[2014-04-30 22:43:45] Beginning TopHat run (v2.0.8b)
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[2014-04-30 22:43:45] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-30 22:43:45] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-30 22:43:45] Checking for Bowtie index files
[2014-04-30 22:43:45] Checking for reference FASTA file
[2014-04-30 22:43:45] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-30 22:43:48] Preparing reads
	 left reads: min. length=60, max. length=101, 23114556 kept reads (11860 discarded)
[2014-04-30 22:53:06] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-30 23:26:30] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-30 23:32:03] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-30 23:37:40] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-30 23:45:11] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-30 23:51:10] Searching for junctions via segment mapping
[2014-05-01 03:32:19] Retrieving sequences for splices
[2014-05-01 03:34:15] Indexing splices
[2014-05-01 03:35:12] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-01 03:43:33] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-01 03:52:09] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-01 04:01:03] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-01 04:09:54] Joining segment hits
[2014-05-01 04:18:58] Reporting output tracks
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[2014-05-01 04:33:57] Run complete: 05:50:12 elapsed