[2014-05-02 05:16:24] Beginning TopHat run (v2.0.8b)
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[2014-05-02 05:16:24] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-02 05:16:24] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-02 05:16:24] Checking for Bowtie index files
[2014-05-02 05:16:24] Checking for reference FASTA file
[2014-05-02 05:16:24] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-02 05:16:27] Preparing reads
	 left reads: min. length=60, max. length=101, 30750542 kept reads (6408 discarded)
[2014-05-02 05:28:49] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-02 06:07:31] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-02 06:11:16] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-02 06:15:17] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-02 06:20:52] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-02 06:24:46] Searching for junctions via segment mapping
[2014-05-02 06:31:02] Retrieving sequences for splices
[2014-05-02 06:32:58] Indexing splices
[2014-05-02 06:33:42] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-02 06:35:05] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-02 06:36:45] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-02 06:38:26] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-02 06:39:58] Joining segment hits
[2014-05-02 06:44:29] Reporting output tracks
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[2014-05-02 07:02:05] Run complete: 01:45:41 elapsed