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% @chr1:113705733, elapsed 0.7s, est remaining 12.6s, peak mem 145MB, user 6.8s, sys 0.3s, output queue size 4
progress 10% @chr2:3671058, elapsed 1.3s, est remaining 11.6s, peak mem 145MB, user 13.1s, sys 0.8s, output queue size 8
progress 15% @chr2:178609108, elapsed 2.0s, est remaining 11.1s, peak mem 145MB, user 19.9s, sys 1.2s, output queue size 12
progress 20% @chr3:57483276, elapsed 2.6s, est remaining 10.2s, peak mem 145MB, user 26.2s, sys 1.6s, output queue size 0
progress 25% @chr4:70598256, elapsed 3.2s, est remaining 9.6s, peak mem 146MB, user 32.8s, sys 2.1s, output queue size 8
progress 30% @chr5:135873921, elapsed 3.9s, est remaining 9.2s, peak mem 147MB, user 40.0s, sys 2.5s, output queue size 4
progress 35% @chr6:104849042, elapsed 4.5s, est remaining 8.4s, peak mem 147MB, user 46.1s, sys 2.9s, output queue size 3
progress 40% @chr7:106284249, elapsed 5.2s, est remaining 7.8s, peak mem 147MB, user 52.9s, sys 3.2s, output queue size 5
progress 45% @chr8:143820566, elapsed 5.9s, est remaining 7.2s, peak mem 148MB, user 59.7s, sys 3.7s, output queue size 1
progress 50% @chr10:21726144, elapsed 6.5s, est remaining 6.5s, peak mem 151MB, user 66.0s, sys 4.1s, output queue size 1
progress 55% @chr11:34136878, elapsed 7.1s, est remaining 5.8s, peak mem 152MB, user 72.5s, sys 4.6s, output queue size 1
progress 60% @chr12:12718707, elapsed 7.8s, est remaining 5.2s, peak mem 153MB, user 78.7s, sys 5.0s, output queue size 10
progress 65% @chr13:32149648, elapsed 8.4s, est remaining 4.5s, peak mem 153MB, user 85.2s, sys 5.5s, output queue size 10
progress 70% @chr15:35381722, elapsed 9.0s, est remaining 3.9s, peak mem 153MB, user 91.6s, sys 5.9s, output queue size 2
progress 75% @chr16:28494582, elapsed 9.7s, est remaining 3.2s, peak mem 153MB, user 98.1s, sys 6.2s, output queue size 0
progress 80% @chr17:40035622, elapsed 10.4s, est remaining 2.6s, peak mem 153MB, user 105.3s, sys 6.6s, output queue size 1
progress 85% @chr19:1806528, elapsed 11.0s, est remaining 1.9s, peak mem 154MB, user 112.1s, sys 7.0s, output queue size 3
progress 90% @chr19:54632916, elapsed 11.7s, est remaining 1.3s, peak mem 154MB, user 118.7s, sys 7.3s, output queue size 1
progress 95% @chr22:31897382, elapsed 13.2s, est remaining 0.7s, peak mem 340MB, user 133.8s, sys 7.8s, output queue size 10
progress 100% @chrY:24834027, elapsed 13.8s, est remaining 0.0s, peak mem 340MB, user 139.9s, sys 8.2s, output queue size 80
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 74586812
output file size: 51111
reads: 1501816
contig: 178193 intervals 76355618 bases
"assemble": 189 calls 0.444 user 0.020 sys 0.458 real
"assemble_addRead": 189 calls 0.000 user 0.000 sys 0.008 real
"assemble_buildGraph": 446 calls 0.182 user 0.010 sys 0.199 real
"assemble_computecigar": 274 calls 0.040 user 0.020 sys 0.068 real
"assemble_kg_build_calcsize": 446 calls 0.127 user 0.000 sys 0.102 real
"assemble_kg_build_clear": 608 calls 0.010 user 0.000 sys 0.008 real
"assemble_kg_build_prepare": 892 calls 0.091 user 0.010 sys 0.098 real
"assemble_kg_build_threading": 284 calls 0.055 user 0.010 sys 0.093 real
"assemble_kg_op1": 284 calls 0.062 user 0.000 sys 0.065 real
"assemble_kg_op2": 284 calls 0.000 user 0.000 sys 0.004 real
"assemble_kg_op3": 284 calls 0.020 user 0.000 sys 0.005 real
"assemble_sg_clean": 274 calls 0.020 user 0.000 sys 0.021 real
"assemble_sg_create": 274 calls 0.010 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 0.020 sys 0.071 real
advance: 189104 calls 15.123 user 0.386 sys 18.780 real
assemble_region: 189 calls 0.484 user 0.040 sys 0.539 real
build_pileup: 70986 calls 0.441 user 0.024 sys 0.460 real
build_stats: 71708 calls 1.959 user 0.027 sys 2.368 real
build_variants: 158 calls 0.010 user 0.000 sys 0.001 real
calc: 128714 calls 2.524 user 0.053 sys 2.998 real
calc_region: 158 calls 1.764 user 0.021 sys 1.898 real
call_region: 158 calls 0.066 user 0.000 sys 0.046 real
clip_region: 347 calls 0.001 user 0.000 sys 0.036 real
done: 1 calls 0.427 user 0.000 sys 0.434 real
execute: 1 calls 0.005 user 0.001 sys 13.801 real
fetch: 743546 calls 0.628 user 0.093 sys 0.912 real
fetch_ref: 745694 calls 1.722 user 0.416 sys 2.740 real
fetch_region: 189 calls 0.000 user 0.000 sys 0.008 real
fetch_vcf: 189104 calls 42.544 user 0.741 sys 55.900 real
idle: 35 calls 0.005 user 0.003 sys 12.859 real
init: 1 calls 0.040 user 0.020 sys 0.059 real
pairhmm: 454 calls 2.988 user 0.029 sys 2.978 real
realign: 158 calls 0.401 user 0.000 sys 0.439 real
region: 367297 calls 2.251 user 0.123 sys 2.545 real
tracker: 367297 calls 0.414 user 0.050 sys 0.555 real
trim_region: 189 calls 0.000 user 0.000 sys 0.002 real
overall: 357535744 mem 156.369 user 10.989 sys 15.106 real