cluster.split issue

Hi all,

I’m trying to troubleshoot a problem from cluster.split.
After having produced the .dist files, the sequences are read and clustered. During that process, I’ve got an error message saying as follows:

Clustering stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.6.dist
Cutoff was 0.155 changed cutoff to 0.06
[ERROR]: Could not open 47468.temp
[ERROR]: std::bad_alloc has occurred in the ClusterSplitCommand class function createProcesses. This error indicates your computer is running out of memory. This is most commonly caused by trying to process a dataset too large, using multiple processors, or a file format issue. If you are running our 32bit version, your memory usage is limited to 4G. If you have more than 4G of RAM and are running a 64bit OS, using our 64bit version may resolve your issue. If you are using multiple processors, try running the command with processors=1, the more processors you use the more memory is required. Also, you may be able to reduce the size of your dataset by using the commands outlined in the Schloss SOP, If you are uable to resolve the issue, please contact Pat Schloss at, and be sure to include the mothur.logFile with your inquiry.

Looking at the first error message ([ERROR]: Could not open 47468.temp), I’ve checked the files produced during the analysis. Apparently, the file "47468.temp” is not been produced, so that’s probably why the command cannot open it and the job has been killed.
Does any of you know where this problem could come from and how to fix it?



That is usually a sign that you don’t have enough RAM to cluster the distance matrix. You likely need to use a higher taxlevel (e.g. 5 or 6), get more RAM, or get better data (