[2014-05-27 13:52:05] Beginning TopHat run (v2.0.8b)
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[2014-05-27 13:52:05] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 13:52:05] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 13:52:05] Checking for Bowtie index files
[2014-05-27 13:52:05] Checking for reference FASTA file
[2014-05-27 13:52:05] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 13:52:07] Preparing reads
	 left reads: min. length=60, max. length=101, 24313815 kept reads (1385 discarded)
[2014-05-27 14:02:52] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 14:49:03] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 14:59:31] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 15:10:22] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 15:20:47] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 15:32:28] Searching for junctions via segment mapping
[2014-05-27 20:43:19] Retrieving sequences for splices
[2014-05-27 20:45:30] Indexing splices
[2014-05-27 20:46:55] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 21:08:26] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-27 21:30:21] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-27 21:52:12] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 22:13:24] Joining segment hits
[2014-05-27 22:21:34] Reporting output tracks
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[2014-05-27 22:37:39] Run complete: 08:45:33 elapsed