[2016-04-07 16:54:11] Beginning TopHat run (v2.0.14)
-----------------------------------------------
[2016-04-07 16:54:11] Checking for Bowtie
		  Bowtie version:	 2.2.5.0
[2016-04-07 16:54:11] Checking for Bowtie index files (genome)..
[2016-04-07 16:54:11] Checking for reference FASTA file
[2016-04-07 16:54:11] Generating SAM header for ../anno/genome
[2016-04-07 16:54:21] Reading known junctions from GTF file
[2016-04-07 16:54:28] Preparing reads
	 left reads: min. length=50, max. length=50, 33854791 kept reads (30306 discarded)
	right reads: min. length=50, max. length=50, 33844866 kept reads (40231 discarded)
[2016-04-07 17:04:09] Building transcriptome data files A8CO_13065_CGTACG/tmp/genes
[2016-04-07 17:04:27] Building Bowtie index from genes.fa
[2016-04-07 17:06:51] Mapping left_kept_reads to transcriptome genes with Bowtie2 
[2016-04-07 17:21:30] Mapping right_kept_reads to transcriptome genes with Bowtie2 
[2016-04-07 17:36:39] Resuming TopHat pipeline with unmapped reads
[2016-04-07 17:36:40] 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 17:41:17] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2016-04-07 17:41:58] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2016-04-07 17:45:28] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2016-04-07 17:46:13] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2016-04-07 17:46:58] Searching for junctions via segment mapping
[2016-04-07 18:01:23] Retrieving sequences for splices
[2016-04-07 18:02:56] Indexing splices
[2016-04-07 18:07:51] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2016-04-07 18:08:45] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2016-04-07 18:09:29] Joining segment hits
[2016-04-07 18:11:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2016-04-07 18:11:59] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2016-04-07 18:12:47] Joining segment hits
[2016-04-07 18:14:27] Reporting output tracks
-----------------------------------------------
[2016-04-07 18:39:29] A summary of the alignment counts can be found in A8CO_13065_CGTACG/align_summary.txt
[2016-04-07 18:39:29] Run complete: 01:45:18 elapsed