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% @chr21:14375652, elapsed 0.1s, est remaining 1.5s, peak mem 117MB, user 0.6s, sys 0.0s, output queue size 27
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 132MB, user 1.1s, sys 0.1s, output queue size 9
progress 20% @chr21:29553555, elapsed 0.2s, est remaining 0.7s, peak mem 138MB, user 1.5s, sys 0.1s, output queue size 4
progress 25% @chr21:31135933, elapsed 0.2s, est remaining 0.6s, peak mem 141MB, user 1.7s, sys 0.1s, output queue size 23
progress 30% @chr21:32325229, elapsed 0.2s, est remaining 0.6s, peak mem 147MB, user 2.0s, sys 0.1s, output queue size 22
progress 35% @chr21:32769814, elapsed 0.3s, est remaining 0.6s, peak mem 147MB, user 2.4s, sys 0.1s, output queue size 49
progress 40% @chr21:33559877, elapsed 0.3s, est remaining 0.5s, peak mem 147MB, user 2.7s, sys 0.1s, output queue size 7
progress 45% @chr21:34521302, elapsed 0.4s, est remaining 0.4s, peak mem 156MB, user 2.9s, sys 0.1s, output queue size 101
progress 50% @chr21:36200331, elapsed 0.7s, est remaining 0.7s, peak mem 234MB, user 4.2s, sys 0.1s, output queue size 38
progress 56% @chr21:34787802, elapsed 0.8s, est remaining 0.6s, peak mem 237MB, user 5.4s, sys 0.2s, output queue size 119
progress 60% @chr21:37490175, elapsed 0.8s, est remaining 0.5s, peak mem 237MB, user 5.6s, sys 0.2s, output queue size 27
progress 65% @chr21:39277251, elapsed 0.8s, est remaining 0.4s, peak mem 243MB, user 5.9s, sys 0.2s, output queue size 59
progress 70% @chr21:39660560, elapsed 0.9s, est remaining 0.4s, peak mem 258MB, user 6.2s, sys 0.2s, output queue size 154
progress 75% @chr21:41480933, elapsed 2.1s, est remaining 0.7s, peak mem 558MB, user 11.4s, sys 0.2s, output queue size 4
progress 80% @chr21:41740838, elapsed 3.8s, est remaining 1.0s, peak mem 567MB, user 28.6s, sys 0.3s, output queue size 39
progress 85% @chr21:42380117, elapsed 4.2s, est remaining 0.7s, peak mem 570MB, user 31.8s, sys 0.3s, output queue size 112
progress 90% @chr21:41990895, elapsed 4.3s, est remaining 0.5s, peak mem 570MB, user 37.7s, sys 0.4s, output queue size 75
progress 95% @chr21:42903182, elapsed 4.3s, est remaining 0.2s, peak mem 570MB, user 38.0s, sys 0.4s, output queue size 46
progress 100% @chr21:44082788, elapsed 4.3s, est remaining 0.0s, peak mem 570MB, user 38.3s, 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: 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 1.229 user 0.050 sys 1.410 real
"assemble_addRead": 237 calls 0.037 user 0.000 sys 0.085 real
"assemble_buildGraph": 494 calls 0.564 user 0.020 sys 0.730 real
"assemble_computecigar": 375 calls 0.401 user 0.021 sys 0.561 real
"assemble_kg_build_calcsize": 494 calls 0.325 user 0.000 sys 0.417 real
"assemble_kg_build_clear": 572 calls 0.036 user 0.000 sys 0.046 real
"assemble_kg_build_prepare": 988 calls 0.375 user 0.030 sys 0.390 real
"assemble_kg_build_threading": 416 calls 0.231 user 0.020 sys 0.302 real
"assemble_kg_op1": 416 calls 0.023 user 0.000 sys 0.049 real
"assemble_kg_op2": 416 calls 0.030 user 0.000 sys 0.018 real
"assemble_kg_op3": 416 calls 0.013 user 0.000 sys 0.012 real
"assemble_sg_clean": 375 calls 0.071 user 0.000 sys 0.060 real
"assemble_sg_create": 375 calls 0.051 user 0.000 sys 0.050 real
"checkGraph": 237 calls 0.000 user 0.000 sys 0.002 real
"findHaplotype": 237 calls 0.470 user 0.021 sys 0.620 real
active: 3201 calls 0.010 user 0.000 sys 0.011 real
advance: 1625 calls 4.002 user 0.193 sys 4.819 real
annotate: 279 calls 0.070 user 0.000 sys 0.056 real
assemble_region: 237 calls 1.743 user 0.071 sys 2.120 real
build_variants: 236 calls 0.000 user 0.000 sys 0.004 real
calc: 3201 calls 0.517 user 0.011 sys 0.570 real
calc_region: 236 calls 23.433 user 0.086 sys 23.769 real
call_region: 236 calls 0.188 user 0.010 sys 0.215 real
clip_region: 473 calls 0.139 user 0.000 sys 0.159 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.004 sys 4.333 real
fetch: 3201 calls 0.399 user 0.036 sys 0.358 real
fetch_db: 236 calls 0.016 user 0.000 sys 0.060 real
fetch_ref: 3438 calls 0.019 user 0.010 sys 0.016 real
fetch_region: 237 calls 0.031 user 0.000 sys 0.051 real
idle: 60 calls 0.061 user 0.000 sys 12.618 real
init: 1 calls 0.030 user 0.010 sys 0.042 real
pairhmm: 9053 calls 39.724 user 0.044 sys 40.766 real
realign: 1302 calls 1.940 user 0.001 sys 1.878 real
region: 3201 calls 33.186 user 0.136 sys 33.456 real
tracker: 3201 calls 0.000 user 0.000 sys 0.010 real
trim_region: 237 calls 0.010 user 0.000 sys 0.007 real
overall: 597823488 mem 50.840 user 0.607 sys 5.458 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory