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% @chr19:49149547, elapsed 0.0s, est remaining 0.2s, peak mem 70MB, user 0.0s, sys 0.0s, output queue size 473
progress 10% @chr19:50657989, elapsed 0.0s, est remaining 0.2s, peak mem 70MB, user 0.0s, sys 0.0s, output queue size 1064
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.1s, peak mem 73MB, user 0.0s, sys 0.1s, output queue size 1429
progress 20% @chr19:54804793, elapsed 0.0s, est remaining 0.1s, peak mem 75MB, user 0.0s, sys 0.1s, output queue size 249
progress 25% @chr19:56221575, elapsed 0.0s, est remaining 0.1s, peak mem 78MB, user 0.0s, sys 0.1s, output queue size 691
progress 30% @chr19:58212161, elapsed 0.0s, est remaining 0.1s, peak mem 78MB, user 0.0s, sys 0.1s, output queue size 936
progress 35% @chr21:29342399, elapsed 0.1s, est remaining 0.2s, peak mem 102MB, user 0.5s, sys 0.2s, output queue size 83
progress 40% @chr21:36245048, elapsed 0.3s, est remaining 0.4s, peak mem 151MB, user 1.6s, sys 0.2s, output queue size 109
progress 45% @chr21:41990895, elapsed 0.9s, est remaining 1.2s, peak mem 286MB, user 6.9s, sys 0.3s, output queue size 130
progress 50% @chr21:45525817, elapsed 1.1s, est remaining 1.1s, peak mem 289MB, user 9.2s, sys 0.4s, output queue size 115
progress 55% @chr22:19444265, elapsed 1.1s, est remaining 0.9s, peak mem 292MB, user 9.9s, sys 0.4s, output queue size 319
progress 60% @chr22:22201834, elapsed 1.1s, est remaining 0.8s, peak mem 292MB, user 9.9s, sys 0.4s, output queue size 799
progress 65% @chr22:23883772, elapsed 1.1s, est remaining 0.6s, peak mem 292MB, user 9.9s, sys 0.4s, output queue size 1017
progress 70% @chr22:29288004, elapsed 1.2s, est remaining 0.5s, peak mem 292MB, user 9.9s, sys 0.4s, output queue size 1522
progress 75% @chr22:31833915, elapsed 1.2s, est remaining 0.4s, peak mem 292MB, user 9.9s, sys 0.4s, output queue size 2067
progress 80% @chr22:37933039, elapsed 1.2s, est remaining 0.3s, peak mem 292MB, user 9.9s, sys 0.5s, output queue size 2627
progress 85% @chr22:41257948, elapsed 1.2s, est remaining 0.2s, peak mem 292MB, user 9.9s, sys 0.5s, output queue size 355
progress 90% @chr22:46256561, elapsed 1.2s, est remaining 0.1s, peak mem 292MB, user 10.0s, sys 0.5s, output queue size 968
progress 95% @chr22:50720184, elapsed 1.2s, est remaining 0.1s, peak mem 292MB, user 10.0s, sys 0.6s, output queue size 1540
progress 100% @chr22:50061583, elapsed 1.2s, est remaining 0.0s, peak mem 292MB, user 10.0s, sys 0.6s, output queue size 2116
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: 71692773
output file size: 77724
reads: 1001089
contig: 9624 intervals 1921786 bases
"assemble": 315 calls 0.542 user 0.010 sys 0.703 real
"assemble_addRead": 315 calls 0.003 user 0.000 sys 0.034 real
"assemble_buildGraph": 650 calls 0.232 user 0.006 sys 0.346 real
"assemble_computecigar": 513 calls 0.297 user 0.016 sys 0.380 real
"assemble_kg_build_calcsize": 650 calls 0.100 user 0.003 sys 0.188 real
"assemble_kg_build_clear": 775 calls 0.009 user 0.000 sys 0.016 real
"assemble_kg_build_prepare": 1300 calls 0.136 user 0.001 sys 0.157 real
"assemble_kg_build_threading": 525 calls 0.128 user 0.003 sys 0.153 real
"assemble_kg_op1": 525 calls 0.029 user 0.001 sys 0.033 real
"assemble_kg_op2": 525 calls 0.007 user 0.000 sys 0.008 real
"assemble_kg_op3": 525 calls 0.000 user 0.000 sys 0.012 real
"assemble_sg_clean": 513 calls 0.036 user 0.000 sys 0.041 real
"assemble_sg_create": 513 calls 0.043 user 0.002 sys 0.054 real
"checkGraph": 315 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 315 calls 0.302 user 0.016 sys 0.399 real
active: 19646 calls 0.013 user 0.000 sys 0.014 real
advance: 10022 calls 2.441 user 0.118 sys 3.102 real
annotate: 358 calls 0.039 user 0.002 sys 0.026 real
assemble_region: 315 calls 0.848 user 0.027 sys 1.140 real
build_variants: 312 calls 0.000 user 0.000 sys 0.001 real
calc: 19646 calls 0.240 user 0.005 sys 0.311 real
calc_region: 312 calls 4.206 user 0.021 sys 4.518 real
call_region: 312 calls 0.081 user 0.002 sys 0.051 real
clip_region: 627 calls 0.060 user 0.000 sys 0.063 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.005 user 0.003 sys 1.261 real
fetch: 19646 calls 0.087 user 0.003 sys 0.140 real
fetch_db: 312 calls 0.007 user 0.004 sys 0.083 real
fetch_ref: 19961 calls 0.021 user 0.006 sys 0.077 real
fetch_region: 315 calls 0.003 user 0.000 sys 0.017 real
idle: 39 calls 0.018 user 0.022 sys 13.143 real
init: 1 calls 0.038 user 0.002 sys 0.043 real
pairhmm: 1803 calls 6.297 user 0.025 sys 7.056 real
realign: 598 calls 0.551 user 0.001 sys 0.524 real
region: 19646 calls 6.760 user 0.092 sys 6.792 real
tracker: 19646 calls 0.011 user 0.001 sys 0.025 real
trim_region: 315 calls 0.012 user 0.000 sys 0.004 real
overall: 306479104 mem 12.827 user 1.057 sys 2.379 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory