[2014-05-29 05:28:39] Beginning TopHat run (v2.0.8b)
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[2014-05-29 05:28:39] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 05:28:39] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 05:28:39] Checking for Bowtie index files
[2014-05-29 05:28:39] Checking for reference FASTA file
[2014-05-29 05:28:39] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 05:28:41] Preparing reads
	 left reads: min. length=60, max. length=101, 34789821 kept reads (483 discarded)
[2014-05-29 05:44:34] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 06:37:47] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 06:42:59] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 06:48:33] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 06:54:23] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 07:00:30] Searching for junctions via segment mapping
[2014-05-29 07:06:28] Retrieving sequences for splices
[2014-05-29 07:08:26] Indexing splices
[2014-05-29 07:09:45] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 07:12:13] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 07:15:35] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 07:18:56] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 07:21:55] Joining segment hits
[2014-05-29 07:27:12] Reporting output tracks
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[2014-05-29 07:47:21] Run complete: 02:18:41 elapsed