Problem running MAFFT
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2.9 years ago

I'm trying to run MAFFT for aligning sequences in .fasta format. I'm working on Ubuntu and using MAFFT version 7.407.

I got MAFFT running on a set of 100 sequences but it's giving me the following error on 500 sequences:

Allocation error ( 3448 x 3448 doublemtx )

I'm running MAFFT using the options --localpair --maxiterate 16 --phylipout --inputorder

Could anyone please help me out as I'm pretty new to this?

alignment sequence • 1.7k views
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You are probably running out of memory. See the tips page for suggestions on how to handle big datasets.

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Wow, this really solved my bug: ApplicationError: Non-zero return code 1 from 'mafft Ref_andOneMore.fasta', message 'nthread = 0' , Time-expending googling didn't help, but your recommended page ("tips") helped.

So I used the --memsave option and it was enough to get it run.

mafft --auto --memsave Ref_andOneMore.fasta > out3.txt
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