[2014-04-30 04:08:14] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2014-04-30 04:08:14] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-30 04:08:14] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-30 04:08:14] Checking for Bowtie index files
[2014-04-30 04:08:14] Checking for reference FASTA file
[2014-04-30 04:08:14] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-30 04:08:16] Preparing reads
	 left reads: min. length=60, max. length=101, 19043186 kept reads (8634 discarded)
[2014-04-30 04:16:03] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-30 04:39:45] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-30 04:41:36] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-30 04:43:39] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-30 04:45:54] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-30 04:48:26] Searching for junctions via segment mapping
[2014-04-30 04:53:06] Retrieving sequences for splices
[2014-04-30 04:55:02] Indexing splices
[2014-04-30 04:55:39] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-30 04:56:33] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-30 04:57:38] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-30 04:58:43] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-30 04:59:47] Joining segment hits
[2014-04-30 05:02:57] Reporting output tracks
-----------------------------------------------
[2014-04-30 05:14:17] Run complete: 01:06:03 elapsed