[2014-05-27 22:37:39] Beginning TopHat run (v2.0.8b)
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[2014-05-27 22:37:39] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 22:37:39] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 22:37:39] Checking for Bowtie index files
[2014-05-27 22:37:39] Checking for reference FASTA file
[2014-05-27 22:37:39] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 22:37:41] Preparing reads
	 left reads: min. length=60, max. length=101, 27347922 kept reads (1068 discarded)
[2014-05-27 22:49:53] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 23:42:45] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 23:57:15] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 00:11:49] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 00:26:17] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 00:43:05] Searching for junctions via segment mapping
[2014-05-28 07:28:29] Retrieving sequences for splices
[2014-05-28 07:30:39] Indexing splices
[2014-05-28 07:32:23] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 08:01:53] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 08:32:13] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 09:02:31] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 09:32:21] Joining segment hits
[2014-05-28 09:41:58] Reporting output tracks
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[2014-05-28 10:00:07] Run complete: 11:22:27 elapsed