[2014-05-29 04:40:09] Beginning TopHat run (v2.0.8b)
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[2014-05-29 04:40:09] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 04:40:09] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 04:40:09] Checking for Bowtie index files
[2014-05-29 04:40:09] Checking for reference FASTA file
[2014-05-29 04:40:09] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 04:40:11] Preparing reads
	 left reads: min. length=60, max. length=101, 38269988 kept reads (1454 discarded)
[2014-05-29 04:57:42] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 05:59:21] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 06:04:15] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 06:09:29] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 06:14:31] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 06:20:12] Searching for junctions via segment mapping
[2014-05-29 06:26:58] Retrieving sequences for splices
[2014-05-29 06:28:53] Indexing splices
[2014-05-29 06:29:28] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 06:36:54] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 06:45:04] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 06:52:54] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 07:01:15] Joining segment hits
[2014-05-29 07:08:46] Reporting output tracks
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[2014-05-29 07:30:11] Run complete: 02:50:01 elapsed