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