[2014-05-29 20:24:30] Beginning TopHat run (v2.0.8b)
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[2014-05-29 20:24:30] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 20:24:30] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 20:24:30] Checking for Bowtie index files
[2014-05-29 20:24:30] Checking for reference FASTA file
[2014-05-29 20:24:30] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 20:24:32] Preparing reads
	 left reads: min. length=60, max. length=101, 25288147 kept reads (1233 discarded)
[2014-05-29 20:35:28] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 21:16:27] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 21:19:35] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 21:23:22] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 21:27:22] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 21:31:54] Searching for junctions via segment mapping
[2014-05-29 22:06:23] Retrieving sequences for splices
[2014-05-29 22:08:31] Indexing splices
[2014-05-29 22:09:34] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 22:12:54] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 22:16:18] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 22:19:49] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 22:23:07] Joining segment hits
[2014-05-29 22:26:49] Reporting output tracks
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[2014-05-29 22:40:39] Run complete: 02:16:08 elapsed