reference: /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 Col_0/ -G /data/www/arabcall/TAIR10_GFF3_genes_transposons.gff /data/arabidopsis/xiang/tair10_um Col_0//Run33_lane2_Col_0_seedling.fastq.flt_1.fq

[Mon May 23 11:05:58 2011] Beginning TopHat run (v1.2.0)
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[Mon May 23 11:05:58 2011] Preparing output location Col_0//
[Mon May 23 11:05:58 2011] Checking for Bowtie index files
[Mon May 23 11:05:58 2011] Checking for reference FASTA file
[Mon May 23 11:05:58 2011] Checking for Bowtie
	Bowtie version:			 0.12.7.0
[Mon May 23 11:05:58 2011] Checking for Samtools
	Samtools Version: 0.1.7
[Mon May 23 11:05:59 2011] Checking reads
	min read length: 82bp, max read length: 82bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon May 23 11:22:21 2011] Reading known junctions from GTF file
[Mon May 23 11:30:41 2011] Mapping reads against tair10_um with Bowtie
[Mon May 23 13:16:31 2011] Joining segment hits
[Mon May 23 13:41:34 2011] Mapping reads against tair10_um with Bowtie(1/3)
[Mon May 23 14:21:13 2011] Mapping reads against tair10_um with Bowtie(2/3)
[Mon May 23 14:52:56 2011] Mapping reads against tair10_um with Bowtie(3/3)
[Mon May 23 15:07:19 2011] Searching for junctions via segment mapping
[Mon May 23 16:19:17 2011] Retrieving sequences for splices
[Mon May 23 16:20:40 2011] Indexing splices
[Mon May 23 16:34:18 2011] Mapping reads against segment_juncs with Bowtie
[Mon May 23 17:23:27 2011] Mapping reads against segment_juncs with Bowtie
[Mon May 23 18:03:00 2011] Mapping reads against segment_juncs with Bowtie
[Mon May 23 18:20:51 2011] Joining segment hits
[Mon May 23 18:38:32 2011] Reporting output tracks
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Run complete [08:20:14 elapsed]
[sam_header_read2] 7 sequences loaded.