# Error in Taxonomy Analysis
**URL:** https://forum.qiime2.org/t/error-in-taxonomy-analysis/8731
**Category:** User Support
**Created:** [March 11, 2019, 4:00pm UTC](https://forum.qiime2.org/t/error-in-taxonomy-analysis/8731 "2019-03-11T16:00:53Z")
**Posts on this page:** 13
**Page:** 1
### Author:  [@Mehrdad](https://forum.qiime2.org/u/Mehrdad)
#### Post date: [March 11, 2019, 4:00pm UTC](https://forum.qiime2.org/t/error-in-taxonomy-analysis/8731/1 "2019-03-11T16:00:53Z")
I got this error. I did not solve it:
qiime feature-classifier classify-sklearn
--i-classifier gg-13-8-99-515-806-nb-classifier.qza **(I used SILVA instead of gg)**
--i-reads rep-seqs.qza \ **(I used rep-seqs from dada2 plugin)**
--o-classification taxonomy.qza
What is the problem?
🙏
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [March 11, 2019, 4:03pm UTC](https://forum.qiime2.org/t/error-in-taxonomy-analysis/8731/2 "2019-03-11T16:03:04Z")
Hey there @Mehrdad, you have several typos in your command. What you wrote is this:
```bash
qiime feature-classifier classify-sklearn \
> > --i-classifier silva-132-99-nb-classifier.qza \
> > --i-reads RepresenDenoisedLibA.qza \
> > --o-classification taxonomylibA.qza
```
Note the ~~6~~ 3 extra `>` at the beginning of line 2, line 3, and line 4. You should not include those:
```bash
qiime feature-classifier classify-sklearn \
--i-classifier silva-132-99-nb-classifier.qza \
--i-reads RepresenDenoisedLibA.qza \
--o-classification taxonomylibA.qza
```
---
### Author:  [@Mehrdad](https://forum.qiime2.org/u/Mehrdad)
#### Post date: [March 11, 2019, 4:31pm UTC](https://forum.qiime2.org/t/error-in-taxonomy-analysis/8731/3 "2019-03-11T16:31:11Z")
Hi Matthew,
On terminal screen I have always this sign (\>), but you are right I had three extra of that. Firstly I offer my thanks.
I put the right form then I got error.
---
### Author:  [@Mehrdad](https://forum.qiime2.org/u/Mehrdad)
#### Post date: [March 11, 2019, 4:41pm UTC](https://forum.qiime2.org/t/error-in-taxonomy-analysis/8731/4 "2019-03-11T16:41:46Z")
I finished dada2 step. And based on the suggestion I am following the next step but I started with taxonomy analysis.
> [@With FeatureData or Without it](https://forum.qiime2.org/t/with-featuredata-or-without-it/8716):
>
> Hi, I already created my feature table but during the taxonomy analysis and the workflow in the tutorial page, I understood that I need feature data. Honestly, I do not have it. It is admittedly required for taxonomy analysis. I do not know! Based on the workflow, it is possible to continue by only feature table. If it is necessary alongside the feature table for the taxonomy analysis how can provide it? Feature Data is coming from two sources: Reference taxonomy, Reference sequence and the qu…
---
### Author:  [@Mehrdad](https://forum.qiime2.org/u/Mehrdad)
#### Post date: [March 11, 2019, 5:11pm UTC](https://forum.qiime2.org/t/error-in-taxonomy-analysis/8731/5 "2019-03-11T17:11:27Z")
I downloaded GreenGen (full length) database from this page:
> **[Data resources — QIIME 2 2019.1.0 documentation](https://docs.qiime2.org/2019.1/data-resources/)**
It worked; however, it did not work once I immediately run the same command with SILVA file. I am interested in working with SILVA database because it highly updated.
What is your idea?
How solve the error?
What is the origin of the error?
thanks
---
### Author:  [@Mehrbod\_Estaki](https://forum.qiime2.org/u/Mehrbod_Estaki)
#### Post date: [March 11, 2019, 9:11pm UTC](https://forum.qiime2.org/t/error-in-taxonomy-analysis/8731/6 "2019-03-11T21:11:00Z")
Hi @Mehrdad,
In order to troubleshoot any error messages it is almost always necessary to see the full error message. Could you rerun your commands with the `--verbose` flag and copy paste the full report please.
---
### Author:  [@Mehrdad](https://forum.qiime2.org/u/Mehrdad)
#### Post date: [March 11, 2019, 10:20pm UTC](https://forum.qiime2.org/t/error-in-taxonomy-analysis/8731/7 "2019-03-11T22:20:28Z")
Hi Mehrbod,
Thanks for the reply!
This the whole error. There you go!
---
### Author:  [@Mehrdad](https://forum.qiime2.org/u/Mehrdad)
#### Post date: [March 11, 2019, 10:20pm UTC](https://forum.qiime2.org/t/error-in-taxonomy-analysis/8731/8 "2019-03-11T22:20:30Z")
**Copy Paste the whole report:**
qiime feature-classifier classify-sklearn --i-classifier silva-132-99-nb-classifier.qza --i-reads RepresenDenoisedLibA.qza --o-classification RepresenDenoisedLibA.qza --verbose
Traceback (most recent call last):
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py", line 274, in **call**
results = action(\*\*arguments)
File "\", line 2, in classify\_sklearn
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound\_callable
output\_types, provenance)
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 365, in _callable\_executor_
output\_views = self.\_callable(\*\*view\_args)
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2\_feature\_classifier/classifier.py", line 212, in classify\_sklearn
reads, classifier, read\_orientation=read\_orientation)
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2\_feature\_classifier/classifier.py", line 169, in \_autodetect\_orientation
result = list(zip(\*predict(first\_n\_reads, classifier, confidence=0.)))
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2\_feature\_classifier/\_skl.py", line 45, in predict
for chunk in \_chunks(reads, chunk\_size)) for m in c)
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/externals/joblib/parallel.py", line 917, in **call**
if self.dispatch\_one\_batch(iterator):
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/externals/joblib/parallel.py", line 759, in dispatch\_one\_batch
self.\_dispatch(tasks)
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/externals/joblib/parallel.py", line 716, in \_dispatch
job = self.\_backend.apply\_async(batch, callback=cb)
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/externals/joblib/\_parallel\_backends.py", line 182, in apply\_async
result = ImmediateResult(func)
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/externals/joblib/\_parallel\_backends.py", line 549, in **init**
self.results = batch()
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/externals/joblib/parallel.py", line 225, in **call**
for func, args, kwargs in self.items]
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/externals/joblib/parallel.py", line 225, in
for func, args, kwargs in self.items]
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2\_feature\_classifier/\_skl.py", line 52, in \_predict\_chunk
return \_predict\_chunk\_with\_conf(pipeline, separator, confidence, chunk)
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2\_feature\_classifier/\_skl.py", line 66, in \_predict\_chunk\_with\_conf
prob\_pos = pipeline.predict\_proba(X)
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/utils/metaestimators.py", line 118, in
out = lambda \*args, \*\*kwargs: self.fn(obj, \*args, \*\*kwargs)
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/pipeline.py", line 382, in predict\_proba
return self.steps[-1][-1].predict\_proba(Xt)
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/naive\_bayes.py", line 104, in predict\_proba
return np.exp(self.predict\_log\_proba(X))
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/naive\_bayes.py", line 84, in predict\_log\_proba
jll = self.\_joint\_log\_likelihood(X)
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/naive\_bayes.py", line 731, in _joint\_log\_likelihood
return (safe\_sparse\_dot(X, self.feature\_log\_prob_.T) +
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/utils/extmath.py", line 168, in safe\_sparse\_dot
ret = a \* b
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/scipy/sparse/base.py", line 473, in **mul**
return self.\_mul\_multivector(other)
File "/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/scipy/sparse/compressed.py", line 482, in \_mul\_multivector
other.ravel(), result.ravel())
MemoryError
Plugin error from feature-classifier:
See above for debug info.
---
### Author:  [@Mehrbod\_Estaki](https://forum.qiime2.org/u/Mehrbod_Estaki)
#### Post date: [March 11, 2019, 11:09pm UTC](https://forum.qiime2.org/t/error-in-taxonomy-analysis/8731/9 "2019-03-11T23:09:39Z")
Hi @Mehrdad,
Thanks! So if I'm not mistaken I believe your MemoryError indicates that you have insufficient RAM for this task. This is pretty common with the Silva dataset due to its size. You can browse around the forum to see what others have done, for ex [here](https://forum.qiime2.org/t/memoryerror-when-running-feature-classifer-with-pre-trained-classifier/566). Ultimately you just need access to more RAM. If that is not an option for you then you could try the Greengenes database which is a lot less memory intensive.
---
### Author:  [@Mehrdad](https://forum.qiime2.org/u/Mehrdad)
#### Post date: [March 18, 2019, 2:19pm UTC](https://forum.qiime2.org/t/error-in-taxonomy-analysis/8731/10 "2019-03-18T14:19:29Z")
Dear @Mehrbod_Estaki,
I read some of the discussions regarding MemoryError I modified the command but I still have error.
Also I tested the --p-n-jobs parameter it did not work and computer totally frosen.
What should I do for solving the memory error?
\*My memory is 16 GiB.
Thanks
---
### Author:  [@Mehrdad](https://forum.qiime2.org/u/Mehrdad)
#### Post date: [March 19, 2019, 12:26pm UTC](https://forum.qiime2.org/t/error-in-taxonomy-analysis/8731/12 "2019-03-19T12:26:40Z")
[https://docs.qiime2.org/2019.1/plugins/available/feature-classifier/classify-sklearn/](https://docs.qiime2.org/2019.1/plugins/available/feature-classifier/classify-sklearn/)
These parameters are not present in the page above, and you have mentioned them in some discussions, by the way.
--p-chunk-size
--p-classify-chunk
---
### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [March 19, 2019, 12:32pm UTC](https://forum.qiime2.org/t/error-in-taxonomy-analysis/8731/13 "2019-03-19T12:32:40Z")
> [@Mehrdad](#):
>
> –p-chunk-size
that is the old name for the `--p-reads-per-batch` parameter in previous releases. Try setting it to 1000 and it may fix your problem. If it does not, and you followed all other tips given above, then you need a more powerful computer to run that command and we cannot help you with that.
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [April 19, 2019, 6:32pm UTC](https://forum.qiime2.org/t/error-in-taxonomy-analysis/8731/14 "2019-04-19T18:32:40Z")
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