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 1.7s, peak mem 118MB, user 0.6s, sys 0.0s, output queue size 30
progress 10% @chr21:21418473, elapsed 0.1s, est remaining 1.1s, peak mem 129MB, user 0.8s, sys 0.0s, output queue size 94
progress 15% @chr21:26934466, elapsed 0.1s, est remaining 0.8s, peak mem 132MB, user 1.1s, sys 0.0s, output queue size 9
progress 20% @chr21:29587366, elapsed 0.2s, est remaining 0.8s, peak mem 143MB, user 1.5s, sys 0.0s, output queue size 102
progress 25% @chr21:30337045, elapsed 0.2s, est remaining 0.7s, peak mem 146MB, user 1.8s, sys 0.0s, output queue size 28
progress 30% @chr21:32349304, elapsed 0.3s, est remaining 0.6s, peak mem 148MB, user 2.2s, sys 0.0s, output queue size 23
progress 35% @chr21:32759777, elapsed 0.3s, est remaining 0.6s, peak mem 148MB, user 2.8s, sys 0.1s, output queue size 19
progress 40% @chr21:33559877, elapsed 0.4s, est remaining 0.5s, peak mem 151MB, user 3.0s, sys 0.1s, output queue size 8
progress 45% @chr21:34870435, elapsed 0.4s, est remaining 0.5s, peak mem 163MB, user 3.2s, sys 0.1s, output queue size 101
progress 50% @chr21:34669389, elapsed 0.8s, est remaining 0.8s, peak mem 239MB, user 4.5s, sys 0.1s, output queue size 52
progress 55% @chr21:36411463, elapsed 0.8s, est remaining 0.7s, peak mem 244MB, user 5.6s, sys 0.2s, output queue size 43
progress 60% @chr21:37478181, elapsed 0.9s, est remaining 0.6s, peak mem 244MB, user 5.8s, sys 0.2s, output queue size 77
progress 65% @chr21:39264460, elapsed 0.9s, est remaining 0.5s, peak mem 255MB, user 6.2s, sys 0.2s, output queue size 58
progress 70% @chr21:41250752, elapsed 1.0s, est remaining 0.4s, peak mem 269MB, user 6.5s, sys 0.2s, output queue size 153
progress 75% @chr21:41488133, elapsed 2.1s, est remaining 0.7s, peak mem 415MB, user 12.4s, sys 0.3s, output queue size 13
progress 80% @chr21:41740838, elapsed 4.1s, est remaining 1.0s, peak mem 502MB, user 27.6s, sys 0.4s, output queue size 36
progress 85% @chr21:42287889, elapsed 4.3s, est remaining 0.8s, peak mem 502MB, user 34.2s, sys 0.4s, output queue size 87
progress 90% @chr21:42413024, elapsed 4.4s, est remaining 0.5s, peak mem 502MB, user 37.0s, sys 0.5s, output queue size 53
progress 95% @chr21:42903182, elapsed 4.4s, est remaining 0.2s, peak mem 502MB, user 37.5s, sys 0.5s, output queue size 42
progress 100% @chr21:44082788, elapsed 4.5s, est remaining 0.0s, peak mem 502MB, user 37.9s, sys 0.5s, output queue size 20
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: 208827488
output file size: 65321
reads: 2481283
contig: 1576 intervals 300011 bases
"assemble": 237 calls 1.156 user 0.042 sys 1.461 real
"assemble_addRead": 237 calls 0.069 user 0.040 sys 0.088 real
"assemble_buildGraph": 494 calls 0.717 user 0.011 sys 0.763 real
"assemble_computecigar": 375 calls 0.506 user 0.001 sys 0.578 real
"assemble_kg_build_calcsize": 494 calls 0.409 user 0.010 sys 0.440 real
"assemble_kg_build_clear": 572 calls 0.050 user 0.000 sys 0.048 real
"assemble_kg_build_prepare": 988 calls 0.210 user 0.025 sys 0.390 real
"assemble_kg_build_threading": 416 calls 0.285 user 0.001 sys 0.311 real
"assemble_kg_op1": 416 calls 0.023 user 0.000 sys 0.051 real
"assemble_kg_op2": 416 calls 0.000 user 0.000 sys 0.019 real
"assemble_kg_op3": 416 calls 0.012 user 0.000 sys 0.012 real
"assemble_sg_clean": 375 calls 0.030 user 0.000 sys 0.064 real
"assemble_sg_create": 375 calls 0.081 user 0.000 sys 0.054 real
"checkGraph": 237 calls 0.000 user 0.000 sys 0.002 real
"findHaplotype": 237 calls 0.555 user 0.001 sys 0.639 real
active: 3201 calls 0.010 user 0.000 sys 0.013 real
advance: 1625 calls 4.408 user 0.168 sys 4.844 real
annotate: 279 calls 0.060 user 0.000 sys 0.063 real
assemble_region: 237 calls 1.789 user 0.083 sys 2.193 real
build_variants: 236 calls 0.020 user 0.000 sys 0.005 real
calc: 3201 calls 0.505 user 0.001 sys 0.616 real
calc_region: 236 calls 22.227 user 0.134 sys 22.615 real
call_region: 236 calls 0.177 user 0.000 sys 0.237 real
clip_region: 473 calls 0.131 user 0.011 sys 0.163 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.002 user 0.000 sys 4.484 real
fetch: 3201 calls 0.327 user 0.000 sys 0.366 real
fetch_db: 236 calls 0.059 user 0.002 sys 0.062 real
fetch_ref: 3438 calls 0.023 user 0.000 sys 0.017 real
fetch_region: 237 calls 0.074 user 0.000 sys 0.041 real
idle: 60 calls 0.049 user 0.000 sys 12.552 real
init: 1 calls 0.041 user 0.009 sys 0.041 real
pairhmm: 9053 calls 40.930 user 0.281 sys 42.299 real
realign: 1302 calls 1.584 user 0.001 sys 1.930 real
region: 3201 calls 32.447 user 0.245 sys 32.975 real
tracker: 3201 calls 0.000 user 0.000 sys 0.011 real
trim_region: 237 calls 0.000 user 0.000 sys 0.007 real
overall: 527130624 mem 52.452 user 0.749 sys 5.599 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory