# Syntax error near unexpected token

**URL:** https://forum.mothur.org/t/syntax-error-near-unexpected-token/21071
**Category:** Commands in mothur
**Created:** [July 25, 2021, 10:11am UTC](https://forum.mothur.org/t/syntax-error-near-unexpected-token/21071 "2021-07-25T10:11:35Z")
**Posts on this page:** 4
**Page:** 1

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### Author: ![1106351165](https://avatars.discourse-cdn.com/v4/letter/1/f4b2a3/32.png) [@1106351165](https://forum.mothur.org/u/1106351165)
#### Post date: [July 25, 2021, 10:11am UTC](https://forum.mothur.org/t/syntax-error-near-unexpected-token/21071/1 "2021-07-25T10:11:35Z")

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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 ‘(’. I have no idea why! Any help would be greatly appreciated.

 ![question](https://canada1.discourse-cdn.com/flex036/uploads/mothur/original/1X/6718a4b5dc372722ea0ddc46e6a6b0ee5f638a74.jpeg)

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### Author: ![SJSalter](https://avatars.discourse-cdn.com/v4/letter/s/e19adc/32.png) [@SJSalter](https://forum.mothur.org/u/SJSalter)
#### Post date: [July 26, 2021, 3:12pm UTC](https://forum.mothur.org/t/syntax-error-near-unexpected-token/21071/2 "2021-07-26T15:12:15Z")

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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 “i” !]

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### Author: ![1106351165](https://avatars.discourse-cdn.com/v4/letter/1/f4b2a3/32.png) [@1106351165](https://forum.mothur.org/u/1106351165)
#### Post date: [July 30, 2021, 1:23pm UTC](https://forum.mothur.org/t/syntax-error-near-unexpected-token/21071/3 "2021-07-30T13:23:11Z")

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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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### Author: ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)
#### Post date: [August 9, 2021, 1:24pm UTC](https://forum.mothur.org/t/syntax-error-near-unexpected-token/21071/4 "2021-08-09T13:24:05Z")

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