[2014-05-05 06:29:15] Beginning TopHat run (v2.0.8b)
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[2014-05-05 06:29:15] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-05 06:29:15] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-05 06:29:15] Checking for Bowtie index files
[2014-05-05 06:29:15] Checking for reference FASTA file
[2014-05-05 06:29:15] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-05 06:29:17] Preparing reads
	 left reads: min. length=60, max. length=101, 29416920 kept reads (8026 discarded)
[2014-05-05 06:41:11] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-05 07:20:06] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-05 07:23:01] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-05 07:26:19] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-05 07:29:55] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-05 07:33:24] Searching for junctions via segment mapping
[2014-05-05 07:38:52] Retrieving sequences for splices
[2014-05-05 07:40:49] Indexing splices
[2014-05-05 07:41:34] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-05 07:42:56] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-05 07:44:32] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-05 07:46:07] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-05 07:47:38] Joining segment hits
[2014-05-05 07:51:31] Reporting output tracks
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[2014-05-05 08:08:45] Run complete: 01:39:30 elapsed