[2014-04-29 09:25:36] Beginning TopHat run (v2.0.8b)
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[2014-04-29 09:25:36] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-29 09:25:36] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-29 09:25:36] Checking for Bowtie index files
[2014-04-29 09:25:36] Checking for reference FASTA file
[2014-04-29 09:25:36] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-29 09:25:38] Preparing reads
	 left reads: min. length=60, max. length=101, 22316849 kept reads (10929 discarded)
[2014-04-29 09:34:36] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-29 10:04:21] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-29 10:07:00] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-29 10:09:55] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-29 10:14:41] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-29 10:17:51] Searching for junctions via segment mapping
[2014-04-29 10:51:16] Retrieving sequences for splices
[2014-04-29 10:53:13] Indexing splices
[2014-04-29 10:54:03] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-29 10:55:46] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-29 10:57:42] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-29 10:59:42] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-29 11:01:33] Joining segment hits
[2014-04-29 11:06:30] Reporting output tracks
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[2014-04-29 11:20:27] Run complete: 01:54:51 elapsed