[2014-04-27 01:21:49] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2014-04-27 01:21:49] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-27 01:21:49] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-27 01:21:49] Checking for Bowtie index files
[2014-04-27 01:21:49] Checking for reference FASTA file
[2014-04-27 01:21:49] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-27 01:21:57] Preparing reads
	 left reads: min. length=60, max. length=101, 17308085 kept reads (11975 discarded)
[2014-04-27 01:29:00] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-27 01:54:18] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-27 01:56:06] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-27 01:58:11] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-27 02:00:35] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-27 02:02:46] Searching for junctions via segment mapping
[2014-04-27 02:09:52] Retrieving sequences for splices
[2014-04-27 02:11:48] Indexing splices
[2014-04-27 02:12:30] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-27 02:13:41] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-27 02:15:05] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-27 02:16:27] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-27 02:17:48] Joining segment hits
[2014-04-27 02:21:17] Reporting output tracks
-----------------------------------------------
[2014-04-27 02:32:48] Run complete: 01:10:59 elapsed