# All commands invalid
**URL:** https://forum.mothur.org/t/all-commands-invalid/1612
**Category:** Commands in mothur
**Created:** [December 11, 2013, 12:28pm UTC](https://forum.mothur.org/t/all-commands-invalid/1612 "2013-12-11T12:28:59Z")
**Posts on this page:** 7
**Page:** 1
### Author:  [@Somebodyatthedoor](https://forum.mothur.org/u/Somebodyatthedoor)
#### Post date: [December 11, 2013, 12:28pm UTC](https://forum.mothur.org/t/all-commands-invalid/1612/1 "2013-12-11T12:28:59Z")
Hi,
I’ve just started using mothur and have ran into a pretty big problem. My institutes IT department have just installed the newest version of MOTHUR (2013-11-22) onto a linux server.
When I try to use a command or use help (command) I get the message that this is an ‘invalid command’. I then get a list of all the valid commands amongst which is the command I just entered. This isn’t due to an accidental space being added as was the case in another post.
Anyone got any ideas?
Cheers,
Laura
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### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [December 11, 2013, 3:19pm UTC](https://forum.mothur.org/t/all-commands-invalid/1612/2 "2013-12-11T15:19:23Z")
Welcome to the mothur community! I would like to help you get up and running. Are you running mothur on a 32bit or 64bit linux server?
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### Author:  [@Somebodyatthedoor](https://forum.mothur.org/u/Somebodyatthedoor)
#### Post date: [December 11, 2013, 3:27pm UTC](https://forum.mothur.org/t/all-commands-invalid/1612/3 "2013-12-11T15:27:24Z")
Thanks for the quick reply. It’s 64 bit.
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### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [December 11, 2013, 4:45pm UTC](https://forum.mothur.org/t/all-commands-invalid/1612/4 "2013-12-11T16:45:08Z")
Can you try running mothur in script mode? From a command prompt, try this: sarahswork$ ./mothur “#help();”
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### Author:  [@Somebodyatthedoor](https://forum.mothur.org/u/Somebodyatthedoor)
#### Post date: [December 11, 2013, 5:00pm UTC](https://forum.mothur.org/t/all-commands-invalid/1612/5 "2013-12-11T17:00:33Z")
Hi,
I tried it in script mode but I still get the invalid command output.
Cheers,
Laura
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### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [December 11, 2013, 7:12pm UTC](https://forum.mothur.org/t/all-commands-invalid/1612/6 "2013-12-11T19:12:42Z")
Did you install the prebuilt executable or did you build from source?
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### Author:  [@Somebodyatthedoor](https://forum.mothur.org/u/Somebodyatthedoor)
#### Post date: [December 12, 2013, 9:54am UTC](https://forum.mothur.org/t/all-commands-invalid/1612/7 "2013-12-12T09:54:47Z")
Hi,
Sorry to have taken up your time but I got into work this morning and it is working fine…
The mystery of IT…
I think this thread can probably be deleted as frankly the problem sounds like it was caused by server gremlins and therefore will be of little use to anyone else.