For the intron size problem, you can fix that by adding the /pseudo attribute. Have a look here to understand the meaning of this attribute.
If you want I have a script that do it automatically. It is called gff3_sp_flag_short_intron.pl and you can find it in the GAAS repository.
It is called agat_sp_flag_short_introns.pl and is part of the of GFF toolkit AGAT.
For this Abutting features error, if the two features are from different genes then it is a bug from their validator. Have a look here.
They advise to remove the exons from the flat file to avoid that type of problem. Otherwise you have to modify location manually.
Thank you @jike-34 for your reply.
I installed all perl dependencies of GAAS to use your scripts gff3_sp_flag_short_intron.pl. I ran it but it also asks the module "BILS :: CheckModule" but mcpan it can not find this module
It just mean that you haven't completed the installation procedure.
Everything starting by BILS is related to a personal library that is within the GAAS repo.
To access them (because it is not the only one needed) 2 choices:
cd GAAS
make install
source profiles/activate_env
or add in your ~/.bashrc or ~/.profile file (provide the correct path):
Thanks @Juke-34 for your help. It is well installed.
I have a quick question, Do you think that the argument --translate of EMBLmyGFF3 is mandatory for submission?
Thank you for your reply. Yes I ran gff3_sp_flag_short_intron.pl without any problem. Except sometimes it put twice / pseudo in the same CDS which is not recommended for a valid file, but it works very well. Thanks again.
I forgot about this duplication of attributes within the EMBL output. Did you find a way to fix it ? Because the validator does not like them...
I have fixed that within EMBLmyGFF3 but I didn't push the fix yet...
you can find some pointers in this blog post already : http://avrilomics.blogspot.com/2018/08/converting-gff3-file-to-embl-to-submit.html