[2016-03-14 17:15:56] Beginning TopHat run (v2.0.14)
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[2016-03-14 17:15:56] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2016-03-14 17:15:56] Checking for Bowtie index files (genome)..
[2016-03-14 17:15:56] Checking for reference FASTA file
	Warning: Could not find FASTA file bowtie2-index/tomato_chr6.fa
[2016-03-14 17:15:56] Reconstituting reference FASTA file from Bowtie index
  Executing: /usr/local/bioinfo/bin/bowtie2-inspect bowtie2-index/tomato_chr6 > aln_tophat_mt/tmp/tomato_chr6.fa
[2016-03-14 17:16:01] Generating SAM header for bowtie2-index/tomato_chr6
[2016-03-14 17:16:02] Preparing reads
	 left reads: min. length=101, max. length=101, 1624611 kept reads (2 discarded)
	right reads: min. length=101, max. length=101, 1624533 kept reads (80 discarded)
[2016-03-14 17:17:18] Mapping left_kept_reads to genome tomato_chr6 with Bowtie2 
[2016-03-14 17:22:30] Mapping left_kept_reads_seg1 to genome tomato_chr6 with Bowtie2 (1/4)
[2016-03-14 17:23:04] Mapping left_kept_reads_seg2 to genome tomato_chr6 with Bowtie2 (2/4)
[2016-03-14 17:23:46] Mapping left_kept_reads_seg3 to genome tomato_chr6 with Bowtie2 (3/4)
[2016-03-14 17:24:18] Mapping left_kept_reads_seg4 to genome tomato_chr6 with Bowtie2 (4/4)
[2016-03-14 17:25:16] Mapping right_kept_reads to genome tomato_chr6 with Bowtie2 
[2016-03-14 17:30:33] Mapping right_kept_reads_seg1 to genome tomato_chr6 with Bowtie2 (1/4)
[2016-03-14 17:31:16] Mapping right_kept_reads_seg2 to genome tomato_chr6 with Bowtie2 (2/4)
[2016-03-14 17:31:54] Mapping right_kept_reads_seg3 to genome tomato_chr6 with Bowtie2 (3/4)
[2016-03-14 17:32:33] Mapping right_kept_reads_seg4 to genome tomato_chr6 with Bowtie2 (4/4)
[2016-03-14 17:33:36] Searching for junctions via segment mapping
[2016-03-14 17:35:36] Retrieving sequences for splices
[2016-03-14 17:35:38] Indexing splices
[2016-03-14 17:35:49] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2016-03-14 17:36:17] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2016-03-14 17:36:43] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2016-03-14 17:37:09] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2016-03-14 17:37:42] Joining segment hits
[2016-03-14 17:38:47] Mapping right_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2016-03-14 17:39:12] Mapping right_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2016-03-14 17:39:42] Mapping right_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2016-03-14 17:40:08] Mapping right_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2016-03-14 17:40:42] Joining segment hits
[2016-03-14 17:41:45] Reporting output tracks
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[2016-03-14 17:47:27] A summary of the alignment counts can be found in aln_tophat_mt/align_summary.txt
[2016-03-14 17:47:27] Run complete: 00:31:31 elapsed