readytowear SILVA 132 Training Error

Library Plugin Support
1

I'm trying to train the SILVA 132 V4 reference database with the animal-distal-gut.qza as the class-weight within qiime feature-classifier fit-classifier-naive-bayes. The command provided on the readytowear GitHub page worked just fine generating the correct classifier artifact:

qiime feature-classifier fit-classifier-naive-bayes \
  --i-reference-reads readytowear/data/gg_13_8/515f-806r/ref-seqs-v4.qza \
  --i-reference-taxonomy readytowear/data/gg_13_8/515f-806r/ref-tax.qza \
  --i-class-weight readytowear/data/gg_13_8/515f-806r/soil-non-saline.qza \
  --o-classifier gg138_v4_soil-non-saline_classifier.qza

When I modify this to the SILVA 132 database and a different weight as below:
'''
qiime feature-classifier fit-classifier-naive-bayes \

--i-reference-reads readytowear/data/silva_132/515f-806r/ref-seqs.qza \

--i-reference-taxonomy readytowear/data/silva_132/515f-806r/ref-tax.qza \

--i-class-weight readytowear/data/silva_132/515f-806r/animal-distal-gut.qza \

--o-classifier silva132_v4_animal-distal-gut_classifier.qza
'''
It throws the following error:
'''
Plugin error from feature-classifier:

Number of priors must match number of classes.
'''
Anyone have any ideas how to resolve this?

1 Like
2

Thanks for reporting this @zlmg2b!

It looks like those class weights somehow got mangled and contain extra taxonomy classes... I am currently testing and regenerating all SILVA 132 class weights to make sure all of these are working, which should take a day or two to finish. I will update you here when that is complete, though you could also most likely generate your own class weights following the tutorial in less time, since you only need animal-distal-gut, not everything.

I am also now making class weights for SILVA 138, so those will be on readytowear soon.

Thanks for your patience!

3 Likes
5

Hi @zlmg2b,
Sorry for the slow turnaround, regenerating all of these data takes a substantial amount of time.

Please re-download the SILVA files from readytowear and proceed.

We have fully replaced the SILVA 132 files with SILVA 138, so that these are fully compatible with the latest release of qiime-compatible SILVA files available in the QIIME 2 data resources. The V4-trimmed sequences are also available in readytowear.

Thanks for bearing with us, and for discovering that the animal distal gut weights had broken!

5 Likes