Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/fe6be0afd233563a374fa5f66e9f3b/ColoN_FFPE_L08_RNA_01_B23LG7FLT4_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/66/36817c11d86294b6f21a9400c73534/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/36817c11d86294b6f21a9400c73534/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/fe6be0afd233563a374fa5f66e9f3b/ColoN_FFPE_L08_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/79d41d845d919e12d76bc84f4807d2/ColoN_FFPE_L08_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (6 inputs)
-ctat genome lib [/tmp/nxf.NMS43luF0E/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.NMS43luF0E/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.NMS43luF0E/./star-fusion.preliminary
-sample contains 108305891 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.NMS43luF0E/ctat_genome_lib_build_dir -J /tmp/nxf.NMS43luF0E/ColoN_FFPE_L08_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.NMS43luF0E/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.NMS43luF0E/ColoN_FFPE_L08_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.NMS43luF0E/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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[1590000], rate=71353.78/min -building interval tree based on /tmp/nxf.NMS43luF0E/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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[1580000], rate=69603.52/min -building interval tree based on /tmp/nxf.NMS43luF0E/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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