[2014-05-27 23:58:08] Beginning TopHat run (v2.0.8b)
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[2014-05-27 23:58:08] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 23:58:08] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 23:58:08] Checking for Bowtie index files
[2014-05-27 23:58:08] Checking for reference FASTA file
[2014-05-27 23:58:08] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 23:58:10] Preparing reads
	 left reads: min. length=60, max. length=101, 26253414 kept reads (1842 discarded)
[2014-05-28 00:09:40] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 00:51:27] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 00:55:23] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 00:59:36] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 01:03:55] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 01:08:42] Searching for junctions via segment mapping
[2014-05-28 01:14:27] Retrieving sequences for splices
[2014-05-28 01:16:22] Indexing splices
[2014-05-28 01:16:48] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 01:20:45] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 01:25:03] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 01:29:27] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 01:34:22] Joining segment hits
[2014-05-28 01:40:31] Reporting output tracks
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[2014-05-28 01:57:23] Run complete: 01:59:15 elapsed