Problem with running analysis script

[MarcNiebel]

Hi, I am struggling to run the analysis script for Phyloscanner after generating my trees. My input command is:

phyloscanner_analyse_trees.R third_iteration/trees_thirditeration/FastTree RunWithoutBlacklisting s,20 --outgroupName "1|a|AF009606" --tipRegex "^(.*)_([0-9]+)read([0-9]+)count([0-9]+)$" --normRefFileName branch_length_normalisation.csv_ByPosition.csv --multifurcationThreshold g --verbose

Below is the output: Warning: replacing previous import ‘ggtree::getRoot’ by ‘phangorn::getRoot’ when loading ‘phyloscannerR’ Error in .stop(output, "parse error:") : parse error: usage: ./phyloscanner_analyse_trees.R [-h] [-og OUTGROUPNAME] [-m MULTIFURCATIONTHRESHOLD] [-b USERBLACKLIST] [-od OUTPUTDIR] [-v] [-npb] [-x TIPREGEX] [-y FILENAMEREGEX] [-tfe TREEFILEEXTENSION] [-cfe CSVFILEEXTENSION] [-pw PDFWIDTH] [-ph PDFRELHEIGHT] [-psb PDFSCALEBARWIDTH] [-rda] [-sd SEED] [-ow] [-nr NORMREFFILENAME] [-ns] [-nc NORMALISATIONCONSTANTS] [-db DUPLICATEBLACKLIST] [-pbk PARSIMONYBLACKLISTK] [-rwt RAWBLACKLISTTHRESHOLD] [-rtt RATIOBLACKLISTTHRESHOLD] [-ub]

Calls: -> res -> .stop Execution halted

Any help would be much appreciated.

Marc

[mdhall272]

Hi Marc,

That's odd - I can't see anything obviously wrong with it. I presume your phyloscanner version is reasonably up to date? (If you update right now you'd need to change --verbose to --verbose 1 or --verbose 2, I made that change today.) Is it possible your shell is seeing special characters that need escaping - the pipes in the outgroup name maybe?

Thanks, Matthew

[MarcNiebel]

Hi Matthew,

Thanks for that tip. Worked with --outgroupName 1|a|AF009606

Best Wishes,

Marc