[2014-05-29 17:15:04] Beginning TopHat run (v2.0.8b)
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[2014-05-29 17:15:04] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 17:15:04] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 17:15:04] Checking for Bowtie index files
[2014-05-29 17:15:04] Checking for reference FASTA file
[2014-05-29 17:15:04] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 17:15:07] Preparing reads
	 left reads: min. length=60, max. length=101, 24862523 kept reads (991 discarded)
[2014-05-29 17:26:26] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 18:01:55] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 18:04:19] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 18:06:47] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 18:09:45] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 18:12:13] Searching for junctions via segment mapping
[2014-05-29 18:15:52] Retrieving sequences for splices
[2014-05-29 18:17:49] Indexing splices
[2014-05-29 18:18:28] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 18:19:30] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 18:20:47] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 18:22:05] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 18:23:08] Joining segment hits
[2014-05-29 18:26:12] Reporting output tracks
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[2014-05-29 18:40:23] Run complete: 01:25:19 elapsed