Schloss SOP tutorial: chimera.uchime error

mothur bugs
1

Hi,
i’m a beginner at mothur and i’ve been trying to understand this very useful tool by following the Schloss SOP tutorial
(http://www.mothur.org/wiki/Schloss_SOP)

Everything was fine until now. I am at the “removing chimera” step and i try to use the command given in the tutorial

mothur > chimera.uchime(fasta=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.fasta, name=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.names, group=GQY1XT001.shhh.good.groups, processors=2)

all i get is

uchime by Robert C. Edgar
http://drive5.com/uchime
This code is donated to the public domain.

Checking sequences from GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.fasta …
sh: /Users/myname/Desktop/Projet: No such file or directory
sh: /Users/myname/Desktop/Projet: No such file or directory
[ERROR]: Could not open GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.uchime.chimera9290.tempF003D142
[ERROR]: Could not open GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.uchime.chimeraF003D000

You must know that my datas are at this folder
/Users/myname/Desktop/Projet\ MNHN\ Coral\ Reef\ Bacterial\ Biodiversity/SchlossSOP

and mothur and uchime are in
/Users/myname/Desktop/Projet\ MNHN\ Coral\ Reef\ Bacterial\ Biodiversity/Mothur/

I think it might be a bug due to the spaces put in my folder name “Projet MNHN Coral Reef Bacterial Biodiversity” but i don’t understand why it bugs now. I had no problem until i use the chimera.uchime command.

Would you know how I could fix this problem?

Thank you for your help.

François

2

What version of mothur are you using?

3

Hi,

i’m using mothur v.1.25.1 on Mac OS X 10.6.

In fact, I’ve solved the problem, as i thought, by removing spaces in my folder’s name.

It could be a thing to know in order to improve the chimera.uchime command.

Thanks for your amazing tool!