cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i reference-NA12878-downsampled-500k.bam -i Sig_18_tissue.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity_padded100bp.bed --algo TNhaplotyper2 --tumor_sample Sig_18_tissue --normal_sample reference-NA12878 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz positive_somatic_control_2.tnseq.vcf.gz --algo OrientationBias --tumor_sample Sig_18_tissue positive_somatic_control_2.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample Sig_18_tissue --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments positive_somatic_control_2.tnseq.segments positive_somatic_control_2.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113698162, elapsed 1.3s, est remaining 24.3s, peak mem 128MB, user 9.7s, sys 1.7s, output queue size 17
progress 10% @chr2:3604215, elapsed 2.5s, est remaining 22.8s, peak mem 128MB, user 18.5s, sys 3.5s, output queue size 84
progress 15% @chr2:178606921, elapsed 3.8s, est remaining 21.5s, peak mem 128MB, user 28.3s, sys 5.2s, output queue size 22
progress 20% @chr3:57498400, elapsed 5.0s, est remaining 20.0s, peak mem 128MB, user 36.8s, sys 7.0s, output queue size 786
progress 25% @chr4:70603777, elapsed 6.4s, est remaining 19.2s, peak mem 128MB, user 45.9s, sys 8.9s, output queue size 423
progress 30% @chr5:135534877, elapsed 7.8s, est remaining 18.2s, peak mem 128MB, user 55.1s, sys 10.6s, output queue size 138
progress 35% @chr6:105124447, elapsed 9.0s, est remaining 16.7s, peak mem 128MB, user 62.9s, sys 12.1s, output queue size 1972
progress 40% @chr7:106248199, elapsed 10.2s, est remaining 15.4s, peak mem 128MB, user 71.8s, sys 13.9s, output queue size 2202
progress 45% @chr8:143810379, elapsed 11.5s, est remaining 14.1s, peak mem 128MB, user 80.6s, sys 15.4s, output queue size 2136
progress 50% @chr10:21673250, elapsed 12.7s, est remaining 12.7s, peak mem 131MB, user 89.2s, sys 17.0s, output queue size 990
progress 55% @chr11:34131281, elapsed 13.9s, est remaining 11.4s, peak mem 131MB, user 97.0s, sys 18.7s, output queue size 3650
progress 60% @chr12:12786809, elapsed 15.1s, est remaining 10.1s, peak mem 134MB, user 105.0s, sys 20.2s, output queue size 522
progress 65% @chr13:32134804, elapsed 16.3s, est remaining 8.8s, peak mem 134MB, user 113.5s, sys 22.0s, output queue size 5236
progress 70% @chr15:35372050, elapsed 17.5s, est remaining 7.5s, peak mem 134MB, user 122.4s, sys 23.2s, output queue size 905
progress 75% @chr16:28501876, elapsed 18.7s, est remaining 6.2s, peak mem 134MB, user 131.3s, sys 24.7s, output queue size 1096
progress 80% @chr17:40034816, elapsed 19.9s, est remaining 5.0s, peak mem 134MB, user 141.2s, sys 26.4s, output queue size 0
progress 85% @chr19:1805788, elapsed 21.1s, est remaining 3.7s, peak mem 134MB, user 150.4s, sys 27.8s, output queue size 109
progress 90% @chr19:54663432, elapsed 22.3s, est remaining 2.5s, peak mem 134MB, user 159.9s, sys 29.1s, output queue size 15
progress 95% @chr22:32099083, elapsed 25.0s, est remaining 1.3s, peak mem 311MB, user 183.3s, sys 31.3s, output queue size 624
progress 100% @chr6_GL000254v2_alt:3891438, elapsed 26.1s, est remaining 0.0s, peak mem 311MB, user 191.1s, sys 32.8s, output queue size 60
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  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: 71721858 93136294
output file size: 53227
reads: 1502521
contig: 178193 intervals 76355618 bases
"assemble": 222 calls 0.713 user 0.047 sys 0.795 real
"assemble_addRead": 222 calls 0.020 user 0.000 sys 0.014 real
"assemble_buildGraph": 498 calls 0.282 user 0.011 sys 0.352 real
"assemble_computecigar": 330 calls 0.117 user 0.015 sys 0.110 real
"assemble_kg_build_calcsize": 498 calls 0.146 user 0.000 sys 0.159 real
"assemble_kg_build_clear": 653 calls 0.051 user 0.001 sys 0.017 real
"assemble_kg_build_prepare": 996 calls 0.206 user 0.021 sys 0.155 real
"assemble_kg_build_threading": 343 calls 0.132 user 0.010 sys 0.184 real
"assemble_kg_op1": 343 calls 0.063 user 0.001 sys 0.107 real
"assemble_kg_op2": 343 calls 0.000 user 0.000 sys 0.007 real
"assemble_kg_op3": 343 calls 0.000 user 0.000 sys 0.009 real
"assemble_sg_clean": 330 calls 0.030 user 0.000 sys 0.040 real
"assemble_sg_create": 330 calls 0.059 user 0.003 sys 0.062 real
"checkGraph": 222 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 222 calls 0.132 user 0.015 sys 0.118 real
advance: 189104 calls 15.335 user 0.853 sys 29.064 real
assemble_region: 222 calls 0.865 user 0.062 sys 0.933 real
build_pileup: 70986 calls 0.598 user 0.050 sys 1.045 real
build_stats: 71711 calls 4.514 user 0.476 sys 4.754 real
build_variants: 179 calls 0.010 user 0.000 sys 0.002 real
calc: 128717 calls 2.926 user 0.127 sys 4.944 real
calc_region: 179 calls 3.391 user 0.051 sys 3.642 real
call_region: 179 calls 0.066 user 0.000 sys 0.089 real
clip_region: 401 calls 0.078 user 0.000 sys 0.068 real
done: 1 calls 0.688 user 0.012 sys 0.702 real
execute: 1 calls 0.000 user 0.017 sys 26.071 real
fetch: 743546 calls 1.409 user 0.147 sys 1.825 real
fetch_ref: 745727 calls 1.523 user 1.057 sys 5.117 real
fetch_region: 222 calls 0.027 user 0.000 sys 0.016 real
fetch_vcf: 189104 calls 38.804 user 2.629 sys 83.491 real
idle: 32 calls 0.002 user 0.002 sys 13.431 real
init: 1 calls 0.078 user 0.009 sys 0.090 real
pairhmm: 838 calls 5.656 user 0.063 sys 5.704 real
realign: 179 calls 0.551 user 0.001 sys 0.695 real
region: 367297 calls 4.374 user 0.149 sys 4.756 real
tracker: 367297 calls 0.546 user 0.178 sys 1.080 real
trim_region: 222 calls 0.002 user 0.000 sys 0.004 real
overall: 326176768 mem 243.246 user 51.739 sys 27.638 real