v1.36.0 problems

mothur bugs
1

Hi
I have installed mothur v 1.36.0 in ubuntu 14.04 LTS according to instructions provided, which includes the use of Boost as a significant deviation from the previous mothur makes. However, neither does mothur recognise the reference.tgz files in the source folder (specified in the makefile before make) nor does it run the command make.biom properly. When i run the command:
mothur > make.biom(shared=final.an.shared, label=0.03, reftaxonomy=gg_13_8_99.gg.tax, constaxonomy=final.an.0.03.cons.taxonomy, picrust=97_otu_map.txt)

constaxonomy is not a valid parameter.
The valid parameters are: shared, contaxonomy, groups, label, inputdir, outputdir, and matrixtype.
picrust is not a valid parameter.
The valid parameters are: shared, contaxonomy, groups, label, inputdir, outputdir, and matrixtype.
reftaxonomy is not a valid parameter.
The valid parameters are: shared, contaxonomy, groups, label, inputdir, outputdir, and matrixtype.
[ERROR]: did not complete make.biom.

Does this mean that mothur v 1.36.0 doesn’t support the picrust option anymore? I am confused. This worked with v 1.35.0 fine.

2

It seems like you may have an old version of mothur in your path. Can you type which mothur at the terminal window to find out? Or check the log file created to see the version number? Also we released a 1.36.1, you can download it here, https://github.com/mothur/mothur/releases/tag/v1.36.1.

3

Thank you, Sarah. You are spot on!..I had recently installed QIIME and the full version installs mothur 1.25.0. I was not aware of that. removed it from the .bashrc. All fixed it seems. thanks much! :slight_smile: