[2014-05-29 07:47:21] Beginning TopHat run (v2.0.8b)
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[2014-05-29 07:47:21] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 07:47:21] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 07:47:21] Checking for Bowtie index files
[2014-05-29 07:47:21] Checking for reference FASTA file
[2014-05-29 07:47:21] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 07:47:24] Preparing reads
	 left reads: min. length=60, max. length=101, 35382675 kept reads (459 discarded)
[2014-05-29 08:04:25] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 08:55:18] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 09:00:33] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 09:06:20] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 09:12:15] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 09:17:16] Searching for junctions via segment mapping
[2014-05-29 09:22:47] Retrieving sequences for splices
[2014-05-29 09:24:53] Indexing splices
[2014-05-29 09:26:25] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 09:29:07] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 09:32:26] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 09:35:46] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 09:38:42] Joining segment hits
[2014-05-29 09:43:23] Reporting output tracks
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[2014-05-29 10:02:40] Run complete: 02:15:18 elapsed