[2014-05-29 20:18:31] Beginning TopHat run (v2.0.8b)
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[2014-05-29 20:18:31] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 20:18:31] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 20:18:31] Checking for Bowtie index files
[2014-05-29 20:18:31] Checking for reference FASTA file
[2014-05-29 20:18:31] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 20:18:33] Preparing reads
	 left reads: min. length=60, max. length=101, 32515450 kept reads (590 discarded)
[2014-05-29 20:31:52] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 21:20:21] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 21:25:12] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 21:30:17] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 21:34:44] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 21:40:28] Searching for junctions via segment mapping
[2014-05-29 21:46:23] Retrieving sequences for splices
[2014-05-29 21:48:34] Indexing splices
[2014-05-29 21:49:47] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 21:52:18] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 21:55:26] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 21:58:37] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 22:01:20] Joining segment hits
[2014-05-29 22:05:33] Reporting output tracks
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[2014-05-29 22:22:28] Run complete: 02:03:56 elapsed