[2014-05-27 12:10:49] Beginning TopHat run (v2.0.8b)
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[2014-05-27 12:10:49] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 12:10:49] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 12:10:49] Checking for Bowtie index files
[2014-05-27 12:10:49] Checking for reference FASTA file
[2014-05-27 12:10:49] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 12:10:51] Preparing reads
	 left reads: min. length=60, max. length=101, 25451295 kept reads (1017 discarded)
[2014-05-27 12:21:55] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 13:01:06] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 13:03:45] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 13:07:02] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 13:10:22] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 13:13:44] Searching for junctions via segment mapping
[2014-05-27 13:18:39] Retrieving sequences for splices
[2014-05-27 13:20:46] Indexing splices
[2014-05-27 13:21:21] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 13:22:39] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-27 13:24:16] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-27 13:26:05] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 13:27:39] Joining segment hits
[2014-05-27 13:31:34] Reporting output tracks
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[2014-05-27 13:45:40] Run complete: 01:34:51 elapsed