[2014-04-27 11:09:58] Beginning TopHat run (v2.0.8b)
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[2014-04-27 11:09:58] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-27 11:09:58] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-27 11:09:58] Checking for Bowtie index files
[2014-04-27 11:09:58] Checking for reference FASTA file
[2014-04-27 11:09:58] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-27 11:10:00] Preparing reads
	 left reads: min. length=60, max. length=101, 19925371 kept reads (9521 discarded)
[2014-04-27 11:18:10] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-27 11:43:14] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-27 11:45:24] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-27 11:47:44] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-27 11:50:26] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-27 11:53:18] Searching for junctions via segment mapping
[2014-04-27 11:58:05] Retrieving sequences for splices
[2014-04-27 12:00:01] Indexing splices
[2014-04-27 12:00:52] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-27 12:01:55] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-27 12:03:11] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-27 12:04:28] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-27 12:05:42] Joining segment hits
[2014-04-27 12:09:07] Reporting output tracks
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[2014-04-27 12:21:02] Run complete: 01:11:04 elapsed