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HYPHY Package >> HyPhy feedback >> Running REL course http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1350619621 Message started by nextday on Oct 18th, 2012 at 9:07pm |
Title: Running REL course Post by nextday on Oct 18th, 2012 at 9:07pm
Hi, I begin to practice Hyphy2.1.2 on window XP follow your Workshop:Vancouver2011:SelectionAnalyses course.
When 1.2 Running REL and after 2 Choose Genetic Code : Universal, the program show the window:branch lengths:condon model/nucleotide model, which is different from your lesson. And after closed condon model/nucleotide model, the program show Model string:. If inputted Default, hyphy show the window Amino Acid Class Model : Default. But after that, it show the bar:Run out of input in buffer during a redirected standard input read. Current task has been terminated. Would you like to see the remaining error meddages, if there are any? After Y, it showed: Model string:default How many datafiles are to be analyzed (>=1):? Reading input file 1/1 ______________READ THE FOLLOWING DATA______________ 19 species:{Rabensburg_isolate,WNFCG,SPU116_89,KUNCG,Italy_1998_equine,PaAn001,KN3829,RO97_50,VLG_4,Ast99,PaH001,Mex03,IS_98,HNY1999,NY99_eqhs,NY99_flamingo,EthAn4766,Chin_01,Eg101}; Total Sites:1857; Distinct Sites:357 A tree was found in the data file: ((((((((((Rabensburg_isolate,(WNFCG,SPU116_89)),KUNCG),(EthAn4766,(Chin_01,Eg101))),(((Italy_1998_equine,PaAn001),(RO97_50,VLG_4)),KN3829)),Ast99),PaH001),IS_98),Mex03),NY99_flamingo),HNY1999,NY99_eqhs) Would you like to use it:(Y/N)? Please enter a 6 character model designation (e.g:010010 defines HKY85): Please enter a 6 character model designation (e.g:010010 defines HKY85): Please enter a 6 character model designation (e.g:010010 defines HKY85): Please enter a 6 character model designation (e.g:010010 defines HKY85): Please enter a 6 character model designation (e.g:010010 defines HKY85): Please enter a 6 character model designation (e.g:010010 defines HKY85): I changed the File:WN NS3.fas to nexus and separated the sequence and tree, but the progress all failed. Vancouver2011:SelectionAnalyses course is the simplest course for Hyphy I found on line. So please tell me how to continue practicing? Thanks a lot! |
Title: Re: Running REL course Post by Sergei on Oct 19th, 2012 at 11:54am
Hi there,
Thanks for letting me know about this discrepancy! I updated the wiki page with the correct instructions. Cheers, Sergei |
Title: Re: Running REL course Post by nextday on Oct 20th, 2012 at 5:31am
Hi, Sergi. Thank you very much for your timely replay and update. The program runs well. I think I need learn more about Hyphy and positive selection.
Have a nice weekend, |
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