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_13.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% @chr1:113682797, elapsed 0.6s, est remaining 11.3s, peak mem 142MB, user 6.0s, sys 0.5s, output queue size 4
progress 10% @chr2:3613211, elapsed 1.2s, est remaining 10.5s, peak mem 142MB, user 11.6s, sys 0.9s, output queue size 5
progress 15% @chr2:178606921, elapsed 1.7s, est remaining 9.9s, peak mem 142MB, user 17.6s, sys 1.3s, output queue size 12
progress 20% @chr3:57498400, elapsed 2.3s, est remaining 9.2s, peak mem 142MB, user 23.1s, sys 1.6s, output queue size 0
progress 25% @chr4:70598256, elapsed 2.9s, est remaining 8.7s, peak mem 142MB, user 29.1s, sys 2.0s, output queue size 6
progress 30% @chr5:135850325, elapsed 3.5s, est remaining 8.2s, peak mem 144MB, user 35.4s, sys 2.4s, output queue size 4
progress 35% @chr6:104849042, elapsed 4.0s, est remaining 7.5s, peak mem 144MB, user 40.8s, sys 2.9s, output queue size 3
progress 40% @chr7:106872437, elapsed 4.6s, est remaining 6.9s, peak mem 144MB, user 46.8s, sys 3.2s, output queue size 2
progress 45% @chr8:143821497, elapsed 5.2s, est remaining 6.4s, peak mem 144MB, user 52.9s, sys 3.6s, output queue size 0
progress 50% @chr10:21713672, elapsed 5.8s, est remaining 5.8s, peak mem 145MB, user 58.8s, sys 4.0s, output queue size 1
progress 55% @chr11:34132025, elapsed 6.3s, est remaining 5.2s, peak mem 145MB, user 64.6s, sys 4.3s, output queue size 1
progress 60% @chr12:12718707, elapsed 6.9s, est remaining 4.6s, peak mem 145MB, user 70.1s, sys 4.6s, output queue size 9
progress 65% @chr13:32134804, elapsed 7.5s, est remaining 4.0s, peak mem 145MB, user 76.0s, sys 5.0s, output queue size 10
progress 70% @chr15:35538174, elapsed 8.0s, est remaining 3.4s, peak mem 145MB, user 81.7s, sys 5.4s, output queue size 0
progress 75% @chr16:28488491, elapsed 8.6s, est remaining 2.9s, peak mem 145MB, user 87.6s, sys 5.7s, output queue size 4
progress 80% @chr17:40035622, elapsed 9.2s, est remaining 2.3s, peak mem 145MB, user 93.9s, sys 6.1s, output queue size 2
progress 85% @chr19:1796611, elapsed 9.8s, est remaining 1.7s, peak mem 147MB, user 99.9s, sys 6.4s, output queue size 3
progress 90% @chr19:54632916, elapsed 10.3s, est remaining 1.1s, peak mem 147MB, user 105.7s, sys 6.7s, output queue size 0
progress 95% @chr22:31944634, elapsed 11.7s, est remaining 0.6s, peak mem 334MB, user 118.9s, sys 7.1s, output queue size 10
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 12.2s, est remaining 0.0s, peak mem 334MB, user 124.1s, sys 7.6s, output queue size 485
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 12 max 192
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 74586807
output file size: 63924
reads: 1501816
contig: 178193 intervals 76355618 bases
"assemble": 256 calls 0.599 user 0.001 sys 0.509 real
"assemble_addRead": 256 calls 0.000 user 0.000 sys 0.008 real
"assemble_buildGraph": 596 calls 0.238 user 0.000 sys 0.227 real
"assemble_computecigar": 383 calls 0.019 user 0.007 sys 0.065 real
"assemble_kg_build_calcsize": 596 calls 0.114 user 0.000 sys 0.120 real
"assemble_kg_build_clear": 796 calls 0.010 user 0.000 sys 0.009 real
"assemble_kg_build_prepare": 1192 calls 0.127 user 0.001 sys 0.104 real
"assemble_kg_build_threading": 396 calls 0.124 user 0.000 sys 0.104 real
"assemble_kg_op1": 396 calls 0.104 user 0.000 sys 0.069 real
"assemble_kg_op2": 396 calls 0.010 user 0.000 sys 0.004 real
"assemble_kg_op3": 396 calls 0.000 user 0.000 sys 0.006 real
"assemble_sg_clean": 383 calls 0.030 user 0.000 sys 0.023 real
"assemble_sg_create": 383 calls 0.049 user 0.000 sys 0.036 real
"checkGraph": 256 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 256 calls 0.019 user 0.007 sys 0.069 real
advance: 189104 calls 11.658 user 0.331 sys 17.197 real
assemble_region: 256 calls 0.618 user 0.008 sys 0.588 real
build_pileup: 70986 calls 0.151 user 0.005 sys 0.366 real
build_stats: 71708 calls 1.638 user 0.052 sys 1.725 real
build_variants: 222 calls 0.000 user 0.000 sys 0.001 real
calc: 128714 calls 1.299 user 0.016 sys 2.293 real
calc_region: 222 calls 1.781 user 0.012 sys 1.884 real
call_region: 222 calls 0.020 user 0.000 sys 0.043 real
clip_region: 478 calls 0.010 user 0.000 sys 0.041 real
done: 1 calls 0.271 user 0.008 sys 0.280 real
execute: 1 calls 0.004 user 0.001 sys 12.198 real
fetch: 743546 calls 0.498 user 0.055 sys 0.647 real
fetch_ref: 745761 calls 1.092 user 0.421 sys 2.596 real
fetch_region: 256 calls 0.010 user 0.000 sys 0.009 real
fetch_vcf: 189104 calls 31.422 user 0.930 sys 50.092 real
idle: 35 calls 0.007 user 0.009 sys 12.650 real
init: 1 calls 0.030 user 0.010 sys 0.047 real
pairhmm: 591 calls 2.771 user 0.011 sys 2.842 real
realign: 222 calls 0.335 user 0.009 sys 0.425 real
region: 367297 calls 2.430 user 0.036 sys 2.556 real
tracker: 367297 calls 0.262 user 0.077 sys 0.419 real
trim_region: 256 calls 0.010 user 0.000 sys 0.002 real
overall: 351199232 mem 137.268 user 10.454 sys 13.457 real