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_Blood.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_Blood --normal_sample reference-NA12878 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz negative_somatic_control_2.tnseq.vcf.gz --algo OrientationBias --tumor_sample Sig_18_Blood negative_somatic_control_2.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample Sig_18_Blood --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments negative_somatic_control_2.tnseq.segments negative_somatic_control_2.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113710154, elapsed 0.6s, est remaining 11.4s, peak mem 145MB, user 5.7s, sys 0.4s, output queue size 4
progress 10% @chr2:3643344, elapsed 1.2s, est remaining 10.4s, peak mem 146MB, user 11.2s, sys 0.7s, output queue size 5
progress 15% @chr2:178606921, elapsed 1.7s, est remaining 9.8s, peak mem 146MB, user 16.9s, sys 1.0s, output queue size 12
progress 20% @chr3:57483276, elapsed 2.3s, est remaining 9.1s, peak mem 146MB, user 22.2s, sys 1.3s, output queue size 0
progress 25% @chr4:70602524, elapsed 2.9s, est remaining 8.6s, peak mem 146MB, user 27.9s, sys 1.7s, output queue size 1
progress 30% @chr5:135873921, elapsed 3.5s, est remaining 8.1s, peak mem 148MB, user 33.9s, sys 2.0s, output queue size 4
progress 35% @chr6:104957999, elapsed 4.0s, est remaining 7.4s, peak mem 149MB, user 39.2s, sys 2.3s, output queue size 3
progress 40% @chr7:106872437, elapsed 4.6s, est remaining 6.8s, peak mem 150MB, user 45.1s, sys 2.6s, output queue size 2
progress 45% @chr8:143821497, elapsed 5.1s, est remaining 6.3s, peak mem 150MB, user 50.9s, sys 2.9s, output queue size 1
progress 50% @chr10:21726144, elapsed 5.7s, est remaining 5.7s, peak mem 151MB, user 56.5s, sys 3.2s, output queue size 1
progress 55% @chr11:34136878, elapsed 6.3s, est remaining 5.1s, peak mem 151MB, user 62.0s, sys 3.5s, output queue size 5
progress 60% @chr12:12718707, elapsed 6.8s, est remaining 4.5s, peak mem 153MB, user 67.5s, sys 3.8s, output queue size 9
progress 65% @chr13:32078734, elapsed 7.4s, est remaining 4.0s, peak mem 153MB, user 73.2s, sys 4.0s, output queue size 10
progress 70% @chr15:35521993, elapsed 8.0s, est remaining 3.4s, peak mem 155MB, user 78.7s, sys 4.3s, output queue size 2
progress 75% @chr16:28483906, elapsed 8.5s, est remaining 2.8s, peak mem 155MB, user 84.2s, sys 4.6s, output queue size 5
progress 80% @chr17:40034816, elapsed 9.1s, est remaining 2.3s, peak mem 155MB, user 90.4s, sys 4.9s, output queue size 0
progress 85% @chr19:1806528, elapsed 9.7s, est remaining 1.7s, peak mem 155MB, user 96.2s, sys 5.2s, output queue size 3
progress 90% @chr19:54632916, elapsed 10.3s, est remaining 1.1s, peak mem 156MB, user 101.7s, sys 5.5s, output queue size 2
progress 95% @chr22:31897382, elapsed 11.5s, est remaining 0.6s, peak mem 337MB, user 114.1s, sys 6.0s, output queue size 10
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 12.0s, est remaining 0.0s, peak mem 337MB, user 119.3s, sys 6.2s, output queue size 7
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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 64
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 74586810
output file size: 51111
reads: 1501816
contig: 178193 intervals 76355618 bases
"assemble": 189 calls 0.408 user 0.001 sys 0.359 real
"assemble_addRead": 189 calls 0.002 user 0.000 sys 0.006 real
"assemble_buildGraph": 446 calls 0.139 user 0.000 sys 0.158 real
"assemble_computecigar": 274 calls 0.017 user 0.010 sys 0.055 real
"assemble_kg_build_calcsize": 446 calls 0.104 user 0.000 sys 0.085 real
"assemble_kg_build_clear": 608 calls 0.003 user 0.000 sys 0.006 real
"assemble_kg_build_prepare": 892 calls 0.125 user 0.000 sys 0.075 real
"assemble_kg_build_threading": 284 calls 0.031 user 0.000 sys 0.069 real
"assemble_kg_op1": 284 calls 0.045 user 0.000 sys 0.047 real
"assemble_kg_op2": 284 calls 0.030 user 0.000 sys 0.004 real
"assemble_kg_op3": 284 calls 0.010 user 0.000 sys 0.004 real
"assemble_sg_clean": 274 calls 0.013 user 0.000 sys 0.017 real
"assemble_sg_create": 274 calls 0.025 user 0.000 sys 0.026 real
"checkGraph": 189 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 189 calls 0.017 user 0.010 sys 0.057 real
advance: 189104 calls 12.795 user 0.358 sys 17.294 real
assemble_region: 189 calls 0.426 user 0.011 sys 0.424 real
build_pileup: 70986 calls 0.238 user 0.011 sys 0.379 real
build_stats: 71708 calls 2.100 user 0.064 sys 1.767 real
build_variants: 158 calls 0.000 user 0.000 sys 0.001 real
calc: 128714 calls 1.542 user 0.035 sys 2.335 real
calc_region: 158 calls 1.323 user 0.011 sys 1.389 real
call_region: 158 calls 0.037 user 0.000 sys 0.031 real
clip_region: 347 calls 0.032 user 0.000 sys 0.030 real
done: 1 calls 0.283 user 0.000 sys 0.286 real
execute: 1 calls 0.003 user 0.001 sys 12.047 real
fetch: 743546 calls 0.572 user 0.011 sys 0.688 real
fetch_ref: 745694 calls 1.425 user 0.359 sys 2.441 real
fetch_region: 189 calls 0.000 user 0.000 sys 0.006 real
fetch_vcf: 189104 calls 34.060 user 0.799 sys 50.415 real
idle: 34 calls 0.001 user 0.008 sys 12.779 real
init: 1 calls 0.050 user 0.000 sys 0.051 real
pairhmm: 454 calls 2.119 user 0.019 sys 2.150 real
realign: 158 calls 0.278 user 0.000 sys 0.335 real
region: 367297 calls 1.788 user 0.039 sys 1.896 real
tracker: 367297 calls 0.262 user 0.016 sys 0.432 real
trim_region: 189 calls 0.010 user 0.000 sys 0.001 real
overall: 354246656 mem 137.675 user 8.719 sys 13.310 real