[2016-04-07 16:52:41] Beginning TopHat run (v2.0.14)
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[2016-04-07 16:52:41] Checking for Bowtie
		  Bowtie version:	 2.2.5.0
[2016-04-07 16:52:41] Checking for Bowtie index files (genome)..
[2016-04-07 16:52:41] Checking for reference FASTA file
[2016-04-07 16:52:41] Generating SAM header for ../anno/genome
[2016-04-07 16:53:00] Reading known junctions from GTF file
[2016-04-07 16:53:06] Preparing reads
	 left reads: min. length=50, max. length=50, 35428086 kept reads (31902 discarded)
	right reads: min. length=50, max. length=50, 35417903 kept reads (42085 discarded)
[2016-04-07 17:03:14] Building transcriptome data files A3DE_13060_TGACCA/tmp/genes
[2016-04-07 17:03:30] Building Bowtie index from genes.fa
[2016-04-07 17:05:54] Mapping left_kept_reads to transcriptome genes with Bowtie2 
[2016-04-07 17:20:47] Mapping right_kept_reads to transcriptome genes with Bowtie2 
[2016-04-07 17:35:46] Resuming TopHat pipeline with unmapped reads
[2016-04-07 17:35:46] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2016-04-07 17:41:11] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2016-04-07 17:42:11] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2016-04-07 17:43:03] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2016-04-07 17:47:51] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2016-04-07 17:48:48] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2016-04-07 17:49:40] Searching for junctions via segment mapping
[2016-04-07 18:06:23] Retrieving sequences for splices
[2016-04-07 18:08:06] Indexing splices
[2016-04-07 18:15:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2016-04-07 18:16:38] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2016-04-07 18:17:42] Joining segment hits
[2016-04-07 18:19:33] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2016-04-07 18:20:36] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2016-04-07 18:21:37] Joining segment hits
[2016-04-07 18:23:26] Reporting output tracks
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[2016-04-07 18:50:08] A summary of the alignment counts can be found in A3DE_13060_TGACCA/align_summary.txt
[2016-04-07 18:50:08] Run complete: 01:57:27 elapsed