mothur > collect.single(shared=final.pick.an.shared, calc=chao-invsimpson, freq=0.25)
I received this message:
Processing group XXX_C-11N-C_V456.V456-BSF517-linker
Floating point exception
And mothur stopped, without quit()
I checked the corresponding sample and it contains only 3 sequences. The same story happened with other datasets when some samples contained less than 4 samples.
It looks like a bug generated by the choosen parameter freq=0.25, when the resulting frequency is smaller than 1.
What do you think?
Why are you using freq=0.25? Remember that freq is the frequency at which data is outputted to the collect files. The smallest freq you’d ever want would be 1.
According to the documentation of collect.single(), I expected to get data based on % of sequences
or you set set the frequency as a percentage of the number of sequences. For example to output after 25%:
mothur > collect.single(list=98_lt_phylip_amazon.fn.list, freq=0.25)
Maybe I missed something
The freq option can take 0.25 as an input. Is your shared file a relabund file, meaning it contains relative abundances?