"Floating point exception" with collect.single

mothur bugs
1

When using:

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

0.03
Floating point exception

And mothur stopped, without quit() :frowning:
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?

2

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.

3

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

4

The freq option can take 0.25 as an input. Is your shared file a relabund file, meaning it contains relative abundances?