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Exiting now due to presumed problems *Got a NULL alignment. Exiting now due to presumed problems* %s output Score %4.2f bits over entire alignment. This will be different from per-alignment scores. See manual for details For computer parsable output, try %s -help or read the manual Scores as bits over a flat simple random model Scores as bits over a synchronous coding model %s #Complete Analysis ------------------------------------------------------------- Starting search...String %s was unable to converted into a start/end policy Could not open single dna sequence in %sCould not build a sequence database on %sI could not read the Comparison matrix file in %s; however, you are using a HMM so it is not needed. Please set the WISECONFIGDIR or WISEPERSONALDIR variable correctly to prevent this message.Could not read Comparison matrix file in %sCould not get gap string number %sCould not get ext string number %sCould not make %s out as query startCould not make %s out as query endWeird aln number string %s... Weird report stagger asked for %sUnable to set global/local switch on threestatedbCould not read hmm from %s Could not build a threestatemodel database from a single tsm. Weird!Proteins can only have local/global startend policies set, not %sCould not read Protein sequence in %sCould not build ThreeStateModel from a single protein sequence...No protein input file! Yikes!Could not get maximum main_block number %sCould not convert %s to a doubleflatCannot interpret [%s] as a null model string 312333333LCould not make default random model Could not read codon table file in %sWCould not open %s as an output file$Name: wise2-2-0 $%s (%s) This program is freely distributed under a GPL. See -version for more info Copyright (c) GRL limited: portions of the code are from separate copyrights spcwise in fasta format Options. In any order, '-' as filename (for any input) means stdin Don't use stdin for databases, as on-the-fly indexing is used Protein type [-protein,-prodb,-hmmer,-pfam] [default - protein] Dna type [-dnas,-dnadb] [default - dnadb] Dna [-tfor] Protein [-s,-t,-g,-e,-m] HMM [-hmmer,-hname] Model [-codon,-subs,-indel,-null] Alg [-kbyte,-alg,-aalg,-aln,-noh] Output [-pretty,-alb,-pal,-block,-divide] Standard [-help,-version,-silent,-quiet,-errorlog] For more help go %s -help. See WWW help at http://www.sanger.ac.uk/Software/Wise2/ %s Protein input type -protein [default] single protein -prodb protein fasta format db -pfam pfam hmm library -pfam2 pfam style model directory (2.1) -hmmer single hmmer 1.x HMM DNA input type -dnadb [default] dna fasta database -dnas a single dna fasta sequence DNA sequence options -tfor search forward strands only Protein comparison options -gap [%3d] gap penalty -ext [%3d] extension penalty -matrix [%s] Comparison matrix HMM options -hname For single hmms, use this as the name, not filename Model options -init [%s] [default/global/local/wing] start-end policy -codon [%s] Codon file -subs [%2.2g] Substitution error rate -indel [%2.2g] Insertion/deletion error rate -null [syn/flat] Random Model as synchronous or flat [default syn] -alln [%s] Probability of matching a NNN codon -flati Flat insert probabilities Algorithm options -alg [333/312] Algorithm used for searching [default %s] -aalg [312/333/333L] Algorithm used for alignment [default %s] -cut [%.2f] Bits cutoff for reporting in search algorithm -ecut [n/a] Evalue cutoff for single protein vs DNA searches. -aln [%d] Max number of alignments (even if above cut) -nohis Don't show histogram on single protein/hmm vs DNA search -report [0] Issue a report every x comparisons (default 0 comparisons) Output options for each alignment [default -pretty -para] -pretty show pretty ascii output -para show parameters -pep show protein translation, splicing frameshifts -mul protein mul format alignments [only for one HMM vs DNA db] -sum show summary output -alb show logical AlnBlock alignment -pal show raw matrix alignment -block [%s] Length of main block in pretty output -divide [%s] divide string for multiple outputs ------------------------------------------------------------- Wise2 - database searching mode unreleasedProgram: %s version: %s released: %s This program is freely distributed under a Gnu Public License. See -version for more info on copyright Bugs and credits to Ewan Birney Algorithm type: EstWise Search algorithm: %s Implementation: %s Single cdna vs protein dbProtein db vs cdna dbSingle protein vs cdna dbSearch mode: %s Protein info from: %s Dna info from: %s Comp Matrix: %s Gap open: %d Gap extension: %d Start/End %s Codon Table: %s Subs error: %2.2g Indel error: %2.2g synchronousNull model: %s modelledProtein Insertion: %s Alignment Alg %s Jan 1 2008%s Version: %s Released: %s Compiled: %s This program is freely distributed under a Gnu Public License The source code is copyright (c) GRL 1998 and others There is no warranty, implied or otherwise on the performance of this program For more information read the GNULICENSE file in the distribution Credits: Ewan Birney wrote the core code. Portions of this code was from HMMer1, written by Sean Eddy Portions of this code was from HMMer2, written by Sean Eddy codon.tablegapgextematrixmstalncodonalgaalgcutecutsubsindelinitallnnulldnasdnadbtforflatihmmerpfam2pfamproteinprodbhnamenohisprettypepmulparasumalbpaldivideblockreportWrong number of arguments (expect 2)! Arg line looked like (after option processing) %s one on one search. 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