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 1.4s, est remaining 27.1s, peak mem 129MB, user 9.7s, sys 1.8s, output queue size 53
progress 10% @chr2:3643344, elapsed 2.7s, est remaining 24.5s, peak mem 129MB, user 19.3s, sys 3.3s, output queue size 6
progress 15% @chr2:178609108, elapsed 3.9s, est remaining 22.4s, peak mem 132MB, user 28.9s, sys 5.1s, output queue size 12
progress 20% @chr3:57508282, elapsed 5.2s, est remaining 20.9s, peak mem 132MB, user 37.9s, sys 6.5s, output queue size 92
progress 25% @chr4:70248898, elapsed 6.6s, est remaining 19.7s, peak mem 132MB, user 47.5s, sys 8.2s, output queue size 1299
progress 30% @chr5:135534877, elapsed 8.1s, est remaining 18.9s, peak mem 132MB, user 57.0s, sys 10.2s, output queue size 3141
progress 35% @chr6:104859467, elapsed 9.3s, est remaining 17.2s, peak mem 132MB, user 65.7s, sys 11.8s, output queue size 3622
progress 40% @chr7:106248199, elapsed 10.6s, est remaining 15.9s, peak mem 132MB, user 75.1s, sys 13.3s, output queue size 3128
progress 45% @chr8:143821497, elapsed 11.8s, est remaining 14.4s, peak mem 132MB, user 84.3s, sys 14.6s, output queue size 228
progress 50% @chr10:21726144, elapsed 13.0s, est remaining 13.0s, peak mem 135MB, user 93.8s, sys 15.8s, output queue size 2
progress 55% @chr11:34132926, elapsed 14.2s, est remaining 11.6s, peak mem 135MB, user 103.2s, sys 17.0s, output queue size 29
progress 60% @chr12:12718707, elapsed 15.3s, est remaining 10.2s, peak mem 135MB, user 111.9s, sys 18.3s, output queue size 11
progress 65% @chr13:32149648, elapsed 16.5s, est remaining 8.9s, peak mem 135MB, user 121.0s, sys 19.6s, output queue size 87
progress 70% @chr15:35381722, elapsed 17.5s, est remaining 7.5s, peak mem 135MB, user 130.0s, sys 20.6s, output queue size 4
progress 75% @chr16:28403418, elapsed 18.6s, est remaining 6.2s, peak mem 135MB, user 138.9s, sys 21.7s, output queue size 13
progress 80% @chr17:40034816, elapsed 19.8s, est remaining 5.0s, peak mem 135MB, user 148.4s, sys 23.1s, output queue size 5
progress 85% @chr19:1805788, elapsed 21.0s, est remaining 3.7s, peak mem 135MB, user 157.7s, sys 24.3s, output queue size 2
progress 90% @chr19:54630974, elapsed 22.2s, est remaining 2.5s, peak mem 135MB, user 167.2s, sys 25.6s, output queue size 3
progress 95% @chr22:31897382, elapsed 24.5s, est remaining 1.3s, peak mem 291MB, user 189.1s, sys 27.1s, output queue size 10
progress 100% @chr6_GL000251v2_alt:3936344, elapsed 25.6s, est remaining 0.0s, peak mem 291MB, user 197.9s, sys 28.4s, output queue size 175
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 384
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 71343278
output file size: 46613
reads: 1501772
contig: 178193 intervals 76355618 bases
"assemble": 183 calls 0.690 user 0.003 sys 0.610 real
"assemble_addRead": 183 calls 0.000 user 0.000 sys 0.010 real
"assemble_buildGraph": 422 calls 0.338 user 0.001 sys 0.271 real
"assemble_computecigar": 264 calls 0.098 user 0.018 sys 0.116 real
"assemble_kg_build_calcsize": 422 calls 0.205 user 0.001 sys 0.139 real
"assemble_kg_build_clear": 573 calls 0.015 user 0.000 sys 0.010 real
"assemble_kg_build_prepare": 844 calls 0.096 user 0.000 sys 0.120 real
"assemble_kg_build_threading": 271 calls 0.134 user 0.000 sys 0.125 real
"assemble_kg_op1": 271 calls 0.064 user 0.001 sys 0.076 real
"assemble_kg_op2": 271 calls 0.000 user 0.000 sys 0.006 real
"assemble_kg_op3": 271 calls 0.000 user 0.000 sys 0.006 real
"assemble_sg_clean": 264 calls 0.050 user 0.000 sys 0.033 real
"assemble_sg_create": 264 calls 0.040 user 0.000 sys 0.048 real
"checkGraph": 183 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 183 calls 0.098 user 0.018 sys 0.121 real
advance: 189104 calls 16.474 user 0.806 sys 29.036 real
assemble_region: 183 calls 0.798 user 0.021 sys 0.745 real
build_pileup: 70974 calls 0.670 user 0.036 sys 1.025 real
build_stats: 71688 calls 4.208 user 0.351 sys 4.488 real
build_variants: 142 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 2.810 user 0.188 sys 4.863 real
calc_region: 142 calls 2.291 user 0.023 sys 2.462 real
call_region: 142 calls 0.029 user 0.000 sys 0.056 real
clip_region: 325 calls 0.042 user 0.000 sys 0.042 real
done: 1 calls 0.656 user 0.000 sys 0.660 real
execute: 1 calls 0.006 user 0.002 sys 25.664 real
fetch: 743546 calls 1.245 user 0.102 sys 1.585 real
fetch_ref: 745688 calls 1.493 user 0.731 sys 4.694 real
fetch_region: 183 calls 0.000 user 0.000 sys 0.011 real
fetch_vcf: 189104 calls 43.815 user 2.516 sys 84.676 real
idle: 35 calls 0.002 user 0.000 sys 13.447 real
init: 1 calls 0.061 user 0.030 sys 0.089 real
pairhmm: 472 calls 4.067 user 0.011 sys 4.168 real
realign: 142 calls 0.368 user 0.000 sys 0.388 real
region: 367297 calls 3.152 user 0.106 sys 3.369 real
tracker: 367297 calls 0.526 user 0.119 sys 1.060 real
trim_region: 183 calls 0.000 user 0.000 sys 0.002 real
overall: 305242112 mem 241.679 user 43.337 sys 27.196 real