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% @chr1:113698162, elapsed 0.7s, est remaining 12.8s, peak mem 145MB, user 6.7s, sys 0.5s, output queue size 4
progress 10% @chr2:3603546, elapsed 1.3s, est remaining 11.8s, peak mem 145MB, user 13.0s, sys 1.0s, output queue size 6
progress 15% @chr2:178587018, elapsed 2.0s, est remaining 11.2s, peak mem 146MB, user 19.8s, sys 1.4s, output queue size 12
progress 20% @chr3:57483276, elapsed 2.6s, est remaining 10.3s, peak mem 146MB, user 26.0s, sys 1.8s, output queue size 0
progress 25% @chr4:70530939, elapsed 3.3s, est remaining 9.8s, peak mem 146MB, user 32.8s, sys 2.2s, output queue size 9
progress 30% @chr5:135534877, elapsed 3.9s, est remaining 9.2s, peak mem 147MB, user 39.8s, sys 2.6s, output queue size 3
progress 35% @chr6:104957999, elapsed 4.5s, est remaining 8.4s, peak mem 149MB, user 46.0s, sys 3.0s, output queue size 3
progress 40% @chr7:106872437, elapsed 5.2s, est remaining 7.8s, peak mem 150MB, user 52.8s, sys 3.5s, output queue size 14
progress 45% @chr8:143821497, elapsed 5.9s, est remaining 7.2s, peak mem 150MB, user 59.7s, sys 3.9s, output queue size 1
progress 50% @chr10:21727756, elapsed 6.5s, est remaining 6.5s, peak mem 153MB, user 66.5s, sys 4.1s, output queue size 2
progress 55% @chr11:34132926, elapsed 7.2s, est remaining 5.9s, peak mem 153MB, user 73.1s, sys 4.5s, output queue size 6
progress 60% @chr12:12718707, elapsed 7.8s, est remaining 5.2s, peak mem 154MB, user 79.3s, sys 5.0s, output queue size 10
progress 65% @chr13:32078734, elapsed 8.4s, est remaining 4.5s, peak mem 154MB, user 85.9s, sys 5.4s, output queue size 10
progress 70% @chr15:35542313, elapsed 9.1s, est remaining 3.9s, peak mem 154MB, user 92.5s, sys 5.8s, output queue size 2
progress 75% @chr16:28494582, elapsed 9.7s, est remaining 3.2s, peak mem 155MB, user 98.8s, sys 6.2s, output queue size 0
progress 80% @chr17:40034816, elapsed 10.4s, est remaining 2.6s, peak mem 155MB, user 106.0s, sys 6.7s, output queue size 7
progress 85% @chr19:1805788, elapsed 11.0s, est remaining 1.9s, peak mem 155MB, user 112.8s, sys 7.1s, output queue size 2
progress 90% @chr19:54630974, elapsed 11.7s, est remaining 1.3s, peak mem 157MB, user 119.5s, sys 7.4s, output queue size 2
progress 95% @chr22:31897382, elapsed 13.2s, est remaining 0.7s, peak mem 331MB, user 134.5s, sys 7.9s, output queue size 10
progress 100% @chrY:5104244, elapsed 13.8s, est remaining 0.0s, peak mem 331MB, user 140.7s, sys 8.3s, output queue size 368
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 64
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 74586800
output file size: 51111
reads: 1501816
contig: 178193 intervals 76355618 bases
"assemble": 189 calls 0.431 user 0.000 sys 0.447 real
"assemble_addRead": 189 calls 0.010 user 0.000 sys 0.007 real
"assemble_buildGraph": 446 calls 0.192 user 0.000 sys 0.194 real
"assemble_computecigar": 274 calls 0.040 user 0.010 sys 0.066 real
"assemble_kg_build_calcsize": 446 calls 0.167 user 0.000 sys 0.101 real
"assemble_kg_build_clear": 608 calls 0.020 user 0.000 sys 0.007 real
"assemble_kg_build_prepare": 892 calls 0.073 user 0.000 sys 0.094 real
"assemble_kg_build_threading": 284 calls 0.026 user 0.000 sys 0.089 real
"assemble_kg_op1": 284 calls 0.086 user 0.000 sys 0.064 real
"assemble_kg_op2": 284 calls 0.000 user 0.000 sys 0.004 real
"assemble_kg_op3": 284 calls 0.000 user 0.000 sys 0.005 real
"assemble_sg_clean": 274 calls 0.010 user 0.000 sys 0.021 real
"assemble_sg_create": 274 calls 0.040 user 0.000 sys 0.032 real
"checkGraph": 189 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 189 calls 0.040 user 0.010 sys 0.069 real
advance: 189104 calls 14.255 user 0.342 sys 18.689 real
assemble_region: 189 calls 0.481 user 0.010 sys 0.525 real
build_pileup: 70986 calls 0.321 user 0.011 sys 0.456 real
build_stats: 71708 calls 1.940 user 0.054 sys 2.250 real
build_variants: 158 calls 0.000 user 0.000 sys 0.001 real
calc: 128714 calls 2.486 user 0.031 sys 2.933 real
calc_region: 158 calls 1.783 user 0.010 sys 1.911 real
call_region: 158 calls 0.010 user 0.000 sys 0.044 real
clip_region: 347 calls 0.110 user 0.000 sys 0.035 real
done: 1 calls 0.480 user 0.000 sys 0.481 real
execute: 1 calls 0.008 user 0.001 sys 13.795 real
fetch: 743546 calls 0.884 user 0.085 sys 0.876 real
fetch_ref: 745694 calls 1.727 user 0.407 sys 2.708 real
fetch_region: 189 calls 0.010 user 0.000 sys 0.008 real
fetch_vcf: 189104 calls 43.303 user 1.000 sys 55.806 real
idle: 35 calls 0.006 user 0.006 sys 12.838 real
init: 1 calls 0.060 user 0.000 sys 0.058 real
pairhmm: 454 calls 2.886 user 0.019 sys 2.964 real
realign: 158 calls 0.417 user 0.000 sys 0.434 real
region: 367297 calls 2.297 user 0.080 sys 2.542 real
tracker: 367297 calls 0.419 user 0.109 sys 0.550 real
trim_region: 189 calls 0.000 user 0.000 sys 0.001 real
overall: 347324416 mem 155.481 user 11.195 sys 15.084 real