[2014-05-06 16:53:52] Beginning TopHat run (v2.0.8b)
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[2014-05-06 16:53:52] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-06 16:53:52] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-06 16:53:52] Checking for Bowtie index files
[2014-05-06 16:53:52] Checking for reference FASTA file
[2014-05-06 16:53:52] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-06 16:53:57] Preparing reads
	 left reads: min. length=60, max. length=101, 34201634 kept reads (13908 discarded)
[2014-05-06 17:07:37] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-06 17:57:46] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-06 18:06:32] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-06 18:16:25] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-06 18:25:21] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-06 18:35:36] Searching for junctions via segment mapping
[2014-05-06 20:10:46] Retrieving sequences for splices
[2014-05-06 20:13:06] Indexing splices
[2014-05-06 20:14:05] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-06 20:42:09] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-06 21:07:34] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-06 21:31:05] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-06 21:54:49] Joining segment hits
[2014-05-06 22:05:48] Reporting output tracks
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[2014-05-06 22:22:24] Run complete: 05:28:31 elapsed