Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/61c72f74b3aacfc4b6c39c8be712c9/aih-tih-sc-522d83-R1_B23WHYVLT4_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/3f/58e1678fb32d6f717cbd7dbe4c9b41/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/58e1678fb32d6f717cbd7dbe4c9b41/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/61c72f74b3aacfc4b6c39c8be712c9/aih-tih-sc-522d83-R1_B23WHYVLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/78e926b96b2588440f4adffc6a8a11/aih-tih-sc-522d83-R1_B23WHYVLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.c2Wf9ChgxY/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.c2Wf9ChgxY/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.c2Wf9ChgxY/./star-fusion.preliminary
-sample contains 294514862 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.c2Wf9ChgxY/ctat_genome_lib_build_dir  -J /tmp/nxf.c2Wf9ChgxY/aih-tih-sc-522d83-R1_B23WHYVLT4_1.Chimeric.out.junction  -O /tmp/nxf.c2Wf9ChgxY/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.c2Wf9ChgxY/aih-tih-sc-522d83-R1_B23WHYVLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.c2Wf9ChgxY/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.12 min).
-mapping reads to genes

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