[2014-05-28 04:48:26] Beginning TopHat run (v2.0.8b)
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[2014-05-28 04:48:26] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 04:48:26] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 04:48:26] Checking for Bowtie index files
[2014-05-28 04:48:26] Checking for reference FASTA file
[2014-05-28 04:48:26] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 04:48:28] Preparing reads
	 left reads: min. length=60, max. length=101, 27563572 kept reads (2190 discarded)
[2014-05-28 05:00:32] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 05:54:08] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 06:10:38] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 06:27:34] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 06:44:16] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 07:03:34] Searching for junctions via segment mapping
[2014-05-28 15:26:24] Retrieving sequences for splices
[2014-05-28 15:28:35] Indexing splices
[2014-05-28 15:30:13] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 16:03:21] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 16:37:50] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 17:12:03] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 17:45:34] Joining segment hits
[2014-05-28 17:56:31] Reporting output tracks
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[2014-05-28 18:15:12] Run complete: 13:26:46 elapsed