chimera.uchime Error

Commands in mothur
1

Hi all,

I’m trying to run the chimera.uchime script with my trimmed and unique sequences fasta file and I keep getting this error:

mothur > chimera.uchime(fasta=stability.trim.contigs.good.unique.good.filter.fasta, count=stability.trim.contigs.good.unique.good.filter.count_table, dereplicate=t)

Unable to open /Users/laurenoconnell/Desktop/Thesis_Data/stability.trim.contigs.good.unique.good.filter.fasta. Trying output directory /Users/laurenoconnell/Desktop/Thesis_Data/mothur/stability.trim.contigs.good.unique.good.filter.fasta
Unable to open /Users/laurenoconnell/Desktop/Thesis_Data/stability.trim.contigs.good.unique.good.filter.count_table. Trying output directory /Users/laurenoconnell/Desktop/Thesis_Data/mothur/stability.trim.contigs.good.unique.good.filter.count_table

Using 1 processors.
/Users/laurenoconnell/Desktop/mothur/uchime file does not exist. Checking path…
[ERROR]: file does not exist. mothur requires the uchime executable.
[ERROR]: did not complete chimera.uchime.

I’ve tried changing my directory but I am still getting the same error.

Does anyone have any suggestions on how to get this command working?

2

mothur doesn’t perform uchime itself, it runs uchime as a separate program. It looks like you don’t have the executable (or don’t have it where mothur expects it). Have you moved mothur from where you originally downloaded/compiled it? If so, see if uchime is there and stick it wherever you’re running mothur from.

3

If you need the uchime executable. It is available for download with our mothur executable versions, http://www.mothur.org/wiki/Download_mothur.

4

I did move my mothur folder from where I downloaded it originally. I moved everything back and was able to get it running. Thanks, much!