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% @chr21:14226759, elapsed 0.6s, est remaining 11.9s, peak mem 224MB, user 3.3s, sys 0.1s, output queue size 55
progress 10% @chr21:25702070, elapsed 0.8s, est remaining 7.6s, peak mem 246MB, user 6.1s, sys 0.2s, output queue size 106
progress 15% @chr21:29034737, elapsed 1.0s, est remaining 5.7s, peak mem 250MB, user 8.2s, sys 0.2s, output queue size 10
progress 20% @chr21:30746851, elapsed 1.2s, est remaining 4.7s, peak mem 260MB, user 10.0s, sys 0.2s, output queue size 10
progress 25% @chr21:32352610, elapsed 1.4s, est remaining 4.2s, peak mem 260MB, user 12.3s, sys 0.2s, output queue size 4
progress 30% @chr21:33352658, elapsed 1.6s, est remaining 3.7s, peak mem 263MB, user 14.4s, sys 0.2s, output queue size 76
progress 35% @chr21:34125241, elapsed 1.9s, est remaining 3.5s, peak mem 283MB, user 16.7s, sys 0.2s, output queue size 74
progress 40% @chr21:36247417, elapsed 2.7s, est remaining 4.1s, peak mem 457MB, user 20.8s, sys 0.3s, output queue size 56
progress 45% @chr21:37125980, elapsed 3.0s, est remaining 3.7s, peak mem 461MB, user 24.4s, sys 0.4s, output queue size 155
progress 50% @chr21:39229212, elapsed 3.2s, est remaining 3.2s, peak mem 465MB, user 27.1s, sys 0.5s, output queue size 42
progress 55% @chr21:41344376, elapsed 3.5s, est remaining 2.9s, peak mem 488MB, user 29.5s, sys 0.5s, output queue size 149
progress 60% @chr21:41810054, elapsed 6.6s, est remaining 4.4s, peak mem 877MB, user 49.7s, sys 0.8s, output queue size 21
progress 65% @chr21:42389827, elapsed 7.0s, est remaining 3.8s, peak mem 900MB, user 55.3s, sys 0.9s, output queue size 113
progress 70% @chr21:43065103, elapsed 7.2s, est remaining 3.1s, peak mem 907MB, user 59.2s, sys 0.9s, output queue size 216
progress 75% @chr21:44120248, elapsed 7.4s, est remaining 2.5s, peak mem 914MB, user 61.5s, sys 0.9s, output queue size 327
progress 80% @chr21:44509099, elapsed 7.8s, est remaining 1.9s, peak mem 929MB, user 64.9s, sys 1.0s, output queue size 437
progress 85% @chr21:44889176, elapsed 8.3s, est remaining 1.5s, peak mem 933MB, user 71.2s, sys 1.0s, output queue size 36
progress 90% @chr21:45991910, elapsed 8.7s, est remaining 1.0s, peak mem 933MB, user 76.1s, sys 1.1s, output queue size 27
progress 95% @chr21:46317108, elapsed 9.2s, est remaining 0.5s, peak mem 933MB, user 81.6s, sys 1.1s, output queue size 15
progress 100% @chr21:46661700, elapsed 9.7s, est remaining 0.0s, peak mem 933MB, user 86.2s, sys 1.1s, output queue size 2
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050654
  features: 1f8bfbff fffa3203
  extended: d19f47ab 00000018
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8175M CPU @ 2.50GHz
threads: 12 max 16
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 4.427 user 0.054 sys 4.407 real
"assemble_addRead": 288 calls 0.100 user 0.000 sys 0.122 real
"assemble_buildGraph": 670 calls 2.351 user 0.002 sys 2.233 real
"assemble_computecigar": 418 calls 0.214 user 0.009 sys 0.233 real
"assemble_kg_build_calcsize": 670 calls 1.374 user 0.000 sys 1.304 real
"assemble_kg_build_clear": 902 calls 0.292 user 0.010 sys 0.181 real
"assemble_kg_build_prepare": 1340 calls 1.054 user 0.042 sys 1.217 real
"assemble_kg_build_threading": 438 calls 0.884 user 0.002 sys 0.843 real
"assemble_kg_op1": 438 calls 0.450 user 0.001 sys 0.458 real
"assemble_kg_op2": 438 calls 0.010 user 0.000 sys 0.011 real
"assemble_kg_op3": 438 calls 0.020 user 0.000 sys 0.011 real
"assemble_sg_clean": 418 calls 0.055 user 0.000 sys 0.071 real
"assemble_sg_create": 418 calls 0.093 user 0.000 sys 0.093 real
"checkGraph": 288 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 288 calls 0.234 user 0.009 sys 0.246 real
advance: 2074 calls 30.274 user 0.737 sys 30.942 real
assemble_region: 288 calls 4.761 user 0.064 sys 4.782 real
build_pileup: 1963 calls 0.270 user 0.000 sys 0.271 real
build_stats: 1987 calls 4.696 user 0.066 sys 4.909 real
build_variants: 215 calls 0.000 user 0.000 sys 0.003 real
calc: 3888 calls 3.576 user 0.000 sys 3.859 real
calc_region: 215 calls 28.927 user 0.045 sys 29.695 real
call_region: 215 calls 0.641 user 0.000 sys 0.535 real
clip_region: 503 calls 0.361 user 0.000 sys 0.383 real
done: 1 calls 1.060 user 0.001 sys 1.066 real
execute: 1 calls 0.005 user 0.001 sys 9.735 real
fetch: 8147 calls 7.198 user 0.011 sys 6.858 real
fetch_ref: 8489 calls 0.127 user 0.010 sys 0.068 real
fetch_region: 288 calls 0.120 user 0.000 sys 0.141 real
fetch_vcf: 2074 calls 0.999 user 0.030 sys 1.099 real
idle: 52 calls 0.072 user 0.000 sys 25.557 real
init: 1 calls 0.089 user 0.001 sys 0.085 real
pairhmm: 4281 calls 51.667 user 0.022 sys 52.004 real
realign: 215 calls 3.557 user 0.006 sys 4.031 real
region: 4053 calls 33.968 user 0.109 sys 34.791 real
tracker: 4053 calls 0.020 user 0.000 sys 0.028 real
trim_region: 288 calls 0.020 user 0.000 sys 0.005 real
overall: 979066880 mem 115.858 user 1.250 sys 12.069 real