cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i reference-NA12878-downsampled-500k.bam -i Sig_18_Blood.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity_padded100bp.bed --algo TNhaplotyper2 --tumor_sample Sig_18_Blood --normal_sample reference-NA12878 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz negative_somatic_control_2.tnseq.vcf.gz --algo OrientationBias --tumor_sample Sig_18_Blood negative_somatic_control_2.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample Sig_18_Blood --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments negative_somatic_control_2.tnseq.segments negative_somatic_control_2.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113706494, elapsed 1.4s, est remaining 27.2s, peak mem 143MB, user 12.7s, sys 1.6s, output queue size 3
progress 10% @chr2:3671058, elapsed 2.9s, est remaining 25.7s, peak mem 143MB, user 25.0s, sys 3.2s, output queue size 6
progress 15% @chr2:178609108, elapsed 4.4s, est remaining 24.8s, peak mem 143MB, user 38.3s, sys 4.6s, output queue size 12
progress 20% @chr3:57483276, elapsed 5.7s, est remaining 22.9s, peak mem 143MB, user 50.0s, sys 6.2s, output queue size 24
progress 25% @chr4:70603777, elapsed 7.1s, est remaining 21.4s, peak mem 143MB, user 62.9s, sys 7.8s, output queue size 8
progress 30% @chr5:135571753, elapsed 8.6s, est remaining 20.1s, peak mem 144MB, user 76.0s, sys 9.5s, output queue size 4
progress 35% @chr6:104791404, elapsed 9.9s, est remaining 18.3s, peak mem 145MB, user 87.5s, sys 10.8s, output queue size 7
progress 40% @chr7:106248199, elapsed 11.2s, est remaining 16.8s, peak mem 146MB, user 100.1s, sys 12.2s, output queue size 22
progress 45% @chr8:143835562, elapsed 12.6s, est remaining 15.4s, peak mem 147MB, user 112.8s, sys 13.8s, output queue size 0
progress 50% @chr10:21727756, elapsed 13.9s, est remaining 13.9s, peak mem 150MB, user 125.5s, sys 15.1s, output queue size 2
progress 55% @chr11:34135075, elapsed 15.2s, est remaining 12.4s, peak mem 151MB, user 137.6s, sys 16.6s, output queue size 6
progress 60% @chr12:12718707, elapsed 16.5s, est remaining 11.0s, peak mem 152MB, user 149.8s, sys 17.8s, output queue size 12
progress 65% @chr13:32078734, elapsed 17.8s, est remaining 9.6s, peak mem 152MB, user 162.2s, sys 19.3s, output queue size 10
progress 70% @chr15:35381722, elapsed 19.1s, est remaining 8.2s, peak mem 153MB, user 174.1s, sys 20.8s, output queue size 2
progress 75% @chr16:28494582, elapsed 20.4s, est remaining 6.8s, peak mem 153MB, user 186.2s, sys 22.3s, output queue size 2
progress 80% @chr17:40034816, elapsed 21.8s, est remaining 5.4s, peak mem 153MB, user 200.0s, sys 23.6s, output queue size 1
progress 85% @chr19:1806528, elapsed 23.1s, est remaining 4.1s, peak mem 153MB, user 213.0s, sys 25.1s, output queue size 3
progress 90% @chr19:54630974, elapsed 24.4s, est remaining 2.7s, peak mem 155MB, user 225.2s, sys 26.4s, output queue size 4
progress 95% @chr22:32068396, elapsed 27.5s, est remaining 1.4s, peak mem 330MB, user 254.6s, sys 28.1s, output queue size 69
progress 100% @chrY:14723017, elapsed 28.9s, est remaining 0.0s, peak mem 330MB, user 266.3s, sys 29.8s, output queue size 458
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: AuthenticAMD
 signature: 00800f12
  features: 178bfbff fed83203
  extended: 209c01a9 00000000
  amd bits: 2fd3fbff 00c001f3
     brand: AMD EPYC 7571
threads: 12 max 64
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 74586802
output file size: 51111
reads: 1501816
contig: 178193 intervals 76355618 bases
"assemble": 189 calls 0.959 user 0.032 sys 0.978 real
"assemble_addRead": 189 calls 0.020 user 0.000 sys 0.015 real
"assemble_buildGraph": 446 calls 0.479 user 0.010 sys 0.442 real
"assemble_computecigar": 274 calls 0.166 user 0.010 sys 0.150 real
"assemble_kg_build_calcsize": 446 calls 0.194 user 0.000 sys 0.228 real
"assemble_kg_build_clear": 608 calls 0.000 user 0.000 sys 0.019 real
"assemble_kg_build_prepare": 892 calls 0.207 user 0.010 sys 0.213 real
"assemble_kg_build_threading": 284 calls 0.286 user 0.010 sys 0.204 real
"assemble_kg_op1": 284 calls 0.080 user 0.010 sys 0.115 real
"assemble_kg_op2": 284 calls 0.020 user 0.000 sys 0.008 real
"assemble_kg_op3": 284 calls 0.000 user 0.000 sys 0.009 real
"assemble_sg_clean": 274 calls 0.011 user 0.000 sys 0.044 real
"assemble_sg_create": 274 calls 0.078 user 0.002 sys 0.068 real
"checkGraph": 189 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 189 calls 0.176 user 0.010 sys 0.157 real
advance: 189104 calls 20.500 user 0.873 sys 32.590 real
assemble_region: 189 calls 1.155 user 0.042 sys 1.154 real
build_pileup: 70986 calls 0.613 user 0.048 sys 1.221 real
build_stats: 71708 calls 5.222 user 0.278 sys 7.106 real
build_variants: 158 calls 0.000 user 0.000 sys 0.002 real
calc: 128714 calls 3.885 user 0.160 sys 6.978 real
calc_region: 158 calls 3.188 user 0.024 sys 3.415 real
call_region: 158 calls 0.149 user 0.000 sys 0.091 real
clip_region: 347 calls 0.061 user 0.000 sys 0.069 real
done: 1 calls 1.226 user 0.004 sys 1.229 real
execute: 1 calls 0.000 user 0.016 sys 28.923 real
fetch: 743546 calls 1.641 user 0.241 sys 2.207 real
fetch_ref: 745694 calls 1.658 user 0.808 sys 5.026 real
fetch_region: 189 calls 0.050 user 0.000 sys 0.017 real
fetch_vcf: 189104 calls 58.088 user 2.699 sys 104.945 real
idle: 47 calls 0.003 user 0.001 sys 25.877 real
init: 1 calls 0.090 user 0.020 sys 0.111 real
pairhmm: 454 calls 5.608 user 0.019 sys 5.670 real
realign: 158 calls 0.602 user 0.000 sys 0.725 real
region: 367297 calls 4.451 user 0.165 sys 4.867 real
tracker: 367297 calls 0.652 user 0.145 sys 1.471 real
trim_region: 189 calls 0.000 user 0.000 sys 0.004 real
overall: 346955776 mem 298.534 user 42.602 sys 31.504 real