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_BL.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_BL --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_1.tnseq.vcf.gz --algo OrientationBias --tumor_sample HCC1395_BL negative_somatic_control_1.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_BL --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments negative_somatic_control_1.tnseq.segments negative_somatic_control_1.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113682797, elapsed 2.1s, est remaining 39.2s, peak mem 138MB, user 9.9s, sys 1.1s, output queue size 43
progress 10% @chr2:3695617, elapsed 4.3s, est remaining 38.6s, peak mem 140MB, user 19.1s, sys 2.0s, output queue size 241
progress 15% @chr2:178615207, elapsed 6.5s, est remaining 36.7s, peak mem 141MB, user 28.8s, sys 3.0s, output queue size 241
progress 20% @chr3:57510690, elapsed 8.5s, est remaining 34.1s, peak mem 143MB, user 37.5s, sys 3.8s, output queue size 221
progress 25% @chr4:70602524, elapsed 10.6s, est remaining 31.9s, peak mem 143MB, user 47.5s, sys 4.8s, output queue size 5
progress 30% @chr5:134743887, elapsed 13.0s, est remaining 30.3s, peak mem 143MB, user 57.4s, sys 5.7s, output queue size 107
progress 35% @chr6:105125291, elapsed 15.0s, est remaining 27.9s, peak mem 143MB, user 66.1s, sys 6.6s, output queue size 143
progress 40% @chr7:106867451, elapsed 17.5s, est remaining 26.2s, peak mem 143MB, user 75.9s, sys 7.3s, output queue size 44
progress 45% @chr8:143597804, elapsed 19.6s, est remaining 24.0s, peak mem 143MB, user 85.8s, sys 8.0s, output queue size 44
progress 50% @chr10:21732799, elapsed 21.7s, est remaining 21.7s, peak mem 146MB, user 95.3s, sys 8.8s, output queue size 102
progress 55% @chr11:34139091, elapsed 24.1s, est remaining 19.8s, peak mem 146MB, user 104.2s, sys 9.6s, output queue size 50
progress 60% @chr12:12987052, elapsed 25.9s, est remaining 17.3s, peak mem 146MB, user 113.3s, sys 10.3s, output queue size 71
progress 65% @chr13:32155391, elapsed 28.2s, est remaining 15.2s, peak mem 146MB, user 122.3s, sys 11.1s, output queue size 53
progress 70% @chr15:35542313, elapsed 30.1s, est remaining 12.9s, peak mem 146MB, user 131.7s, sys 11.8s, output queue size 60
progress 75% @chr16:28494999, elapsed 32.1s, est remaining 10.7s, peak mem 148MB, user 141.0s, sys 12.5s, output queue size 70
progress 80% @chr17:40084510, elapsed 34.1s, est remaining 8.5s, peak mem 148MB, user 151.1s, sys 13.3s, output queue size 73
progress 85% @chr19:1810522, elapsed 36.1s, est remaining 6.4s, peak mem 148MB, user 161.0s, sys 14.0s, output queue size 66
progress 90% @chr19:54663432, elapsed 38.2s, est remaining 4.2s, peak mem 148MB, user 170.5s, sys 14.7s, output queue size 136
progress 95% @chr22:32082974, elapsed 42.1s, est remaining 2.2s, peak mem 316MB, user 194.5s, sys 15.9s, output queue size 491
progress 100% @chrY:19741218, elapsed 43.9s, est remaining 0.0s, peak mem 316MB, user 203.1s, sys 16.7s, output queue size 813
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000606a6
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef 40417f5e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 128
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 71637313
output file size: 46618
reads: 1501772
contig: 178193 intervals 76355618 bases
"assemble": 184 calls 0.662 user 0.030 sys 0.974 real
"assemble_addRead": 184 calls 0.030 user 0.000 sys 0.025 real
"assemble_buildGraph": 424 calls 0.240 user 0.010 sys 0.413 real
"assemble_computecigar": 266 calls 0.140 user 0.038 sys 0.203 real
"assemble_kg_build_calcsize": 424 calls 0.096 user 0.000 sys 0.199 real
"assemble_kg_build_clear": 575 calls 0.010 user 0.000 sys 0.015 real
"assemble_kg_build_prepare": 848 calls 0.147 user 0.020 sys 0.216 real
"assemble_kg_build_threading": 273 calls 0.134 user 0.000 sys 0.196 real
"assemble_kg_op1": 273 calls 0.136 user 0.000 sys 0.130 real
"assemble_kg_op2": 273 calls 0.000 user 0.000 sys 0.007 real
"assemble_kg_op3": 273 calls 0.000 user 0.000 sys 0.007 real
"assemble_sg_clean": 266 calls 0.050 user 0.000 sys 0.058 real
"assemble_sg_create": 266 calls 0.050 user 0.000 sys 0.067 real
"checkGraph": 184 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 184 calls 0.140 user 0.038 sys 0.209 real
advance: 189104 calls 19.184 user 0.529 sys 39.907 real
assemble_region: 184 calls 0.843 user 0.069 sys 1.221 real
build_pileup: 70974 calls 0.702 user 0.022 sys 1.547 real
build_stats: 71688 calls 4.675 user 0.104 sys 8.641 real
build_variants: 142 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 6.118 user 0.099 sys 12.386 real
calc_region: 142 calls 3.081 user 0.043 sys 4.160 real
call_region: 142 calls 0.054 user 0.000 sys 0.076 real
clip_region: 326 calls 0.033 user 0.000 sys 0.066 real
done: 1 calls 0.979 user 0.000 sys 0.993 real
execute: 1 calls 0.004 user 0.011 sys 43.943 real
fetch: 743546 calls 1.323 user 0.214 sys 2.518 real
fetch_ref: 745689 calls 2.276 user 0.854 sys 6.491 real
fetch_region: 184 calls 0.010 user 0.000 sys 0.012 real
fetch_vcf: 189104 calls 66.894 user 1.349 sys 135.309 real
idle: 47 calls 0.024 user 0.003 sys 25.873 real
init: 1 calls 0.088 user 0.020 sys 0.110 real
pairhmm: 472 calls 5.445 user 0.021 sys 6.876 real
realign: 142 calls 0.501 user 0.001 sys 0.757 real
region: 367297 calls 3.984 user 0.163 sys 5.638 real
tracker: 367297 calls 0.915 user 0.149 sys 2.093 real
trim_region: 184 calls 0.000 user 0.000 sys 0.003 real
overall: 331436032 mem 226.246 user 18.660 sys 46.564 real