a problem about get.lineage


I use mothur v.1.25.1 ,Windows 32Bit Version.
When I tried get.lineage command to get a unique sequence, a problem came to me:

mothur > get.lineage(taxonomy=finala.taxonomy,taxon=Archaea(100);Euryarchaeota(100);Halobacteria(100);Halobacteriales(100);Deep_Sea_Hydrothermal_Vent_Gp_6(DHVEG-6)(100);,name=finala.abund.names,group=finala.abund.groups,fasta=finala.abund.fasta)

[ERROR]: MHVG)(100 has occurred in the GetLineageCommand class function getTaxons. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.

I think it could caused by (DHVEG-6), because it also happened to taxon=Archaea(100);Euryarchaeota(100);Thermoplasmata(100);South_African_Goldmine_Gp(SAGMEG)(100);

How to solve this problem?

Thank you

Mothur thinks the only thing in wrapped in parenthesis’ is a confidence score. Version 1.28 will make mothur more flexible and resolve this issue. You will want to escape the ‘-’ character as well since mothur uses the ‘-’ to separate the list of taxons you would like to search for.


Thanks! I replaced () with _ in finala.taxonomy and it works!