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% @chr21:14373617, elapsed 0.1s, est remaining 2.2s, peak mem 106MB, user 0.9s, sys 0.0s, output queue size 27
progress 10% @chr21:21468662, elapsed 0.1s, est remaining 1.3s, peak mem 117MB, user 1.2s, sys 0.0s, output queue size 94
progress 15% @chr21:26929886, elapsed 0.2s, est remaining 1.1s, peak mem 126MB, user 1.6s, sys 0.0s, output queue size 9
progress 20% @chr21:29553555, elapsed 0.3s, est remaining 1.1s, peak mem 138MB, user 2.1s, sys 0.1s, output queue size 98
progress 25% @chr21:30592446, elapsed 0.3s, est remaining 1.0s, peak mem 141MB, user 2.5s, sys 0.1s, output queue size 22
progress 30% @chr21:32355449, elapsed 0.4s, est remaining 0.9s, peak mem 147MB, user 2.9s, sys 0.1s, output queue size 90
progress 35% @chr21:32762096, elapsed 0.5s, est remaining 0.9s, peak mem 148MB, user 3.5s, sys 0.1s, output queue size 51
progress 40% @chr21:33559230, elapsed 0.5s, est remaining 0.7s, peak mem 150MB, user 4.0s, sys 0.1s, output queue size 7
progress 45% @chr21:34834409, elapsed 0.5s, est remaining 0.6s, peak mem 159MB, user 4.2s, sys 0.2s, output queue size 101
progress 50% @chr21:33549476, elapsed 1.0s, est remaining 1.0s, peak mem 238MB, user 5.3s, sys 0.2s, output queue size 150
progress 56% @chr21:34787802, elapsed 1.1s, est remaining 0.9s, peak mem 240MB, user 7.6s, sys 0.2s, output queue size 118
progress 60% @chr21:37490175, elapsed 1.1s, est remaining 0.8s, peak mem 240MB, user 7.8s, sys 0.2s, output queue size 76
progress 65% @chr21:39278743, elapsed 1.2s, est remaining 0.6s, peak mem 246MB, user 8.2s, sys 0.2s, output queue size 59
progress 70% @chr21:41250752, elapsed 1.2s, est remaining 0.5s, peak mem 258MB, user 8.6s, sys 0.3s, output queue size 153
progress 75% @chr21:41491493, elapsed 3.2s, est remaining 1.1s, peak mem 451MB, user 16.3s, sys 0.4s, output queue size 4
progress 80% @chr21:41861563, elapsed 5.5s, est remaining 1.4s, peak mem 520MB, user 39.6s, sys 0.7s, output queue size 38
progress 85% @chr21:41990895, elapsed 6.7s, est remaining 1.2s, peak mem 521MB, user 49.3s, sys 0.8s, output queue size 107
progress 90% @chr21:42896927, elapsed 7.0s, est remaining 0.8s, peak mem 521MB, user 56.1s, sys 0.9s, output queue size 194
progress 96% @chr21:41501693, elapsed 7.2s, est remaining 0.3s, peak mem 521MB, user 60.6s, sys 1.0s, output queue size 280
progress 100% @chr21:43789630, elapsed 7.2s, est remaining 0.0s, peak mem 521MB, user 61.0s, sys 1.1s, output queue size 54
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
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 1.839 user 0.119 sys 2.182 real
"assemble_addRead": 238 calls 0.060 user 0.000 sys 0.123 real
"assemble_buildGraph": 495 calls 0.979 user 0.020 sys 1.144 real
"assemble_computecigar": 379 calls 0.825 user 0.031 sys 0.933 real
"assemble_kg_build_calcsize": 495 calls 0.581 user 0.000 sys 0.666 real
"assemble_kg_build_clear": 574 calls 0.068 user 0.000 sys 0.069 real
"assemble_kg_build_prepare": 990 calls 0.476 user 0.089 sys 0.616 real
"assemble_kg_build_threading": 416 calls 0.398 user 0.020 sys 0.461 real
"assemble_kg_op1": 416 calls 0.044 user 0.008 sys 0.070 real
"assemble_kg_op2": 416 calls 0.010 user 0.000 sys 0.023 real
"assemble_kg_op3": 416 calls 0.013 user 0.000 sys 0.015 real
"assemble_sg_clean": 379 calls 0.051 user 0.000 sys 0.088 real
"assemble_sg_create": 379 calls 0.105 user 0.001 sys 0.079 real
"checkGraph": 238 calls 0.010 user 0.000 sys 0.002 real
"findHaplotype": 238 calls 0.903 user 0.032 sys 1.011 real
active: 3201 calls 0.000 user 0.000 sys 0.031 real
advance: 1625 calls 5.574 user 0.366 sys 6.392 real
annotate: 279 calls 0.099 user 0.000 sys 0.094 real
assemble_region: 238 calls 2.812 user 0.151 sys 3.321 real
build_variants: 236 calls 0.000 user 0.000 sys 0.007 real
calc: 3201 calls 0.820 user 0.000 sys 1.008 real
calc_region: 236 calls 37.059 user 0.364 sys 37.680 real
call_region: 236 calls 0.266 user 0.000 sys 0.322 real
clip_region: 474 calls 0.112 user 0.025 sys 0.253 real
done: 1 calls 0.000 user 0.000 sys 0.003 real
execute: 1 calls 0.001 user 0.001 sys 7.223 real
fetch: 3201 calls 0.449 user 0.099 sys 0.552 real
fetch_db: 236 calls 0.033 user 0.000 sys 0.091 real
fetch_ref: 3439 calls 0.038 user 0.000 sys 0.022 real
fetch_region: 238 calls 0.025 user 0.000 sys 0.040 real
idle: 56 calls 0.062 user 0.001 sys 12.793 real
init: 1 calls 0.039 user 0.020 sys 0.053 real
pairhmm: 9072 calls 68.984 user 0.463 sys 70.207 real
realign: 1314 calls 2.909 user 0.042 sys 3.103 real
region: 3201 calls 53.965 user 0.525 sys 54.782 real
tracker: 3201 calls 0.010 user 0.010 sys 0.027 real
trim_region: 238 calls 0.030 user 0.000 sys 0.010 real
overall: 547282944 mem 84.439 user 1.533 sys 8.400 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory