[2014-05-28 01:01:42] Beginning TopHat run (v2.0.8b)
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[2014-05-28 01:01:42] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 01:01:42] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 01:01:42] Checking for Bowtie index files
[2014-05-28 01:01:42] Checking for reference FASTA file
[2014-05-28 01:01:42] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 01:01:45] Preparing reads
	 left reads: min. length=60, max. length=101, 24912910 kept reads (3904 discarded)
[2014-05-28 01:12:31] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 01:49:35] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 01:52:07] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 01:55:25] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 01:58:55] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 02:02:29] Searching for junctions via segment mapping
[2014-05-28 02:11:48] Retrieving sequences for splices
[2014-05-28 02:13:57] Indexing splices
[2014-05-28 02:14:55] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 02:16:34] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 02:18:29] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 02:20:25] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 02:22:16] Joining segment hits
[2014-05-28 02:25:42] Reporting output tracks
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[2014-05-28 02:40:13] Run complete: 01:38:30 elapsed