[2014-04-30 10:53:58] Beginning TopHat run (v2.0.8b)
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[2014-04-30 10:53:58] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-30 10:53:58] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-30 10:53:58] Checking for Bowtie index files
[2014-04-30 10:53:58] Checking for reference FASTA file
[2014-04-30 10:53:58] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-30 10:54:00] Preparing reads
	 left reads: min. length=60, max. length=101, 21277944 kept reads (10734 discarded)
[2014-04-30 11:02:37] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-30 11:29:03] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-30 11:31:09] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-30 11:33:31] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-30 11:36:19] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-30 11:39:09] Searching for junctions via segment mapping
[2014-04-30 11:44:12] Retrieving sequences for splices
[2014-04-30 11:46:07] Indexing splices
[2014-04-30 11:46:44] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-30 11:47:44] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-30 11:48:57] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-30 11:50:10] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-30 11:51:20] Joining segment hits
[2014-04-30 11:54:46] Reporting output tracks
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[2014-04-30 12:07:08] Run complete: 01:13:09 elapsed