mothur

Remove.rare taking a long time to run

#1

Hi,

I am trying to remove rare OTUs using the remove.rare command. Since I generated my list with a count table, I also included that in the command.

It has been running for about two days now. My list was based on unique sequences (not clustered based on 0.03), as I am working with data where SNPs are important for allele designation.

Is there any way to increase the speed of this process? I notice I cannot designate how many processors to use, and looking at the task manager it looks like it is only using one.

Any help is greatly appreciated.

#2

Can you post the exact syntax you are using? ALso, what happens if you only provide the list file and not the count table?

Pat

#3

Hi Pat,

This has been resolved. I took your advice to contact mothur.bugs@gmail.com (via a twitter response).

The person helped immensely.

mothur > remove.rare(shared=mhc.shared, nseqs=2, label=0.0)
Your file does not include the label 0.0. I will use 0.
0

Output File Names: 
/Users/joel/Desktop/rare/mhc.0.pick.shared

mothur > list.otus(shared=current)
Using /Users/joel/Desktop/rare/mhc.0.pick.shared as input file for the shared parameter.
0

Output File Names: 
/Users/joel/Desktop/rare/mhc.0.pick.0.otulabels

mothur > get.otus(list=mhc.list, accnos=mhc.0.pick.0.otulabels)
You did not provide a label, I will use the first label in your inputfile.
Selected 95143 OTUs from your list file.

Output File Names: 
/Users/joel/Desktop/rare/mhc.0.pick.list

mothur > list.seqs(list=current)
Using /Users/joel/Desktop/rare/mhc.0.pick.list as input file for the list parameter.

Output File Names: 
/Users/joel/Desktop/rare/mhc.0.pick.accnos

mothur > get.seqs(count=mhc.count_table)
Using /Users/joel/Desktop/rare/mhc.0.pick.accnos as input file for the accnos parameter.
Selected 542001 sequences from your count file.

Output File Names: 
/Users/joel/Desktop/rare/mhc.pick.count_table