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 0.9s, est remaining 17.2s, peak mem 145MB, user 9.1s, sys 0.5s, output queue size 3
progress 10% @chr2:3603546, elapsed 1.7s, est remaining 15.5s, peak mem 145MB, user 17.4s, sys 1.2s, output queue size 6
progress 15% @chr2:178606921, elapsed 2.6s, est remaining 14.9s, peak mem 146MB, user 26.4s, sys 1.9s, output queue size 12
progress 20% @chr3:57508282, elapsed 3.5s, est remaining 13.8s, peak mem 147MB, user 34.9s, sys 2.4s, output queue size 0
progress 25% @chr4:70603160, elapsed 4.3s, est remaining 13.0s, peak mem 148MB, user 44.0s, sys 2.9s, output queue size 3
progress 30% @chr5:135850325, elapsed 5.2s, est remaining 12.2s, peak mem 149MB, user 53.3s, sys 3.5s, output queue size 4
progress 35% @chr6:104791404, elapsed 6.0s, est remaining 11.2s, peak mem 151MB, user 61.5s, sys 4.1s, output queue size 7
progress 40% @chr7:106248199, elapsed 6.9s, est remaining 10.4s, peak mem 153MB, user 70.5s, sys 4.6s, output queue size 20
progress 45% @chr8:143835562, elapsed 7.8s, est remaining 9.6s, peak mem 154MB, user 79.7s, sys 5.0s, output queue size 3
progress 50% @chr10:21670349, elapsed 8.7s, est remaining 8.7s, peak mem 156MB, user 88.4s, sys 5.6s, output queue size 1
progress 55% @chr11:34130713, elapsed 9.5s, est remaining 7.8s, peak mem 156MB, user 97.0s, sys 6.1s, output queue size 5
progress 60% @chr12:12786809, elapsed 10.3s, est remaining 6.9s, peak mem 156MB, user 105.0s, sys 6.6s, output queue size 3
progress 65% @chr13:32149648, elapsed 11.2s, est remaining 6.0s, peak mem 156MB, user 113.5s, sys 7.2s, output queue size 0
progress 70% @chr15:35084093, elapsed 11.9s, est remaining 5.1s, peak mem 156MB, user 121.4s, sys 7.8s, output queue size 5
progress 75% @chr16:28489190, elapsed 12.7s, est remaining 4.2s, peak mem 156MB, user 129.8s, sys 8.3s, output queue size 4
progress 80% @chr17:40034816, elapsed 13.6s, est remaining 3.4s, peak mem 156MB, user 138.7s, sys 8.9s, output queue size 1
progress 85% @chr19:1652201, elapsed 14.4s, est remaining 2.5s, peak mem 156MB, user 147.2s, sys 9.5s, output queue size 16
progress 90% @chr19:54662811, elapsed 15.2s, est remaining 1.7s, peak mem 158MB, user 155.7s, sys 10.0s, output queue size 6
progress 95% @chr22:32043182, elapsed 17.1s, est remaining 0.9s, peak mem 329MB, user 175.3s, sys 10.7s, output queue size 3
progress 100% @chrY:14840313, elapsed 17.9s, est remaining 0.0s, peak mem 330MB, user 183.0s, sys 11.3s, output queue size 236
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 71692772
output file size: 46614
reads: 1501772
contig: 178193 intervals 76355618 bases
"assemble": 183 calls 0.550 user 0.007 sys 0.557 real
"assemble_addRead": 183 calls 0.000 user 0.000 sys 0.010 real
"assemble_buildGraph": 422 calls 0.246 user 0.007 sys 0.238 real
"assemble_computecigar": 264 calls 0.080 user 0.009 sys 0.104 real
"assemble_kg_build_calcsize": 422 calls 0.145 user 0.000 sys 0.118 real
"assemble_kg_build_clear": 573 calls 0.020 user 0.000 sys 0.010 real
"assemble_kg_build_prepare": 844 calls 0.079 user 0.000 sys 0.114 real
"assemble_kg_build_threading": 271 calls 0.085 user 0.007 sys 0.113 real
"assemble_kg_op1": 271 calls 0.057 user 0.000 sys 0.076 real
"assemble_kg_op2": 271 calls 0.000 user 0.000 sys 0.005 real
"assemble_kg_op3": 271 calls 0.000 user 0.000 sys 0.005 real
"assemble_sg_clean": 264 calls 0.050 user 0.000 sys 0.029 real
"assemble_sg_create": 264 calls 0.063 user 0.000 sys 0.044 real
"checkGraph": 183 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 183 calls 0.090 user 0.009 sys 0.108 real
advance: 189104 calls 19.430 user 0.458 sys 23.243 real
assemble_region: 183 calls 0.641 user 0.017 sys 0.677 real
build_pileup: 70974 calls 0.479 user 0.013 sys 0.677 real
build_stats: 71688 calls 3.078 user 0.070 sys 3.622 real
build_variants: 142 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 4.222 user 0.070 sys 5.164 real
calc_region: 142 calls 2.883 user 0.025 sys 2.932 real
call_region: 142 calls 0.045 user 0.000 sys 0.052 real
clip_region: 325 calls 0.032 user 0.000 sys 0.035 real
done: 1 calls 0.428 user 0.010 sys 0.444 real
execute: 1 calls 0.005 user 0.001 sys 17.911 real
fetch: 743546 calls 0.883 user 0.072 sys 1.163 real
fetch_ref: 745688 calls 2.116 user 0.449 sys 3.081 real
fetch_region: 183 calls 0.020 user 0.000 sys 0.008 real
fetch_vcf: 189104 calls 56.193 user 1.239 sys 72.302 real
idle: 35 calls 0.008 user 0.012 sys 12.829 real
init: 1 calls 0.050 user 0.010 sys 0.058 real
pairhmm: 472 calls 4.301 user 0.032 sys 4.371 real
realign: 142 calls 0.436 user 0.000 sys 0.417 real
region: 367297 calls 3.592 user 0.089 sys 3.747 real
tracker: 367297 calls 0.635 user 0.089 sys 0.872 real
trim_region: 183 calls 0.000 user 0.000 sys 0.002 real
overall: 346337280 mem 203.616 user 15.011 sys 19.204 real