[2019-04-29 17:13:29] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-04-29 17:13:29] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-29 17:13:31] Checking for Bowtie index files (genome)..
[2019-04-29 17:13:31] Checking for reference FASTA file
[2019-04-29 17:13:31] Generating SAM header for Bowtie2Index/genome
[2019-04-29 17:13:37] Reading known junctions from GTF file
[2019-04-29 17:13:41] Preparing reads
	 left reads: min. length=35, max. length=43, 5639912 kept reads (25072 discarded)
	right reads: min. length=35, max. length=43, 5640079 kept reads (24905 discarded)
[2019-04-29 17:18:43] Building transcriptome data files /scratch/5765348.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-29 17:19:03] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-29 17:27:45] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 17:31:06] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 17:35:03] 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
[2019-04-29 17:35:03] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 17:36:51] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 17:38:14] Searching for junctions via segment mapping
[2019-04-29 17:40:24] Retrieving sequences for splices
[2019-04-29 17:42:37] Indexing splices
Building a SMALL index
[2019-04-29 17:42:59] Mapping left_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie2 (1/1)
[2019-04-29 17:43:03] Joining segment hits
[2019-04-29 17:46:30] Mapping right_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie2 (1/1)
[2019-04-29 17:46:34] Joining segment hits
[2019-04-29 17:49:57] Reporting output tracks
-----------------------------------------------
[2019-04-29 17:59:02] A summary of the alignment counts can be found in /scratch/5765348.1.linga/tophat2/align_summary.txt
[2019-04-29 17:59:02] Run complete: 00:45:33 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 4 files...