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HyPhy standalone analyses
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SCUEAL-WG tool #22

Open juanledesma78 opened 2 years ago

juanledesma78 commented 2 years ago

Dear hyphy team,

I would like to use SCUEL-WG tool on HIV whole genomes we have generated so that we can study their subtype and the presence of potential recombinants.

I have installed hyphy using bioconda
HYPHY 2.5.8(MP) for Linux on x86_64

and then cloned the hyphy-analyses and try to run the script using this

$ cd hyphy-analyses/SCUEAL-WG/
$ hyphy ./SCUEALfullG.bf --alignment ../testRS.fas

But I have got this error

Error:
Could not read command file from '/localdisk/software/SCUEAL_fullG/SCUEAL-master/TopLevel/MPIScreenFASTA.bf' (expanded to '/localdisk/software/SCUEAL_fullG/SCUEAL-master/TopLevel/MPIScreenFASTA.bf') in call to ExecuteAFile("/localdisk/software/SCUEAL_fullG/SCUEAL-master/TopLevel/MPIScreenFASTA.bf", /home/juan/hyphy-analyses/SCUEAL-WG/./, inArguments);

Function call stack
1 :  ExecuteAFile("/localdisk/software/SCUEAL_fullG/SCUEAL-master/TopLevel/MPIScreenFASTA.bf", /home/juan/hyphy-analyses/SCUEAL-WG/./, inArguments);

    Keyword arguments:
        {
         "alignment":"../testRS.fas"
        }
-------

Check errors.log for execution error details.

I am not familiar with hyphy so I would appreciate any help/advice on how to use SCUEAL-WG, as it would be very useful for us.

Regards

Juan