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_tumor.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_tumor --normal_sample reference-NA12878 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz positive_somatic_control_1.tnseq.vcf.gz --algo OrientationBias --tumor_sample HCC1395_tumor positive_somatic_control_1.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_tumor --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments positive_somatic_control_1.tnseq.segments positive_somatic_control_1.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113699604, elapsed 1.3s, est remaining 25.3s, peak mem 143MB, user 12.2s, sys 1.6s, output queue size 4
progress 10% @chr2:3673975, elapsed 2.6s, est remaining 23.1s, peak mem 144MB, user 23.7s, sys 3.0s, output queue size 1
progress 15% @chr2:178606921, elapsed 3.8s, est remaining 21.7s, peak mem 144MB, user 35.9s, sys 4.3s, output queue size 12
progress 20% @chr3:57471372, elapsed 5.1s, est remaining 20.4s, peak mem 144MB, user 47.7s, sys 5.8s, output queue size 8
progress 25% @chr4:70603160, elapsed 6.5s, est remaining 19.6s, peak mem 144MB, user 60.6s, sys 7.5s, output queue size 4
progress 30% @chr5:135534877, elapsed 7.9s, est remaining 18.5s, peak mem 146MB, user 73.7s, sys 9.0s, output queue size 3
progress 35% @chr6:104850807, elapsed 9.2s, est remaining 17.1s, peak mem 147MB, user 85.5s, sys 10.4s, output queue size 3
progress 40% @chr7:106284249, elapsed 10.5s, est remaining 15.8s, peak mem 148MB, user 98.2s, sys 11.8s, output queue size 6
progress 45% @chr8:143810379, elapsed 11.8s, est remaining 14.5s, peak mem 149MB, user 110.9s, sys 13.2s, output queue size 2
progress 50% @chr10:21726144, elapsed 13.2s, est remaining 13.2s, peak mem 150MB, user 123.7s, sys 14.4s, output queue size 2
progress 55% @chr11:34132926, elapsed 14.5s, est remaining 11.8s, peak mem 152MB, user 135.8s, sys 15.8s, output queue size 0
progress 60% @chr12:12718707, elapsed 15.7s, est remaining 10.4s, peak mem 154MB, user 147.3s, sys 17.1s, output queue size 12
progress 65% @chr13:32149648, elapsed 17.0s, est remaining 9.1s, peak mem 154MB, user 159.8s, sys 18.5s, output queue size 10
progress 70% @chr15:35372050, elapsed 18.2s, est remaining 7.8s, peak mem 155MB, user 172.0s, sys 19.7s, output queue size 4
progress 75% @chr16:28494582, elapsed 19.5s, est remaining 6.5s, peak mem 155MB, user 184.0s, sys 20.9s, output queue size 6
progress 80% @chr17:40034816, elapsed 20.8s, est remaining 5.2s, peak mem 155MB, user 197.4s, sys 21.9s, output queue size 2
progress 85% @chr19:1799847, elapsed 22.1s, est remaining 3.9s, peak mem 156MB, user 209.9s, sys 23.2s, output queue size 2
progress 90% @chr19:54632916, elapsed 23.4s, est remaining 2.6s, peak mem 156MB, user 222.2s, sys 24.4s, output queue size 3
progress 95% @chr22:31944634, elapsed 26.3s, est remaining 1.4s, peak mem 332MB, user 251.3s, sys 26.1s, output queue size 10
progress 100% @chrY:23265607, elapsed 27.6s, est remaining 0.0s, peak mem 333MB, user 262.6s, sys 27.5s, output queue size 89
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 81484542
output file size: 50711
reads: 1502003
contig: 178193 intervals 76355618 bases
"assemble": 207 calls 0.938 user 0.013 sys 0.908 real
"assemble_addRead": 207 calls 0.000 user 0.000 sys 0.014 real
"assemble_buildGraph": 465 calls 0.361 user 0.000 sys 0.410 real
"assemble_computecigar": 304 calls 0.183 user 0.037 sys 0.221 real
"assemble_kg_build_calcsize": 465 calls 0.181 user 0.000 sys 0.202 real
"assemble_kg_build_clear": 618 calls 0.020 user 0.000 sys 0.016 real
"assemble_kg_build_prepare": 930 calls 0.200 user 0.010 sys 0.179 real
"assemble_kg_build_threading": 312 calls 0.170 user 0.000 sys 0.200 real
"assemble_kg_op1": 312 calls 0.152 user 0.000 sys 0.107 real
"assemble_kg_op2": 312 calls 0.000 user 0.000 sys 0.008 real
"assemble_kg_op3": 312 calls 0.020 user 0.000 sys 0.009 real
"assemble_sg_clean": 304 calls 0.030 user 0.000 sys 0.048 real
"assemble_sg_create": 304 calls 0.115 user 0.003 sys 0.075 real
"checkGraph": 207 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 207 calls 0.183 user 0.037 sys 0.230 real
advance: 189104 calls 20.361 user 0.711 sys 32.521 real
assemble_region: 207 calls 1.131 user 0.051 sys 1.156 real
build_pileup: 70976 calls 0.819 user 0.042 sys 1.181 real
build_stats: 71686 calls 4.746 user 0.125 sys 6.561 real
build_variants: 162 calls 0.000 user 0.000 sys 0.002 real
calc: 128670 calls 4.459 user 0.156 sys 6.819 real
calc_region: 162 calls 3.419 user 0.017 sys 3.573 real
call_region: 162 calls 0.066 user 0.000 sys 0.077 real
clip_region: 369 calls 0.100 user 0.000 sys 0.058 real
done: 1 calls 1.289 user 0.004 sys 1.298 real
execute: 1 calls 0.000 user 0.015 sys 27.591 real
fetch: 743546 calls 1.516 user 0.208 sys 2.078 real
fetch_ref: 745712 calls 1.756 user 0.977 sys 4.931 real
fetch_region: 207 calls 0.017 user 0.000 sys 0.016 real
fetch_vcf: 189104 calls 61.042 user 2.859 sys 104.557 real
idle: 47 calls 0.001 user 0.001 sys 25.903 real
init: 1 calls 0.090 user 0.020 sys 0.112 real
pairhmm: 466 calls 5.751 user 0.013 sys 5.789 real
realign: 162 calls 0.548 user 0.000 sys 0.571 real
region: 367297 calls 4.630 user 0.148 sys 5.022 real
tracker: 367297 calls 0.649 user 0.160 sys 1.403 real
trim_region: 207 calls 0.000 user 0.000 sys 0.004 real
overall: 349331456 mem 294.788 user 39.338 sys 30.192 real