Feature-classifier plugin error

[Egeo]

Hello all,

I’m training a classifier with the SILVA 99% OTUs dataset and have a plugin error when I run the feature-classifier fit. I used the unaligned reference sequences. Has anyone else had this problem?

Here is the pipeline:

qiime tools import
–type ‘FeatureData[Sequence]’
–input-path silva132_99.fna
–output-path 99_otus.qza

qiime tools import
–type ‘FeatureData[Taxonomy]’
–source-format HeaderlessTSVTaxonomyFormat
–input-path consensus_taxonomy_all_levels.txt
–output-path ref-taxonomy.qza

qiime feature-classifier extract-reads
–i-sequences 99_otus.qza
–p-f-primer GTGYCAGCMGCCGCGGTAA
–p-r-primer GGACTACNVGGGTWTCTAAT
–o-reads ref-seqs.qza

qiime feature-classifier fit-classifier-naive-bayes
–i-reference-reads ref-seqs.qza
–i-reference-taxonomy ref-taxonomy.qza
–o-classifier classifier_silva_99_trimmed.qza

Plugin error from feature-classifier:
Debug info has been saved to /tmp/qiime2-q2cli-err-1iyh64p2.log

Thanks!

[Nicholas_Bokulich]

Hi @Egeo,
The error is written to this temporary file:

/tmp/qiime2-q2cli-err-1iyh64p2.log

You can use

less /tmp/qiime2-q2cli-err-1iyh64p2.log

to read the contents of that file.

Or else run:

qiime feature-classifier fit-classifier-naive-bayes \
  --i-reference-reads ref-seqs.qza \
  --i-reference-taxonomy ref-taxonomy.qza \
  --o-classifier classifier_silva_99_trimmed.qza \
  --verbose

To see the full error. (Adding the --verbose flag to any command causes the error to be printed to your terminal instead of to a temp file)

Once you have that error, please search this forum to see if that error message has been reported previously. If you get stuck, please share the full error traceback with us and we will give you a hand!

Thanks!