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/c8/d496de8d3a5dd936e0b30cc528b0d4/.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-rnd-pltf-dev-nextflow-scratch-01/work/c8/d496de8d3a5dd936e0b30cc528b0d4/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/466dd7fa69e785d7453832220f228b/1173_PCB-T1-TDNA-01_B23MHVNLT4_1_vs_1173_PCB-N1-BDNA-02_A23MHW3LT4_1.manta_fusion.somatic_sv.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/466dd7fa69e785d7453832220f228b/1173_PCB-T1-TDNA-01_B23MHVNLT4_1_vs_1173_PCB-N1-BDNA-02_A23MHW3LT4_1.manta_fusion.somatic_sv.vcf.gz.tbi
==> STAGING COMPLETE (6 inputs)

[annotateFusionVcf] Loading gene BED: protein_coding_genes.bed
[annotateFusionVcf] Loading actionable BED: foresight_panel_for_manta.bed
[annotateFusionVcf] Annotating VCF...
[annotateFusionVcf] WARNING: could not identify tumor sample by name (['1173_PCB-N1-BDNA-02_A23MHW3LT4_1', '1173_PCB-T1-TDNA-01_B23MHVNLT4_1']) — falling back to positional heuristic (column 1). FUSION_TUMOR_VAF / FUSION_NORMAL_VAF may be incorrect.
[annotateFusionVcf] Done.