[2014-04-29 15:46:08] Beginning TopHat run (v2.0.8b)
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[2014-04-29 15:46:08] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-29 15:46:08] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-29 15:46:08] Checking for Bowtie index files
[2014-04-29 15:46:08] Checking for reference FASTA file
[2014-04-29 15:46:08] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-29 15:46:11] Preparing reads
	 left reads: min. length=60, max. length=101, 21974950 kept reads (12756 discarded)
[2014-04-29 15:55:07] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-29 16:21:46] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-29 16:24:02] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-29 16:26:29] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-29 16:29:17] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-29 16:32:13] Searching for junctions via segment mapping
[2014-04-29 16:36:28] Retrieving sequences for splices
[2014-04-29 16:38:27] Indexing splices
[2014-04-29 16:39:03] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-29 16:40:12] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-29 16:41:34] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-29 16:42:58] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-29 16:44:19] Joining segment hits
[2014-04-29 16:47:53] Reporting output tracks
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[2014-04-29 17:01:38] Run complete: 01:15:30 elapsed