Closed HY-Zeng closed 1 year ago
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,
Stale issue message
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.
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 :
Error: Can't create empty trees.
Function call stack 1 : [namespace = IhfQMUVv] Topology T = (tree_string);
2 : [namespace = PVYXSyMj] result=trees.ExtractTreeInfo(trees.GetTreeString(look_for_newick_tree));
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)};
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")]);
AHA_FADE.txt