[2014-04-29 22:03:30] Beginning TopHat run (v2.0.8b)
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[2014-04-29 22:03:30] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-29 22:03:30] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-29 22:03:30] Checking for Bowtie index files
[2014-04-29 22:03:30] Checking for reference FASTA file
[2014-04-29 22:03:30] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-29 22:03:32] Preparing reads
	 left reads: min. length=60, max. length=101, 20414588 kept reads (9408 discarded)
[2014-04-29 22:11:48] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-29 22:36:57] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-29 22:38:56] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-29 22:41:13] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-29 22:43:50] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-29 22:46:34] Searching for junctions via segment mapping
[2014-04-29 22:50:25] Retrieving sequences for splices
[2014-04-29 22:52:22] Indexing splices
[2014-04-29 22:52:58] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-29 22:54:04] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-29 22:55:22] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-29 22:56:39] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-29 22:57:54] Joining segment hits
[2014-04-29 23:01:20] Reporting output tracks
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[2014-04-29 23:14:04] Run complete: 01:10:34 elapsed