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% @chr19:49136724, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 374
progress 10% @chr19:50625897, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 972
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 1344
progress 20% @chr19:54813842, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 1724
progress 25% @chr19:56221575, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 2162
progress 30% @chr19:58242206, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 2404
progress 35% @chr21:30282168, elapsed 0.1s, est remaining 0.2s, peak mem 108MB, user 0.8s, sys 0.1s, output queue size 83
progress 40% @chr21:36460976, elapsed 0.3s, est remaining 0.4s, peak mem 156MB, user 1.7s, sys 0.2s, output queue size 107
progress 45% @chr21:42388403, elapsed 1.2s, est remaining 1.5s, peak mem 285MB, user 10.0s, sys 0.2s, output queue size 113
progress 50% @chr21:45514976, elapsed 1.5s, est remaining 1.5s, peak mem 300MB, user 12.8s, sys 0.3s, output queue size 5
progress 55% @chr22:19435638, elapsed 1.5s, est remaining 1.3s, peak mem 300MB, user 13.3s, sys 0.3s, output queue size 380
progress 60% @chr22:22195903, elapsed 1.5s, est remaining 1.0s, peak mem 300MB, user 13.4s, sys 0.4s, output queue size 859
progress 65% @chr22:23883772, elapsed 1.5s, est remaining 0.8s, peak mem 300MB, user 13.4s, sys 0.4s, output queue size 1077
progress 70% @chr22:29288004, elapsed 1.6s, est remaining 0.7s, peak mem 300MB, user 13.4s, sys 0.4s, output queue size 1586
progress 75% @chr22:31814992, elapsed 1.6s, est remaining 0.5s, peak mem 300MB, user 13.4s, sys 0.4s, output queue size 2127
progress 80% @chr22:37959346, elapsed 1.6s, est remaining 0.4s, peak mem 300MB, user 13.4s, sys 0.6s, output queue size 2692
progress 85% @chr22:41240874, elapsed 1.6s, est remaining 0.3s, peak mem 300MB, user 13.4s, sys 0.6s, output queue size 511
progress 90% @chr22:46256561, elapsed 1.6s, est remaining 0.2s, peak mem 300MB, user 13.4s, sys 0.6s, output queue size 1117
progress 95% @chr22:50720184, elapsed 1.6s, est remaining 0.1s, peak mem 300MB, user 13.5s, sys 0.7s, output queue size 1702
progress 100% @chrY:23248763, elapsed 1.7s, est remaining 0.0s, peak mem 300MB, user 13.5s, sys 0.8s, output queue size 2274
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 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74586799
output file size: 79931
reads: 1001133
contig: 9624 intervals 1921786 bases
"assemble": 324 calls 0.768 user 0.001 sys 0.811 real
"assemble_addRead": 324 calls 0.028 user 0.000 sys 0.038 real
"assemble_buildGraph": 688 calls 0.391 user 0.000 sys 0.408 real
"assemble_computecigar": 523 calls 0.255 user 0.000 sys 0.386 real
"assemble_kg_build_calcsize": 688 calls 0.195 user 0.000 sys 0.229 real
"assemble_kg_build_clear": 826 calls 0.012 user 0.000 sys 0.019 real
"assemble_kg_build_prepare": 1376 calls 0.216 user 0.000 sys 0.190 real
"assemble_kg_build_threading": 550 calls 0.196 user 0.000 sys 0.174 real
"assemble_kg_op1": 550 calls 0.033 user 0.000 sys 0.035 real
"assemble_kg_op2": 550 calls 0.010 user 0.000 sys 0.010 real
"assemble_kg_op3": 550 calls 0.011 user 0.000 sys 0.012 real
"assemble_sg_clean": 523 calls 0.018 user 0.000 sys 0.041 real
"assemble_sg_create": 523 calls 0.025 user 0.001 sys 0.054 real
"checkGraph": 324 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 324 calls 0.262 user 0.000 sys 0.405 real
active: 19646 calls 0.002 user 0.000 sys 0.015 real
advance: 10022 calls 2.389 user 0.081 sys 3.079 real
annotate: 394 calls 0.008 user 0.000 sys 0.032 real
assemble_region: 324 calls 1.071 user 0.001 sys 1.258 real
build_variants: 322 calls 0.000 user 0.000 sys 0.002 real
calc: 19646 calls 0.254 user 0.004 sys 0.309 real
calc_region: 322 calls 6.473 user 0.002 sys 6.749 real
call_region: 322 calls 0.030 user 0.000 sys 0.060 real
clip_region: 646 calls 0.055 user 0.000 sys 0.078 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.005 sys 1.776 real
fetch: 19646 calls 0.212 user 0.024 sys 0.150 real
fetch_db: 322 calls 0.040 user 0.000 sys 0.085 real
fetch_ref: 19970 calls 0.011 user 0.032 sys 0.079 real
fetch_region: 324 calls 0.010 user 0.000 sys 0.017 real
idle: 41 calls 0.005 user 0.006 sys 13.799 real
init: 1 calls 0.005 user 0.035 sys 0.042 real
pairhmm: 2270 calls 10.176 user 0.000 sys 10.853 real
realign: 697 calls 0.443 user 0.000 sys 0.719 real
region: 19646 calls 10.048 user 0.025 sys 10.002 real
tracker: 19646 calls 0.016 user 0.004 sys 0.023 real
trim_region: 324 calls 0.001 user 0.000 sys 0.004 real
overall: 314707968 mem 16.961 user 1.335 sys 2.889 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory