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% @chr1:113682797, elapsed 1.4s, est remaining 26.0s, peak mem 143MB, user 12.4s, sys 1.7s, output queue size 3
progress 10% @chr2:3643344, elapsed 2.6s, est remaining 23.4s, peak mem 143MB, user 24.1s, sys 3.2s, output queue size 1
progress 15% @chr2:178606921, elapsed 4.0s, est remaining 22.7s, peak mem 144MB, user 36.8s, sys 4.9s, output queue size 12
progress 20% @chr3:57483276, elapsed 5.3s, est remaining 21.2s, peak mem 144MB, user 48.9s, sys 6.0s, output queue size 11
progress 25% @chr4:70530939, elapsed 6.7s, est remaining 20.0s, peak mem 145MB, user 61.5s, sys 7.8s, output queue size 7
progress 30% @chr5:135571753, elapsed 8.0s, est remaining 18.8s, peak mem 146MB, user 74.4s, sys 9.2s, output queue size 4
progress 35% @chr6:104957999, elapsed 9.3s, est remaining 17.3s, peak mem 147MB, user 85.7s, sys 10.6s, output queue size 2
progress 40% @chr7:106879419, elapsed 10.6s, est remaining 16.0s, peak mem 149MB, user 98.6s, sys 11.9s, output queue size 6
progress 45% @chr8:143835562, elapsed 12.0s, est remaining 14.6s, peak mem 151MB, user 111.0s, sys 13.4s, output queue size 0
progress 50% @chr10:21726144, elapsed 13.2s, est remaining 13.2s, peak mem 154MB, user 123.4s, sys 14.6s, output queue size 21
progress 55% @chr11:34136542, elapsed 14.5s, est remaining 11.9s, peak mem 154MB, user 135.5s, sys 16.1s, output queue size 0
progress 60% @chr12:12718707, elapsed 15.7s, est remaining 10.5s, peak mem 155MB, user 147.1s, sys 17.2s, output queue size 13
progress 65% @chr13:32078734, elapsed 17.0s, est remaining 9.2s, peak mem 155MB, user 159.4s, sys 18.5s, output queue size 10
progress 70% @chr15:35521993, elapsed 18.3s, est remaining 7.8s, peak mem 156MB, user 171.3s, sys 19.8s, output queue size 0
progress 75% @chr16:28488491, elapsed 19.5s, est remaining 6.5s, peak mem 157MB, user 183.4s, sys 21.2s, output queue size 2
progress 80% @chr17:40034816, elapsed 20.9s, est remaining 5.2s, peak mem 157MB, user 196.3s, sys 22.4s, output queue size 1
progress 85% @chr19:1796611, elapsed 22.2s, est remaining 3.9s, peak mem 158MB, user 209.2s, sys 23.5s, output queue size 3
progress 90% @chr19:54630974, elapsed 23.4s, est remaining 2.6s, peak mem 159MB, user 221.3s, sys 24.6s, output queue size 2
progress 95% @chr22:32068396, elapsed 26.4s, est remaining 1.4s, peak mem 336MB, user 250.4s, sys 26.4s, output queue size 10
progress 100% @chrY:24805357, elapsed 27.6s, est remaining 0.0s, peak mem 336MB, user 261.5s, sys 27.6s, output queue size 480
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 81484560
output file size: 50711
reads: 1502003
contig: 178193 intervals 76355618 bases
"assemble": 207 calls 0.932 user 0.011 sys 0.905 real
"assemble_addRead": 207 calls 0.000 user 0.000 sys 0.013 real
"assemble_buildGraph": 465 calls 0.384 user 0.010 sys 0.409 real
"assemble_computecigar": 304 calls 0.172 user 0.028 sys 0.219 real
"assemble_kg_build_calcsize": 465 calls 0.105 user 0.000 sys 0.199 real
"assemble_kg_build_clear": 618 calls 0.036 user 0.000 sys 0.016 real
"assemble_kg_build_prepare": 930 calls 0.221 user 0.000 sys 0.177 real
"assemble_kg_build_threading": 312 calls 0.258 user 0.010 sys 0.202 real
"assemble_kg_op1": 312 calls 0.100 user 0.000 sys 0.106 real
"assemble_kg_op2": 312 calls 0.000 user 0.000 sys 0.008 real
"assemble_kg_op3": 312 calls 0.000 user 0.000 sys 0.009 real
"assemble_sg_clean": 304 calls 0.066 user 0.000 sys 0.048 real
"assemble_sg_create": 304 calls 0.055 user 0.000 sys 0.075 real
"checkGraph": 207 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 207 calls 0.172 user 0.028 sys 0.227 real
advance: 189104 calls 21.411 user 0.802 sys 32.545 real
assemble_region: 207 calls 1.103 user 0.039 sys 1.149 real
build_pileup: 70976 calls 0.589 user 0.046 sys 1.166 real
build_stats: 71686 calls 5.043 user 0.269 sys 6.501 real
build_variants: 162 calls 0.000 user 0.000 sys 0.002 real
calc: 128670 calls 4.028 user 0.133 sys 6.812 real
calc_region: 162 calls 3.429 user 0.053 sys 3.649 real
call_region: 162 calls 0.090 user 0.000 sys 0.075 real
clip_region: 369 calls 0.030 user 0.000 sys 0.057 real
done: 1 calls 1.230 user 0.010 sys 1.248 real
execute: 1 calls 0.012 user 0.000 sys 27.654 real
fetch: 743546 calls 1.482 user 0.247 sys 2.061 real
fetch_ref: 745712 calls 1.704 user 0.991 sys 4.847 real
fetch_region: 207 calls 0.010 user 0.000 sys 0.016 real
fetch_vcf: 189104 calls 61.769 user 2.793 sys 104.270 real
idle: 47 calls 0.001 user 0.002 sys 25.900 real
init: 1 calls 0.120 user 0.000 sys 0.114 real
pairhmm: 466 calls 5.902 user 0.037 sys 5.934 real
realign: 162 calls 0.460 user 0.000 sys 0.563 real
region: 367297 calls 4.642 user 0.154 sys 5.092 real
tracker: 367297 calls 0.769 user 0.127 sys 1.404 real
trim_region: 207 calls 0.010 user 0.000 sys 0.004 real
overall: 353124352 mem 294.251 user 39.391 sys 30.241 real