[2014-05-28 19:50:32] Beginning TopHat run (v2.0.8b)
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[2014-05-28 19:50:32] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 19:50:32] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 19:50:32] Checking for Bowtie index files
[2014-05-28 19:50:32] Checking for reference FASTA file
[2014-05-28 19:50:32] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 19:50:34] Preparing reads
	 left reads: min. length=60, max. length=101, 26128748 kept reads (1802 discarded)
[2014-05-28 20:03:32] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 20:45:59] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 20:49:49] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 20:53:55] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 20:58:05] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 21:02:56] Searching for junctions via segment mapping
[2014-05-28 21:09:24] Retrieving sequences for splices
[2014-05-28 21:11:32] Indexing splices
[2014-05-28 21:12:09] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 21:16:31] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 21:21:15] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 21:25:52] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 21:30:52] Joining segment hits
[2014-05-28 21:36:06] Reporting output tracks
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[2014-05-28 21:52:09] Run complete: 02:01:37 elapsed