[2014-04-29 12:50:32] Beginning TopHat run (v2.0.8b)
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[2014-04-29 12:50:32] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-29 12:50:32] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-29 12:50:32] Checking for Bowtie index files
[2014-04-29 12:50:32] Checking for reference FASTA file
[2014-04-29 12:50:32] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-29 12:50:34] Preparing reads
	 left reads: min. length=60, max. length=101, 23090507 kept reads (10909 discarded)
[2014-04-29 12:59:53] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-29 13:30:08] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-29 13:32:51] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-29 13:35:53] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-29 13:41:06] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-29 13:44:23] Searching for junctions via segment mapping
[2014-04-29 14:00:43] Retrieving sequences for splices
[2014-04-29 14:02:40] Indexing splices
[2014-04-29 14:03:27] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-29 14:05:01] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-29 14:06:49] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-29 14:08:39] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-29 14:10:25] Joining segment hits
[2014-04-29 14:14:39] Reporting output tracks
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[2014-04-29 14:28:41] Run complete: 01:38:09 elapsed