mothur

Importing data into mothur


#1

Hi there,

I am sorry if this turns out to be a very stupid question, but I’ve been struggling with this for quite some time now, and haven’t been able to figure it out.

While running commands on Mothur, if suppose the system hangs/mothur crashes et al (basically, I need to restart the Mothur interface again), is there any way to continue working from the stage where I was prior to restarting the interface, or do I have to again start analysis from scratch?

So, in other words, can I import data from anywhere along the analysis process using some relevant command which i am not aware of, and continue my analysis? Or do I have to start again from the initial stability.files creation step?

I would be extremely grateful for any insight into this matter.

Thanks.


#2

Hi,
don’t worry, you don’t need to start from scratch every time!
By default for data from analysis is stored in the folder you started mothur from.
You can change this by using set.dir(input=/PATH/TO/YOUR/ANALYSIS/ and output=/PATH/TO/YOUR/ANALYSIS/). You don’t need to import data as you can specify which files to use in the mothur command. The arguments fasta= or count= take file names or “current”. Current only works, when mothur knows which files to use. It will use the last files used or created. With current() you get an output on all files mothur uses for the analysis at the moment. So basically, when you want to continue your analysis you set the working directory with set.dir() and than specify the files to use by their filenames. If you are unsure what the last files created were named, just look into the logfiles stored in the same folder from where you ran mothur. I can highly recommend the Mothur SOP, which describes all this and the whole analysis process perfectly. Hope this help.


#3

Thanks a ton. I also found out that creating commands as a batch file and exporting them to the software also works fine. I shall try the way you suggested. I forgot about the set.dir!


closed #4

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