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/9c/09b686503a4d5a651e9cd829726866/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/09b686503a4d5a651e9cd829726866/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/56621d824dd2d84a26a662511fff89/aih-tih-sc-a49d10-R1_B23WHYVLT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/56621d824dd2d84a26a662511fff89/aih-tih-sc-a49d10-R1_B23WHYVLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/6d7ca363a05a8bc1603d6c2c89591c/aih-tih-sc-a49d10-R1_B23WHYVLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.ZJ2IcX5BoS/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.ZJ2IcX5BoS/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.ZJ2IcX5BoS/./star-fusion.preliminary
-sample contains 295122042 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.ZJ2IcX5BoS/ctat_genome_lib_build_dir  -J /tmp/nxf.ZJ2IcX5BoS/aih-tih-sc-a49d10-R1_B23WHYVLT4_1.Chimeric.out.junction  -O /tmp/nxf.ZJ2IcX5BoS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.ZJ2IcX5BoS/aih-tih-sc-a49d10-R1_B23WHYVLT4_1.Chimeric.out.junction