[2014-05-28 13:31:35] Beginning TopHat run (v2.0.8b)
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[2014-05-28 13:31:35] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 13:31:35] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 13:31:35] Checking for Bowtie index files
[2014-05-28 13:31:35] Checking for reference FASTA file
[2014-05-28 13:31:35] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 13:31:38] Preparing reads
	 left reads: min. length=60, max. length=101, 24985827 kept reads (1551 discarded)
[2014-05-28 13:42:41] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 14:21:06] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 14:24:19] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 14:27:55] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 14:31:34] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 14:35:15] Searching for junctions via segment mapping
[2014-05-28 14:40:09] Retrieving sequences for splices
[2014-05-28 14:42:21] Indexing splices
[2014-05-28 14:43:20] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 14:45:07] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 14:47:14] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 14:49:25] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 14:51:24] Joining segment hits
[2014-05-28 14:55:02] Reporting output tracks
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[2014-05-28 15:09:37] Run complete: 01:38:01 elapsed