[2014-04-29 05:36:33] Beginning TopHat run (v2.0.8b)
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[2014-04-29 05:36:33] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-29 05:36:33] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-29 05:36:33] Checking for Bowtie index files
[2014-04-29 05:36:33] Checking for reference FASTA file
[2014-04-29 05:36:33] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-29 05:36:36] Preparing reads
	 left reads: min. length=60, max. length=101, 20955423 kept reads (9647 discarded)
[2014-04-29 05:45:00] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-29 06:12:26] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-29 06:14:58] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-29 06:17:46] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-29 06:22:26] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-29 06:25:33] Searching for junctions via segment mapping
[2014-04-29 06:54:05] Retrieving sequences for splices
[2014-04-29 06:56:06] Indexing splices
[2014-04-29 06:56:54] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-29 06:58:37] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-29 07:00:34] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-29 07:02:37] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-29 07:04:35] Joining segment hits
[2014-04-29 07:08:42] Reporting output tracks
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[2014-04-29 07:20:58] Run complete: 01:44:25 elapsed