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% @chr1:113704566, elapsed 1.5s, est remaining 28.3s, peak mem 142MB, user 12.9s, sys 1.9s, output queue size 4
progress 10% @chr2:3643344, elapsed 2.8s, est remaining 25.4s, peak mem 143MB, user 25.1s, sys 3.5s, output queue size 5
progress 15% @chr2:178606921, elapsed 4.2s, est remaining 24.0s, peak mem 144MB, user 37.8s, sys 5.1s, output queue size 12
progress 20% @chr3:57483276, elapsed 5.5s, est remaining 21.9s, peak mem 144MB, user 49.7s, sys 6.4s, output queue size 11
progress 25% @chr4:70529084, elapsed 6.8s, est remaining 20.5s, peak mem 144MB, user 62.5s, sys 7.9s, output queue size 9
progress 30% @chr5:135571753, elapsed 8.2s, est remaining 19.2s, peak mem 145MB, user 75.3s, sys 9.6s, output queue size 4
progress 35% @chr6:104843123, elapsed 9.4s, est remaining 17.5s, peak mem 146MB, user 86.5s, sys 10.9s, output queue size 3
progress 40% @chr7:106248199, elapsed 10.7s, est remaining 16.1s, peak mem 147MB, user 99.2s, sys 12.1s, output queue size 19
progress 45% @chr8:143821497, elapsed 12.0s, est remaining 14.7s, peak mem 149MB, user 112.1s, sys 13.4s, output queue size 1
progress 50% @chr10:21726144, elapsed 13.3s, est remaining 13.3s, peak mem 152MB, user 124.4s, sys 14.9s, output queue size 2
progress 55% @chr11:34136542, elapsed 14.6s, est remaining 12.0s, peak mem 152MB, user 136.4s, sys 16.5s, output queue size 0
progress 60% @chr12:12718707, elapsed 15.8s, est remaining 10.6s, peak mem 154MB, user 148.2s, sys 17.9s, output queue size 12
progress 65% @chr13:32078734, elapsed 17.1s, est remaining 9.2s, peak mem 154MB, user 160.4s, sys 19.5s, output queue size 10
progress 70% @chr15:35538174, elapsed 18.4s, est remaining 7.9s, peak mem 155MB, user 172.5s, sys 20.7s, output queue size 9
progress 75% @chr16:28470989, elapsed 19.7s, est remaining 6.6s, peak mem 155MB, user 184.8s, sys 21.9s, output queue size 8
progress 80% @chr17:40034816, elapsed 21.0s, est remaining 5.3s, peak mem 155MB, user 198.0s, sys 23.1s, output queue size 0
progress 85% @chr19:1796611, elapsed 22.3s, est remaining 3.9s, peak mem 156MB, user 210.5s, sys 24.5s, output queue size 3
progress 90% @chr19:54632916, elapsed 23.6s, est remaining 2.6s, peak mem 157MB, user 223.2s, sys 25.7s, output queue size 12
progress 95% @chr22:32068396, elapsed 26.5s, est remaining 1.4s, peak mem 327MB, user 251.6s, sys 27.3s, output queue size 5
progress 100% @chrY:57106233, elapsed 27.6s, est remaining 0.0s, peak mem 327MB, user 261.2s, sys 28.7s, output queue size 199
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 71692776
output file size: 46614
reads: 1501772
contig: 178193 intervals 76355618 bases
"assemble": 183 calls 0.861 user 0.036 sys 0.857 real
"assemble_addRead": 183 calls 0.020 user 0.000 sys 0.013 real
"assemble_buildGraph": 422 calls 0.410 user 0.018 sys 0.377 real
"assemble_computecigar": 264 calls 0.130 user 0.000 sys 0.161 real
"assemble_kg_build_calcsize": 422 calls 0.217 user 0.000 sys 0.190 real
"assemble_kg_build_clear": 573 calls 0.000 user 0.000 sys 0.016 real
"assemble_kg_build_prepare": 844 calls 0.133 user 0.010 sys 0.192 real
"assemble_kg_build_threading": 271 calls 0.184 user 0.018 sys 0.178 real
"assemble_kg_op1": 271 calls 0.160 user 0.000 sys 0.099 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 0.010 user 0.000 sys 0.041 real
"assemble_sg_create": 264 calls 0.057 user 0.008 sys 0.063 real
"checkGraph": 183 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 183 calls 0.130 user 0.000 sys 0.168 real
advance: 189104 calls 19.629 user 0.813 sys 31.788 real
assemble_region: 183 calls 1.011 user 0.036 sys 1.041 real
build_pileup: 70974 calls 0.717 user 0.038 sys 1.170 real
build_stats: 71688 calls 4.821 user 0.169 sys 6.607 real
build_variants: 142 calls 0.000 user 0.000 sys 0.002 real
calc: 128670 calls 3.960 user 0.158 sys 6.783 real
calc_region: 142 calls 4.233 user 0.018 sys 4.306 real
call_region: 142 calls 0.070 user 0.000 sys 0.076 real
clip_region: 325 calls 0.079 user 0.000 sys 0.053 real
done: 1 calls 1.262 user 0.001 sys 1.270 real
execute: 1 calls 0.014 user 0.001 sys 27.579 real
fetch: 743546 calls 1.456 user 0.167 sys 2.026 real
fetch_ref: 745688 calls 2.037 user 0.802 sys 4.820 real
fetch_region: 183 calls 0.006 user 0.000 sys 0.013 real
fetch_vcf: 189104 calls 59.268 user 2.920 sys 103.668 real
idle: 47 calls 0.006 user 0.007 sys 26.227 real
init: 1 calls 0.120 user 0.020 sys 0.139 real
pairhmm: 472 calls 6.426 user 0.010 sys 6.426 real
realign: 142 calls 0.503 user 0.006 sys 0.543 real
region: 367297 calls 5.328 user 0.183 sys 5.634 real
tracker: 367297 calls 0.609 user 0.159 sys 1.415 real
trim_region: 183 calls 0.010 user 0.000 sys 0.003 real
overall: 343474176 mem 292.279 user 41.009 sys 30.229 real