[2014-05-27 20:01:31] Beginning TopHat run (v2.0.8b)
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[2014-05-27 20:01:31] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 20:01:31] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 20:01:31] Checking for Bowtie index files
[2014-05-27 20:01:31] Checking for reference FASTA file
[2014-05-27 20:01:31] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 20:01:33] Preparing reads
	 left reads: min. length=60, max. length=101, 26560945 kept reads (1889 discarded)
[2014-05-27 20:13:21] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 20:56:06] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 20:59:56] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 21:04:04] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 21:08:14] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 21:13:05] Searching for junctions via segment mapping
[2014-05-27 21:19:11] Retrieving sequences for splices
[2014-05-27 21:21:20] Indexing splices
[2014-05-27 21:21:52] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 21:25:55] 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 21:34:41] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 21:39:14] Joining segment hits
[2014-05-27 21:44:18] Reporting output tracks
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[2014-05-27 22:00:30] Run complete: 01:58:59 elapsed