[2014-05-29 11:17:31] Beginning TopHat run (v2.0.8b)
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[2014-05-29 11:17:31] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 11:17:31] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 11:17:31] Checking for Bowtie index files
[2014-05-29 11:17:31] Checking for reference FASTA file
[2014-05-29 11:17:31] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 11:17:33] Preparing reads
	 left reads: min. length=60, max. length=101, 29889024 kept reads (1222 discarded)
[2014-05-29 11:30:06] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 12:11:13] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 12:13:52] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 12:16:51] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 12:20:15] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 12:24:12] Searching for junctions via segment mapping
[2014-05-29 12:29:11] Retrieving sequences for splices
[2014-05-29 12:31:18] Indexing splices
[2014-05-29 12:32:09] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 12:33:39] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 12:35:29] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 12:37:19] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 12:38:55] Joining segment hits
[2014-05-29 12:42:50] Reporting output tracks
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[2014-05-29 12:59:08] Run complete: 01:41:36 elapsed