[2014-04-26 08:08:54] Beginning TopHat run (v2.0.8b)
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[2014-04-26 08:08:54] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-26 08:08:54] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-26 08:08:54] Checking for Bowtie index files
[2014-04-26 08:08:54] Checking for reference FASTA file
[2014-04-26 08:08:54] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-26 08:08:57] Preparing reads
	 left reads: min. length=60, max. length=101, 23371845 kept reads (8495 discarded)
[2014-04-26 08:18:25] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-26 08:52:51] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-26 08:55:07] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-26 08:57:44] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-26 09:00:29] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-26 09:03:19] Searching for junctions via segment mapping
[2014-04-26 09:12:52] Retrieving sequences for splices
[2014-04-26 09:14:48] Indexing splices
[2014-04-26 09:15:41] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-26 09:17:14] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-26 09:19:03] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-26 09:20:48] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-26 09:22:34] Joining segment hits
[2014-04-26 09:27:00] Reporting output tracks
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[2014-04-26 09:42:08] Run complete: 01:33:14 elapsed