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% @chr1:113705733, elapsed 1.5s, est remaining 28.3s, peak mem 144MB, user 12.9s, sys 1.9s, output queue size 3
progress 10% @chr2:3643344, elapsed 2.9s, est remaining 26.4s, peak mem 144MB, user 25.3s, sys 3.5s, output queue size 6
progress 15% @chr2:178600754, elapsed 4.4s, est remaining 24.7s, peak mem 145MB, user 38.2s, sys 5.2s, output queue size 13
progress 20% @chr3:57489409, elapsed 5.6s, est remaining 22.5s, peak mem 145MB, user 49.8s, sys 6.9s, output queue size 10
progress 25% @chr4:70596899, elapsed 7.0s, est remaining 21.1s, peak mem 145MB, user 63.0s, sys 8.4s, output queue size 10
progress 30% @chr5:135534877, elapsed 8.5s, est remaining 19.7s, peak mem 148MB, user 76.0s, sys 9.9s, output queue size 2
progress 35% @chr6:104850807, elapsed 9.7s, est remaining 18.0s, peak mem 148MB, user 87.6s, sys 11.4s, output queue size 7
progress 40% @chr7:106248199, elapsed 11.1s, est remaining 16.6s, peak mem 149MB, user 100.6s, sys 12.8s, output queue size 19
progress 45% @chr8:143820566, elapsed 12.4s, est remaining 15.2s, peak mem 149MB, user 113.5s, sys 14.2s, output queue size 1
progress 50% @chr10:21726144, elapsed 13.8s, est remaining 13.8s, peak mem 151MB, user 125.8s, sys 15.9s, output queue size 2
progress 55% @chr11:34136878, elapsed 15.1s, est remaining 12.4s, peak mem 151MB, user 138.0s, sys 17.3s, output queue size 6
progress 60% @chr12:12718707, elapsed 16.4s, est remaining 10.9s, peak mem 151MB, user 150.0s, sys 18.6s, output queue size 12
progress 65% @chr13:32078734, elapsed 17.8s, est remaining 9.6s, peak mem 151MB, user 163.0s, sys 19.9s, output queue size 10
progress 70% @chr15:35450585, elapsed 19.1s, est remaining 8.2s, peak mem 152MB, user 175.4s, sys 21.1s, output queue size 0
progress 75% @chr16:28494582, elapsed 20.3s, est remaining 6.8s, peak mem 153MB, user 187.5s, sys 22.4s, output queue size 4
progress 80% @chr17:40035622, elapsed 21.7s, est remaining 5.4s, peak mem 153MB, user 200.8s, sys 23.8s, output queue size 2
progress 85% @chr19:1805788, elapsed 23.1s, est remaining 4.1s, peak mem 154MB, user 214.1s, sys 25.2s, output queue size 2
progress 90% @chr19:54630974, elapsed 24.4s, est remaining 2.7s, peak mem 154MB, user 226.7s, sys 26.5s, output queue size 4
progress 95% @chr22:32067867, elapsed 27.5s, est remaining 1.4s, peak mem 351MB, user 255.1s, sys 28.2s, output queue size 75
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 28.6s, est remaining 0.0s, peak mem 351MB, user 265.2s, sys 30.1s, output queue size 7
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 93248813
output file size: 53230
reads: 1502521
contig: 178193 intervals 76355618 bases
"assemble": 221 calls 0.895 user 0.001 sys 0.934 real
"assemble_addRead": 221 calls 0.001 user 0.009 sys 0.014 real
"assemble_buildGraph": 496 calls 0.421 user 0.001 sys 0.419 real
"assemble_computecigar": 329 calls 0.111 user 0.019 sys 0.150 real
"assemble_kg_build_calcsize": 496 calls 0.190 user 0.000 sys 0.198 real
"assemble_kg_build_clear": 650 calls 0.000 user 0.000 sys 0.015 real
"assemble_kg_build_prepare": 992 calls 0.244 user 0.000 sys 0.189 real
"assemble_kg_build_threading": 342 calls 0.231 user 0.000 sys 0.213 real
"assemble_kg_op1": 342 calls 0.063 user 0.000 sys 0.120 real
"assemble_kg_op2": 342 calls 0.001 user 0.000 sys 0.009 real
"assemble_kg_op3": 342 calls 0.010 user 0.000 sys 0.010 real
"assemble_sg_clean": 329 calls 0.060 user 0.000 sys 0.047 real
"assemble_sg_create": 329 calls 0.042 user 0.000 sys 0.074 real
"checkGraph": 221 calls 0.010 user 0.000 sys 0.001 real
"findHaplotype": 221 calls 0.141 user 0.019 sys 0.158 real
advance: 189104 calls 18.117 user 0.848 sys 31.752 real
assemble_region: 221 calls 1.047 user 0.029 sys 1.109 real
build_pileup: 70986 calls 0.789 user 0.048 sys 1.208 real
build_stats: 71711 calls 5.008 user 0.214 sys 6.884 real
build_variants: 178 calls 0.000 user 0.000 sys 0.002 real
calc: 128717 calls 3.993 user 0.168 sys 6.767 real
calc_region: 178 calls 4.841 user 0.063 sys 5.135 real
call_region: 178 calls 0.105 user 0.000 sys 0.106 real
clip_region: 399 calls 0.070 user 0.000 sys 0.071 real
done: 1 calls 1.347 user 0.029 sys 1.382 real
execute: 1 calls 0.006 user 0.011 sys 28.667 real
fetch: 743546 calls 1.324 user 0.186 sys 1.942 real
fetch_ref: 745726 calls 1.698 user 0.867 sys 4.988 real
fetch_region: 221 calls 0.010 user 0.000 sys 0.015 real
fetch_vcf: 189104 calls 55.758 user 2.865 sys 104.844 real
idle: 47 calls 0.014 user 0.011 sys 26.018 real
init: 1 calls 0.086 user 0.029 sys 0.119 real
pairhmm: 837 calls 8.029 user 0.040 sys 8.127 real
realign: 178 calls 0.810 user 0.010 sys 0.950 real
region: 367297 calls 5.965 user 0.159 sys 6.539 real
tracker: 367297 calls 0.675 user 0.138 sys 1.457 real
trim_region: 221 calls 0.000 user 0.000 sys 0.003 real
overall: 368488448 mem 298.866 user 42.641 sys 31.326 real