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kfuku52 / csubst

Molecular convergence detection
BSD 3-Clause "New" or "Revised" License
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There is no target branch combination at K = 2. #55

Closed kfuku52 closed 8 months ago

kfuku52 commented 8 months ago 
Python version: 3.9.15 | packaged by conda-forge | (main, Nov 22 2022, 08:45:29)  [GCC 10.4.0]
CSUBST version: 1.4.0
CSUBST command: /opt/conda/envs/biotools/bin/csubst analyze --genetic_code 1 --infile_type iqtree --alignment_file ./HOG0001050.iqtree.anc/csubst.fasta --rooted_tree_file ./HOG0001050.iqtree.anc/csubst.nwk --iqtree_treefile ./HOG0001050.iqtree.anc/csubst.treefile --iqtree_state ./HOG0001050.iqtree.anc/csubst.state --iqtree_rate ./HOG0001050.iqtree.anc/csubst.rate --iqtree_iqtree ./HOG0001050.iqtree.anc/csubst.iqtree --iqtree_log ./HOG0001050.iqtree.anc/csubst.log --iqtree_model ECMK07+F+R4 --iqtree_redo no --max_arity 10 --exhaustive_until 1 --cutoff_stat OCNany2spe,2.0|omegaCany2spe,3.0 --max_combination 10000 --fg_exclude_wg no --fg_stem_only no --mg_sister no --exclude_sister_pair yes --ml_anc no --b yes --s no --cs no --cb yes --bs no --cbs no --calc_quantile no --omegaC_method submodel --asrv each --threads 1 --calibrate_longtail yes --float_type 32 --foreground /gfe_data/species_trait/species_trait.tsv --fg_format 2
kfuku52 commented 8 months ago

This happened when foreground.tsv has the first column with values like Arabidopsis_thaliana rather than Arabidopsis_thaliana_.* for the regex search of gene names like Arabidopsis_thaliana_AT0G00000 in the input gene tree.

kfuku52 commented 8 months ago

This is actually a bug. In addition to the above input anomaly, CSUBST terminates without examining branch combinations when one of multiple traits (with --fg_format 2) has no combination to examine.