Error with 'unexpected input'' when conducting LefSe analysis

1

Hello, Thanks for your development of GALAXY for LefSe analysis.

I wanna report my error about ‘unexpected input’.
I tried to conduct LefSe analysis with taxa data (exported from Qiime). My data don’t have any subclass.

A first column is about taxa information in form of “p__|c__|o__|f__|g__|s__”.
And a first row stands for ‘Infection result’, the 2nd row stands for ‘sample_id’ which selected as index.
Actually, it works when using “k__|p__|c__|o__|f__|g__|s__” (longer name) so it may not the problem regarding ‘out of range’.

I tried to remove ‘[’ ‘]’ after looking some advice in website (link: Lefse Error in (function (file = "", n = NULL, text = NULL, prompt = "?", keep.source = getOption("keep.source"), - #4 by rickmortyforever), but it didn’t work.

Also, i tried to change ‘__’ to ‘_’ to reduce the length of each taxa name. Also, I changed the option to ‘one-to-all (less stricted)’

I guess the input number of lowest level (species level) may exceed the range so it could not be analyzed LefSe effect size and other downstream analysis. (maybe in case of “k__|p__|c__|o__|f__|g__|s__” just parsed the name before species (|s__)?

Please give me an advice to debug this case. Thanks in advance!**

2

I solved the problem although I didn’t certain that this is the correct approach.
I rename the all unclassifed name (" __ ") to inform their level (e.g. p__, c__).
Then it works.

If there is an another idea, please tell me!

1 Like
3

it also works only change the taxon name start with " __ " to “p__”.