ytabatabaee / castles Goto Github PK

Hello!
I am trying to use CASTLES to estimate branch lengths of a species tree topology I generated with ASTRAL. I was able to annotate the species tree topology with a local installation of ASTER. However, when I run castles.py, I get this error:

Number of species: 55
Number of genes: 5969

Calculating lengths in post-order traversal of internal nodes:
Traceback (most recent call last):
File "/home/avehi/Biotools/CASTLES-1.3.0/castles.py", line 306, in
castles(st, gts, tns)
File "/home/avehi/Biotools/CASTLES-1.3.0/castles.py", line 210, in castles
label_dict = process_node_annotation(node.label)
File "/home/avehi/Biotools/CASTLES-1.3.0/castles.py", line 21, in process_node_annotation
label_dict['support'] = float(annotations[1])
IndexError: list index out of range

The input files are rather large but I could email them to you, if you'd like.

Thanks very much in advance!!

If I am correct, then theoretically this should work with duplicate taxa in gene trees, however I get this error when trying to use a species-tree inferred under ASTRAL, with a collection of gene-trees:

dendropy.dataio.newickreader.NewickReader.NewickReaderDuplicateTaxonError: Error parsing data source 'castle_gt_input.trees' on line 1 at column 1481: Multiple occurrences of the same taxa on trees are not supported: trees with duplicate node labels can only be processed if the labels are not parsed as operational taxonomic unit concepts but instead as simply node labels by specifying 'suppress_internal_node_taxa=True, suppress_leaf_node_taxa=True'.

When trying to add these flags though I also get errors:
castles.py: error: unrecognized arguments: suppress_internal_node_taxa=True, suppress_leaf_node_taxa=True

castles.py: error: unrecognized arguments: suppress_internal_node_taxa=True suppress_leaf_node_taxa=True