cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i reference-NA12878-downsampled-500k.bam -i HCC1395_tumor.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 HCC1395_tumor --normal_sample reference-NA12878 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz positive_somatic_control_1.tnseq.vcf.gz --algo OrientationBias --tumor_sample HCC1395_tumor positive_somatic_control_1.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_tumor --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments positive_somatic_control_1.tnseq.segments positive_somatic_control_1.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113706494, elapsed 0.7s, est remaining 12.5s, peak mem 144MB, user 6.8s, sys 0.4s, output queue size 4
progress 10% @chr2:3643344, elapsed 1.3s, est remaining 11.6s, peak mem 145MB, user 13.1s, sys 0.9s, output queue size 6
progress 15% @chr2:178606921, elapsed 2.0s, est remaining 11.1s, peak mem 146MB, user 20.0s, sys 1.3s, output queue size 12
progress 20% @chr3:57483276, elapsed 2.6s, est remaining 10.2s, peak mem 146MB, user 26.3s, sys 1.6s, output queue size 0
progress 25% @chr4:70596899, elapsed 3.2s, est remaining 9.6s, peak mem 146MB, user 33.2s, sys 2.0s, output queue size 4
progress 30% @chr5:135850325, elapsed 3.9s, est remaining 9.1s, peak mem 149MB, user 40.1s, sys 2.4s, output queue size 4
progress 35% @chr6:104849042, elapsed 4.5s, est remaining 8.4s, peak mem 149MB, user 46.4s, sys 2.7s, output queue size 3
progress 40% @chr7:106882017, elapsed 5.2s, est remaining 7.7s, peak mem 149MB, user 53.0s, sys 3.1s, output queue size 2
progress 45% @chr8:143821497, elapsed 5.8s, est remaining 7.1s, peak mem 151MB, user 59.9s, sys 3.4s, output queue size 1
progress 50% @chr10:21713672, elapsed 6.5s, est remaining 6.5s, peak mem 153MB, user 66.5s, sys 3.8s, output queue size 1
progress 55% @chr11:34132025, elapsed 7.1s, est remaining 5.8s, peak mem 154MB, user 73.1s, sys 4.2s, output queue size 1
progress 60% @chr12:12718707, elapsed 7.7s, est remaining 5.1s, peak mem 154MB, user 79.4s, sys 4.5s, output queue size 11
progress 65% @chr13:32124502, elapsed 8.3s, est remaining 4.5s, peak mem 154MB, user 86.0s, sys 5.0s, output queue size 6
progress 70% @chr15:34969439, elapsed 9.0s, est remaining 3.8s, peak mem 154MB, user 92.6s, sys 5.4s, output queue size 6
progress 75% @chr16:28494582, elapsed 9.6s, est remaining 3.2s, peak mem 154MB, user 98.9s, sys 5.9s, output queue size 0
progress 80% @chr17:40034816, elapsed 10.3s, est remaining 2.6s, peak mem 154MB, user 106.1s, sys 6.2s, output queue size 2
progress 85% @chr19:1805788, elapsed 10.9s, est remaining 1.9s, peak mem 154MB, user 112.9s, sys 6.6s, output queue size 2
progress 90% @chr19:54632916, elapsed 11.5s, est remaining 1.3s, peak mem 155MB, user 119.5s, sys 7.0s, output queue size 0
progress 95% @chr22:31897382, elapsed 13.0s, est remaining 0.7s, peak mem 326MB, user 134.4s, sys 7.6s, output queue size 10
progress 100% @chrY:21912069, elapsed 13.6s, est remaining 0.0s, peak mem 326MB, user 140.5s, sys 8.0s, output queue size 437
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 81484554
output file size: 50711
reads: 1502003
contig: 178193 intervals 76355618 bases
"assemble": 207 calls 0.348 user 0.007 sys 0.407 real
"assemble_addRead": 207 calls 0.010 user 0.010 sys 0.007 real
"assemble_buildGraph": 465 calls 0.159 user 0.000 sys 0.174 real
"assemble_computecigar": 304 calls 0.108 user 0.009 sys 0.086 real
"assemble_kg_build_calcsize": 465 calls 0.057 user 0.000 sys 0.084 real
"assemble_kg_build_clear": 618 calls 0.011 user 0.000 sys 0.007 real
"assemble_kg_build_prepare": 930 calls 0.128 user 0.000 sys 0.078 real
"assemble_kg_build_threading": 312 calls 0.082 user 0.000 sys 0.087 real
"assemble_kg_op1": 312 calls 0.030 user 0.007 sys 0.058 real
"assemble_kg_op2": 312 calls 0.000 user 0.000 sys 0.004 real
"assemble_kg_op3": 312 calls 0.000 user 0.000 sys 0.005 real
"assemble_sg_clean": 304 calls 0.000 user 0.000 sys 0.022 real
"assemble_sg_create": 304 calls 0.020 user 0.000 sys 0.035 real
"checkGraph": 207 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 207 calls 0.108 user 0.009 sys 0.089 real
advance: 189104 calls 15.007 user 0.312 sys 18.787 real
assemble_region: 207 calls 0.467 user 0.026 sys 0.505 real
build_pileup: 70976 calls 0.367 user 0.011 sys 0.449 real
build_stats: 71686 calls 1.887 user 0.044 sys 2.159 real
build_variants: 162 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 2.320 user 0.023 sys 2.867 real
calc_region: 162 calls 1.656 user 0.024 sys 1.758 real
call_region: 162 calls 0.010 user 0.000 sys 0.037 real
clip_region: 369 calls 0.020 user 0.000 sys 0.028 real
done: 1 calls 0.441 user 0.009 sys 0.455 real
execute: 1 calls 0.003 user 0.001 sys 13.619 real
fetch: 743546 calls 0.535 user 0.050 sys 0.837 real
fetch_ref: 745712 calls 1.789 user 0.508 sys 2.705 real
fetch_region: 207 calls 0.000 user 0.000 sys 0.007 real
fetch_vcf: 189104 calls 43.919 user 0.734 sys 55.491 real
idle: 34 calls 0.009 user 0.008 sys 12.851 real
init: 1 calls 0.031 user 0.029 sys 0.058 real
pairhmm: 466 calls 2.893 user 0.026 sys 2.967 real
realign: 162 calls 0.281 user 0.000 sys 0.336 real
region: 367297 calls 2.161 user 0.107 sys 2.368 real
tracker: 367297 calls 0.286 user 0.052 sys 0.540 real
trim_region: 207 calls 0.000 user 0.000 sys 0.002 real
overall: 342794240 mem 154.663 user 10.614 sys 14.911 real