[2014-04-26 11:13:22] Beginning TopHat run (v2.0.8b)
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[2014-04-26 11:13:22] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-26 11:13:22] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-26 11:13:22] Checking for Bowtie index files
[2014-04-26 11:13:22] Checking for reference FASTA file
[2014-04-26 11:13:22] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-26 11:13:24] Preparing reads
	 left reads: min. length=60, max. length=101, 24238453 kept reads (9221 discarded)
[2014-04-26 11:23:13] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-26 11:54:32] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-26 11:57:37] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-26 12:00:55] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-26 12:04:44] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-26 12:08:17] Searching for junctions via segment mapping
[2014-04-26 13:03:46] Retrieving sequences for splices
[2014-04-26 13:05:42] Indexing splices
[2014-04-26 13:06:29] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-26 13:08:48] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-26 13:11:21] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-26 13:13:56] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-26 13:16:31] Joining segment hits
[2014-04-26 13:21:13] Reporting output tracks
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[2014-04-26 13:35:38] Run complete: 02:22:16 elapsed