[2014-05-29 11:23:26] Beginning TopHat run (v2.0.8b)
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[2014-05-29 11:23:26] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 11:23:26] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 11:23:26] Checking for Bowtie index files
[2014-05-29 11:23:26] Checking for reference FASTA file
[2014-05-29 11:23:26] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 11:23:28] Preparing reads
	 left reads: min. length=60, max. length=101, 28910987 kept reads (675 discarded)
[2014-05-29 11:37:33] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 12:16:41] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 12:19:15] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 12:22:03] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 12:25:00] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 12:27:53] Searching for junctions via segment mapping
[2014-05-29 12:31:43] Retrieving sequences for splices
[2014-05-29 12:33:39] Indexing splices
[2014-05-29 12:34:28] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 12:35:43] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 12:37:31] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 12:39:20] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 12:40:54] Joining segment hits
[2014-05-29 12:44:55] Reporting output tracks
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[2014-05-29 13:01:39] Run complete: 01:38:12 elapsed