Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/d53752eec1705ef1e2b3a42e2ba1e8/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/e6264cb7b8d1033447aa12304f4c8d/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.Chimeric.out.junction
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/10/9a13a43b9c2da1f48b5eb11d38ee82/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/9a13a43b9c2da1f48b5eb11d38ee82/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/d53752eec1705ef1e2b3a42e2ba1e8/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
-ctat genome lib [/tmp/nxf.iJTxWVSnCM/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.iJTxWVSnCM/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.iJTxWVSnCM/./star-fusion.preliminary
-sample contains 295205705 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.iJTxWVSnCM/ctat_genome_lib_build_dir -J /tmp/nxf.iJTxWVSnCM/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.Chimeric.out.junction -O /tmp/nxf.iJTxWVSnCM/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.iJTxWVSnCM/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.iJTxWVSnCM/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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[2490000], rate=51322.57/min -building interval tree based on /tmp/nxf.iJTxWVSnCM/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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