[2014-05-01 21:40:58] Beginning TopHat run (v2.0.8b)
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[2014-05-01 21:40:58] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-01 21:40:58] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-01 21:40:58] Checking for Bowtie index files
[2014-05-01 21:40:58] Checking for reference FASTA file
[2014-05-01 21:40:58] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-01 21:41:00] Preparing reads
	 left reads: min. length=60, max. length=101, 21129310 kept reads (10278 discarded)
[2014-05-01 21:49:28] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-01 22:16:01] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-01 22:19:27] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-01 22:22:56] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-01 22:26:16] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-01 22:30:18] Searching for junctions via segment mapping
[2014-05-01 23:42:09] Retrieving sequences for splices
[2014-05-01 23:44:05] Indexing splices
[2014-05-01 23:44:55] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-01 23:52:09] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-01 23:59:09] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-02 00:05:42] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-02 00:13:24] Joining segment hits
[2014-05-02 00:21:48] Reporting output tracks
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[2014-05-02 00:33:52] Run complete: 02:52:54 elapsed