Bug in classify.seqs

mothur bugs
1

Hello, all.
I got a problem here. I have a fasta file and a tax file (its.fasta and its.tax) changed from the UNITE_public database. When I run the test.fas with classify.seqs, I keep getting a bug report as following:
mothur > classify.seqs(fasta=current,group=current,reference=its.fasta,taxonomy=its.tax)
Using test.fas as input file for the fasta parameter.
Using test.txt as input file for the group parameter.

Using 2 processors.
Generating search database… DONE.
It took 200 seconds generate search database.

Reading in the its.tax taxonomy… DONE.
Calculating template taxonomy tree… DONE.
Calculating template probabilities… [ERROR]: std::bad_alloc has occurred in the Bayesian class function Bayesian. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.

I don’t know how to get through this trouble, please help me.
Best wishes

Susie

2

Hi Susie,
The error you are getting indicates you are running out of memory. Your template files have almost 300,000 sequences. I ran your files successfully with processors=1. It requires a little over 2G of RAM. The more processors you use the more memory is required. I would suggest running the command with processors=1.
Kindly,
Sarah

3

Hi, Sarah.
Thanks for your help…I will try it again.

Susie :slight_smile:

4

Hi, Sarah,
I tried it again as you recommended, but the problem still came out. Does this have anything to do with the Mothur version which I use? I’m using mothur v.1.28.0 on windows XP.

Susie

5

How much RAM does your computer have?

6

The computer with windows XP system has 3G RAM. I finally find out that it works well on a Ubuntu system with only 2G RAM.