OK, so now I have another issue, related to the "Run Custom" suggestion: Using the HYPHYMP version, after "run custom" you are asked about "rate variation options", and you can select multiple options.. Typing in d gets you past this bank of selections and on to the 'distribution options'..
When I try to implement this into the wrapper file and using the MPI version, it does not work, seems to not accept the 'd' command to complete this set of selections..
Batchfile:
Code:inputOptions = {};
inputOptions ["00"] = PATH_TO_CURRENT_BF + ".." + DIRECTORY_SEPARATOR + "data" + DIRECTORY_SEPARATOR + "data1.txt";
inputOptions ["01"] = "Universal";
inputOptions ["02"] = "y";
inputOptions ["03"] = "Codon Model";
inputOptions ["04"] = "MG94xREV";
inputOptions ["05"] = "Run Custom";
inputOptions ["06"] = "Dual";
inputOptions ["07"] = "d";
inputOptions ["08"] = "Independent Discrete";
inputOptions ["09"] = "Randomized";
inputOptions ["10"] = "3";
inputOptions ["11"] = "3";
inputOptions ["12"] = PATH_TO_CURRENT_BF + ".." + DIRECTORY_SEPARATOR + "Results" + DIRECTORY_SEPARATOR + "testingREL751.txt";;
ExecuteAFile (HYPHY_BASE_DIRECTORY + "TemplateBatchFiles" + DIRECTORY_SEPARATOR + "dNdSRateAnalysis.bf", inputOptions);
error:
Code:Master node received an error:
Not a valid (or duplicate) option: 'd' passed to Choice List (with multiple selections) 'Rate Variation Models' using redirected stdin input
Call stack
2 : Choice List for Rate Variation Models with choice list:SKIP_NONE. Store result in modelTypes
1 : ExecuteAFile from file HYPHY_BASE_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"dNdSRateAnalysis.bf" using basepath /home/macmanes/hyphy1/TestSuite/REL/. reading input from inputOptions
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mpirun noticed that process rank 0 with PID 7431 on node macmanes exited on signal 11 (Segmentation fault).
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I get basically the same error when not using the 'd' option.