[2014-05-29 16:17:42] Beginning TopHat run (v2.0.8b)
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[2014-05-29 16:17:42] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 16:17:42] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 16:17:42] Checking for Bowtie index files
[2014-05-29 16:17:42] Checking for reference FASTA file
[2014-05-29 16:17:42] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 16:17:44] Preparing reads
	 left reads: min. length=60, max. length=101, 21620011 kept reads (1635 discarded)
[2014-05-29 16:27:26] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 17:01:37] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 17:04:39] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 17:07:59] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 17:11:24] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 17:14:56] Searching for junctions via segment mapping
[2014-05-29 17:26:56] Retrieving sequences for splices
[2014-05-29 17:29:04] Indexing splices
[2014-05-29 17:29:52] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 17:31:51] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 17:34:06] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 17:36:22] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 17:38:32] Joining segment hits
[2014-05-29 17:42:34] Reporting output tracks
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[2014-05-29 17:56:08] Run complete: 01:38:25 elapsed