reference: /Net/mus/data/arabidopsis/xiang/tair10_um.fa
tophat --num-threads 4 --library-type fr-firststrand --mate-inner-dist 38 --mate-std-dev 40 --max-multihits 10 --coverage-search --microexon-search -o Tsu_0/ -G /Net/mus/data/www/arabcall/TAIR10_GFF3_genes_transposons.gff /Net/mus/data/arabidopsis/xiang/tair10_um Tsu_0//Run34_lane3_Tsu_0_seedling.flt_1.fq

[Mon May 23 14:14:46 2011] Beginning TopHat run (v1.2.0)
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[Mon May 23 14:14:46 2011] Preparing output location Tsu_0//
[Mon May 23 14:14:46 2011] Checking for Bowtie index files
[Mon May 23 14:14:46 2011] Checking for reference FASTA file
[Mon May 23 14:14:46 2011] Checking for Bowtie
	Bowtie version:			 0.12.7.0
[Mon May 23 14:14:46 2011] Checking for Samtools
	Samtools Version: 0.1.7
[Mon May 23 14:14:48 2011] Checking reads
	min read length: 82bp, max read length: 82bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon May 23 14:54:18 2011] Reading known junctions from GTF file
[Mon May 23 15:20:52 2011] Mapping reads against tair10_um with Bowtie
[Mon May 23 18:34:00 2011] Joining segment hits
[Mon May 23 19:35:04 2011] Mapping reads against tair10_um with Bowtie(1/3)
[Mon May 23 20:30:16 2011] Mapping reads against tair10_um with Bowtie(2/3)
[Mon May 23 21:26:04 2011] Mapping reads against tair10_um with Bowtie(3/3)
[Mon May 23 22:00:18 2011] Searching for junctions via segment mapping
[Mon May 23 23:41:29 2011] Retrieving sequences for splices
[Mon May 23 23:42:29 2011] Indexing splices
[Mon May 23 23:51:31 2011] Mapping reads against segment_juncs with Bowtie
[Tue May 24 00:43:08 2011] Mapping reads against segment_juncs with Bowtie
[Tue May 24 01:33:04 2011] Mapping reads against segment_juncs with Bowtie
[Tue May 24 01:57:16 2011] Joining segment hits
[Tue May 24 02:29:04 2011] Reporting output tracks
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Run complete [13:39:48 elapsed]
[sam_header_read2] 7 sequences loaded.