ERROR with 'flip=t' at linux?


The pipeline shows error at linux while doing ‘flip=t’ at command "align.seqs(fasta=stability.trim.contigs.good.unique.fasta, reference=silva.nr_v123.align, flip=t). However, same command with same data are running at window platform. I tried with, versions.

Could you please get find my error? Thanks


Reading in the silva.nr_v128.align template sequences… DONE.

It took 200 to read 190661 sequences.

Aligning sequences from stability.trim.contigs.good.unique.fasta …

[ERROR]: std::bad_alloc has occurred in the Nast class function getSimilarityScore. 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.

The problem is that the windows version cannot access as much of your RAM as the linux version. That is what the error message is indicating.


But, i think the window version is able to run ‘flip=t’ and at linux showing error with flip=t. So, Window version is using more RAM.