search

BDI-pathogens / phyloscanner

Phylogenetics between and within hosts at once, all along the genome.
GNU General Public License v3.0
47 stars 14 forks source link

Problem with running second script #28

Closed MarcNiebel closed 6 years ago

MarcNiebel commented 6 years ago

Hi Matthew,

I have a files of tree files which have been generated by FastTree. I am trying to use these in your script for analysing the trees. My command is:

../../../../../phyloscanner/phyloscanner_analysetrees.R AlignedReadsInWindow P102_P110multitrans s,20 --outgroupName AF009606 --allowMultiTrans --tipRegex "^(.*)([0-9]+)read([0-9]+)count([0-9]+)$" --normRefFileName ../../../../1a_ORF.csv_ByPosition.csv --multifurcationThreshold g --verbose 2

The error I get is:

Warning: replacing previous import ‘ggtree::getRoot’ by ‘phangorn::getRoot’ when loading ‘phyloscannerR’ Random number seed is 197906578 Error in phyloscanner.analyse.trees(tree.directory, tree.file.regex, reconstruction.mode, : unused arguments (verbosity, no.progress.bars) Execution halted

Could you possible clarify which arguments are required. I am not sure I understand the error. Previous iterations of the above code worked fine.

Kind Regards,

Marc

mdhall272 commented 6 years ago

Hi Marc,

Are the files beginning AlignedReadsInWindow_ tree files? And is there more than one of them?

This isn't anything you did - it's an internal function that's seeing the wrong arguments. I'm unclear why as yet.

MarcNiebel commented 6 years ago

Yes there are 50 of them which have the format: AlignedReadsInWindow_1081_to_1260.tree (example)

mdhall272 commented 6 years ago

What was different about the earlier iterations that worked?

MarcNiebel commented 6 years ago

Nothing except I did it about a month ago and recently updated the scripts

mdhall272 commented 6 years ago

Maybe quickest if you just run the attached instead and tell me what the output is. I suspect some argument is being split into a vector.

phyloscanner_analyse_trees_DEBUG.txt

MarcNiebel commented 6 years ago

Do I just run it instead of normal script?

mdhall272 commented 6 years ago

Yes. Github didn't like ".R" as a file extension, but it's just a modification of the same script.

MarcNiebel commented 6 years ago

Actually resolved it by re-installing the R package(phyloscannerR) without having to implement the debug version. Thanks for your help.

Marc

mdhall272 commented 6 years ago

Reinstalling the package should probably be suggestion number 1 in a FAQ for problems with phyloscannerR! Thanks for letting me know.