[2014-04-28 09:16:48] Beginning TopHat run (v2.0.8b)
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[2014-04-28 09:16:48] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-28 09:16:48] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-28 09:16:48] Checking for Bowtie index files
[2014-04-28 09:16:48] Checking for reference FASTA file
[2014-04-28 09:16:48] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-28 09:16:54] Preparing reads
	 left reads: min. length=60, max. length=101, 23106179 kept reads (13679 discarded)
[2014-04-28 09:26:00] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-28 09:56:19] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-28 10:00:36] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-28 10:04:50] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-28 10:11:07] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-28 10:15:19] Searching for junctions via segment mapping
[2014-04-28 11:24:03] Retrieving sequences for splices
[2014-04-28 11:26:00] Indexing splices
[2014-04-28 11:26:54] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-28 11:34:37] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-28 11:41:50] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-28 11:48:39] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-28 11:56:36] Joining segment hits
[2014-04-28 12:05:55] Reporting output tracks
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[2014-04-28 12:18:57] Run complete: 03:02:08 elapsed