[2014-05-27 12:19:52] Beginning TopHat run (v2.0.8b)
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[2014-05-27 12:19:52] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 12:19:52] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 12:19:52] Checking for Bowtie index files
[2014-05-27 12:19:52] Checking for reference FASTA file
[2014-05-27 12:19:52] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 12:19:54] Preparing reads
	 left reads: min. length=60, max. length=101, 24510357 kept reads (585 discarded)
[2014-05-27 12:29:59] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 13:12:04] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 13:15:00] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 13:17:35] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 13:20:15] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 13:22:59] Searching for junctions via segment mapping
[2014-05-27 13:27:22] Retrieving sequences for splices
[2014-05-27 13:29:26] Indexing splices
[2014-05-27 13:30:07] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 13:31:44] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-27 13:33:39] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-27 13:35:36] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 13:37:20] Joining segment hits
[2014-05-27 13:41:36] Reporting output tracks
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[2014-05-27 13:56:58] Run complete: 01:37:06 elapsed