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% @chr21:14485912, elapsed 0.1s, est remaining 2.1s, peak mem 115MB, user 1.0s, sys 0.0s, output queue size 2
progress 10% @chr21:21484455, elapsed 0.2s, est remaining 1.4s, peak mem 129MB, user 1.2s, sys 0.0s, output queue size 94
progress 15% @chr21:28879870, elapsed 0.2s, est remaining 1.1s, peak mem 132MB, user 1.6s, sys 0.0s, output queue size 9
progress 20% @chr21:28966370, elapsed 0.3s, est remaining 1.1s, peak mem 144MB, user 2.4s, sys 0.0s, output queue size 62
progress 25% @chr21:30541657, elapsed 0.3s, est remaining 1.0s, peak mem 145MB, user 2.8s, sys 0.0s, output queue size 23
progress 30% @chr21:32349304, elapsed 0.4s, est remaining 0.9s, peak mem 148MB, user 3.2s, sys 0.0s, output queue size 23
progress 35% @chr21:33241923, elapsed 0.5s, est remaining 0.9s, peak mem 149MB, user 3.9s, sys 0.1s, output queue size 50
progress 40% @chr21:33575778, elapsed 0.5s, est remaining 0.7s, peak mem 150MB, user 4.2s, sys 0.1s, output queue size 6
progress 45% @chr21:34518084, elapsed 0.5s, est remaining 0.7s, peak mem 161MB, user 4.6s, sys 0.1s, output queue size 100
progress 50% @chr21:36208715, elapsed 0.7s, est remaining 0.7s, peak mem 227MB, user 5.3s, sys 0.1s, output queue size 38
progress 55% @chr21:36368988, elapsed 1.2s, est remaining 1.0s, peak mem 242MB, user 8.2s, sys 0.1s, output queue size 85
progress 60% @chr21:37240496, elapsed 1.2s, est remaining 0.8s, peak mem 242MB, user 9.1s, sys 0.2s, output queue size 76
progress 65% @chr21:38819503, elapsed 1.3s, est remaining 0.7s, peak mem 249MB, user 9.6s, sys 0.2s, output queue size 59
progress 70% @chr21:41250752, elapsed 1.4s, est remaining 0.6s, peak mem 266MB, user 10.0s, sys 0.2s, output queue size 153
progress 75% @chr21:41464388, elapsed 3.2s, est remaining 1.1s, peak mem 459MB, user 18.8s, sys 0.4s, output queue size 14
progress 80% @chr21:41490173, elapsed 4.9s, est remaining 1.2s, peak mem 513MB, user 34.1s, sys 0.4s, output queue size 38
progress 85% @chr21:42395324, elapsed 5.9s, est remaining 1.0s, peak mem 521MB, user 41.4s, sys 0.4s, output queue size 116
progress 90% @chr21:42918524, elapsed 6.1s, est remaining 0.7s, peak mem 521MB, user 45.8s, sys 0.5s, output queue size 194
progress 96% @chr21:41501693, elapsed 6.2s, est remaining 0.3s, peak mem 521MB, user 49.5s, sys 0.5s, output queue size 264
progress 100% @chr21:44082788, elapsed 6.3s, est remaining 0.0s, peak mem 521MB, user 49.9s, sys 0.5s, output queue size 20
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
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 1.705 user 0.099 sys 2.115 real
"assemble_addRead": 237 calls 0.138 user 0.000 sys 0.120 real
"assemble_buildGraph": 494 calls 0.884 user 0.016 sys 1.089 real
"assemble_computecigar": 375 calls 0.794 user 0.008 sys 0.835 real
"assemble_kg_build_calcsize": 494 calls 0.459 user 0.000 sys 0.632 real
"assemble_kg_build_clear": 572 calls 0.049 user 0.000 sys 0.066 real
"assemble_kg_build_prepare": 988 calls 0.424 user 0.074 sys 0.608 real
"assemble_kg_build_threading": 416 calls 0.424 user 0.016 sys 0.440 real
"assemble_kg_op1": 416 calls 0.056 user 0.000 sys 0.072 real
"assemble_kg_op2": 416 calls 0.051 user 0.000 sys 0.025 real
"assemble_kg_op3": 416 calls 0.029 user 0.000 sys 0.016 real
"assemble_sg_clean": 375 calls 0.051 user 0.000 sys 0.089 real
"assemble_sg_create": 375 calls 0.065 user 0.000 sys 0.075 real
"checkGraph": 237 calls 0.000 user 0.000 sys 0.002 real
"findHaplotype": 237 calls 0.882 user 0.008 sys 0.922 real
active: 3201 calls 0.034 user 0.000 sys 0.020 real
advance: 1625 calls 6.343 user 0.214 sys 6.739 real
annotate: 279 calls 0.111 user 0.000 sys 0.093 real
assemble_region: 237 calls 2.724 user 0.107 sys 3.163 real
build_variants: 236 calls 0.000 user 0.000 sys 0.006 real
calc: 3201 calls 0.985 user 0.000 sys 1.121 real
calc_region: 236 calls 29.192 user 0.101 sys 29.604 real
call_region: 236 calls 0.285 user 0.010 sys 0.341 real
clip_region: 473 calls 0.158 user 0.000 sys 0.239 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.001 sys 6.274 real
fetch: 3201 calls 0.641 user 0.020 sys 0.618 real
fetch_db: 236 calls 0.039 user 0.000 sys 0.086 real
fetch_ref: 3438 calls 0.025 user 0.000 sys 0.022 real
fetch_region: 237 calls 0.021 user 0.009 sys 0.058 real
idle: 60 calls 0.062 user 0.000 sys 12.747 real
init: 1 calls 0.045 user 0.009 sys 0.056 real
pairhmm: 9053 calls 57.766 user 0.132 sys 58.978 real
realign: 1302 calls 2.158 user 0.000 sys 2.521 real
region: 3201 calls 41.700 user 0.216 sys 42.508 real
tracker: 3201 calls 0.000 user 0.000 sys 0.015 real
trim_region: 237 calls 0.010 user 0.000 sys 0.011 real
overall: 546676736 mem 73.690 user 0.709 sys 7.434 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory