[2014-04-28 00:37:22] Beginning TopHat run (v2.0.8b)
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[2014-04-28 00:37:22] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-28 00:37:22] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-28 00:37:22] Checking for Bowtie index files
[2014-04-28 00:37:22] Checking for reference FASTA file
[2014-04-28 00:37:22] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-28 00:37:25] Preparing reads
	 left reads: min. length=60, max. length=101, 24023169 kept reads (11981 discarded)
[2014-04-28 00:46:56] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-28 01:17:17] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-28 01:21:30] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-28 01:25:40] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-28 01:29:44] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-28 01:34:10] Searching for junctions via segment mapping
[2014-04-28 03:01:44] Retrieving sequences for splices
[2014-04-28 03:03:45] Indexing splices
[2014-04-28 03:04:38] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-28 03:14:10] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-28 03:23:07] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-28 03:31:38] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-28 03:41:28] Joining segment hits
[2014-04-28 03:51:41] Reporting output tracks
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[2014-04-28 04:05:42] Run complete: 03:28:20 elapsed