Installation

Commands in mothur
1

I am completely new to these types of programs C++ command lines etc, I think I have installed the program mothur and X-code. I am on a macbook and have a terminal window open and typed the command ./mothur and I have a command line that says mothur >

So is this an indication it is installed correctly and in the installation guide it says hopefully, mothur will open in the interactive mode. How do I know if this is the interactive mode or not?

Please keep answers simple! Thank you

2

Yep, sounds like you’ve got it right if you are seeing mothur >

3

Thank you, where is the best place to go now to know what to do now. I am totally new to command lines etc. I have a memory stick from NGS sequencing company that has bioinformatics done and in the mothur folder there are 4 files that I need to open but don’t know how to, so need some idiots guide!

4

Have you followed the MiSeq SOP? http://www.mothur.org/wiki/MiSeq_SOP

5

In the installation wiki on mothur is says about a makefile. “If you are analyzing large data sets (e.g. from pyrosequencing) in OS X and you have more than 2 GB of RAM in your computer, you can add a flag to the make file to use 64-bit pointers by opening the makefile and changing the lines that read:” I don’t seem to have/can’t find a makefile within the mothur folder.

Is there something I am doing wrong?

Thanks

6

You don’t need to run make because you already have mothur :slight_smile: so you can ignore that message.

  1. Move your files into the mothur folder.
  2. From command prompt: mothur Carrie$ ./mothur
  3. You should now see:
    …
    When using, please cite:
    Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type ‘help()’ for information on the commands that are available

Type ‘quit()’ to exit program



mothur >
  1. Type commands at the “mothur >” prompt you would like to run.
  2. Follow Pat’s example analysis to help you become familiar with mothur’s commands. http://www.mothur.org/wiki/MiSeq_SOP
7

Yes I’m trying to work through it but the first command I’m supposed to put in doesn’t work.

mothur > make.contigs(file=stability.files, processors=8)
Unable to open stability.files. Trying default /Users/Carrie/Desktop/mothur/stability.files
Unable to open /Users/Carrie/Desktop/mothur/stability.files. Trying mothur’s location /Users/Carrie/Desktop/mothur/stability.files
Unable to open /Users/Carrie/Desktop/mothur/stability.files

Using 8 processors.
[ERROR]: did not complete make.contigs.

8

Where is the stability.file located? Could you have a hidden extension remaining? For example if you didn’t decompress a file. http://www.mothur.org/wiki/Frequently_asked_questions#Mothur_can.27t_find_my_input_files

9

The stability.file is in the MiSeq_SOP folder on the desktop, sorry I know this is probably simple but I’ve never used command lines before so these programs are totally out of my depth

Thanks

10

Hello

I am also new, so maybe I can help you :wink:

You need to make sure that the “stability.file” is typed exactly as the name of the “stability.file” that you have on your computer. You also need to make sure that “stability.file” is within the mothur folder. When I received this error (similar as you did): "cant find the ...file..", its usually one of these two reasons. For learning how to use command lines, I would search for tutorials/websites for basic training. For example this one: http://cli.learncodethehardway.org/book/.

11

Thank you. I will take a look at that crash course. ATM I am trying to wrap my head around what is on the NGS memory stick, so I may be back to this in a while!

12

Hi

Try to check if you have the rest of the files in mothur folder (Not in a subdirectory) as well as stability.file other way mothur is not going to find them. You need to paste all the files from MySeq_SOP in mothur folder.

Good luck!!!