[2014-04-29 02:18:24] Beginning TopHat run (v2.0.8b)
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[2014-04-29 02:18:24] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-29 02:18:24] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-29 02:18:24] Checking for Bowtie index files
[2014-04-29 02:18:24] Checking for reference FASTA file
[2014-04-29 02:18:24] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-29 02:18:29] Preparing reads
	 left reads: min. length=60, max. length=101, 24119714 kept reads (11110 discarded)
[2014-04-29 02:28:15] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-29 02:59:26] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-29 03:02:06] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-29 03:04:58] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-29 03:08:13] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-29 03:11:44] Searching for junctions via segment mapping
[2014-04-29 03:33:13] Retrieving sequences for splices
[2014-04-29 03:35:10] Indexing splices
[2014-04-29 03:35:58] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-29 03:37:44] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-29 03:39:46] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-29 03:41:50] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-29 03:43:48] Joining segment hits
[2014-04-29 03:48:00] Reporting output tracks
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[2014-04-29 04:02:04] Run complete: 01:43:39 elapsed