Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/MantaFusion/foresight_panel_for_manta.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/8120cacb902423f5536878d7b09099/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/MantaFusion/protein_coding_genes.bed
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/MantaFusion/model.pkl
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/273080a5ecb33307d3ba4eff54f940/659_csY-T1-TDNA-1_A23FG3YLT4_1_vs_659_csY-N1-BDNA-1_A23FG3YLT4_1.manta_fusion.somatic_sv.annotated.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/8120cacb902423f5536878d7b09099/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/273080a5ecb33307d3ba4eff54f940/659_csY-T1-TDNA-1_A23FG3YLT4_1_vs_659_csY-N1-BDNA-1_A23FG3YLT4_1.manta_fusion.somatic_sv.annotated.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/MantaFusion/cosmic_fusion.tsv.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/MantaFusion/pon
==> STAGING COMPLETE (9 inputs)

[predict] Loading model from model.pkl …
  36 features loaded
[predict] Loading PoN from pon …
  1D bins: 43,871  2D pairs: 39,238
[predict] Loading COSMIC from cosmic_fusion.tsv.gz …
  614 gene-pair orientations
[predict] Loading gene annotator from protein_coding_genes.bed …
[predict] Loading target panel from foresight_panel_for_manta.bed …
  201,779 panel intervals across 26 contigs
[predict] Tumor sample ID: '659_csY-T1-TDNA-1_A23FG3YLT4_1'  Normal sample ID: '659_csY-N1-BDNA-1_A23FG3YLT4_1'
[predict] Parsing VCF 659_csY-T1-TDNA-1_A23FG3YLT4_1_vs_659_csY-N1-BDNA-1_A23FG3YLT4_1.manta_fusion.somatic_sv.annotated.vcf.gz …
  98 calls parsed (after intergenic/same-gene/on_panel filter)
  32 killed by hard filters → 66 surviving
  is_paralog_of_higher_score_call=1 for 0/66 calls
[predict] Scored 66 calls: 22 PASS at threshold 0.15
  After events_match dedup: 37 calls (21 PASS)
  Final call set: 37 calls (21 PASS)
[predict] Writing 659_csY-T1-TDNA-1_A23FG3YLT4_1_vs_659_csY-N1-BDNA-1_A23FG3YLT4_1.manta_fusion.somatic_sv.scored.vcf.gz …
[predict] Writing 659_csY-T1-TDNA-1_A23FG3YLT4_1_vs_659_csY-N1-BDNA-1_A23FG3YLT4_1.manta_fusion.fusion_calls.tsv …
[predict] Done.