PhyloscannerR error: Cannot normalise branch lengths from file without window cooardinates in tree IDs

[magosil86]

Hi Matthew,

I recently upgraded to v1.8.0 and tried the example dataset provided with phyloscannerR, however I am running into the following issue: Warning in initialise.phyloscanner(tree.file.directory, tree.file.regex, : Cannot normalise branch lengths from file without window cooardinates in tree IDs (which are usually file suffixes); tree branch lengths will not be normalised.

Minimum working example: Data: ptyr10_patients.txt ptyr10_trees_newick.zip

call to phyloscanner_analyse_trees.R: phyloscanner/phyloscanner_analyse_trees.R "ptyr10_trees_newick/" ptyr1 s,20 --allowMultiTrans --fileNameRegex "^\D*([0-9]+)_to_([0-9]+)\D*$" --maxReadsPerHost 50 --multifurcationThreshold 1e-05 --noProgressBars --normRefFileName "phyloscanner/phyloscannerR/inst/HIV_DistanceNormalisationOverGenome.csv" --normStandardiseGagPol --outgroupName "REF_CPX_AF460972" --outputRDA --overwrite --parsimonyBlacklistK 20 --ratioBlacklistThreshold 0 --rawBlacklistThreshold 20 --readCountsMatterOnZeroLengthBranches --relaxedAncestry --seed 42 --tipRegex "^(.*)_fq[0-9]+_read_([0-9]+)_count_([0-9]+)$" --verbose 1

Any suggestions?

Thanks

[mdhall272]

That --fileNameRegex doesn't work now, but the new default one does on that data.

[magosil86]

It works now, thanks for the tip Matthew!