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/24/6c24f450d64421a9f5be68a1229b89/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/6c24f450d64421a9f5be68a1229b89/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/21d4bf98653f54f2a6e87973fd4b81/aih-tih-sc-3e91d2-R1_B23WHYVLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/4d7d5db6c134add7930cd84e61b6f2/aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/21d4bf98653f54f2a6e87973fd4b81/aih-tih-sc-3e91d2-R1_B23WHYVLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.3GYIMc1UCq/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.3GYIMc1UCq/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.3GYIMc1UCq/./star-fusion.preliminary
-sample contains 295193843 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.3GYIMc1UCq/ctat_genome_lib_build_dir  -J /tmp/nxf.3GYIMc1UCq/aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.Chimeric.out.junction  -O /tmp/nxf.3GYIMc1UCq/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.3GYIMc1UCq/aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.3GYIMc1UCq/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

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