Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/2c9dfb5f668afe393178fd797014f4/aih-tih-sc-c35cc3-R1_A23YTGFLT4_1_1.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/4a/2c9dfb5f668afe393178fd797014f4/aih-tih-sc-c35cc3-R1_A23YTGFLT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/7442c04f1418069db0f60d06d640b6/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/7442c04f1418069db0f60d06d640b6/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/3122602c176b1f7f7f007aecc2210b/aih-tih-sc-c35cc3-R1_A23YTGFLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.OBq4PHyrMH/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.OBq4PHyrMH/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.OBq4PHyrMH/./star-fusion.preliminary
-sample contains 250686040 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.OBq4PHyrMH/ctat_genome_lib_build_dir  -J /tmp/nxf.OBq4PHyrMH/aih-tih-sc-c35cc3-R1_A23YTGFLT4_1.Chimeric.out.junction  -O /tmp/nxf.OBq4PHyrMH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.OBq4PHyrMH/aih-tih-sc-c35cc3-R1_A23YTGFLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.OBq4PHyrMH/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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[2210000], rate=57179.82/min -building interval tree based on /tmp/nxf.OBq4PHyrMH/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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[2210000], rate=56666.67/min -building interval tree based on /tmp/nxf.OBq4PHyrMH/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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[2200000], rate=49162.01/min -building interval tree based on /tmp/nxf.OBq4PHyrMH/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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[2200000], rate=44325.05/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.OBq4PHyrMH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.OBq4PHyrMH/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.OBq4PHyrMH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.OBq4PHyrMH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.OBq4PHyrMH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

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