Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/dna_daq/stored-normals/reference-NA12878-downsampled-500k.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/dna_daq/stored-normals/reference-NA12878-downsampled-500k.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_padded_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity_padded100bp.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/5606fbb6c8bff9bc17b430929b15df/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/5e824146ba07eb6f65d51147020cd4/Sig_18_tissue.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/5e824146ba07eb6f65d51147020cd4/Sig_18_tissue.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/5606fbb6c8bff9bc17b430929b15df/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
==> STAGING COMPLETE (14 inputs)

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% @chr1:113705733, elapsed 1.2s, est remaining 22.5s, peak mem 148MB, user 10.7s, sys 0.6s, output queue size 5
progress 10% @chr2:3678368, elapsed 2.3s, est remaining 20.7s, peak mem 149MB, user 20.8s, sys 1.4s, output queue size 6
progress 15% @chr2:178609108, elapsed 3.5s, est remaining 20.0s, peak mem 151MB, user 31.4s, sys 2.0s, output queue size 12
progress 20% @chr3:57509040, elapsed 4.6s, est remaining 18.3s, peak mem 152MB, user 40.6s, sys 2.6s, output queue size 0
progress 25% @chr4:70603160, elapsed 5.7s, est remaining 17.2s, peak mem 152MB, user 50.9s, sys 3.3s, output queue size 9
progress 30% @chr5:135534877, elapsed 6.9s, est remaining 16.0s, peak mem 155MB, user 61.0s, sys 4.1s, output queue size 3
progress 35% @chr6:104849042, elapsed 8.0s, est remaining 14.9s, peak mem 157MB, user 70.6s, sys 4.9s, output queue size 3
progress 40% @chr7:106248199, elapsed 9.2s, est remaining 13.8s, peak mem 158MB, user 82.0s, sys 5.4s, output queue size 21
progress 45% @chr8:143835562, elapsed 10.4s, est remaining 12.7s, peak mem 159MB, user 93.0s, sys 6.0s, output queue size 3
progress 50% @chr10:21514996, elapsed 11.5s, est remaining 11.5s, peak mem 161MB, user 103.9s, sys 6.6s, output queue size 14
progress 55% @chr11:34135075, elapsed 12.7s, est remaining 10.4s, peak mem 162MB, user 114.6s, sys 7.1s, output queue size 0
progress 60% @chr12:12718707, elapsed 13.7s, est remaining 9.1s, peak mem 163MB, user 124.0s, sys 7.7s, output queue size 25
progress 65% @chr13:32078734, elapsed 14.9s, est remaining 8.0s, peak mem 163MB, user 134.1s, sys 8.4s, output queue size 10
progress 70% @chr15:35521993, elapsed 16.0s, est remaining 6.9s, peak mem 164MB, user 144.6s, sys 8.9s, output queue size 3
progress 75% @chr16:28486247, elapsed 17.1s, est remaining 5.7s, peak mem 165MB, user 154.8s, sys 9.5s, output queue size 4
progress 80% @chr17:40032956, elapsed 18.4s, est remaining 4.6s, peak mem 165MB, user 166.5s, sys 10.2s, output queue size 1
progress 85% @chr19:1809543, elapsed 19.5s, est remaining 3.4s, peak mem 165MB, user 176.1s, sys 10.9s, output queue size 3
progress 90% @chr19:54630974, elapsed 20.5s, est remaining 2.3s, peak mem 166MB, user 186.0s, sys 11.5s, output queue size 6
progress 95% @chr22:32081766, elapsed 23.4s, est remaining 1.2s, peak mem 363MB, user 212.1s, sys 12.5s, output queue size 10
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 24.4s, est remaining 0.0s, peak mem 363MB, user 221.2s, sys 13.2s, output queue size 421
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050654
  features: 1f8bfbff fffa3203
  extended: d19f47ab 00000018
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8175M CPU @ 2.50GHz
threads: 12 max 16
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 93248821
output file size: 53230
reads: 1502521
contig: 178193 intervals 76355618 bases
"assemble": 221 calls 0.756 user 0.017 sys 0.893 real
"assemble_addRead": 221 calls 0.040 user 0.020 sys 0.018 real
"assemble_buildGraph": 496 calls 0.336 user 0.016 sys 0.403 real
"assemble_computecigar": 329 calls 0.090 user 0.010 sys 0.145 real
"assemble_kg_build_calcsize": 496 calls 0.140 user 0.000 sys 0.183 real
"assemble_kg_build_clear": 650 calls 0.010 user 0.000 sys 0.017 real
"assemble_kg_build_prepare": 992 calls 0.149 user 0.001 sys 0.169 real
"assemble_kg_build_threading": 342 calls 0.186 user 0.006 sys 0.211 real
"assemble_kg_op1": 342 calls 0.094 user 0.000 sys 0.120 real
"assemble_kg_op2": 342 calls 0.000 user 0.000 sys 0.008 real
"assemble_kg_op3": 342 calls 0.010 user 0.000 sys 0.009 real
"assemble_sg_clean": 329 calls 0.040 user 0.000 sys 0.048 real
"assemble_sg_create": 329 calls 0.060 user 0.000 sys 0.071 real
"checkGraph": 221 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 221 calls 0.090 user 0.010 sys 0.152 real
advance: 189104 calls 23.923 user 0.617 sys 30.374 real
assemble_region: 221 calls 0.887 user 0.046 sys 1.066 real
build_pileup: 70986 calls 0.905 user 0.019 sys 1.049 real
build_stats: 71711 calls 4.050 user 0.112 sys 5.279 real
build_variants: 178 calls 0.000 user 0.000 sys 0.002 real
calc: 128717 calls 5.423 user 0.115 sys 7.520 real
calc_region: 178 calls 4.643 user 0.023 sys 4.684 real
call_region: 178 calls 0.090 user 0.000 sys 0.094 real
clip_region: 399 calls 0.089 user 0.000 sys 0.067 real
done: 1 calls 0.702 user 0.000 sys 0.708 real
execute: 1 calls 0.006 user 0.001 sys 24.438 real
fetch: 743546 calls 1.289 user 0.149 sys 1.736 real
fetch_ref: 745726 calls 3.124 user 0.566 sys 5.296 real
fetch_region: 221 calls 0.030 user 0.000 sys 0.014 real
fetch_vcf: 189104 calls 72.010 user 1.608 sys 97.141 real
idle: 35 calls 0.003 user 0.001 sys 13.384 real
init: 1 calls 0.070 user 0.020 sys 0.085 real
pairhmm: 837 calls 8.475 user 0.018 sys 8.399 real
realign: 178 calls 0.885 user 0.000 sys 0.872 real
region: 367297 calls 5.695 user 0.153 sys 6.044 real
tracker: 367297 calls 1.045 user 0.099 sys 1.386 real
trim_region: 221 calls 0.000 user 0.000 sys 0.003 real
overall: 381620224 mem 277.500 user 18.560 sys 25.863 real