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% @chr1:113711646, elapsed 0.7s, est remaining 13.1s, peak mem 144MB, user 6.8s, sys 0.5s, output queue size 3
progress 10% @chr2:3643344, elapsed 1.3s, est remaining 11.9s, peak mem 144MB, user 13.1s, sys 1.0s, output queue size 6
progress 15% @chr2:178606921, elapsed 2.0s, est remaining 11.3s, peak mem 144MB, user 20.0s, sys 1.5s, output queue size 12
progress 20% @chr3:57498400, elapsed 2.6s, est remaining 10.4s, peak mem 145MB, user 26.2s, sys 1.8s, output queue size 0
progress 25% @chr4:70480699, elapsed 3.3s, est remaining 9.8s, peak mem 145MB, user 33.0s, sys 2.3s, output queue size 16
progress 30% @chr5:135850325, elapsed 4.0s, est remaining 9.2s, peak mem 147MB, user 39.9s, sys 2.8s, output queue size 4
progress 35% @chr6:104957999, elapsed 4.6s, est remaining 8.5s, peak mem 149MB, user 45.9s, sys 3.3s, output queue size 2
progress 40% @chr7:106284249, elapsed 5.3s, est remaining 7.9s, peak mem 150MB, user 52.7s, sys 3.7s, output queue size 5
progress 45% @chr8:143813211, elapsed 5.9s, est remaining 7.3s, peak mem 150MB, user 59.4s, sys 4.0s, output queue size 0
progress 50% @chr10:21726144, elapsed 6.6s, est remaining 6.6s, peak mem 152MB, user 66.0s, sys 4.3s, output queue size 2
progress 55% @chr11:34132025, elapsed 7.2s, est remaining 5.9s, peak mem 152MB, user 72.2s, sys 4.8s, output queue size 1
progress 60% @chr12:12718707, elapsed 7.8s, est remaining 5.2s, peak mem 152MB, user 78.5s, sys 5.2s, output queue size 9
progress 65% @chr13:32078734, elapsed 8.5s, est remaining 4.6s, peak mem 152MB, user 85.3s, sys 5.6s, output queue size 10
progress 70% @chr15:35381722, elapsed 9.1s, est remaining 3.9s, peak mem 153MB, user 91.7s, sys 6.1s, output queue size 2
progress 75% @chr16:28494582, elapsed 9.8s, est remaining 3.3s, peak mem 154MB, user 98.1s, sys 6.5s, output queue size 0
progress 80% @chr17:40034816, elapsed 10.5s, est remaining 2.6s, peak mem 154MB, user 105.3s, sys 6.9s, output queue size 0
progress 85% @chr19:1806528, elapsed 11.1s, est remaining 2.0s, peak mem 154MB, user 112.1s, sys 7.4s, output queue size 3
progress 90% @chr19:54630974, elapsed 11.8s, est remaining 1.3s, peak mem 155MB, user 118.6s, sys 7.8s, output queue size 2
progress 95% @chr22:31944634, elapsed 13.4s, est remaining 0.7s, peak mem 339MB, user 133.7s, sys 8.6s, output queue size 10
progress 100% @chrY:20589384, elapsed 14.0s, est remaining 0.0s, peak mem 339MB, user 139.6s, sys 9.1s, output queue size 452
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 74586797
output file size: 51111
reads: 1501816
contig: 178193 intervals 76355618 bases
"assemble": 189 calls 0.511 user 0.010 sys 0.477 real
"assemble_addRead": 189 calls 0.030 user 0.000 sys 0.009 real
"assemble_buildGraph": 446 calls 0.240 user 0.010 sys 0.208 real
"assemble_computecigar": 274 calls 0.110 user 0.000 sys 0.070 real
"assemble_kg_build_calcsize": 446 calls 0.144 user 0.000 sys 0.103 real
"assemble_kg_build_clear": 608 calls 0.020 user 0.000 sys 0.009 real
"assemble_kg_build_prepare": 892 calls 0.107 user 0.000 sys 0.103 real
"assemble_kg_build_threading": 284 calls 0.091 user 0.009 sys 0.099 real
"assemble_kg_op1": 284 calls 0.065 user 0.000 sys 0.066 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 0.033 real
"checkGraph": 189 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 189 calls 0.110 user 0.000 sys 0.073 real
advance: 189104 calls 15.064 user 0.448 sys 18.992 real
assemble_region: 189 calls 0.651 user 0.010 sys 0.561 real
build_pileup: 70986 calls 0.361 user 0.018 sys 0.470 real
build_stats: 71708 calls 2.614 user 0.097 sys 2.716 real
build_variants: 158 calls 0.000 user 0.000 sys 0.001 real
calc: 128714 calls 2.552 user 0.061 sys 3.100 real
calc_region: 158 calls 1.664 user 0.023 sys 1.870 real
call_region: 158 calls 0.077 user 0.000 sys 0.049 real
clip_region: 347 calls 0.060 user 0.000 sys 0.039 real
done: 1 calls 0.491 user 0.000 sys 0.491 real
execute: 1 calls 0.002 user 0.010 sys 13.992 real
fetch: 743546 calls 0.824 user 0.092 sys 1.018 real
fetch_ref: 745694 calls 1.356 user 0.389 sys 2.778 real
fetch_region: 189 calls 0.000 user 0.000 sys 0.010 real
fetch_vcf: 189104 calls 41.348 user 1.066 sys 56.038 real
idle: 35 calls 0.003 user 0.006 sys 12.910 real
init: 1 calls 0.050 user 0.010 sys 0.059 real
pairhmm: 454 calls 2.787 user 0.020 sys 2.994 real
realign: 158 calls 0.403 user 0.000 sys 0.442 real
region: 367297 calls 2.389 user 0.100 sys 2.544 real
tracker: 367297 calls 0.353 user 0.070 sys 0.580 real
trim_region: 189 calls 0.000 user 0.010 sys 0.002 real
overall: 356335616 mem 157.348 user 12.186 sys 15.315 real