What's wrong with my classification+evaluation code for Silva database?

Technical Support
1

This is the code I used (modified a bit compared to the original which was for gg database (Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt).

Output
Output837×386 9.45 KB

qiime rescript evaluate-fit-classifier
--i-sequences silva-138.1-ssu-nr99-seqs-derep-uniq.qza
--i-taxonomy silva-138.1-ssu-nr99-tax-derep-uniq.qza
--o-classifier silva-138.1-ssu-nr99-classifier.qza
--o-observed-taxonomy silva99-taxonomy-predicted-taxonomy.qza
--o-evaluation silva99-taxonomy-fit-classifier-evaluation.qzv

Should I limit my output to just classifier? Or is there a problem that I renamed the output files of observed taxonomy and evaluation? Your help is much appreciated; thank you!

2

Hi @susan.pyakurel,

When entering commands on multiple lines are you ending each line with a backslash (\) character ? Using \ tells the terminal that you are not yet done entering the command. Otherwise it will interpret each line as a separate, or incomplete, command.

For example, you can enter the command in one of two ways, like this:

qiime rescript evaluate-fit-classifier \
    --i-sequences silva-138.1-ssu-nr99-seqs-derep-uniq.qza \
    --i-taxonomy silva-138.1-ssu-nr99-tax-derep-uniq.qza \
    --o-classifier silva-138.1-ssu-nr99-classifier.qza \
    --o-observed-taxonomy silva99-taxonomy-predicted-taxonomy.qza \
    --o-evaluation silva99-taxonomy-fit-classifier-evaluation.qzv

or

qiime rescript evaluate-fit-classifier --i-sequences silva-138.1-ssu-nr99-seqs-derep-uniq.qza --i-taxonomy silva-138.1-ssu-nr99-tax-derep-uniq.qza --o-classifier silva-138.1-ssu-nr99-classifier.qza --o-observed-taxonomy silva99-taxonomy-predicted-taxonomy.qza --o-evaluation silva99-taxonomy-fit-classifier-evaluation.qzv
1 Like
3

Oh!! I just looked at this picture and found my mistake. There is one backlash missing. Let me try after getting that \ there and see if works. Thanks again.

4

It worked, thank you. Took a good 9 hours though with 32G and 24 processors.

What do you think of this? How could I make it better?

Output
Output1257×625 13.7 KB

.

1 Like
5

Great! :sparkler:

That plot looks good to me. I think you are good to move ahead. :pickup_truck:

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