cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr14_64122012-64122133.bed.gz -i 659_bTo-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant 659_bTo-N1-BDNA-1_B23KFG5LT4_1.haplotyper.chr14_64122012-64122133.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr14:95086229, elapsed 3.0s, est remaining 57.2s, peak mem 566MB, user 20.1s, sys 0.4s, output queue size 365
progress 10% @chr15:40934548, elapsed 17.4s, est remaining 156.5s, peak mem 1052MB, user 153.2s, sys 1.3s, output queue size 64
progress 15% @chr15:63939232, elapsed 20.5s, est remaining 116.2s, peak mem 1150MB, user 175.4s, sys 1.6s, output queue size 13
progress 20% @chr15:88039211, elapsed 27.8s, est remaining 111.3s, peak mem 1782MB, user 218.4s, sys 1.9s, output queue size 23
progress 25% @chr16:1953956, elapsed 40.6s, est remaining 121.8s, peak mem 1906MB, user 360.9s, sys 3.0s, output queue size 26
progress 30% @chr16:23494303, elapsed 46.4s, est remaining 108.3s, peak mem 1906MB, user 404.0s, sys 3.4s, output queue size 51
progress 35% @chr16:66608309, elapsed 49.3s, est remaining 91.6s, peak mem 1906MB, user 428.1s, sys 3.9s, output queue size 57
progress 40% @chr16:89226694, elapsed 55.1s, est remaining 82.6s, peak mem 1906MB, user 469.2s, sys 4.2s, output queue size 13
progress 45% @chr17:10198208, elapsed 60.2s, est remaining 73.6s, peak mem 1906MB, user 511.2s, sys 4.6s, output queue size 31
progress 50% @chr17:36195798, elapsed 65.4s, est remaining 65.4s, peak mem 1906MB, user 547.7s, sys 5.0s, output queue size 25
progress 55% @chr17:45104859, elapsed 73.7s, est remaining 60.3s, peak mem 1906MB, user 617.3s, sys 5.5s, output queue size 17
progress 60% @chr17:68420189, elapsed 77.7s, est remaining 51.8s, peak mem 1906MB, user 645.6s, sys 5.9s, output queue size 33
progress 65% @chr18:6215750, elapsed 83.1s, est remaining 44.8s, peak mem 1906MB, user 681.2s, sys 6.2s, output queue size 29
progress 70% @chr18:62368701, elapsed 88.6s, est remaining 38.0s, peak mem 1906MB, user 724.6s, sys 6.6s, output queue size 111
progress 75% @chr19:6921713, elapsed 95.7s, est remaining 31.9s, peak mem 1906MB, user 772.3s, sys 7.1s, output queue size 13
progress 80% @chr19:8945497, elapsed 106.4s, est remaining 26.6s, peak mem 1906MB, user 840.9s, sys 7.6s, output queue size 1683
progress 85% @chr19:37127128, elapsed 108.9s, est remaining 19.2s, peak mem 1906MB, user 862.7s, sys 7.9s, output queue size 44
progress 90% @chr19:46493558, elapsed 112.4s, est remaining 12.5s, peak mem 1906MB, user 892.1s, sys 8.2s, output queue size 29
progress 95% @chr20:36919328, elapsed 115.0s, est remaining 6.1s, peak mem 1906MB, user 912.1s, sys 8.6s, output queue size 12
progress 100% @chr20:63698643, elapsed 119.4s, est remaining 0.0s, peak mem 1906MB, user 943.3s, sys 9.1s, output queue size 155
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: 26295681376
output file size: 1135193
reads: 312450139
contig: 48152 intervals 9000028 bases
"assemble": 6206 calls 30.365 user 0.240 sys 36.708 real
"assemble_addRead": 6206 calls 1.702 user 0.087 sys 2.190 real
"assemble_buildGraph": 13005 calls 16.948 user 0.066 sys 20.178 real
"assemble_computecigar": 10043 calls 9.705 user 0.065 sys 10.659 real
"assemble_kg_build_calcsize": 13005 calls 9.983 user 0.027 sys 11.981 real
"assemble_kg_build_clear": 15280 calls 1.334 user 0.010 sys 1.429 real
"assemble_kg_build_prepare": 26010 calls 7.789 user 0.145 sys 9.281 real
"assemble_kg_build_threading": 10730 calls 6.537 user 0.029 sys 7.796 real
"assemble_kg_op1": 10730 calls 0.728 user 0.010 sys 1.131 real
"assemble_kg_op2": 10730 calls 0.351 user 0.000 sys 0.333 real
"assemble_kg_op3": 10730 calls 0.192 user 0.000 sys 0.312 real
"assemble_sg_clean": 10043 calls 1.059 user 0.000 sys 1.354 real
"assemble_sg_create": 10043 calls 1.189 user 0.000 sys 1.445 real
"checkGraph": 6206 calls 0.000 user 0.000 sys 0.032 real
"findHaplotype": 6206 calls 10.375 user 0.065 sys 11.558 real
active: 97912 calls 0.394 user 0.010 sys 0.425 real
advance: 49760 calls 308.245 user 5.546 sys 322.407 real
annotate: 7275 calls 0.981 user 0.003 sys 1.527 real
assemble_region: 6206 calls 42.506 user 0.401 sys 50.556 real
build_variants: 6147 calls 0.067 user 0.000 sys 0.085 real
calc: 97912 calls 29.056 user 0.065 sys 31.745 real
calc_region: 6147 calls 392.879 user 0.457 sys 402.040 real
call_region: 6147 calls 3.812 user 0.003 sys 5.172 real
clip_region: 12353 calls 3.864 user 0.058 sys 4.719 real
done: 1 calls 0.007 user 0.000 sys 0.007 real
execute: 1 calls 0.000 user 0.011 sys 119.434 real
fetch: 97912 calls 20.943 user 0.265 sys 21.667 real
fetch_db: 6147 calls 2.976 user 0.116 sys 2.530 real
fetch_ref: 104118 calls 3.605 user 0.184 sys 0.788 real
fetch_region: 6206 calls 2.057 user 0.000 sys 2.171 real
idle: 114 calls 0.371 user 0.000 sys 12.989 real
init: 1 calls 0.026 user 0.019 sys 0.048 real
pairhmm: 163716 calls 908.477 user 0.260 sys 923.883 real
realign: 27341 calls 36.548 user 0.030 sys 44.603 real
region: 97912 calls 574.980 user 0.980 sys 580.636 real
tracker: 97912 calls 0.521 user 0.026 sys 0.575 real
trim_region: 6206 calls 0.123 user 0.000 sys 0.139 real
overall: 1999364096 mem 1409.546 user 10.329 sys 120.695 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory