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% @chr19:49138205, elapsed 0.0s, est remaining 0.2s, peak mem 69MB, user 0.0s, sys 0.0s, output queue size 458
progress 10% @chr19:50625393, elapsed 0.0s, est remaining 0.2s, peak mem 69MB, user 0.0s, sys 0.0s, output queue size 1058
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.2s, peak mem 69MB, user 0.1s, sys 0.0s, output queue size 1089
progress 20% @chr19:54866522, elapsed 0.0s, est remaining 0.2s, peak mem 69MB, user 0.1s, sys 0.0s, output queue size 1501
progress 25% @chr19:56413959, elapsed 0.0s, est remaining 0.1s, peak mem 69MB, user 0.1s, sys 0.0s, output queue size 1941
progress 30% @chr19:58260851, elapsed 0.1s, est remaining 0.1s, peak mem 69MB, user 0.1s, sys 0.0s, output queue size 2160
progress 35% @chr21:30215248, elapsed 0.2s, est remaining 0.3s, peak mem 99MB, user 0.8s, sys 0.2s, output queue size 23
progress 40% @chr21:36719821, elapsed 0.4s, est remaining 0.5s, peak mem 132MB, user 1.6s, sys 0.3s, output queue size 107
progress 45% @chr21:41497133, elapsed 1.2s, est remaining 1.5s, peak mem 249MB, user 9.5s, sys 0.4s, output queue size 123
progress 50% @chr21:45497050, elapsed 1.5s, est remaining 1.5s, peak mem 258MB, user 12.2s, sys 0.4s, output queue size 66
progress 55% @chr22:19233166, elapsed 1.6s, est remaining 1.3s, peak mem 261MB, user 12.7s, sys 0.5s, output queue size 250
progress 60% @chr22:22162280, elapsed 1.6s, est remaining 1.1s, peak mem 261MB, user 12.7s, sys 0.5s, output queue size 732
progress 65% @chr22:23883772, elapsed 1.6s, est remaining 0.9s, peak mem 261MB, user 12.7s, sys 0.5s, output queue size 946
progress 70% @chr22:29288004, elapsed 1.6s, est remaining 0.7s, peak mem 261MB, user 12.8s, sys 0.5s, output queue size 1454
progress 75% @chr22:31845018, elapsed 1.6s, est remaining 0.5s, peak mem 261MB, user 12.8s, sys 0.5s, output queue size 305
progress 80% @chr22:37970687, elapsed 1.6s, est remaining 0.4s, peak mem 261MB, user 12.8s, sys 0.5s, output queue size 872
progress 85% @chr22:41264664, elapsed 1.6s, est remaining 0.3s, peak mem 261MB, user 12.8s, sys 0.6s, output queue size 1386
progress 90% @chr22:46256561, elapsed 1.7s, est remaining 0.2s, peak mem 261MB, user 12.8s, sys 0.6s, output queue size 2000
progress 95% @chr22:50730721, elapsed 1.7s, est remaining 0.1s, peak mem 261MB, user 12.8s, sys 0.6s, output queue size 2569
progress 100% @chrY:19715352, elapsed 1.7s, est remaining 0.0s, peak mem 261MB, user 12.8s, sys 0.6s, output queue size 3147
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: 74586810
output file size: 79931
reads: 1001133
contig: 9624 intervals 1921786 bases
"assemble": 324 calls 0.679 user 0.018 sys 0.879 real
"assemble_addRead": 324 calls 0.007 user 0.000 sys 0.044 real
"assemble_buildGraph": 688 calls 0.345 user 0.005 sys 0.440 real
"assemble_computecigar": 523 calls 0.343 user 0.022 sys 0.412 real
"assemble_kg_build_calcsize": 688 calls 0.195 user 0.000 sys 0.243 real
"assemble_kg_build_clear": 826 calls 0.046 user 0.000 sys 0.022 real
"assemble_kg_build_prepare": 1376 calls 0.220 user 0.008 sys 0.212 real
"assemble_kg_build_threading": 550 calls 0.133 user 0.005 sys 0.191 real
"assemble_kg_op1": 550 calls 0.033 user 0.000 sys 0.038 real
"assemble_kg_op2": 550 calls 0.000 user 0.000 sys 0.010 real
"assemble_kg_op3": 550 calls 0.012 user 0.000 sys 0.012 real
"assemble_sg_clean": 523 calls 0.004 user 0.000 sys 0.043 real
"assemble_sg_create": 523 calls 0.021 user 0.005 sys 0.057 real
"checkGraph": 324 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 324 calls 0.343 user 0.022 sys 0.432 real
active: 19646 calls 0.009 user 0.000 sys 0.016 real
advance: 10022 calls 2.326 user 0.157 sys 3.155 real
annotate: 394 calls 0.019 user 0.000 sys 0.036 real
assemble_region: 324 calls 1.028 user 0.041 sys 1.358 real
build_variants: 322 calls 0.000 user 0.000 sys 0.002 real
calc: 19646 calls 0.235 user 0.000 sys 0.330 real
calc_region: 322 calls 6.066 user 0.067 sys 6.421 real
call_region: 322 calls 0.052 user 0.000 sys 0.068 real
clip_region: 646 calls 0.046 user 0.001 sys 0.088 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.002 user 0.000 sys 1.864 real
fetch: 19646 calls 0.221 user 0.017 sys 0.187 real
fetch_db: 322 calls 0.022 user 0.001 sys 0.089 real
fetch_ref: 19970 calls 0.010 user 0.015 sys 0.081 real
fetch_region: 324 calls 0.000 user 0.000 sys 0.018 real
idle: 39 calls 0.005 user 0.007 sys 14.506 real
init: 1 calls 0.047 user 0.003 sys 0.043 real
pairhmm: 2270 calls 10.417 user 0.052 sys 10.986 real
realign: 697 calls 0.450 user 0.006 sys 0.734 real
region: 19646 calls 9.276 user 0.141 sys 9.489 real
tracker: 19646 calls 0.015 user 0.000 sys 0.026 real
trim_region: 324 calls 0.010 user 0.000 sys 0.005 real
overall: 273813504 mem 17.394 user 1.174 sys 2.979 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory