[2014-04-27 10:05:55] Beginning TopHat run (v2.0.8b)
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[2014-04-27 10:05:55] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-27 10:05:55] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-27 10:05:55] Checking for Bowtie index files
[2014-04-27 10:05:55] Checking for reference FASTA file
[2014-04-27 10:05:55] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-27 10:05:58] Preparing reads
	 left reads: min. length=60, max. length=101, 17743773 kept reads (8041 discarded)
[2014-04-27 10:13:16] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-27 10:35:28] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-27 10:37:26] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-27 10:39:32] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-27 10:41:52] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-27 10:44:24] Searching for junctions via segment mapping
[2014-04-27 10:48:50] Retrieving sequences for splices
[2014-04-27 10:50:47] Indexing splices
[2014-04-27 10:51:41] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-27 10:52:38] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-27 10:53:45] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-27 10:54:53] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-27 10:56:00] Joining segment hits
[2014-04-27 10:59:13] Reporting output tracks
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[2014-04-27 11:09:57] Run complete: 01:04:02 elapsed