[2014-04-30 18:39:35] Beginning TopHat run (v2.0.8b)
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[2014-04-30 18:39:35] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-30 18:39:35] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-30 18:39:35] Checking for Bowtie index files
[2014-04-30 18:39:35] Checking for reference FASTA file
[2014-04-30 18:39:35] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-30 18:39:38] Preparing reads
	 left reads: min. length=60, max. length=101, 21109069 kept reads (10937 discarded)
[2014-04-30 18:48:08] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-30 19:17:44] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-30 19:22:00] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-30 19:26:30] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-30 19:33:24] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-30 19:37:57] Searching for junctions via segment mapping
[2014-04-30 21:59:18] Retrieving sequences for splices
[2014-04-30 22:01:14] Indexing splices
[2014-04-30 22:02:05] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-30 22:07:08] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-30 22:12:31] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-30 22:17:58] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-30 22:23:27] Joining segment hits
[2014-04-30 22:30:22] Reporting output tracks
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[2014-04-30 22:43:45] Run complete: 04:04:10 elapsed