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% @chr1:113724659, elapsed 1.2s, est remaining 22.4s, peak mem 144MB, user 11.3s, sys 0.7s, output queue size 5
progress 10% @chr2:3625914, elapsed 2.3s, est remaining 20.9s, peak mem 146MB, user 21.8s, sys 1.3s, output queue size 5
progress 15% @chr2:178588438, elapsed 3.5s, est remaining 19.9s, peak mem 147MB, user 32.3s, sys 2.0s, output queue size 9
progress 20% @chr3:57472446, elapsed 4.6s, est remaining 18.5s, peak mem 147MB, user 42.3s, sys 2.7s, output queue size 1
progress 25% @chr4:70603777, elapsed 5.8s, est remaining 17.5s, peak mem 148MB, user 53.3s, sys 3.4s, output queue size 8
progress 30% @chr5:135850325, elapsed 7.0s, est remaining 16.4s, peak mem 151MB, user 64.9s, sys 4.1s, output queue size 4
progress 35% @chr6:104849042, elapsed 8.1s, est remaining 15.0s, peak mem 152MB, user 75.5s, sys 4.8s, output queue size 3
progress 40% @chr7:106879419, elapsed 9.2s, est remaining 13.9s, peak mem 153MB, user 86.1s, sys 5.4s, output queue size 4
progress 45% @chr8:143821497, elapsed 10.4s, est remaining 12.7s, peak mem 153MB, user 97.2s, sys 6.2s, output queue size 1
progress 50% @chr10:21514996, elapsed 11.5s, est remaining 11.5s, peak mem 156MB, user 108.4s, sys 6.8s, output queue size 17
progress 55% @chr11:34135075, elapsed 12.6s, est remaining 10.3s, peak mem 156MB, user 119.2s, sys 7.5s, output queue size 4
progress 60% @chr12:12718707, elapsed 13.6s, est remaining 9.0s, peak mem 156MB, user 129.5s, sys 8.1s, output queue size 6
progress 65% @chr13:32078734, elapsed 14.6s, est remaining 7.9s, peak mem 156MB, user 139.7s, sys 8.8s, output queue size 10
progress 70% @chr15:35538174, elapsed 15.7s, est remaining 6.7s, peak mem 157MB, user 150.3s, sys 9.4s, output queue size 3
progress 75% @chr16:28491382, elapsed 16.9s, est remaining 5.6s, peak mem 158MB, user 161.0s, sys 9.9s, output queue size 1
progress 80% @chr17:40076771, elapsed 18.0s, est remaining 4.5s, peak mem 158MB, user 173.0s, sys 10.5s, output queue size 1
progress 85% @chr19:1795775, elapsed 19.2s, est remaining 3.4s, peak mem 159MB, user 185.2s, sys 11.0s, output queue size 14
progress 90% @chr19:54630974, elapsed 20.3s, est remaining 2.3s, peak mem 160MB, user 195.8s, sys 11.6s, output queue size 6
progress 95% @chr22:31944634, elapsed 23.2s, est remaining 1.2s, peak mem 362MB, user 224.2s, sys 12.7s, output queue size 10
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 24.2s, est remaining 0.0s, peak mem 362MB, user 232.2s, sys 13.3s, output queue size 424
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050654
  features: 1f8bfbff fffa320b
  extended: d19f47ab 00000018
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8175M CPU @ 2.50GHz
threads: 12 max 48
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 93248816
output file size: 53230
reads: 1502521
contig: 178193 intervals 76355618 bases
"assemble": 221 calls 0.820 user 0.011 sys 0.912 real
"assemble_addRead": 221 calls 0.000 user 0.000 sys 0.019 real
"assemble_buildGraph": 496 calls 0.341 user 0.010 sys 0.410 real
"assemble_computecigar": 329 calls 0.160 user 0.020 sys 0.136 real
"assemble_kg_build_calcsize": 496 calls 0.146 user 0.000 sys 0.183 real
"assemble_kg_build_clear": 650 calls 0.000 user 0.000 sys 0.020 real
"assemble_kg_build_prepare": 992 calls 0.189 user 0.002 sys 0.175 real
"assemble_kg_build_threading": 342 calls 0.195 user 0.010 sys 0.217 real
"assemble_kg_op1": 342 calls 0.100 user 0.000 sys 0.122 real
"assemble_kg_op2": 342 calls 0.010 user 0.000 sys 0.008 real
"assemble_kg_op3": 342 calls 0.010 user 0.000 sys 0.009 real
"assemble_sg_clean": 329 calls 0.050 user 0.000 sys 0.046 real
"assemble_sg_create": 329 calls 0.080 user 0.000 sys 0.070 real
"checkGraph": 221 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 221 calls 0.170 user 0.020 sys 0.143 real
advance: 189104 calls 24.929 user 0.559 sys 30.307 real
assemble_region: 221 calls 1.000 user 0.031 sys 1.077 real
build_pileup: 70986 calls 0.649 user 0.020 sys 1.047 real
build_stats: 71711 calls 4.427 user 0.122 sys 5.503 real
build_variants: 178 calls 0.000 user 0.000 sys 0.002 real
calc: 128717 calls 5.846 user 0.117 sys 7.494 real
calc_region: 178 calls 4.907 user 0.021 sys 5.090 real
call_region: 178 calls 0.090 user 0.000 sys 0.094 real
clip_region: 399 calls 0.070 user 0.000 sys 0.074 real
done: 1 calls 0.672 user 0.000 sys 0.677 real
execute: 1 calls 0.005 user 0.011 sys 24.219 real
fetch: 743546 calls 1.547 user 0.164 sys 1.935 real
fetch_ref: 745726 calls 3.339 user 0.688 sys 5.391 real
fetch_region: 221 calls 0.010 user 0.000 sys 0.016 real
fetch_vcf: 189104 calls 74.928 user 1.588 sys 96.257 real
idle: 35 calls 0.043 user 0.007 sys 13.328 real
init: 1 calls 0.079 user 0.001 sys 0.084 real
pairhmm: 837 calls 7.990 user 0.020 sys 8.117 real
realign: 178 calls 0.798 user 0.000 sys 0.854 real
region: 367297 calls 6.057 user 0.100 sys 6.460 real
tracker: 367297 calls 0.917 user 0.070 sys 1.361 real
trim_region: 221 calls 0.000 user 0.000 sys 0.003 real
overall: 379645952 mem 275.960 user 18.566 sys 25.639 real