[2018-05-11 13:06:47] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-05-11 13:06:47] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-05-11 13:06:47] Checking for Bowtie index files (genome)..
[2018-05-11 13:06:47] Checking for reference FASTA file
[2018-05-11 13:06:47] Generating SAM header for Bowtie2Index/genome
[2018-05-11 13:06:49] Reading known junctions from GTF file
[2018-05-11 13:06:51] Preparing reads
	 left reads: min. length=33, max. length=33, 15583711 kept reads (7556 discarded)
[2018-05-11 13:09:01] Building transcriptome data files /scratch/6177253.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-05-11 13:09:10] Building Bowtie index from RefSeq_GeneBody.fa
[2018-05-11 13:14:03] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-05-11 13:17:44] 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
[2018-05-11 13:17:44] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-05-11 13:18:59] Searching for junctions via segment mapping
[2018-05-11 13:20:02] Retrieving sequences for splices
[2018-05-11 13:21:09] Indexing splices
Building a SMALL index
[2018-05-11 13:21:19] Mapping left_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie2 (1/1)
[2018-05-11 13:21:21] Joining segment hits
[2018-05-11 13:24:23] Reporting output tracks
-----------------------------------------------
[2018-05-11 13:28:32] A summary of the alignment counts can be found in /scratch/6177253.1.p8/tophat2/align_summary.txt
[2018-05-11 13:28:32] Run complete: 00:21:45 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 4 files...