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_Blood.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_Blood --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_2.tnseq.vcf.gz --algo OrientationBias --tumor_sample Sig_18_Blood negative_somatic_control_2.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample Sig_18_Blood --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments negative_somatic_control_2.tnseq.segments negative_somatic_control_2.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113705733, elapsed 1.0s, est remaining 19.4s, peak mem 117MB, user 8.5s, sys 0.7s, output queue size 4
progress 10% @chr2:3613211, elapsed 1.8s, est remaining 16.2s, peak mem 117MB, user 15.7s, sys 1.3s, output queue size 6
progress 15% @chr2:178588438, elapsed 2.6s, est remaining 14.6s, peak mem 117MB, user 22.8s, sys 2.0s, output queue size 9
progress 20% @chr3:57498400, elapsed 3.4s, est remaining 13.7s, peak mem 117MB, user 29.6s, sys 2.8s, output queue size 2
progress 25% @chr4:70530939, elapsed 4.2s, est remaining 12.7s, peak mem 117MB, user 37.1s, sys 3.3s, output queue size 8
progress 30% @chr5:135534877, elapsed 5.0s, est remaining 11.7s, peak mem 117MB, user 44.3s, sys 3.9s, output queue size 4
progress 35% @chr6:104957999, elapsed 5.7s, est remaining 10.6s, peak mem 117MB, user 50.9s, sys 4.4s, output queue size 3
progress 40% @chr7:106284249, elapsed 6.5s, est remaining 9.8s, peak mem 117MB, user 58.1s, sys 5.0s, output queue size 6
progress 45% @chr8:143820566, elapsed 7.3s, est remaining 8.9s, peak mem 117MB, user 65.5s, sys 5.6s, output queue size 1
progress 50% @chr10:21713672, elapsed 8.1s, est remaining 8.1s, peak mem 120MB, user 72.3s, sys 6.2s, output queue size 1
progress 55% @chr11:34124202, elapsed 8.9s, est remaining 7.3s, peak mem 120MB, user 79.3s, sys 6.8s, output queue size 5
progress 60% @chr12:12718707, elapsed 9.6s, est remaining 6.4s, peak mem 120MB, user 86.3s, sys 7.3s, output queue size 12
progress 65% @chr13:32149648, elapsed 10.4s, est remaining 5.6s, peak mem 120MB, user 93.3s, sys 7.8s, output queue size 0
progress 70% @chr15:35521993, elapsed 11.2s, est remaining 4.8s, peak mem 120MB, user 100.2s, sys 8.5s, output queue size 6
progress 75% @chr16:28486247, elapsed 11.9s, est remaining 4.0s, peak mem 120MB, user 107.1s, sys 9.1s, output queue size 4
progress 80% @chr17:40036016, elapsed 12.7s, est remaining 3.2s, peak mem 120MB, user 115.0s, sys 9.5s, output queue size 1
progress 85% @chr19:1796611, elapsed 13.5s, est remaining 2.4s, peak mem 120MB, user 122.5s, sys 10.0s, output queue size 3
progress 90% @chr19:54632364, elapsed 14.4s, est remaining 1.6s, peak mem 120MB, user 130.1s, sys 10.5s, output queue size 2
progress 95% @chr22:32081766, elapsed 16.1s, est remaining 0.8s, peak mem 270MB, user 146.9s, sys 11.2s, output queue size 5
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 16.9s, est remaining 0.0s, peak mem 270MB, user 153.5s, sys 11.7s, output queue size 419
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 74586806
output file size: 51111
reads: 1501816
contig: 178193 intervals 76355618 bases
"assemble": 189 calls 0.474 user 0.014 sys 0.494 real
"assemble_addRead": 189 calls 0.000 user 0.000 sys 0.008 real
"assemble_buildGraph": 446 calls 0.211 user 0.006 sys 0.217 real
"assemble_computecigar": 274 calls 0.068 user 0.000 sys 0.078 real
"assemble_kg_build_calcsize": 446 calls 0.101 user 0.006 sys 0.113 real
"assemble_kg_build_clear": 608 calls 0.010 user 0.000 sys 0.009 real
"assemble_kg_build_prepare": 892 calls 0.087 user 0.003 sys 0.108 real
"assemble_kg_build_threading": 284 calls 0.100 user 0.000 sys 0.098 real
"assemble_kg_op1": 284 calls 0.080 user 0.004 sys 0.062 real
"assemble_kg_op2": 284 calls 0.011 user 0.000 sys 0.005 real
"assemble_kg_op3": 284 calls 0.003 user 0.000 sys 0.005 real
"assemble_sg_clean": 274 calls 0.001 user 0.000 sys 0.023 real
"assemble_sg_create": 274 calls 0.057 user 0.000 sys 0.035 real
"checkGraph": 189 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 189 calls 0.068 user 0.000 sys 0.081 real
advance: 189104 calls 16.115 user 0.481 sys 22.280 real
assemble_region: 189 calls 0.542 user 0.014 sys 0.586 real
build_pileup: 70986 calls 0.494 user 0.016 sys 0.599 real
build_stats: 71708 calls 2.912 user 0.080 sys 2.802 real
build_variants: 158 calls 0.000 user 0.000 sys 0.001 real
calc: 128714 calls 2.255 user 0.090 sys 3.439 real
calc_region: 158 calls 1.793 user 0.003 sys 1.963 real
call_region: 158 calls 0.042 user 0.000 sys 0.044 real
clip_region: 347 calls 0.020 user 0.000 sys 0.038 real
done: 1 calls 0.429 user 0.000 sys 0.431 real
execute: 1 calls 0.002 user 0.011 sys 16.866 real
fetch: 743546 calls 1.047 user 0.056 sys 1.081 real
fetch_ref: 745694 calls 2.689 user 0.803 sys 3.495 real
fetch_region: 189 calls 0.010 user 0.000 sys 0.009 real
fetch_vcf: 189104 calls 43.365 user 1.510 sys 65.710 real
idle: 35 calls 0.001 user 0.001 sys 13.579 real
init: 1 calls 0.068 user 0.029 sys 0.091 real
pairhmm: 454 calls 2.779 user 0.014 sys 2.842 real
realign: 158 calls 0.344 user 0.000 sys 0.434 real
region: 367297 calls 2.385 user 0.040 sys 2.665 real
tracker: 367297 calls 0.357 user 0.078 sys 0.664 real
trim_region: 189 calls 0.001 user 0.000 sys 0.002 real
overall: 283238400 mem 183.102 user 16.935 sys 18.394 real