cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta --interval_padding 100 -i 869_BIT-N1-BDNA-1_B23H3TCLT3_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 869_BIT-N1-BDNA-1_B23H3TCLT3_1 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon.hotspot_protected.raw.vcf.gz 869_BIT-N1-BDNA-1_B23H3TCLT3_1.tnseq_tumor_only.vcf.gz --algo OrientationBias --tumor_sample 869_BIT-N1-BDNA-1_B23H3TCLT3_1 869_BIT-N1-BDNA-1_B23H3TCLT3_1.tnseq_tumor_only.orientation_data.tsv --algo ContaminationModel --tumor_sample 869_BIT-N1-BDNA-1_B23H3TCLT3_1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments 869_BIT-N1-BDNA-1_B23H3TCLT3_1.tnseq_tumor_only.segments 869_BIT-N1-BDNA-1_B23H3TCLT3_1.tnseq_tumor_only.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113738010, elapsed 32.1s, est remaining 609.6s, peak mem 1117MB, user 269.9s, sys 6.8s, output queue size 320
progress 10% @chr2:3767654, elapsed 71.7s, est remaining 645.7s, peak mem 1238MB, user 596.4s, sys 10.7s, output queue size 451
progress 15% @chr2:178551530, elapsed 123.2s, est remaining 698.2s, peak mem 1501MB, user 1009.0s, sys 15.2s, output queue size 141
progress 20% @chr3:57507543, elapsed 169.3s, est remaining 677.3s, peak mem 1535MB, user 1404.8s, sys 19.0s, output queue size 54
progress 25% @chr4:70778269, elapsed 221.1s, est remaining 663.2s, peak mem 1535MB, user 1787.3s, sys 23.2s, output queue size 302
progress 30% @chr5:135873921, elapsed 249.6s, est remaining 582.5s, peak mem 1535MB, user 2034.2s, sys 27.3s, output queue size 275
progress 35% @chr6:105373269, elapsed 356.4s, est remaining 661.8s, peak mem 1596MB, user 2889.0s, sys 33.9s, output queue size 559
progress 40% @chr7:107690024, elapsed 429.7s, est remaining 644.5s, peak mem 1714MB, user 3475.0s, sys 38.9s, output queue size 589
progress 45% @chr8:143933898, elapsed 508.3s, est remaining 621.2s, peak mem 1804MB, user 4162.7s, sys 44.8s, output queue size 740
progress 50% @chr10:21713672, elapsed 574.1s, est remaining 574.1s, peak mem 1855MB, user 4688.9s, sys 50.1s, output queue size 59
progress 55% @chr11:34154165, elapsed 617.2s, est remaining 505.0s, peak mem 1855MB, user 5031.2s, sys 55.1s, output queue size 187
progress 60% @chr12:14681256, elapsed 664.2s, est remaining 442.8s, peak mem 1855MB, user 5427.3s, sys 59.8s, output queue size 212
progress 65% @chr13:32170912, elapsed 706.7s, est remaining 380.5s, peak mem 1855MB, user 5803.8s, sys 64.6s, output queue size 196
progress 70% @chr15:34981259, elapsed 780.1s, est remaining 334.3s, peak mem 1870MB, user 6491.8s, sys 70.1s, output queue size 304
progress 75% @chr16:28501876, elapsed 834.9s, est remaining 278.3s, peak mem 1870MB, user 7005.5s, sys 74.6s, output queue size 147
progress 80% @chr17:40096343, elapsed 877.3s, est remaining 219.3s, peak mem 1888MB, user 7370.7s, sys 79.1s, output queue size 158
progress 85% @chr19:1795775, elapsed 924.7s, est remaining 163.2s, peak mem 1888MB, user 7790.3s, sys 83.6s, output queue size 35
progress 90% @chr19:54630974, elapsed 981.3s, est remaining 109.0s, peak mem 1895MB, user 8221.7s, sys 87.8s, output queue size 307
progress 95% @chr22:32151387, elapsed 1036.3s, est remaining 54.5s, peak mem 1973MB, user 8697.3s, sys 92.7s, output queue size 68
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 1062.6s, est remaining 0.0s, peak mem 1973MB, user 8925.8s, sys 96.4s, output queue size 7
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: AuthenticAMD
 signature: 00800f12
  features: 178bfbff fed83203
  extended: 209c01a9 00000000
  amd bits: 2fd3fbff 00c001f3
     brand: AMD EPYC 7571
threads: 12 max 64
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 29885560762
output file size: 6410505
reads: 411013043
contig: 178193 intervals 76355618 bases
"assemble": 38788 calls 541.482 user 2.821 sys 548.599 real
"assemble_addRead": 38788 calls 15.633 user 0.144 sys 15.884 real
"assemble_buildGraph": 82476 calls 286.184 user 0.887 sys 291.591 real
"assemble_computecigar": 62084 calls 33.794 user 0.492 sys 34.659 real
"assemble_kg_build_calcsize": 82476 calls 145.276 user 0.186 sys 148.583 real
"assemble_kg_build_clear": 101778 calls 22.936 user 0.144 sys 22.815 real
"assemble_kg_build_prepare": 164952 calls 130.615 user 1.072 sys 132.213 real
"assemble_kg_build_threading": 63174 calls 133.834 user 0.383 sys 135.577 real
"assemble_kg_op1": 63174 calls 56.626 user 0.275 sys 56.689 real
"assemble_kg_op2": 63174 calls 1.340 user 0.040 sys 1.340 real
"assemble_kg_op3": 63174 calls 1.909 user 0.010 sys 2.087 real
"assemble_sg_clean": 62084 calls 9.927 user 0.039 sys 10.130 real
"assemble_sg_create": 62084 calls 14.506 user 0.085 sys 14.930 real
"checkGraph": 38788 calls 0.260 user 0.000 sys 0.261 real
"findHaplotype": 38788 calls 36.768 user 0.621 sys 37.710 real
advance: 189104 calls 1838.196 user 37.897 sys 1874.351 real
assemble_region: 38788 calls 594.901 user 3.686 sys 603.281 real
build_pileup: 186833 calls 26.225 user 0.158 sys 26.536 real
build_stats: 187773 calls 648.314 user 7.014 sys 666.843 real
build_variants: 35055 calls 0.441 user 0.010 sys 0.402 real
calc: 364819 calls 265.080 user 0.694 sys 277.705 real
calc_region: 35055 calls 4271.166 user 5.892 sys 4331.271 real
call_region: 35055 calls 92.336 user 0.488 sys 93.391 real
clip_region: 73843 calls 72.913 user 0.213 sys 73.977 real
done: 1 calls 101.837 user 0.899 sys 102.753 real
execute: 1 calls 0.002 user 0.011 sys 1062.648 real
fetch: 743546 calls 540.568 user 3.231 sys 558.708 real
fetch_ref: 784293 calls 28.445 user 2.745 sys 8.345 real
fetch_region: 38788 calls 20.665 user 0.157 sys 21.022 real
fetch_vcf: 189104 calls 84.048 user 2.240 sys 89.385 real
idle: 1269 calls 0.139 user 0.009 sys 1239.446 real
init: 1 calls 0.066 user 0.049 sys 0.120 real
pairhmm: 637394 calls 7157.535 user 5.284 sys 7183.958 real
realign: 35055 calls 530.311 user 0.854 sys 566.126 real
region: 367297 calls 4918.730 user 10.249 sys 4988.691 real
tracker: 367297 calls 2.472 user 0.185 sys 2.802 real
trim_region: 38788 calls 0.943 user 0.030 sys 0.975 real
overall: 2343444480 mem 12710.882 user 110.906 sys 1166.821 real