[2014-05-24 19:11:30] Beginning TopHat run (v2.0.8b)
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[2014-05-24 19:11:30] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-24 19:11:30] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-24 19:11:30] Checking for Bowtie index files
[2014-05-24 19:11:30] Checking for reference FASTA file
[2014-05-24 19:11:30] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-24 19:11:32] Preparing reads
	 left reads: min. length=60, max. length=101, 22306671 kept reads (907 discarded)
[2014-05-24 19:22:38] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-24 19:56:56] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-24 19:59:36] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-24 20:02:26] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-24 20:04:45] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-24 20:07:52] Searching for junctions via segment mapping
[2014-05-24 20:12:54] Retrieving sequences for splices
[2014-05-24 20:14:57] Indexing splices
[2014-05-24 20:15:39] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-24 20:17:04] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-24 20:18:32] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-24 20:19:57] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-24 20:21:23] Joining segment hits
[2014-05-24 20:24:39] Reporting output tracks
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[2014-05-24 20:36:48] Run complete: 01:25:17 elapsed