[2016-03-14 17:15:37] Beginning TopHat run (v2.0.14)
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[2016-03-14 17:15:37] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2016-03-14 17:15:37] Checking for Bowtie index files (genome)..
[2016-03-14 17:15:37] Checking for reference FASTA file
	Warning: Could not find FASTA file bowtie2-index/tomato_chr6.fa
[2016-03-14 17:15:37] Reconstituting reference FASTA file from Bowtie index
  Executing: /usr/local/bioinfo/bin/bowtie2-inspect bowtie2-index/tomato_chr6 > aln_tophat_wt/tmp/tomato_chr6.fa
[2016-03-14 17:15:43] Generating SAM header for bowtie2-index/tomato_chr6
[2016-03-14 17:15:50] Preparing reads
	 left reads: min. length=101, max. length=101, 1340546 kept reads (0 discarded)
	right reads: min. length=101, max. length=101, 1340463 kept reads (83 discarded)
[2016-03-14 17:16:54] Mapping left_kept_reads to genome tomato_chr6 with Bowtie2 
[2016-03-14 17:21:33] Mapping left_kept_reads_seg1 to genome tomato_chr6 with Bowtie2 (1/4)
[2016-03-14 17:22:17] Mapping left_kept_reads_seg2 to genome tomato_chr6 with Bowtie2 (2/4)
[2016-03-14 17:22:50] Mapping left_kept_reads_seg3 to genome tomato_chr6 with Bowtie2 (3/4)
[2016-03-14 17:23:23] Mapping left_kept_reads_seg4 to genome tomato_chr6 with Bowtie2 (4/4)
[2016-03-14 17:24:11] Mapping right_kept_reads to genome tomato_chr6 with Bowtie2 
[2016-03-14 17:28:26] Mapping right_kept_reads_seg1 to genome tomato_chr6 with Bowtie2 (1/4)
[2016-03-14 17:28:59] Mapping right_kept_reads_seg2 to genome tomato_chr6 with Bowtie2 (2/4)
[2016-03-14 17:29:34] Mapping right_kept_reads_seg3 to genome tomato_chr6 with Bowtie2 (3/4)
[2016-03-14 17:30:11] Mapping right_kept_reads_seg4 to genome tomato_chr6 with Bowtie2 (4/4)
[2016-03-14 17:31:02] Searching for junctions via segment mapping
[2016-03-14 17:32:43] Retrieving sequences for splices
[2016-03-14 17:32:45] Indexing splices
[2016-03-14 17:32:55] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2016-03-14 17:33:15] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2016-03-14 17:33:39] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2016-03-14 17:34:02] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2016-03-14 17:34:30] Joining segment hits
[2016-03-14 17:35:24] Mapping right_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2016-03-14 17:35:46] Mapping right_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2016-03-14 17:36:13] Mapping right_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2016-03-14 17:36:35] Mapping right_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2016-03-14 17:37:00] Joining segment hits
[2016-03-14 17:37:48] Reporting output tracks
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[2016-03-14 17:42:16] A summary of the alignment counts can be found in aln_tophat_wt/align_summary.txt
[2016-03-14 17:42:16] Run complete: 00:26:40 elapsed