EMBL flatfile not compatible with PAGIT RATT

[nbisweden]

EMBL flatfile not compatible with PAGIT RATT

[Juke34]

The EMBL file created using EMBLmyGFF3 is made for submission purpose. So there is a slight difference between the an EMBL file for submission and a released one.
One of this difference is the header of a fasta sequence that is originally:
>sequence1

and becomes with EMBLmyGFF3:

AC XXX;
XX
AC * _sequence1

I guess RATT is confused with the line AC XXX;or/and the difference between the name sequence1and *_sequence1.
In a EMBL fille released you will end with only 1 AC line with the official name retained for the sequence, most likely:

AC sequence1

In a future version we can think to introduce an option to get an EMBL fomat "ready to use" not for submission pupose. Until then you will have to find a way to replace those line as indicated. I think it will solve the problem.

[VenithaB]

Off-topic!

Is this really an error? It sounds more like a heads-up. Also according to the documentation:

The name of each sequence in the fasta description,
MUST be the same name as its corresponding embl file. So if your embl file is call Tuberculosis.embl, in your reference.fasta file,
the description has to be
>Tuberculsosis
ATTGCGTACG
...

I have always interpreted that to mean that the description of each sequence in the reference .fasta file must have the same name as the .embl file. But it's great that this difference between a submitted and accepted .embl is clarified; it's good to edit the file.

[peritob]

Thanks so much for your quick response and useful advice. I will make some changes to the file and try again with RATT.

[peritob]

Thanks VenithaB, yes I read the documentation but was still unclear where the problem in .embl was.
Happy to close this thread now - as it is going off topic into RATT (which incidentally needs an early perl version). Thanks for all the help :)