This appears to be similar to this forum post where the problem was conda-forge moving some packages. Could that be the problem again and the environment files can be updated to solve?
Are you able to upgrade to the latest version of conda? You're using a fairly old version - I think that conda handles these virtual packages (like glibc) a bit differently in more modern versions of conda.
Updating to the latest version of conda allowed the install, but I think something is still wrong.
When I try to make a classifier using reference reads and taxonomy files from a previous version of Q2 I get an error that the files aren't Q2 artifacts.
qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads silva_ref_seqs.qza --i-referenc
e-taxonomy silva_taxonomy_99_7Levs.qza --o-classifier classifier_q2-2021.4_silva-132_99_7Levs_341-806_classif
ier.qza
(1/2) Invalid value for '--i-reference-reads': 'silva_ref_seqs.qza' is not a
QIIME 2 Artifact (.qza)
(2/2) Invalid value for '--i-reference-taxonomy':
'silva_taxonomy_99_7Levs.qza' is not a QIIME 2 Artifact (.qza)
Here's the new output from Conda info:
active environment : qiime2-2021.4
active env location : /home/saatkinson/anaconda3/envs/qiime2-2021.4
shell level : 2
user config file : /home/saatkinson/.condarc
populated config files : /home/saatkinson/.condarc
conda version : 4.10.1
conda-build version : not installed
python version : 3.6.13.final.0
virtual packages : __linux=4.4.0=0
__glibc=2.31=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/saatkinson/anaconda3 (writable)
conda av data dir : /home/saatkinson/anaconda3/etc/conda
conda av metadata url : https://repo.anaconda.com/pkgs/main
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://conda.anaconda.org/bioconda/linux-64
https://conda.anaconda.org/bioconda/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/saatkinson/anaconda3/pkgs
/home/saatkinson/.conda/pkgs
envs directories : /home/saatkinson/anaconda3/envs
/home/saatkinson/.conda/envs
platform : linux-64
user-agent : conda/4.10.1 requests/2.25.1 CPython/3.6.13 Linux/4.4.0-17763-Microsoft ubuntu/20.0
4 glibc/2.31
UID:GID : 1000:1000
netrc file : None
offline mode : False
How I updated conda:
For those with similar problems, updating conda with conda update conda gave this error:
Solving environment: failed
InvalidVersionSpecError: Invalid version spec: =2.7
I followed the directions in this GitHub issue to fix it.
Hmm, let's take a closer look at that. QIIME 2 artifacts are guaranteed to be backwards compatible - perhaps some other issue is at play here? Can you run the following:
Ok, good, I was pretty sure they were supposed to be backward compatible. Glad I'm not crazy lol!
Here's the output of the command. There's more information here.
qiime tools validate silva_ref_seqs.qza
Traceback (most recent call last):
File "/home/saatkinson/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/builtin/tools.py", li
ne 409, in validate
result = qiime2.sdk.Result.load(path)
File "/home/saatkinson/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/result.py", line
66, in load
archiver = archive.Archiver.load(filepath)
File "/home/saatkinson/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/core/archive/archive
r.py", line 299, in load
archive = cls.get_archive(filepath)
File "/home/saatkinson/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/core/archive/archive
r.py", line 264, in get_archive
raise ValueError("%s is not a QIIME archive." % filepath)
ValueError: silva_ref_seqs.qza is not a QIIME archive.
There was a problem loading silva_ref_seqs.qza as a QIIME 2 Result:
silva_ref_seqs.qza is not a QIIME archive.
See above for debug info.
Well, something looks strange here. Did you move or copy this file from one place to another recently? If so, maybe double check that it fully copied over and didn't become corrupt during the transfer. Otherwise, you can send me a download link for this file, I can perform some forensic analysis (read: poke at it until I come up with some ideas) and let you know.
