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/a2/229f2c83c12c992c172b2153a6837b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/229f2c83c12c992c172b2153a6837b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/db4a0c4c037910b4fdcbb09ccd8363/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/9fbeb399ad8501a1dfe1c2c262afd7/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/9fbeb399ad8501a1dfe1c2c262afd7/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.NvXdA0Nk0J/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.NvXdA0Nk0J/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.NvXdA0Nk0J/./star-fusion.preliminary
-sample contains 13685877 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.NvXdA0Nk0J/ctat_genome_lib_build_dir  -J /tmp/nxf.NvXdA0Nk0J/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction  -O /tmp/nxf.NvXdA0Nk0J/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.NvXdA0Nk0J/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction