cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta --interval_padding 100 -i HCC1395_BL.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed --algo TNhaplotyper2 --tumor_sample HCC1395_BL --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon.hotspot_protected.raw.vcf.gz HCC1395_BL.tnseq_tumor_only.vcf.gz --algo OrientationBias --tumor_sample HCC1395_BL HCC1395_BL.tnseq_tumor_only.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_BL --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments HCC1395_BL.tnseq_tumor_only.segments HCC1395_BL.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 2.2s, peak mem 154MB, user 0.5s, sys 0.1s, output queue size 54
progress 10% @chr21:25698577, elapsed 0.2s, est remaining 1.6s, peak mem 162MB, user 1.3s, sys 0.1s, output queue size 106
progress 15% @chr21:29027814, elapsed 0.2s, est remaining 1.3s, peak mem 167MB, user 2.0s, sys 0.1s, output queue size 36
progress 20% @chr21:30812929, elapsed 0.3s, est remaining 1.1s, peak mem 170MB, user 2.5s, sys 0.1s, output queue size 16
progress 25% @chr21:32346856, elapsed 0.3s, est remaining 1.0s, peak mem 173MB, user 3.3s, sys 0.1s, output queue size 63
progress 30% @chr21:33426784, elapsed 0.4s, est remaining 1.0s, peak mem 176MB, user 4.1s, sys 0.1s, output queue size 75
progress 35% @chr21:33914350, elapsed 0.5s, est remaining 0.9s, peak mem 180MB, user 4.7s, sys 0.1s, output queue size 74
progress 40% @chr21:36337632, elapsed 0.6s, est remaining 0.8s, peak mem 231MB, user 5.4s, sys 0.2s, output queue size 174
progress 45% @chr21:37185606, elapsed 0.7s, est remaining 0.9s, peak mem 236MB, user 6.2s, sys 0.2s, output queue size 164
progress 50% @chr21:39198663, elapsed 0.8s, est remaining 0.8s, peak mem 255MB, user 7.0s, sys 0.2s, output queue size 263
progress 55% @chr21:41382310, elapsed 0.9s, est remaining 0.7s, peak mem 264MB, user 7.5s, sys 0.2s, output queue size 369
progress 60% @chr21:41823218, elapsed 1.3s, est remaining 0.8s, peak mem 349MB, user 10.3s, sys 0.3s, output queue size 29
progress 65% @chr21:41497033, elapsed 1.4s, est remaining 0.8s, peak mem 367MB, user 12.2s, sys 0.4s, output queue size 109
progress 70% @chr21:43071885, elapsed 1.5s, est remaining 0.6s, peak mem 371MB, user 12.9s, sys 0.4s, output queue size 216
progress 75% @chr21:44119287, elapsed 1.6s, est remaining 0.5s, peak mem 374MB, user 13.4s, sys 0.4s, output queue size 327
progress 80% @chr21:44435031, elapsed 1.6s, est remaining 0.4s, peak mem 374MB, user 14.2s, sys 0.4s, output queue size 429
progress 85% @chr21:44906815, elapsed 1.7s, est remaining 0.3s, peak mem 374MB, user 14.9s, sys 0.4s, output queue size 503
progress 90% @chr21:46001861, elapsed 1.8s, est remaining 0.2s, peak mem 375MB, user 15.7s, sys 0.4s, output queue size 614
progress 95% @chr21:41501593, elapsed 1.9s, est remaining 0.1s, peak mem 375MB, user 17.0s, sys 0.4s, output queue size 714
progress 100% @chr21:46661700, elapsed 1.9s, est remaining 0.0s, peak mem 375MB, user 17.8s, sys 0.5s, output queue size 2
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: AuthenticAMD
 signature: 00830f10
  features: 178bfbff fed83203
  extended: 219c01a9 00400000
  amd bits: 2fd3fbff 004001f3
     brand: AMD EPYC 7R32
threads: 12 max 32
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 163002590
output file size: 51811
reads: 1955548
contig: 1979 intervals 801713 bases
"assemble": 227 calls 0.821 user 0.003 sys 0.908 real
"assemble_addRead": 227 calls 0.020 user 0.000 sys 0.020 real
"assemble_buildGraph": 511 calls 0.390 user 0.001 sys 0.430 real
"assemble_computecigar": 321 calls 0.170 user 0.039 sys 0.171 real
"assemble_kg_build_calcsize": 511 calls 0.208 user 0.000 sys 0.247 real
"assemble_kg_build_clear": 699 calls 0.010 user 0.000 sys 0.020 real
"assemble_kg_build_prepare": 1022 calls 0.225 user 0.002 sys 0.225 real
"assemble_kg_build_threading": 323 calls 0.182 user 0.001 sys 0.172 real
"assemble_kg_op1": 323 calls 0.067 user 0.000 sys 0.100 real
"assemble_kg_op2": 323 calls 0.010 user 0.000 sys 0.006 real
"assemble_kg_op3": 323 calls 0.000 user 0.000 sys 0.006 real
"assemble_sg_clean": 321 calls 0.030 user 0.000 sys 0.033 real
"assemble_sg_create": 321 calls 0.045 user 0.000 sys 0.049 real
"checkGraph": 227 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 227 calls 0.170 user 0.042 sys 0.178 real
advance: 2074 calls 6.166 user 0.207 sys 6.459 real
assemble_region: 227 calls 1.011 user 0.045 sys 1.109 real
build_pileup: 1957 calls 0.076 user 0.010 sys 0.055 real
build_stats: 1979 calls 1.635 user 0.050 sys 1.848 real
build_variants: 179 calls 0.000 user 0.000 sys 0.001 real
calc: 3869 calls 0.983 user 0.001 sys 0.861 real
calc_region: 179 calls 4.073 user 0.008 sys 4.140 real
call_region: 179 calls 0.077 user 0.000 sys 0.081 real
clip_region: 406 calls 0.107 user 0.001 sys 0.064 real
done: 1 calls 0.754 user 0.010 sys 0.764 real
execute: 1 calls 0.003 user 0.001 sys 1.944 real
fetch: 8147 calls 1.063 user 0.003 sys 1.022 real
fetch_ref: 8428 calls 0.025 user 0.012 sys 0.039 real
fetch_region: 227 calls 0.040 user 0.000 sys 0.017 real
fetch_vcf: 2074 calls 0.563 user 0.030 sys 0.784 real
idle: 40 calls 0.071 user 0.000 sys 13.107 real
init: 1 calls 0.070 user 0.010 sys 0.073 real
pairhmm: 1058 calls 7.366 user 0.020 sys 7.417 real
realign: 179 calls 0.649 user 0.000 sys 0.726 real
region: 4053 calls 5.183 user 0.053 sys 5.299 real
tracker: 4053 calls 0.000 user 0.010 sys 0.015 real
trim_region: 227 calls 0.000 user 0.000 sys 0.003 real
overall: 394489856 mem 23.534 user 0.608 sys 3.254 real