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/46/1f2e8948827d6364f3ed65a9cf09ba/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/38e039e8e18e618818086c0c2abc34/aih-tih-sc-446670-R1_B23WHYVLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/1f2e8948827d6364f3ed65a9cf09ba/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/38e039e8e18e618818086c0c2abc34/aih-tih-sc-446670-R1_B23WHYVLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/e95e58a1d4bce64d368d2c09cb7636/aih-tih-sc-446670-R1_B23WHYVLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (6 inputs)
-ctat genome lib [/tmp/nxf.ZKvbNRKf7e/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.ZKvbNRKf7e/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.ZKvbNRKf7e/./star-fusion.preliminary
-sample contains 222001508 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.ZKvbNRKf7e/ctat_genome_lib_build_dir -J /tmp/nxf.ZKvbNRKf7e/aih-tih-sc-446670-R1_B23WHYVLT4_1.Chimeric.out.junction -O /tmp/nxf.ZKvbNRKf7e/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.ZKvbNRKf7e/aih-tih-sc-446670-R1_B23WHYVLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.ZKvbNRKf7e/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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[1950000], rate=44184.29/min -building interval tree based on /tmp/nxf.ZKvbNRKf7e/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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[1950000], rate=42238.27/min -building interval tree based on /tmp/nxf.ZKvbNRKf7e/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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[1270000], rate=45931.28/min
[1280000], rate=46126.13/min
[1290000], rate=46264.20/min
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[1310000], rate=45724.26/min
[1320000], rate=45179.69/min
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[1440000], rate=38263.95/min
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[1470000], rate=37740.69/min
[1480000], rate=37643.07/min
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[1540000], rate=37408.91/min
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[1580000], rate=37485.17/min
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[1620000], rate=37442.22/min
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[1660000], rate=37684.45/min
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[1710000], rate=38112.93/min
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[1740000], rate=38410.60/min
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[1760000], rate=38512.04/min
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[1790000], rate=38716.65/min
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[1910000], rate=36932.00/min
[1920000], rate=36840.42/min
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[1940000], rate=36742.42/min