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_tissue.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_tissue --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_2.tnseq.vcf.gz --algo OrientationBias --tumor_sample Sig_18_tissue positive_somatic_control_2.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample Sig_18_tissue --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments positive_somatic_control_2.tnseq.segments positive_somatic_control_2.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113713179, elapsed 2.0s, est remaining 37.6s, peak mem 139MB, user 9.4s, sys 0.8s, output queue size 81
progress 10% @chr2:3678368, elapsed 3.6s, est remaining 32.5s, peak mem 140MB, user 18.5s, sys 1.7s, output queue size 64
progress 15% @chr2:178619521, elapsed 5.4s, est remaining 30.5s, peak mem 140MB, user 28.5s, sys 2.7s, output queue size 33
progress 20% @chr3:57503916, elapsed 7.1s, est remaining 28.5s, peak mem 140MB, user 37.1s, sys 3.5s, output queue size 125
progress 25% @chr4:70606085, elapsed 9.1s, est remaining 27.4s, peak mem 140MB, user 46.9s, sys 4.4s, output queue size 201
progress 30% @chr5:135852463, elapsed 11.0s, est remaining 25.7s, peak mem 142MB, user 56.5s, sys 5.4s, output queue size 314
progress 35% @chr6:100643931, elapsed 12.7s, est remaining 23.6s, peak mem 142MB, user 65.5s, sys 6.1s, output queue size 69
progress 40% @chr7:106284249, elapsed 14.3s, est remaining 21.5s, peak mem 142MB, user 75.5s, sys 6.8s, output queue size 18
progress 45% @chr8:143812717, elapsed 16.1s, est remaining 19.7s, peak mem 142MB, user 85.6s, sys 7.6s, output queue size 2
progress 50% @chr10:21682125, elapsed 17.8s, est remaining 17.8s, peak mem 143MB, user 95.2s, sys 8.6s, output queue size 93
progress 55% @chr11:34132025, elapsed 19.5s, est remaining 15.9s, peak mem 143MB, user 104.7s, sys 9.6s, output queue size 99
progress 60% @chr12:11810059, elapsed 21.1s, est remaining 14.1s, peak mem 143MB, user 113.6s, sys 10.6s, output queue size 91
progress 65% @chr13:32179575, elapsed 22.7s, est remaining 12.2s, peak mem 143MB, user 123.5s, sys 11.5s, output queue size 57
progress 70% @chr15:35542313, elapsed 24.5s, est remaining 10.5s, peak mem 143MB, user 133.0s, sys 12.2s, output queue size 50
progress 75% @chr16:28494999, elapsed 26.3s, est remaining 8.8s, peak mem 143MB, user 142.4s, sys 13.0s, output queue size 221
progress 80% @chr17:40077408, elapsed 28.3s, est remaining 7.1s, peak mem 143MB, user 152.6s, sys 13.9s, output queue size 242
progress 85% @chr19:1815966, elapsed 30.1s, est remaining 5.3s, peak mem 143MB, user 162.5s, sys 14.8s, output queue size 77
progress 90% @chr19:54636394, elapsed 31.6s, est remaining 3.5s, peak mem 143MB, user 172.3s, sys 15.5s, output queue size 96
progress 95% @chr22:32086120, elapsed 35.1s, est remaining 1.8s, peak mem 337MB, user 196.0s, sys 16.5s, output queue size 265
progress 100% @chrY:24854733, elapsed 36.6s, est remaining 0.0s, peak mem 337MB, user 205.1s, sys 17.0s, output queue size 45
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  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 93237272
output file size: 53231
reads: 1502521
contig: 178193 intervals 76355618 bases
"assemble": 222 calls 0.659 user 0.021 sys 0.944 real
"assemble_addRead": 222 calls 0.000 user 0.000 sys 0.012 real
"assemble_buildGraph": 498 calls 0.325 user 0.021 sys 0.463 real
"assemble_computecigar": 330 calls 0.096 user 0.000 sys 0.142 real
"assemble_kg_build_calcsize": 498 calls 0.152 user 0.001 sys 0.234 real
"assemble_kg_build_clear": 653 calls 0.020 user 0.000 sys 0.012 real
"assemble_kg_build_prepare": 996 calls 0.105 user 0.000 sys 0.164 real
"assemble_kg_build_threading": 343 calls 0.143 user 0.020 sys 0.212 real
"assemble_kg_op1": 343 calls 0.060 user 0.000 sys 0.114 real
"assemble_kg_op2": 343 calls 0.006 user 0.000 sys 0.007 real
"assemble_kg_op3": 343 calls 0.000 user 0.000 sys 0.008 real
"assemble_sg_clean": 330 calls 0.060 user 0.000 sys 0.059 real
"assemble_sg_create": 330 calls 0.038 user 0.000 sys 0.068 real
"checkGraph": 222 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 222 calls 0.116 user 0.000 sys 0.148 real
advance: 189104 calls 21.481 user 0.710 sys 38.505 real
assemble_region: 222 calls 0.775 user 0.021 sys 1.108 real
build_pileup: 70986 calls 0.755 user 0.039 sys 1.469 real
build_stats: 71711 calls 3.889 user 0.131 sys 5.920 real
build_variants: 179 calls 0.004 user 0.000 sys 0.002 real
calc: 128717 calls 4.438 user 0.065 sys 7.319 real
calc_region: 179 calls 3.491 user 0.010 sys 4.681 real
call_region: 179 calls 0.070 user 0.000 sys 0.112 real
clip_region: 401 calls 0.061 user 0.000 sys 0.081 real
done: 1 calls 0.706 user 0.000 sys 0.731 real
execute: 1 calls 0.001 user 0.010 sys 36.659 real
fetch: 743546 calls 1.089 user 0.087 sys 1.883 real
fetch_ref: 745727 calls 2.138 user 1.231 sys 6.072 real
fetch_region: 222 calls 0.010 user 0.000 sys 0.012 real
fetch_vcf: 189104 calls 69.895 user 1.631 sys 120.022 real
idle: 35 calls 0.001 user 0.001 sys 13.376 real
init: 1 calls 0.050 user 0.030 sys 0.088 real
pairhmm: 838 calls 6.020 user 0.017 sys 7.209 real
realign: 179 calls 0.667 user 0.000 sys 0.956 real
region: 367297 calls 4.333 user 0.065 sys 5.980 real
tracker: 367297 calls 0.762 user 0.146 sys 1.394 real
trim_region: 222 calls 0.000 user 0.000 sys 0.003 real
overall: 353566720 mem 233.869 user 18.970 sys 38.154 real