[2014-05-29 08:08:35] Beginning TopHat run (v2.0.8b)
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[2014-05-29 08:08:35] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 08:08:35] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 08:08:35] Checking for Bowtie index files
[2014-05-29 08:08:35] Checking for reference FASTA file
[2014-05-29 08:08:35] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 08:08:37] Preparing reads
	 left reads: min. length=60, max. length=101, 21518076 kept reads (1614 discarded)
[2014-05-29 08:17:11] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 08:48:46] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 08:53:38] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 08:58:52] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 09:03:38] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 09:09:04] Searching for junctions via segment mapping
[2014-05-29 09:51:07] Retrieving sequences for splices
[2014-05-29 09:53:17] Indexing splices
[2014-05-29 09:54:04] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 10:09:44] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 10:24:56] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 10:38:42] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 10:56:05] Joining segment hits
[2014-05-29 11:05:35] Reporting output tracks
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[2014-05-29 11:17:30] Run complete: 03:08:54 elapsed