Feature-classifier missing options

[F_Mauthe]

Hi everyone!

I have imported reference sequences and taxonomy and now want to filter out sequences that are not Glomeromycota. When I use feature-classifier classify-consensus-blast

qiime feature-classifier classify-consensus-blast
--i-query frequency-filtered-rep-seqs.qza
--i-reference-reads cacao_seqs.qza
--i-reference-taxonomy taxonomy.qza
--p-query-cov 0.95
--p-perc-identity 0.95 \
--p-maxaccepts 1 \
--o-classification Blast_rep_taxonomy-CQ-95-95-1.qza

I always get this error:

(1/3) Missing option '--o-classification'. ("--output-dir" may also be used)

(2/3) Missing option '--o-search-results'. ("--output-dir" may also be used)

(3/3) Got unexpected extra argument ( )

frequency-filtered-rep-seqs.qza (82.5 KB)
cacao_seqs.qza (1.2 MB)
taxonomy.qza (10.0 KB)

What am I doing wrong?
Does anyone know what the reason could be?

I am grateful for any advice.

kind regards
Franzi

[colinvwood (Colin Wood)]

Hello @F_Mauthe,

It looks like there is a space after the backslash in the --p-perc-identity option. Remove that space and make sure all other backslashes have no spaces after them and you should be good to go.

--p-perc-identity 0.95 \ <-- trailing space (bad)
--p-perc-identity 0.95 \<-- no trailing space (good)