# Importing downloaded latest UNITE database for ITS classifier training
**URL:** https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687
**Category:** User Support
**Created:** [December 17, 2021, 9:48pm UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687 "2021-12-17T21:48:23Z")
**Posts on this page:** 19
**Page:** 1
### Author:  [@bettya](https://forum.qiime2.org/u/bettya)
#### Post date: [December 17, 2021, 9:48pm UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687/1 "2021-12-17T21:48:23Z")
Can anyone please help me with importing the latest UNITE qiime2 ITS trainer?
I have been struggling with the file which has a .gz format:
# qiime tools import \
--type 'FeatureData[Sequence]'
--input-path "C:\Users\User\Desktop\qiime2-ITS1\C5547B97AAA979E45F79DC4C8C4B12113389343D7588716B5AD330F8BDB300C9\C5547B97AAA979E45F79DC4C8C4B12113389343D7588716B5AD330F8BDB300C9.tar"
--output-path unite.qza
qiime tools import
--type 'FeatureData[Taxonomy]'
--input-format HeaderlessTSVTaxonomyFormat
--input-path sh\_taxonomy\_qiime\_ver7\_dynamic\_01.12.2017.txt
--output-path unite-taxonomy.qza
I used the above command and I got error
qiime tools import
--type 'FeatureData[Taxonomy]'
--input-format HeaderlessTSVTaxonomyFormat
--input-path sh\_taxonomy\_qiime\_ver7\_dynamic\_01.12.2017.txt
--output-path unite-taxonomy.qza
I used the above command and I got an error, can anyone put me through.
Regards.
Betty
---
### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [December 20, 2021, 5:49am UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687/2 "2021-12-20T05:49:07Z")
Hello Betty,
**EDIT: Since this post was written in 2021, I've built [ready to use UNITE classifiers for Qiime2](https://github.com/colinbrislawn/unite-train/).**
* * *
Original post:
It's good to see you on the forums again. Thanks for posting the commands you ran.
It looks like the UNITE team distributes files in the .tgz format. That's a tar file compressed with .gz, so we will have to uncompress it to see the files inside.
📦 🔜 🗃
After downloading this file, try extracting it with a command like this:
```bash
cd path/to/the/dowloaded/file
tar -xf C5547B97AAA979E45F79DC4C8C4B12113389343D7588716B5AD330F8BDB300C9.tgz
```
When I run this command, it extracts the .tgz file and makes a new directory called `sh_qiime_release_10.05.2021`.
Where you able to extract that .tgz file and see that directory?
I can see this directory when I run `ls -alh`
```bash
(base) cbrisl@MacBook-Air Downloads % ls -alht
total 1947200
drwxr-xr-x+ 84 cbrisl staff 2.6K Dec 20 00:36 ..
drwx------@ 161 cbrisl staff 5.0K Dec 20 00:35 .
-rw-r--r--@ 1 cbrisl staff 48M Dec 20 00:32 C5547B97AAA979E45F79DC4C8C4B12113389343D7588716B5AD330F8BDB300C9.tgz
drwxr-xr-x@ 10 cbrisl staff 320B May 10 2021 sh_qiime_release_10.05.2021
...
```
Inside that directory are the files you can import into Qiime2:
```bash
(base) cbrisl@MacBook-Air Downloads % ls -alht sh_qiime_release_10.05.2021
total 213456
drwx------@ 161 cbrisl staff 5.0K Dec 20 00:35 ..
drwxr-xr-x@ 10 cbrisl staff 320B May 10 2021 .
drwxr-xr-x@ 8 cbrisl staff 256B May 10 2021 developer
-rw-r--r--@ 1 cbrisl staff 33K May 10 2021 QIIME_ITS_readme_10.05.2021.pdf
-rw-r--r--@ 1 cbrisl staff 7.9M May 10 2021 sh_taxonomy_qiime_ver8_dynamic_10.05.2021.txt
-rw-r--r--@ 1 cbrisl staff 8.2M May 10 2021 sh_taxonomy_qiime_ver8_99_10.05.2021.txt
-rw-r--r--@ 1 cbrisl staff 5.6M May 10 2021 sh_taxonomy_qiime_ver8_97_10.05.2021.txt
-rw-r--r--@ 1 cbrisl staff 30M May 10 2021 sh_refs_qiime_ver8_dynamic_10.05.2021.fasta
-rw-r--r--@ 1 cbrisl staff 31M May 10 2021 sh_refs_qiime_ver8_99_10.05.2021.fasta
-rw-r--r--@ 1 cbrisl staff 22M May 10 2021 sh_refs_qiime_ver8_97_10.05.2021.fasta
```
Let me know if you were able to extract that .tgz file and could see the Qiime2 compatible files inside.
Colin 🐳
---
### Author:  [@bettya](https://forum.qiime2.org/u/bettya)
#### Post date: [December 22, 2021, 10:25pm UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687/3 "2021-12-22T22:25:46Z")
Hi Colin
Thanks a bunch. It pretty much works out.
Another issue I have is that I am struggling to train the classifier. I used this command line:
qiime feature-classifier fit-classifier-naive-bayes
--i-reference-reads unite-taxonomy.qza
--i-reference-taxonomy unite.qza
--o-classifier unite-ver8\_99\_10.05.2021.qza
Output
There were some problems with the command:
(1/2) Invalid value for '--i-reference-reads': Expected an artifact of at
least type FeatureData[Sequence]. An artifact of type FeatureData[Taxonomy]
was provided.
(2/2) Invalid value for '--i-reference-taxonomy': Expected an artifact of at
least type FeatureData[Taxonomy]. An artifact of type FeatureData[Sequence]
was provided.
My question is that, which of these files should I import for the training?
I have these 2 files imported already to qiime2: unite-taxonomy.qza and unite.qza
I am working on ITS 1 and 2 data now on y virtual box.
Please advice.
---
### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [December 22, 2021, 11:49pm UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687/4 "2021-12-22T23:49:33Z")
I'm glad this worked out, and you got these files imported!
I think this next error should be pretty quick to address:
> [@bettya](#):
>
> There were some problems with the command:
> (1/2) Invalid value for '--i-reference-reads': Expected an artifact of at
> least type FeatureData[Sequence]. An artifact of type FeatureData[Taxonomy]
> was provided.
> (2/2) Invalid value for '--i-reference-taxonomy': Expected an artifact of at
> least type FeatureData[Taxonomy]. An artifact of type FeatureData[Sequence]
> was provided.
Looks like these two input files got switched. Try this:
```bash
--i-reference-reads unite.qza
--i-reference-taxonomy unite-taxonomy.qza
```
---
### Author:  [@bettya](https://forum.qiime2.org/u/bettya)
#### Post date: [December 24, 2021, 1:08pm UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687/5 "2021-12-24T13:08:57Z")
Hi Collin
Thank you for the correction. I changed it just like you directed and the command ran but did not complete. This is the command I used:
qiime feature-classifier fit-classifier-naive-bayes
--i-reference-reads unite.qza
--i-reference-taxonomy unite-taxonomy.qza
--o-classifier unite-ver8\_99\_10.05.2021.qza
It returned as "Killed"
I realised after searching the forum that quite a number of people have challenge training classifiers.
Can you please advise what this means?
Also, if you can share an already trained classifier with me, I wouldn't mind.
I must submit the fungi results on resumption in January 2022.
Regards.
---
### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [December 24, 2021, 5:39pm UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687/6 "2021-12-24T17:39:21Z")
Ah, OK. Thanks for telling me more.
The status of 'Killed' means that the computer or server you are running this on intentionally canceled the command, often this is because it ran out of RAM / memory. Training a classifier does take a lot of memory, so this is probably what happened.
How much memory does your computer or VM have? Could you run this command on a server or computer with more memory so that the command will be able to complete?
EDIT: I forgot to mention this! If you are ok with using an older version of UNITE and Qiime2, then you could use [the pretrained UNITE v8.0 classifiers](https://forum.qiime2.org/t/unite-v-8-0-2018-11-18-classifiers-for-qiime2-available-here/8750). This way you can avoid this `fit-classifier-naive-bayes` step that requires so much RAM, and move on to the classifying your ASVs! Let me know if you would like to try that.
---
### Author:  [@bettya](https://forum.qiime2.org/u/bettya)
#### Post date: [December 28, 2021, 9:26pm UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687/7 "2021-12-28T21:26:08Z")
Hi
I downloaded the dynamic version of the classifier and I used this command:
qiime feature-classifier classify-sklearn
--i-classifier unite-ver8-dynamic-classifier.qza
--i-reads dada2-single-end-rep-seqs.qza
--o-classification taxonomy.qza
I got this error:
Plugin error from feature-classifier:
The scikit-learn version (0.20.2) used to generate this artifact does not match the current version of scikit-learn installed (0.23.1). Please retrain your classifier for your current deployment to prevent data-corruption errors.
Debug info has been saved to /tmp/qiime2-q2cli-err-09bfhzi1.log
Verbose error log:
raceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/commands.py", line 329, in **call**
results = action(\*\*arguments)
File "", line 2, in classify\_sklearn
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/action.py", line 234, in bound\_callable
spec.view\_type, recorder)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/result.py", line 289, in \_view
result = transformation(self.\_archiver.data\_dir)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/core/transform.py", line 70, in transformation
new\_view = transformer(view)
File "/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/q2\_feature\_classifier/\_taxonomic\_classifier.py", line 64, in \_1
% (sklearn\_version, sklearn. **version** ))
ValueError: The scikit-learn version (0.20.2) used to generate this artifact does not match the current version of scikit-learn installed (0.23.1). Please retrain your classifier for your current deployment to prevent data-corruption errors.
How do I resolve this error?
Kindly assist.
Thanks and regards.
---
### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [December 28, 2021, 9:45pm UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687/8 "2021-12-28T21:45:51Z")
The [UNITE classifiers I linked above](https://forum.qiime2.org/t/unite-v-8-0-2018-11-18-classifiers-for-qiime2-available-here/8750) were trained with qiime2 2019.1, so you will have to [install that older version of Qiime](https://docs.qiime2.org/2019.1/install/native/#install-qiime-2-within-a-conda-environment) in a conda environment to use it.
Let me know if you need a hand installing `qiime2-2019.1` or if you run into any more issues getting the classifier to run.
---
### Author:  [@bettya](https://forum.qiime2.org/u/bettya)
#### Post date: [December 28, 2021, 11:59pm UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687/9 "2021-12-28T23:59:39Z")
Hi
Thank you for the tip.
I will like to inform you that I am using a virtual machine with the latest qiime2 installed on my windows laptop.
How do I install qiime2-2019 in a conda environment?
Do you know any tutorial I can follow to install the qiime2-2019.1 on the virtual box?
Thank you for your help.
Betty
---
### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [December 29, 2021, 1:55am UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687/10 "2021-12-29T01:55:32Z")
You can download the qiime2-2019.1 image here!
[https://data.qiime2.org/distro/core/virtualbox-images.txt](https://data.qiime2.org/distro/core/virtualbox-images.txt)
(You did mention you were using a VM, I should have remembered that.)
---
### Author:  [@bettya](https://forum.qiime2.org/u/bettya)
#### Post date: [December 30, 2021, 8:35pm UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687/11 "2021-12-30T20:35:01Z")
Hi Colin
Thanks for the support. Merry Xmas to you!
I downloaded the qiime2 2019.1 version and ran the classifier and I got this error:
qiime feature-classifier classify-sklearn \
> --i-classifier unite-ver8-dynamic-classifier.qza
> --i-reads dada2-single-end-rep-seqs.qza
> --o-classification taxonomy.qza
> --verbose
Traceback (most recent call last):
File "/home/qiime2/miniconda/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/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 225, in bound\_callable
spec.view\_type, recorder)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/result.py", line 287, in \_view
result = transformation(self.\_archiver.data\_dir)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/core/transform.py", line 70, in transformation
new\_view = transformer(view)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2\_feature\_classifier/\_taxonomic\_classifier.py", line 72, in \_1
pipeline = joblib.load(os.path.join(dirname, 'sklearn\_pipeline.pkl'))
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/externals/joblib/numpy\_pickle.py", line 598, in load
obj = \_unpickle(fobj, filename, mmap\_mode)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/externals/joblib/numpy\_pickle.py", line 526, in \_unpickle
obj = unpickler.load()
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/pickle.py", line 1050, in load
dispatchkey[0]
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/externals/joblib/numpy\_pickle.py", line 352, in load\_build
self.stack.append(array\_wrapper.read(self))
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/externals/joblib/numpy\_pickle.py", line 195, in read
array = self.read\_array(unpickler)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/externals/joblib/numpy\_pickle.py", line 141, in read\_array
array = unpickler.np.empty(count, dtype=self.dtype)
MemoryError
Plugin error from feature-classifier:
See above for debug info.
Kindly help with this.
Regards.
---
### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [December 30, 2021, 9:25pm UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687/12 "2021-12-30T21:25:34Z")
Hello again Betty,
Did you check you errors for clues? 🔎
> [@bettya](#):
>
> packages/sklearn/externals/joblib/numpy\_pickle.py", line 141, in read\_array
> array = unpickler.np.empty(count, dtype=self.dtype)
> MemoryError
I saw it says MemoryError, which is probably because there's not enough memory on this machine.
How much memory / RAM do you have on your host Windows machine?
How much memory have you allocated to your VM?
You could also try reducing the number reads-per-batch, say using `--p-reads-per-batch 1000`, and see if that helps reduce the memory needed so the command can finish.
---
### Author:  [@bettya](https://forum.qiime2.org/u/bettya)
#### Post date: [December 30, 2021, 11:35pm UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687/13 "2021-12-30T23:35:18Z")
Hi Colin
Thanks for the information.
Yes, I read the debug info, I just want to double-check with you.
I am unable to run the command even after reducing the per read to 500.
Is there any other way out that you can advise?
My laptop is overstretched already, just need to get a better machine.
Thank you for your assistance.
Much regards.
---
### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [December 31, 2021, 3:36pm UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687/14 "2021-12-31T15:36:48Z")
Huh... I wonder what's the minimum needed ram needed for this classier.
How much memory / RAM do you have on your host Windows machine?
How much memory have you allocated to your VM?
---
### Author:  [@bettya](https://forum.qiime2.org/u/bettya)
#### Post date: [January 4, 2022, 8:53pm UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687/15 "2022-01-04T20:53:25Z")
Hi Colin
Thank you for your help.
I was trying to use another machine to run the classifier but I am yet to do it.
I have an 8GB machine and I allocated 2084 MB for the VM.
Regards.
---
### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [January 7, 2022, 5:00am UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687/16 "2022-01-07T05:00:19Z")
Hello Betty,
> [@bettya](#):
>
> I have an 8GB machine and I allocated 2084 MB for the VM.
Thanks for telling me more.
Having 8 GB on the host machine and 2 GB for the VM is pretty limiting. Try closing all other programs on the host machine and increasing the memory allocated to the VM to 6 GB (or 6000 MB).
Let me know how it goes. I think the best solution will be to find a machine with more memory to run this step, so let me know if you find that too!
---
### Author:  [@bettya](https://forum.qiime2.org/u/bettya)
#### Post date: [January 19, 2022, 11:15am UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687/17 "2022-01-19T11:15:58Z")
Dear Colin
Compliments of the new year to you, again.
I waited for resumption at my workplace and I tried the classifier again but I am still unable to do it.
I allocated 7GB to the VM but it is not working, I do not know why, because I read that I need about 6GB ram to run the classifier command.
I actually do not know what to do as I have to submit this result before the end of the month.
I now know that machine resources are a vital part of data analysis.
Any suggestion or help from your side?
Much thanks.
Betty
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [January 19, 2022, 6:27pm UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687/18 "2022-01-19T18:27:52Z")
Hi @bettya - as @colinbrislawn has mentioned a few times above, the machine you're trying to run this analysis on might not be capable of supporting these commands. Do you have access to an institutional HPC? Or a department server? Many funding agencies also provide free or low-cost compute infrastructure for awardees.
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [February 20, 2022, 12:28am UTC](https://forum.qiime2.org/t/importing-downloaded-latest-unite-database-for-its-classifier-training/21687/19 "2022-02-20T00:28:43Z")
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