[2014-05-05 09:49:14] Beginning TopHat run (v2.0.8b)
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[2014-05-05 09:49:14] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-05 09:49:14] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-05 09:49:14] Checking for Bowtie index files
[2014-05-05 09:49:14] Checking for reference FASTA file
[2014-05-05 09:49:14] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-05 09:49:16] Preparing reads
	 left reads: min. length=60, max. length=101, 29394086 kept reads (6862 discarded)
[2014-05-05 10:01:14] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-05 10:37:42] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-05 10:41:10] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-05 10:44:51] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-05 10:49:49] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-05 10:53:30] Searching for junctions via segment mapping
[2014-05-05 10:58:50] Retrieving sequences for splices
[2014-05-05 11:00:46] Indexing splices
[2014-05-05 11:01:39] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-05 11:03:04] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-05 11:04:46] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-05 11:06:31] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-05 11:08:09] Joining segment hits
[2014-05-05 11:12:35] Reporting output tracks
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[2014-05-05 11:29:01] Run complete: 01:39:46 elapsed