Comments (5)
Perhaps "orthologyGroups/orthologyGroups.%s.list" would be more convenient as an input file, which can be obtained with a little processing of the Orthofiner results
from agora.
Hi,
sorry for the late answer. NHX is a newick format with additional annotation on each nod and leaf.
Some tools for computing gene trees (reconciliated or not with the species tree) can output NHX (see ProfileNJ , treerecs, Treebest).
As a reminder, AGORA run with NHX trees reconciliated with species tree.
Nevertheless, as you previously mentioned, AGORA can run with orthology groups.
I hope it will resolve your problem. Don't hesitate to ask any other question if needed.
regards,
Alexandra
from agora.
Thank you for your reply, it helps a lot
I have a new problem, I use orthogroup as the input file but the program runs too fast, it runs in 2-3 minutes and the software is installed without any problem (./checkAgoraIntegrity.sh). There are also no obvious errors in the log files.
Maybe I'll have to try using "GeneTreeForest"?
My Linux: Centos 8.5
from agora.
When a look a the bottom of log2.txt... I can read:
"Status: 0 to do, 1 running, 9 done, 0 failed -- 10 total
Waiting ...
task 9 report: 6.95752 sec CPU time / 3.6729 sec elapsed = 189.429% CPU usage, 64.0195 MB RAM
task 9 is now finished (status 0)
Workflow complete
Workflow report: 145.498 sec CPU time / 89.9035 sec elapsed = 161.838% CPU usage, 1052.43 MB RAM"
So agora just run on your data...
You should have results in result_vertebrates/ancGenomes/vertebrates-workflow/
from agora.
Thanks a lot !
It was so fast, it was all running in 2 minutes
from agora.
Related Issues (20)
- divergence times with Agora
- Too many contiguous ancestral regions (CARs) HOT 2
- Lack of chromosomal information HOT 1
- input file issue HOT 2
- Plotting agora results plus a general question HOT 12
- Breakpoint regions mapping to reference chromosomes HOT 1
- ValueError when runnig misc.compareGenomes.py HOT 1
- Error when running agora-basic.py HOT 5
- Agora in living sps HOT 1
- Error Running agora-basic.py: "assert oldName not in seen" HOT 5
- Request for Custom Scripts: Rearrangement Breakpoints filtering and Interchromosomal Rearrangement Identification
- Clarification on Identifying Successive Genomes and Synthetic Blocks between Ancestral Nodes and Extant Genomes in PhylDiag HOT 2
- Creating input for analysis HOT 4
- How to locate the support scores of the AGORA adjacency graph for adjacent genes in ancGenome?
- Orthology groups correspond to HOGs? HOT 2
- Agora-generic pipeline seems to be “stuck” for several days after adding 1 more genome HOT 4
- AssertionError in ALL.reformatGeneFamilies.py HOT 4
- drawKaryotype trouble HOT 2
- Purpose of ENSEMBL.buildProteinTrees HOT 5
- Visualization of results HOT 1
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 agora.