Is it truly impossible to use the SILVA database with RESCRIPt on VirtualBox?

Hi, everyone.
First of all, thank you so much for reading my post as a QIIME2 newbie. :smiling_face_with_tear:

I'm running QIIME 2 Core - 2022.2 (1654113933) with conda 4.13.0 on VirtualBox

I'm trying this post, "[Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt]"

In this post, I tried the Getting SILVA data: Hard Mode here, but wget did not gunzip to gz, so I downloaded the 4 files below directly from the SILVA v138.1 archive site.

  • tax_slv_ssu_138.1.txt.gz
  • taxmap_slv_ssu_ref_nr_138.1.txt.gz
  • tax_slv_ssu_138.1.tre.gz
    the sequence file:
  • SILVA_138.1_SSURef_Nr99_tax_silva_trunc.fasta.gz

(So I have a total of 8 files, gzed and not gzed)

And I installed RESCRIPT from the following site.


The problem starts with “Import silva files into QIIME2

When I tried to import the taxonomy rank file:

qiime tools import
--type 'FeatureData[SILVATaxonomy]'
--input-path tax_slv_ssu_138.1.txt
--output-path taxranks-silva-138.1-ssu-nr99.qza

Preformatted text I got the following error

No module named 'q2_types_genomics'
(RESCRIPT install: "ModuleNotFoundError: No module named 'q2_types_genomics'")

So I referred to this post that raised the same error, where before referring to the code SoilRotifer told, I clicked “here” to download the latest version of QIIME2 right below the code.

After entering this code

conda install -c conda-forge -c bioconda -c qiime2
-c released
-c defaults xmltodict 'q2-types-genomics>2023.5' ncbi-datasets-pylib

pip install git+https://github.com/bokulich-lab/RESCRIPt.git

qiime dev refresh-cache

qiime rescript --help

The results like this pictures



I tried again, but the same error popped up like this picture

so I re-entered the code that SoilRotifer replied to in the ModuleNotFoundError poster I mentioned earlier (the code is below).

conda activate qiime2-2023.2
conda create -y -n rescript
conda activate rescript
conda install
-c conda-forge -c bioconda -c qiime2 -c 2023.2-tested -c defaults
qiime2 q2cli q2templates q2-types q2-longitudinal q2-feature-classifier 'q2-types-genomics>2023.2'
"pandas>=0.25.3" xmltodict ncbi-datasets-pylib

pip install git+https://github.com/bokulich-lab/RESCRIPt.git


And then, I tried again But another error appeared like this

I can't solve this error because I've looked for advice on other similar errors, and the only thing I've found is that it's about the qiime installation.

Error
/usr/bin/qiime: 52: exec: /usr/lib/qiime/bin/tools.py: not found


Based on the errors and workarounds so far, I'm guessing that I need the required version of qiime2 to run Rescripts. Is this correct?
But the thing that bothers me is that no matter how much I update qiime with code, the version of qiime2 core in this virtualbox is 2022.2, so I don't know if it will work.
I need to install qiime2 core to run in the virtualbox, but even if I look in the qiime2 documentation, it is not updated to 2022-2.

All the things that ran earlier were due to the version of qiime2 core on virtualbox, right?
plz help me :sob: :sob: :sob:

Correct. You are running a very old version of QIIME 2, which is not compatible with the latest version of RESCRIPt. If you'd like to use the latest version you need to download and install QIIME 2 (2024.5).

Otherwise you'll have to look at the install instructions for older versions of RESCRIPt i.e. 2022.8 and earlier.

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Using the VirtualBox image you have right now, you can install a newer version of Qiime2 side by side with the old one simply by using a new conda environment.

This lets you use new Qiime2 features and plugins without downloading a new VM image!

https://docs.qiime2.org/2024.5/install/native/

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Hi @colinbrislawn !

I tried this, but it didn't work....
I'm going to change the VirtualBox to Ubuntu WSL and try again!!

Thanks for your kind reply and have a nice day!

-modori0227-

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Hi @SoilRotifer

Aha, I missed that there was a way to use an older version of RESCRIPt.

Thank you for your kind reply! I think using old versions of Qiime2 and RESCRIPt feels a bit unsettling, so I'm going to move to another tool(like Ubuntu) in VirtualBox to use the latest version.:sweat_smile::sweat_smile:
Thanks again

-modori0227--

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