[2014-04-28 04:05:42] Beginning TopHat run (v2.0.8b)
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[2014-04-28 04:05:42] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-28 04:05:42] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-28 04:05:42] Checking for Bowtie index files
[2014-04-28 04:05:42] Checking for reference FASTA file
[2014-04-28 04:05:42] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-28 04:05:46] Preparing reads
	 left reads: min. length=60, max. length=101, 19543945 kept reads (9779 discarded)
[2014-04-28 04:13:29] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-28 04:37:58] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-28 04:41:18] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-28 04:44:38] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-28 04:47:56] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-28 04:51:30] Searching for junctions via segment mapping
[2014-04-28 05:54:47] Retrieving sequences for splices
[2014-04-28 05:56:50] Indexing splices
[2014-04-28 05:57:37] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-28 06:05:08] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-28 06:12:06] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-28 06:18:33] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-28 06:26:15] Joining segment hits
[2014-04-28 06:34:34] Reporting output tracks
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[2014-04-28 06:46:00] Run complete: 02:40:17 elapsed