[2014-05-28 00:06:43] Beginning TopHat run (v2.0.8b)
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[2014-05-28 00:06:43] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 00:06:43] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 00:06:43] Checking for Bowtie index files
[2014-05-28 00:06:43] Checking for reference FASTA file
[2014-05-28 00:06:43] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 00:06:46] Preparing reads
	 left reads: min. length=60, max. length=101, 26074067 kept reads (2467 discarded)
[2014-05-28 00:18:34] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 00:54:41] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 00:57:08] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 00:59:51] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 01:02:39] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 01:05:25] Searching for junctions via segment mapping
[2014-05-28 01:09:47] Retrieving sequences for splices
[2014-05-28 01:11:45] Indexing splices
[2014-05-28 01:12:30] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 01:14:06] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 01:16:07] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 01:18:10] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 01:20:02] Joining segment hits
[2014-05-28 01:23:57] Reporting output tracks
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[2014-05-28 01:39:34] Run complete: 01:32:51 elapsed