cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i reference-NA12878.bam -i FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity_padded100bp.bed --algo TNhaplotyper2 --tumor_sample FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1 --normal_sample reference-NA12878 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz positive_somatic_control_1.tnseq.vcf.gz --algo OrientationBias --tumor_sample FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1 positive_somatic_control_1.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1 --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments positive_somatic_control_1.tnseq.segments positive_somatic_control_1.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:112712644, elapsed 90.2s, est remaining 1713.9s, peak mem 3234MB, user 825.6s, sys 11.1s, output queue size 51
progress 10% @chr2:3726903, elapsed 247.4s, est remaining 2226.9s, peak mem 3590MB, user 2211.9s, sys 18.7s, output queue size 39
progress 15% @chr2:178600754, elapsed 390.0s, est remaining 2210.2s, peak mem 4763MB, user 3494.0s, sys 26.5s, output queue size 27
progress 20% @chr3:57503916, elapsed 509.3s, est remaining 2037.1s, peak mem 4763MB, user 4647.5s, sys 33.2s, output queue size 6
progress 25% @chr4:70782991, elapsed 620.6s, est remaining 1861.7s, peak mem 4775MB, user 5637.6s, sys 39.7s, output queue size 298
progress 30% @chr5:135893920, elapsed 715.4s, est remaining 1669.2s, peak mem 4830MB, user 6430.0s, sys 45.1s, output queue size 276
progress 35% @chr6:105368803, elapsed 1040.0s, est remaining 1931.4s, peak mem 5320MB, user 9446.3s, sys 53.3s, output queue size 560
progress 40% @chr7:107790948, elapsed 1290.1s, est remaining 1935.2s, peak mem 5799MB, user 11391.9s, sys 63.3s, output queue size 622
progress 45% @chr8:143936879, elapsed 1526.2s, est remaining 1865.4s, peak mem 7749MB, user 13865.5s, sys 73.9s, output queue size 742
progress 50% @chr10:21733404, elapsed 1686.3s, est remaining 1686.3s, peak mem 7794MB, user 15406.2s, sys 82.4s, output queue size 19
progress 55% @chr11:34154601, elapsed 1833.7s, est remaining 1500.3s, peak mem 7794MB, user 16775.7s, sys 88.4s, output queue size 187
progress 60% @chr12:14915389, elapsed 2020.3s, est remaining 1346.9s, peak mem 7794MB, user 18343.1s, sys 96.8s, output queue size 219
progress 65% @chr13:32228356, elapsed 2173.5s, est remaining 1170.3s, peak mem 7794MB, user 19743.2s, sys 104.9s, output queue size 195
progress 70% @chr15:38516097, elapsed 2515.4s, est remaining 1078.0s, peak mem 8200MB, user 22849.5s, sys 114.1s, output queue size 1113
progress 75% @chr16:28342507, elapsed 2666.0s, est remaining 888.7s, peak mem 8200MB, user 24638.7s, sys 122.0s, output queue size 140
progress 80% @chr17:40133434, elapsed 2782.4s, est remaining 695.6s, peak mem 8200MB, user 25751.2s, sys 129.1s, output queue size 158
progress 85% @chr19:1815966, elapsed 2952.7s, est remaining 521.1s, peak mem 8200MB, user 27309.3s, sys 137.9s, output queue size 34
progress 90% @chr19:54573779, elapsed 3131.9s, est remaining 348.0s, peak mem 8200MB, user 28911.7s, sys 145.9s, output queue size 21
progress 95% @chr22:32149440, elapsed 3298.1s, est remaining 173.6s, peak mem 8200MB, user 30507.6s, sys 154.6s, output queue size 67
progress 100% @chrX:154531292, elapsed 3412.3s, est remaining 0.0s, peak mem 8200MB, user 31519.0s, sys 160.7s, output queue size 651
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050654
  features: bfebfbff 7ffefbff
  extended: d39ffffb 00000018
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8175M CPU @ 2.50GHz
threads: 12 max 96
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 23476805429 105664775977
output file size: 20599434
reads: 1553251308
contig: 178193 intervals 76355618 bases
"assemble": 86852 calls 2119.238 user 4.256 sys 2130.469 real
"assemble_addRead": 86852 calls 66.322 user 0.769 sys 68.670 real
"assemble_buildGraph": 182732 calls 1082.896 user 1.123 sys 1087.141 real
"assemble_computecigar": 142397 calls 62.806 user 0.344 sys 63.282 real
"assemble_kg_build_calcsize": 182732 calls 551.221 user 0.197 sys 552.546 real
"assemble_kg_build_clear": 218920 calls 117.484 user 0.251 sys 118.790 real
"assemble_kg_build_prepare": 365464 calls 594.876 user 2.062 sys 598.555 real
"assemble_kg_build_threading": 146544 calls 493.960 user 0.388 sys 495.148 real
"assemble_kg_op1": 146544 calls 218.039 user 0.202 sys 219.915 real
"assemble_kg_op2": 146544 calls 2.038 user 0.060 sys 2.233 real
"assemble_kg_op3": 146544 calls 4.291 user 0.080 sys 4.322 real
"assemble_sg_clean": 142397 calls 19.497 user 0.043 sys 19.163 real
"assemble_sg_create": 142397 calls 25.139 user 0.017 sys 24.779 real
"checkGraph": 86852 calls 0.410 user 0.020 sys 0.443 real
"findHaplotype": 86852 calls 70.053 user 0.413 sys 70.797 real
advance: 189104 calls 6253.048 user 110.902 sys 6357.195 real
assemble_region: 86852 calls 2257.818 user 5.651 sys 2272.470 real
build_pileup: 187013 calls 41.551 user 0.095 sys 42.207 real
build_stats: 188097 calls 797.582 user 4.365 sys 813.186 real
build_variants: 81829 calls 0.726 user 0.020 sys 0.710 real
calc: 365421 calls 557.725 user 0.389 sys 570.330 real
calc_region: 81829 calls 19011.548 user 11.194 sys 19116.715 real
call_region: 81829 calls 294.124 user 0.761 sys 301.380 real
clip_region: 168681 calls 264.455 user 0.653 sys 267.218 real
done: 1 calls 60.067 user 1.142 sys 61.243 real
execute: 1 calls 0.000 user 0.009 sys 3412.342 real
fetch: 743546 calls 1488.413 user 4.072 sys 1530.359 real
fetch_ref: 832357 calls 29.991 user 1.822 sys 8.116 real
fetch_region: 86852 calls 115.741 user 0.586 sys 117.621 real
fetch_vcf: 189104 calls 67.661 user 2.009 sys 71.892 real
idle: 809 calls 0.256 user 0.000 sys 754.676 real
init: 1 calls 0.049 user 0.039 sys 0.088 real
pairhmm: 2584532 calls 25865.918 user 2.155 sys 25928.565 real
realign: 81829 calls 1525.657 user 0.860 sys 1646.902 real
region: 367297 calls 21494.363 user 18.383 sys 21619.045 real
tracker: 367297 calls 2.799 user 0.080 sys 3.170 real
trim_region: 86852 calls 1.542 user 0.030 sys 1.419 real
overall: 8738627584 mem 40734.893 user 168.495 sys 3475.502 real