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% @chr1:113711646, elapsed 0.8s, est remaining 15.8s, peak mem 123MB, user 8.0s, sys 0.4s, output queue size 5
progress 10% @chr2:3671058, elapsed 1.6s, est remaining 14.1s, peak mem 123MB, user 15.0s, sys 1.0s, output queue size 5
progress 15% @chr2:178588438, elapsed 2.3s, est remaining 13.3s, peak mem 123MB, user 22.2s, sys 1.7s, output queue size 11
progress 20% @chr3:57509040, elapsed 3.1s, est remaining 12.4s, peak mem 123MB, user 28.6s, sys 2.4s, output queue size 2
progress 25% @chr4:70632551, elapsed 3.8s, est remaining 11.5s, peak mem 123MB, user 35.3s, sys 2.9s, output queue size 9
progress 30% @chr5:135534877, elapsed 4.6s, est remaining 10.7s, peak mem 123MB, user 42.1s, sys 3.4s, output queue size 3
progress 35% @chr6:104957151, elapsed 5.2s, est remaining 9.7s, peak mem 123MB, user 47.9s, sys 3.9s, output queue size 6
progress 40% @chr7:106248199, elapsed 5.9s, est remaining 8.9s, peak mem 123MB, user 54.6s, sys 4.3s, output queue size 16
progress 45% @chr8:143820566, elapsed 6.7s, est remaining 8.1s, peak mem 123MB, user 61.7s, sys 4.8s, output queue size 1
progress 50% @chr10:21726144, elapsed 7.5s, est remaining 7.5s, peak mem 123MB, user 69.1s, sys 5.3s, output queue size 1
progress 55% @chr11:34124202, elapsed 8.3s, est remaining 6.8s, peak mem 123MB, user 76.3s, sys 5.8s, output queue size 5
progress 60% @chr12:12718707, elapsed 9.0s, est remaining 6.0s, peak mem 123MB, user 82.7s, sys 6.4s, output queue size 14
progress 65% @chr13:32136771, elapsed 9.7s, est remaining 5.2s, peak mem 123MB, user 89.8s, sys 6.8s, output queue size 3
progress 70% @chr15:35538174, elapsed 10.4s, est remaining 4.5s, peak mem 123MB, user 96.7s, sys 7.3s, output queue size 2
progress 75% @chr16:28494582, elapsed 11.2s, est remaining 3.7s, peak mem 123MB, user 103.1s, sys 7.8s, output queue size 0
progress 80% @chr17:40034816, elapsed 11.9s, est remaining 3.0s, peak mem 123MB, user 109.7s, sys 8.3s, output queue size 1
progress 85% @chr19:1806528, elapsed 12.5s, est remaining 2.2s, peak mem 123MB, user 116.1s, sys 8.8s, output queue size 3
progress 90% @chr19:54630974, elapsed 13.2s, est remaining 1.5s, peak mem 123MB, user 122.6s, sys 9.3s, output queue size 3
progress 95% @chr22:32043182, elapsed 14.8s, est remaining 0.8s, peak mem 291MB, user 137.8s, sys 10.1s, output queue size 10
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 15.4s, est remaining 0.0s, peak mem 291MB, user 143.9s, sys 10.6s, output queue size 416
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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 384
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 71692769
output file size: 46614
reads: 1501772
contig: 178193 intervals 76355618 bases
"assemble": 183 calls 0.401 user 0.009 sys 0.426 real
"assemble_addRead": 183 calls 0.001 user 0.000 sys 0.007 real
"assemble_buildGraph": 422 calls 0.131 user 0.007 sys 0.182 real
"assemble_computecigar": 264 calls 0.045 user 0.000 sys 0.076 real
"assemble_kg_build_calcsize": 422 calls 0.081 user 0.000 sys 0.093 real
"assemble_kg_build_clear": 573 calls 0.003 user 0.000 sys 0.008 real
"assemble_kg_build_prepare": 844 calls 0.109 user 0.000 sys 0.091 real
"assemble_kg_build_threading": 271 calls 0.047 user 0.007 sys 0.084 real
"assemble_kg_op1": 271 calls 0.027 user 0.000 sys 0.055 real
"assemble_kg_op2": 271 calls 0.004 user 0.000 sys 0.004 real
"assemble_kg_op3": 271 calls 0.000 user 0.000 sys 0.005 real
"assemble_sg_clean": 264 calls 0.015 user 0.000 sys 0.021 real
"assemble_sg_create": 264 calls 0.047 user 0.002 sys 0.032 real
"checkGraph": 183 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 183 calls 0.055 user 0.000 sys 0.080 real
advance: 189104 calls 13.187 user 0.556 sys 20.660 real
assemble_region: 183 calls 0.457 user 0.009 sys 0.515 real
build_pileup: 70974 calls 0.274 user 0.015 sys 0.494 real
build_stats: 71688 calls 2.945 user 0.100 sys 2.428 real
build_variants: 142 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 2.293 user 0.059 sys 3.052 real
calc_region: 142 calls 1.799 user 0.011 sys 1.900 real
call_region: 142 calls 0.041 user 0.000 sys 0.036 real
clip_region: 325 calls 0.050 user 0.000 sys 0.029 real
done: 1 calls 0.480 user 0.000 sys 0.480 real
execute: 1 calls 0.005 user 0.002 sys 15.418 real
fetch: 743546 calls 1.203 user 0.089 sys 0.934 real
fetch_ref: 745688 calls 1.709 user 0.528 sys 3.094 real
fetch_region: 183 calls 0.010 user 0.000 sys 0.007 real
fetch_vcf: 189104 calls 36.800 user 1.090 sys 61.373 real
idle: 35 calls 0.003 user 0.005 sys 12.858 real
init: 1 calls 0.060 user 0.000 sys 0.058 real
pairhmm: 472 calls 2.611 user 0.029 sys 2.836 real
realign: 142 calls 0.238 user 0.000 sys 0.305 real
region: 367297 calls 2.299 user 0.048 sys 2.517 real
tracker: 367297 calls 0.333 user 0.047 sys 0.579 real
trim_region: 183 calls 0.000 user 0.000 sys 0.002 real
overall: 305270784 mem 169.064 user 15.756 sys 16.737 real