[2014-05-02 02:08:23] Beginning TopHat run (v2.0.8b)
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[2014-05-02 02:08:23] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-02 02:08:23] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-02 02:08:23] Checking for Bowtie index files
[2014-05-02 02:08:23] Checking for reference FASTA file
[2014-05-02 02:08:23] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-02 02:08:26] Preparing reads
	 left reads: min. length=60, max. length=101, 29958625 kept reads (6075 discarded)
[2014-05-02 02:20:32] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-02 02:57:02] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-02 02:59:51] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-02 03:03:03] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-02 03:06:39] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-02 03:10:18] Searching for junctions via segment mapping
[2014-05-02 03:17:28] Retrieving sequences for splices
[2014-05-02 03:19:24] Indexing splices
[2014-05-02 03:20:11] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-02 03:21:31] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-02 03:23:05] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-02 03:24:40] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-02 03:26:10] Joining segment hits
[2014-05-02 03:30:09] Reporting output tracks
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[2014-05-02 03:47:41] Run complete: 01:39:18 elapsed