[2016-04-07 16:52:11] Beginning TopHat run (v2.0.14)
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[2016-04-07 16:52:11] Checking for Bowtie
		  Bowtie version:	 2.2.5.0
[2016-04-07 16:52:11] Checking for Bowtie index files (genome)..
[2016-04-07 16:52:11] Checking for reference FASTA file
[2016-04-07 16:52:11] Generating SAM header for ../anno/genome
[2016-04-07 16:52:36] Reading known junctions from GTF file
[2016-04-07 16:52:43] Preparing reads
	 left reads: min. length=50, max. length=50, 28864969 kept reads (25706 discarded)
	right reads: min. length=50, max. length=50, 28855610 kept reads (35065 discarded)
[2016-04-07 17:00:52] Building transcriptome data files A3CO_13059_CGATGT/tmp/genes
[2016-04-07 17:01:22] Building Bowtie index from genes.fa
[2016-04-07 17:03:46] Mapping left_kept_reads to transcriptome genes with Bowtie2 
[2016-04-07 17:14:24] Mapping right_kept_reads to transcriptome genes with Bowtie2 
[2016-04-07 17:25:25] Resuming TopHat pipeline with unmapped reads
[2016-04-07 17:25:25] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2016-04-07 17:29:51] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2016-04-07 17:30:47] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2016-04-07 17:31:42] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2016-04-07 17:35:46] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2016-04-07 17:36:40] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2016-04-07 17:37:33] Searching for junctions via segment mapping
[2016-04-07 17:51:50] Retrieving sequences for splices
[2016-04-07 17:53:24] Indexing splices
[2016-04-07 17:58:54] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2016-04-07 18:00:01] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2016-04-07 18:00:59] Joining segment hits
[2016-04-07 18:02:40] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2016-04-07 18:03:40] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2016-04-07 18:04:38] Joining segment hits
[2016-04-07 18:06:20] Reporting output tracks
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[2016-04-07 18:26:42] A summary of the alignment counts can be found in A3CO_13059_CGATGT/align_summary.txt
[2016-04-07 18:26:42] Run complete: 01:34:31 elapsed