[2014-04-28 06:46:00] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2014-04-28 06:46:00] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-28 06:46:00] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-28 06:46:00] Checking for Bowtie index files
[2014-04-28 06:46:00] Checking for reference FASTA file
[2014-04-28 06:46:00] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-28 06:46:07] Preparing reads
	 left reads: min. length=60, max. length=101, 21807297 kept reads (13035 discarded)
[2014-04-28 06:54:37] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-28 07:23:06] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-28 07:26:48] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-28 07:30:37] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-28 07:37:16] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-28 07:41:15] Searching for junctions via segment mapping
[2014-04-28 08:28:01] Retrieving sequences for splices
[2014-04-28 08:29:58] Indexing splices
[2014-04-28 08:30:45] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-28 08:37:03] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-28 08:43:09] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-28 08:49:14] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-28 08:56:18] Joining segment hits
[2014-04-28 09:04:32] Reporting output tracks
-----------------------------------------------
[2014-04-28 09:16:48] Run complete: 02:30:47 elapsed