DADA2 Quality Control ERROR

[matthewbur (Matthew Burdick)]

Hello. I am currently using Qiime2-2020.11 and began receiving an error during my quality control step for the first time.

Code:
qiime dada2 denoise-paired
--i-demultiplexed-seqs demux.qza
--p-trim-left-f 19
--p-trim-left-r 16
--p-trunc-len-f 220 \
--p-trunc-len-r 200 \
--o-table table.qza
--o-representative-sequences rep-seqs.qza
--o-denoising-stats denoising-stats.qza

Errors:
(1/5) Missing option '--p-trunc-len-r'.
(2/5) Missing option '--o-table'. ("--output-dir" may also be used)
(3/5) Missing option '--o-representative-sequences'. ("--output-dir" may also be used)
(4/5) Missing option '--o-denoising-stats'. ("--output-dir" may also be used)
(5/5) Got unexpected extra argument ( )
zsh: command not found: --p-trunc-len-r
zsh: command not found: --o-table

I am not sure why this started happening. The code was working just fine earlier in the day. Any suggestions as too what may resolve the issue is appreciated.

Thanks!

[Nicholas_Bokulich]

Welcome @matthewbur!

See here:

–o-denoising stats: command not found

@farhad63, The issue is that your command is separated onto multiple lines. Put your entire command on a single line like to prevent this issue from occurring. Alternatively, put a backslash character (\) at the end of each line to let the computer know that your command continues onto the next line. You will note this is what is done in the QIIME 2 documentation — breaking up the command onto multiple lines makes it easier to read in the tutorial, but requires the backslashes to the computer …

@matthewbur

The code was working just fine earlier in the day

You probably copied/pasted from earlier and/or changed a line and forgot to add the backslash to the end of the line.

Good luck!