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% @chr19:49136724, elapsed 0.0s, est remaining 0.2s, peak mem 70MB, user 0.0s, sys 0.0s, output queue size 333
progress 10% @chr19:50625897, elapsed 0.0s, est remaining 0.2s, peak mem 70MB, user 0.0s, sys 0.0s, output queue size 930
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.1s, peak mem 70MB, user 0.1s, sys 0.0s, output queue size 1302
progress 20% @chr19:54906523, elapsed 0.0s, est remaining 0.1s, peak mem 75MB, user 0.1s, sys 0.0s, output queue size 1714
progress 25% @chr19:56208449, elapsed 0.0s, est remaining 0.1s, peak mem 76MB, user 0.1s, sys 0.1s, output queue size 2125
progress 30% @chr19:58212161, elapsed 0.0s, est remaining 0.1s, peak mem 76MB, user 0.1s, sys 0.1s, output queue size 2366
progress 35% @chr21:28966370, elapsed 0.1s, est remaining 0.2s, peak mem 99MB, user 0.6s, sys 0.1s, output queue size 83
progress 40% @chr21:36245048, elapsed 0.3s, est remaining 0.4s, peak mem 151MB, user 1.5s, sys 0.2s, output queue size 110
progress 45% @chr21:42381982, elapsed 0.9s, est remaining 1.1s, peak mem 267MB, user 7.0s, sys 0.2s, output queue size 112
progress 50% @chr21:45510064, elapsed 1.1s, est remaining 1.1s, peak mem 271MB, user 8.9s, sys 0.3s, output queue size 118
progress 55% @chr22:19433265, elapsed 1.1s, est remaining 0.9s, peak mem 274MB, user 9.5s, sys 0.3s, output queue size 473
progress 60% @chr22:22353210, elapsed 1.1s, est remaining 0.8s, peak mem 274MB, user 9.6s, sys 0.3s, output queue size 422
progress 65% @chr22:23884623, elapsed 1.1s, est remaining 0.6s, peak mem 274MB, user 9.7s, sys 0.3s, output queue size 633
progress 70% @chr22:29286684, elapsed 1.2s, est remaining 0.5s, peak mem 274MB, user 9.7s, sys 0.4s, output queue size 1140
progress 75% @chr22:31814992, elapsed 1.2s, est remaining 0.4s, peak mem 274MB, user 9.7s, sys 0.4s, output queue size 1679
progress 80% @chr22:37944175, elapsed 1.2s, est remaining 0.3s, peak mem 274MB, user 9.7s, sys 0.4s, output queue size 2241
progress 85% @chr22:41249729, elapsed 1.2s, est remaining 0.2s, peak mem 274MB, user 9.7s, sys 0.4s, output queue size 2762
progress 90% @chr22:46256561, elapsed 1.2s, est remaining 0.1s, peak mem 274MB, user 9.7s, sys 0.5s, output queue size 3377
progress 95% @chr22:50720184, elapsed 1.2s, est remaining 0.1s, peak mem 274MB, user 9.7s, sys 0.5s, output queue size 3952
progress 100% @chrY:12722108, elapsed 1.2s, est remaining 0.0s, peak mem 274MB, user 9.8s, sys 0.5s, output queue size 4524
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 71637313
output file size: 77769
reads: 1001089
contig: 9624 intervals 1921786 bases
"assemble": 315 calls 0.524 user 0.010 sys 0.694 real
"assemble_addRead": 315 calls 0.054 user 0.000 sys 0.036 real
"assemble_buildGraph": 650 calls 0.217 user 0.006 sys 0.342 real
"assemble_computecigar": 513 calls 0.278 user 0.010 sys 0.376 real
"assemble_kg_build_calcsize": 650 calls 0.093 user 0.000 sys 0.186 real
"assemble_kg_build_clear": 775 calls 0.003 user 0.000 sys 0.015 real
"assemble_kg_build_prepare": 1300 calls 0.103 user 0.002 sys 0.154 real
"assemble_kg_build_threading": 525 calls 0.122 user 0.006 sys 0.152 real
"assemble_kg_op1": 525 calls 0.036 user 0.000 sys 0.033 real
"assemble_kg_op2": 525 calls 0.016 user 0.000 sys 0.009 real
"assemble_kg_op3": 525 calls 0.002 user 0.000 sys 0.011 real
"assemble_sg_clean": 513 calls 0.054 user 0.001 sys 0.041 real
"assemble_sg_create": 513 calls 0.080 user 0.002 sys 0.053 real
"checkGraph": 315 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 315 calls 0.281 user 0.010 sys 0.395 real
active: 19646 calls 0.010 user 0.000 sys 0.014 real
advance: 10022 calls 2.311 user 0.096 sys 3.069 real
annotate: 358 calls 0.014 user 0.000 sys 0.028 real
assemble_region: 315 calls 0.860 user 0.020 sys 1.128 real
build_variants: 312 calls 0.000 user 0.000 sys 0.002 real
calc: 19646 calls 0.239 user 0.000 sys 0.298 real
calc_region: 312 calls 3.818 user 0.016 sys 4.185 real
call_region: 312 calls 0.015 user 0.000 sys 0.053 real
clip_region: 627 calls 0.052 user 0.000 sys 0.067 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.001 user 0.000 sys 1.276 real
fetch: 19646 calls 0.172 user 0.008 sys 0.156 real
fetch_db: 312 calls 0.040 user 0.000 sys 0.082 real
fetch_ref: 19961 calls 0.001 user 0.003 sys 0.079 real
fetch_region: 315 calls 0.015 user 0.000 sys 0.016 real
idle: 39 calls 0.011 user 0.005 sys 13.299 real
init: 1 calls 0.040 user 0.000 sys 0.045 real
pairhmm: 1785 calls 6.329 user 0.033 sys 6.940 real
realign: 598 calls 0.433 user 0.001 sys 0.522 real
region: 19646 calls 6.457 user 0.053 sys 6.462 real
tracker: 19646 calls 0.015 user 0.002 sys 0.025 real
trim_region: 315 calls 0.000 user 0.000 sys 0.004 real
overall: 288124928 mem 12.929 user 0.997 sys 2.395 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory