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itsmeludo / PhylOligo

Bioinformatics / Explore oligonucleotide composition similarity between assembly contigs or scaffolds to detect contaminant DNA.
GNU General Public License v3.0
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Error in identify.phylo #15

Open abhiraj1105 opened 1 year ago

abhiraj1105 commented 1 year ago

hello

i installed PhylOligo and ran the phylopreprocess.py and phyloligo.py with no problems. however when i ran phyloselect.R after some time it flashed the tree for a secend then halted with below

phyloselect.R -d -m -i barcode03_HAC_flye_medaka.JSD.mat -a barcode03_HAC_flye_medaka_phylopreprocess.fasta

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

lowess

null device 1 Click close to a node. Right-click to exit. Error in identify.phylo(phy, quiet = TRUE) : could not find function "" Calls: clade_select Execution halted

would greatly appreciate some help resolving the issue

thanks

giacomomutti commented 1 year ago

Hey, I was having the same issue and I solved it by substituting identify.phylo to graphics::identify in the source code. I am not sure it's the perfect solution but it works! Cheers