Comments (9)
Yes, I think it should be possible to invert the order of the ranks and include the complete lineage.... let me have a look into this and I'll get back to you asap.
from emg-viral-pipeline.
Hey, thx @Ales-ibt !
Yes agree, inverting the ranks would make more sense probably. Having the full ranks shown should be also possible with the NCBI taxonomy file @guille0387 , or?
Regarding the Caudovirales vs Caudoviricetes: actually Caudovirales should not be in the pipeline anymore bc the taxa was discontinued by ICTV. We added the following warning mssg when running VIRify:
Warning: --meta_version v4 does not include the following discontinued virus taxa
(according to ICTV) anymore and they have been excluded from the dataset.
- Allolevivirus
- Autographivirinae
- Buttersvirus
- Caudovirales
- Chungbukvirus
- Incheonvirus
- Leviviridae
- Levivirus
- Mandarivirus
- Pbi1virus
- Phicbkvirus
- Radnorvirus
- Sitaravirus
- Vidavervirus
- Myoviridae
- Siphoviridae
- Podoviridae
- Viunavirus
- Orthohepevirus
- Klosneuvirus
- Hendrixvirus
- Rubulavirus
- Avulavirus
- Catovirus
- Nucleorhabdovirus
- Viunavirus
- Gammalipothrixvirus
- Peduovirinae
- Sedoreovirinae
Did you still had Caudovirales in your results? Can you try a fresh installation and most importantly re-download of the database files? Maybe an old database file was still used.
from emg-viral-pipeline.
I created a new branch called out_lineage with modifications in the contig taxonomic assignment script. The output should now reflect the suggestions that Ales made. I tested it with the two mock datasets we used in the paper and it worked, but perhaps Ales would like to try it with her own data? Let me know if you have any issues.
from emg-viral-pipeline.
Great, thx @guille0387 ! Looks also good for me. @Ales-ibt can you give it a try as well? thx!
from emg-viral-pipeline.
Great, I'll run a test and be back to you soon.
from emg-viral-pipeline.
Hello, sorry about taking that long to be back. I updated the NCBI database and now I have the correct Caudoviricetes annotation :D. I also tested the pipeline on the out_lineage branch and I can see the complete lineages beautifully sorted on the 08-final/taxonomy/*prodigal_annotation_taxonomy.tsv, thank you so much for this. The only detail is that this fix is not reflected on the GFF output file.
Thank you again!
Ales
from emg-viral-pipeline.
Awesome, thanks for checking, @Ales-ibt !
@guille0387 can you also do the GFF fix and then we could merge that into dev
@mberacochea
from emg-viral-pipeline.
Excellent @guille0387!, thank you for that fix. Let me know if you need a hand fixing the GFF.
from emg-viral-pipeline.
from emg-viral-pipeline.
Related Issues (20)
- Unable to locate package docker-ce-cli HOT 1
- `annotate:ratio_evalue (1)` terminated with an error exit status (1) -- 'nextflow-autodownload-databases' Is a directory error HOT 1
- Can Prodigal-GV make 'real world' difference compared to original Prodigal? HOT 2
- Update ViPhOGs to remove old models that are associated with discontinued viral taxa HOT 5
- CWL discontinued
- No space left in /tmp HOT 2
- preprocess:rename idle state HOT 12
- Fix sankey plot visualization for undefined ranks
- Imitervirales assignment although not well supported by ViPhOGs
- Repository may be corrupted HOT 3
- Issue for running on ARM64-based Linux VM HOT 5
- wrapper_phage_contigs_sorter_iPlant HOT 1
- [Feature Request] Conda Distribution for Taxonomic Identification HOT 1
- Input file name collision on 'annotate:write_gff' HOT 2
- COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes
- Missing process or function with name 'getFileSystem' HOT 3
- Not able to run "nextflow pull EBI-Metagenomics/emg-viral-pipeline" HOT 2
- Error executing process > 'annotate:hmmscan_viphogs (1)'
- CheckV failed HOT 4
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 emg-viral-pipeline.