[2014-04-26 06:11:22] Beginning TopHat run (v2.0.8b)
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[2014-04-26 06:11:22] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-26 06:11:22] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-26 06:11:22] Checking for Bowtie index files
[2014-04-26 06:11:22] Checking for reference FASTA file
[2014-04-26 06:11:22] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-26 06:11:26] Preparing reads
	 left reads: min. length=60, max. length=101, 25019832 kept reads (8194 discarded)
[2014-04-26 06:21:31] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-26 06:53:43] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-26 06:56:47] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-26 07:00:04] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-26 07:04:22] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-26 07:08:04] Searching for junctions via segment mapping
[2014-04-26 07:38:54] Retrieving sequences for splices
[2014-04-26 07:40:50] Indexing splices
[2014-04-26 07:41:41] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-26 07:43:30] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-26 07:45:35] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-26 07:47:40] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-26 07:49:39] Joining segment hits
[2014-04-26 07:54:05] Reporting output tracks
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[2014-04-26 08:08:54] Run complete: 01:57:31 elapsed