[2014-04-28 20:40:05] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2014-04-28 20:40:05] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-28 20:40:05] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-28 20:40:05] Checking for Bowtie index files
[2014-04-28 20:40:05] Checking for reference FASTA file
[2014-04-28 20:40:05] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-28 20:40:14] Preparing reads
	 left reads: min. length=60, max. length=101, 20515751 kept reads (10931 discarded)
[2014-04-28 20:48:35] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-28 21:15:42] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-28 21:18:12] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-28 21:20:37] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-28 21:23:27] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-28 21:25:58] Searching for junctions via segment mapping
[2014-04-28 21:29:49] Retrieving sequences for splices
[2014-04-28 21:31:54] Indexing splices
[2014-04-28 21:32:36] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-28 21:33:27] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-28 21:34:27] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-28 21:35:28] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-28 21:36:28] Joining segment hits
[2014-04-28 21:39:42] Reporting output tracks
-----------------------------------------------
[2014-04-28 21:51:32] Run complete: 01:11:26 elapsed