cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i HCC1395_BL.recal.bam -i HCC1395_tumor.recal.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% @chr21:14226759, elapsed 0.3s, est remaining 5.0s, peak mem 174MB, user 2.1s, sys 0.1s, output queue size 57
progress 10% @chr21:25693656, elapsed 0.4s, est remaining 3.5s, peak mem 192MB, user 3.3s, sys 0.1s, output queue size 106
progress 15% @chr21:29037176, elapsed 0.5s, est remaining 2.8s, peak mem 210MB, user 4.6s, sys 0.1s, output queue size 39
progress 20% @chr21:30812929, elapsed 0.6s, est remaining 2.4s, peak mem 222MB, user 5.8s, sys 0.1s, output queue size 10
progress 25% @chr21:32352610, elapsed 0.7s, est remaining 2.2s, peak mem 222MB, user 7.4s, sys 0.2s, output queue size 6
progress 30% @chr21:33410736, elapsed 0.9s, est remaining 2.0s, peak mem 231MB, user 8.7s, sys 0.2s, output queue size 25
progress 35% @chr21:34073601, elapsed 1.0s, est remaining 1.9s, peak mem 243MB, user 10.2s, sys 0.2s, output queue size 74
progress 40% @chr21:36344479, elapsed 1.5s, est remaining 2.3s, peak mem 438MB, user 12.4s, sys 0.2s, output queue size 173
progress 45% @chr21:37125980, elapsed 1.7s, est remaining 2.1s, peak mem 444MB, user 15.5s, sys 0.3s, output queue size 157
progress 50% @chr21:39229212, elapsed 1.9s, est remaining 1.9s, peak mem 453MB, user 17.2s, sys 0.3s, output queue size 43
progress 55% @chr21:41346913, elapsed 2.0s, est remaining 1.6s, peak mem 480MB, user 18.5s, sys 0.3s, output queue size 149
progress 60% @chr21:41746513, elapsed 3.6s, est remaining 2.4s, peak mem 822MB, user 27.0s, sys 0.6s, output queue size 23
progress 65% @chr21:41495593, elapsed 3.8s, est remaining 2.1s, peak mem 845MB, user 34.1s, sys 0.7s, output queue size 100
progress 70% @chr21:43071885, elapsed 3.9s, est remaining 1.7s, peak mem 845MB, user 35.4s, sys 0.7s, output queue size 216
progress 75% @chr21:44126800, elapsed 4.1s, est remaining 1.4s, peak mem 848MB, user 36.8s, sys 0.7s, output queue size 327
progress 80% @chr21:44330098, elapsed 4.3s, est remaining 1.1s, peak mem 848MB, user 39.3s, sys 0.7s, output queue size 431
progress 85% @chr21:45204455, elapsed 4.7s, est remaining 0.8s, peak mem 851MB, user 42.4s, sys 0.8s, output queue size 504
progress 90% @chr21:45991910, elapsed 4.9s, est remaining 0.5s, peak mem 851MB, user 46.9s, sys 0.9s, output queue size 28
progress 95% @chr21:46314616, elapsed 5.2s, est remaining 0.3s, peak mem 851MB, user 49.9s, sys 0.9s, output queue size 15
progress 100% @chr21:46661700, elapsed 5.5s, est remaining 0.0s, peak mem 851MB, user 52.3s, sys 0.9s, output queue size 2
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 12 max 384
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 111697681 274742098
output file size: 78467
reads: 4941615
contig: 1979 intervals 801713 bases
"assemble": 479 calls 3.476 user 0.059 sys 3.472 real
"assemble_addRead": 479 calls 0.097 user 0.000 sys 0.104 real
"assemble_buildGraph": 1069 calls 1.945 user 0.020 sys 1.760 real
"assemble_computecigar": 748 calls 0.110 user 0.000 sys 0.116 real
"assemble_kg_build_calcsize": 1069 calls 1.147 user 0.000 sys 1.018 real
"assemble_kg_build_clear": 1371 calls 0.070 user 0.000 sys 0.132 real
"assemble_kg_build_prepare": 2138 calls 0.817 user 0.029 sys 0.921 real
"assemble_kg_build_threading": 767 calls 0.788 user 0.020 sys 0.695 real
"assemble_kg_op1": 767 calls 0.338 user 0.000 sys 0.377 real
"assemble_kg_op2": 767 calls 0.020 user 0.000 sys 0.008 real
"assemble_kg_op3": 767 calls 0.010 user 0.000 sys 0.011 real
"assemble_sg_clean": 748 calls 0.051 user 0.000 sys 0.055 real
"assemble_sg_create": 748 calls 0.054 user 0.000 sys 0.088 real
"checkGraph": 479 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 479 calls 0.120 user 0.000 sys 0.124 real
advance: 2074 calls 18.799 user 0.540 sys 19.508 real
assemble_region: 479 calls 3.693 user 0.060 sys 3.706 real
build_pileup: 1964 calls 0.091 user 0.000 sys 0.168 real
build_stats: 1986 calls 2.601 user 0.045 sys 2.576 real
build_variants: 264 calls 0.000 user 0.000 sys 0.002 real
calc: 3875 calls 1.636 user 0.000 sys 1.820 real
calc_region: 264 calls 16.894 user 0.035 sys 17.311 real
call_region: 264 calls 0.296 user 0.000 sys 0.332 real
clip_region: 743 calls 0.344 user 0.000 sys 0.306 real
done: 1 calls 0.675 user 0.020 sys 0.704 real
execute: 1 calls 0.003 user 0.001 sys 5.451 real
fetch: 8147 calls 4.472 user 0.071 sys 4.457 real
fetch_ref: 8680 calls 0.061 user 0.010 sys 0.046 real
fetch_region: 479 calls 0.153 user 0.000 sys 0.137 real
fetch_vcf: 2074 calls 0.607 user 0.000 sys 0.734 real
idle: 49 calls 0.113 user 0.000 sys 13.052 real
init: 1 calls 0.050 user 0.010 sys 0.057 real
pairhmm: 4065 calls 24.034 user 0.050 sys 24.274 real
realign: 264 calls 2.492 user 0.006 sys 2.779 real
region: 4053 calls 20.890 user 0.095 sys 21.318 real
tracker: 4053 calls 0.020 user 0.000 sys 0.017 real
trim_region: 479 calls 0.000 user 0.000 sys 0.003 real
overall: 892821504 mem 64.355 user 1.049 sys 6.716 real