[2014-04-27 06:34:27] Beginning TopHat run (v2.0.8b)
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[2014-04-27 06:34:27] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-27 06:34:27] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-27 06:34:27] Checking for Bowtie index files
[2014-04-27 06:34:27] Checking for reference FASTA file
[2014-04-27 06:34:27] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-27 06:34:30] Preparing reads
	 left reads: min. length=60, max. length=101, 19950191 kept reads (9159 discarded)
[2014-04-27 06:42:42] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-27 07:07:56] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-27 07:10:03] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-27 07:12:23] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-27 07:15:09] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-27 07:18:03] Searching for junctions via segment mapping
[2014-04-27 07:22:38] Retrieving sequences for splices
[2014-04-27 07:24:36] Indexing splices
[2014-04-27 07:25:32] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-27 07:26:34] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-27 07:27:49] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-27 07:29:04] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-27 07:30:19] Joining segment hits
[2014-04-27 07:33:41] Reporting output tracks
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[2014-04-27 07:45:38] Run complete: 01:11:10 elapsed