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% @chr19:49139668, elapsed 0.0s, est remaining 0.3s, peak mem 73MB, user 0.0s, sys 0.0s, output queue size 451
progress 10% @chr19:50629294, elapsed 0.0s, est remaining 0.3s, peak mem 76MB, user 0.0s, sys 0.1s, output queue size 725
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.2s, peak mem 79MB, user 0.0s, sys 0.1s, output queue size 1090
progress 20% @chr19:54633016, elapsed 0.0s, est remaining 0.2s, peak mem 82MB, user 0.0s, sys 0.1s, output queue size 1477
progress 25% @chr19:56301968, elapsed 0.1s, est remaining 0.2s, peak mem 83MB, user 0.0s, sys 0.2s, output queue size 1931
progress 30% @chr19:58260851, elapsed 0.1s, est remaining 0.1s, peak mem 84MB, user 0.0s, sys 0.2s, output queue size 2160
progress 35% @chr21:29342399, elapsed 0.1s, est remaining 0.3s, peak mem 109MB, user 0.6s, sys 0.3s, output queue size 118
progress 40% @chr21:36741717, elapsed 0.4s, est remaining 0.5s, peak mem 162MB, user 1.8s, sys 0.4s, output queue size 113
progress 45% @chr21:42381982, elapsed 1.3s, est remaining 1.6s, peak mem 286MB, user 9.8s, sys 0.4s, output queue size 112
progress 50% @chr21:45515658, elapsed 1.4s, est remaining 1.4s, peak mem 289MB, user 12.0s, sys 0.5s, output queue size 115
progress 55% @chr22:18169844, elapsed 1.5s, est remaining 1.3s, peak mem 293MB, user 12.8s, sys 0.5s, output queue size 346
progress 60% @chr22:22214908, elapsed 1.6s, est remaining 1.0s, peak mem 293MB, user 12.8s, sys 0.6s, output queue size 331
progress 65% @chr22:23966915, elapsed 1.6s, est remaining 0.8s, peak mem 293MB, user 12.8s, sys 0.6s, output queue size 558
progress 70% @chr22:29294124, elapsed 1.6s, est remaining 0.7s, peak mem 293MB, user 12.9s, sys 0.6s, output queue size 1057
progress 75% @chr22:31836972, elapsed 1.6s, est remaining 0.5s, peak mem 293MB, user 12.9s, sys 0.6s, output queue size 1599
progress 80% @chr22:37953047, elapsed 1.6s, est remaining 0.4s, peak mem 293MB, user 12.9s, sys 0.7s, output queue size 2163
progress 85% @chr22:41257948, elapsed 1.6s, est remaining 0.3s, peak mem 293MB, user 12.9s, sys 0.7s, output queue size 2685
progress 90% @chr22:46256561, elapsed 1.6s, est remaining 0.2s, peak mem 293MB, user 12.9s, sys 0.7s, output queue size 3293
progress 95% @chr22:50730721, elapsed 1.7s, est remaining 0.1s, peak mem 293MB, user 12.9s, sys 0.8s, output queue size 461
progress 100% @chrY:21522383, elapsed 1.7s, est remaining 0.0s, peak mem 293MB, user 12.9s, sys 0.8s, output queue size 1039
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 128
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692767
output file size: 77724
reads: 1001089
contig: 9624 intervals 1921786 bases
"assemble": 315 calls 0.718 user 0.024 sys 0.920 real
"assemble_addRead": 315 calls 0.046 user 0.000 sys 0.047 real
"assemble_buildGraph": 650 calls 0.373 user 0.002 sys 0.440 real
"assemble_computecigar": 513 calls 0.497 user 0.003 sys 0.519 real
"assemble_kg_build_calcsize": 650 calls 0.196 user 0.000 sys 0.231 real
"assemble_kg_build_clear": 775 calls 0.041 user 0.001 sys 0.022 real
"assemble_kg_build_prepare": 1300 calls 0.198 user 0.019 sys 0.213 real
"assemble_kg_build_threading": 525 calls 0.167 user 0.002 sys 0.203 real
"assemble_kg_op1": 525 calls 0.027 user 0.000 sys 0.045 real
"assemble_kg_op2": 525 calls 0.008 user 0.000 sys 0.010 real
"assemble_kg_op3": 525 calls 0.000 user 0.000 sys 0.013 real
"assemble_sg_clean": 513 calls 0.001 user 0.000 sys 0.054 real
"assemble_sg_create": 513 calls 0.052 user 0.002 sys 0.074 real
"checkGraph": 315 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 315 calls 0.532 user 0.003 sys 0.546 real
active: 19646 calls 0.004 user 0.000 sys 0.023 real
advance: 10022 calls 2.804 user 0.123 sys 3.567 real
annotate: 358 calls 0.027 user 0.000 sys 0.037 real
assemble_region: 315 calls 1.296 user 0.027 sys 1.517 real
build_variants: 312 calls 0.000 user 0.000 sys 0.002 real
calc: 19646 calls 0.354 user 0.014 sys 0.440 real
calc_region: 312 calls 5.172 user 0.018 sys 5.544 real
call_region: 312 calls 0.050 user 0.000 sys 0.067 real
clip_region: 627 calls 0.061 user 0.000 sys 0.087 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.007 user 0.003 sys 1.800 real
fetch: 19646 calls 0.355 user 0.007 sys 0.233 real
fetch_db: 312 calls 0.030 user 0.001 sys 0.097 real
fetch_ref: 19961 calls 0.028 user 0.005 sys 0.097 real
fetch_region: 315 calls 0.030 user 0.000 sys 0.029 real
idle: 39 calls 0.003 user 0.011 sys 13.903 real
init: 1 calls 0.039 user 0.001 sys 0.047 real
pairhmm: 1803 calls 9.083 user 0.014 sys 9.914 real
realign: 598 calls 0.665 user 0.016 sys 0.695 real
region: 19646 calls 8.903 user 0.104 sys 9.179 real
tracker: 19646 calls 0.015 user 0.004 sys 0.035 real
trim_region: 315 calls 0.010 user 0.000 sys 0.006 real
overall: 307904512 mem 16.862 user 1.476 sys 2.931 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory