[2018-05-09 17:04:53] Beginning TopHat run (v2.1.1)
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[2018-05-09 17:04:53] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-05-09 17:04:53] Checking for Bowtie index files (genome)..
[2018-05-09 17:04:53] Checking for reference FASTA file
[2018-05-09 17:04:53] Generating SAM header for Bowtie2Index/genome
[2018-05-09 17:04:57] Reading known junctions from GTF file
[2018-05-09 17:05:01] Preparing reads
	 left reads: min. length=33, max. length=33, 18184516 kept reads (40189 discarded)
[2018-05-09 17:08:46] Building transcriptome data files /scratch/6136169.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-05-09 17:09:05] Building Bowtie index from RefSeq_GeneBody.fa
[2018-05-09 17:17:36] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-05-09 17:38:56] 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
[2018-05-09 17:38:56] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-05-09 17:43:51] Searching for junctions via segment mapping
[2018-05-09 17:45:51] Retrieving sequences for splices
[2018-05-09 17:47:51] Indexing splices
Building a SMALL index
[2018-05-09 17:48:08] Mapping left_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie2 (1/1)
[2018-05-09 17:48:12] Joining segment hits
[2018-05-09 17:55:23] Reporting output tracks
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[2018-05-09 18:05:54] A summary of the alignment counts can be found in /scratch/6136169.1.linga/tophat2/align_summary.txt
[2018-05-09 18:05:54] Run complete: 01:01:00 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 4 files...