[2014-05-02 07:02:06] Beginning TopHat run (v2.0.8b)
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[2014-05-02 07:02:06] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-02 07:02:06] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-02 07:02:06] Checking for Bowtie index files
[2014-05-02 07:02:06] Checking for reference FASTA file
[2014-05-02 07:02:06] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-02 07:02:08] Preparing reads
	 left reads: min. length=60, max. length=101, 26381987 kept reads (5653 discarded)
[2014-05-02 07:12:44] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-02 07:53:28] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-02 08:02:47] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-02 08:12:27] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-02 08:22:08] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-02 08:32:17] Searching for junctions via segment mapping
[2014-05-02 17:16:06] Retrieving sequences for splices
[2014-05-02 17:18:04] Indexing splices
[2014-05-02 17:19:28] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-02 17:33:52] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-02 17:48:21] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-02 18:03:01] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-02 18:18:05] Joining segment hits
[2014-05-02 18:30:57] Reporting output tracks
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[2014-05-02 18:49:12] Run complete: 11:47:06 elapsed