[2014-05-27 17:48:26] Beginning TopHat run (v2.0.8b)
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[2014-05-27 17:48:26] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 17:48:26] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 17:48:26] Checking for Bowtie index files
[2014-05-27 17:48:26] Checking for reference FASTA file
[2014-05-27 17:48:26] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 17:48:28] Preparing reads
	 left reads: min. length=60, max. length=101, 28918704 kept reads (1148 discarded)
[2014-05-27 18:01:17] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 18:48:34] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 18:52:57] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 18:57:46] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 19:02:39] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 19:08:04] Searching for junctions via segment mapping
[2014-05-27 19:14:52] Retrieving sequences for splices
[2014-05-27 19:17:02] Indexing splices
[2014-05-27 19:17:36] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 19:22:33] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-27 19:27:52] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-27 19:33:08] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 19:38:33] Joining segment hits
[2014-05-27 19:44:11] Reporting output tracks
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[2014-05-27 20:01:26] Run complete: 02:13:00 elapsed