[2014-05-27 22:00:30] Beginning TopHat run (v2.0.8b)
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[2014-05-27 22:00:30] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 22:00:30] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 22:00:30] Checking for Bowtie index files
[2014-05-27 22:00:30] Checking for reference FASTA file
[2014-05-27 22:00:30] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 22:00:32] Preparing reads
	 left reads: min. length=60, max. length=101, 25522238 kept reads (1398 discarded)
[2014-05-27 22:11:42] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 22:53:20] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 22:57:17] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 23:01:34] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 23:05:50] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 23:10:34] Searching for junctions via segment mapping
[2014-05-27 23:16:30] Retrieving sequences for splices
[2014-05-27 23:18:40] Indexing splices
[2014-05-27 23:19:11] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 23:23:24] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-27 23:28:08] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-27 23:32:41] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 23:37:27] Joining segment hits
[2014-05-27 23:42:32] Reporting output tracks
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[2014-05-27 23:58:08] Run complete: 01:57:38 elapsed