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% @chr1:113697605, elapsed 1.5s, est remaining 28.3s, peak mem 141MB, user 12.8s, sys 1.9s, output queue size 5
progress 10% @chr2:3643344, elapsed 2.8s, est remaining 25.2s, peak mem 141MB, user 24.7s, sys 3.5s, output queue size 5
progress 15% @chr2:178609108, elapsed 4.1s, est remaining 23.5s, peak mem 143MB, user 36.9s, sys 4.9s, output queue size 12
progress 20% @chr3:57498400, elapsed 5.4s, est remaining 21.7s, peak mem 143MB, user 48.8s, sys 6.4s, output queue size 0
progress 25% @chr4:70596899, elapsed 6.9s, est remaining 20.6s, peak mem 143MB, user 61.6s, sys 8.1s, output queue size 4
progress 30% @chr5:135534877, elapsed 8.3s, est remaining 19.4s, peak mem 145MB, user 74.7s, sys 9.7s, output queue size 4
progress 35% @chr6:104791404, elapsed 9.6s, est remaining 17.8s, peak mem 147MB, user 86.2s, sys 11.1s, output queue size 7
progress 40% @chr7:106284249, elapsed 10.9s, est remaining 16.4s, peak mem 148MB, user 98.6s, sys 12.7s, output queue size 5
progress 45% @chr8:143810379, elapsed 12.3s, est remaining 15.0s, peak mem 149MB, user 111.3s, sys 14.1s, output queue size 2
progress 50% @chr10:21682125, elapsed 13.6s, est remaining 13.6s, peak mem 151MB, user 123.6s, sys 15.6s, output queue size 13
progress 55% @chr11:34136542, elapsed 14.9s, est remaining 12.2s, peak mem 152MB, user 135.7s, sys 16.8s, output queue size 0
progress 60% @chr12:12718707, elapsed 16.1s, est remaining 10.8s, peak mem 152MB, user 147.3s, sys 18.2s, output queue size 10
progress 65% @chr13:32124502, elapsed 17.5s, est remaining 9.4s, peak mem 152MB, user 159.8s, sys 19.5s, output queue size 10
progress 70% @chr15:35521993, elapsed 18.8s, est remaining 8.1s, peak mem 153MB, user 172.1s, sys 20.9s, output queue size 2
progress 75% @chr16:28488491, elapsed 20.1s, est remaining 6.7s, peak mem 154MB, user 184.4s, sys 22.2s, output queue size 4
progress 80% @chr17:40032956, elapsed 21.5s, est remaining 5.4s, peak mem 155MB, user 197.8s, sys 23.5s, output queue size 2
progress 85% @chr19:1806528, elapsed 22.8s, est remaining 4.0s, peak mem 155MB, user 210.1s, sys 24.9s, output queue size 3
progress 90% @chr19:54630974, elapsed 24.1s, est remaining 2.7s, peak mem 156MB, user 222.5s, sys 26.2s, output queue size 4
progress 95% @chr22:31937816, elapsed 27.1s, est remaining 1.4s, peak mem 342MB, user 251.5s, sys 28.0s, output queue size 1209
progress 100% @chrY:20759768, elapsed 28.4s, est remaining 0.0s, peak mem 342MB, user 263.1s, sys 29.6s, output queue size 203
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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 74586799
output file size: 51111
reads: 1501816
contig: 178193 intervals 76355618 bases
"assemble": 189 calls 0.958 user 0.040 sys 0.980 real
"assemble_addRead": 189 calls 0.030 user 0.000 sys 0.015 real
"assemble_buildGraph": 446 calls 0.463 user 0.018 sys 0.441 real
"assemble_computecigar": 274 calls 0.119 user 0.000 sys 0.152 real
"assemble_kg_build_calcsize": 446 calls 0.287 user 0.000 sys 0.227 real
"assemble_kg_build_clear": 608 calls 0.010 user 0.000 sys 0.019 real
"assemble_kg_build_prepare": 892 calls 0.184 user 0.019 sys 0.217 real
"assemble_kg_build_threading": 284 calls 0.176 user 0.018 sys 0.204 real
"assemble_kg_op1": 284 calls 0.090 user 0.000 sys 0.115 real
"assemble_kg_op2": 284 calls 0.000 user 0.000 sys 0.008 real
"assemble_kg_op3": 284 calls 0.010 user 0.000 sys 0.009 real
"assemble_sg_clean": 274 calls 0.052 user 0.000 sys 0.045 real
"assemble_sg_create": 274 calls 0.060 user 0.000 sys 0.066 real
"checkGraph": 189 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 189 calls 0.139 user 0.000 sys 0.158 real
advance: 189104 calls 19.414 user 0.831 sys 32.305 real
assemble_region: 189 calls 1.127 user 0.040 sys 1.157 real
build_pileup: 70986 calls 0.823 user 0.065 sys 1.200 real
build_stats: 71708 calls 5.305 user 0.346 sys 6.958 real
build_variants: 158 calls 0.000 user 0.000 sys 0.002 real
calc: 128714 calls 4.075 user 0.224 sys 6.897 real
calc_region: 158 calls 3.119 user 0.023 sys 3.404 real
call_region: 158 calls 0.119 user 0.000 sys 0.087 real
clip_region: 347 calls 0.055 user 0.000 sys 0.068 real
done: 1 calls 1.237 user 0.001 sys 1.238 real
execute: 1 calls 0.001 user 0.010 sys 28.389 real
fetch: 743546 calls 1.348 user 0.175 sys 2.166 real
fetch_ref: 745694 calls 1.891 user 0.810 sys 5.026 real
fetch_region: 189 calls 0.000 user 0.000 sys 0.017 real
fetch_vcf: 189104 calls 57.908 user 2.995 sys 104.199 real
idle: 47 calls 0.013 user 0.004 sys 25.900 real
init: 1 calls 0.080 user 0.030 sys 0.111 real
pairhmm: 454 calls 5.404 user 0.020 sys 5.536 real
realign: 158 calls 0.613 user 0.007 sys 0.720 real
region: 367297 calls 4.322 user 0.167 sys 4.859 real
tracker: 367297 calls 0.687 user 0.178 sys 1.463 real
trim_region: 189 calls 0.000 user 0.000 sys 0.004 real
overall: 358711296 mem 294.846 user 42.487 sys 30.966 real