cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr21_5117103-5117231.bed.gz -i Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant Sig_18_Blood.haplotyper.chr21_5117103-5117231.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:14373617, elapsed 0.1s, est remaining 1.2s, peak mem 111MB, user 0.4s, sys 0.0s, output queue size 37
progress 10% @chr21:21477291, elapsed 0.1s, est remaining 1.0s, peak mem 126MB, user 0.8s, sys 0.1s, output queue size 94
progress 15% @chr21:28882160, elapsed 0.1s, est remaining 0.8s, peak mem 129MB, user 1.0s, sys 0.1s, output queue size 9
progress 20% @chr21:29159941, elapsed 0.2s, est remaining 0.8s, peak mem 138MB, user 1.4s, sys 0.1s, output queue size 59
progress 25% @chr21:31124522, elapsed 0.2s, est remaining 0.7s, peak mem 138MB, user 1.7s, sys 0.1s, output queue size 22
progress 30% @chr21:32325229, elapsed 0.3s, est remaining 0.6s, peak mem 141MB, user 2.0s, sys 0.1s, output queue size 22
progress 35% @chr21:32771326, elapsed 0.3s, est remaining 0.6s, peak mem 144MB, user 2.4s, sys 0.1s, output queue size 55
progress 40% @chr21:33559587, elapsed 0.3s, est remaining 0.5s, peak mem 144MB, user 2.7s, sys 0.1s, output queue size 7
progress 45% @chr21:34709357, elapsed 0.4s, est remaining 0.4s, peak mem 150MB, user 2.9s, sys 0.1s, output queue size 100
progress 50% @chr21:36200331, elapsed 0.5s, est remaining 0.5s, peak mem 210MB, user 3.5s, sys 0.1s, output queue size 38
progress 56% @chr21:34787802, elapsed 0.8s, est remaining 0.6s, peak mem 222MB, user 5.7s, sys 0.2s, output queue size 117
progress 60% @chr21:36744728, elapsed 0.8s, est remaining 0.5s, peak mem 225MB, user 5.8s, sys 0.2s, output queue size 75
progress 65% @chr21:39270283, elapsed 0.9s, est remaining 0.5s, peak mem 237MB, user 6.2s, sys 0.2s, output queue size 58
progress 70% @chr21:41250752, elapsed 0.9s, est remaining 0.4s, peak mem 255MB, user 6.4s, sys 0.2s, output queue size 154
progress 75% @chr21:41495693, elapsed 2.2s, est remaining 0.7s, peak mem 423MB, user 11.7s, sys 0.3s, output queue size 4
progress 80% @chr21:41740838, elapsed 3.5s, est remaining 0.9s, peak mem 492MB, user 24.8s, sys 0.4s, output queue size 34
progress 85% @chr21:42388929, elapsed 4.1s, est remaining 0.7s, peak mem 495MB, user 30.3s, sys 0.5s, output queue size 117
progress 90% @chr21:42896927, elapsed 4.2s, est remaining 0.5s, peak mem 495MB, user 33.3s, sys 0.5s, output queue size 194
progress 95% @chr21:43967946, elapsed 4.3s, est remaining 0.2s, peak mem 495MB, user 33.8s, sys 0.6s, output queue size 299
progress 100% @chr21:44082788, elapsed 4.4s, est remaining 0.0s, peak mem 495MB, user 36.5s, sys 0.6s, output queue size 20
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 12 max 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 208827488
output file size: 65321
reads: 2481283
contig: 1576 intervals 300011 bases
"assemble": 237 calls 1.210 user 0.088 sys 1.442 real
"assemble_addRead": 237 calls 0.049 user 0.022 sys 0.104 real
"assemble_buildGraph": 494 calls 0.574 user 0.008 sys 0.733 real
"assemble_computecigar": 375 calls 0.607 user 0.008 sys 0.575 real
"assemble_kg_build_calcsize": 494 calls 0.360 user 0.000 sys 0.420 real
"assemble_kg_build_clear": 572 calls 0.012 user 0.000 sys 0.047 real
"assemble_kg_build_prepare": 988 calls 0.366 user 0.079 sys 0.413 real
"assemble_kg_build_threading": 416 calls 0.214 user 0.008 sys 0.302 real
"assemble_kg_op1": 416 calls 0.020 user 0.000 sys 0.049 real
"assemble_kg_op2": 416 calls 0.040 user 0.000 sys 0.019 real
"assemble_kg_op3": 416 calls 0.031 user 0.000 sys 0.012 real
"assemble_sg_clean": 375 calls 0.117 user 0.000 sys 0.061 real
"assemble_sg_create": 375 calls 0.013 user 0.000 sys 0.051 real
"checkGraph": 237 calls 0.000 user 0.000 sys 0.002 real
"findHaplotype": 237 calls 0.647 user 0.008 sys 0.635 real
active: 3201 calls 0.026 user 0.010 sys 0.011 real
advance: 1625 calls 4.250 user 0.230 sys 4.893 real
annotate: 279 calls 0.029 user 0.000 sys 0.067 real
assemble_region: 237 calls 1.916 user 0.117 sys 2.186 real
build_variants: 236 calls 0.007 user 0.000 sys 0.006 real
calc: 3201 calls 0.453 user 0.000 sys 0.591 real
calc_region: 236 calls 20.796 user 0.120 sys 21.121 real
call_region: 236 calls 0.182 user 0.000 sys 0.240 real
clip_region: 473 calls 0.143 user 0.001 sys 0.174 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.002 user 0.003 sys 4.420 real
fetch: 3201 calls 0.379 user 0.054 sys 0.395 real
fetch_db: 236 calls 0.005 user 0.000 sys 0.060 real
fetch_ref: 3438 calls 0.007 user 0.000 sys 0.017 real
fetch_region: 237 calls 0.031 user 0.000 sys 0.039 real
idle: 80 calls 0.034 user 0.001 sys 12.561 real
init: 1 calls 0.020 user 0.020 sys 0.042 real
pairhmm: 9053 calls 40.151 user 0.129 sys 41.419 real
realign: 1302 calls 1.819 user 0.004 sys 1.927 real
region: 3201 calls 31.238 user 0.210 sys 31.619 real
tracker: 3201 calls 0.011 user 0.010 sys 0.012 real
trim_region: 237 calls 0.000 user 0.000 sys 0.007 real
overall: 519180288 mem 51.628 user 0.758 sys 5.535 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory