[2014-04-29 04:02:04] Beginning TopHat run (v2.0.8b)
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[2014-04-29 04:02:04] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-29 04:02:04] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-29 04:02:04] Checking for Bowtie index files
[2014-04-29 04:02:04] Checking for reference FASTA file
[2014-04-29 04:02:04] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-29 04:02:06] Preparing reads
	 left reads: min. length=60, max. length=101, 18223378 kept reads (9164 discarded)
[2014-04-29 04:09:30] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-29 04:33:27] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-29 04:35:27] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-29 04:37:43] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-29 04:40:15] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-29 04:42:55] Searching for junctions via segment mapping
[2014-04-29 05:12:32] Retrieving sequences for splices
[2014-04-29 05:14:28] Indexing splices
[2014-04-29 05:15:18] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-29 05:16:45] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-29 05:18:27] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-29 05:20:08] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-29 05:21:53] Joining segment hits
[2014-04-29 05:25:29] Reporting output tracks
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[2014-04-29 05:36:32] Run complete: 01:34:28 elapsed