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% @chr1:113682797, elapsed 1.2s, est remaining 23.3s, peak mem 143MB, user 11.1s, sys 1.6s, output queue size 5
progress 10% @chr2:3603546, elapsed 2.5s, est remaining 22.1s, peak mem 144MB, user 22.2s, sys 3.2s, output queue size 6
progress 15% @chr2:178606921, elapsed 3.9s, est remaining 21.9s, peak mem 145MB, user 35.0s, sys 4.7s, output queue size 12
progress 20% @chr3:57483276, elapsed 5.2s, est remaining 20.9s, peak mem 145MB, user 47.0s, sys 6.0s, output queue size 2
progress 25% @chr4:70480699, elapsed 6.7s, est remaining 20.0s, peak mem 145MB, user 59.7s, sys 7.6s, output queue size 15
progress 30% @chr5:135873921, elapsed 8.1s, est remaining 18.8s, peak mem 149MB, user 72.3s, sys 9.1s, output queue size 4
progress 35% @chr6:104957999, elapsed 9.3s, est remaining 17.3s, peak mem 149MB, user 83.7s, sys 10.4s, output queue size 3
progress 40% @chr7:106284249, elapsed 10.7s, est remaining 16.0s, peak mem 151MB, user 96.1s, sys 12.0s, output queue size 5
progress 45% @chr8:143820566, elapsed 12.0s, est remaining 14.7s, peak mem 152MB, user 108.7s, sys 13.3s, output queue size 3
progress 50% @chr10:21514996, elapsed 13.3s, est remaining 13.3s, peak mem 154MB, user 120.7s, sys 14.7s, output queue size 14
progress 55% @chr11:34132025, elapsed 14.6s, est remaining 11.9s, peak mem 155MB, user 132.8s, sys 16.2s, output queue size 9
progress 60% @chr12:12718707, elapsed 15.9s, est remaining 10.6s, peak mem 155MB, user 144.4s, sys 17.6s, output queue size 15
progress 65% @chr13:32078734, elapsed 17.2s, est remaining 9.2s, peak mem 156MB, user 156.9s, sys 18.9s, output queue size 10
progress 70% @chr15:35372050, elapsed 18.5s, est remaining 7.9s, peak mem 156MB, user 169.1s, sys 20.3s, output queue size 9
progress 75% @chr16:28489190, elapsed 19.7s, est remaining 6.6s, peak mem 156MB, user 181.0s, sys 21.6s, output queue size 2
progress 80% @chr17:40034816, elapsed 21.1s, est remaining 5.3s, peak mem 156MB, user 194.0s, sys 22.9s, output queue size 1
progress 85% @chr19:1652201, elapsed 22.4s, est remaining 4.0s, peak mem 157MB, user 206.3s, sys 24.2s, output queue size 15
progress 90% @chr19:54630974, elapsed 23.7s, est remaining 2.6s, peak mem 157MB, user 218.5s, sys 25.3s, output queue size 2
progress 95% @chr22:32081766, elapsed 27.0s, est remaining 1.4s, peak mem 354MB, user 250.6s, sys 27.0s, output queue size 528
progress 100% @chrY:20761184, elapsed 28.2s, est remaining 0.0s, peak mem 354MB, user 261.8s, sys 28.4s, output queue size 445
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 93248819
output file size: 53230
reads: 1502521
contig: 178193 intervals 76355618 bases
"assemble": 221 calls 1.001 user 0.038 sys 1.095 real
"assemble_addRead": 221 calls 0.021 user 0.009 sys 0.017 real
"assemble_buildGraph": 496 calls 0.492 user 0.018 sys 0.502 real
"assemble_computecigar": 329 calls 0.165 user 0.009 sys 0.174 real
"assemble_kg_build_calcsize": 496 calls 0.240 user 0.000 sys 0.244 real
"assemble_kg_build_clear": 650 calls 0.040 user 0.000 sys 0.022 real
"assemble_kg_build_prepare": 992 calls 0.156 user 0.000 sys 0.215 real
"assemble_kg_build_threading": 342 calls 0.232 user 0.018 sys 0.248 real
"assemble_kg_op1": 342 calls 0.102 user 0.010 sys 0.140 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 0.060 user 0.000 sys 0.055 real
"assemble_sg_create": 329 calls 0.104 user 0.000 sys 0.082 real
"checkGraph": 221 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 221 calls 0.182 user 0.009 sys 0.183 real
advance: 189104 calls 19.017 user 0.876 sys 32.165 real
assemble_region: 221 calls 1.203 user 0.056 sys 1.300 real
build_pileup: 70986 calls 0.656 user 0.032 sys 1.148 real
build_stats: 71711 calls 4.439 user 0.187 sys 6.815 real
build_variants: 178 calls 0.000 user 0.000 sys 0.002 real
calc: 128717 calls 3.733 user 0.111 sys 6.776 real
calc_region: 178 calls 5.599 user 0.044 sys 5.796 real
call_region: 178 calls 0.130 user 0.000 sys 0.120 real
clip_region: 399 calls 0.070 user 0.000 sys 0.084 real
done: 1 calls 1.326 user 0.002 sys 1.331 real
execute: 1 calls 0.006 user 0.011 sys 28.284 real
fetch: 743546 calls 1.516 user 0.211 sys 2.122 real
fetch_ref: 745726 calls 1.718 user 0.789 sys 4.844 real
fetch_region: 221 calls 0.010 user 0.000 sys 0.018 real
fetch_vcf: 189104 calls 54.098 user 2.365 sys 102.954 real
idle: 47 calls 0.009 user 0.006 sys 25.854 real
init: 1 calls 0.090 user 0.020 sys 0.111 real
pairhmm: 837 calls 9.357 user 0.039 sys 9.486 real
realign: 178 calls 0.974 user 0.000 sys 1.026 real
region: 367297 calls 6.893 user 0.209 sys 7.394 real
tracker: 367297 calls 0.627 user 0.112 sys 1.383 real
trim_region: 221 calls 0.000 user 0.000 sys 0.004 real
overall: 372174848 mem 294.825 user 40.937 sys 30.849 real