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/58/bdee4b3239095e6081b7022694c96e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/f18a5b139b63b36f009877db350ae0/dna_s763_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/bdee4b3239095e6081b7022694c96e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/f18a5b139b63b36f009877db350ae0/dna_s763_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/a9cb9d9c67c57aa1c70d6d41eb7024/dna_s763.Chimeric.out.junction
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.ttcV39Xe0P/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.ttcV39Xe0P/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.ttcV39Xe0P/./star-fusion.preliminary
-sample contains 149617648 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.ttcV39Xe0P/ctat_genome_lib_build_dir  -J /tmp/nxf.ttcV39Xe0P/dna_s763.Chimeric.out.junction  -O /tmp/nxf.ttcV39Xe0P/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.ttcV39Xe0P/dna_s763.Chimeric.out.junction
-building interval tree based on /tmp/nxf.ttcV39Xe0P/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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[840000], rate=54961.83/min -building interval tree based on /tmp/nxf.ttcV39Xe0P/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

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