[2014-05-05 08:08:45] Beginning TopHat run (v2.0.8b)
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[2014-05-05 08:08:45] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-05 08:08:45] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-05 08:08:45] Checking for Bowtie index files
[2014-05-05 08:08:45] Checking for reference FASTA file
[2014-05-05 08:08:45] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-05 08:08:47] Preparing reads
	 left reads: min. length=60, max. length=101, 28073076 kept reads (7476 discarded)
[2014-05-05 08:20:06] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-05 08:56:23] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-05 08:59:15] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-05 09:02:24] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-05 09:05:48] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-05 09:09:20] Searching for junctions via segment mapping
[2014-05-05 09:17:42] Retrieving sequences for splices
[2014-05-05 09:19:43] Indexing splices
[2014-05-05 09:20:34] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-05 09:22:16] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-05 09:24:16] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-05 09:26:17] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-05 09:28:17] Joining segment hits
[2014-05-05 09:32:29] Reporting output tracks
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[2014-05-05 09:49:14] Run complete: 01:40:29 elapsed