[2014-05-06 02:28:32] Beginning TopHat run (v2.0.8b)
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[2014-05-06 02:28:32] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-06 02:28:33] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-06 02:28:33] Checking for Bowtie index files
[2014-05-06 02:28:33] Checking for reference FASTA file
[2014-05-06 02:28:33] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-06 02:28:49] Preparing reads
	 left reads: min. length=60, max. length=101, 27214065 kept reads (9879 discarded)
[2014-05-06 02:39:56] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-06 03:19:50] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-06 03:23:04] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-06 03:26:18] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-06 03:29:42] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-06 03:33:04] Searching for junctions via segment mapping
[2014-05-06 03:48:47] Retrieving sequences for splices
[2014-05-06 03:50:46] Indexing splices
[2014-05-06 03:51:39] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-06 03:53:08] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-06 03:54:50] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-06 03:56:30] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-06 03:58:09] Joining segment hits
[2014-05-06 04:02:45] Reporting output tracks
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[2014-05-06 04:21:19] Run complete: 01:52:46 elapsed