OMA standalone error

Question

[pbravakos]

I am trying to run OMA as a standalone program with Espirit enabled. I get the following error message:

Reading 4761692 characters from file Cache/DB/Str01_Jun18_Spades.db
Pre-processing input (DNA)
89 sequences within 89 entries considered
Creating file Cache/DB/Str01_Jun18_Spades.db.map for mapping
Building new Pat index in file Cache/DB/Str01_Jun18_Spades.db.tree with 4756132 entries
Pat index with 4756132 entries
 sorted, from "A</SEQ></E>\n<E><ID>" to "XXXXXXXXXXXXXXXXXXX"
1533645354.662245 - 1 - [pid 14006]: Computing Pseudomonas_1W1-1A vs Pseudomonas_sp_R2A2 (Part 1 of 1) Mem: 0.399GB
Error, 'sequence 1 is too long'

Does anybody know what can be done to fix this? Thanks

[GenoMax]

Tagging: adrian.altenhoff

Answer 1

[Adrian Altenhoff]

Hi @pbravakos

currently Esprit works only on protein sequences, or in principle coding DNA (but parameters certainly have not been optimised for that). The error you get indicates that you probably are using also intronic gene sequences or even entire contigs.

[pbravakos]

Yes i am using contigs, so it is the wrong tool for the job. Thanks