[2014-05-27 12:17:29] Beginning TopHat run (v2.0.8b)
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[2014-05-27 12:17:29] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 12:17:29] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 12:17:29] Checking for Bowtie index files
[2014-05-27 12:17:29] Checking for reference FASTA file
[2014-05-27 12:17:29] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 12:17:31] Preparing reads
	 left reads: min. length=60, max. length=101, 28895775 kept reads (717 discarded)
[2014-05-27 12:28:58] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 13:27:38] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 13:48:02] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 14:07:55] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 14:28:44] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 14:52:39] Searching for junctions via segment mapping
[2014-05-28 01:22:27] Retrieving sequences for splices
[2014-05-28 01:24:32] Indexing splices
[2014-05-28 01:26:55] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 02:10:56] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 02:56:54] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 03:42:36] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 04:26:16] Joining segment hits
[2014-05-28 04:37:23] Reporting output tracks
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[2014-05-28 04:58:37] Run complete: 16:41:08 elapsed