[2014-05-02 03:47:41] Beginning TopHat run (v2.0.8b)
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[2014-05-02 03:47:41] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-02 03:47:41] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-02 03:47:41] Checking for Bowtie index files
[2014-05-02 03:47:41] Checking for reference FASTA file
[2014-05-02 03:47:41] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-02 03:47:44] Preparing reads
	 left reads: min. length=60, max. length=101, 26243755 kept reads (5341 discarded)
[2014-05-02 03:58:24] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-02 04:31:10] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-02 04:33:49] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-02 04:36:40] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-02 04:39:48] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-02 04:43:06] Searching for junctions via segment mapping
[2014-05-02 04:49:05] Retrieving sequences for splices
[2014-05-02 04:51:01] Indexing splices
[2014-05-02 04:51:45] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-02 04:52:57] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-02 04:54:23] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-02 04:55:48] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-02 04:57:10] Joining segment hits
[2014-05-02 05:00:53] Reporting output tracks
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[2014-05-02 05:16:24] Run complete: 01:28:42 elapsed