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_tissue.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_tissue --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_2.tnseq.vcf.gz --algo OrientationBias --tumor_sample Sig_18_tissue positive_somatic_control_2.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample Sig_18_tissue --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments positive_somatic_control_2.tnseq.segments positive_somatic_control_2.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113710154, elapsed 1.3s, est remaining 24.8s, peak mem 143MB, user 12.1s, sys 1.5s, output queue size 5
progress 10% @chr2:3671058, elapsed 2.5s, est remaining 22.9s, peak mem 144MB, user 24.0s, sys 2.7s, output queue size 5
progress 15% @chr2:178613651, elapsed 4.0s, est remaining 22.6s, peak mem 145MB, user 37.3s, sys 4.2s, output queue size 12
progress 20% @chr3:57472446, elapsed 5.3s, est remaining 21.1s, peak mem 145MB, user 49.3s, sys 5.6s, output queue size 3
progress 25% @chr4:70596899, elapsed 6.7s, est remaining 20.0s, peak mem 146MB, user 61.9s, sys 7.2s, output queue size 8
progress 30% @chr5:135534877, elapsed 8.1s, est remaining 18.8s, peak mem 148MB, user 74.8s, sys 8.7s, output queue size 4
progress 35% @chr6:104849042, elapsed 9.3s, est remaining 17.3s, peak mem 149MB, user 86.4s, sys 10.0s, output queue size 3
progress 40% @chr7:106248199, elapsed 10.7s, est remaining 16.0s, peak mem 151MB, user 99.0s, sys 11.5s, output queue size 18
progress 45% @chr8:143824213, elapsed 12.0s, est remaining 14.7s, peak mem 151MB, user 111.7s, sys 12.8s, output queue size 1
progress 50% @chr10:21682125, elapsed 13.3s, est remaining 13.3s, peak mem 157MB, user 124.2s, sys 14.1s, output queue size 2
progress 55% @chr11:34132926, elapsed 14.6s, est remaining 12.0s, peak mem 157MB, user 136.2s, sys 15.4s, output queue size 0
progress 60% @chr12:12718707, elapsed 15.9s, est remaining 10.6s, peak mem 158MB, user 148.2s, sys 16.6s, output queue size 13
progress 65% @chr13:32078734, elapsed 17.2s, est remaining 9.2s, peak mem 159MB, user 160.4s, sys 18.1s, output queue size 10
progress 70% @chr15:35372050, elapsed 18.4s, est remaining 7.9s, peak mem 159MB, user 172.3s, sys 19.4s, output queue size 4
progress 75% @chr16:28488491, elapsed 19.7s, est remaining 6.6s, peak mem 160MB, user 184.4s, sys 20.9s, output queue size 4
progress 80% @chr17:40036016, elapsed 21.1s, est remaining 5.3s, peak mem 160MB, user 197.7s, sys 22.1s, output queue size 1
progress 85% @chr19:1796611, elapsed 22.4s, est remaining 4.0s, peak mem 161MB, user 210.2s, sys 23.3s, output queue size 3
progress 90% @chr19:54573779, elapsed 23.6s, est remaining 2.6s, peak mem 161MB, user 222.6s, sys 24.4s, output queue size 12
progress 95% @chr22:31897382, elapsed 27.0s, est remaining 1.4s, peak mem 353MB, user 254.3s, sys 26.0s, output queue size 10
progress 100% @chrY:24803156, elapsed 28.2s, est remaining 0.0s, peak mem 353MB, user 265.8s, sys 27.4s, output queue size 160
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 93248830
output file size: 53230
reads: 1502521
contig: 178193 intervals 76355618 bases
"assemble": 221 calls 0.947 user 0.001 sys 1.081 real
"assemble_addRead": 221 calls 0.030 user 0.000 sys 0.017 real
"assemble_buildGraph": 496 calls 0.437 user 0.001 sys 0.499 real
"assemble_computecigar": 329 calls 0.250 user 0.010 sys 0.181 real
"assemble_kg_build_calcsize": 496 calls 0.220 user 0.000 sys 0.245 real
"assemble_kg_build_clear": 650 calls 0.030 user 0.000 sys 0.021 real
"assemble_kg_build_prepare": 992 calls 0.150 user 0.000 sys 0.209 real
"assemble_kg_build_threading": 342 calls 0.217 user 0.001 sys 0.244 real
"assemble_kg_op1": 342 calls 0.157 user 0.000 sys 0.137 real
"assemble_kg_op2": 342 calls 0.020 user 0.000 sys 0.010 real
"assemble_kg_op3": 342 calls 0.020 user 0.000 sys 0.010 real
"assemble_sg_clean": 329 calls 0.030 user 0.000 sys 0.055 real
"assemble_sg_create": 329 calls 0.053 user 0.000 sys 0.081 real
"checkGraph": 221 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 221 calls 0.280 user 0.010 sys 0.190 real
advance: 189104 calls 21.529 user 0.816 sys 32.733 real
assemble_region: 221 calls 1.257 user 0.011 sys 1.294 real
build_pileup: 70986 calls 0.791 user 0.018 sys 1.181 real
build_stats: 71711 calls 5.099 user 0.170 sys 6.885 real
build_variants: 178 calls 0.000 user 0.000 sys 0.002 real
calc: 128717 calls 4.638 user 0.127 sys 6.923 real
calc_region: 178 calls 5.118 user 0.023 sys 5.428 real
call_region: 178 calls 0.110 user 0.000 sys 0.123 real
clip_region: 399 calls 0.100 user 0.000 sys 0.085 real
done: 1 calls 1.337 user 0.000 sys 1.336 real
execute: 1 calls 0.008 user 0.002 sys 28.273 real
fetch: 743546 calls 1.525 user 0.228 sys 2.131 real
fetch_ref: 745726 calls 1.890 user 0.843 sys 4.925 real
fetch_region: 221 calls 0.010 user 0.000 sys 0.017 real
fetch_vcf: 189104 calls 61.224 user 2.850 sys 104.941 real
idle: 47 calls 0.008 user 0.002 sys 25.822 real
init: 1 calls 0.110 user 0.010 sys 0.111 real
pairhmm: 837 calls 9.438 user 0.021 sys 9.551 real
realign: 178 calls 0.968 user 0.000 sys 1.047 real
region: 367297 calls 6.523 user 0.080 sys 7.024 real
tracker: 367297 calls 0.903 user 0.139 sys 1.420 real
trim_region: 221 calls 0.020 user 0.000 sys 0.005 real
overall: 370626560 mem 300.715 user 39.538 sys 30.843 real