[2014-05-03 17:59:34] Beginning TopHat run (v2.0.8b)
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[2014-05-03 17:59:34] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-03 17:59:34] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-03 17:59:34] Checking for Bowtie index files
[2014-05-03 17:59:34] Checking for reference FASTA file
[2014-05-03 17:59:34] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-03 17:59:36] Preparing reads
	 left reads: min. length=60, max. length=101, 26271893 kept reads (4419 discarded)
[2014-05-03 18:10:35] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-03 18:46:33] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-03 18:51:59] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-03 18:57:44] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-03 19:03:14] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-03 19:09:26] Searching for junctions via segment mapping
[2014-05-03 23:12:17] Retrieving sequences for splices
[2014-05-03 23:14:13] Indexing splices
[2014-05-03 23:15:18] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-03 23:23:20] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-03 23:31:49] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-03 23:40:12] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-03 23:48:42] Joining segment hits
[2014-05-03 23:57:27] Reporting output tracks
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[2014-05-04 00:14:34] Run complete: 06:15:00 elapsed