[2014-05-05 22:27:58] Beginning TopHat run (v2.0.8b)
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[2014-05-05 22:27:58] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-05 22:27:58] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-05 22:27:58] Checking for Bowtie index files
[2014-05-05 22:27:58] Checking for reference FASTA file
[2014-05-05 22:27:58] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-05 22:28:18] Preparing reads
	 left reads: min. length=60, max. length=101, 29605003 kept reads (7129 discarded)
[2014-05-05 22:40:25] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-05 23:22:06] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-05 23:25:09] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-05 23:28:25] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-05 23:31:48] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-05 23:35:23] Searching for junctions via segment mapping
[2014-05-05 23:51:44] Retrieving sequences for splices
[2014-05-05 23:53:47] Indexing splices
[2014-05-05 23:54:55] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-05 23:57:33] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-06 00:00:30] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-06 00:03:20] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-06 00:06:24] Joining segment hits
[2014-05-06 00:12:22] Reporting output tracks
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[2014-05-06 00:33:14] Run complete: 02:05:15 elapsed