[2014-04-30 06:23:19] Beginning TopHat run (v2.0.8b)
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[2014-04-30 06:23:19] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-30 06:23:19] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-30 06:23:19] Checking for Bowtie index files
[2014-04-30 06:23:19] Checking for reference FASTA file
[2014-04-30 06:23:19] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-30 06:23:22] Preparing reads
	 left reads: min. length=60, max. length=101, 20861845 kept reads (10455 discarded)
[2014-04-30 06:31:52] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-30 06:58:07] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-30 07:00:08] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-30 07:02:23] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-30 07:05:00] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-30 07:07:42] Searching for junctions via segment mapping
[2014-04-30 07:12:32] Retrieving sequences for splices
[2014-04-30 07:14:28] Indexing splices
[2014-04-30 07:15:08] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-30 07:16:04] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-30 07:17:12] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-30 07:18:20] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-30 07:19:27] Joining segment hits
[2014-04-30 07:22:47] Reporting output tracks
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[2014-04-30 07:35:11] Run complete: 01:11:51 elapsed