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% @chr1:113703957, elapsed 1.4s, est remaining 26.5s, peak mem 143MB, user 13.0s, sys 1.3s, output queue size 4
progress 10% @chr2:3625914, elapsed 2.6s, est remaining 23.8s, peak mem 143MB, user 24.6s, sys 2.7s, output queue size 5
progress 15% @chr2:178588438, elapsed 4.1s, est remaining 23.3s, peak mem 145MB, user 37.7s, sys 4.2s, output queue size 12
progress 20% @chr3:57483276, elapsed 5.5s, est remaining 21.8s, peak mem 145MB, user 49.6s, sys 5.8s, output queue size 0
progress 25% @chr4:70598256, elapsed 6.9s, est remaining 20.8s, peak mem 145MB, user 62.6s, sys 7.5s, output queue size 7
progress 30% @chr5:135850325, elapsed 8.4s, est remaining 19.5s, peak mem 146MB, user 75.8s, sys 9.0s, output queue size 4
progress 35% @chr6:104957999, elapsed 9.7s, est remaining 17.9s, peak mem 146MB, user 87.7s, sys 10.5s, output queue size 2
progress 40% @chr7:106248199, elapsed 11.0s, est remaining 16.5s, peak mem 147MB, user 100.2s, sys 12.0s, output queue size 17
progress 45% @chr8:143835562, elapsed 12.4s, est remaining 15.1s, peak mem 148MB, user 113.2s, sys 13.3s, output queue size 0
progress 50% @chr10:21670349, elapsed 13.7s, est remaining 13.7s, peak mem 151MB, user 125.5s, sys 14.7s, output queue size 3
progress 55% @chr11:34135075, elapsed 14.9s, est remaining 12.2s, peak mem 153MB, user 137.6s, sys 16.0s, output queue size 5
progress 60% @chr12:12718707, elapsed 16.2s, est remaining 10.8s, peak mem 153MB, user 149.3s, sys 17.4s, output queue size 13
progress 65% @chr13:32078734, elapsed 17.5s, est remaining 9.4s, peak mem 154MB, user 161.6s, sys 18.9s, output queue size 10
progress 70% @chr15:35381722, elapsed 18.8s, est remaining 8.1s, peak mem 154MB, user 173.8s, sys 20.2s, output queue size 2
progress 75% @chr16:28482005, elapsed 20.1s, est remaining 6.7s, peak mem 155MB, user 185.5s, sys 21.6s, output queue size 6
progress 80% @chr17:40076771, elapsed 21.5s, est remaining 5.4s, peak mem 155MB, user 198.6s, sys 22.9s, output queue size 3
progress 85% @chr19:1806528, elapsed 22.8s, est remaining 4.0s, peak mem 155MB, user 211.1s, sys 24.3s, output queue size 3
progress 90% @chr19:54630974, elapsed 24.1s, est remaining 2.7s, peak mem 157MB, user 223.6s, sys 25.4s, output queue size 4
progress 95% @chr22:32068396, elapsed 27.1s, est remaining 1.4s, peak mem 336MB, user 253.0s, sys 26.9s, output queue size 467
progress 100% @chrY:18546688, elapsed 28.4s, est remaining 0.0s, peak mem 336MB, user 264.4s, sys 28.4s, output queue size 445
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 74586815
output file size: 51111
reads: 1501816
contig: 178193 intervals 76355618 bases
"assemble": 189 calls 0.880 user 0.000 sys 0.962 real
"assemble_addRead": 189 calls 0.020 user 0.000 sys 0.015 real
"assemble_buildGraph": 446 calls 0.430 user 0.000 sys 0.436 real
"assemble_computecigar": 274 calls 0.120 user 0.020 sys 0.148 real
"assemble_kg_build_calcsize": 446 calls 0.270 user 0.000 sys 0.229 real
"assemble_kg_build_clear": 608 calls 0.030 user 0.000 sys 0.019 real
"assemble_kg_build_prepare": 892 calls 0.150 user 0.000 sys 0.213 real
"assemble_kg_build_threading": 284 calls 0.150 user 0.000 sys 0.197 real
"assemble_kg_op1": 284 calls 0.130 user 0.000 sys 0.112 real
"assemble_kg_op2": 284 calls 0.010 user 0.000 sys 0.008 real
"assemble_kg_op3": 284 calls 0.000 user 0.000 sys 0.008 real
"assemble_sg_clean": 274 calls 0.020 user 0.000 sys 0.044 real
"assemble_sg_create": 274 calls 0.090 user 0.000 sys 0.065 real
"checkGraph": 189 calls 0.006 user 0.000 sys 0.001 real
"findHaplotype": 189 calls 0.120 user 0.020 sys 0.155 real
advance: 189104 calls 20.284 user 0.852 sys 32.200 real
assemble_region: 189 calls 1.026 user 0.020 sys 1.136 real
build_pileup: 70986 calls 0.765 user 0.044 sys 1.189 real
build_stats: 71708 calls 4.742 user 0.188 sys 6.885 real
build_variants: 158 calls 0.000 user 0.000 sys 0.002 real
calc: 128714 calls 4.253 user 0.146 sys 6.887 real
calc_region: 158 calls 3.548 user 0.006 sys 3.715 real
call_region: 158 calls 0.114 user 0.000 sys 0.087 real
clip_region: 347 calls 0.060 user 0.000 sys 0.067 real
done: 1 calls 1.214 user 0.006 sys 1.224 real
execute: 1 calls 0.000 user 0.017 sys 28.413 real
fetch: 743546 calls 1.398 user 0.251 sys 2.113 real
fetch_ref: 745694 calls 1.545 user 0.815 sys 4.976 real
fetch_region: 189 calls 0.020 user 0.000 sys 0.017 real
fetch_vcf: 189104 calls 58.470 user 2.809 sys 104.611 real
idle: 47 calls 0.001 user 0.001 sys 25.898 real
init: 1 calls 0.080 user 0.030 sys 0.111 real
pairhmm: 454 calls 5.712 user 0.010 sys 5.756 real
realign: 158 calls 0.710 user 0.000 sys 0.713 real
region: 367297 calls 4.665 user 0.136 sys 5.145 real
tracker: 367297 calls 0.605 user 0.117 sys 1.425 real
trim_region: 189 calls 0.010 user 0.000 sys 0.004 real
overall: 353091584 mem 296.547 user 41.007 sys 31.009 real