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 1.3s, est remaining 25.1s, peak mem 143MB, user 12.1s, sys 1.5s, output queue size 3
progress 10% @chr2:3625914, elapsed 2.6s, est remaining 23.3s, peak mem 144MB, user 24.2s, sys 2.7s, output queue size 5
progress 15% @chr2:178588438, elapsed 4.1s, est remaining 23.1s, peak mem 145MB, user 37.2s, sys 4.3s, output queue size 9
progress 20% @chr3:57472446, elapsed 5.4s, est remaining 21.6s, peak mem 146MB, user 49.0s, sys 5.7s, output queue size 1
progress 25% @chr4:70530939, elapsed 6.8s, est remaining 20.5s, peak mem 147MB, user 61.8s, sys 7.2s, output queue size 8
progress 30% @chr5:135571753, elapsed 8.2s, est remaining 19.2s, peak mem 148MB, user 74.5s, sys 9.1s, output queue size 4
progress 35% @chr6:104957999, elapsed 9.5s, est remaining 17.6s, peak mem 149MB, user 86.1s, sys 10.2s, output queue size 3
progress 40% @chr7:106284249, elapsed 10.8s, est remaining 16.2s, peak mem 150MB, user 99.0s, sys 11.5s, output queue size 6
progress 45% @chr8:143821497, elapsed 12.1s, est remaining 14.8s, peak mem 151MB, user 111.9s, sys 12.8s, output queue size 1
progress 50% @chr10:21514996, elapsed 13.5s, est remaining 13.5s, peak mem 155MB, user 124.5s, sys 14.0s, output queue size 13
progress 55% @chr11:34136878, elapsed 14.8s, est remaining 12.1s, peak mem 155MB, user 136.7s, sys 15.4s, output queue size 2
progress 60% @chr12:12718707, elapsed 16.0s, est remaining 10.7s, peak mem 155MB, user 148.6s, sys 16.5s, output queue size 12
progress 65% @chr13:32134804, elapsed 17.3s, est remaining 9.3s, peak mem 156MB, user 161.0s, sys 17.9s, output queue size 4
progress 70% @chr15:35372050, elapsed 18.6s, est remaining 8.0s, peak mem 157MB, user 173.0s, sys 19.1s, output queue size 4
progress 75% @chr16:28488491, elapsed 19.8s, est remaining 6.6s, peak mem 159MB, user 185.0s, sys 20.3s, output queue size 2
progress 80% @chr17:40034816, elapsed 21.2s, est remaining 5.3s, peak mem 159MB, user 197.9s, sys 21.7s, output queue size 3
progress 85% @chr19:1805788, elapsed 22.4s, est remaining 4.0s, peak mem 160MB, user 210.4s, sys 23.0s, output queue size 2
progress 90% @chr19:54632916, elapsed 23.7s, est remaining 2.6s, peak mem 161MB, user 222.6s, sys 24.1s, output queue size 1
progress 95% @chr22:31944634, elapsed 26.7s, est remaining 1.4s, peak mem 344MB, user 252.6s, sys 25.7s, output queue size 10
progress 100% @chrY:23191952, elapsed 27.9s, est remaining 0.0s, peak mem 344MB, user 263.6s, sys 27.2s, output queue size 113
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: AuthenticAMD
 signature: 00800f12
  features: 178bfbff fed83203
  extended: 209c01a9 00000000
  amd bits: 2fd3fbff 00c001f3
     brand: AMD EPYC 7571
threads: 12 max 64
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 71692767
output file size: 46614
reads: 1501772
contig: 178193 intervals 76355618 bases
"assemble": 183 calls 0.856 user 0.038 sys 0.873 real
"assemble_addRead": 183 calls 0.020 user 0.000 sys 0.013 real
"assemble_buildGraph": 422 calls 0.323 user 0.000 sys 0.386 real
"assemble_computecigar": 264 calls 0.151 user 0.009 sys 0.172 real
"assemble_kg_build_calcsize": 422 calls 0.110 user 0.000 sys 0.197 real
"assemble_kg_build_clear": 573 calls 0.000 user 0.000 sys 0.015 real
"assemble_kg_build_prepare": 844 calls 0.251 user 0.029 sys 0.191 real
"assemble_kg_build_threading": 271 calls 0.213 user 0.000 sys 0.181 real
"assemble_kg_op1": 271 calls 0.105 user 0.000 sys 0.100 real
"assemble_kg_op2": 271 calls 0.010 user 0.000 sys 0.008 real
"assemble_kg_op3": 271 calls 0.010 user 0.000 sys 0.008 real
"assemble_sg_clean": 264 calls 0.046 user 0.009 sys 0.044 real
"assemble_sg_create": 264 calls 0.050 user 0.000 sys 0.066 real
"checkGraph": 183 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 183 calls 0.151 user 0.009 sys 0.180 real
advance: 189104 calls 20.171 user 0.898 sys 32.271 real
assemble_region: 183 calls 1.027 user 0.047 sys 1.069 real
build_pileup: 70974 calls 0.908 user 0.007 sys 1.175 real
build_stats: 71688 calls 4.715 user 0.208 sys 6.580 real
build_variants: 142 calls 0.000 user 0.000 sys 0.002 real
calc: 128670 calls 4.283 user 0.247 sys 6.853 real
calc_region: 142 calls 4.379 user 0.011 sys 4.455 real
call_region: 142 calls 0.100 user 0.000 sys 0.077 real
clip_region: 325 calls 0.080 user 0.000 sys 0.055 real
done: 1 calls 1.297 user 0.000 sys 1.298 real
execute: 1 calls 0.005 user 0.012 sys 27.936 real
fetch: 743546 calls 1.354 user 0.178 sys 2.044 real
fetch_ref: 745688 calls 1.863 user 0.949 sys 4.868 real
fetch_region: 183 calls 0.020 user 0.000 sys 0.014 real
fetch_vcf: 189104 calls 63.044 user 2.810 sys 104.933 real
idle: 47 calls 0.002 user 0.001 sys 25.959 real
init: 1 calls 0.080 user 0.040 sys 0.119 real
pairhmm: 472 calls 6.603 user 0.020 sys 6.651 real
realign: 142 calls 0.534 user 0.000 sys 0.563 real
region: 367297 calls 5.525 user 0.143 sys 5.816 real
tracker: 367297 calls 0.738 user 0.142 sys 1.397 real
trim_region: 183 calls 0.000 user 0.000 sys 0.004 real
overall: 360796160 mem 295.852 user 39.075 sys 30.565 real