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.recal.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% @chr21:10569437, elapsed 0.1s, est remaining 1.5s, peak mem 112MB, user 0.6s, sys 0.0s, output queue size 39
progress 10% @chr21:18297734, elapsed 0.1s, est remaining 0.9s, peak mem 121MB, user 0.8s, sys 0.0s, output queue size 94
progress 15% @chr21:26842339, elapsed 0.1s, est remaining 0.7s, peak mem 126MB, user 1.0s, sys 0.1s, output queue size 14
progress 20% @chr21:29329487, elapsed 0.2s, est remaining 0.7s, peak mem 139MB, user 1.4s, sys 0.1s, output queue size 21
progress 25% @chr21:30592446, elapsed 0.2s, est remaining 0.6s, peak mem 142MB, user 1.6s, sys 0.1s, output queue size 23
progress 30% @chr21:30829435, elapsed 0.2s, est remaining 0.6s, peak mem 147MB, user 1.9s, sys 0.1s, output queue size 88
progress 35% @chr21:32751119, elapsed 0.3s, est remaining 0.6s, peak mem 150MB, user 2.3s, sys 0.1s, output queue size 50
progress 40% @chr21:33559877, elapsed 0.3s, est remaining 0.5s, peak mem 151MB, user 2.5s, sys 0.1s, output queue size 25
progress 45% @chr21:33865151, elapsed 0.3s, est remaining 0.4s, peak mem 159MB, user 2.7s, sys 0.1s, output queue size 100
progress 50% @chr21:36200331, elapsed 0.7s, est remaining 0.7s, peak mem 246MB, user 3.7s, sys 0.1s, output queue size 39
progress 56% @chr21:34787802, elapsed 0.7s, est remaining 0.6s, peak mem 249MB, user 4.7s, sys 0.1s, output queue size 112
progress 60% @chr21:37472684, elapsed 0.7s, est remaining 0.5s, peak mem 249MB, user 4.8s, sys 0.1s, output queue size 27
progress 65% @chr21:39278743, elapsed 0.8s, est remaining 0.4s, peak mem 260MB, user 5.1s, sys 0.1s, output queue size 59
progress 70% @chr21:41338378, elapsed 0.8s, est remaining 0.3s, peak mem 272MB, user 5.3s, sys 0.1s, output queue size 154
progress 75% @chr21:38380028, elapsed 2.0s, est remaining 0.7s, peak mem 422MB, user 12.7s, sys 0.2s, output queue size 204
progress 80% @chr21:41801240, elapsed 3.6s, est remaining 0.9s, peak mem 505MB, user 27.5s, sys 0.3s, output queue size 43
progress 85% @chr21:41497133, elapsed 4.2s, est remaining 0.7s, peak mem 506MB, user 34.6s, sys 0.3s, output queue size 103
progress 90% @chr21:42876702, elapsed 4.5s, est remaining 0.5s, peak mem 506MB, user 36.3s, sys 0.3s, output queue size 193
progress 95% @chr21:42903182, elapsed 4.5s, est remaining 0.2s, peak mem 506MB, user 39.0s, sys 0.4s, output queue size 45
progress 100% @chr21:44082788, elapsed 4.6s, est remaining 0.0s, peak mem 506MB, user 39.3s, sys 0.4s, 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: 138653580
output file size: 65431
reads: 1685487
contig: 1576 intervals 300011 bases
"assemble": 238 calls 1.118 user 0.020 sys 1.400 real
"assemble_addRead": 238 calls 0.081 user 0.000 sys 0.075 real
"assemble_buildGraph": 495 calls 0.515 user 0.001 sys 0.737 real
"assemble_computecigar": 379 calls 0.520 user 0.031 sys 0.555 real
"assemble_kg_build_calcsize": 495 calls 0.280 user 0.000 sys 0.434 real
"assemble_kg_build_clear": 574 calls 0.075 user 0.000 sys 0.047 real
"assemble_kg_build_prepare": 990 calls 0.328 user 0.020 sys 0.381 real
"assemble_kg_build_threading": 416 calls 0.220 user 0.000 sys 0.293 real
"assemble_kg_op1": 416 calls 0.045 user 0.000 sys 0.045 real
"assemble_kg_op2": 416 calls 0.010 user 0.000 sys 0.017 real
"assemble_kg_op3": 416 calls 0.007 user 0.000 sys 0.011 real
"assemble_sg_clean": 379 calls 0.022 user 0.000 sys 0.057 real
"assemble_sg_create": 379 calls 0.044 user 0.000 sys 0.050 real
"checkGraph": 238 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 238 calls 0.620 user 0.031 sys 0.606 real
active: 3201 calls 0.020 user 0.000 sys 0.019 real
advance: 1625 calls 3.614 user 0.162 sys 4.151 real
annotate: 279 calls 0.046 user 0.000 sys 0.054 real
assemble_region: 238 calls 1.819 user 0.052 sys 2.085 real
build_variants: 236 calls 0.000 user 0.000 sys 0.004 real
calc: 3201 calls 0.375 user 0.000 sys 0.534 real
calc_region: 236 calls 22.509 user 0.026 sys 22.755 real
call_region: 236 calls 0.191 user 0.000 sys 0.204 real
clip_region: 474 calls 0.125 user 0.000 sys 0.158 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.002 user 0.002 sys 4.573 real
fetch: 3201 calls 0.361 user 0.018 sys 0.284 real
fetch_db: 236 calls 0.037 user 0.006 sys 0.060 real
fetch_ref: 3439 calls 0.017 user 0.010 sys 0.017 real
fetch_region: 238 calls 0.058 user 0.000 sys 0.028 real
idle: 56 calls 0.051 user 0.000 sys 12.293 real
init: 1 calls 0.029 user 0.011 sys 0.042 real
pairhmm: 9072 calls 43.831 user 0.053 sys 44.401 real
realign: 1314 calls 1.234 user 0.000 sys 1.999 real
region: 3201 calls 34.822 user 0.113 sys 35.068 real
tracker: 3201 calls 0.031 user 0.000 sys 0.017 real
trim_region: 238 calls 0.006 user 0.000 sys 0.007 real
overall: 531165184 mem 53.856 user 0.480 sys 5.738 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory