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 Oy_0/ -G /Net/mus/data/www/arabcall/TAIR10_GFF3_genes_transposons.gff /Net/mus/data/arabidopsis/xiang/tair10_um Oy_0//Run33_lane5_Oy_0_seedling.fastq.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 Oy_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 14:46:50 2011] Reading known junctions from GTF file
[Mon May 23 15:17:45 2011] Mapping reads against tair10_um with Bowtie
[Mon May 23 18:33:36 2011] Joining segment hits
[Mon May 23 19:34:18 2011] Mapping reads against tair10_um with Bowtie(1/3)
[Mon May 23 20:29:11 2011] Mapping reads against tair10_um with Bowtie(2/3)
[Mon May 23 21:23:32 2011] Mapping reads against tair10_um with Bowtie(3/3)
[Mon May 23 21:56:20 2011] Searching for junctions via segment mapping
[Mon May 23 23:39:27 2011] Retrieving sequences for splices
[Mon May 23 23:40:28 2011] Indexing splices
[Mon May 23 23:50:35 2011] Mapping reads against segment_juncs with Bowtie
[Tue May 24 00:40:12 2011] Mapping reads against segment_juncs with Bowtie
[Tue May 24 01:30:21 2011] Mapping reads against segment_juncs with Bowtie
[Tue May 24 01:54:13 2011] Joining segment hits
[Tue May 24 02:37:45 2011] Reporting output tracks
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Run complete [13:38:39 elapsed]
[sam_header_read2] 7 sequences loaded.