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medvedevgroup / SibeliaZ

A fast whole-genome aligner based on de Bruijn graphs
http://medvedevgroup.com/
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sibeliaZ outputs #47

Open runxuan opened 1 year ago

runxuan commented 1 year ago

Hi,

on the Readme page, I have the impression that the output will contain two files, a GFF file "blocks_coords.gff" containing coordinates of the blocks, and file "alignment.maf" with the actual alignment.

However, i have run sibeliaz on my data twice and I only got "blocks_coords.gff" on both times with "alignment.maf" missing. There is no error message given. Have I done anything wrong here? any parameter needs to be turned on/off?

Also I want to generate a pan-genome graph in gfa format. I suppose this can be achieved through generating "alignment.maf"?

Thanks a lot!

Best regards,

Runxuan

iminkin commented 1 year ago

Hi,

This sounds like a bug. What is the dataset you are trying to align? Number of genomes, their size and type.

runxuan commented 1 year ago

Thanks a lot for your reply IIlia. I am aligning genomes from 20 different barley genotypes. Each barley genotype genome is around 5.1G bp in size. Barley is diploid with 7 chromosomes, but there are many unanchored fragments in addition in the fasta files.

Please let me know if you need further info.

Thanks

Runxuan