[2014-04-29 11:20:27] Beginning TopHat run (v2.0.8b)
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[2014-04-29 11:20:27] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-29 11:20:27] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-29 11:20:27] Checking for Bowtie index files
[2014-04-29 11:20:27] Checking for reference FASTA file
[2014-04-29 11:20:27] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-29 11:20:43] Preparing reads
	 left reads: min. length=60, max. length=101, 19608293 kept reads (8487 discarded)
[2014-04-29 11:28:43] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-29 11:53:52] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-29 11:56:04] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-29 11:58:29] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-29 12:01:11] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-29 12:04:02] Searching for junctions via segment mapping
[2014-04-29 12:25:38] Retrieving sequences for splices
[2014-04-29 12:27:36] Indexing splices
[2014-04-29 12:28:24] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-29 12:29:51] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-29 12:31:31] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-29 12:33:13] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-29 12:34:53] Joining segment hits
[2014-04-29 12:38:45] Reporting output tracks
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[2014-04-29 12:50:31] Run complete: 01:30:03 elapsed