Comments (7)
Could you relaunch with '-vvv' option to have more verbose information ?
Thx
from emblmygff3.
Of course, please attached log file.
EMBLmyGFF3.test.log
from emblmygff3.
Ok then it's related to a bug we are aware of: #32
We shouldn't stop the tool but just raise a WARNING and not report the value in the output.
It's because the KEGG database (from the dbxref attribute) is not among accepted databases at ENA.
Here the list of databases accepted: https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/
A way would be to remove those information or edit the legal_dbxref.json
to add those DB among the list of accepted one. In the second case you will create an EMBL file that do not strictly follow the ENA specification and I'm no sure how ENA will handle it.
Another thing, I realised recently that ENA do not keep DB_xref information when it's processed by their pipeline. I'm still waiting for information about it from them, but the only information I got is: "We get rid of DB_xref information and redo our own functional information"...
At the end I don't really know how the db_xref data is handle by ENA.
from emblmygff3.
Great, so I guess the safest way for now is to remove this attribute from the GFF. Will try to do that.
Many thanks for the prompt support.
from emblmygff3.
As your annotation comes from NBIS I guess several other DB reported in the dbxref attribute are not supported by ENA. Here is the list of DB we can report that are not accepted by ENA:
"KOG",
"KEGG",
"MetaCyc",
"Reactome",
"UniPathway"
from emblmygff3.
Removing these values from the dbxref attribute solves this error.
from emblmygff3.
fixed in release 1.2.5
from emblmygff3.
Related Issues (20)
- How to add in comment or CC line HOT 1
- Webin-CLI validation failing due to duplicated feature locations in EMBLmyGFF3 flat file HOT 2
- thank you HOT 1
- ImportError Bio.Alphabet error HOT 1
- What the option "-a accesion" parameter should to be set(means:What type?) HOT 3
- TypeError: read() takes 1 positional argument but 2 were given? HOT 3
- attribute formats broken across several lines HOT 2
- Use of example data HOT 2
- Contigs are disorganised in the EMBL file HOT 10
- Warning qualifier unknown db_xref HOT 1
- Translation problem HOT 2
- Reporting the line number of the problematic input GFF3 files when parsing error is triggered HOT 2
- BioPython 1.81 installs via conda, but needs an older version HOT 2
- if I can specify certain python source during python setup.py install HOT 2
- Not for ENA submission: Sequence too short
- Installation issue EMBLmyGFF3 & python version requirements
- Translation when circular genome and ORF in the cut of the assembly HOT 1
- unexpected keyword argument 'strand' HOT 3
- Gene sorting compared to fasta HOT 4
- Bug when specifying -g mitochrondrion (or plastid)
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from emblmygff3.