[2014-05-29 06:27:49] Beginning TopHat run (v2.0.8b)
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[2014-05-29 06:27:49] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 06:27:49] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 06:27:49] Checking for Bowtie index files
[2014-05-29 06:27:49] Checking for reference FASTA file
[2014-05-29 06:27:49] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 06:27:51] Preparing reads
	 left reads: min. length=60, max. length=101, 23094542 kept reads (1050 discarded)
[2014-05-29 06:39:25] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 07:17:36] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 07:20:37] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 07:24:02] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 07:27:29] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 07:31:02] Searching for junctions via segment mapping
[2014-05-29 07:37:49] Retrieving sequences for splices
[2014-05-29 07:39:46] Indexing splices
[2014-05-29 07:40:46] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 07:42:55] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 07:45:29] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 07:48:00] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 07:50:25] Joining segment hits
[2014-05-29 07:54:02] Reporting output tracks
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[2014-05-29 08:07:34] Run complete: 01:39:45 elapsed