[2014-05-06 17:11:24] Beginning TopHat run (v2.0.8b)
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[2014-05-06 17:11:24] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-06 17:11:24] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-06 17:11:24] Checking for Bowtie index files
[2014-05-06 17:11:24] Checking for reference FASTA file
[2014-05-06 17:11:24] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-06 17:11:30] Preparing reads
	 left reads: min. length=60, max. length=101, 29769745 kept reads (9873 discarded)
[2014-05-06 17:25:20] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-06 18:08:05] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-06 18:16:42] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-06 18:24:58] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-06 18:32:35] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-06 18:40:13] Searching for junctions via segment mapping
[2014-05-06 19:39:54] Retrieving sequences for splices
[2014-05-06 19:42:12] Indexing splices
[2014-05-06 19:43:06] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-06 20:06:48] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-06 20:26:47] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-06 20:46:25] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-06 21:11:00] Joining segment hits
[2014-05-06 21:22:59] Reporting output tracks
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[2014-05-06 21:40:28] Run complete: 04:29:04 elapsed