cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta --interval_padding 100 -i Sig_18_Blood.recalibrated.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% @chr21:14381103, elapsed 0.1s, est remaining 2.1s, peak mem 152MB, user 0.8s, sys 0.0s, output queue size 56
progress 10% @chr21:25592712, elapsed 0.2s, est remaining 1.7s, peak mem 163MB, user 1.6s, sys 0.1s, output queue size 28
progress 15% @chr21:29038235, elapsed 0.3s, est remaining 1.5s, peak mem 172MB, user 2.4s, sys 0.1s, output queue size 39
progress 20% @chr21:30592346, elapsed 0.3s, est remaining 1.3s, peak mem 176MB, user 3.1s, sys 0.1s, output queue size 8
progress 25% @chr21:32366518, elapsed 0.4s, est remaining 1.2s, peak mem 179MB, user 3.9s, sys 0.1s, output queue size 9
progress 30% @chr21:33355216, elapsed 0.5s, est remaining 1.1s, peak mem 183MB, user 4.7s, sys 0.1s, output queue size 75
progress 35% @chr21:33888052, elapsed 0.6s, est remaining 1.0s, peak mem 191MB, user 5.6s, sys 0.1s, output queue size 74
progress 40% @chr21:36288945, elapsed 1.0s, est remaining 1.6s, peak mem 270MB, user 6.5s, sys 0.2s, output queue size 169
progress 45% @chr21:37186949, elapsed 1.2s, est remaining 1.4s, peak mem 275MB, user 7.8s, sys 0.2s, output queue size 166
progress 50% @chr21:39277151, elapsed 1.3s, est remaining 1.3s, peak mem 295MB, user 10.0s, sys 0.2s, output queue size 265
progress 55% @chr21:41357008, elapsed 1.4s, est remaining 1.2s, peak mem 303MB, user 11.7s, sys 0.2s, output queue size 149
progress 60% @chr21:41756425, elapsed 2.4s, est remaining 1.6s, peak mem 461MB, user 15.0s, sys 0.4s, output queue size 16
progress 65% @chr21:42375616, elapsed 2.8s, est remaining 1.5s, peak mem 478MB, user 18.6s, sys 0.4s, output queue size 107
progress 70% @chr21:42903082, elapsed 2.9s, est remaining 1.2s, peak mem 478MB, user 21.8s, sys 0.5s, output queue size 218
progress 75% @chr21:44124480, elapsed 3.0s, est remaining 1.0s, peak mem 478MB, user 22.6s, sys 0.5s, output queue size 327
progress 80% @chr21:44499683, elapsed 3.1s, est remaining 0.8s, peak mem 478MB, user 23.7s, sys 0.5s, output queue size 435
progress 85% @chr21:45285578, elapsed 3.2s, est remaining 0.6s, peak mem 482MB, user 24.7s, sys 0.6s, output queue size 515
progress 90% @chr21:45998797, elapsed 3.4s, est remaining 0.4s, peak mem 482MB, user 26.2s, sys 0.6s, output queue size 611
progress 95% @chr21:41501593, elapsed 3.5s, est remaining 0.2s, peak mem 482MB, user 29.0s, sys 0.6s, output queue size 707
progress 100% @chr21:46334297, elapsed 3.7s, est remaining 0.0s, peak mem 482MB, user 30.3s, sys 0.7s, output queue size 91
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050654
  features: 1f8bfbff fffa320b
  extended: d19f47ab 00000018
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8175M CPU @ 2.50GHz
threads: 12 max 96
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 208827488
output file size: 57860
reads: 2481283
contig: 1979 intervals 801713 bases
"assemble": 236 calls 1.443 user 0.010 sys 1.524 real
"assemble_addRead": 236 calls 0.090 user 0.000 sys 0.037 real
"assemble_buildGraph": 545 calls 0.746 user 0.000 sys 0.721 real
"assemble_computecigar": 331 calls 0.154 user 0.030 sys 0.166 real
"assemble_kg_build_calcsize": 545 calls 0.380 user 0.000 sys 0.406 real
"assemble_kg_build_clear": 752 calls 0.040 user 0.000 sys 0.051 real
"assemble_kg_build_prepare": 1090 calls 0.391 user 0.010 sys 0.402 real
"assemble_kg_build_threading": 338 calls 0.346 user 0.000 sys 0.287 real
"assemble_kg_op1": 338 calls 0.133 user 0.000 sys 0.176 real
"assemble_kg_op2": 338 calls 0.000 user 0.000 sys 0.008 real
"assemble_kg_op3": 338 calls 0.000 user 0.000 sys 0.008 real
"assemble_sg_clean": 331 calls 0.056 user 0.000 sys 0.042 real
"assemble_sg_create": 331 calls 0.028 user 0.000 sys 0.056 real
"checkGraph": 236 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 236 calls 0.154 user 0.030 sys 0.174 real
advance: 2074 calls 8.758 user 0.311 sys 9.320 real
assemble_region: 236 calls 1.687 user 0.050 sys 1.739 real
build_pileup: 1969 calls 0.090 user 0.000 sys 0.084 real
build_stats: 1999 calls 2.527 user 0.111 sys 2.611 real
build_variants: 195 calls 0.000 user 0.000 sys 0.002 real
calc: 3915 calls 1.392 user 0.010 sys 1.232 real
calc_region: 195 calls 10.187 user 0.013 sys 10.339 real
call_region: 195 calls 0.194 user 0.000 sys 0.165 real
clip_region: 431 calls 0.100 user 0.000 sys 0.131 real
done: 1 calls 0.766 user 0.000 sys 0.767 real
execute: 1 calls 0.002 user 0.000 sys 3.703 real
fetch: 8147 calls 1.782 user 0.003 sys 1.941 real
fetch_ref: 8437 calls 0.056 user 0.027 sys 0.064 real
fetch_region: 236 calls 0.050 user 0.000 sys 0.038 real
fetch_vcf: 2074 calls 0.756 user 0.009 sys 0.850 real
idle: 40 calls 0.051 user 0.000 sys 13.545 real
init: 1 calls 0.065 user 0.019 sys 0.081 real
pairhmm: 2129 calls 20.441 user 0.040 sys 20.642 real
realign: 195 calls 1.390 user 0.000 sys 1.549 real
region: 4053 calls 11.934 user 0.063 sys 12.178 real
tracker: 4053 calls 0.010 user 0.020 sys 0.018 real
trim_region: 236 calls 0.000 user 0.000 sys 0.004 real
overall: 508526592 mem 43.980 user 0.870 sys 5.054 real