[2014-05-02 18:49:13] Beginning TopHat run (v2.0.8b)
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[2014-05-02 18:49:13] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-02 18:49:13] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-02 18:49:13] Checking for Bowtie index files
[2014-05-02 18:49:13] Checking for reference FASTA file
[2014-05-02 18:49:13] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-02 18:49:25] Preparing reads
	 left reads: min. length=60, max. length=101, 31166012 kept reads (5690 discarded)
[2014-05-02 19:02:00] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-02 19:40:31] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-02 19:44:19] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-02 19:48:23] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-02 19:53:40] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-02 19:58:21] Searching for junctions via segment mapping
[2014-05-02 20:04:55] Retrieving sequences for splices
[2014-05-02 20:06:52] Indexing splices
[2014-05-02 20:07:57] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-02 20:09:40] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-02 20:11:44] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-02 20:13:49] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-02 20:15:49] Joining segment hits
[2014-05-02 20:20:27] Reporting output tracks
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[2014-05-02 20:38:01] Run complete: 01:48:48 elapsed