[2016-04-07 16:52:45] Beginning TopHat run (v2.0.14)
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[2016-04-07 16:52:45] Checking for Bowtie
		  Bowtie version:	 2.2.5.0
[2016-04-07 16:52:46] Checking for Bowtie index files (genome)..
[2016-04-07 16:52:46] Checking for reference FASTA file
[2016-04-07 16:52:46] Generating SAM header for ../anno/genome
[2016-04-07 16:52:56] Reading known junctions from GTF file
[2016-04-07 16:53:03] Preparing reads
	 left reads: min. length=50, max. length=50, 31857188 kept reads (28402 discarded)
	right reads: min. length=50, max. length=50, 31847311 kept reads (38279 discarded)
[2016-04-07 17:02:05] Building transcriptome data files A6CO_13061_CAGATC/tmp/genes
[2016-04-07 17:02:23] Building Bowtie index from genes.fa
[2016-04-07 17:04:47] Mapping left_kept_reads to transcriptome genes with Bowtie2 
[2016-04-07 17:16:48] Mapping right_kept_reads to transcriptome genes with Bowtie2 
[2016-04-07 17:29:04] Resuming TopHat pipeline with unmapped reads
[2016-04-07 17:29:04] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2016-04-07 17:35:40] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2016-04-07 17:37:13] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2016-04-07 17:38:53] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2016-04-07 17:45:30] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2016-04-07 17:47:34] 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 18:16:24] Retrieving sequences for splices
[2016-04-07 18:18:06] Indexing splices
[2016-04-07 18:25:38] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2016-04-07 18:27:18] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2016-04-07 18:29:16] Joining segment hits
[2016-04-07 18:31:11] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2016-04-07 18:33:19] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2016-04-07 18:36:07] Joining segment hits
[2016-04-07 18:38:17] Reporting output tracks
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[2016-04-07 18:59:33] A summary of the alignment counts can be found in A6CO_13061_CAGATC/align_summary.txt
[2016-04-07 18:59:33] Run complete: 02:06:48 elapsed