[2014-04-28 13:29:52] Beginning TopHat run (v2.0.8b)
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[2014-04-28 13:29:52] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-28 13:29:52] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-28 13:29:52] Checking for Bowtie index files
[2014-04-28 13:29:52] Checking for reference FASTA file
[2014-04-28 13:29:52] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-28 13:29:54] Preparing reads
	 left reads: min. length=60, max. length=101, 22367228 kept reads (11232 discarded)
[2014-04-28 13:39:00] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-28 14:07:55] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-28 14:10:09] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-28 14:12:40] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-28 14:15:45] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-28 14:18:36] Searching for junctions via segment mapping
[2014-04-28 14:22:24] Retrieving sequences for splices
[2014-04-28 14:24:22] Indexing splices
[2014-04-28 14:25:07] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-28 14:26:02] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-28 14:27:09] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-28 14:28:16] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-28 14:29:21] Joining segment hits
[2014-04-28 14:32:37] Reporting output tracks
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[2014-04-28 14:45:04] Run complete: 01:15:12 elapsed