Hi Sergei,
Thanks again for the response!! The revised batch file you attached gave me a directory error:
Quote:Error:
Could not read command file in ExecuteAFile from: /usr/local/src/hyphy/HYPHY/TemplateBatchFiles/HYPHY_LIB_DIRECTORY+"TemplateBatch
Files"+DIRECTORY_SEPARATOR+"TemplateModels"+DIRECTORY_SEPARATOR+"chooseGeneticCo
de.def"
Function call stack
1 : ExecuteAFile from file HYPHY_LIB_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"TemplateModels"+DI
RECTORY_SEPARATOR+"chooseGeneticCode.def" using basepath /usr/local/src/hyphy/HYPHY/TemplateBatchFiles/.
I changed HYPHY_LIB_DIRECTORY to HYPHY_BASE_DIRECTORY and, once again, the first file runs and the wrapper breaks running the second file. Here is the error:
Quote:Error:
Cannot reuse the filter 'dsf' because it is already being used by likelihood function 'three_LF', and the two likelihood functions impose different leaf-to-sequence mapping. Create a copy the filter and pass it to the second likelihood function to resolve this issue.
Function call stack
1 : Construct the following likelihood function:dsf ; givenTree ;
Standard input redirect:
Empty Associative List-------
2 : ExecuteAFile from file filetoExe using basepath /. reading input from inputRedirect
{"01":"Universal",
"02":"/FASTA_CDS/test2.nex",
"03":"/FASTA_CDS/test2.tree",
"04":"WILD",
"05":"",
"06":"/FASTA_CDS/test2.out"}
I really appreciate your help. Please let me know if there is any further info I can provide you that could help sort this out.
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