[2014-05-04 00:14:34] Beginning TopHat run (v2.0.8b)
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[2014-05-04 00:14:34] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-04 00:14:34] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-04 00:14:34] Checking for Bowtie index files
[2014-05-04 00:14:34] Checking for reference FASTA file
[2014-05-04 00:14:34] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-04 00:14:37] Preparing reads
	 left reads: min. length=60, max. length=101, 27412939 kept reads (4681 discarded)
[2014-05-04 00:25:41] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-04 01:08:29] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-04 01:18:08] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-04 01:28:15] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-04 01:37:54] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-04 01:49:20] Searching for junctions via segment mapping
[2014-05-04 11:25:42] Retrieving sequences for splices
[2014-05-04 11:27:39] Indexing splices
[2014-05-04 11:29:05] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-04 11:45:09] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-04 12:01:19] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-04 12:17:33] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-04 12:34:00] Joining segment hits
[2014-05-04 12:47:05] Reporting output tracks
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[2014-05-04 13:06:58] Run complete: 12:52:23 elapsed