[2014-04-26 21:00:05] Beginning TopHat run (v2.0.8b)
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[2014-04-26 21:00:05] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-26 21:00:05] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-26 21:00:05] Checking for Bowtie index files
[2014-04-26 21:00:05] Checking for reference FASTA file
[2014-04-26 21:00:05] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-26 21:00:09] Preparing reads
	 left reads: min. length=60, max. length=101, 29044605 kept reads (8059 discarded)
[2014-04-26 21:11:53] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-26 21:46:24] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-26 21:49:07] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-26 21:52:05] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-26 21:55:18] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-26 21:58:45] Searching for junctions via segment mapping
[2014-04-26 22:03:18] Retrieving sequences for splices
[2014-04-26 22:05:15] Indexing splices
[2014-04-26 22:05:55] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-26 22:07:28] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-26 22:09:16] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-26 22:11:03] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-26 22:12:46] Joining segment hits
[2014-04-26 22:16:52] Reporting output tracks
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[2014-04-26 22:34:47] Run complete: 01:34:41 elapsed