[2014-04-29 07:20:58] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2014-04-29 07:20:58] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-29 07:20:58] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-29 07:20:58] Checking for Bowtie index files
[2014-04-29 07:20:58] Checking for reference FASTA file
[2014-04-29 07:20:58] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-29 07:21:00] Preparing reads
	 left reads: min. length=60, max. length=101, 21950104 kept reads (10666 discarded)
[2014-04-29 07:29:52] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-29 07:58:55] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-29 08:01:40] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-29 08:04:41] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-29 08:09:15] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-29 08:12:36] Searching for junctions via segment mapping
[2014-04-29 08:57:35] Retrieving sequences for splices
[2014-04-29 08:59:32] Indexing splices
[2014-04-29 09:00:18] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-29 09:02:09] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-29 09:04:16] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-29 09:06:26] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-29 09:08:40] Joining segment hits
[2014-04-29 09:12:51] Reporting output tracks
-----------------------------------------------
[2014-04-29 09:25:36] Run complete: 02:04:37 elapsed