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% @chr1:119937813, elapsed 66.0s, est remaining 1253.1s, peak mem 3868MB, user 591.4s, sys 7.9s, output queue size 164
progress 10% @chr1:243499720, elapsed 195.0s, est remaining 1755.4s, peak mem 4976MB, user 1558.3s, sys 14.0s, output queue size 1131
progress 15% @chr2:189083984, elapsed 276.7s, est remaining 1567.8s, peak mem 5409MB, user 2218.8s, sys 19.1s, output queue size 333
progress 20% @chr3:97871842, elapsed 351.0s, est remaining 1404.1s, peak mem 5441MB, user 2888.9s, sys 24.4s, output queue size 408
progress 25% @chr4:88463855, elapsed 412.3s, est remaining 1237.0s, peak mem 5474MB, user 3406.4s, sys 29.0s, output queue size 86
progress 30% @chr5:147509478, elapsed 463.6s, est remaining 1081.8s, peak mem 5474MB, user 3771.1s, sys 32.3s, output queue size 198
progress 35% @chr6:131733588, elapsed 582.6s, est remaining 1081.9s, peak mem 5631MB, user 4750.8s, sys 37.4s, output queue size 608
progress 40% @chr7:128877484, elapsed 713.0s, est remaining 1069.4s, peak mem 6061MB, user 5664.6s, sys 42.6s, output queue size 1563
progress 45% @chr9:990041, elapsed 793.7s, est remaining 970.1s, peak mem 6061MB, user 6382.4s, sys 46.8s, output queue size 159
progress 50% @chr10:32901570, elapsed 861.2s, est remaining 861.2s, peak mem 6190MB, user 6969.8s, sys 51.5s, output queue size 74
progress 55% @chr11:49037478, elapsed 997.5s, est remaining 816.2s, peak mem 6190MB, user 7896.8s, sys 55.6s, output queue size 3358
progress 60% @chr12:22506711, elapsed 1079.5s, est remaining 719.7s, peak mem 6190MB, user 8618.6s, sys 59.5s, output queue size 640
progress 65% @chr13:49259346, elapsed 1167.4s, est remaining 628.6s, peak mem 6190MB, user 9283.1s, sys 64.6s, output queue size 54
progress 70% @chr15:43160681, elapsed 1334.3s, est remaining 571.8s, peak mem 6190MB, user 10604.6s, sys 68.9s, output queue size 454
progress 75% @chr16:30892586, elapsed 1429.1s, est remaining 476.4s, peak mem 6248MB, user 11541.6s, sys 74.0s, output queue size 22
progress 80% @chr17:42562612, elapsed 1495.4s, est remaining 373.8s, peak mem 6248MB, user 12171.2s, sys 79.3s, output queue size 56
progress 85% @chr19:5749101, elapsed 1576.9s, est remaining 278.3s, peak mem 6248MB, user 12807.9s, sys 83.4s, output queue size 426
progress 90% @chr19:55852081, elapsed 1656.7s, est remaining 184.1s, peak mem 6248MB, user 13480.2s, sys 87.6s, output queue size 78
progress 95% @chr22:36504515, elapsed 1739.4s, est remaining 91.5s, peak mem 6840MB, user 14227.5s, sys 92.9s, output queue size 2
progress 100% @chrY:25622443, elapsed 1788.4s, est remaining 0.0s, peak mem 6840MB, user 14645.9s, sys 96.4s, 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: 26263832747 103367536517
output file size: 2942516
reads: 1658552174
contig: 201779 intervals 37922265 bases
"assemble": 16113 calls 583.628 user 0.597 sys 585.891 real
"assemble_addRead": 16113 calls 19.071 user 0.100 sys 19.376 real
"assemble_buildGraph": 36499 calls 283.805 user 0.211 sys 284.641 real
"assemble_computecigar": 24753 calls 10.191 user 0.001 sys 10.136 real
"assemble_kg_build_calcsize": 36499 calls 147.206 user 0.049 sys 148.742 real
"assemble_kg_build_clear": 46017 calls 36.408 user 0.050 sys 36.990 real
"assemble_kg_build_prepare": 72998 calls 174.409 user 0.255 sys 174.756 real
"assemble_kg_build_threading": 26981 calls 122.154 user 0.112 sys 121.062 real
"assemble_kg_op1": 26981 calls 63.929 user 0.044 sys 64.728 real
"assemble_kg_op2": 26981 calls 0.594 user 0.000 sys 0.660 real
"assemble_kg_op3": 26981 calls 0.655 user 0.000 sys 0.719 real
"assemble_sg_clean": 24753 calls 3.375 user 0.000 sys 3.242 real
"assemble_sg_create": 24753 calls 3.578 user 0.000 sys 3.535 real
"checkGraph": 16113 calls 0.110 user 0.010 sys 0.090 real
"findHaplotype": 16113 calls 12.584 user 0.001 sys 12.499 real
advance: 208647 calls 5836.478 user 73.420 sys 5897.959 real
assemble_region: 16113 calls 615.657 user 0.721 sys 618.154 real
build_pileup: 202447 calls 26.414 user 0.087 sys 26.356 real
build_stats: 207329 calls 452.154 user 1.368 sys 459.514 real
build_variants: 11455 calls 0.142 user 0.000 sys 0.159 real
calc: 407987 calls 452.544 user 0.353 sys 466.558 real
calc_region: 11455 calls 5232.020 user 2.227 sys 5247.182 real
call_region: 11455 calls 103.262 user 0.052 sys 104.891 real
clip_region: 27568 calls 81.429 user 0.079 sys 81.047 real
done: 1 calls 23.140 user 0.139 sys 23.283 real
execute: 1 calls 0.004 user 0.002 sys 1788.375 real
fetch: 821727 calls 1308.141 user 1.386 sys 1350.597 real
fetch_ref: 843833 calls 28.380 user 1.393 sys 5.356 real
fetch_region: 16113 calls 45.743 user 0.025 sys 45.935 real
fetch_vcf: 208647 calls 59.303 user 1.211 sys 63.604 real
idle: 311 calls 0.069 user 0.000 sys 290.663 real
init: 1 calls 0.029 user 0.030 sys 0.062 real
pairhmm: 1390548 calls 11089.940 user 1.684 sys 11102.848 real
realign: 11455 calls 604.048 user 0.228 sys 627.210 real
region: 410426 calls 5931.426 user 3.175 sys 5949.724 real
tracker: 410426 calls 1.436 user 0.081 sys 1.419 real
trim_region: 16113 calls 0.288 user 0.000 sys 0.278 real
overall: 7172890624 mem 21362.891 user 101.082 sys 1812.918 real