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/8f/e71429953647dce55f47702945295f/659_3g-T1-TDNA-1_B23KCHGLT4_1_vs_659_3g-N1-BDNA-1_B23MHTGLT4_1.manta_fusion.somatic_sv.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/ece895531ccd2291483dbd61736c7a/.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/8d/ece895531ccd2291483dbd61736c7a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/e71429953647dce55f47702945295f/659_3g-T1-TDNA-1_B23KCHGLT4_1_vs_659_3g-N1-BDNA-1_B23MHTGLT4_1.manta_fusion.somatic_sv.vcf.gz
==> 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 (['659_3g-N1-BDNA-1_B23MHTGLT4_1', '659_3g-T1-TDNA-1_B23KCHGLT4_1']) — falling back to positional heuristic (column 1). FUSION_TUMOR_VAF / FUSION_NORMAL_VAF may be incorrect.
[annotateFusionVcf] Done.