[2018-05-13 12:13:11] Beginning TopHat run (v2.1.1)
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[2018-05-13 12:13:11] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-05-13 12:13:11] Checking for Bowtie index files (genome)..
[2018-05-13 12:13:11] Checking for reference FASTA file
[2018-05-13 12:13:11] Generating SAM header for Bowtie2Index/genome
[2018-05-13 12:13:14] Reading known junctions from GTF file
[2018-05-13 12:13:18] Preparing reads
	 left reads: min. length=33, max. length=33, 16901553 kept reads (7248 discarded)
[2018-05-13 12:16:35] Building transcriptome data files /scratch/6184261.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-05-13 12:16:54] Building Bowtie index from RefSeq_GeneBody.fa
[2018-05-13 12:24:34] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-05-13 12:50:26] 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 12:50:26] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-05-13 12:55:30] Searching for junctions via segment mapping
[2018-05-13 12:57:25] Retrieving sequences for splices
[2018-05-13 12:59:30] Indexing splices
Building a SMALL index
[2018-05-13 12:59:51] Mapping left_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie2 (1/1)
[2018-05-13 12:59:54] Joining segment hits
[2018-05-13 13:06:47] Reporting output tracks
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[2018-05-13 13:18:35] A summary of the alignment counts can be found in /scratch/6184261.1.linga/tophat2/align_summary.txt
[2018-05-13 13:18:35] Run complete: 01:05:24 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 3 files...