[2014-04-26 18:06:22] Beginning TopHat run (v2.0.8b)
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[2014-04-26 18:06:22] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-26 18:06:22] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-26 18:06:22] Checking for Bowtie index files
[2014-04-26 18:06:22] Checking for reference FASTA file
[2014-04-26 18:06:22] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-26 18:06:27] Preparing reads
	 left reads: min. length=60, max. length=101, 27346185 kept reads (8593 discarded)
[2014-04-26 18:17:53] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-26 18:51:02] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-26 18:53:58] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-26 18:57:05] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-26 19:00:52] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-26 19:04:25] Searching for junctions via segment mapping
[2014-04-26 19:08:54] Retrieving sequences for splices
[2014-04-26 19:10:52] Indexing splices
[2014-04-26 19:11:30] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-26 19:12:59] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-26 19:14:39] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-26 19:16:21] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-26 19:18:01] Joining segment hits
[2014-04-26 19:22:13] Reporting output tracks
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[2014-04-26 19:38:48] Run complete: 01:32:25 elapsed