Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/0ea271aced377f5c45034c38f825d1/HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz
  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/17/9b4f4d0d2440914bb1306fc1316719/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/9b4f4d0d2440914bb1306fc1316719/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/0ea271aced377f5c45034c38f825d1/HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/e5962f723520d871d112f3d8bb3238/HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.bnyI9uLbYq/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.bnyI9uLbYq/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.bnyI9uLbYq/./star-fusion.preliminary
-sample contains 68408748 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.bnyI9uLbYq/ctat_genome_lib_build_dir  -J /tmp/nxf.bnyI9uLbYq/HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1.Chimeric.out.junction  -O /tmp/nxf.bnyI9uLbYq/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.bnyI9uLbYq/HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1.Chimeric.out.junction