[2018-05-13 12:13:15] Beginning TopHat run (v2.1.1)
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[2018-05-13 12:13:15] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-05-13 12:13:15] Checking for Bowtie index files (genome)..
[2018-05-13 12:13:15] Checking for reference FASTA file
[2018-05-13 12:13:15] Generating SAM header for Bowtie2Index/genome
[2018-05-13 12:13:21] Reading known junctions from GTF file
[2018-05-13 12:13:27] Preparing reads
	 left reads: min. length=33, max. length=33, 14887142 kept reads (6740 discarded)
[2018-05-13 12:16:51] Building transcriptome data files /scratch/6184254.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-05-13 12:17:16] Building Bowtie index from RefSeq_GeneBody.fa
[2018-05-13 12:27:37] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-05-13 12:35:31] Resuming TopHat pipeline with unmapped reads
Warning: you have only one segment per read.
	If the read length is greater than or equal to 45bp,
	we strongly recommend that you decrease --segment-length to about half the read length because TopHat will work better with multiple segments
[2018-05-13 12:35:31] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-05-13 12:40:05] Searching for junctions via segment mapping
[2018-05-13 12:42:13] Retrieving sequences for splices
[2018-05-13 12:44:24] Indexing splices
Building a SMALL index
[2018-05-13 12:44:46] Mapping left_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie2 (1/1)
[2018-05-13 12:44:49] Joining segment hits
[2018-05-13 12:52:02] Reporting output tracks
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[2018-05-13 12:59:34] A summary of the alignment counts can be found in /scratch/6184254.1.linga/tophat2/align_summary.txt
[2018-05-13 12:59:34] Run complete: 00:46:19 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 4 files...