[2014-05-29 14:39:54] Beginning TopHat run (v2.0.8b)
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[2014-05-29 14:39:54] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 14:39:54] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 14:39:54] Checking for Bowtie index files
[2014-05-29 14:39:54] Checking for reference FASTA file
[2014-05-29 14:39:54] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 14:39:57] Preparing reads
	 left reads: min. length=60, max. length=101, 28497705 kept reads (743 discarded)
[2014-05-29 14:53:14] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 15:30:10] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 15:33:26] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 15:37:01] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 15:40:39] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 15:44:05] Searching for junctions via segment mapping
[2014-05-29 15:47:54] Retrieving sequences for splices
[2014-05-29 15:49:51] Indexing splices
[2014-05-29 15:50:30] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 15:51:46] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 15:53:36] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 15:55:24] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 15:56:59] Joining segment hits
[2014-05-29 16:01:07] Reporting output tracks
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[2014-05-29 16:17:29] Run complete: 01:37:35 elapsed