# Make.file command

**URL:** <https://forum.mothur.org/t/make-file-command/21375>\
**Category:** Commands in mothur\
**Created:** [April 16, 2022, 8:33pm UTC](https://forum.mothur.org/t/make-file-command/21375 "2022-04-16T20:33:36Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Hira](https://avatars.discourse-cdn.com/v4/letter/h/7993a0/32.png) [@Hira](https://forum.mothur.org/u/Hira)\
**Post date:** [April 16, 2022, 8:33pm UTC](https://forum.mothur.org/t/make-file-command/21375/1 "2022-04-16T20:33:36Z")

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I need help with this make.file command. I get this error as given in the attached images. I am following the MiSeq SOP tutorial.

 ![Screenshot 2022-04-17 at 1.28.13 AM](https://canada1.discourse-cdn.com/flex036/uploads/mothur/original/1X/d31710f0791a1de278aaf20821a7b9b57327f6af.png)  
 ![Screenshot 2022-04-17 at 1.30.50 AM](https://canada1.discourse-cdn.com/flex036/uploads/mothur/original/1X/f40c58d8dde4be96349d3732478df5549ae72765.png)

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**Author:** ![leocadio](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/leocadio/32/203_2.png) [@leocadio](https://forum.mothur.org/u/leocadio)\
**Post date:** [April 18, 2022, 2:09pm UTC](https://forum.mothur.org/t/make-file-command/21375/2 "2022-04-18T14:09:45Z")

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Hello Hira

it is not finding the folder Miseq\_Sop.

i am not very familiar with mac, but could you check where is mothur creating the log file? THat is the directory where mothur is running, and where Miseq\_Sop should be placed. I had problems in the past with students since they were running mothur, but IOs run the software in a directory that is NOT where the executable is (as windows does). You can also give mothur the full address to Miseq\_Sop instead. That would do the trick too.

Leo

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**Author:** ![Hira](https://avatars.discourse-cdn.com/v4/letter/h/7993a0/32.png) [@Hira](https://forum.mothur.org/u/Hira)\
**Post date:** [April 18, 2022, 2:33pm UTC](https://forum.mothur.org/t/make-file-command/21375/3 "2022-04-18T14:33:01Z")

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I gave mothur the full address to Miseq\_Sop and the command worked.  
Thank you very much.  
Regards  
Hira

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**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:** [April 19, 2022, 4:56pm UTC](https://forum.mothur.org/t/make-file-command/21375/4 "2022-04-19T16:56:42Z")

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From the mothur command prompt, you can run `system(ls)` to see what mothur can see from your current working directory. I suspect the directory you had given `inputdir` in `make.contigs` isn’t there.

Pat

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**Author:** ![Hira](https://avatars.discourse-cdn.com/v4/letter/h/7993a0/32.png) [@Hira](https://forum.mothur.org/u/Hira)\
**Post date:** [April 20, 2022, 6:28am UTC](https://forum.mothur.org/t/make-file-command/21375/5 "2022-04-20T06:28:30Z")

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Yes I have resolved this issue.  
Thank you.  
Regards  
Hira

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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:** [April 30, 2022, 6:29am UTC](https://forum.mothur.org/t/make-file-command/21375/6 "2022-04-30T06:29:26Z")

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