[2014-05-24 21:53:28] Beginning TopHat run (v2.0.8b)
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[2014-05-24 21:53:28] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-24 21:53:28] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-24 21:53:28] Checking for Bowtie index files
[2014-05-24 21:53:28] Checking for reference FASTA file
[2014-05-24 21:53:28] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-24 21:53:31] Preparing reads
	 left reads: min. length=60, max. length=101, 23166536 kept reads (3110 discarded)
[2014-05-24 22:04:04] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-24 22:34:31] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-24 22:36:41] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-24 22:39:04] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-24 22:41:33] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-24 22:44:00] Searching for junctions via segment mapping
[2014-05-24 22:47:59] Retrieving sequences for splices
[2014-05-24 22:49:54] Indexing splices
[2014-05-24 22:50:27] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-24 22:51:32] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-24 22:52:51] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-24 22:54:08] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-24 22:55:14] Joining segment hits
[2014-05-24 22:58:16] Reporting output tracks
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[2014-05-24 23:10:24] Run complete: 01:16:56 elapsed