[2014-04-28 23:23:24] Beginning TopHat run (v2.0.8b)
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[2014-04-28 23:23:24] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-28 23:23:24] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-28 23:23:24] Checking for Bowtie index files
[2014-04-28 23:23:24] Checking for reference FASTA file
[2014-04-28 23:23:24] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-28 23:23:28] Preparing reads
	 left reads: min. length=60, max. length=101, 22546395 kept reads (14263 discarded)
[2014-04-28 23:32:18] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-29 00:00:17] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-29 00:03:56] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-29 00:07:42] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-29 00:11:18] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-29 00:15:16] Searching for junctions via segment mapping
[2014-04-29 01:21:45] Retrieving sequences for splices
[2014-04-29 01:23:41] Indexing splices
[2014-04-29 01:24:26] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-29 01:32:22] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-29 01:39:47] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-29 01:47:24] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-29 01:56:50] Joining segment hits
[2014-04-29 02:05:33] Reporting output tracks
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[2014-04-29 02:18:24] Run complete: 02:54:59 elapsed