[2014-04-26 22:34:47] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2014-04-26 22:34:47] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-26 22:34:47] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-26 22:34:47] Checking for Bowtie index files
[2014-04-26 22:34:47] Checking for reference FASTA file
[2014-04-26 22:34:47] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-26 22:34:50] Preparing reads
	 left reads: min. length=60, max. length=101, 20828655 kept reads (11741 discarded)
[2014-04-26 22:43:19] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-26 23:13:30] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-26 23:15:32] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-26 23:17:53] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-26 23:20:32] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-26 23:23:06] Searching for junctions via segment mapping
[2014-04-26 23:31:34] Retrieving sequences for splices
[2014-04-26 23:33:31] Indexing splices
[2014-04-26 23:34:26] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-26 23:35:50] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-26 23:37:27] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-26 23:39:05] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-26 23:40:46] Joining segment hits
[2014-04-26 23:44:43] Reporting output tracks
-----------------------------------------------
[2014-04-26 23:58:41] Run complete: 01:23:54 elapsed