ASTRAL issue

[jiyideanjiao]

I used the "tree" option with backbone.nwk and the alignments of 12 genes including 2538 species. I always got error message "In cluster species/output/udance/3, 1 gene tree(s) with lower than 0.80 median lpp are discarded.
ASTRAL job on partition species/output/udance/3 has failed. Check the log file species/output/udance/3/astral.incremental.log for further information."

When I check the astral.incremental.log file, it shows as below:

11 trees read from species/output/udance/3/astral_input.trees
All output trees will be arbitrarily rooted at species1232

Shutting down threading
Exception in thread "main" java.lang.RuntimeException: Error: Leptothorax_acervorum was not seen in main input trees.
at phylonet.coalescent.TaxonIdentifier.taxonId(TaxonIdentifier.java:38)
at phylonet.coalescent.CommandLine.readInputTrees(CommandLine.java:833)
at phylonet.coalescent.CommandLine.runInference(CommandLine.java:639)
at phylonet.coalescent.CommandLine.process(CommandLine.java:549)
at phylonet.coalescent.CommandLineMP.process(CommandLineMP.java:194)
at phylonet.coalescent.CommandLineMP.main(CommandLineMP.java:229)"

Do you have any idea to figure out this issue? Thanks

[balabanmetin]

It must be related to the fact that one of twelve gene trees is discarded because it is low quality ("lower than 0.80 median lpp"). The missing species (Leptothorax_acervorum) is probably present in the backbone tree but none of the remaining 11 gene trees. Please confirm by searching this species in the astral_input.trees. If this is the case, you can resolve this by increasing gene filtering threshold to 1.0, which disables gene filtering (all 12 will be used by ASTRAL):

  # 1D k-means-based (k=2) outlier gene detection parameter. Centroid difference must be 
  # larger than this value to designate the first cluster as outliers.
  outlier_difference: 0.1

I am currently on vacation. I am planning on resolving this 7 days later if this does not help.

[balabanmetin]

A bad gene tree can occur due to failed or bad MSA or lack of phylogenetic signal in the gene.

[jiyideanjiao]

Get it. thanks very much!

[balabanmetin]

Is the issue resolved?

[jiyideanjiao]

still got error message at ASTRAL step