[2014-04-27 07:45:38] Beginning TopHat run (v2.0.8b)
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[2014-04-27 07:45:38] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-27 07:45:38] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-27 07:45:38] Checking for Bowtie index files
[2014-04-27 07:45:38] Checking for reference FASTA file
[2014-04-27 07:45:38] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-27 07:45:40] Preparing reads
	 left reads: min. length=60, max. length=101, 19536144 kept reads (9282 discarded)
[2014-04-27 07:53:40] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-27 08:17:35] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-27 08:19:44] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-27 08:22:06] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-27 08:24:49] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-27 08:27:40] Searching for junctions via segment mapping
[2014-04-27 08:32:18] Retrieving sequences for splices
[2014-04-27 08:34:20] Indexing splices
[2014-04-27 08:35:21] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-27 08:36:26] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-27 08:37:44] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-27 08:39:03] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-27 08:40:19] Joining segment hits
[2014-04-27 08:43:47] Reporting output tracks
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[2014-04-27 08:55:18] Run complete: 01:09:40 elapsed