[2014-05-27 15:28:42] Beginning TopHat run (v2.0.8b)
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[2014-05-27 15:28:42] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 15:28:42] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 15:28:42] Checking for Bowtie index files
[2014-05-27 15:28:42] Checking for reference FASTA file
[2014-05-27 15:28:42] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 15:28:44] Preparing reads
	 left reads: min. length=60, max. length=101, 25261691 kept reads (1279 discarded)
[2014-05-27 15:38:54] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 16:25:01] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 16:36:09] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 16:46:56] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 16:57:41] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 17:09:44] Searching for junctions via segment mapping
[2014-05-27 22:14:42] Retrieving sequences for splices
[2014-05-27 22:16:43] Indexing splices
[2014-05-27 22:18:00] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 22:39:11] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-27 23:00:17] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-27 23:20:07] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 23:41:44] Joining segment hits
[2014-05-27 23:51:06] Reporting output tracks
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[2014-05-28 00:06:43] Run complete: 08:38:00 elapsed