[2014-05-28 06:22:12] Beginning TopHat run (v2.0.8b)
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[2014-05-28 06:22:12] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 06:22:12] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 06:22:12] Checking for Bowtie index files
[2014-05-28 06:22:12] Checking for reference FASTA file
[2014-05-28 06:22:12] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 06:22:14] Preparing reads
	 left reads: min. length=60, max. length=101, 24838893 kept reads (2763 discarded)
[2014-05-28 06:32:16] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 07:05:36] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 07:08:08] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 07:10:57] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 07:13:51] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 07:16:44] Searching for junctions via segment mapping
[2014-05-28 07:23:36] Retrieving sequences for splices
[2014-05-28 07:25:34] Indexing splices
[2014-05-28 07:26:26] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 07:28:23] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 07:30:42] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 07:32:59] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 07:35:09] Joining segment hits
[2014-05-28 07:38:52] Reporting output tracks
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[2014-05-28 07:52:35] Run complete: 01:30:23 elapsed