# Make.file problem

**URL:** <https://forum.mothur.org/t/make-file-problem/3097>\
**Category:** Commands in mothur\
**Created:** [January 29, 2017, 8:01pm UTC](https://forum.mothur.org/t/make-file-problem/3097 "2017-01-29T20:01:59Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![santiago](https://avatars.discourse-cdn.com/v4/letter/s/3bc359/32.png) [@santiago](https://forum.mothur.org/u/santiago)\
**Post date:** [January 29, 2017, 8:01pm UTC](https://forum.mothur.org/t/make-file-problem/3097/1 "2017-01-29T20:01:59Z")

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Hi there,

I come here in search of your kindly help please.

I trying to analize some sequences, I saw the example called MiSeq\_SOP and the first step in the analysis is to make a file of your sequences.

I am ashame because I can not start. I try the first step with the command make.file and the program responses:

“Ls” is not recognized as an internal or external command, program or executable batch file. Unable to find any fastq files in your directory.

Someone can help me please, what im doing bad?..

thank you very much in advance, best regards.

Santiago.

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<div class="post-metadata">

**Author:** ![santiago](https://avatars.discourse-cdn.com/v4/letter/s/3bc359/32.png) [@santiago](https://forum.mothur.org/u/santiago)\
**Post date:** [January 29, 2017, 9:02pm UTC](https://forum.mothur.org/t/make-file-problem/3097/2 "2017-01-29T21:02:27Z")

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Here are the commands I used:

make.file(inputdir=MiSeq\_SOP, type=fastq, prefix=stability)

Setting input directory to: MiSeq\_SOP  
“ls” no se reconoce como un comando interno o externo,  
programa o archivo por lotes ejecutable.  
[WARNING]: Unable to find any fastq files in your directory.

Output File Names:

Thank you all

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<div class="post-metadata">

**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\
**Post date:** [January 30, 2017, 1:54pm UTC](https://forum.mothur.org/t/make-file-problem/3097/3 "2017-01-30T13:54:23Z")

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You need to type

```nohighlight
system(ls)

```

at the mothur prompt. Also, if you could post the English version of the error messages that would be helpful in the future.

Thanks!  
Pat