the problem of training a feature classifier

[QIN]

hi, dear qiime2 developers
this is my first time to use qiime2, i feel very unconfident about my question,
my problem is about the time for training the feature classifier,
it has been taken over one week, but there is no error, so i am confused..
there is details,
the version:
(qiime2-2022.2) user@Ubuntu:~/Documents/QIN 18s 22.08.08/$ qiime --version
q2cli version 2022.2.0

and the command:

(qiime2-2022.2) user@Ubuntu:~/Documents/QIN 18s 22.08.08/fastq$ qiime feature-classifier extract-reads \

--input-path 'home/user/Documents/QIN 18s 22.08.08/sliva-138-99-seqs(1).qza
--p-f-primer TTGTACACACCGCCC
--p-r-primer CCTTCYGCAGGTTCACCTAC
--o-reads ref-seqs.qza

i downloaded the dataset on this website:
https://data.qiime2.org/2022.2/common/silva-138-99-tax.qza.
is there problem with my command? or is there some methods to make this step faster?
or if there is no way, can i just skip this step?
thank you for any help!!

[lizgehret]

Hi @QIN,

Welcome to the forum!

Apologies for the delay in response on this - I am checking in with a few of my colleagues and we will circle back shortly. Thanks!

[SoilRotifer (Mike Robeson)]

Hi @QIN,

I assume you mean that you've downloaded the sequence and taxonomy files from the Data resources page? Note, this links to the latest 2022.8 version of . If you are using 2022.2 then use the drop-menu on the upper left of the page to navigate to the version you are using and download those files.

I highly recommend that you avoid including spaces or special characters, i.e. parenthesis, etc... in your folder or file path names. They can cause some software tools, or parts of some software tools, to behave unexpectedly. Perhaps rename your QIN 18s 22.08.08 folder to QIN_18s_22.08.08 and rename the sliva-138-99-seqs(1).qza file to sliva-138-99-seqs.qza. Then re-run the command.

I noticed that you have a quote ' that is not closed on this line:

--input-path 'home/user/Documents/QIN 18s 22.08.08/sliva-138-99-seqs(1).qza

perhaps add ' at the end of this line? If this is the issue, it explains why it appears to have been running for a long time. That is, it is not actually running, but expecting you to close the quote before starting anything.