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% @chr19:49152310, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 262
progress 10% @chr19:50625393, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 842
progress 15% @chr19:52704937, elapsed 0.0s, est remaining 0.1s, peak mem 75MB, user 0.1s, sys 0.0s, output queue size 1209
progress 20% @chr19:54889649, elapsed 0.0s, est remaining 0.1s, peak mem 78MB, user 0.1s, sys 0.0s, output queue size 1624
progress 25% @chr19:56422891, elapsed 0.0s, est remaining 0.1s, peak mem 78MB, user 0.1s, sys 0.0s, output queue size 2060
progress 30% @chr19:58212161, elapsed 0.0s, est remaining 0.1s, peak mem 81MB, user 0.1s, sys 0.1s, output queue size 2278
progress 35% @chr21:29342399, elapsed 0.1s, est remaining 0.2s, peak mem 106MB, user 0.5s, sys 0.2s, output queue size 83
progress 40% @chr21:36743387, elapsed 0.3s, est remaining 0.4s, peak mem 154MB, user 1.4s, sys 0.2s, output queue size 114
progress 45% @chr21:42395324, elapsed 0.9s, est remaining 1.1s, peak mem 263MB, user 6.7s, sys 0.3s, output queue size 113
progress 50% @chr21:45525817, elapsed 1.0s, est remaining 1.0s, peak mem 270MB, user 8.6s, sys 0.3s, output queue size 116
progress 55% @chr22:19447665, elapsed 1.1s, est remaining 0.9s, peak mem 270MB, user 9.3s, sys 0.3s, output queue size 372
progress 60% @chr22:22214908, elapsed 1.1s, est remaining 0.7s, peak mem 270MB, user 9.3s, sys 0.3s, output queue size 850
progress 65% @chr22:23884623, elapsed 1.1s, est remaining 0.6s, peak mem 270MB, user 9.3s, sys 0.3s, output queue size 1069
progress 70% @chr22:29288004, elapsed 1.1s, est remaining 0.5s, peak mem 270MB, user 9.3s, sys 0.4s, output queue size 1574
progress 75% @chr22:31838685, elapsed 1.1s, est remaining 0.4s, peak mem 270MB, user 9.4s, sys 0.4s, output queue size 2114
progress 80% @chr22:37945042, elapsed 1.2s, est remaining 0.3s, peak mem 270MB, user 9.4s, sys 0.4s, output queue size 606
progress 85% @chr22:41274600, elapsed 1.2s, est remaining 0.2s, peak mem 270MB, user 9.4s, sys 0.4s, output queue size 1128
progress 90% @chr22:46256561, elapsed 1.2s, est remaining 0.1s, peak mem 270MB, user 9.4s, sys 0.4s, output queue size 1734
progress 95% @chr22:50720184, elapsed 1.2s, est remaining 0.1s, peak mem 270MB, user 9.4s, sys 0.4s, output queue size 2308
progress 100% @chr6_GL000254v2_alt:3891538, elapsed 1.2s, est remaining 0.0s, peak mem 270MB, user 9.4s, sys 0.5s, output queue size 2884
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 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692764
output file size: 77724
reads: 1001089
contig: 9624 intervals 1921786 bases
"assemble": 315 calls 0.470 user 0.017 sys 0.682 real
"assemble_addRead": 315 calls 0.010 user 0.000 sys 0.031 real
"assemble_buildGraph": 650 calls 0.181 user 0.011 sys 0.338 real
"assemble_computecigar": 513 calls 0.324 user 0.003 sys 0.372 real
"assemble_kg_build_calcsize": 650 calls 0.098 user 0.000 sys 0.185 real
"assemble_kg_build_clear": 775 calls 0.028 user 0.003 sys 0.015 real
"assemble_kg_build_prepare": 1300 calls 0.131 user 0.002 sys 0.150 real
"assemble_kg_build_threading": 525 calls 0.077 user 0.011 sys 0.149 real
"assemble_kg_op1": 525 calls 0.018 user 0.000 sys 0.032 real
"assemble_kg_op2": 525 calls 0.011 user 0.000 sys 0.008 real
"assemble_kg_op3": 525 calls 0.010 user 0.000 sys 0.011 real
"assemble_sg_clean": 513 calls 0.024 user 0.000 sys 0.040 real
"assemble_sg_create": 513 calls 0.030 user 0.001 sys 0.053 real
"checkGraph": 315 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 315 calls 0.349 user 0.003 sys 0.392 real
active: 19646 calls 0.005 user 0.000 sys 0.013 real
advance: 10022 calls 2.352 user 0.122 sys 3.044 real
annotate: 358 calls 0.029 user 0.000 sys 0.025 real
assemble_region: 315 calls 0.838 user 0.020 sys 1.108 real
build_variants: 312 calls 0.000 user 0.000 sys 0.001 real
calc: 19646 calls 0.150 user 0.001 sys 0.294 real
calc_region: 312 calls 3.932 user 0.038 sys 4.316 real
call_region: 312 calls 0.039 user 0.000 sys 0.048 real
clip_region: 627 calls 0.029 user 0.000 sys 0.062 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.002 user 0.001 sys 1.258 real
fetch: 19646 calls 0.090 user 0.009 sys 0.133 real
fetch_db: 312 calls 0.018 user 0.000 sys 0.080 real
fetch_ref: 19961 calls 0.003 user 0.001 sys 0.073 real
fetch_region: 315 calls 0.010 user 0.000 sys 0.013 real
idle: 39 calls 0.014 user 0.021 sys 13.164 real
init: 1 calls 0.030 user 0.010 sys 0.040 real
pairhmm: 1803 calls 6.473 user 0.032 sys 6.956 real
realign: 598 calls 0.297 user 0.000 sys 0.517 real
region: 19646 calls 6.275 user 0.091 sys 6.274 real
tracker: 19646 calls 0.019 user 0.007 sys 0.023 real
trim_region: 315 calls 0.000 user 0.000 sys 0.004 real
overall: 283959296 mem 12.707 user 0.783 sys 2.372 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory