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% @chr1:110672982, elapsed 1.9s, est remaining 36.7s, peak mem 139MB, user 10.0s, sys 0.9s, output queue size 291
progress 10% @chr2:3682842, elapsed 3.7s, est remaining 33.6s, peak mem 140MB, user 19.0s, sys 1.8s, output queue size 61
progress 15% @chr2:178616379, elapsed 5.8s, est remaining 32.8s, peak mem 141MB, user 28.4s, sys 2.7s, output queue size 154
progress 20% @chr3:57510690, elapsed 7.6s, est remaining 30.2s, peak mem 141MB, user 37.4s, sys 3.5s, output queue size 113
progress 25% @chr4:70641915, elapsed 9.9s, est remaining 29.7s, peak mem 142MB, user 46.8s, sys 4.3s, output queue size 101
progress 30% @chr5:135534877, elapsed 11.9s, est remaining 27.8s, peak mem 143MB, user 56.7s, sys 5.2s, output queue size 182
progress 35% @chr6:104850807, elapsed 13.8s, est remaining 25.6s, peak mem 144MB, user 65.6s, sys 5.7s, output queue size 133
progress 40% @chr7:106867451, elapsed 15.7s, est remaining 23.6s, peak mem 145MB, user 75.0s, sys 6.7s, output queue size 169
progress 45% @chr8:143816420, elapsed 17.8s, est remaining 21.8s, peak mem 145MB, user 84.8s, sys 7.5s, output queue size 39
progress 50% @chr10:21733404, elapsed 20.0s, est remaining 20.0s, peak mem 146MB, user 94.3s, sys 8.2s, output queue size 58
progress 55% @chr11:34140300, elapsed 22.1s, est remaining 18.1s, peak mem 148MB, user 103.1s, sys 9.0s, output queue size 92
progress 60% @chr12:11752319, elapsed 24.3s, est remaining 16.2s, peak mem 148MB, user 111.7s, sys 9.7s, output queue size 102
progress 65% @chr13:32179575, elapsed 26.5s, est remaining 14.3s, peak mem 148MB, user 120.7s, sys 10.7s, output queue size 127
progress 70% @chr15:36657733, elapsed 28.8s, est remaining 12.3s, peak mem 148MB, user 129.8s, sys 11.5s, output queue size 108
progress 75% @chr16:28494999, elapsed 30.8s, est remaining 10.3s, peak mem 149MB, user 138.6s, sys 12.4s, output queue size 90
progress 80% @chr17:40053198, elapsed 32.8s, est remaining 8.2s, peak mem 149MB, user 148.2s, sys 13.3s, output queue size 41
progress 85% @chr19:1810522, elapsed 35.1s, est remaining 6.2s, peak mem 149MB, user 157.4s, sys 14.3s, output queue size 208
progress 90% @chr19:54635457, elapsed 37.1s, est remaining 4.1s, peak mem 149MB, user 166.2s, sys 15.2s, output queue size 278
progress 95% @chr22:32084800, elapsed 41.1s, est remaining 2.2s, peak mem 325MB, user 189.4s, sys 16.4s, output queue size 297
progress 100% @chrY:23169898, elapsed 43.0s, est remaining 0.0s, peak mem 325MB, user 197.9s, sys 17.2s, output queue size 191
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000606a6
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef 40417f5e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 128
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 74559500
output file size: 51111
reads: 1501816
contig: 178193 intervals 76355618 bases
"assemble": 189 calls 0.834 user 0.025 sys 1.258 real
"assemble_addRead": 189 calls 0.013 user 0.009 sys 0.030 real
"assemble_buildGraph": 446 calls 0.383 user 0.010 sys 0.624 real
"assemble_computecigar": 274 calls 0.072 user 0.020 sys 0.153 real
"assemble_kg_build_calcsize": 446 calls 0.214 user 0.000 sys 0.309 real
"assemble_kg_build_clear": 608 calls 0.020 user 0.000 sys 0.018 real
"assemble_kg_build_prepare": 892 calls 0.167 user 0.000 sys 0.273 real
"assemble_kg_build_threading": 284 calls 0.159 user 0.010 sys 0.286 real
"assemble_kg_op1": 284 calls 0.062 user 0.008 sys 0.153 real
"assemble_kg_op2": 284 calls 0.000 user 0.000 sys 0.006 real
"assemble_kg_op3": 284 calls 0.030 user 0.000 sys 0.017 real
"assemble_sg_clean": 274 calls 0.030 user 0.000 sys 0.058 real
"assemble_sg_create": 274 calls 0.054 user 0.000 sys 0.067 real
"checkGraph": 189 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 189 calls 0.083 user 0.020 sys 0.161 real
advance: 189104 calls 19.004 user 0.619 sys 40.102 real
assemble_region: 189 calls 0.930 user 0.054 sys 1.452 real
build_pileup: 70986 calls 0.833 user 0.019 sys 1.717 real
build_stats: 71708 calls 4.535 user 0.166 sys 8.550 real
build_variants: 158 calls 0.000 user 0.000 sys 0.001 real
calc: 128714 calls 6.163 user 0.090 sys 11.843 real
calc_region: 158 calls 2.796 user 0.005 sys 4.303 real
call_region: 158 calls 0.054 user 0.000 sys 0.076 real
clip_region: 347 calls 0.050 user 0.000 sys 0.085 real
done: 1 calls 0.923 user 0.000 sys 0.943 real
execute: 1 calls 0.002 user 0.010 sys 43.062 real
fetch: 743546 calls 1.431 user 0.193 sys 2.605 real
fetch_ref: 745694 calls 2.626 user 0.894 sys 6.685 real
fetch_region: 189 calls 0.020 user 0.000 sys 0.034 real
fetch_vcf: 189104 calls 66.624 user 1.363 sys 132.582 real
idle: 35 calls 0.003 user 0.001 sys 13.777 real
init: 1 calls 0.100 user 0.010 sys 0.110 real
pairhmm: 454 calls 4.845 user 0.002 sys 6.723 real
realign: 158 calls 0.560 user 0.000 sys 0.868 real
region: 367297 calls 3.807 user 0.163 sys 6.108 real
tracker: 367297 calls 0.759 user 0.085 sys 1.852 real
trim_region: 189 calls 0.000 user 0.000 sys 0.003 real
overall: 341065728 mem 221.252 user 19.109 sys 44.726 real