[2014-05-05 15:02:16] Beginning TopHat run (v2.0.8b)
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[2014-05-05 15:02:16] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-05 15:02:16] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-05 15:02:16] Checking for Bowtie index files
[2014-05-05 15:02:16] Checking for reference FASTA file
[2014-05-05 15:02:16] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-05 15:02:19] Preparing reads
	 left reads: min. length=60, max. length=101, 29467771 kept reads (6169 discarded)
[2014-05-05 15:14:13] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-05 15:51:12] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-05 15:54:38] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-05 15:58:32] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-05 16:02:34] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-05 16:07:05] Searching for junctions via segment mapping
[2014-05-05 16:14:35] Retrieving sequences for splices
[2014-05-05 16:16:30] Indexing splices
[2014-05-05 16:17:00] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-05 16:20:25] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-05 16:24:07] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-05 16:27:43] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-05 16:31:39] Joining segment hits
[2014-05-05 16:38:12] Reporting output tracks
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[2014-05-05 16:56:48] Run complete: 01:54:32 elapsed