Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/ec8732ea0ed0b9762962840c526ca4/RT4_FFPE_RNA_0001_B23LG7FLT4_3.Chimeric.out.junction
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/ecc0861bbf06d8cbfd0b1b13911d89/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/ecc0861bbf06d8cbfd0b1b13911d89/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/b4510de809756b64db798086196579/RT4_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/b4510de809756b64db798086196579/RT4_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.Ao3Kz9C99n/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.Ao3Kz9C99n/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.Ao3Kz9C99n/./star-fusion.preliminary
-sample contains 294496681 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.Ao3Kz9C99n/ctat_genome_lib_build_dir  -J /tmp/nxf.Ao3Kz9C99n/RT4_FFPE_RNA_0001_B23LG7FLT4_3.Chimeric.out.junction  -O /tmp/nxf.Ao3Kz9C99n/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.Ao3Kz9C99n/RT4_FFPE_RNA_0001_B23LG7FLT4_3.Chimeric.out.junction