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% @chr19:49134639, elapsed 0.0s, est remaining 0.5s, peak mem 70MB, user 0.0s, sys 0.0s, output queue size 450
progress 10% @chr19:50632286, elapsed 0.0s, est remaining 0.4s, peak mem 70MB, user 0.1s, sys 0.0s, output queue size 522
progress 15% @chr19:52553107, elapsed 0.1s, est remaining 0.3s, peak mem 70MB, user 0.1s, sys 0.0s, output queue size 887
progress 20% @chr19:54813690, elapsed 0.1s, est remaining 0.3s, peak mem 70MB, user 0.1s, sys 0.0s, output queue size 1273
progress 25% @chr19:56221575, elapsed 0.1s, est remaining 0.2s, peak mem 70MB, user 0.1s, sys 0.0s, output queue size 1712
progress 30% @chr19:58260851, elapsed 0.1s, est remaining 0.2s, peak mem 72MB, user 0.1s, sys 0.0s, output queue size 1959
progress 35% @chr21:30425394, elapsed 0.2s, est remaining 0.3s, peak mem 108MB, user 0.8s, sys 0.2s, output queue size 82
progress 40% @chr21:36723045, elapsed 0.4s, est remaining 0.5s, peak mem 156MB, user 2.0s, sys 0.2s, output queue size 107
progress 45% @chr21:42447057, elapsed 1.2s, est remaining 1.5s, peak mem 276MB, user 9.8s, sys 0.3s, output queue size 128
progress 50% @chr21:45505358, elapsed 1.5s, est remaining 1.5s, peak mem 283MB, user 12.9s, sys 0.5s, output queue size 8
progress 55% @chr22:19433265, elapsed 1.6s, est remaining 1.3s, peak mem 283MB, user 13.4s, sys 0.5s, output queue size 373
progress 60% @chr22:22201834, elapsed 1.6s, est remaining 1.1s, peak mem 283MB, user 13.5s, sys 0.5s, output queue size 344
progress 65% @chr22:23882459, elapsed 1.6s, est remaining 0.9s, peak mem 283MB, user 13.5s, sys 0.5s, output queue size 561
progress 70% @chr22:29288004, elapsed 1.6s, est remaining 0.7s, peak mem 283MB, user 13.5s, sys 0.6s, output queue size 1065
progress 75% @chr22:31845018, elapsed 1.6s, est remaining 0.5s, peak mem 283MB, user 13.5s, sys 0.6s, output queue size 1615
progress 80% @chr22:37940709, elapsed 1.6s, est remaining 0.4s, peak mem 283MB, user 13.5s, sys 0.6s, output queue size 2172
progress 85% @chr22:41357177, elapsed 1.7s, est remaining 0.3s, peak mem 283MB, user 13.5s, sys 0.6s, output queue size 2721
progress 90% @chr22:41154977, elapsed 1.7s, est remaining 0.2s, peak mem 283MB, user 13.5s, sys 0.7s, output queue size 3316
progress 95% @chr22:50720184, elapsed 1.7s, est remaining 0.1s, peak mem 283MB, user 13.5s, sys 0.7s, output queue size 3882
progress 100% @chrY:19735352, elapsed 1.7s, est remaining 0.0s, peak mem 283MB, user 13.5s, sys 0.8s, output queue size 4455
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 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74586806
output file size: 79931
reads: 1001133
contig: 9624 intervals 1921786 bases
"assemble": 324 calls 0.683 user 0.030 sys 0.876 real
"assemble_addRead": 324 calls 0.002 user 0.000 sys 0.043 real
"assemble_buildGraph": 688 calls 0.345 user 0.001 sys 0.442 real
"assemble_computecigar": 523 calls 0.312 user 0.015 sys 0.414 real
"assemble_kg_build_calcsize": 688 calls 0.209 user 0.000 sys 0.249 real
"assemble_kg_build_clear": 826 calls 0.001 user 0.000 sys 0.022 real
"assemble_kg_build_prepare": 1376 calls 0.143 user 0.015 sys 0.204 real
"assemble_kg_build_threading": 550 calls 0.134 user 0.000 sys 0.187 real
"assemble_kg_op1": 550 calls 0.028 user 0.000 sys 0.037 real
"assemble_kg_op2": 550 calls 0.002 user 0.000 sys 0.010 real
"assemble_kg_op3": 550 calls 0.000 user 0.000 sys 0.012 real
"assemble_sg_clean": 523 calls 0.031 user 0.000 sys 0.045 real
"assemble_sg_create": 523 calls 0.066 user 0.004 sys 0.059 real
"checkGraph": 324 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 324 calls 0.341 user 0.015 sys 0.434 real
active: 19646 calls 0.001 user 0.000 sys 0.017 real
advance: 10022 calls 2.542 user 0.124 sys 3.267 real
annotate: 394 calls 0.013 user 0.000 sys 0.036 real
assemble_region: 324 calls 1.025 user 0.045 sys 1.357 real
build_variants: 322 calls 0.000 user 0.000 sys 0.002 real
calc: 19646 calls 0.142 user 0.020 sys 0.368 real
calc_region: 322 calls 6.326 user 0.126 sys 6.777 real
call_region: 322 calls 0.026 user 0.000 sys 0.068 real
clip_region: 646 calls 0.054 user 0.000 sys 0.088 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.001 user 0.000 sys 1.745 real
fetch: 19646 calls 0.116 user 0.016 sys 0.188 real
fetch_db: 322 calls 0.011 user 0.000 sys 0.092 real
fetch_ref: 19970 calls 0.016 user 0.004 sys 0.080 real
fetch_region: 324 calls 0.032 user 0.000 sys 0.021 real
idle: 39 calls 0.002 user 0.001 sys 13.132 real
init: 1 calls 0.035 user 0.000 sys 0.045 real
pairhmm: 2270 calls 10.785 user 0.135 sys 11.359 real
realign: 697 calls 0.554 user 0.000 sys 0.756 real
region: 19646 calls 10.145 user 0.193 sys 10.351 real
tracker: 19646 calls 0.003 user 0.000 sys 0.027 real
trim_region: 324 calls 0.022 user 0.000 sys 0.005 real
overall: 297197568 mem 17.789 user 1.236 sys 2.863 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory