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% @chr1:113711646, elapsed 1.5s, est remaining 28.9s, peak mem 142MB, user 13.0s, sys 1.8s, output queue size 3
progress 10% @chr2:3643344, elapsed 3.0s, est remaining 26.6s, peak mem 143MB, user 25.3s, sys 3.5s, output queue size 1
progress 15% @chr2:178609108, elapsed 4.4s, est remaining 25.1s, peak mem 144MB, user 38.5s, sys 5.0s, output queue size 12
progress 20% @chr3:57483276, elapsed 5.8s, est remaining 23.1s, peak mem 144MB, user 50.6s, sys 6.5s, output queue size 2
progress 25% @chr4:70603777, elapsed 7.2s, est remaining 21.6s, peak mem 144MB, user 63.3s, sys 8.3s, output queue size 10
progress 30% @chr5:135534877, elapsed 8.6s, est remaining 20.2s, peak mem 146MB, user 76.5s, sys 10.1s, output queue size 11
progress 35% @chr6:104957999, elapsed 9.9s, est remaining 18.5s, peak mem 146MB, user 88.4s, sys 11.6s, output queue size 3
progress 40% @chr7:106872437, elapsed 11.3s, est remaining 17.0s, peak mem 146MB, user 101.4s, sys 13.2s, output queue size 2
progress 45% @chr8:143821497, elapsed 12.7s, est remaining 15.5s, peak mem 146MB, user 114.5s, sys 14.7s, output queue size 0
progress 50% @chr10:21726144, elapsed 14.1s, est remaining 14.1s, peak mem 148MB, user 127.3s, sys 16.1s, output queue size 2
progress 55% @chr11:34136542, elapsed 15.4s, est remaining 12.6s, peak mem 148MB, user 139.6s, sys 17.6s, output queue size 3
progress 60% @chr12:12718707, elapsed 16.7s, est remaining 11.1s, peak mem 148MB, user 151.6s, sys 18.8s, output queue size 13
progress 65% @chr13:32078734, elapsed 18.0s, est remaining 9.7s, peak mem 148MB, user 164.2s, sys 20.6s, output queue size 10
progress 70% @chr15:34960674, elapsed 19.3s, est remaining 8.3s, peak mem 149MB, user 176.3s, sys 22.1s, output queue size 8
progress 75% @chr16:28494582, elapsed 20.7s, est remaining 6.9s, peak mem 151MB, user 189.0s, sys 23.4s, output queue size 6
progress 80% @chr17:40032956, elapsed 22.0s, est remaining 5.5s, peak mem 152MB, user 202.3s, sys 24.6s, output queue size 1
progress 85% @chr19:1806528, elapsed 23.3s, est remaining 4.1s, peak mem 152MB, user 214.6s, sys 25.9s, output queue size 3
progress 90% @chr19:54630974, elapsed 24.7s, est remaining 2.7s, peak mem 152MB, user 227.1s, sys 27.1s, output queue size 4
progress 95% @chr22:32067867, elapsed 27.8s, est remaining 1.5s, peak mem 332MB, user 257.3s, sys 28.8s, output queue size 10
progress 100% @chrY:21905713, elapsed 28.9s, est remaining 0.0s, peak mem 332MB, user 267.7s, sys 30.0s, output queue size 455
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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 71692763
output file size: 46614
reads: 1501772
contig: 178193 intervals 76355618 bases
"assemble": 183 calls 0.944 user 0.040 sys 0.918 real
"assemble_addRead": 183 calls 0.010 user 0.000 sys 0.014 real
"assemble_buildGraph": 422 calls 0.447 user 0.020 sys 0.406 real
"assemble_computecigar": 264 calls 0.169 user 0.010 sys 0.176 real
"assemble_kg_build_calcsize": 422 calls 0.220 user 0.010 sys 0.204 real
"assemble_kg_build_clear": 573 calls 0.020 user 0.000 sys 0.017 real
"assemble_kg_build_prepare": 844 calls 0.217 user 0.019 sys 0.201 real
"assemble_kg_build_threading": 271 calls 0.217 user 0.010 sys 0.192 real
"assemble_kg_op1": 271 calls 0.108 user 0.000 sys 0.105 real
"assemble_kg_op2": 271 calls 0.010 user 0.000 sys 0.008 real
"assemble_kg_op3": 271 calls 0.020 user 0.000 sys 0.008 real
"assemble_sg_clean": 264 calls 0.031 user 0.000 sys 0.045 real
"assemble_sg_create": 264 calls 0.063 user 0.000 sys 0.068 real
"checkGraph": 183 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 183 calls 0.197 user 0.020 sys 0.184 real
advance: 189104 calls 19.122 user 0.749 sys 32.523 real
assemble_region: 183 calls 1.152 user 0.060 sys 1.119 real
build_pileup: 70974 calls 0.683 user 0.065 sys 1.208 real
build_stats: 71688 calls 4.701 user 0.321 sys 6.965 real
build_variants: 142 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 3.831 user 0.161 sys 6.947 real
calc_region: 142 calls 4.130 user 0.007 sys 4.250 real
call_region: 142 calls 0.066 user 0.000 sys 0.079 real
clip_region: 325 calls 0.053 user 0.000 sys 0.059 real
done: 1 calls 1.244 user 0.011 sys 1.262 real
execute: 1 calls 0.005 user 0.011 sys 28.888 real
fetch: 743546 calls 1.622 user 0.157 sys 2.206 real
fetch_ref: 745688 calls 1.647 user 0.765 sys 5.012 real
fetch_region: 183 calls 0.001 user 0.000 sys 0.015 real
fetch_vcf: 189104 calls 54.144 user 2.723 sys 105.418 real
idle: 47 calls 0.002 user 0.001 sys 26.071 real
init: 1 calls 0.110 user 0.020 sys 0.122 real
pairhmm: 472 calls 6.585 user 0.010 sys 6.689 real
realign: 142 calls 0.534 user 0.000 sys 0.560 real
region: 367297 calls 5.349 user 0.112 sys 5.664 real
tracker: 367297 calls 0.615 user 0.105 sys 1.454 real
trim_region: 183 calls 0.010 user 0.000 sys 0.005 real
overall: 348868608 mem 299.162 user 42.984 sys 31.566 real