[2019-06-24 21:23:18] Beginning TopHat run (v2.1.1)
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[2019-06-24 21:23:18] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 21:23:18] Checking for Bowtie index files (genome)..
[2019-06-24 21:23:18] Checking for reference FASTA file
[2019-06-24 21:23:18] Generating SAM header for Bowtie2Index/genome
[2019-06-24 21:23:21] Reading known junctions from GTF file
[2019-06-24 21:23:24] Preparing reads
	 left reads: min. length=32, max. length=36, 13355729 kept reads (77135 discarded)
	right reads: min. length=32, max. length=36, 12996020 kept reads (436844 discarded)
[2019-06-24 21:28:35] Building transcriptome data files /scratch/7056804.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 21:28:50] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 21:34:45] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 21:38:46] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2