Error running Mafft alignment

[Camilla (Camilla Diotallevi)]

Hi all,
I have been trying to run mafft alignement but it keeps failing.
The error that I got is: --i- sequences command not found

Here the commands:
qiime alignment mafft \
--i-sequences rep-seqs.qza
--p-n-threads 1
--o-alignment fitered_Alignment.qza
Could somebody help me to understand why?

PS: I have activated the conda enviroment

Thank you
Camilla

[colinbrislawn (Colin J Brislawn)]

Hello Camilla,

@Camilla

PS: I have activated the conda environment

Perfect! We are off to a good start!

The "command not found" makes me wonder there is an issue with the multi-line command and the slashes at the end of the line

I think this command should work

qiime alignment mafft \
--i-sequences rep-seqs.qza \
--p-n-threads 1 \
--o-alignment fitered_Alignment.qza

Noticed how I added the \ back slashes \ after each line accept the last one, and the \ is the very last character on the line.
(If the line ends with slash and a space \ it causes errors)

Let me know how well that works for you,
Colin

[Camilla (Camilla Diotallevi)]

Thank you Colin!! Now it works

Camilla