FADE cannot recognize my tree file

[HY-Zeng]

Hello, this is my input file, I just append the tree file to the end of my alignment text, but it can not work. How can I solve this problem? With best wishes.

Analysis Description

FADE (FUBAR Approach to Directional Evolution) is a fast method to test
whether or not a subset of sites in a protein alignment evolve towards a
particular residue along a subset of branches at accelerated rates
compared to reference model. FADE uses a random effects model and latent
Dirichlet allocation (LDA) - inspired approximation methods to allocate
sites to rate classes.

• Requirements: A protein alignment and a rooted phylogenetic tree (optionally
  annotated with {})

• Citation: TBD

• Written by: Sergei L Kosakovsky Pond

• Contact Information: spond@temple.edu

• Analysis Version: 0.2

Save FADE cache to :

cache –> /home/datamonkey/datamonkey-js-server/production/app/fade/output/637ced0d1da9092e2690a25a.FADE.cache
FADE will write cache and result files to /home/datamonkey/datamonkey-js-server/production/app/fade/output/637ced0d1da9092e2690a25a.FADE.cache and /home/datamonkey/datamonkey-js-server/production/app/fade/output/637ced0d1da9092e2690a25a.FADE.json, respectively

Error:
Can't create empty trees.

Function call stack
1 : [namespace = IhfQMUVv] Topology T = (tree_string);

Keyword arguments:
	{
	 "branches":"All",
	 "burn-in":"1000000",
	 "chain":"5",
	 "chains":"2000000",
	 "concentration_parameter":"0.5",
	 "grid":"20",
	 "method":"Variational-Bayes",
	 "model":"GTR",
	 "samples":"100",
	 "tree":"/home/datamonkey/datamonkey-js-server/production/app/fade/output/637ced0d1da9092e2690a25a.tre"
	}

---

2 : [namespace = PVYXSyMj] result=trees.ExtractTreeInfo(trees.GetTreeString(look_for_newick_tree));

Keyword arguments:
	{
	 "branches":"All",
	 "burn-in":"1000000",
	 "chain":"5",
	 "chains":"2000000",
	 "concentration_parameter":"0.5",
	 "grid":"20",
	 "method":"Variational-Bayes",
	 "model":"GTR",
	 "samples":"100",
	 "tree":"/home/datamonkey/datamonkey-js-server/production/app/fade/output/637ced0d1da9092e2690a25a.tre"
	}

---

3 : [namespace = nucuyAzF] partrees+{utility.getGlobalValue("terms.data.name"):partitions[i][0],utility.getGlobalValue("terms.data.filter_string"):partitions[i][1],utility.getGlobalValue("terms.data.tree"):trees.LoadAnnotatedTopologyAndMap(tree_matrix[i][1],mapping)};

Keyword arguments:
	{
	 "branches":"All",
	 "burn-in":"1000000",
	 "chain":"5",
	 "chains":"2000000",
	 "concentration_parameter":"0.5",
	 "grid":"20",
	 "method":"Variational-Bayes",
	 "model":"GTR",
	 "samples":"100",
	 "tree":"/home/datamonkey/datamonkey-js-server/production/app/fade/output/637ced0d1da9092e2690a25a.tre"
	}

---

4 : fade.partitions_and_trees=trees.LoadAnnotatedTreeTopology.match_partitions(fade.alignment_info[utility.getGlobalValue("terms.data.partitions")],fade.alignment_info[utility.getGlobalValue("terms.data.name_mapping")]);

Keyword arguments:
	{
	 "branches":"All",
	 "burn-in":"1000000",
	 "chain":"5",
	 "chains":"2000000",
	 "concentration_parameter":"0.5",
	 "grid":"20",
	 "method":"Variational-Bayes",
	 "model":"GTR",
	 "samples":"100",
	 "tree":"/home/datamonkey/datamonkey-js-server/production/app/fade/output/637ced0d1da9092e2690a25a.tre"
	}

---

AHA_FADE.txt

[jzehr]

Dear @HY-Zeng,

Sorry for the delay.

I was able to run your file using HyPhy version 2.5.43(MP) with the command:

hyphy fade --alignment AHA_FADE.txt  --branches All --grid 20 --model GTR --method Variational-Bayes --chain 5 --chains 2000000 --burn-in 1000000 --samples 100 --concentration_parameter 0.5 --output AHA_FADE.FADE.json 

It looks like the output file is too large to share here, could I place your data at a retrievable spot on our server for you? This would mean that the results would temporarily be public. Let me know if that would be ok, otherwise we can come up with another way to share the data.

Once you have your data, it can be viewed here.

Let me know if you have any other questions.

Best,

[github-actions]

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