[2014-05-27 10:32:40] Beginning TopHat run (v2.0.8b)
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[2014-05-27 10:32:40] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 10:32:40] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 10:32:40] Checking for Bowtie index files
[2014-05-27 10:32:40] Checking for reference FASTA file
[2014-05-27 10:32:40] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 10:32:52] Preparing reads
	 left reads: min. length=60, max. length=101, 29771652 kept reads (616 discarded)
[2014-05-27 10:44:58] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 11:30:30] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 11:33:55] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 11:37:50] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 11:41:56] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 11:45:21] Searching for junctions via segment mapping
[2014-05-27 11:50:19] Retrieving sequences for splices
[2014-05-27 11:52:21] Indexing splices
[2014-05-27 11:53:02] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 11:54:52] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-27 11:57:07] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-27 11:59:19] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 12:01:00] Joining segment hits
[2014-05-27 12:04:36] Reporting output tracks
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[2014-05-27 12:19:52] Run complete: 01:47:12 elapsed