[2014-04-27 13:22:24] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2014-04-27 13:22:24] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-27 13:22:24] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-27 13:22:24] Checking for Bowtie index files
[2014-04-27 13:22:24] Checking for reference FASTA file
[2014-04-27 13:22:24] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-27 13:22:26] Preparing reads
	 left reads: min. length=60, max. length=101, 22685421 kept reads (11981 discarded)
[2014-04-27 13:31:22] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-27 13:59:06] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-27 14:02:51] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-27 14:06:28] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-27 14:10:09] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-27 14:14:04] Searching for junctions via segment mapping
[2014-04-27 15:17:25] Retrieving sequences for splices
[2014-04-27 15:19:22] Indexing splices
[2014-04-27 15:20:10] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-27 15:28:44] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-27 15:36:26] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-27 15:43:29] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-27 15:52:00] Joining segment hits
[2014-04-27 16:00:53] Reporting output tracks
-----------------------------------------------
[2014-04-27 16:14:14] Run complete: 02:51:49 elapsed