[2014-05-28 06:21:47] Beginning TopHat run (v2.0.8b)
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[2014-05-28 06:21:47] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 06:21:47] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 06:21:47] Checking for Bowtie index files
[2014-05-28 06:21:47] Checking for reference FASTA file
[2014-05-28 06:21:47] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 06:21:50] Preparing reads
	 left reads: min. length=60, max. length=101, 24732965 kept reads (2609 discarded)
[2014-05-28 06:33:50] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 07:08:42] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 07:12:17] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 07:16:10] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 07:20:09] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 07:24:23] Searching for junctions via segment mapping
[2014-05-28 07:36:20] Retrieving sequences for splices
[2014-05-28 07:38:25] Indexing splices
[2014-05-28 07:39:17] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 07:48:53] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 07:58:28] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 08:07:58] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 08:18:36] Joining segment hits
[2014-05-28 08:27:07] Reporting output tracks
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[2014-05-28 08:43:38] Run complete: 02:21:50 elapsed