[2014-04-25 22:58:26] Beginning TopHat run (v2.0.8b)
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[2014-04-25 22:58:26] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-25 22:58:26] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-25 22:58:26] Checking for Bowtie index files
[2014-04-25 22:58:26] Checking for reference FASTA file
[2014-04-25 22:58:26] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-25 22:58:29] Preparing reads
	 left reads: min. length=60, max. length=101, 24666821 kept reads (7495 discarded)
[2014-04-25 23:08:28] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-25 23:40:02] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-25 23:42:23] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-25 23:45:05] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-25 23:48:04] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-25 23:51:05] Searching for junctions via segment mapping
[2014-04-25 23:55:14] Retrieving sequences for splices
[2014-04-25 23:57:12] Indexing splices
[2014-04-25 23:57:55] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-25 23:58:55] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-26 00:00:04] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-26 00:01:14] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-26 00:02:22] Joining segment hits
[2014-04-26 00:05:46] Reporting output tracks
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[2014-04-26 00:19:55] Run complete: 01:21:28 elapsed