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 0.7s, est remaining 12.8s, peak mem 145MB, user 6.8s, sys 0.4s, output queue size 4
progress 10% @chr2:3671058, elapsed 1.3s, est remaining 11.7s, peak mem 145MB, user 13.4s, sys 0.7s, output queue size 5
progress 15% @chr2:178609108, elapsed 2.0s, est remaining 11.1s, peak mem 145MB, user 20.1s, sys 1.1s, output queue size 12
progress 20% @chr3:57483276, elapsed 2.5s, est remaining 10.2s, peak mem 145MB, user 26.3s, sys 1.5s, output queue size 0
progress 25% @chr4:70598256, elapsed 3.2s, est remaining 9.6s, peak mem 145MB, user 33.0s, sys 2.0s, output queue size 6
progress 30% @chr5:135873921, elapsed 3.9s, est remaining 9.0s, peak mem 148MB, user 39.6s, sys 2.6s, output queue size 4
progress 35% @chr6:104957999, elapsed 4.5s, est remaining 8.3s, peak mem 150MB, user 45.9s, sys 2.9s, output queue size 2
progress 40% @chr7:106284249, elapsed 5.1s, est remaining 7.7s, peak mem 151MB, user 52.5s, sys 3.3s, output queue size 5
progress 45% @chr8:143821497, elapsed 5.8s, est remaining 7.0s, peak mem 151MB, user 59.4s, sys 3.7s, output queue size 1
progress 50% @chr10:21726144, elapsed 6.4s, est remaining 6.4s, peak mem 154MB, user 66.0s, sys 4.0s, output queue size 1
progress 55% @chr11:34132025, elapsed 7.0s, est remaining 5.7s, peak mem 154MB, user 72.5s, sys 4.3s, output queue size 1
progress 60% @chr12:12718707, elapsed 7.6s, est remaining 5.1s, peak mem 155MB, user 78.6s, sys 4.7s, output queue size 10
progress 65% @chr13:32149648, elapsed 8.3s, est remaining 4.5s, peak mem 155MB, user 85.3s, sys 5.0s, output queue size 1
progress 70% @chr15:35381722, elapsed 8.9s, est remaining 3.8s, peak mem 155MB, user 91.6s, sys 5.5s, output queue size 2
progress 75% @chr16:28494582, elapsed 9.5s, est remaining 3.2s, peak mem 156MB, user 98.0s, sys 6.0s, output queue size 0
progress 80% @chr17:40034816, elapsed 10.2s, est remaining 2.5s, peak mem 156MB, user 105.1s, sys 6.3s, output queue size 1
progress 85% @chr19:1805788, elapsed 10.8s, est remaining 1.9s, peak mem 156MB, user 111.9s, sys 6.6s, output queue size 2
progress 90% @chr19:54632916, elapsed 11.5s, est remaining 1.3s, peak mem 156MB, user 118.4s, sys 6.9s, output queue size 2
progress 95% @chr22:31897382, elapsed 13.1s, est remaining 0.7s, peak mem 346MB, user 135.0s, sys 7.3s, output queue size 10
progress 100% @chr6_GL000251v2_alt:3933919, elapsed 13.7s, est remaining 0.0s, peak mem 347MB, user 141.0s, sys 7.7s, output queue size 40
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 64
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 93248822
output file size: 53230
reads: 1502521
contig: 178193 intervals 76355618 bases
"assemble": 221 calls 0.517 user 0.001 sys 0.495 real
"assemble_addRead": 221 calls 0.010 user 0.000 sys 0.008 real
"assemble_buildGraph": 496 calls 0.255 user 0.000 sys 0.214 real
"assemble_computecigar": 329 calls 0.044 user 0.014 sys 0.078 real
"assemble_kg_build_calcsize": 496 calls 0.165 user 0.000 sys 0.103 real
"assemble_kg_build_clear": 650 calls 0.010 user 0.000 sys 0.008 real
"assemble_kg_build_prepare": 992 calls 0.156 user 0.001 sys 0.096 real
"assemble_kg_build_threading": 342 calls 0.090 user 0.000 sys 0.107 real
"assemble_kg_op1": 342 calls 0.055 user 0.000 sys 0.077 real
"assemble_kg_op2": 342 calls 0.000 user 0.000 sys 0.005 real
"assemble_kg_op3": 342 calls 0.000 user 0.000 sys 0.006 real
"assemble_sg_clean": 329 calls 0.019 user 0.000 sys 0.025 real
"assemble_sg_create": 329 calls 0.003 user 0.000 sys 0.038 real
"checkGraph": 221 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 221 calls 0.054 user 0.014 sys 0.082 real
advance: 189104 calls 14.752 user 0.289 sys 18.763 real
assemble_region: 221 calls 0.582 user 0.025 sys 0.587 real
build_pileup: 70986 calls 0.347 user 0.013 sys 0.448 real
build_stats: 71711 calls 1.930 user 0.038 sys 2.268 real
build_variants: 178 calls 0.000 user 0.000 sys 0.001 real
calc: 128717 calls 2.118 user 0.017 sys 2.892 real
calc_region: 178 calls 2.931 user 0.017 sys 2.968 real
call_region: 178 calls 0.070 user 0.000 sys 0.059 real
clip_region: 399 calls 0.050 user 0.000 sys 0.043 real
done: 1 calls 0.463 user 0.000 sys 0.472 real
execute: 1 calls 0.003 user 0.001 sys 13.747 real
fetch: 743546 calls 0.686 user 0.085 sys 0.887 real
fetch_ref: 745726 calls 1.868 user 0.456 sys 2.698 real
fetch_region: 221 calls 0.020 user 0.000 sys 0.009 real
fetch_vcf: 189104 calls 43.291 user 0.806 sys 55.439 real
idle: 35 calls 0.003 user 0.002 sys 12.872 real
init: 1 calls 0.060 user 0.000 sys 0.058 real
pairhmm: 837 calls 4.772 user 0.015 sys 4.758 real
realign: 178 calls 0.574 user 0.000 sys 0.619 real
region: 367297 calls 3.569 user 0.097 sys 3.664 real
tracker: 367297 calls 0.415 user 0.066 sys 0.539 real
trim_region: 221 calls 0.000 user 0.000 sys 0.002 real
overall: 363900928 mem 157.182 user 10.402 sys 15.040 real