[2014-04-28 21:51:32] Beginning TopHat run (v2.0.8b)
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[2014-04-28 21:51:32] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-28 21:51:32] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-28 21:51:32] Checking for Bowtie index files
[2014-04-28 21:51:32] Checking for reference FASTA file
[2014-04-28 21:51:32] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-28 21:51:37] Preparing reads
	 left reads: min. length=60, max. length=101, 17494805 kept reads (13259 discarded)
[2014-04-28 21:58:48] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-28 22:22:01] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-28 22:24:11] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-28 22:26:37] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-28 22:29:21] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-28 22:32:04] Searching for junctions via segment mapping
[2014-04-28 22:54:33] Retrieving sequences for splices
[2014-04-28 22:56:34] Indexing splices
[2014-04-28 22:57:17] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-28 22:59:26] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-28 23:01:52] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-28 23:04:17] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-28 23:06:49] Joining segment hits
[2014-04-28 23:12:21] Reporting output tracks
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[2014-04-28 23:23:24] Run complete: 01:31:51 elapsed