[2014-04-27 08:55:18] Beginning TopHat run (v2.0.8b)
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[2014-04-27 08:55:18] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-27 08:55:18] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-27 08:55:18] Checking for Bowtie index files
[2014-04-27 08:55:18] Checking for reference FASTA file
[2014-04-27 08:55:18] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-27 08:55:20] Preparing reads
	 left reads: min. length=60, max. length=101, 19550130 kept reads (9274 discarded)
[2014-04-27 09:03:21] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-27 09:28:05] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-27 09:30:14] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-27 09:32:34] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-27 09:35:22] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-27 09:38:13] Searching for junctions via segment mapping
[2014-04-27 09:43:00] Retrieving sequences for splices
[2014-04-27 09:44:56] Indexing splices
[2014-04-27 09:45:55] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-27 09:46:57] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-27 09:48:14] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-27 09:49:31] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-27 09:50:45] Joining segment hits
[2014-04-27 09:54:12] Reporting output tracks
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[2014-04-27 10:05:55] Run complete: 01:10:37 elapsed