cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i 1029_0W2-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam -i 1029_0W2-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_0W2-T1-TDNA-1_A23KCGYLT4_1 --normal_sample 1029_0W2-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_0W2.tnseq.vcf.gz --algo OrientationBias --tumor_sample 1029_0W2-T1-TDNA-1_A23KCGYLT4_1 1029_0W2.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample 1029_0W2-T1-TDNA-1_A23KCGYLT4_1 --normal_sample 1029_0W2-N1-BDNA-1_B23KGCJLT4_1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments 1029_0W2.tnseq.segments 1029_0W2.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119922603, elapsed 37.8s, est remaining 718.4s, peak mem 2235MB, user 348.0s, sys 4.8s, output queue size 162
progress 10% @chr2:20670464, elapsed 91.0s, est remaining 819.0s, peak mem 2689MB, user 816.1s, sys 8.7s, output queue size 640
progress 15% @chr2:189666133, elapsed 165.3s, est remaining 936.6s, peak mem 3337MB, user 1376.4s, sys 13.5s, output queue size 396
progress 20% @chr3:98264285, elapsed 249.7s, est remaining 998.6s, peak mem 3337MB, user 2072.1s, sys 17.3s, output queue size 414
progress 25% @chr4:88479353, elapsed 306.8s, est remaining 920.4s, peak mem 3482MB, user 2540.6s, sys 21.5s, output queue size 86
progress 30% @chr5:147632680, elapsed 344.8s, est remaining 804.6s, peak mem 3571MB, user 2848.5s, sys 24.5s, output queue size 196
progress 35% @chr6:131738031, elapsed 417.5s, est remaining 775.4s, peak mem 3668MB, user 3457.5s, sys 29.0s, output queue size 607
progress 40% @chr7:128857118, elapsed 570.8s, est remaining 856.2s, peak mem 4082MB, user 4603.8s, sys 33.3s, output queue size 1562
progress 45% @chr9:990041, elapsed 692.9s, est remaining 846.8s, peak mem 4570MB, user 5704.9s, sys 38.9s, output queue size 86
progress 50% @chr10:32854400, elapsed 762.1s, est remaining 762.1s, peak mem 4659MB, user 6309.6s, sys 42.5s, output queue size 68
progress 55% @chr11:48164380, elapsed 829.0s, est remaining 678.3s, peak mem 4666MB, user 6875.2s, sys 45.9s, output queue size 74
progress 60% @chr12:21765723, elapsed 908.6s, est remaining 605.7s, peak mem 4721MB, user 7555.2s, sys 49.3s, output queue size 638
progress 65% @chr13:49476476, elapsed 966.1s, est remaining 520.2s, peak mem 4721MB, user 8021.7s, sys 52.6s, output queue size 556
progress 70% @chr15:43134257, elapsed 1028.9s, est remaining 440.9s, peak mem 4721MB, user 8575.1s, sys 55.8s, output queue size 457
progress 75% @chr16:30949290, elapsed 1114.5s, est remaining 371.5s, peak mem 4728MB, user 9385.7s, sys 59.1s, output queue size 21
progress 80% @chr17:42587834, elapsed 1177.8s, est remaining 294.4s, peak mem 4728MB, user 9969.9s, sys 63.4s, output queue size 121
progress 85% @chr19:5708342, elapsed 1242.7s, est remaining 219.3s, peak mem 4728MB, user 10499.1s, sys 66.8s, output queue size 400
progress 90% @chr19:55772602, elapsed 1303.8s, est remaining 144.9s, peak mem 4752MB, user 11019.4s, sys 70.1s, output queue size 61
progress 95% @chr22:36497991, elapsed 1374.4s, est remaining 72.3s, peak mem 4912MB, user 11647.3s, sys 74.1s, output queue size 3
progress 100% @chrY:25622443, elapsed 1412.0s, est remaining 0.0s, peak mem 4912MB, user 11982.9s, sys 77.0s, output queue size 31
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: 26404493781 76694971856
output file size: 3820928
reads: 1263973677
contig: 201779 intervals 37922265 bases
"assemble": 30670 calls 731.157 user 0.769 sys 735.665 real
"assemble_addRead": 30670 calls 23.616 user 0.060 sys 23.419 real
"assemble_buildGraph": 66441 calls 362.408 user 0.262 sys 364.283 real
"assemble_computecigar": 49074 calls 11.378 user 0.030 sys 11.322 real
"assemble_kg_build_calcsize": 66441 calls 174.039 user 0.065 sys 175.803 real
"assemble_kg_build_clear": 79729 calls 36.883 user 0.084 sys 37.602 real
"assemble_kg_build_prepare": 132882 calls 196.050 user 0.224 sys 196.396 real
"assemble_kg_build_threading": 53153 calls 177.529 user 0.127 sys 177.659 real
"assemble_kg_op1": 53153 calls 101.529 user 0.071 sys 102.230 real
"assemble_kg_op2": 53153 calls 0.871 user 0.000 sys 0.868 real
"assemble_kg_op3": 53153 calls 1.228 user 0.000 sys 1.229 real
"assemble_sg_clean": 49074 calls 4.641 user 0.010 sys 4.589 real
"assemble_sg_create": 49074 calls 6.068 user 0.000 sys 6.348 real
"checkGraph": 30670 calls 0.070 user 0.000 sys 0.119 real
"findHaplotype": 30670 calls 13.490 user 0.030 sys 13.485 real
advance: 208647 calls 4279.500 user 55.443 sys 4322.249 real
assemble_region: 30670 calls 768.804 user 0.879 sys 773.201 real
build_pileup: 202454 calls 17.349 user 0.030 sys 17.743 real
build_stats: 207279 calls 325.535 user 0.790 sys 334.707 real
build_variants: 16597 calls 0.153 user 0.000 sys 0.170 real
calc: 407887 calls 333.246 user 0.436 sys 351.083 real
calc_region: 16597 calls 4739.235 user 2.388 sys 4759.918 real
call_region: 16597 calls 84.916 user 0.081 sys 86.651 real
clip_region: 47267 calls 83.650 user 0.051 sys 83.983 real
done: 1 calls 51.408 user 0.310 sys 51.726 real
execute: 1 calls 0.005 user 0.001 sys 1412.037 real
fetch: 821727 calls 924.497 user 1.385 sys 955.436 real
fetch_ref: 858390 calls 25.477 user 1.299 sys 5.182 real
fetch_region: 30670 calls 49.668 user 0.025 sys 50.631 real
fetch_vcf: 208647 calls 58.145 user 1.211 sys 62.819 real
idle: 647 calls 0.043 user 0.010 sys 625.883 real
init: 1 calls 0.049 user 0.010 sys 0.062 real
pairhmm: 1027941 calls 8859.617 user 1.752 sys 8868.771 real
realign: 16597 calls 521.673 user 0.130 sys 550.368 real
region: 410426 calls 5600.987 user 3.421 sys 5627.236 real
tracker: 410426 calls 1.569 user 0.060 sys 1.692 real
trim_region: 30670 calls 0.294 user 0.000 sys 0.312 real
overall: 5666971648 mem 16889.401 user 81.071 sys 1464.737 real