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% @chr19:49142804, elapsed 0.0s, est remaining 0.4s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 50
progress 10% @chr19:50625393, elapsed 0.0s, est remaining 0.3s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 643
progress 15% @chr19:52553107, elapsed 0.1s, est remaining 0.3s, peak mem 72MB, user 0.0s, sys 0.3s, output queue size 1005
progress 20% @chr19:54829928, elapsed 0.1s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.3s, output queue size 1401
progress 25% @chr19:56383863, elapsed 0.1s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.3s, output queue size 1850
progress 30% @chr19:58338254, elapsed 0.1s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.4s, output queue size 2083
progress 35% @chr21:29342399, elapsed 0.2s, est remaining 0.3s, peak mem 90MB, user 0.4s, sys 0.5s, output queue size 355
progress 40% @chr21:36460976, elapsed 0.3s, est remaining 0.5s, peak mem 141MB, user 1.3s, sys 0.7s, output queue size 105
progress 45% @chr21:42413410, elapsed 0.9s, est remaining 1.1s, peak mem 243MB, user 6.6s, sys 0.8s, output queue size 121
progress 50% @chr21:45525817, elapsed 1.1s, est remaining 1.1s, peak mem 249MB, user 8.6s, sys 0.8s, output queue size 115
progress 55% @chr22:19494507, elapsed 1.2s, est remaining 1.0s, peak mem 252MB, user 9.3s, sys 0.9s, output queue size 339
progress 60% @chr22:22195903, elapsed 1.2s, est remaining 0.8s, peak mem 252MB, user 9.3s, sys 0.9s, output queue size 801
progress 65% @chr22:23868481, elapsed 1.2s, est remaining 0.7s, peak mem 252MB, user 9.3s, sys 1.0s, output queue size 1016
progress 70% @chr22:29288004, elapsed 1.2s, est remaining 0.5s, peak mem 252MB, user 9.3s, sys 1.1s, output queue size 1524
progress 75% @chr22:31814992, elapsed 1.2s, est remaining 0.4s, peak mem 252MB, user 9.3s, sys 1.1s, output queue size 2065
progress 80% @chr22:37970687, elapsed 1.3s, est remaining 0.3s, peak mem 252MB, user 9.4s, sys 1.2s, output queue size 2635
progress 85% @chr22:41249330, elapsed 1.3s, est remaining 0.2s, peak mem 252MB, user 9.4s, sys 1.3s, output queue size 34
progress 90% @chr22:46256561, elapsed 1.3s, est remaining 0.1s, peak mem 252MB, user 9.4s, sys 1.4s, output queue size 643
progress 95% @chr22:50730721, elapsed 1.3s, est remaining 0.1s, peak mem 252MB, user 9.4s, sys 1.5s, output queue size 1236
progress 100% @chrY:630898, elapsed 1.3s, est remaining 0.0s, peak mem 252MB, user 9.4s, sys 1.5s, output queue size 1796
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692759
output file size: 77724
reads: 1001089
contig: 9624 intervals 1921786 bases
"assemble": 315 calls 0.495 user 0.037 sys 0.719 real
"assemble_addRead": 315 calls 0.020 user 0.000 sys 0.046 real
"assemble_buildGraph": 650 calls 0.246 user 0.012 sys 0.347 real
"assemble_computecigar": 513 calls 0.288 user 0.006 sys 0.382 real
"assemble_kg_build_calcsize": 650 calls 0.166 user 0.001 sys 0.186 real
"assemble_kg_build_clear": 775 calls 0.032 user 0.000 sys 0.017 real
"assemble_kg_build_prepare": 1300 calls 0.107 user 0.012 sys 0.167 real
"assemble_kg_build_threading": 525 calls 0.073 user 0.011 sys 0.156 real
"assemble_kg_op1": 525 calls 0.028 user 0.002 sys 0.035 real
"assemble_kg_op2": 525 calls 0.001 user 0.000 sys 0.009 real
"assemble_kg_op3": 525 calls 0.004 user 0.000 sys 0.012 real
"assemble_sg_clean": 513 calls 0.023 user 0.000 sys 0.042 real
"assemble_sg_create": 513 calls 0.046 user 0.009 sys 0.054 real
"checkGraph": 315 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 315 calls 0.298 user 0.006 sys 0.402 real
active: 19646 calls 0.008 user 0.010 sys 0.014 real
advance: 10022 calls 2.240 user 0.131 sys 3.062 real
annotate: 358 calls 0.013 user 0.000 sys 0.029 real
assemble_region: 315 calls 0.813 user 0.043 sys 1.172 real
build_variants: 312 calls 0.000 user 0.000 sys 0.002 real
calc: 19646 calls 0.133 user 0.002 sys 0.296 real
calc_region: 312 calls 3.706 user 0.071 sys 4.127 real
call_region: 312 calls 0.014 user 0.001 sys 0.056 real
clip_region: 627 calls 0.025 user 0.002 sys 0.071 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.001 user 0.000 sys 1.395 real
fetch: 19646 calls 0.214 user 0.013 sys 0.154 real
fetch_db: 312 calls 0.022 user 0.000 sys 0.083 real
fetch_ref: 19961 calls 0.021 user 0.015 sys 0.093 real
fetch_region: 315 calls 0.019 user 0.000 sys 0.014 real
idle: 39 calls 0.009 user 0.013 sys 13.286 real
init: 1 calls 0.039 user 0.001 sys 0.042 real
pairhmm: 1803 calls 6.655 user 0.072 sys 7.028 real
realign: 598 calls 0.378 user 0.011 sys 0.530 real
region: 19646 calls 6.295 user 0.223 sys 6.546 real
tracker: 19646 calls 0.006 user 0.001 sys 0.025 real
trim_region: 315 calls 0.000 user 0.000 sys 0.004 real
overall: 264376320 mem 12.500 user 2.221 sys 2.513 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory