[2014-05-28 15:09:37] Beginning TopHat run (v2.0.8b)
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[2014-05-28 15:09:37] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 15:09:37] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 15:09:37] Checking for Bowtie index files
[2014-05-28 15:09:37] Checking for reference FASTA file
[2014-05-28 15:09:37] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 15:09:39] Preparing reads
	 left reads: min. length=60, max. length=101, 21158005 kept reads (1865 discarded)
[2014-05-28 15:19:04] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 15:51:31] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 15:54:14] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 15:57:19] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 16:00:25] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 16:03:37] Searching for junctions via segment mapping
[2014-05-28 16:08:01] Retrieving sequences for splices
[2014-05-28 16:10:13] Indexing splices
[2014-05-28 16:11:05] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 16:12:26] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 16:14:08] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 16:15:50] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 16:17:27] Joining segment hits
[2014-05-28 16:20:53] Reporting output tracks
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[2014-05-28 16:33:35] Run complete: 01:23:57 elapsed