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/01/9d9f2d79fef56ae93aa6f3406f2044/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/9d9f2d79fef56ae93aa6f3406f2044/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/938abe7f19a8b6af90edbca74e3d06/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/e35c7f0885f15376d1b8c37e635d7f/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/e35c7f0885f15376d1b8c37e635d7f/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.mlnM3yrIL4/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.mlnM3yrIL4/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.mlnM3yrIL4/./star-fusion.preliminary
-sample contains 193153107 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.mlnM3yrIL4/ctat_genome_lib_build_dir  -J /tmp/nxf.mlnM3yrIL4/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.Chimeric.out.junction  -O /tmp/nxf.mlnM3yrIL4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.mlnM3yrIL4/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.Chimeric.out.junction