cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i HCC1395_BL.recalibrated.bam -i HCC1395_tumor.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21_padded100bp.bed --algo TNhaplotyper2 --tumor_sample HCC1395_tumor --normal_sample HCC1395_BL --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz HCC1395_tumor_vs_HCC1395_BL.tnseq.vcf.gz --algo OrientationBias --tumor_sample HCC1395_tumor HCC1395_tumor_vs_HCC1395_BL.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_tumor --normal_sample HCC1395_BL --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments HCC1395_tumor_vs_HCC1395_BL.tnseq.segments HCC1395_tumor_vs_HCC1395_BL.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:14373517, elapsed 0.6s, est remaining 12.0s, peak mem 220MB, user 2.7s, sys 0.1s, output queue size 57
progress 10% @chr21:21508751, elapsed 0.8s, est remaining 7.4s, peak mem 242MB, user 5.4s, sys 0.2s, output queue size 18
progress 15% @chr21:29037176, elapsed 1.0s, est remaining 5.6s, peak mem 242MB, user 7.2s, sys 0.2s, output queue size 23
progress 20% @chr21:30620558, elapsed 1.2s, est remaining 4.6s, peak mem 250MB, user 9.1s, sys 0.2s, output queue size 10
progress 25% @chr21:32372407, elapsed 1.4s, est remaining 4.1s, peak mem 252MB, user 11.5s, sys 0.2s, output queue size 10
progress 30% @chr21:33343168, elapsed 1.6s, est remaining 3.7s, peak mem 255MB, user 13.5s, sys 0.3s, output queue size 75
progress 35% @chr21:34385378, elapsed 1.9s, est remaining 3.5s, peak mem 275MB, user 16.1s, sys 0.3s, output queue size 74
progress 40% @chr21:36277875, elapsed 2.7s, est remaining 4.0s, peak mem 454MB, user 19.8s, sys 0.3s, output queue size 67
progress 45% @chr21:36936349, elapsed 2.9s, est remaining 3.5s, peak mem 456MB, user 22.7s, sys 0.5s, output queue size 162
progress 50% @chr21:39196159, elapsed 3.0s, est remaining 3.0s, peak mem 473MB, user 25.6s, sys 0.5s, output queue size 43
progress 55% @chr21:41338278, elapsed 3.2s, est remaining 2.7s, peak mem 496MB, user 27.5s, sys 0.5s, output queue size 149
progress 60% @chr21:41820967, elapsed 5.8s, est remaining 3.8s, peak mem 857MB, user 42.8s, sys 1.1s, output queue size 25
progress 65% @chr21:42382933, elapsed 6.0s, est remaining 3.2s, peak mem 889MB, user 48.9s, sys 1.3s, output queue size 109
progress 70% @chr21:43529654, elapsed 6.2s, est remaining 2.7s, peak mem 889MB, user 50.4s, sys 1.4s, output queue size 227
progress 75% @chr21:44118663, elapsed 6.3s, est remaining 2.1s, peak mem 897MB, user 53.0s, sys 1.4s, output queue size 327
progress 80% @chr21:44423545, elapsed 6.6s, est remaining 1.7s, peak mem 903MB, user 55.8s, sys 1.5s, output queue size 431
progress 85% @chr21:45220736, elapsed 7.1s, est remaining 1.3s, peak mem 903MB, user 59.5s, sys 1.5s, output queue size 504
progress 90% @chr21:45991910, elapsed 7.4s, est remaining 0.8s, peak mem 903MB, user 64.2s, sys 1.7s, output queue size 27
progress 95% @chr21:46314616, elapsed 7.8s, est remaining 0.4s, peak mem 903MB, user 68.3s, sys 1.7s, output queue size 15
progress 100% @chr21:46558123, elapsed 8.2s, est remaining 0.0s, peak mem 903MB, user 71.7s, sys 1.7s, output queue size 19
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050657
  features: 1f8bfbff fffa320b
  extended: d19f47ab 00000018
  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: 163002590 333302564
output file size: 71258
reads: 7311657
contig: 1979 intervals 801713 bases
"assemble": 288 calls 3.811 user 0.071 sys 3.853 real
"assemble_addRead": 288 calls 0.090 user 0.000 sys 0.114 real
"assemble_buildGraph": 670 calls 1.850 user 0.000 sys 1.862 real
"assemble_computecigar": 418 calls 0.216 user 0.000 sys 0.243 real
"assemble_kg_build_calcsize": 670 calls 1.010 user 0.000 sys 1.072 real
"assemble_kg_build_clear": 902 calls 0.110 user 0.010 sys 0.158 real
"assemble_kg_build_prepare": 1340 calls 1.157 user 0.040 sys 1.135 real
"assemble_kg_build_threading": 438 calls 0.790 user 0.000 sys 0.716 real
"assemble_kg_op1": 438 calls 0.351 user 0.010 sys 0.430 real
"assemble_kg_op2": 438 calls 0.000 user 0.000 sys 0.009 real
"assemble_kg_op3": 438 calls 0.010 user 0.000 sys 0.010 real
"assemble_sg_clean": 418 calls 0.063 user 0.000 sys 0.059 real
"assemble_sg_create": 418 calls 0.107 user 0.000 sys 0.077 real
"checkGraph": 288 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 288 calls 0.216 user 0.000 sys 0.256 real
advance: 2074 calls 24.687 user 0.945 sys 26.252 real
assemble_region: 288 calls 4.127 user 0.071 sys 4.230 real
build_pileup: 1963 calls 0.110 user 0.000 sys 0.232 real
build_stats: 1987 calls 4.343 user 0.145 sys 4.204 real
build_variants: 215 calls 0.000 user 0.000 sys 0.002 real
calc: 3888 calls 3.000 user 0.011 sys 3.187 real
calc_region: 215 calls 23.471 user 0.184 sys 24.360 real
call_region: 215 calls 0.411 user 0.010 sys 0.472 real
clip_region: 503 calls 0.215 user 0.000 sys 0.333 real
done: 1 calls 1.079 user 0.000 sys 1.084 real
execute: 1 calls 0.005 user 0.002 sys 8.185 real
fetch: 8147 calls 6.407 user 0.054 sys 6.313 real
fetch_ref: 8489 calls 0.083 user 0.014 sys 0.069 real
fetch_region: 288 calls 0.170 user 0.020 sys 0.145 real
fetch_vcf: 2074 calls 1.059 user 0.021 sys 0.959 real
idle: 49 calls 0.065 user 0.000 sys 25.519 real
init: 1 calls 0.060 user 0.020 sys 0.084 real
pairhmm: 4281 calls 41.934 user 0.226 sys 42.379 real
realign: 215 calls 2.858 user 0.030 sys 3.228 real
region: 4053 calls 27.847 user 0.276 sys 28.890 real
tracker: 4053 calls 0.023 user 0.000 sys 0.023 real
trim_region: 288 calls 0.000 user 0.000 sys 0.004 real
overall: 947253248 mem 96.005 user 1.990 sys 10.528 real