[2014-05-29 06:14:45] Beginning TopHat run (v2.0.8b)
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[2014-05-29 06:14:45] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 06:14:45] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 06:14:45] Checking for Bowtie index files
[2014-05-29 06:14:45] Checking for reference FASTA file
[2014-05-29 06:14:45] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 06:14:48] Preparing reads
	 left reads: min. length=60, max. length=101, 34775326 kept reads (132 discarded)
[2014-05-29 06:30:35] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 07:20:05] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 07:24:18] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 07:28:45] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 07:33:13] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 07:38:09] Searching for junctions via segment mapping
[2014-05-29 07:44:04] Retrieving sequences for splices
[2014-05-29 07:46:14] Indexing splices
[2014-05-29 07:47:39] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 07:50:33] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 07:54:11] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 07:57:47] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 08:00:52] Joining segment hits
[2014-05-29 08:05:57] Reporting output tracks
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[2014-05-29 08:23:26] Run complete: 02:08:41 elapsed