cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i Sig_18_Blood.recalibrated.bam -i Sig_18_tissue.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21_padded100bp.bed --algo TNhaplotyper2 --tumor_sample Sig_18_tissue --normal_sample Sig_18_Blood --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz custom_Sig_18_tumor_normal.tnseq.vcf.gz --algo OrientationBias --tumor_sample Sig_18_tissue custom_Sig_18_tumor_normal.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample Sig_18_tissue --normal_sample Sig_18_Blood --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments custom_Sig_18_tumor_normal.tnseq.segments custom_Sig_18_tumor_normal.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:10595882, elapsed 0.5s, est remaining 10.3s, peak mem 308MB, user 3.7s, sys 0.1s, output queue size 56
progress 10% @chr21:21432008, elapsed 1.0s, est remaining 8.6s, peak mem 356MB, user 7.0s, sys 0.2s, output queue size 16
progress 15% @chr21:28992664, elapsed 1.4s, est remaining 7.7s, peak mem 376MB, user 10.5s, sys 0.3s, output queue size 11
progress 20% @chr21:31038152, elapsed 1.7s, est remaining 6.6s, peak mem 418MB, user 13.2s, sys 0.3s, output queue size 16
progress 25% @chr21:32378345, elapsed 2.4s, est remaining 7.3s, peak mem 424MB, user 17.9s, sys 0.4s, output queue size 65
progress 30% @chr21:33348991, elapsed 2.8s, est remaining 6.5s, peak mem 437MB, user 21.7s, sys 0.4s, output queue size 24
progress 35% @chr21:34142308, elapsed 3.1s, est remaining 5.8s, peak mem 458MB, user 24.7s, sys 0.5s, output queue size 74
progress 40% @chr21:36281383, elapsed 6.6s, est remaining 9.9s, peak mem 821MB, user 30.7s, sys 0.5s, output queue size 68
progress 45% @chr21:37152851, elapsed 7.2s, est remaining 8.8s, peak mem 824MB, user 41.2s, sys 0.6s, output queue size 160
progress 50% @chr21:39238379, elapsed 7.7s, est remaining 7.7s, peak mem 881MB, user 48.9s, sys 0.7s, output queue size 242
progress 55% @chr21:41338278, elapsed 8.6s, est remaining 7.0s, peak mem 967MB, user 57.5s, sys 0.8s, output queue size 149
progress 60% @chr21:41509513, elapsed 14.6s, est remaining 9.7s, peak mem 1791MB, user 92.0s, sys 1.3s, output queue size 21
progress 65% @chr21:42362379, elapsed 16.0s, est remaining 8.6s, peak mem 1838MB, user 108.0s, sys 1.4s, output queue size 102
progress 70% @chr21:43107351, elapsed 16.4s, est remaining 7.0s, peak mem 1838MB, user 116.9s, sys 1.5s, output queue size 219
progress 75% @chr21:44118663, elapsed 16.6s, est remaining 5.5s, peak mem 1838MB, user 120.0s, sys 1.5s, output queue size 327
progress 80% @chr21:44233457, elapsed 17.1s, est remaining 4.3s, peak mem 1838MB, user 124.1s, sys 1.6s, output queue size 434
progress 85% @chr21:45175630, elapsed 17.8s, est remaining 3.1s, peak mem 1838MB, user 130.0s, sys 1.7s, output queue size 517
progress 90% @chr21:46116277, elapsed 18.6s, est remaining 2.1s, peak mem 1838MB, user 136.0s, sys 1.7s, output queue size 611
progress 95% @chr21:41501593, elapsed 19.1s, est remaining 1.0s, peak mem 1838MB, user 147.9s, sys 1.8s, output queue size 706
progress 100% @chr21:46334297, elapsed 20.2s, est remaining 0.0s, peak mem 1838MB, user 155.3s, sys 1.8s, output queue size 91
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 208827488 728301144
output file size: 95376
reads: 14812996
contig: 1979 intervals 801713 bases
"assemble": 405 calls 9.212 user 0.070 sys 9.381 real
"assemble_addRead": 405 calls 0.252 user 0.010 sys 0.295 real
"assemble_buildGraph": 944 calls 4.668 user 0.010 sys 4.500 real
"assemble_computecigar": 561 calls 0.220 user 0.020 sys 0.252 real
"assemble_kg_build_calcsize": 944 calls 2.442 user 0.000 sys 2.535 real
"assemble_kg_build_clear": 1284 calls 0.725 user 0.000 sys 0.642 real
"assemble_kg_build_prepare": 1888 calls 2.609 user 0.060 sys 2.800 real
"assemble_kg_build_threading": 604 calls 1.823 user 0.000 sys 1.692 real
"assemble_kg_op1": 604 calls 0.956 user 0.010 sys 1.021 real
"assemble_kg_op2": 604 calls 0.010 user 0.000 sys 0.016 real
"assemble_kg_op3": 604 calls 0.000 user 0.000 sys 0.013 real
"assemble_sg_clean": 561 calls 0.047 user 0.000 sys 0.087 real
"assemble_sg_create": 561 calls 0.105 user 0.000 sys 0.079 real
"checkGraph": 405 calls 0.000 user 0.000 sys 0.002 real
"findHaplotype": 405 calls 0.250 user 0.020 sys 0.289 real
advance: 2074 calls 32.922 user 1.164 sys 34.456 real
assemble_region: 405 calls 9.714 user 0.100 sys 9.975 real
build_pileup: 1976 calls 0.485 user 0.000 sys 0.481 real
build_stats: 2008 calls 7.528 user 0.151 sys 7.739 real
build_variants: 297 calls 0.010 user 0.000 sys 0.005 real
calc: 3928 calls 4.572 user 0.001 sys 4.551 real
calc_region: 297 calls 77.049 user 0.117 sys 77.542 real
call_region: 297 calls 1.785 user 0.000 sys 1.766 real
clip_region: 702 calls 1.257 user 0.000 sys 1.276 real
done: 1 calls 1.286 user 0.011 sys 1.299 real
execute: 1 calls 0.003 user 0.001 sys 20.200 real
fetch: 8147 calls 13.440 user 0.033 sys 13.454 real
fetch_ref: 8606 calls 0.034 user 0.020 sys 0.048 real
fetch_region: 405 calls 0.548 user 0.000 sys 0.521 real
fetch_vcf: 2074 calls 0.563 user 0.020 sys 0.698 real
idle: 47 calls 0.059 user 0.000 sys 26.380 real
init: 1 calls 0.050 user 0.010 sys 0.061 real
pairhmm: 24353 calls 144.562 user 0.122 sys 144.709 real
realign: 297 calls 11.078 user 0.000 sys 11.691 real
region: 4053 calls 87.844 user 0.217 sys 88.606 real
tracker: 4053 calls 0.030 user 0.000 sys 0.024 real
trim_region: 405 calls 0.010 user 0.000 sys 0.008 real
overall: 1928151040 mem 239.639 user 1.979 sys 22.454 real