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% @chr1:113711646, elapsed 1.4s, est remaining 26.9s, peak mem 141MB, user 12.5s, sys 1.6s, output queue size 4
progress 10% @chr2:3643344, elapsed 2.9s, est remaining 25.7s, peak mem 141MB, user 25.2s, sys 3.1s, output queue size 5
progress 15% @chr2:178604608, elapsed 4.4s, est remaining 24.7s, peak mem 143MB, user 38.3s, sys 4.8s, output queue size 12
progress 20% @chr3:57471372, elapsed 5.7s, est remaining 22.9s, peak mem 143MB, user 50.2s, sys 6.3s, output queue size 10
progress 25% @chr4:70602524, elapsed 7.2s, est remaining 21.7s, peak mem 144MB, user 63.2s, sys 8.0s, output queue size 7
progress 30% @chr5:135449354, elapsed 8.7s, est remaining 20.2s, peak mem 146MB, user 76.0s, sys 9.6s, output queue size 4
progress 35% @chr6:104957999, elapsed 10.0s, est remaining 18.5s, peak mem 148MB, user 88.1s, sys 10.8s, output queue size 3
progress 40% @chr7:106248199, elapsed 11.3s, est remaining 17.0s, peak mem 149MB, user 101.1s, sys 12.2s, output queue size 18
progress 45% @chr8:143810379, elapsed 12.7s, est remaining 15.5s, peak mem 149MB, user 114.2s, sys 13.7s, output queue size 3
progress 50% @chr10:21514996, elapsed 14.0s, est remaining 14.0s, peak mem 151MB, user 126.5s, sys 15.1s, output queue size 13
progress 55% @chr11:34124202, elapsed 15.4s, est remaining 12.6s, peak mem 151MB, user 138.9s, sys 16.5s, output queue size 5
progress 60% @chr12:12718707, elapsed 16.6s, est remaining 11.1s, peak mem 153MB, user 151.2s, sys 17.8s, output queue size 10
progress 65% @chr13:32078734, elapsed 18.1s, est remaining 9.7s, peak mem 153MB, user 164.5s, sys 19.0s, output queue size 10
progress 70% @chr15:35538174, elapsed 19.4s, est remaining 8.3s, peak mem 153MB, user 176.9s, sys 20.3s, output queue size 4
progress 75% @chr16:28488491, elapsed 20.8s, est remaining 6.9s, peak mem 153MB, user 189.3s, sys 21.5s, output queue size 4
progress 80% @chr17:40035622, elapsed 22.2s, est remaining 5.5s, peak mem 153MB, user 202.5s, sys 23.0s, output queue size 1
progress 85% @chr19:1799847, elapsed 23.5s, est remaining 4.1s, peak mem 154MB, user 215.2s, sys 24.4s, output queue size 3
progress 90% @chr19:54573779, elapsed 24.8s, est remaining 2.8s, peak mem 155MB, user 227.3s, sys 25.8s, output queue size 13
progress 95% @chr22:32067867, elapsed 27.8s, est remaining 1.5s, peak mem 331MB, user 256.5s, sys 27.5s, output queue size 233
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 28.9s, est remaining 0.0s, peak mem 331MB, user 267.1s, sys 28.8s, output queue size 251
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 74586805
output file size: 51111
reads: 1501816
contig: 178193 intervals 76355618 bases
"assemble": 189 calls 0.942 user 0.014 sys 0.970 real
"assemble_addRead": 189 calls 0.013 user 0.000 sys 0.015 real
"assemble_buildGraph": 446 calls 0.461 user 0.003 sys 0.436 real
"assemble_computecigar": 274 calls 0.136 user 0.009 sys 0.147 real
"assemble_kg_build_calcsize": 446 calls 0.243 user 0.000 sys 0.226 real
"assemble_kg_build_clear": 608 calls 0.010 user 0.000 sys 0.020 real
"assemble_kg_build_prepare": 892 calls 0.189 user 0.010 sys 0.214 real
"assemble_kg_build_threading": 284 calls 0.208 user 0.003 sys 0.199 real
"assemble_kg_op1": 284 calls 0.133 user 0.000 sys 0.113 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 0.045 user 0.000 sys 0.045 real
"assemble_sg_create": 274 calls 0.065 user 0.000 sys 0.066 real
"checkGraph": 189 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 189 calls 0.136 user 0.009 sys 0.153 real
advance: 189104 calls 19.683 user 0.839 sys 32.463 real
assemble_region: 189 calls 1.102 user 0.023 sys 1.142 real
build_pileup: 70986 calls 0.698 user 0.027 sys 1.219 real
build_stats: 71708 calls 5.139 user 0.244 sys 6.966 real
build_variants: 158 calls 0.010 user 0.000 sys 0.002 real
calc: 128714 calls 4.214 user 0.168 sys 6.974 real
calc_region: 158 calls 3.425 user 0.005 sys 3.688 real
call_region: 158 calls 0.072 user 0.000 sys 0.089 real
clip_region: 347 calls 0.050 user 0.000 sys 0.067 real
done: 1 calls 1.223 user 0.027 sys 1.255 real
execute: 1 calls 0.003 user 0.010 sys 28.964 real
fetch: 743546 calls 1.709 user 0.251 sys 2.218 real
fetch_ref: 745694 calls 1.470 user 0.718 sys 4.987 real
fetch_region: 189 calls 0.026 user 0.000 sys 0.017 real
fetch_vcf: 189104 calls 55.884 user 2.781 sys 104.909 real
idle: 46 calls 0.003 user 0.001 sys 26.027 real
init: 1 calls 0.100 user 0.010 sys 0.111 real
pairhmm: 454 calls 5.576 user 0.014 sys 5.637 real
realign: 158 calls 0.637 user 0.000 sys 0.708 real
region: 367297 calls 4.653 user 0.102 sys 5.128 real
tracker: 367297 calls 0.757 user 0.121 sys 1.460 real
trim_region: 189 calls 0.000 user 0.000 sys 0.004 real
overall: 347631616 mem 298.405 user 42.059 sys 31.589 real