cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam -i 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed --algo TNhaplotyper2 --tumor_sample 1029_0I-T1-TDNA-1_A23KCGYLT4_1 --normal_sample 1029_0I-N1-BDNA-1_B23KGCJLT4_1 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz 1029_0I.tnseq.vcf.gz --algo OrientationBias --tumor_sample 1029_0I-T1-TDNA-1_A23KCGYLT4_1 1029_0I.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample 1029_0I-T1-TDNA-1_A23KCGYLT4_1 --normal_sample 1029_0I-N1-BDNA-1_B23KGCJLT4_1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments 1029_0I.tnseq.segments 1029_0I.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119622705, elapsed 98.5s, est remaining 1871.0s, peak mem 3684MB, user 889.7s, sys 14.0s, output queue size 165
progress 10% @chr2:20670464, elapsed 305.4s, est remaining 2748.5s, peak mem 5104MB, user 2425.9s, sys 27.0s, output queue size 636
progress 15% @chr2:185788643, elapsed 435.1s, est remaining 2465.8s, peak mem 5651MB, user 3510.6s, sys 36.3s, output queue size 215
progress 20% @chr3:98784945, elapsed 553.6s, est remaining 2214.3s, peak mem 5651MB, user 4584.0s, sys 43.9s, output queue size 422
progress 25% @chr4:88463532, elapsed 650.1s, est remaining 1950.4s, peak mem 5697MB, user 5386.7s, sys 50.3s, output queue size 87
progress 30% @chr5:147509478, elapsed 729.8s, est remaining 1703.0s, peak mem 5697MB, user 5969.3s, sys 55.3s, output queue size 197
progress 35% @chr6:131733588, elapsed 913.9s, est remaining 1697.2s, peak mem 5925MB, user 7449.0s, sys 62.2s, output queue size 607
progress 40% @chr7:128866410, elapsed 1119.4s, est remaining 1679.1s, peak mem 6153MB, user 8852.0s, sys 70.1s, output queue size 1561
progress 45% @chr9:1051614, elapsed 1242.7s, est remaining 1518.8s, peak mem 6153MB, user 9920.1s, sys 76.5s, output queue size 16
progress 50% @chr10:32922640, elapsed 1348.0s, est remaining 1348.0s, peak mem 6204MB, user 10794.6s, sys 83.0s, output queue size 143
progress 55% @chr11:49037478, elapsed 1563.8s, est remaining 1279.5s, peak mem 6204MB, user 12133.9s, sys 89.2s, output queue size 3358
progress 60% @chr12:22201552, elapsed 1689.6s, est remaining 1126.4s, peak mem 6236MB, user 13258.4s, sys 95.9s, output queue size 639
progress 65% @chr13:49278350, elapsed 1824.6s, est remaining 982.5s, peak mem 6308MB, user 14244.5s, sys 103.0s, output queue size 55
progress 70% @chr15:43085984, elapsed 2082.7s, est remaining 892.6s, peak mem 6308MB, user 16225.2s, sys 109.2s, output queue size 453
progress 75% @chr16:30946730, elapsed 2211.5s, est remaining 737.2s, peak mem 6423MB, user 17474.2s, sys 117.6s, output queue size 21
progress 80% @chr17:42562612, elapsed 2299.8s, est remaining 575.0s, peak mem 6423MB, user 18302.6s, sys 124.1s, output queue size 56
progress 85% @chr19:5763215, elapsed 2410.4s, est remaining 425.4s, peak mem 6423MB, user 19121.3s, sys 130.0s, output queue size 426
progress 90% @chr19:55761801, elapsed 2518.6s, est remaining 279.8s, peak mem 6423MB, user 20006.3s, sys 135.4s, output queue size 78
progress 95% @chr22:36504515, elapsed 2630.6s, est remaining 138.5s, peak mem 6742MB, user 21006.0s, sys 142.3s, output queue size 3
progress 100% @chrY:25622443, elapsed 2696.5s, est remaining 0.0s, peak mem 6742MB, user 21560.8s, sys 147.0s, output queue size 31
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050657
  features: bfebfbff 7ffefbff
  extended: d39ff7eb 00000818
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz
threads: 12 max 96
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 26263832747 103367536517
output file size: 2942516
reads: 1658552174
contig: 201779 intervals 37922265 bases
"assemble": 16113 calls 899.987 user 1.488 sys 901.602 real
"assemble_addRead": 16113 calls 28.000 user 0.164 sys 28.249 real
"assemble_buildGraph": 36499 calls 451.936 user 0.271 sys 453.058 real
"assemble_computecigar": 24753 calls 16.860 user 0.064 sys 17.023 real
"assemble_kg_build_calcsize": 36499 calls 231.555 user 0.121 sys 231.753 real
"assemble_kg_build_clear": 46017 calls 64.826 user 0.104 sys 64.114 real
"assemble_kg_build_prepare": 72998 calls 254.278 user 0.815 sys 255.321 real
"assemble_kg_build_threading": 26981 calls 194.212 user 0.101 sys 195.414 real
"assemble_kg_op1": 26981 calls 96.748 user 0.128 sys 97.137 real
"assemble_kg_op2": 26981 calls 0.913 user 0.020 sys 0.887 real
"assemble_kg_op3": 26981 calls 1.087 user 0.010 sys 1.023 real
"assemble_sg_clean": 24753 calls 5.127 user 0.023 sys 5.199 real
"assemble_sg_create": 24753 calls 6.073 user 0.000 sys 5.425 real
"checkGraph": 16113 calls 0.150 user 0.000 sys 0.127 real
"findHaplotype": 16113 calls 20.147 user 0.084 sys 20.466 real
advance: 208647 calls 8367.859 user 107.595 sys 8472.026 real
assemble_region: 16113 calls 948.605 user 1.736 sys 950.887 real
build_pileup: 202447 calls 43.627 user 0.095 sys 44.440 real
build_stats: 207329 calls 729.951 user 2.701 sys 735.796 real
build_variants: 11455 calls 0.260 user 0.000 sys 0.234 real
calc: 407987 calls 749.719 user 0.641 sys 763.382 real
calc_region: 11455 calls 7781.356 user 5.273 sys 7812.010 real
call_region: 11455 calls 165.794 user 0.260 sys 167.631 real
clip_region: 27568 calls 115.421 user 0.206 sys 115.210 real
done: 1 calls 33.217 user 0.309 sys 33.530 real
execute: 1 calls 0.000 user 0.009 sys 2696.554 real
fetch: 821727 calls 1887.207 user 3.663 sys 1929.238 real
fetch_ref: 843833 calls 31.394 user 1.904 sys 7.081 real
fetch_region: 16113 calls 59.265 user 0.236 sys 59.449 real
fetch_vcf: 208647 calls 85.211 user 1.920 sys 90.134 real
idle: 431 calls 0.051 user 0.001 sys 411.954 real
init: 1 calls 0.065 user 0.018 sys 0.090 real
pairhmm: 1390548 calls 17334.206 user 8.410 sys 17352.737 real
realign: 11455 calls 735.124 user 0.495 sys 760.076 real
region: 410426 calls 8844.667 user 7.548 sys 8878.313 real
tracker: 410426 calls 1.855 user 0.053 sys 2.073 real
trim_region: 16113 calls 0.520 user 0.000 sys 0.399 real
overall: 7070359552 mem 32206.820 user 159.025 sys 2731.419 real