[2014-04-26 15:07:26] Beginning TopHat run (v2.0.8b)
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[2014-04-26 15:07:26] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-26 15:07:26] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-26 15:07:26] Checking for Bowtie index files
[2014-04-26 15:07:26] Checking for reference FASTA file
[2014-04-26 15:07:26] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-26 15:07:28] Preparing reads
	 left reads: min. length=60, max. length=101, 26000404 kept reads (6438 discarded)
[2014-04-26 15:17:55] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-26 15:48:41] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-26 15:51:22] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-26 15:54:18] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-26 15:57:55] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-26 16:01:14] Searching for junctions via segment mapping
[2014-04-26 16:05:32] Retrieving sequences for splices
[2014-04-26 16:07:28] Indexing splices
[2014-04-26 16:08:10] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-26 16:09:31] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-26 16:11:05] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-26 16:12:43] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-26 16:14:16] Joining segment hits
[2014-04-26 16:18:20] Reporting output tracks
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[2014-04-26 16:35:36] Run complete: 01:28:09 elapsed