[2014-04-26 09:42:08] Beginning TopHat run (v2.0.8b)
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[2014-04-26 09:42:08] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-26 09:42:08] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-26 09:42:08] Checking for Bowtie index files
[2014-04-26 09:42:08] Checking for reference FASTA file
[2014-04-26 09:42:08] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-26 09:42:10] Preparing reads
	 left reads: min. length=60, max. length=101, 22674696 kept reads (10136 discarded)
[2014-04-26 09:51:26] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-26 10:20:34] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-26 10:22:55] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-26 10:25:31] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-26 10:28:18] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-26 10:31:20] Searching for junctions via segment mapping
[2014-04-26 10:47:22] Retrieving sequences for splices
[2014-04-26 10:49:18] Indexing splices
[2014-04-26 10:49:59] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-26 10:51:21] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-26 10:52:54] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-26 10:54:25] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-26 10:55:51] Joining segment hits
[2014-04-26 10:59:35] Reporting output tracks
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[2014-04-26 11:13:22] Run complete: 01:31:13 elapsed