search

medvedevgroup / SibeliaZ

A fast whole-genome aligner based on de Bruijn graphs
http://medvedevgroup.com/
Other
140 stars 19 forks source link

Empty MAF file in output #12

Open ShoumikSaha opened 4 years ago

ShoumikSaha commented 4 years ago

I'm getting just one line in MAF file of output - "maf version=1" and fasta files in 'blocks' folder. I'm using a 4GB ram, is it not enough? Even I tried with so small input file and still not getting any information in MAF file. It will be so helpful if I get MAF format. Thanks in advance.

iminkin commented 4 years ago

@ShoumikSaha ,

Sorry for the late reply. Unfortunately, SibeliaZ requires large amounts of memory to produce the resulting alignment even for small outputs. This is due to the high memory consumption of the aligner we use, spoa. So yes, 4GB is enough to produce the collinear blocks, but not their alignment. The reason why we use spoa as a default aligner is its high-speed which is crucial for long inputs, but we might add an option for a slower and more memory-frugal global aligner when the speed is not crucial.

ShoumikSaha commented 4 years ago

Thanks for your reply. In my case, speed is not crucial. I need the alignments. Is there any option available now for global aligner with limited memory?

iminkin commented 4 years ago

@ShoumikSaha , not right now. If you don't have an access to a machine with larger memory right away, an option worth considering is renting one on Amazon/Azure.