[2014-05-03 05:38:35] Beginning TopHat run (v2.0.8b)
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[2014-05-03 05:38:35] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-03 05:38:35] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-03 05:38:35] Checking for Bowtie index files
[2014-05-03 05:38:35] Checking for reference FASTA file
[2014-05-03 05:38:35] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-03 05:38:37] Preparing reads
	 left reads: min. length=60, max. length=101, 30113789 kept reads (6875 discarded)
[2014-05-03 05:50:42] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-03 06:36:04] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-03 06:45:52] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-03 06:55:59] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-03 07:05:43] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-03 07:16:45] Searching for junctions via segment mapping
[2014-05-03 16:17:07] Retrieving sequences for splices
[2014-05-03 16:19:04] Indexing splices
[2014-05-03 16:20:38] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-03 16:36:25] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-03 16:52:40] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-03 17:08:56] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-03 17:25:24] Joining segment hits
[2014-05-03 17:38:44] Reporting output tracks
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[2014-05-03 17:59:34] Run complete: 12:20:58 elapsed