[2014-05-05 02:47:09] Beginning TopHat run (v2.0.8b)
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[2014-05-05 02:47:09] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-05 02:47:09] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-05 02:47:09] Checking for Bowtie index files
[2014-05-05 02:47:09] Checking for reference FASTA file
[2014-05-05 02:47:09] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-05 02:47:11] Preparing reads
	 left reads: min. length=60, max. length=101, 29598742 kept reads (5878 discarded)
[2014-05-05 02:59:12] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-05 03:38:33] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-05 03:41:23] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-05 03:44:37] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-05 03:48:05] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-05 03:51:37] Searching for junctions via segment mapping
[2014-05-05 03:57:04] Retrieving sequences for splices
[2014-05-05 03:59:00] Indexing splices
[2014-05-05 03:59:55] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-05 04:01:16] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-05 04:02:53] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-05 04:04:31] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-05 04:06:08] Joining segment hits
[2014-05-05 04:10:04] Reporting output tracks
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[2014-05-05 04:27:25] Run complete: 01:40:16 elapsed