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% @chr1:113704566, elapsed 1.9s, est remaining 36.8s, peak mem 143MB, user 9.3s, sys 0.9s, output queue size 65
progress 10% @chr2:1942882, elapsed 3.9s, est remaining 35.3s, peak mem 144MB, user 18.0s, sys 1.9s, output queue size 48
progress 15% @chr2:178619521, elapsed 6.1s, est remaining 34.8s, peak mem 145MB, user 27.4s, sys 2.7s, output queue size 107
progress 20% @chr3:57508282, elapsed 8.1s, est remaining 32.3s, peak mem 146MB, user 36.0s, sys 3.4s, output queue size 97
progress 25% @chr4:70248898, elapsed 10.2s, est remaining 30.5s, peak mem 146MB, user 45.6s, sys 4.2s, output queue size 321
progress 30% @chr5:135446274, elapsed 12.5s, est remaining 29.1s, peak mem 147MB, user 55.2s, sys 5.1s, output queue size 132
progress 35% @chr6:105078314, elapsed 14.4s, est remaining 26.8s, peak mem 148MB, user 63.5s, sys 5.9s, output queue size 235
progress 40% @chr7:106905009, elapsed 16.3s, est remaining 24.5s, peak mem 148MB, user 72.9s, sys 6.8s, output queue size 175
progress 45% @chr8:143836939, elapsed 18.4s, est remaining 22.5s, peak mem 148MB, user 82.3s, sys 7.8s, output queue size 124
progress 50% @chr10:21727756, elapsed 20.4s, est remaining 20.4s, peak mem 152MB, user 91.5s, sys 8.6s, output queue size 79
progress 55% @chr11:34136542, elapsed 22.3s, est remaining 18.2s, peak mem 153MB, user 100.8s, sys 9.4s, output queue size 152
progress 60% @chr12:12829323, elapsed 24.2s, est remaining 16.1s, peak mem 153MB, user 109.5s, sys 10.2s, output queue size 36
progress 65% @chr13:32175446, elapsed 26.3s, est remaining 14.1s, peak mem 153MB, user 118.5s, sys 11.0s, output queue size 78
progress 70% @chr15:34363913, elapsed 28.1s, est remaining 12.0s, peak mem 153MB, user 127.7s, sys 11.6s, output queue size 70
progress 75% @chr16:27464220, elapsed 29.9s, est remaining 10.0s, peak mem 153MB, user 136.9s, sys 12.4s, output queue size 245
progress 80% @chr17:40088142, elapsed 32.0s, est remaining 8.0s, peak mem 153MB, user 146.6s, sys 13.4s, output queue size 158
progress 85% @chr19:1819834, elapsed 34.0s, est remaining 6.0s, peak mem 153MB, user 156.1s, sys 14.2s, output queue size 161
progress 90% @chr19:54663432, elapsed 36.0s, est remaining 4.0s, peak mem 154MB, user 165.3s, sys 14.9s, output queue size 142
progress 95% @chr22:32091512, elapsed 39.8s, est remaining 2.1s, peak mem 334MB, user 188.8s, sys 16.0s, output queue size 749
progress 100% @chrY:56960292, elapsed 41.8s, est remaining 0.0s, peak mem 334MB, user 197.1s, sys 16.7s, output queue size 1489
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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 74381931
output file size: 51110
reads: 1501816
contig: 178193 intervals 76355618 bases
"assemble": 189 calls 0.788 user 0.011 sys 1.081 real
"assemble_addRead": 189 calls 0.000 user 0.000 sys 0.017 real
"assemble_buildGraph": 446 calls 0.355 user 0.000 sys 0.458 real
"assemble_computecigar": 274 calls 0.060 user 0.010 sys 0.185 real
"assemble_kg_build_calcsize": 446 calls 0.172 user 0.000 sys 0.216 real
"assemble_kg_build_clear": 608 calls 0.010 user 0.000 sys 0.028 real
"assemble_kg_build_prepare": 892 calls 0.154 user 0.010 sys 0.203 real
"assemble_kg_build_threading": 284 calls 0.173 user 0.000 sys 0.233 real
"assemble_kg_op1": 284 calls 0.080 user 0.000 sys 0.156 real
"assemble_kg_op2": 284 calls 0.000 user 0.000 sys 0.007 real
"assemble_kg_op3": 284 calls 0.010 user 0.000 sys 0.007 real
"assemble_sg_clean": 274 calls 0.083 user 0.000 sys 0.040 real
"assemble_sg_create": 274 calls 0.020 user 0.000 sys 0.067 real
"checkGraph": 189 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 189 calls 0.060 user 0.010 sys 0.190 real
advance: 189104 calls 18.635 user 0.547 sys 36.663 real
assemble_region: 189 calls 0.848 user 0.021 sys 1.290 real
build_pileup: 70986 calls 0.584 user 0.013 sys 1.340 real
build_stats: 71708 calls 4.675 user 0.145 sys 8.678 real
build_variants: 158 calls 0.000 user 0.000 sys 0.001 real
calc: 128714 calls 6.245 user 0.161 sys 10.886 real
calc_region: 158 calls 2.843 user 0.011 sys 3.842 real
call_region: 158 calls 0.091 user 0.000 sys 0.134 real
clip_region: 347 calls 0.100 user 0.000 sys 0.095 real
done: 1 calls 0.943 user 0.000 sys 0.947 real
execute: 1 calls 0.004 user 0.011 sys 41.829 real
fetch: 743546 calls 1.683 user 0.146 sys 2.676 real
fetch_ref: 745694 calls 2.333 user 0.630 sys 6.171 real
fetch_region: 189 calls 0.020 user 0.000 sys 0.025 real
fetch_vcf: 189104 calls 63.017 user 1.540 sys 121.268 real
idle: 47 calls 0.005 user 0.004 sys 26.102 real
init: 1 calls 0.100 user 0.000 sys 0.123 real
pairhmm: 454 calls 4.858 user 0.029 sys 5.977 real
realign: 158 calls 0.529 user 0.000 sys 0.862 real
region: 367297 calls 3.814 user 0.084 sys 5.395 real
tracker: 367297 calls 1.039 user 0.077 sys 1.944 real
trim_region: 189 calls 0.000 user 0.000 sys 0.003 real
overall: 351215616 mem 224.006 user 19.106 sys 44.444 real