[2016-04-07 16:53:09] Beginning TopHat run (v2.0.14)
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[2016-04-07 16:53:09] Checking for Bowtie
		  Bowtie version:	 2.2.5.0
[2016-04-07 16:53:10] Checking for Bowtie index files (genome)..
[2016-04-07 16:53:10] Checking for reference FASTA file
[2016-04-07 16:53:10] Generating SAM header for ../anno/genome
[2016-04-07 16:53:20] Reading known junctions from GTF file
[2016-04-07 16:53:27] Preparing reads
	 left reads: min. length=50, max. length=50, 33294650 kept reads (30187 discarded)
	right reads: min. length=50, max. length=50, 33284714 kept reads (40123 discarded)
[2016-04-07 17:03:04] Building transcriptome data files A7DE_13064_GATCAG/tmp/genes
[2016-04-07 17:03:23] Building Bowtie index from genes.fa
[2016-04-07 17:05:33] Mapping left_kept_reads to transcriptome genes with Bowtie2 
[2016-04-07 17:18:25] Mapping right_kept_reads to transcriptome genes with Bowtie2 
[2016-04-07 17:31:40] Resuming TopHat pipeline with unmapped reads
[2016-04-07 17:31:41] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2016-04-07 17:36:07] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2016-04-07 17:36:58] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2016-04-07 17:37:45] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2016-04-07 17:41:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2016-04-07 17:42:51] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2016-04-07 17:43:42] Searching for junctions via segment mapping
[2016-04-07 18:00:58] Retrieving sequences for splices
[2016-04-07 18:02:41] Indexing splices
[2016-04-07 18:12:02] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2016-04-07 18:13:39] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2016-04-07 18:14:59] Joining segment hits
[2016-04-07 18:17:16] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2016-04-07 18:18:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2016-04-07 18:20:07] Joining segment hits
[2016-04-07 18:22:24] Reporting output tracks
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[2016-04-07 18:47:22] A summary of the alignment counts can be found in A7DE_13064_GATCAG/align_summary.txt
[2016-04-07 18:47:22] Run complete: 01:54:12 elapsed