[2016-04-07 16:54:47] Beginning TopHat run (v2.0.14)
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[2016-04-07 16:54:47] Checking for Bowtie
		  Bowtie version:	 2.2.5.0
[2016-04-07 16:54:47] Checking for Bowtie index files (genome)..
[2016-04-07 16:54:47] Checking for reference FASTA file
[2016-04-07 16:54:47] Generating SAM header for ../anno/genome
[2016-04-07 16:54:58] Reading known junctions from GTF file
[2016-04-07 16:55:04] Preparing reads
	 left reads: min. length=50, max. length=50, 33489937 kept reads (29611 discarded)
	right reads: min. length=50, max. length=50, 33480762 kept reads (38786 discarded)
[2016-04-07 17:04:45] Building transcriptome data files A8DE_13066_ATTCCT/tmp/genes
[2016-04-07 17:05:03] Building Bowtie index from genes.fa
[2016-04-07 17:07:26] Mapping left_kept_reads to transcriptome genes with Bowtie2 
[2016-04-07 17:21:35] Mapping right_kept_reads to transcriptome genes with Bowtie2 
[2016-04-07 17:35:42] Resuming TopHat pipeline with unmapped reads
[2016-04-07 17:35:42] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2016-04-07 17:40:31] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2016-04-07 17:41:13] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2016-04-07 17:41:53] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2016-04-07 17:46:08] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2016-04-07 17:46:55] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2016-04-07 17:47:39] Searching for junctions via segment mapping
[2016-04-07 18:03:13] Retrieving sequences for splices
[2016-04-07 18:04:50] Indexing splices
[2016-04-07 18:11:36] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2016-04-07 18:12:35] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2016-04-07 18:13:28] Joining segment hits
[2016-04-07 18:15:14] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2016-04-07 18:16:11] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2016-04-07 18:17:07] Joining segment hits
[2016-04-07 18:18:55] Reporting output tracks
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[2016-04-07 18:43:56] A summary of the alignment counts can be found in A8DE_13066_ATTCCT/align_summary.txt
[2016-04-07 18:43:56] Run complete: 01:49:09 elapsed