[2014-05-24 20:36:48] Beginning TopHat run (v2.0.8b)
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[2014-05-24 20:36:48] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-24 20:36:48] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-24 20:36:48] Checking for Bowtie index files
[2014-05-24 20:36:48] Checking for reference FASTA file
[2014-05-24 20:36:48] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-24 20:36:50] Preparing reads
	 left reads: min. length=60, max. length=101, 21971951 kept reads (2001 discarded)
[2014-05-24 20:46:17] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-24 21:22:02] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-24 21:25:05] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-24 21:28:03] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-24 21:31:21] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-24 21:35:17] Searching for junctions via segment mapping
[2014-05-24 21:41:04] Retrieving sequences for splices
[2014-05-24 21:43:02] Indexing splices
[2014-05-24 21:43:29] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-24 21:47:23] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-24 21:51:15] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-24 21:55:04] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-24 21:59:12] Joining segment hits
[2014-05-24 22:03:46] Reporting output tracks
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[2014-05-24 22:18:16] Run complete: 01:41:27 elapsed