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% @chr1:119935015, elapsed 45.0s, est remaining 854.6s, peak mem 3493MB, user 451.4s, sys 6.7s, output queue size 163
progress 10% @chr2:17785862, elapsed 107.7s, est remaining 969.2s, peak mem 3942MB, user 1022.1s, sys 11.5s, output queue size 641
progress 15% @chr2:189676491, elapsed 173.8s, est remaining 984.6s, peak mem 4515MB, user 1605.8s, sys 16.4s, output queue size 401
progress 20% @chr3:97871842, elapsed 248.0s, est remaining 992.0s, peak mem 4593MB, user 2253.5s, sys 20.6s, output queue size 400
progress 25% @chr4:88463855, elapsed 301.6s, est remaining 904.8s, peak mem 4780MB, user 2719.5s, sys 25.0s, output queue size 86
progress 30% @chr5:147617911, elapsed 349.2s, est remaining 814.8s, peak mem 4832MB, user 3118.7s, sys 28.6s, output queue size 196
progress 35% @chr6:131737355, elapsed 462.1s, est remaining 858.1s, peak mem 5013MB, user 4003.0s, sys 35.6s, output queue size 608
progress 40% @chr7:128841454, elapsed 583.6s, est remaining 875.4s, peak mem 5258MB, user 4931.3s, sys 40.7s, output queue size 543
progress 45% @chr9:1051614, elapsed 668.7s, est remaining 817.3s, peak mem 5374MB, user 5745.8s, sys 45.7s, output queue size 157
progress 50% @chr10:32848596, elapsed 733.5s, est remaining 733.5s, peak mem 5374MB, user 6326.1s, sys 50.0s, output queue size 74
progress 55% @chr11:48136039, elapsed 808.8s, est remaining 661.7s, peak mem 5374MB, user 6936.2s, sys 54.4s, output queue size 14
progress 60% @chr12:22474751, elapsed 877.3s, est remaining 584.9s, peak mem 5411MB, user 7559.7s, sys 58.8s, output queue size 638
progress 65% @chr13:49476476, elapsed 943.8s, est remaining 508.2s, peak mem 5411MB, user 8106.8s, sys 62.6s, output queue size 557
progress 70% @chr15:43149029, elapsed 1054.2s, est remaining 451.8s, peak mem 5411MB, user 9011.1s, sys 66.5s, output queue size 454
progress 75% @chr16:30947052, elapsed 1127.3s, est remaining 375.8s, peak mem 5443MB, user 9708.9s, sys 70.8s, output queue size 21
progress 80% @chr17:42585125, elapsed 1193.9s, est remaining 298.5s, peak mem 5443MB, user 10327.2s, sys 75.4s, output queue size 120
progress 85% @chr19:5699027, elapsed 1255.0s, est remaining 221.5s, peak mem 5509MB, user 10853.0s, sys 79.3s, output queue size 403
progress 90% @chr19:55731999, elapsed 1313.4s, est remaining 145.9s, peak mem 5509MB, user 11369.5s, sys 82.6s, output queue size 61
progress 95% @chr22:36504098, elapsed 1377.0s, est remaining 72.5s, peak mem 5596MB, user 11955.4s, sys 86.6s, output queue size 27
progress 100% @chrY:25622443, elapsed 1414.4s, est remaining 0.0s, peak mem 5596MB, user 12300.4s, sys 89.8s, 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: 32844732891 88906492583
output file size: 2016845
reads: 1796723445
contig: 201779 intervals 37922265 bases
"assemble": 17899 calls 570.277 user 0.564 sys 572.437 real
"assemble_addRead": 17899 calls 20.561 user 0.087 sys 20.770 real
"assemble_buildGraph": 40125 calls 286.503 user 0.166 sys 287.844 real
"assemble_computecigar": 27403 calls 7.660 user 0.012 sys 7.731 real
"assemble_kg_build_calcsize": 40125 calls 143.204 user 0.068 sys 142.779 real
"assemble_kg_build_clear": 50157 calls 35.619 user 0.041 sys 35.879 real
"assemble_kg_build_prepare": 80250 calls 161.196 user 0.254 sys 162.647 real
"assemble_kg_build_threading": 30093 calls 131.791 user 0.058 sys 133.501 real
"assemble_kg_op1": 30093 calls 64.796 user 0.050 sys 64.527 real
"assemble_kg_op2": 30093 calls 0.574 user 0.000 sys 0.559 real
"assemble_kg_op3": 30093 calls 0.716 user 0.010 sys 0.731 real
"assemble_sg_clean": 27403 calls 2.933 user 0.000 sys 2.904 real
"assemble_sg_create": 27403 calls 3.447 user 0.010 sys 3.667 real
"checkGraph": 17899 calls 0.120 user 0.000 sys 0.078 real
"findHaplotype": 17899 calls 9.415 user 0.020 sys 9.622 real
advance: 208647 calls 5423.887 user 67.384 sys 5474.731 real
assemble_region: 17899 calls 600.693 user 0.701 sys 603.291 real
build_pileup: 202436 calls 23.193 user 0.040 sys 23.668 real
build_stats: 207249 calls 375.631 user 0.365 sys 384.457 real
build_variants: 8278 calls 0.130 user 0.000 sys 0.135 real
calc: 407824 calls 414.430 user 0.336 sys 428.113 real
calc_region: 8278 calls 3465.105 user 2.076 sys 3484.752 real
call_region: 8278 calls 71.931 user 0.020 sys 72.499 real
clip_region: 26177 calls 69.905 user 0.054 sys 69.659 real
done: 1 calls 49.496 user 0.226 sys 49.734 real
execute: 1 calls 0.004 user 0.002 sys 1414.422 real
fetch: 821727 calls 1320.748 user 1.421 sys 1365.147 real
fetch_ref: 845619 calls 27.722 user 1.273 sys 5.395 real
fetch_region: 17899 calls 54.828 user 0.030 sys 54.837 real
fetch_vcf: 208647 calls 61.224 user 1.615 sys 63.859 real
idle: 623 calls 0.062 user 0.000 sys 602.246 real
init: 1 calls 0.039 user 0.020 sys 0.062 real
pairhmm: 908704 calls 7356.144 user 2.087 sys 7367.104 real
realign: 8278 calls 489.307 user 0.173 sys 508.911 real
region: 410426 calls 4159.871 user 2.933 sys 4182.689 real
tracker: 410426 calls 1.498 user 0.080 sys 1.593 real
trim_region: 17899 calls 0.283 user 0.000 sys 0.235 real
overall: 6247530496 mem 16906.303 user 94.722 sys 1465.138 real