cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i 1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam -i 1029_11H-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_11H-T1-TDNA-1_B23KFCWLT4_1 --normal_sample 1029_11H-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_11H.tnseq.vcf.gz --algo OrientationBias --tumor_sample 1029_11H-T1-TDNA-1_B23KFCWLT4_1 1029_11H.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample 1029_11H-T1-TDNA-1_B23KFCWLT4_1 --normal_sample 1029_11H-N1-BDNA-1_B23KGCJLT4_1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments 1029_11H.tnseq.segments 1029_11H.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119937238, elapsed 61.7s, est remaining 1171.6s, peak mem 2986MB, user 568.9s, sys 9.9s, output queue size 164
progress 10% @chr2:21001730, elapsed 194.1s, est remaining 1747.2s, peak mem 4447MB, user 1616.2s, sys 18.2s, output queue size 639
progress 15% @chr2:185788643, elapsed 310.1s, est remaining 1757.2s, peak mem 5013MB, user 2523.3s, sys 25.4s, output queue size 281
progress 20% @chr3:98784945, elapsed 444.4s, est remaining 1777.7s, peak mem 5091MB, user 3707.3s, sys 32.6s, output queue size 422
progress 25% @chr4:88479353, elapsed 557.7s, est remaining 1673.1s, peak mem 5385MB, user 4668.9s, sys 39.9s, output queue size 87
progress 30% @chr5:147631413, elapsed 644.1s, est remaining 1503.0s, peak mem 5598MB, user 5320.9s, sys 44.8s, output queue size 198
progress 35% @chr6:131864506, elapsed 858.4s, est remaining 1594.3s, peak mem 5660MB, user 6904.8s, sys 51.2s, output queue size 621
progress 40% @chr7:128858336, elapsed 1084.8s, est remaining 1627.2s, peak mem 6216MB, user 8493.9s, sys 59.5s, output queue size 1562
progress 45% @chr9:977002, elapsed 1252.1s, est remaining 1530.4s, peak mem 6291MB, user 9987.3s, sys 66.5s, output queue size 15
progress 50% @chr10:32854400, elapsed 1391.4s, est remaining 1391.4s, peak mem 6685MB, user 11117.7s, sys 74.0s, output queue size 68
progress 55% @chr11:48167204, elapsed 1557.2s, est remaining 1274.1s, peak mem 6685MB, user 12433.4s, sys 80.8s, output queue size 74
progress 60% @chr12:21765723, elapsed 1670.9s, est remaining 1113.9s, peak mem 6685MB, user 13429.4s, sys 86.7s, output queue size 75
progress 65% @chr13:49513059, elapsed 1817.4s, est remaining 978.6s, peak mem 6685MB, user 14484.6s, sys 93.3s, output queue size 557
progress 70% @chr15:43148755, elapsed 2066.9s, est remaining 885.8s, peak mem 7882MB, user 16424.1s, sys 101.4s, output queue size 454
progress 75% @chr16:30953185, elapsed 2165.9s, est remaining 722.0s, peak mem 7882MB, user 17373.6s, sys 107.4s, output queue size 22
progress 80% @chr17:42586765, elapsed 2271.9s, est remaining 568.0s, peak mem 7882MB, user 18381.9s, sys 114.1s, output queue size 121
progress 85% @chr19:5708342, elapsed 2427.5s, est remaining 428.4s, peak mem 7882MB, user 19529.2s, sys 121.2s, output queue size 400
progress 90% @chr19:55621751, elapsed 2530.1s, est remaining 281.1s, peak mem 7882MB, user 20408.2s, sys 126.5s, output queue size 50
progress 95% @chr22:36504515, elapsed 2620.8s, est remaining 137.9s, peak mem 7882MB, user 21165.3s, sys 131.6s, output queue size 0
progress 100% @chr6_GL000254v2_alt:3881705, elapsed 2749.3s, est remaining 0.0s, peak mem 7882MB, user 22166.5s, sys 137.7s, output queue size 1
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: 34853343684 99946753954
output file size: 2168680
reads: 2014757509
contig: 201779 intervals 37922265 bases
"assemble": 18996 calls 1078.341 user 1.008 sys 1080.206 real
"assemble_addRead": 18996 calls 35.882 user 0.220 sys 36.142 real
"assemble_buildGraph": 42882 calls 560.093 user 0.204 sys 560.474 real
"assemble_computecigar": 28846 calls 14.464 user 0.100 sys 14.510 real
"assemble_kg_build_calcsize": 42882 calls 273.326 user 0.051 sys 274.883 real
"assemble_kg_build_clear": 53660 calls 79.803 user 0.071 sys 79.279 real
"assemble_kg_build_prepare": 85764 calls 290.113 user 0.602 sys 290.522 real
"assemble_kg_build_threading": 32104 calls 258.977 user 0.092 sys 258.108 real
"assemble_kg_op1": 32104 calls 117.310 user 0.052 sys 118.689 real
"assemble_kg_op2": 32104 calls 1.020 user 0.000 sys 0.910 real
"assemble_kg_op3": 32104 calls 1.197 user 0.000 sys 1.171 real
"assemble_sg_clean": 28846 calls 4.630 user 0.010 sys 4.850 real
"assemble_sg_create": 28846 calls 5.793 user 0.000 sys 5.891 real
"checkGraph": 18996 calls 0.140 user 0.000 sys 0.111 real
"findHaplotype": 18996 calls 17.351 user 0.141 sys 17.737 real
advance: 208647 calls 8802.255 user 104.730 sys 8908.200 real
assemble_region: 18996 calls 1132.246 user 1.388 sys 1134.713 real
build_pileup: 202458 calls 43.623 user 0.051 sys 44.224 real
build_stats: 207057 calls 690.059 user 1.185 sys 692.095 real
build_variants: 8360 calls 0.189 user 0.010 sys 0.222 real
calc: 407430 calls 784.902 user 0.264 sys 800.756 real
calc_region: 8360 calls 7463.952 user 2.500 sys 7499.272 real
call_region: 8360 calls 157.627 user 0.290 sys 158.153 real
clip_region: 27356 calls 123.368 user 0.161 sys 123.454 real
done: 1 calls 66.483 user 0.880 sys 67.371 real
execute: 1 calls 0.000 user 0.010 sys 2749.346 real
fetch: 821727 calls 2157.516 user 2.509 sys 2197.428 real
fetch_ref: 846716 calls 30.906 user 1.962 sys 7.164 real
fetch_region: 18996 calls 81.673 user 0.100 sys 81.508 real
fetch_vcf: 208647 calls 85.704 user 2.126 sys 89.194 real
idle: 839 calls 0.055 user 0.000 sys 818.749 real
init: 1 calls 0.058 user 0.029 sys 0.092 real
pairhmm: 1205859 calls 17021.969 user 1.641 sys 17031.549 real
realign: 8360 calls 785.310 user 0.165 sys 807.578 real
region: 410426 calls 8747.321 user 4.309 sys 8785.629 real
tracker: 410426 calls 2.380 user 0.061 sys 2.448 real
trim_region: 18996 calls 0.335 user 0.000 sys 0.371 real
overall: 8352186368 mem 32881.380 user 145.359 sys 2818.491 real