[2014-05-28 18:58:45] Beginning TopHat run (v2.0.8b)
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[2014-05-28 18:58:45] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 18:58:45] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 18:58:45] Checking for Bowtie index files
[2014-05-28 18:58:45] Checking for reference FASTA file
[2014-05-28 18:58:45] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 18:58:47] Preparing reads
	 left reads: min. length=60, max. length=101, 25044372 kept reads (528 discarded)
[2014-05-28 19:09:36] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 19:51:28] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 19:55:34] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 19:59:57] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 20:04:26] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 20:09:32] Searching for junctions via segment mapping
[2014-05-28 20:17:36] Retrieving sequences for splices
[2014-05-28 20:19:40] Indexing splices
[2014-05-28 20:20:20] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 20:25:25] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 20:30:51] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 20:36:10] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 20:41:52] Joining segment hits
[2014-05-28 20:48:14] Reporting output tracks
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[2014-05-28 21:04:27] Run complete: 02:05:42 elapsed