Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/afd9e5adf4029fe6dd9c25524bee53/aih-tih-sc-070e1d-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/5d/100e62abc0e9747d4ac0bbf7dd68c5/aih-tih-sc-070e1d-R1_B23WHYVLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/cfc56e726f37d7c576ed24c9a61616/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/cfc56e726f37d7c576ed24c9a61616/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/100e62abc0e9747d4ac0bbf7dd68c5/aih-tih-sc-070e1d-R1_B23WHYVLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
-ctat genome lib [/tmp/nxf.dGyJOHbUvY/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.dGyJOHbUvY/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.dGyJOHbUvY/./star-fusion.preliminary
-sample contains 276483938 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.dGyJOHbUvY/ctat_genome_lib_build_dir -J /tmp/nxf.dGyJOHbUvY/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.Chimeric.out.junction -O /tmp/nxf.dGyJOHbUvY/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.dGyJOHbUvY/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.dGyJOHbUvY/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
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-building interval tree based on /tmp/nxf.dGyJOHbUvY/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
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-building interval tree based on /tmp/nxf.dGyJOHbUvY/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
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