Using MOTHUR v.1.40 I am trying to construct a .biom file to use it on PICRUSt with the command ‘make.biom’. This is what I do (following biom format for PICRUST):
classify.seqs(fasta=my_data.fasta, template=gg_13_5.fasta, taxonomy=gg_13_5_taxonomy_fin.tax) make.biom(shared=my_data.phylip.opti_mcc.0.03.subsample.shared, label=0.03, reftaxonomy=gg_13_5_taxonomy_fin.tax, constaxonomy=my_data.gg_13_5_taxonomy_fin.wang.taxonomy, picrust=97_otu_map.map)
And I get the following error on my logfile (the terminal automatically shutdown):
[ERROR]: std::bad_allocRAM used: 1.95832Gigabytes . Total Ram: 7.90855Gigabytes. 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 unable to resolve the issue, please contact Pat Schloss at email@example.com, and be sure to include the mothur.logFile with your inquiry.
The dataset is not so big (I’ve also tried with a subsampled file of only 100 seqs), the version is the 64 bit one, so maybe is a file format error? Or a problem between versions of GreenGrenes data base? I also tried with the 99_otu_map version and I still have the same problem
I was wondering how to get a .cons.taxonomy from a ‘classfy.seqs’ command, since maybe this is the main issue?? I tried to run ‘classify.otu’ after ‘classify.seqs’ and I get a cons.taxonomy file that can subsequently be used for ‘make.file’, but instead of .biom output file I get a ‘.sum’ output file that does not reflect abundance of each OTU per sample (taken from the ‘.shared’ file?), as it is suposed to show when following PICRUSt tutorial.
How can I solve this problem?
Thanks a lot