[2014-04-28 18:14:22] Beginning TopHat run (v2.0.8b)
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[2014-04-28 18:14:22] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-28 18:14:22] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-28 18:14:22] Checking for Bowtie index files
[2014-04-28 18:14:22] Checking for reference FASTA file
[2014-04-28 18:14:22] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-28 18:14:47] Preparing reads
	 left reads: min. length=60, max. length=101, 21645581 kept reads (11799 discarded)
[2014-04-28 18:23:41] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-28 18:55:28] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-28 18:57:37] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-28 19:00:00] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-28 19:02:45] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-28 19:05:23] Searching for junctions via segment mapping
[2014-04-28 19:09:27] Retrieving sequences for splices
[2014-04-28 19:11:39] Indexing splices
[2014-04-28 19:12:25] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-28 19:13:27] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-28 19:14:42] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-28 19:15:55] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-28 19:17:04] Joining segment hits
[2014-04-28 19:20:36] Reporting output tracks
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[2014-04-28 19:33:17] Run complete: 01:18:55 elapsed