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_tissue.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_tissue --normal_sample reference-NA12878 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz positive_somatic_control_2.tnseq.vcf.gz --algo OrientationBias --tumor_sample Sig_18_tissue positive_somatic_control_2.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample Sig_18_tissue --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments positive_somatic_control_2.tnseq.segments positive_somatic_control_2.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113700694, elapsed 1.4s, est remaining 25.7s, peak mem 142MB, user 12.4s, sys 1.7s, output queue size 4
progress 10% @chr2:3643344, elapsed 2.7s, est remaining 24.7s, peak mem 143MB, user 24.8s, sys 3.1s, output queue size 7
progress 15% @chr2:178606921, elapsed 4.2s, est remaining 24.1s, peak mem 144MB, user 37.9s, sys 4.8s, output queue size 12
progress 20% @chr3:57498400, elapsed 5.6s, est remaining 22.4s, peak mem 144MB, user 50.2s, sys 6.1s, output queue size 27
progress 25% @chr4:70598256, elapsed 7.1s, est remaining 21.2s, peak mem 144MB, user 63.1s, sys 7.7s, output queue size 3
progress 30% @chr5:135534877, elapsed 8.5s, est remaining 19.9s, peak mem 147MB, user 76.1s, sys 9.4s, output queue size 3
progress 35% @chr6:104791404, elapsed 9.8s, est remaining 18.3s, peak mem 147MB, user 88.1s, sys 10.6s, output queue size 7
progress 40% @chr7:106248199, elapsed 11.2s, est remaining 16.8s, peak mem 149MB, user 100.9s, sys 12.2s, output queue size 17
progress 45% @chr8:143835562, elapsed 12.5s, est remaining 15.3s, peak mem 151MB, user 113.7s, sys 13.5s, output queue size 1
progress 50% @chr10:21514996, elapsed 13.8s, est remaining 13.8s, peak mem 153MB, user 125.6s, sys 15.2s, output queue size 14
progress 55% @chr11:34136542, elapsed 15.1s, est remaining 12.4s, peak mem 153MB, user 138.1s, sys 16.7s, output queue size 0
progress 60% @chr12:12718707, elapsed 16.4s, est remaining 10.9s, peak mem 153MB, user 150.0s, sys 18.0s, output queue size 13
progress 65% @chr13:32078734, elapsed 17.8s, est remaining 9.6s, peak mem 153MB, user 162.8s, sys 19.6s, output queue size 10
progress 70% @chr15:35538174, elapsed 19.1s, est remaining 8.2s, peak mem 153MB, user 175.0s, sys 21.1s, output queue size 8
progress 75% @chr16:28489190, elapsed 20.4s, est remaining 6.8s, peak mem 154MB, user 187.3s, sys 22.4s, output queue size 4
progress 80% @chr17:40032956, elapsed 21.8s, est remaining 5.5s, peak mem 154MB, user 200.5s, sys 23.7s, output queue size 2
progress 85% @chr19:1806528, elapsed 23.1s, est remaining 4.1s, peak mem 154MB, user 212.5s, sys 25.3s, output queue size 2
progress 90% @chr19:54630974, elapsed 24.4s, est remaining 2.7s, peak mem 154MB, user 224.9s, sys 26.3s, output queue size 3
progress 95% @chr22:32043182, elapsed 27.9s, est remaining 1.5s, peak mem 356MB, user 257.1s, sys 28.1s, output queue size 789
progress 100% @chrY:23191952, elapsed 29.2s, est remaining 0.0s, peak mem 356MB, user 268.4s, sys 29.8s, output queue size 328
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 93248819
output file size: 53230
reads: 1502521
contig: 178193 intervals 76355618 bases
"assemble": 221 calls 1.043 user 0.046 sys 1.132 real
"assemble_addRead": 221 calls 0.030 user 0.000 sys 0.018 real
"assemble_buildGraph": 496 calls 0.509 user 0.025 sys 0.522 real
"assemble_computecigar": 329 calls 0.165 user 0.000 sys 0.184 real
"assemble_kg_build_calcsize": 496 calls 0.201 user 0.000 sys 0.257 real
"assemble_kg_build_clear": 650 calls 0.030 user 0.000 sys 0.022 real
"assemble_kg_build_prepare": 992 calls 0.239 user 0.020 sys 0.223 real
"assemble_kg_build_threading": 342 calls 0.288 user 0.025 sys 0.254 real
"assemble_kg_op1": 342 calls 0.072 user 0.000 sys 0.143 real
"assemble_kg_op2": 342 calls 0.000 user 0.000 sys 0.009 real
"assemble_kg_op3": 342 calls 0.000 user 0.000 sys 0.010 real
"assemble_sg_clean": 329 calls 0.061 user 0.000 sys 0.056 real
"assemble_sg_create": 329 calls 0.071 user 0.000 sys 0.083 real
"checkGraph": 221 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 221 calls 0.170 user 0.000 sys 0.193 real
advance: 189104 calls 20.140 user 0.815 sys 32.770 real
assemble_region: 221 calls 1.243 user 0.047 sys 1.348 real
build_pileup: 70986 calls 0.686 user 0.023 sys 1.199 real
build_stats: 71711 calls 5.073 user 0.247 sys 7.042 real
build_variants: 178 calls 0.020 user 0.000 sys 0.002 real
calc: 128717 calls 4.400 user 0.157 sys 6.940 real
calc_region: 178 calls 5.696 user 0.036 sys 5.774 real
call_region: 178 calls 0.114 user 0.000 sys 0.124 real
clip_region: 399 calls 0.050 user 0.000 sys 0.086 real
done: 1 calls 1.339 user 0.000 sys 1.342 real
execute: 1 calls 0.004 user 0.011 sys 29.195 real
fetch: 743546 calls 1.555 user 0.195 sys 2.184 real
fetch_ref: 745726 calls 1.707 user 1.008 sys 5.074 real
fetch_region: 221 calls 0.000 user 0.000 sys 0.019 real
fetch_vcf: 189104 calls 56.674 user 2.904 sys 105.044 real
idle: 47 calls 0.007 user 0.010 sys 25.967 real
init: 1 calls 0.106 user 0.009 sys 0.118 real
pairhmm: 837 calls 9.416 user 0.013 sys 9.294 real
realign: 178 calls 1.080 user 0.011 sys 1.090 real
region: 367297 calls 6.974 user 0.152 sys 7.426 real
tracker: 367297 calls 0.684 user 0.177 sys 1.435 real
trim_region: 221 calls 0.000 user 0.000 sys 0.004 real
overall: 374329344 mem 301.214 user 43.243 sys 31.776 real