[2014-04-26 01:52:35] Beginning TopHat run (v2.0.8b)
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[2014-04-26 01:52:35] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-26 01:52:35] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-26 01:52:35] Checking for Bowtie index files
[2014-04-26 01:52:35] Checking for reference FASTA file
[2014-04-26 01:52:35] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-26 01:52:37] Preparing reads
	 left reads: min. length=60, max. length=101, 26784844 kept reads (7444 discarded)
[2014-04-26 02:03:26] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-26 02:37:55] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-26 02:40:28] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-26 02:43:19] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-26 02:46:27] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-26 02:49:40] Searching for junctions via segment mapping
[2014-04-26 02:53:50] Retrieving sequences for splices
[2014-04-26 02:55:52] Indexing splices
[2014-04-26 02:56:43] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-26 02:57:46] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-26 02:59:03] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-26 03:00:19] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-26 03:01:33] Joining segment hits
[2014-04-26 03:05:03] Reporting output tracks
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[2014-04-26 03:20:16] Run complete: 01:27:41 elapsed