Question: OMA standalone error
gravatar for pbravakos
24 months ago by
pbravakos0 wrote:

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/ 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

ADD COMMENTlink modified 24 months ago by adrian.altenhoff650 • written 24 months ago by pbravakos0

Tagging: adrian.altenhoff

ADD REPLYlink written 24 months ago by genomax87k
gravatar for adrian.altenhoff
24 months ago by
adrian.altenhoff650 wrote:

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.

ADD COMMENTlink written 24 months ago by adrian.altenhoff650

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

ADD REPLYlink written 24 months ago by pbravakos0
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