cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr19_47340800-47341813.bed.gz -i Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_2.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr19:49133796, elapsed 0.0s, est remaining 0.3s, peak mem 66MB, user 0.0s, sys 0.0s, output queue size 476
progress 10% @chr19:50629784, elapsed 0.0s, est remaining 0.3s, peak mem 66MB, user 0.0s, sys 0.1s, output queue size 549
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.2s, peak mem 66MB, user 0.0s, sys 0.1s, output queue size 921
progress 20% @chr19:54813842, elapsed 0.1s, est remaining 0.2s, peak mem 66MB, user 0.0s, sys 0.2s, output queue size 1302
progress 25% @chr19:56221575, elapsed 0.1s, est remaining 0.2s, peak mem 66MB, user 0.0s, sys 0.2s, output queue size 1738
progress 30% @chr19:58212161, elapsed 0.1s, est remaining 0.2s, peak mem 66MB, user 0.0s, sys 0.2s, output queue size 1985
progress 35% @chr21:30319403, elapsed 0.2s, est remaining 0.3s, peak mem 99MB, user 0.8s, sys 0.4s, output queue size 82
progress 40% @chr21:36460976, elapsed 0.3s, est remaining 0.5s, peak mem 147MB, user 1.8s, sys 0.4s, output queue size 106
progress 45% @chr21:42383033, elapsed 1.2s, est remaining 1.5s, peak mem 258MB, user 9.5s, sys 0.5s, output queue size 112
progress 50% @chr21:45514976, elapsed 1.5s, est remaining 1.5s, peak mem 267MB, user 12.1s, sys 0.5s, output queue size 3
progress 55% @chr22:19435638, elapsed 1.6s, est remaining 1.3s, peak mem 267MB, user 12.7s, sys 0.6s, output queue size 236
progress 60% @chr22:22162280, elapsed 1.6s, est remaining 1.1s, peak mem 267MB, user 12.7s, sys 0.6s, output queue size 721
progress 65% @chr22:23875117, elapsed 1.6s, est remaining 0.9s, peak mem 267MB, user 12.7s, sys 0.6s, output queue size 935
progress 70% @chr22:29294124, elapsed 1.6s, est remaining 0.7s, peak mem 267MB, user 12.8s, sys 0.7s, output queue size 1441
progress 75% @chr22:31838685, elapsed 1.6s, est remaining 0.5s, peak mem 267MB, user 12.8s, sys 0.8s, output queue size 622
progress 80% @chr22:37937080, elapsed 1.7s, est remaining 0.4s, peak mem 267MB, user 12.8s, sys 0.8s, output queue size 1185
progress 85% @chr22:41254308, elapsed 1.7s, est remaining 0.3s, peak mem 267MB, user 12.8s, sys 0.9s, output queue size 1703
progress 90% @chr22:46256561, elapsed 1.7s, est remaining 0.2s, peak mem 267MB, user 12.8s, sys 1.0s, output queue size 2323
progress 95% @chrY:312766, elapsed 1.7s, est remaining 0.1s, peak mem 267MB, user 12.8s, sys 1.1s, output queue size 2914
progress 100% @chrY:20592341, elapsed 1.7s, est remaining 0.0s, peak mem 267MB, user 12.8s, sys 1.1s, output queue size 3468
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 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74586797
output file size: 79932
reads: 1001133
contig: 9624 intervals 1921786 bases
"assemble": 324 calls 0.639 user 0.009 sys 0.890 real
"assemble_addRead": 324 calls 0.067 user 0.004 sys 0.053 real
"assemble_buildGraph": 688 calls 0.347 user 0.001 sys 0.441 real
"assemble_computecigar": 523 calls 0.355 user 0.009 sys 0.422 real
"assemble_kg_build_calcsize": 688 calls 0.199 user 0.000 sys 0.245 real
"assemble_kg_build_clear": 826 calls 0.011 user 0.000 sys 0.023 real
"assemble_kg_build_prepare": 1376 calls 0.149 user 0.006 sys 0.219 real
"assemble_kg_build_threading": 550 calls 0.147 user 0.001 sys 0.189 real
"assemble_kg_op1": 550 calls 0.020 user 0.001 sys 0.038 real
"assemble_kg_op2": 550 calls 0.000 user 0.000 sys 0.010 real
"assemble_kg_op3": 550 calls 0.014 user 0.000 sys 0.012 real
"assemble_sg_clean": 523 calls 0.023 user 0.000 sys 0.044 real
"assemble_sg_create": 523 calls 0.044 user 0.001 sys 0.058 real
"checkGraph": 324 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 324 calls 0.393 user 0.009 sys 0.443 real
active: 19646 calls 0.010 user 0.000 sys 0.015 real
advance: 10022 calls 2.438 user 0.093 sys 3.198 real
annotate: 394 calls 0.011 user 0.000 sys 0.038 real
assemble_region: 324 calls 1.110 user 0.023 sys 1.390 real
build_variants: 322 calls 0.000 user 0.000 sys 0.003 real
calc: 19646 calls 0.233 user 0.005 sys 0.344 real
calc_region: 322 calls 5.862 user 0.065 sys 6.279 real
call_region: 322 calls 0.035 user 0.000 sys 0.072 real
clip_region: 646 calls 0.109 user 0.007 sys 0.095 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.002 user 0.001 sys 1.813 real
fetch: 19646 calls 0.250 user 0.017 sys 0.204 real
fetch_db: 322 calls 0.038 user 0.007 sys 0.091 real
fetch_ref: 19970 calls 0.014 user 0.008 sys 0.090 real
fetch_region: 324 calls 0.017 user 0.000 sys 0.022 real
idle: 39 calls 0.005 user 0.006 sys 13.916 real
init: 1 calls 0.039 user 0.030 sys 0.066 real
pairhmm: 2270 calls 10.482 user 0.056 sys 11.138 real
realign: 697 calls 0.507 user 0.000 sys 0.743 real
region: 19646 calls 9.413 user 0.116 sys 9.577 real
tracker: 19646 calls 0.019 user 0.015 sys 0.028 real
trim_region: 324 calls 0.000 user 0.000 sys 0.005 real
overall: 280104960 mem 17.577 user 1.842 sys 2.976 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory