mothur

Syntax error near unexpected token

Hi there I am working on a bioinformatics assignment and I am new to using mothur and have almost 0 experience using it, i have encountered an error and have absolutely 0 idea how to fix it. Anyways here it is, when i try to run the command "mothur > make.file(inputdir=PATH./MiSeq_SOP, type=fastq, prefix=stability), I get an error saying -bash: syntax error near unexpected token ā€˜(ā€™. I have no idea why! Any help would be greatly appreciated.

Hello! The error suggests you are putting a mothur command directly into the terminal? If so, first execute mothur by typing:
mothur
(or whatever path-to-mothur you need). If you are on a server with a submission system like LSF then you will need to specify that it is an interactive job, for example:
bsub -Is mothur

Once mothur is running you will have the prompt:
mothur >
And then you can type the command itself, for example:
make.file(inputdir=./miseqsopdata/MiSeq_SOP, type=fastq, prefix=stability)

Good luck with your assignment!

[Edit: note that the command bsub -Is is a capital ā€œiā€ !]

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Thankyou! I have revised path-to-mothur from bashrc profile, now, it is start to run when I execute mothor command. I very appreciate for your help.

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