[2014-04-27 02:32:48] Beginning TopHat run (v2.0.8b)
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[2014-04-27 02:32:48] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-27 02:32:48] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-27 02:32:48] Checking for Bowtie index files
[2014-04-27 02:32:48] Checking for reference FASTA file
[2014-04-27 02:32:48] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-27 02:32:50] Preparing reads
	 left reads: min. length=60, max. length=101, 18053462 kept reads (10446 discarded)
[2014-04-27 02:40:05] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-27 03:05:59] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-27 03:08:18] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-27 03:10:53] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-27 03:16:36] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-27 03:19:07] Searching for junctions via segment mapping
[2014-04-27 03:26:22] Retrieving sequences for splices
[2014-04-27 03:28:18] Indexing splices
[2014-04-27 03:29:02] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-27 03:31:22] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-27 03:33:54] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-27 03:36:26] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-27 03:39:15] Joining segment hits
[2014-04-27 03:45:23] Reporting output tracks
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[2014-04-27 03:57:14] Run complete: 01:24:26 elapsed