[2014-05-28 21:52:33] Beginning TopHat run (v2.0.8b)
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[2014-05-28 21:52:33] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 21:52:33] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 21:52:33] Checking for Bowtie index files
[2014-05-28 21:52:33] Checking for reference FASTA file
[2014-05-28 21:52:33] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 21:52:36] Preparing reads
	 left reads: min. length=60, max. length=101, 23218516 kept reads (644 discarded)
[2014-05-28 22:02:59] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 22:40:46] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 22:44:34] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 22:48:41] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 22:52:57] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 22:57:42] Searching for junctions via segment mapping
[2014-05-28 23:04:06] Retrieving sequences for splices
[2014-05-28 23:06:13] Indexing splices
[2014-05-28 23:06:49] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 23:11:51] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 23:17:12] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 23:22:12] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 23:27:50] Joining segment hits
[2014-05-28 23:33:10] Reporting output tracks
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[2014-05-28 23:47:11] Run complete: 01:54:38 elapsed