[2014-05-24 20:00:28] Beginning TopHat run (v2.0.8b)
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[2014-05-24 20:00:28] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-24 20:00:28] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-24 20:00:28] Checking for Bowtie index files
[2014-05-24 20:00:28] Checking for reference FASTA file
[2014-05-24 20:00:28] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-24 20:00:30] Preparing reads
	 left reads: min. length=60, max. length=101, 23412467 kept reads (4475 discarded)
[2014-05-24 20:12:01] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-24 20:48:27] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-24 20:50:37] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-24 20:52:55] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-24 20:55:23] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-24 20:58:13] Searching for junctions via segment mapping
[2014-05-24 21:02:41] Retrieving sequences for splices
[2014-05-24 21:04:46] Indexing splices
[2014-05-24 21:05:17] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-24 21:06:34] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-24 21:08:10] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-24 21:09:44] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-24 21:11:12] Joining segment hits
[2014-05-24 21:14:35] Reporting output tracks
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[2014-05-24 21:27:10] Run complete: 01:26:42 elapsed