[2014-05-27 23:09:03] Beginning TopHat run (v2.0.8b)
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[2014-05-27 23:09:03] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 23:09:03] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 23:09:03] Checking for Bowtie index files
[2014-05-27 23:09:03] Checking for reference FASTA file
[2014-05-27 23:09:03] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 23:09:06] Preparing reads
	 left reads: min. length=60, max. length=101, 26872567 kept reads (1011 discarded)
[2014-05-27 23:21:40] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 00:02:35] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 00:05:38] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 00:08:51] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 00:12:11] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 00:15:46] Searching for junctions via segment mapping
[2014-05-28 00:21:45] Retrieving sequences for splices
[2014-05-28 00:23:54] Indexing splices
[2014-05-28 00:24:32] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 00:28:23] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 00:32:42] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 00:36:53] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 00:41:15] Joining segment hits
[2014-05-28 00:46:33] Reporting output tracks
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[2014-05-28 01:01:42] Run complete: 01:52:38 elapsed