[2014-05-06 04:21:20] Beginning TopHat run (v2.0.8b)
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[2014-05-06 04:21:20] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-06 04:21:20] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-06 04:21:20] Checking for Bowtie index files
[2014-05-06 04:21:20] Checking for reference FASTA file
[2014-05-06 04:21:20] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-06 04:21:34] Preparing reads
	 left reads: min. length=60, max. length=101, 28128325 kept reads (11547 discarded)
[2014-05-06 04:33:08] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-06 05:16:06] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-06 05:19:39] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-06 05:23:17] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-06 05:26:59] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-06 05:30:26] Searching for junctions via segment mapping
[2014-05-06 05:40:23] Retrieving sequences for splices
[2014-05-06 05:42:24] Indexing splices
[2014-05-06 05:43:22] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-06 05:45:09] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-06 05:47:10] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-06 05:49:05] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-06 05:51:02] Joining segment hits
[2014-05-06 05:56:38] Reporting output tracks
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[2014-05-06 06:16:43] Run complete: 01:55:23 elapsed