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% @chr21:14521050, elapsed 0.7s, est remaining 13.8s, peak mem 217MB, user 3.2s, sys 0.3s, output queue size 55
progress 10% @chr21:25593793, elapsed 1.0s, est remaining 8.7s, peak mem 234MB, user 6.9s, sys 0.4s, output queue size 7
progress 15% @chr21:29038235, elapsed 1.2s, est remaining 6.7s, peak mem 248MB, user 9.1s, sys 0.6s, output queue size 39
progress 20% @chr21:30812929, elapsed 1.4s, est remaining 5.4s, peak mem 254MB, user 11.1s, sys 0.6s, output queue size 10
progress 25% @chr21:32346856, elapsed 1.6s, est remaining 4.8s, peak mem 258MB, user 13.7s, sys 0.7s, output queue size 8
progress 30% @chr21:33426784, elapsed 1.8s, est remaining 4.3s, peak mem 261MB, user 15.9s, sys 0.7s, output queue size 76
progress 35% @chr21:33914350, elapsed 2.1s, est remaining 4.0s, peak mem 277MB, user 18.7s, sys 0.8s, output queue size 74
progress 40% @chr21:36280185, elapsed 3.1s, est remaining 4.6s, peak mem 459MB, user 22.3s, sys 0.9s, output queue size 68
progress 45% @chr21:34886741, elapsed 3.3s, est remaining 4.1s, peak mem 463MB, user 26.8s, sys 1.2s, output queue size 159
progress 50% @chr21:39196159, elapsed 3.5s, est remaining 3.5s, peak mem 478MB, user 29.5s, sys 1.2s, output queue size 44
progress 55% @chr21:41357008, elapsed 3.8s, est remaining 3.1s, peak mem 504MB, user 31.9s, sys 1.3s, output queue size 148
progress 60% @chr21:41810054, elapsed 6.9s, est remaining 4.6s, peak mem 836MB, user 53.8s, sys 2.0s, output queue size 14
progress 65% @chr21:42406208, elapsed 7.2s, est remaining 3.9s, peak mem 859MB, user 57.1s, sys 2.1s, output queue size 114
progress 70% @chr21:43417443, elapsed 7.4s, est remaining 3.2s, peak mem 859MB, user 60.0s, sys 2.2s, output queue size 227
progress 75% @chr21:44120248, elapsed 7.6s, est remaining 2.5s, peak mem 860MB, user 63.3s, sys 2.5s, output queue size 326
progress 80% @chr21:44413791, elapsed 8.0s, est remaining 2.0s, peak mem 883MB, user 66.7s, sys 2.7s, output queue size 431
progress 85% @chr21:45221918, elapsed 8.7s, est remaining 1.5s, peak mem 884MB, user 71.1s, sys 2.9s, output queue size 507
progress 90% @chr21:45986844, elapsed 9.0s, est remaining 1.0s, peak mem 884MB, user 77.6s, sys 3.1s, output queue size 28
progress 95% @chr21:46283968, elapsed 9.5s, est remaining 0.5s, peak mem 884MB, user 82.7s, sys 3.3s, output queue size 12
progress 100% @chr21:46558123, elapsed 10.0s, est remaining 0.0s, peak mem 884MB, user 87.1s, sys 3.4s, output queue size 19
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: AuthenticAMD
 signature: 00800f12
  features: 178bfbff fed83203
  extended: 209c01a9 00000000
  amd bits: 2fd3fbff 00c001f3
     brand: AMD EPYC 7571
threads: 12 max 64
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 4.691 user 0.218 sys 4.865 real
"assemble_addRead": 288 calls 0.081 user 0.000 sys 0.118 real
"assemble_buildGraph": 670 calls 2.333 user 0.051 sys 2.467 real
"assemble_computecigar": 418 calls 0.231 user 0.011 sys 0.299 real
"assemble_kg_build_calcsize": 670 calls 1.340 user 0.025 sys 1.515 real
"assemble_kg_build_clear": 902 calls 0.196 user 0.036 sys 0.194 real
"assemble_kg_build_prepare": 1340 calls 1.404 user 0.107 sys 1.399 real
"assemble_kg_build_threading": 438 calls 0.913 user 0.012 sys 0.870 real
"assemble_kg_op1": 438 calls 0.468 user 0.017 sys 0.461 real
"assemble_kg_op2": 438 calls 0.014 user 0.000 sys 0.013 real
"assemble_kg_op3": 438 calls 0.020 user 0.000 sys 0.011 real
"assemble_sg_clean": 418 calls 0.084 user 0.000 sys 0.074 real
"assemble_sg_create": 418 calls 0.040 user 0.010 sys 0.096 real
"checkGraph": 288 calls 0.000 user 0.000 sys 0.002 real
"findHaplotype": 288 calls 0.254 user 0.011 sys 0.316 real
advance: 2074 calls 29.988 user 1.829 sys 32.074 real
assemble_region: 288 calls 5.035 user 0.228 sys 5.308 real
build_pileup: 1963 calls 0.264 user 0.010 sys 0.346 real
build_stats: 1987 calls 5.666 user 0.235 sys 5.884 real
build_variants: 215 calls 0.000 user 0.000 sys 0.003 real
calc: 3888 calls 3.711 user 0.022 sys 3.709 real
calc_region: 215 calls 29.163 user 0.263 sys 30.298 real
call_region: 215 calls 0.613 user 0.037 sys 0.610 real
clip_region: 503 calls 0.469 user 0.024 sys 0.420 real
done: 1 calls 2.021 user 0.027 sys 2.052 real
execute: 1 calls 0.008 user 0.002 sys 10.034 real
fetch: 8147 calls 6.193 user 0.160 sys 6.817 real
fetch_ref: 8489 calls 0.062 user 0.025 sys 0.072 real
fetch_region: 288 calls 0.123 user 0.001 sys 0.146 real
fetch_vcf: 2074 calls 1.080 user 0.056 sys 1.128 real
idle: 59 calls 0.049 user 0.001 sys 38.352 real
init: 1 calls 0.088 user 0.051 sys 0.139 real
pairhmm: 4281 calls 50.945 user 0.337 sys 51.495 real
realign: 215 calls 4.061 user 0.050 sys 4.506 real
region: 4053 calls 34.527 user 0.493 sys 35.947 real
tracker: 4053 calls 0.040 user 0.010 sys 0.029 real
trim_region: 288 calls 0.000 user 0.000 sys 0.006 real
overall: 927035392 mem 117.473 user 4.000 sys 13.561 real