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% @chr21:14592522, elapsed 0.2s, est remaining 3.8s, peak mem 180MB, user 1.5s, sys 0.1s, output queue size 55
progress 10% @chr21:25698577, elapsed 0.3s, est remaining 2.5s, peak mem 195MB, user 2.3s, sys 0.1s, output queue size 106
progress 15% @chr21:29037176, elapsed 0.4s, est remaining 2.0s, peak mem 204MB, user 3.2s, sys 0.1s, output queue size 39
progress 20% @chr21:30746851, elapsed 0.4s, est remaining 1.7s, peak mem 213MB, user 4.1s, sys 0.1s, output queue size 10
progress 25% @chr21:32346856, elapsed 0.5s, est remaining 1.6s, peak mem 219MB, user 5.2s, sys 0.1s, output queue size 9
progress 30% @chr21:33343168, elapsed 0.6s, est remaining 1.5s, peak mem 225MB, user 6.2s, sys 0.1s, output queue size 24
progress 35% @chr21:33903426, elapsed 0.8s, est remaining 1.4s, peak mem 246MB, user 7.3s, sys 0.1s, output queue size 74
progress 40% @chr21:36341299, elapsed 1.2s, est remaining 1.8s, peak mem 432MB, user 9.0s, sys 0.2s, output queue size 173
progress 45% @chr21:36936349, elapsed 1.3s, est remaining 1.6s, peak mem 441MB, user 11.6s, sys 0.3s, output queue size 156
progress 50% @chr21:39238379, elapsed 1.4s, est remaining 1.4s, peak mem 450MB, user 12.4s, sys 0.3s, output queue size 261
progress 55% @chr21:41344376, elapsed 1.6s, est remaining 1.3s, peak mem 474MB, user 14.1s, sys 0.3s, output queue size 149
progress 60% @chr21:41821803, elapsed 2.8s, est remaining 1.9s, peak mem 828MB, user 21.5s, sys 0.7s, output queue size 27
progress 65% @chr21:42287789, elapsed 3.0s, est remaining 1.6s, peak mem 828MB, user 25.1s, sys 0.8s, output queue size 104
progress 70% @chr21:43169000, elapsed 3.1s, est remaining 1.3s, peak mem 828MB, user 27.6s, sys 0.8s, output queue size 216
progress 75% @chr21:44115591, elapsed 3.2s, est remaining 1.1s, peak mem 828MB, user 28.7s, sys 0.8s, output queue size 327
progress 80% @chr21:44521783, elapsed 3.5s, est remaining 0.9s, peak mem 843MB, user 30.4s, sys 0.9s, output queue size 435
progress 85% @chr21:45184823, elapsed 3.8s, est remaining 0.7s, peak mem 849MB, user 32.8s, sys 0.9s, output queue size 506
progress 90% @chr21:46003291, elapsed 4.0s, est remaining 0.4s, peak mem 849MB, user 35.5s, sys 0.9s, output queue size 613
progress 95% @chr21:46283968, elapsed 4.2s, est remaining 0.2s, peak mem 849MB, user 38.9s, sys 1.0s, output queue size 14
progress 100% @chr21:46661700, elapsed 4.4s, est remaining 0.0s, peak mem 849MB, user 40.9s, sys 1.0s, 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 2.737 user 0.042 sys 2.747 real
"assemble_addRead": 479 calls 0.088 user 0.000 sys 0.076 real
"assemble_buildGraph": 1069 calls 1.414 user 0.011 sys 1.387 real
"assemble_computecigar": 748 calls 0.061 user 0.000 sys 0.096 real
"assemble_kg_build_calcsize": 1069 calls 0.760 user 0.000 sys 0.805 real
"assemble_kg_build_clear": 1371 calls 0.120 user 0.000 sys 0.098 real
"assemble_kg_build_prepare": 2138 calls 0.759 user 0.030 sys 0.727 real
"assemble_kg_build_threading": 767 calls 0.614 user 0.000 sys 0.545 real
"assemble_kg_op1": 767 calls 0.243 user 0.001 sys 0.305 real
"assemble_kg_op2": 767 calls 0.000 user 0.000 sys 0.007 real
"assemble_kg_op3": 767 calls 0.000 user 0.000 sys 0.010 real
"assemble_sg_clean": 748 calls 0.046 user 0.000 sys 0.045 real
"assemble_sg_create": 748 calls 0.092 user 0.000 sys 0.072 real
"checkGraph": 479 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 479 calls 0.061 user 0.000 sys 0.103 real
advance: 2074 calls 15.545 user 0.619 sys 16.693 real
assemble_region: 479 calls 2.887 user 0.042 sys 2.932 real
build_pileup: 1964 calls 0.100 user 0.000 sys 0.106 real
build_stats: 1986 calls 2.018 user 0.036 sys 1.867 real
build_variants: 264 calls 0.000 user 0.000 sys 0.002 real
calc: 3875 calls 1.458 user 0.002 sys 1.260 real
calc_region: 264 calls 12.889 user 0.117 sys 13.307 real
call_region: 264 calls 0.236 user 0.020 sys 0.264 real
clip_region: 743 calls 0.231 user 0.000 sys 0.237 real
done: 1 calls 0.463 user 0.000 sys 0.465 real
execute: 1 calls 0.001 user 0.001 sys 4.420 real
fetch: 8147 calls 2.934 user 0.072 sys 3.045 real
fetch_ref: 8680 calls 0.037 user 0.010 sys 0.039 real
fetch_region: 479 calls 0.138 user 0.000 sys 0.105 real
fetch_vcf: 2074 calls 0.553 user 0.014 sys 0.601 real
idle: 38 calls 0.078 user 0.000 sys 13.101 real
init: 1 calls 0.031 user 0.034 sys 0.065 real
pairhmm: 4065 calls 19.943 user 0.112 sys 20.140 real
realign: 264 calls 2.076 user 0.011 sys 2.389 real
region: 4053 calls 16.014 user 0.159 sys 16.466 real
tracker: 4053 calls 0.026 user 0.000 sys 0.012 real
trim_region: 479 calls 0.000 user 0.000 sys 0.002 real
overall: 891142144 mem 51.902 user 1.277 sys 5.735 real