cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i 1029_16G-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam -i 1029_16G-T1-TDNA-1_B23KFCWLT4_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_16G-T1-TDNA-1_B23KFCWLT4_1 --normal_sample 1029_16G-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_16G.tnseq.vcf.gz --algo OrientationBias --tumor_sample 1029_16G-T1-TDNA-1_B23KFCWLT4_1 1029_16G.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample 1029_16G-T1-TDNA-1_B23KFCWLT4_1 --normal_sample 1029_16G-N1-BDNA-1_B23KGCJLT4_1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments 1029_16G.tnseq.segments 1029_16G.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119935388, elapsed 61.1s, est remaining 1161.3s, peak mem 3619MB, user 596.7s, sys 13.1s, output queue size 163
progress 10% @chr2:21001730, elapsed 153.2s, est remaining 1378.6s, peak mem 4157MB, user 1400.6s, sys 23.9s, output queue size 641
progress 15% @chr2:189676491, elapsed 256.4s, est remaining 1453.0s, peak mem 4661MB, user 2312.2s, sys 32.0s, output queue size 400
progress 20% @chr3:98390666, elapsed 376.5s, est remaining 1505.9s, peak mem 4670MB, user 3349.0s, sys 42.7s, output queue size 399
progress 25% @chr4:88479353, elapsed 460.7s, est remaining 1382.1s, peak mem 4823MB, user 4068.3s, sys 51.0s, output queue size 87
progress 30% @chr5:147617911, elapsed 537.8s, est remaining 1255.0s, peak mem 4823MB, user 4714.5s, sys 56.5s, output queue size 197
progress 35% @chr6:127144950, elapsed 717.0s, est remaining 1331.6s, peak mem 4878MB, user 6122.0s, sys 63.8s, output queue size 574
progress 40% @chr7:128794348, elapsed 914.0s, est remaining 1371.0s, peak mem 5138MB, user 7566.6s, sys 70.7s, output queue size 144
progress 45% @chr9:846960, elapsed 1049.9s, est remaining 1283.2s, peak mem 5384MB, user 8843.0s, sys 77.5s, output queue size 15
progress 50% @chr10:32845243, elapsed 1150.2s, est remaining 1150.2s, peak mem 5384MB, user 9739.2s, sys 83.4s, output queue size 69
progress 55% @chr11:48149447, elapsed 1264.8s, est remaining 1034.8s, peak mem 5384MB, user 10686.8s, sys 89.2s, output queue size 5
progress 60% @chr12:22478313, elapsed 1369.8s, est remaining 913.2s, peak mem 5442MB, user 11629.4s, sys 96.0s, output queue size 637
progress 65% @chr13:49267490, elapsed 1470.0s, est remaining 791.6s, peak mem 5442MB, user 12443.6s, sys 102.1s, output queue size 55
progress 70% @chr15:43160681, elapsed 1645.5s, est remaining 705.2s, peak mem 5499MB, user 13902.6s, sys 107.9s, output queue size 454
progress 75% @chr16:30953185, elapsed 1753.3s, est remaining 584.4s, peak mem 5502MB, user 14920.8s, sys 114.3s, output queue size 22
progress 80% @chr17:42585125, elapsed 1856.1s, est remaining 464.0s, peak mem 5502MB, user 15869.4s, sys 120.3s, output queue size 121
progress 85% @chr19:5714183, elapsed 1949.7s, est remaining 344.1s, peak mem 5594MB, user 16655.1s, sys 125.6s, output queue size 403
progress 90% @chr19:55861992, elapsed 2039.9s, est remaining 226.7s, peak mem 5594MB, user 17433.6s, sys 130.8s, output queue size 63
progress 95% @chr22:36300851, elapsed 2142.2s, est remaining 112.7s, peak mem 5735MB, user 18358.2s, sys 137.1s, output queue size 27
progress 100% @chrY:25622443, elapsed 2198.5s, est remaining 0.0s, peak mem 5735MB, user 18876.3s, sys 141.3s, 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: 32844732891 88906492583
output file size: 2016845
reads: 1796723445
contig: 201779 intervals 37922265 bases
"assemble": 17899 calls 921.475 user 1.511 sys 923.777 real
"assemble_addRead": 17899 calls 31.585 user 0.175 sys 31.289 real
"assemble_buildGraph": 40125 calls 482.593 user 0.579 sys 484.074 real
"assemble_computecigar": 27403 calls 13.185 user 0.120 sys 13.397 real
"assemble_kg_build_calcsize": 40125 calls 237.893 user 0.310 sys 238.885 real
"assemble_kg_build_clear": 50157 calls 66.601 user 0.137 sys 66.519 real
"assemble_kg_build_prepare": 80250 calls 242.576 user 0.582 sys 243.003 real
"assemble_kg_build_threading": 30093 calls 222.445 user 0.179 sys 223.520 real
"assemble_kg_op1": 30093 calls 101.734 user 0.114 sys 101.265 real
"assemble_kg_op2": 30093 calls 0.899 user 0.000 sys 0.772 real
"assemble_kg_op3": 30093 calls 1.130 user 0.020 sys 1.050 real
"assemble_sg_clean": 27403 calls 4.666 user 0.010 sys 4.801 real
"assemble_sg_create": 27403 calls 5.525 user 0.008 sys 5.844 real
"checkGraph": 17899 calls 0.090 user 0.010 sys 0.112 real
"findHaplotype": 17899 calls 16.046 user 0.140 sys 16.236 real
advance: 208647 calls 8076.669 user 103.263 sys 8176.348 real
assemble_region: 17899 calls 969.737 user 1.855 sys 971.969 real
build_pileup: 202436 calls 41.402 user 0.111 sys 41.843 real
build_stats: 207249 calls 631.965 user 1.655 sys 637.054 real
build_variants: 8278 calls 0.270 user 0.000 sys 0.203 real
calc: 407824 calls 726.853 user 1.116 sys 743.563 real
calc_region: 8278 calls 5471.758 user 5.060 sys 5509.503 real
call_region: 8278 calls 119.925 user 0.199 sys 121.099 real
clip_region: 26177 calls 103.709 user 0.257 sys 104.116 real
done: 1 calls 71.649 user 0.729 sys 72.386 real
execute: 1 calls 0.000 user 0.009 sys 2198.550 real
fetch: 821727 calls 1938.178 user 3.949 sys 1981.146 real
fetch_ref: 845619 calls 31.635 user 1.772 sys 7.170 real
fetch_region: 17899 calls 69.692 user 0.266 sys 70.710 real
fetch_vcf: 208647 calls 90.856 user 2.011 sys 92.992 real
idle: 899 calls 0.077 user 0.003 sys 879.301 real
init: 1 calls 0.070 user 0.010 sys 0.088 real
pairhmm: 908704 calls 11910.604 user 8.011 sys 11923.851 real
realign: 8278 calls 633.179 user 0.548 sys 654.175 real
region: 410426 calls 6571.242 user 7.559 sys 6612.535 real
tracker: 410426 calls 2.475 user 0.099 sys 2.494 real
trim_region: 17899 calls 0.320 user 0.000 sys 0.345 real
overall: 6369452032 mem 26270.435 user 152.275 sys 2272.621 real