[2014-05-29 06:12:59] Beginning TopHat run (v2.0.8b)
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[2014-05-29 06:12:59] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 06:12:59] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 06:12:59] Checking for Bowtie index files
[2014-05-29 06:12:59] Checking for reference FASTA file
[2014-05-29 06:12:59] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 06:13:01] Preparing reads
	 left reads: min. length=60, max. length=101, 29876405 kept reads (369 discarded)
[2014-05-29 06:25:49] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 07:12:06] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 07:15:52] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 07:20:19] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 07:25:12] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 07:30:32] Searching for junctions via segment mapping
[2014-05-29 07:36:11] Retrieving sequences for splices
[2014-05-29 07:38:16] Indexing splices
[2014-05-29 07:39:20] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 07:41:22] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 07:44:11] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 07:46:59] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 07:49:23] Joining segment hits
[2014-05-29 07:53:19] Reporting output tracks
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[2014-05-29 08:08:35] Run complete: 01:55:35 elapsed