[2014-05-29 10:03:07] Beginning TopHat run (v2.0.8b)
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[2014-05-29 10:03:07] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 10:03:07] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 10:03:07] Checking for Bowtie index files
[2014-05-29 10:03:07] Checking for reference FASTA file
[2014-05-29 10:03:07] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 10:03:09] Preparing reads
	 left reads: min. length=60, max. length=101, 21659213 kept reads (507 discarded)
[2014-05-29 10:12:54] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 10:43:39] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 10:45:39] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 10:47:49] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 10:50:18] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 10:53:09] Searching for junctions via segment mapping
[2014-05-29 10:57:50] Retrieving sequences for splices
[2014-05-29 10:59:56] Indexing splices
[2014-05-29 11:00:45] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 11:01:59] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 11:03:21] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 11:04:45] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 11:06:02] Joining segment hits
[2014-05-29 11:09:51] Reporting output tracks
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[2014-05-29 11:23:26] Run complete: 01:20:18 elapsed