Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/3006ec1b3b7e0765e0ccf058eecbe8/aih-tih-sc-a3a521-R1_B23WHYVLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/c85ca183333d802a35c2ce3af97062/aih-tih-sc-a3a521-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/90/3006ec1b3b7e0765e0ccf058eecbe8/aih-tih-sc-a3a521-R1_B23WHYVLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/63d53160d5c5846463109a1372b1b1/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/63d53160d5c5846463109a1372b1b1/.command.run
==> STAGING COMPLETE (6 inputs)
-ctat genome lib [/tmp/nxf.cqAG4CNWIa/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.cqAG4CNWIa/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.cqAG4CNWIa/./star-fusion.preliminary
-sample contains 294969847 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.cqAG4CNWIa/ctat_genome_lib_build_dir -J /tmp/nxf.cqAG4CNWIa/aih-tih-sc-a3a521-R1_B23WHYVLT4_1.Chimeric.out.junction -O /tmp/nxf.cqAG4CNWIa/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.cqAG4CNWIa/aih-tih-sc-a3a521-R1_B23WHYVLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.cqAG4CNWIa/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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[2410000], rate=43164.18/min -building interval tree based on /tmp/nxf.cqAG4CNWIa/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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[2410000], rate=39944.75/min -building interval tree based on /tmp/nxf.cqAG4CNWIa/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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