error for uchime and chimera slayer on linux system

mothur bugs
1

I am currently running mothur on a linux server system. When I use the uchime command I receive the following error message
Using 1 processors.
/usr/local/bin/uchime file does not exist. Checking path…
[ERROR]: file does not exist. mothur requires the uchime executable.
[ERROR]: did not complete chimera.uchime.

I also get the following error messages when I try chimera slayer
Only reporting sequence supported by 90% of bootstrapped results.
[ERROR]: /usr/local/bin/blast/bin/formatdb file does not exist. mothur requires formatdb.exe.
[ERROR]: /usr/local/bin/blast/bin/blastall file does not exist. mothur requires blastall.exe.
[ERROR]: /usr/local/bin/blast/bin/megablast file does not exist. mothur requires megablast.exe.

I have run the analysis on a stand alone desktop with the same files it works okay. Does anyone know how to fix the error on the linux system?
thanks

2

For chimera.uchime, did you try moving the uchime executable to /usr/local/bin/uchime? For chimera.slayer, you can move the blast folder to /usr/local/bin, or set your blast location using the blastlocation parameter.

3

Hello

We encountered the same problem. We tried to create a “local” library in our user name directory as suggested but with no success. It look like Mothur cannot find the UCHIME.

Any suggestions?

thank you
Hila

4

I’ve never had this problem on our linux computers, but I have noticed that if you try to run mothur installed in the QIIME virtual machine, the same problem happens with uchime - it’s in the same directory as mothur, but can’t be found.

5

Have you tried putting uchime in the same folder as mothur’s exe?

6

i have encountered a similar problem. May i ask what is the uchime executable?? I have downloaded both “gold” database and uchine2.40 from their site but nothing worked.shall i change the name of the file or something ?

7

The uchime executable is released with the executable versions of mothur, https://github.com/mothur/mothur/releases/tag/v1.36.1. It is also built as part the build process when you build mothur from source yourself. The file will be named uchime on Linux/Max machines, or uchime.exe on Windows machines. Mothur’s wrapper command, chimera.uchime http://www.mothur.org/wiki/Chimera.uchime, is design to work with the version of uchime released with mothur’s executable and source. Mothur’s chimera.uchime command prepares the inputs, runs the uchime executable, and assembles the results.