[2016-04-07 16:52:40] Beginning TopHat run (v2.0.14)
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[2016-04-07 16:52:40] Checking for Bowtie
		  Bowtie version:	 2.2.5.0
[2016-04-07 16:52:40] Checking for Bowtie index files (genome)..
[2016-04-07 16:52:40] Checking for reference FASTA file
[2016-04-07 16:52:40] Generating SAM header for ../anno/genome
[2016-04-07 16:52:48] Reading known junctions from GTF file
[2016-04-07 16:52:55] Preparing reads
	 left reads: min. length=50, max. length=50, 34296765 kept reads (30334 discarded)
	right reads: min. length=50, max. length=50, 34287739 kept reads (39360 discarded)
[2016-04-07 17:03:21] Building transcriptome data files A6DE_13062_CCGTCC/tmp/genes
[2016-04-07 17:03:38] Building Bowtie index from genes.fa
[2016-04-07 17:05:48] Mapping left_kept_reads to transcriptome genes with Bowtie2 
[2016-04-07 17:19:32] Mapping right_kept_reads to transcriptome genes with Bowtie2 
[2016-04-07 17:33:15] Resuming TopHat pipeline with unmapped reads
[2016-04-07 17:33:16] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2016-04-07 17:38:12] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2016-04-07 17:39:04] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2016-04-07 17:39:53] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2016-04-07 17:44:33] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2016-04-07 17:45:37] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2016-04-07 17:46:40] Searching for junctions via segment mapping
[2016-04-07 18:08:04] Retrieving sequences for splices
[2016-04-07 18:09:48] Indexing splices
[2016-04-07 18:19:13] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2016-04-07 18:20:41] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2016-04-07 18:22:03] Joining segment hits
[2016-04-07 18:24:29] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2016-04-07 18:26:02] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2016-04-07 18:27:46] Joining segment hits
[2016-04-07 18:30:09] Reporting output tracks
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[2016-04-07 18:56:21] A summary of the alignment counts can be found in A6DE_13062_CCGTCC/align_summary.txt
[2016-04-07 18:56:21] Run complete: 02:03:41 elapsed