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% @chr1:113682797, elapsed 1.0s, est remaining 18.8s, peak mem 145MB, user 9.3s, sys 0.7s, output queue size 2
progress 10% @chr2:3673975, elapsed 1.9s, est remaining 17.5s, peak mem 145MB, user 18.4s, sys 1.3s, output queue size 6
progress 15% @chr2:178598406, elapsed 3.1s, est remaining 17.5s, peak mem 146MB, user 29.3s, sys 1.9s, output queue size 11
progress 20% @chr3:57471372, elapsed 4.1s, est remaining 16.5s, peak mem 147MB, user 39.3s, sys 2.5s, output queue size 2
progress 25% @chr4:70532355, elapsed 5.2s, est remaining 15.7s, peak mem 147MB, user 50.9s, sys 3.2s, output queue size 6
progress 30% @chr5:135834748, elapsed 6.4s, est remaining 14.9s, peak mem 149MB, user 62.6s, sys 3.9s, output queue size 4
progress 35% @chr6:104843123, elapsed 7.5s, est remaining 13.8s, peak mem 150MB, user 73.2s, sys 4.7s, output queue size 2
progress 40% @chr7:106284249, elapsed 8.6s, est remaining 12.9s, peak mem 152MB, user 84.6s, sys 5.3s, output queue size 5
progress 45% @chr8:143810379, elapsed 9.8s, est remaining 11.9s, peak mem 152MB, user 95.8s, sys 6.0s, output queue size 2
progress 50% @chr10:21514996, elapsed 10.9s, est remaining 10.9s, peak mem 153MB, user 106.8s, sys 6.7s, output queue size 18
progress 55% @chr11:34132025, elapsed 12.0s, est remaining 9.8s, peak mem 154MB, user 116.8s, sys 7.3s, output queue size 1
progress 60% @chr12:12718707, elapsed 13.1s, est remaining 8.8s, peak mem 155MB, user 127.2s, sys 8.0s, output queue size 15
progress 65% @chr13:32078734, elapsed 14.3s, est remaining 7.7s, peak mem 155MB, user 138.6s, sys 8.6s, output queue size 10
progress 70% @chr15:35084093, elapsed 15.4s, est remaining 6.6s, peak mem 156MB, user 149.8s, sys 9.3s, output queue size 5
progress 75% @chr16:28491382, elapsed 16.4s, est remaining 5.5s, peak mem 156MB, user 160.6s, sys 10.0s, output queue size 1
progress 80% @chr17:40032956, elapsed 17.4s, est remaining 4.4s, peak mem 157MB, user 171.5s, sys 10.4s, output queue size 1
progress 85% @chr19:1806528, elapsed 18.4s, est remaining 3.3s, peak mem 158MB, user 181.6s, sys 11.1s, output queue size 4
progress 90% @chr19:54665030, elapsed 19.4s, est remaining 2.2s, peak mem 158MB, user 192.1s, sys 11.6s, output queue size 6
progress 95% @chr22:32067867, elapsed 21.7s, est remaining 1.1s, peak mem 335MB, user 215.5s, sys 12.4s, output queue size 5
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 22.7s, est remaining 0.0s, peak mem 335MB, user 224.6s, sys 13.0s, output queue size 7
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050654
  features: 1f8bfbff fffa320b
  extended: d19f47ab 00000018
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8175M CPU @ 2.50GHz
threads: 12 max 48
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 74586810
output file size: 51111
reads: 1501816
contig: 178193 intervals 76355618 bases
"assemble": 189 calls 0.767 user 0.020 sys 0.750 real
"assemble_addRead": 189 calls 0.010 user 0.000 sys 0.014 real
"assemble_buildGraph": 446 calls 0.324 user 0.019 sys 0.335 real
"assemble_computecigar": 274 calls 0.111 user 0.009 sys 0.113 real
"assemble_kg_build_calcsize": 446 calls 0.168 user 0.000 sys 0.161 real
"assemble_kg_build_clear": 608 calls 0.020 user 0.000 sys 0.015 real
"assemble_kg_build_prepare": 892 calls 0.190 user 0.000 sys 0.163 real
"assemble_kg_build_threading": 284 calls 0.147 user 0.019 sys 0.166 real
"assemble_kg_op1": 284 calls 0.080 user 0.000 sys 0.092 real
"assemble_kg_op2": 284 calls 0.003 user 0.000 sys 0.006 real
"assemble_kg_op3": 284 calls 0.000 user 0.000 sys 0.007 real
"assemble_sg_clean": 274 calls 0.058 user 0.000 sys 0.035 real
"assemble_sg_create": 274 calls 0.032 user 0.000 sys 0.051 real
"checkGraph": 189 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 189 calls 0.111 user 0.009 sys 0.118 real
advance: 189104 calls 23.196 user 0.448 sys 28.665 real
assemble_region: 189 calls 0.887 user 0.029 sys 0.885 real
build_pileup: 70986 calls 0.668 user 0.029 sys 0.990 real
build_stats: 71708 calls 3.985 user 0.064 sys 4.991 real
build_variants: 158 calls 0.000 user 0.000 sys 0.001 real
calc: 128714 calls 4.895 user 0.055 sys 6.871 real
calc_region: 158 calls 2.784 user 0.001 sys 2.971 real
call_region: 158 calls 0.098 user 0.000 sys 0.065 real
clip_region: 347 calls 0.050 user 0.000 sys 0.054 real
done: 1 calls 0.638 user 0.000 sys 0.639 real
execute: 1 calls 0.004 user 0.011 sys 22.712 real
fetch: 743546 calls 1.356 user 0.119 sys 1.744 real
fetch_ref: 745694 calls 3.031 user 0.808 sys 5.314 real
fetch_region: 189 calls 0.000 user 0.000 sys 0.013 real
fetch_vcf: 189104 calls 72.659 user 1.578 sys 91.967 real
idle: 35 calls 0.009 user 0.002 sys 13.317 real
init: 1 calls 0.060 user 0.020 sys 0.084 real
pairhmm: 454 calls 4.546 user 0.020 sys 4.585 real
realign: 158 calls 0.505 user 0.000 sys 0.564 real
region: 367297 calls 3.858 user 0.066 sys 4.133 real
tracker: 367297 calls 0.894 user 0.126 sys 1.280 real
trim_region: 189 calls 0.000 user 0.000 sys 0.003 real
overall: 352096256 mem 259.061 user 18.478 sys 24.132 real