cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i reference-NA12878-downsampled-500k.bam -i HCC1395_BL.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 HCC1395_BL --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_1.tnseq.vcf.gz --algo OrientationBias --tumor_sample HCC1395_BL negative_somatic_control_1.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_BL --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments negative_somatic_control_1.tnseq.segments negative_somatic_control_1.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113682112, 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 2.6s, est remaining 23.8s, peak mem 143MB, user 24.2s, sys 3.4s, output queue size 6
progress 15% @chr2:178600754, elapsed 4.0s, est remaining 22.7s, peak mem 143MB, user 36.6s, sys 5.0s, output queue size 12
progress 20% @chr3:57489409, elapsed 5.3s, est remaining 21.3s, peak mem 144MB, user 48.6s, sys 6.4s, output queue size 0
progress 25% @chr4:70598256, elapsed 6.7s, est remaining 20.2s, peak mem 144MB, user 61.8s, sys 7.9s, output queue size 8
progress 30% @chr5:135571753, elapsed 8.2s, est remaining 19.1s, peak mem 146MB, user 75.2s, sys 9.5s, output queue size 4
progress 35% @chr6:104957999, elapsed 9.5s, est remaining 17.7s, peak mem 148MB, user 87.3s, sys 10.8s, output queue size 2
progress 40% @chr7:106284249, elapsed 10.9s, est remaining 16.4s, peak mem 148MB, user 100.0s, sys 12.4s, output queue size 5
progress 45% @chr8:143821497, elapsed 12.3s, est remaining 15.1s, peak mem 149MB, user 113.0s, sys 13.8s, output queue size 1
progress 50% @chr10:21514996, elapsed 13.7s, est remaining 13.7s, peak mem 151MB, user 126.1s, sys 15.0s, output queue size 13
progress 55% @chr11:34136878, elapsed 15.0s, est remaining 12.3s, peak mem 151MB, user 138.7s, sys 16.4s, output queue size 2
progress 60% @chr12:12718707, elapsed 16.3s, est remaining 10.9s, peak mem 152MB, user 150.4s, sys 18.0s, output queue size 10
progress 65% @chr13:32078734, elapsed 17.7s, est remaining 9.5s, peak mem 152MB, user 162.7s, sys 19.4s, output queue size 10
progress 70% @chr15:35381722, elapsed 19.0s, est remaining 8.1s, peak mem 152MB, user 175.4s, sys 20.8s, output queue size 2
progress 75% @chr16:28494582, elapsed 20.3s, est remaining 6.8s, peak mem 152MB, user 187.6s, sys 22.3s, output queue size 4
progress 80% @chr17:40034816, elapsed 21.8s, est remaining 5.4s, peak mem 153MB, user 201.2s, sys 23.7s, output queue size 3
progress 85% @chr19:1652201, elapsed 23.1s, est remaining 4.1s, peak mem 153MB, user 214.3s, sys 25.2s, output queue size 15
progress 90% @chr19:54630974, elapsed 24.5s, est remaining 2.7s, peak mem 154MB, user 226.9s, sys 26.5s, output queue size 2
progress 95% @chr22:32068396, elapsed 27.6s, est remaining 1.5s, peak mem 335MB, user 256.9s, sys 28.4s, output queue size 10
progress 100% @chrY:21542591, elapsed 28.8s, est remaining 0.0s, peak mem 335MB, user 267.8s, sys 29.8s, output queue size 507
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 71692759
output file size: 46614
reads: 1501772
contig: 178193 intervals 76355618 bases
"assemble": 183 calls 0.928 user 0.022 sys 0.889 real
"assemble_addRead": 183 calls 0.010 user 0.000 sys 0.013 real
"assemble_buildGraph": 422 calls 0.439 user 0.010 sys 0.392 real
"assemble_computecigar": 264 calls 0.150 user 0.020 sys 0.177 real
"assemble_kg_build_calcsize": 422 calls 0.207 user 0.010 sys 0.199 real
"assemble_kg_build_clear": 573 calls 0.022 user 0.000 sys 0.016 real
"assemble_kg_build_prepare": 844 calls 0.174 user 0.011 sys 0.193 real
"assemble_kg_build_threading": 271 calls 0.212 user 0.000 sys 0.184 real
"assemble_kg_op1": 271 calls 0.103 user 0.000 sys 0.102 real
"assemble_kg_op2": 271 calls 0.020 user 0.000 sys 0.008 real
"assemble_kg_op3": 271 calls 0.000 user 0.000 sys 0.008 real
"assemble_sg_clean": 264 calls 0.054 user 0.000 sys 0.046 real
"assemble_sg_create": 264 calls 0.038 user 0.001 sys 0.067 real
"checkGraph": 183 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 183 calls 0.150 user 0.020 sys 0.185 real
advance: 189104 calls 20.707 user 0.901 sys 32.703 real
assemble_region: 183 calls 1.088 user 0.042 sys 1.091 real
build_pileup: 70974 calls 0.692 user 0.060 sys 1.206 real
build_stats: 71688 calls 4.704 user 0.243 sys 6.888 real
build_variants: 142 calls 0.000 user 0.000 sys 0.002 real
calc: 128670 calls 4.204 user 0.144 sys 6.977 real
calc_region: 142 calls 4.316 user 0.034 sys 4.385 real
call_region: 142 calls 0.090 user 0.010 sys 0.078 real
clip_region: 325 calls 0.060 user 0.000 sys 0.055 real
done: 1 calls 1.255 user 0.000 sys 1.259 real
execute: 1 calls 0.003 user 0.011 sys 28.801 real
fetch: 743546 calls 1.542 user 0.217 sys 2.116 real
fetch_ref: 745688 calls 1.546 user 0.883 sys 5.079 real
fetch_region: 183 calls 0.000 user 0.000 sys 0.014 real
fetch_vcf: 189104 calls 59.458 user 3.056 sys 106.273 real
idle: 47 calls 0.003 user 0.001 sys 26.400 real
init: 1 calls 0.120 user 0.020 sys 0.142 real
pairhmm: 472 calls 6.885 user 0.031 sys 6.858 real
realign: 142 calls 0.561 user 0.009 sys 0.579 real
region: 367297 calls 5.502 user 0.143 sys 5.771 real
tracker: 367297 calls 0.813 user 0.166 sys 1.463 real
trim_region: 183 calls 0.000 user 0.000 sys 0.004 real
overall: 351891456 mem 300.649 user 42.618 sys 31.452 real