16S metagenomics with MOTHUR

Commands in mothur
1

hi to all,

I am a new member in this forum and wish to learn from a scratch.
I have 16S sequnces from Sanger platform,whenever I want to work on them using Mothur, it always says “Using 1 processors” for example: after setting my sequence in fasta file format and tried to do “summary.seqs (fasta=nameoffile.fasta)” it alwatys says unable to open file, using 1 processor, Error - did not complete summary.seqs. can someone assist me what wrong am I doing?

Thanks

Kilaza

2

This error occurs when you are running mothur from a folder that is different from where your data are. The way around this is to use the command prompt to navigate to the folder with your data and then launch mothur. If you type system(dir) [for windows] or system(ls) [for mac/linux] you should see your file name in the output.

3

Thanks for your input, I was able to solve the problem