[2014-05-27 15:34:23] Beginning TopHat run (v2.0.8b)
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[2014-05-27 15:34:23] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 15:34:23] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 15:34:23] Checking for Bowtie index files
[2014-05-27 15:34:23] Checking for reference FASTA file
[2014-05-27 15:34:23] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 15:34:25] Preparing reads
	 left reads: min. length=60, max. length=101, 26890211 kept reads (2297 discarded)
[2014-05-27 15:46:36] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 16:26:25] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 16:29:38] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 16:33:09] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 16:36:48] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 16:40:33] Searching for junctions via segment mapping
[2014-05-27 16:46:10] Retrieving sequences for splices
[2014-05-27 16:48:16] Indexing splices
[2014-05-27 16:49:14] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 16:51:07] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-27 16:53:17] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-27 16:55:29] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 16:57:37] Joining segment hits
[2014-05-27 17:01:52] Reporting output tracks
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[2014-05-27 17:17:51] Run complete: 01:43:28 elapsed