fdog.assembly with metaeuk is running slowly

[bheimbu]

Dear @trvinh,

sry, it's me again Bastian. I'm playing around with fdog.assembly and realized when I run it with augustus, it's fairly quick but with metaeuk it takes ages and it also uses a lot of RAM (like 721G). I'm using the Uniref90 database which is about 60G. I'm using fdog.assembly without the option --parallel and only 1 core, otherwise I'm getting errors like Can not allocate data memory in SequenceLookup etc.

Do you have any suggestions for me how to handle this better? Here would be my job script.

Cheers Bastian

[HannahBioI]

Hi Bastian,

Thanks for asking. Do you also get the Can not allocate data memory in SequenceLookup error when using Augustus? Or is this only an issue with MetaEuk? I have not yet encountered this problem, but I will look into it.

Bests,

Hannah

[bheimbu]

Hi Hannah,

how is it going? Nice to hear you. I'm not getting this error when I use Augustus.

Cheers Bastian