[2014-04-30 12:07:08] Beginning TopHat run (v2.0.8b)
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[2014-04-30 12:07:08] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-30 12:07:08] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-30 12:07:08] Checking for Bowtie index files
[2014-04-30 12:07:08] Checking for reference FASTA file
[2014-04-30 12:07:08] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-30 12:07:10] Preparing reads
	 left reads: min. length=60, max. length=101, 16843979 kept reads (9111 discarded)
[2014-04-30 12:13:58] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-30 12:40:14] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-30 12:45:17] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-30 12:50:32] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-30 12:55:51] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-30 13:01:48] Searching for junctions via segment mapping
[2014-04-30 17:42:58] Retrieving sequences for splices
[2014-04-30 17:44:54] Indexing splices
[2014-04-30 17:45:54] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-30 17:54:05] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-30 18:02:28] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-30 18:10:51] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-30 18:19:27] Joining segment hits
[2014-04-30 18:27:33] Reporting output tracks
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[2014-04-30 18:39:35] Run complete: 06:32:27 elapsed