[2014-04-27 05:20:53] Beginning TopHat run (v2.0.8b)
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[2014-04-27 05:20:53] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-27 05:20:53] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-27 05:20:53] Checking for Bowtie index files
[2014-04-27 05:20:53] Checking for reference FASTA file
[2014-04-27 05:20:53] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-27 05:20:56] Preparing reads
	 left reads: min. length=60, max. length=101, 19353117 kept reads (9109 discarded)
[2014-04-27 05:28:45] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-27 05:53:37] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-27 05:56:01] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-27 05:58:36] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-27 06:04:24] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-27 06:07:17] Searching for junctions via segment mapping
[2014-04-27 06:12:01] Retrieving sequences for splices
[2014-04-27 06:13:59] Indexing splices
[2014-04-27 06:14:50] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-27 06:15:54] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-27 06:17:09] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-27 06:18:29] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-27 06:19:42] Joining segment hits
[2014-04-27 06:23:16] Reporting output tracks
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[2014-04-27 06:34:27] Run complete: 01:13:33 elapsed