cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr19_47340800-47341813.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr19:49139668, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 463
progress 10% @chr19:50625393, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 1060
progress 15% @chr19:52704937, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 299
progress 20% @chr19:54889649, elapsed 0.0s, est remaining 0.1s, peak mem 75MB, user 0.0s, sys 0.1s, output queue size 713
progress 25% @chr19:56383863, elapsed 0.0s, est remaining 0.1s, peak mem 76MB, user 0.0s, sys 0.1s, output queue size 1143
progress 30% @chr19:58212161, elapsed 0.0s, est remaining 0.1s, peak mem 76MB, user 0.0s, sys 0.1s, output queue size 1365
progress 35% @chr21:29342399, elapsed 0.1s, est remaining 0.2s, peak mem 100MB, user 0.5s, sys 0.2s, output queue size 83
progress 40% @chr21:36460976, elapsed 0.3s, est remaining 0.4s, peak mem 151MB, user 1.6s, sys 0.3s, output queue size 105
progress 45% @chr21:42426697, elapsed 0.8s, est remaining 1.0s, peak mem 253MB, user 6.7s, sys 0.4s, output queue size 121
progress 50% @chr21:45525817, elapsed 1.1s, est remaining 1.1s, peak mem 262MB, user 8.7s, sys 0.4s, output queue size 116
progress 55% @chr22:19432555, elapsed 1.1s, est remaining 0.9s, peak mem 262MB, user 9.4s, sys 0.5s, output queue size 355
progress 60% @chr22:22244946, elapsed 1.1s, est remaining 0.8s, peak mem 262MB, user 9.4s, sys 0.5s, output queue size 748
progress 65% @chr22:23894772, elapsed 1.1s, est remaining 0.6s, peak mem 262MB, user 9.4s, sys 0.5s, output queue size 967
progress 70% @chr22:29288004, elapsed 1.1s, est remaining 0.5s, peak mem 262MB, user 9.4s, sys 0.5s, output queue size 1473
progress 75% @chr22:31814992, elapsed 1.1s, est remaining 0.4s, peak mem 262MB, user 9.4s, sys 0.5s, output queue size 2012
progress 80% @chr22:37947281, elapsed 1.2s, est remaining 0.3s, peak mem 262MB, user 9.5s, sys 0.6s, output queue size 512
progress 85% @chr22:41254308, elapsed 1.2s, est remaining 0.2s, peak mem 262MB, user 9.5s, sys 0.6s, output queue size 1033
progress 90% @chr22:46256561, elapsed 1.2s, est remaining 0.1s, peak mem 262MB, user 9.5s, sys 0.6s, output queue size 1653
progress 95% @chr22:50730721, elapsed 1.2s, est remaining 0.1s, peak mem 262MB, user 9.5s, sys 0.6s, output queue size 2218
progress 100% @chrY:13705225, elapsed 1.2s, est remaining 0.0s, peak mem 262MB, user 9.5s, sys 0.7s, output queue size 2796
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  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: 77725
reads: 1001089
contig: 9624 intervals 1921786 bases
"assemble": 315 calls 0.509 user 0.005 sys 0.687 real
"assemble_addRead": 315 calls 0.006 user 0.000 sys 0.032 real
"assemble_buildGraph": 650 calls 0.211 user 0.002 sys 0.342 real
"assemble_computecigar": 513 calls 0.292 user 0.008 sys 0.365 real
"assemble_kg_build_calcsize": 650 calls 0.126 user 0.001 sys 0.188 real
"assemble_kg_build_clear": 775 calls 0.023 user 0.000 sys 0.015 real
"assemble_kg_build_prepare": 1300 calls 0.159 user 0.003 sys 0.150 real
"assemble_kg_build_threading": 525 calls 0.086 user 0.000 sys 0.150 real
"assemble_kg_op1": 525 calls 0.022 user 0.000 sys 0.032 real
"assemble_kg_op2": 525 calls 0.001 user 0.000 sys 0.008 real
"assemble_kg_op3": 525 calls 0.000 user 0.000 sys 0.011 real
"assemble_sg_clean": 513 calls 0.031 user 0.000 sys 0.040 real
"assemble_sg_create": 513 calls 0.037 user 0.001 sys 0.053 real
"checkGraph": 315 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 315 calls 0.304 user 0.008 sys 0.383 real
active: 19646 calls 0.000 user 0.000 sys 0.013 real
advance: 10022 calls 2.316 user 0.096 sys 2.991 real
annotate: 358 calls 0.022 user 0.000 sys 0.026 real
assemble_region: 315 calls 0.819 user 0.013 sys 1.105 real
build_variants: 312 calls 0.000 user 0.000 sys 0.001 real
calc: 19646 calls 0.239 user 0.001 sys 0.304 real
calc_region: 312 calls 3.839 user 0.029 sys 4.179 real
call_region: 312 calls 0.032 user 0.000 sys 0.049 real
clip_region: 627 calls 0.004 user 0.000 sys 0.063 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.009 user 0.001 sys 1.257 real
fetch: 19646 calls 0.178 user 0.012 sys 0.139 real
fetch_db: 312 calls 0.010 user 0.013 sys 0.081 real
fetch_ref: 19961 calls 0.027 user 0.001 sys 0.072 real
fetch_region: 315 calls 0.030 user 0.000 sys 0.014 real
idle: 39 calls 0.021 user 0.005 sys 13.158 real
init: 1 calls 0.039 user 0.001 sys 0.041 real
pairhmm: 1809 calls 6.359 user 0.048 sys 7.003 real
realign: 598 calls 0.397 user 0.002 sys 0.519 real
region: 19646 calls 6.299 user 0.097 sys 6.352 real
tracker: 19646 calls 0.013 user 0.000 sys 0.023 real
trim_region: 315 calls 0.000 user 0.000 sys 0.004 real
overall: 275517440 mem 12.652 user 1.039 sys 2.367 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory