35276
progress 90% @chrX:55001546, elapsed 0.8s, est remaining 0.1s, peak mem 231MB, user 0.5s, sys 2.6s, output queue size 37625
progress 95% @chrX:111722793, elapsed 0.8s, est remaining 0.0s, peak mem 237MB, user 0.6s, sys 2.8s, output queue size 39557
progress 100% @chrX:156009816, elapsed 0.8s, est remaining 0.0s, peak mem 252MB, user 0.6s, sys 2.9s, output queue size 41777
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 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692772
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 0.010 user 0.002 sys 0.019 real
advance: 47638 calls 0.006 user 0.009 sys 0.026 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.000 real
calc: 93348 calls 0.008 user 0.011 sys 0.019 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 0.004 user 0.002 sys 1.686 real
fetch: 93348 calls 0.010 user 0.000 sys 0.020 real
fetch_ref: 93349 calls 0.050 user 0.063 sys 0.365 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.007 user 0.030 sys 22.710 real
init: 1 calls 0.043 user 0.000 sys 0.043 real
region: 93348 calls 0.001 user 0.006 sys 0.023 real
tracker: 93348 calls 0.011 user 0.002 sys 0.089 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 267522048 mem 1.220 user 5.023 sys 2.809 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory