[2014-05-29 13:01:39] Beginning TopHat run (v2.0.8b)
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[2014-05-29 13:01:39] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 13:01:39] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 13:01:39] Checking for Bowtie index files
[2014-05-29 13:01:39] Checking for reference FASTA file
[2014-05-29 13:01:39] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 13:01:41] Preparing reads
	 left reads: min. length=60, max. length=101, 23393739 kept reads (1315 discarded)
[2014-05-29 13:11:29] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 13:49:10] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 13:54:07] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 13:59:51] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 14:05:09] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 14:11:05] Searching for junctions via segment mapping
[2014-05-29 14:56:06] Retrieving sequences for splices
[2014-05-29 14:58:16] Indexing splices
[2014-05-29 14:59:10] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 15:13:42] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 15:28:43] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 15:43:03] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 16:00:09] Joining segment hits
[2014-05-29 16:09:30] Reporting output tracks
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[2014-05-29 16:23:42] Run complete: 03:22:03 elapsed