cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta --interval_padding 100 -i Sig_18_Blood.recal.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed --algo TNhaplotyper2 --tumor_sample Sig_18_Blood --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon.hotspot_protected.raw.vcf.gz Sig_18_Blood.tnseq_tumor_only.vcf.gz --algo OrientationBias --tumor_sample Sig_18_Blood Sig_18_Blood.tnseq_tumor_only.orientation_data.tsv --algo ContaminationModel --tumor_sample Sig_18_Blood --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments Sig_18_Blood.tnseq_tumor_only.segments Sig_18_Blood.tnseq_tumor_only.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:14373517, elapsed 0.1s, est remaining 1.2s, peak mem 132MB, user 0.3s, sys 0.1s, output queue size 55
progress 10% @chr21:14964616, elapsed 0.1s, est remaining 1.0s, peak mem 144MB, user 0.9s, sys 0.1s, output queue size 104
progress 15% @chr21:26965188, elapsed 0.1s, est remaining 0.8s, peak mem 150MB, user 1.2s, sys 0.2s, output queue size 38
progress 20% @chr21:31038152, elapsed 0.2s, est remaining 0.7s, peak mem 153MB, user 1.7s, sys 0.2s, output queue size 10
progress 25% @chr21:32355349, elapsed 0.2s, est remaining 0.7s, peak mem 156MB, user 2.1s, sys 0.2s, output queue size 9
progress 30% @chr21:33426784, elapsed 0.3s, est remaining 0.6s, peak mem 165MB, user 2.6s, sys 0.2s, output queue size 75
progress 35% @chr21:33912189, elapsed 0.3s, est remaining 0.6s, peak mem 171MB, user 3.1s, sys 0.2s, output queue size 74
progress 40% @chr21:36293220, elapsed 0.4s, est remaining 0.7s, peak mem 234MB, user 3.6s, sys 0.2s, output queue size 169
progress 45% @chr21:37152851, elapsed 0.6s, est remaining 0.7s, peak mem 237MB, user 4.4s, sys 0.2s, output queue size 161
progress 50% @chr21:39196159, elapsed 0.7s, est remaining 0.7s, peak mem 249MB, user 5.2s, sys 0.2s, output queue size 264
progress 55% @chr21:41345586, elapsed 0.7s, est remaining 0.6s, peak mem 252MB, user 6.0s, sys 0.3s, output queue size 149
progress 60% @chr21:41801140, elapsed 1.3s, est remaining 0.9s, peak mem 397MB, user 7.9s, sys 0.4s, output queue size 18
progress 65% @chr21:42347386, elapsed 1.5s, est remaining 0.8s, peak mem 409MB, user 10.9s, sys 0.4s, output queue size 103
progress 70% @chr21:43100353, elapsed 1.6s, est remaining 0.7s, peak mem 409MB, user 12.0s, sys 0.4s, output queue size 219
progress 75% @chr21:44122077, elapsed 1.6s, est remaining 0.5s, peak mem 409MB, user 12.6s, sys 0.4s, output queue size 328
progress 80% @chr21:44233457, elapsed 1.7s, est remaining 0.4s, peak mem 412MB, user 13.4s, sys 0.4s, output queue size 433
progress 85% @chr21:45265382, elapsed 1.8s, est remaining 0.3s, peak mem 415MB, user 13.9s, sys 0.4s, output queue size 516
progress 90% @chr21:46111377, elapsed 1.9s, est remaining 0.2s, peak mem 415MB, user 14.7s, sys 0.5s, output queue size 610
progress 95% @chr21:46381594, elapsed 1.9s, est remaining 0.1s, peak mem 415MB, user 15.3s, sys 0.5s, output queue size 720
progress 100% @chr21:46334297, elapsed 2.1s, est remaining 0.0s, peak mem 415MB, user 17.1s, sys 0.6s, output queue size 91
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: 138653580
output file size: 66383
reads: 1685487
contig: 1979 intervals 801713 bases
"assemble": 401 calls 1.044 user 0.025 sys 1.140 real
"assemble_addRead": 401 calls 0.020 user 0.000 sys 0.025 real
"assemble_buildGraph": 861 calls 0.462 user 0.002 sys 0.536 real
"assemble_computecigar": 629 calls 0.055 user 0.000 sys 0.078 real
"assemble_kg_build_calcsize": 861 calls 0.286 user 0.000 sys 0.307 real
"assemble_kg_build_clear": 1084 calls 0.037 user 0.000 sys 0.031 real
"assemble_kg_build_prepare": 1722 calls 0.257 user 0.023 sys 0.277 real
"assemble_kg_build_threading": 638 calls 0.169 user 0.001 sys 0.215 real
"assemble_kg_op1": 638 calls 0.116 user 0.000 sys 0.134 real
"assemble_kg_op2": 638 calls 0.000 user 0.000 sys 0.005 real
"assemble_kg_op3": 638 calls 0.000 user 0.000 sys 0.008 real
"assemble_sg_clean": 629 calls 0.024 user 0.000 sys 0.037 real
"assemble_sg_create": 629 calls 0.110 user 0.000 sys 0.060 real
"checkGraph": 401 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 401 calls 0.065 user 0.000 sys 0.082 real
advance: 2074 calls 5.006 user 0.224 sys 5.688 real
assemble_region: 401 calls 1.139 user 0.025 sys 1.251 real
build_pileup: 1970 calls 0.050 user 0.000 sys 0.041 real
build_stats: 2000 calls 1.124 user 0.080 sys 1.286 real
build_variants: 266 calls 0.000 user 0.000 sys 0.001 real
calc: 3907 calls 0.583 user 0.001 sys 0.588 real
calc_region: 266 calls 5.603 user 0.019 sys 5.692 real
call_region: 266 calls 0.099 user 0.001 sys 0.100 real
clip_region: 667 calls 0.065 user 0.000 sys 0.099 real
done: 1 calls 0.302 user 0.000 sys 0.306 real
execute: 1 calls 0.004 user 0.001 sys 2.074 real
fetch: 8147 calls 1.031 user 0.033 sys 0.950 real
fetch_ref: 8602 calls 0.044 user 0.003 sys 0.038 real
fetch_region: 401 calls 0.040 user 0.000 sys 0.024 real
fetch_vcf: 2074 calls 0.570 user 0.010 sys 0.591 real
idle: 37 calls 0.027 user 0.000 sys 12.878 real
init: 1 calls 0.050 user 0.000 sys 0.049 real
pairhmm: 1975 calls 10.305 user 0.042 sys 10.315 real
realign: 266 calls 1.045 user 0.000 sys 1.207 real
region: 4053 calls 6.815 user 0.054 sys 7.013 real
tracker: 4053 calls 0.007 user 0.010 sys 0.011 real
trim_region: 401 calls 0.000 user 0.000 sys 0.002 real
overall: 435642368 mem 24.111 user 0.657 sys 3.283 real