[2014-05-28 11:55:48] Beginning TopHat run (v2.0.8b)
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[2014-05-28 11:55:48] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 11:55:48] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 11:55:48] Checking for Bowtie index files
[2014-05-28 11:55:48] Checking for reference FASTA file
[2014-05-28 11:55:48] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 11:55:50] Preparing reads
	 left reads: min. length=60, max. length=101, 25983107 kept reads (1469 discarded)
[2014-05-28 12:07:34] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 12:47:14] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 12:50:34] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 12:54:16] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 12:58:04] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 13:01:59] Searching for junctions via segment mapping
[2014-05-28 13:06:43] Retrieving sequences for splices
[2014-05-28 13:08:51] Indexing splices
[2014-05-28 13:09:49] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 13:11:36] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 13:13:48] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 13:16:01] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 13:18:00] Joining segment hits
[2014-05-28 13:21:38] Reporting output tracks
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[2014-05-28 13:36:46] Run complete: 01:40:58 elapsed