Dear mothur team,
I have difficulties of running make.biom command in mothur since it results error message saying memory issue in the server, though the server had enough RAM for this (64Gb RAM).
The command I used for classifying my sequences (based on RDP database) with the reference GreenGene database was,
"mothur > make.biom(shared=Dilhani_otutab.mothur, label=usearch, reftaxonomy=99_otu_taxonomy.txt, constaxonomy=Dilhani_utax.txt, picrust=97_otu_map.txt)
The error command I got from mothur,
[ERROR]: std::bad_alloc has occurred in the MakeBiomCommand class function getMetadata. 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, http://www.mothur.org/wiki/Schloss_SOP. If you are uable to resolve the issue, please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.parallels@ubuntu:~/Downloads$ "
I have emailed all the input files and mothur log files into “mothur.bugs@gmail.com” for your reference. Could you please advise me if you see there is something wrong with the input files.
Thank you.
Dilhanide.