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% @chr1:113711646, elapsed 0.6s, est remaining 11.8s, peak mem 122MB, user 5.5s, sys 0.6s, output queue size 4
progress 10% @chr2:3671058, elapsed 1.2s, est remaining 10.8s, peak mem 122MB, user 10.8s, sys 0.9s, output queue size 5
progress 15% @chr2:178588438, elapsed 1.8s, est remaining 10.4s, peak mem 125MB, user 16.3s, sys 1.5s, output queue size 8
progress 20% @chr3:57483276, elapsed 2.4s, est remaining 9.7s, peak mem 125MB, user 21.5s, sys 2.0s, output queue size 0
progress 25% @chr4:70598256, elapsed 3.0s, est remaining 9.1s, peak mem 125MB, user 27.2s, sys 2.4s, output queue size 4
progress 30% @chr5:135873921, elapsed 3.7s, est remaining 8.7s, peak mem 128MB, user 32.9s, sys 3.0s, output queue size 4
progress 35% @chr6:104832942, elapsed 4.3s, est remaining 7.9s, peak mem 128MB, user 38.0s, sys 3.5s, output queue size 3
progress 40% @chr7:106284249, elapsed 4.9s, est remaining 7.3s, peak mem 128MB, user 43.5s, sys 4.0s, output queue size 14
progress 45% @chr8:143820566, elapsed 5.5s, est remaining 6.7s, peak mem 128MB, user 49.1s, sys 4.4s, output queue size 1
progress 50% @chr10:21726144, elapsed 6.1s, est remaining 6.1s, peak mem 131MB, user 54.6s, sys 4.8s, output queue size 1
progress 55% @chr11:34132025, elapsed 6.6s, est remaining 5.4s, peak mem 131MB, user 59.9s, sys 5.2s, output queue size 2
progress 60% @chr12:12718707, elapsed 7.2s, est remaining 4.8s, peak mem 131MB, user 64.8s, sys 5.7s, output queue size 9
progress 65% @chr13:32134804, elapsed 7.8s, est remaining 4.2s, peak mem 131MB, user 70.1s, sys 6.1s, output queue size 10
progress 70% @chr15:35521993, elapsed 8.4s, est remaining 3.6s, peak mem 131MB, user 75.4s, sys 6.5s, output queue size 4
progress 75% @chr16:28494582, elapsed 8.9s, est remaining 3.0s, peak mem 131MB, user 80.8s, sys 6.9s, output queue size 0
progress 80% @chr17:40076771, elapsed 9.6s, est remaining 2.4s, peak mem 131MB, user 86.6s, sys 7.3s, output queue size 3
progress 85% @chr19:1805788, elapsed 10.2s, est remaining 1.8s, peak mem 131MB, user 92.3s, sys 7.7s, output queue size 2
progress 90% @chr19:54630974, elapsed 10.8s, est remaining 1.2s, peak mem 131MB, user 97.9s, sys 7.9s, output queue size 4
progress 95% @chr22:31897382, elapsed 12.2s, est remaining 0.6s, peak mem 311MB, user 111.2s, sys 8.7s, output queue size 10
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 12.8s, est remaining 0.0s, peak mem 311MB, user 116.5s, sys 9.1s, output queue size 492
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  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 93248814
output file size: 53230
reads: 1502521
contig: 178193 intervals 76355618 bases
"assemble": 221 calls 0.408 user 0.005 sys 0.419 real
"assemble_addRead": 221 calls 0.000 user 0.006 sys 0.007 real
"assemble_buildGraph": 496 calls 0.120 user 0.004 sys 0.181 real
"assemble_computecigar": 329 calls 0.060 user 0.000 sys 0.065 real
"assemble_kg_build_calcsize": 496 calls 0.065 user 0.003 sys 0.087 real
"assemble_kg_build_clear": 650 calls 0.025 user 0.000 sys 0.007 real
"assemble_kg_build_prepare": 992 calls 0.071 user 0.001 sys 0.082 real
"assemble_kg_build_threading": 342 calls 0.055 user 0.001 sys 0.090 real
"assemble_kg_op1": 342 calls 0.122 user 0.000 sys 0.060 real
"assemble_kg_op2": 342 calls 0.000 user 0.000 sys 0.004 real
"assemble_kg_op3": 342 calls 0.000 user 0.000 sys 0.005 real
"assemble_sg_clean": 329 calls 0.056 user 0.000 sys 0.023 real
"assemble_sg_create": 329 calls 0.013 user 0.000 sys 0.034 real
"checkGraph": 221 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 221 calls 0.061 user 0.000 sys 0.068 real
advance: 189104 calls 11.523 user 0.481 sys 17.620 real
assemble_region: 221 calls 0.469 user 0.011 sys 0.496 real
build_pileup: 70986 calls 0.277 user 0.010 sys 0.394 real
build_stats: 71711 calls 2.500 user 0.142 sys 1.899 real
build_variants: 178 calls 0.000 user 0.000 sys 0.001 real
calc: 128717 calls 1.329 user 0.041 sys 2.362 real
calc_region: 178 calls 2.018 user 0.017 sys 2.071 real
call_region: 178 calls 0.058 user 0.000 sys 0.046 real
clip_region: 399 calls 0.035 user 0.002 sys 0.037 real
done: 1 calls 0.301 user 0.009 sys 0.311 real
execute: 1 calls 0.004 user 0.001 sys 12.809 real
fetch: 743546 calls 1.053 user 0.098 sys 0.757 real
fetch_ref: 745726 calls 1.185 user 0.527 sys 2.828 real
fetch_region: 221 calls 0.000 user 0.000 sys 0.007 real
fetch_vcf: 189104 calls 27.472 user 0.924 sys 50.279 real
idle: 35 calls 0.002 user 0.000 sys 12.728 real
init: 1 calls 0.040 user 0.010 sys 0.051 real
pairhmm: 837 calls 3.395 user 0.015 sys 3.431 real
realign: 178 calls 0.435 user 0.000 sys 0.480 real
region: 367297 calls 2.510 user 0.050 sys 2.653 real
tracker: 367297 calls 0.287 user 0.052 sys 0.450 real
trim_region: 221 calls 0.000 user 0.000 sys 0.002 real
overall: 326713344 mem 140.781 user 13.445 sys 14.106 real