# make.file warning: unable to find any fastq files in your directory

**URL:** <https://forum.mothur.org/t/make-file-warning-unable-to-find-any-fastq-files-in-your-directory/2922>\
**Category:** Commands in mothur\
**Created:** [July 18, 2016, 7:08pm UTC](https://forum.mothur.org/t/make-file-warning-unable-to-find-any-fastq-files-in-your-directory/2922 "2016-07-18T19:08:59Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![MISSIZXM](https://avatars.discourse-cdn.com/v4/letter/m/85f322/32.png) [@MISSIZXM](https://forum.mothur.org/u/MISSIZXM)\
**Post date:** [July 18, 2016, 7:08pm UTC](https://forum.mothur.org/t/make-file-warning-unable-to-find-any-fastq-files-in-your-directory/2922/1 "2016-07-18T19:08:59Z")

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I’m using Mothur 1.37.4 on a Windows 64-bit PC. I set the input directory to a folder called “sample 01”, and I used “get.current” command to confirm it.

I tried to use “make.file” command to generate a “files” file, but it didn’t work. Mothur kept sending me warning messages: “file not found-”\*fastq". Unable to find any fastq files in your directory." It’s interesting that when I use “fastq.info”, Mothur can read those fastq files, but only one at a time.

Please help me solve this problem. Thanks!!!

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**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [August 1, 2016, 5:16pm UTC](https://forum.mothur.org/t/make-file-warning-unable-to-find-any-fastq-files-in-your-directory/2922/2 "2016-08-01T17:16:50Z")

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Could you run the command in debug mode and post the results?

mothur \> set.dir(input=yourInputDirectory, debug=t)  
mothur \> make.file(…)

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<div class="post-metadata">

**Author:** ![MISSIZXM](https://avatars.discourse-cdn.com/v4/letter/m/85f322/32.png) [@MISSIZXM](https://forum.mothur.org/u/MISSIZXM)\
**Post date:** [August 9, 2016, 5:41pm UTC](https://forum.mothur.org/t/make-file-warning-unable-to-find-any-fastq-files-in-your-directory/2922/3 "2016-08-09T17:41:15Z")

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> [@westcott](#):
>
> Could you run the command in debug mode and post the results?
> 
> mothur \> set.dir(input=yourInputDirectory, debug=t)  
> mothur \> make.file(…)

Here are the results:

"mothur \> make.file(inputdir=C:\Users\Missi.HICHNER296\Desktop\sample01)

[DEBUG]: removed C:\Users\Missi.HICHNER296\Desktop\sample01\temp1470764249  
[DEBUG]: removed C:\Users\Missi.HICHNER296\Desktop\sample01\temp1470764249  
Setting input directory to: C:\Users\Missi.HICHNER296\Desktop\sample01  
[DEBUG]: removed C:\Users\Missi.HICHNER296\Desktop\sample01\temp1470764249  
find “C:\Users\Missi.HICHNER296\Desktop\sample01” -maxdepth 1 -name “_.fastq" \> “C:\Users\Missi.HICHNER296\Desktop\sample01\fileList.temp”  
File not found - "_.fastq”  
[DEBUG]: removed C:\Users\Missi.HICHNER296\Desktop\sample01\fileList.temp  
[WARNING]: Unable to find any fastq files in your directory.

Output File Names:"

Thank you!

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<div class="post-metadata">

**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [August 9, 2016, 7:57pm UTC](https://forum.mothur.org/t/make-file-warning-unable-to-find-any-fastq-files-in-your-directory/2922/4 "2016-08-09T19:57:11Z")

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Is the name of the directory C:\Users\Missi.HICHNER296\Desktop\sample01 or C:\Users\Missi.HICHNER296\Desktop\sample 01 with a space?

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<div class="post-metadata">

**Author:** ![MISSIZXM](https://avatars.discourse-cdn.com/v4/letter/m/85f322/32.png) [@MISSIZXM](https://forum.mothur.org/u/MISSIZXM)\
**Post date:** [August 10, 2016, 6:08pm UTC](https://forum.mothur.org/t/make-file-warning-unable-to-find-any-fastq-files-in-your-directory/2922/5 "2016-08-10T18:08:18Z")

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> [@westcott](#):
>
> Is the name of the directory C:\Users\Missi.HICHNER296\Desktop\sample01 or C:\Users\Missi.HICHNER296\Desktop\sample 01 with a space?

Sample01, no space

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**Author:** ![tallcuppajoe](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/tallcuppajoe/32/6_2.png) [@tallcuppajoe](https://forum.mothur.org/u/tallcuppajoe)\
**Post date:** [October 19, 2016, 8:12pm UTC](https://forum.mothur.org/t/make-file-warning-unable-to-find-any-fastq-files-in-your-directory/2922/6 "2016-10-19T20:12:18Z")

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I’m having this exact same problem with .gz files.