Can't install qiime2

ShevchenkoAlla · September 17, 2024, 4:36pm

Hello.
I can't install qiime2, unfortunately I tried to install pircust and after I updated ubuntu (sudo update - uprgade) I cant install pircust, no qiime2. I am kind of lost.

I dont know what to do
I would appreciate help.

It looks like this

conda env create -n qiime2-amplicon-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml
Channels:

released
bioconda
conda-forge
defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(950): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.11-r43hdfd78af_1'.
Rolling back transaction: done
class: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.11-r43hdfd78af_1
location of failed script: /home/alla/mambaforge/envs/qiime2-amplicon-2024.5/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==

==> script output <==
stdout:
stderr: QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
++ dirname -- /home/alla/mambaforge/envs/qiime2-amplicon-2024.5/bin/installBiocDataPackage.sh

SCRIPT_DIR=/home/alla/mambaforge/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages
json=/home/alla/mambaforge/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."genomeinfodbdata-1.2.11".fn' /home/alla/mambaforge/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages/dataURLs.json
FN='"GenomeInfoDbData_1.2.11.tar.gz"'
IFS=
read -r value
++ yq '."genomeinfodbdata-1.2.11".urls' /home/alla/mambaforge/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages/dataURLs.json
URLS+=($value)
IFS=
read -r value
URLS+=($value)
IFS=
read -r value
URLS+=($value)
IFS=
read -r value
++ yq '."genomeinfodbdata-1.2.11".md5' /home/alla/mambaforge/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages/dataURLs.json
MD5='"2a4cbfc2031992fed3c9445f450890a2"'
STAGING=/home/alla/mambaforge/envs/qiime2-amplicon-2024.5/share/genomeinfodbdata-1.2.11
mkdir -p /home/alla/mambaforge/envs/qiime2-amplicon-2024.5/share/genomeinfodbdata-1.2.11
TARBALL='/home/alla/mambaforge/envs/qiime2-amplicon-2024.5/share/genomeinfodbdata-1.2.11/"GenomeInfoDbData_1.2.11.tar.gz"'
SUCCESS=0
for URL in ${URLS[@]}
++ echo '"https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz"'
++ tr -d '"'
URL=https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz
++ echo '"2a4cbfc2031992fed3c9445f450890a2"'
++ tr -d '"'
MD5=2a4cbfc2031992fed3c9445f450890a2
curl -L https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 416 100 416 0 0 2161 0 --:--:-- --:--:-- --:--:-- 2166

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transfer closed with 4418943 bytes remaining to read

return code: 18

kwargs:
{}

Traceback (most recent call last):
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/exception_handler.py", line 18, in call
return func(*args, **kwargs)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/cli/main.py", line 84, in main_subshell
exit_code = do_call(args, parser)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/cli/conda_argparse.py", line 200, in do_call
result = getattr(module, func_name)(args, parser)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/notices/core.py", line 132, in wrapper
return func(*args, **kwargs)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/cli/main_env_create.py", line 170, in execute
result[installer_type] = installer.install(
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/env/installers/conda.py", line 63, in install
unlink_link_transaction.execute()
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/core/link.py", line 354, in execute
self._execute(
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/core/link.py", line 970, in _execute
raise CondaMultiError(
conda.CondaMultiErrorclass: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.11-r43hdfd78af_1
location of failed script: /home/alla/mambaforge/envs/qiime2-amplicon-2024.5/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==

==> script output <==
stdout:
stderr: QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
++ dirname -- /home/alla/mambaforge/envs/qiime2-amplicon-2024.5/bin/installBiocDataPackage.sh

SCRIPT_DIR=/home/alla/mambaforge/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages
json=/home/alla/mambaforge/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."genomeinfodbdata-1.2.11".fn' /home/alla/mambaforge/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages/dataURLs.json
FN='"GenomeInfoDbData_1.2.11.tar.gz"'
IFS=
read -r value
++ yq '."genomeinfodbdata-1.2.11".urls' /home/alla/mambaforge/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages/dataURLs.json
URLS+=($value)
IFS=
read -r value
URLS+=($value)
IFS=
read -r value
URLS+=($value)
IFS=
read -r value
++ yq '."genomeinfodbdata-1.2.11".md5' /home/alla/mambaforge/envs/qiime2-amplicon-2024.5/bin/../share/bioconductor-data-packages/dataURLs.json
MD5='"2a4cbfc2031992fed3c9445f450890a2"'
STAGING=/home/alla/mambaforge/envs/qiime2-amplicon-2024.5/share/genomeinfodbdata-1.2.11
mkdir -p /home/alla/mambaforge/envs/qiime2-amplicon-2024.5/share/genomeinfodbdata-1.2.11
TARBALL='/home/alla/mambaforge/envs/qiime2-amplicon-2024.5/share/genomeinfodbdata-1.2.11/"GenomeInfoDbData_1.2.11.tar.gz"'
SUCCESS=0
for URL in ${URLS[@]}
++ echo '"https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz"'
++ tr -d '"'
URL=https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz
++ echo '"2a4cbfc2031992fed3c9445f450890a2"'
++ tr -d '"'
MD5=2a4cbfc2031992fed3c9445f450890a2
curl -L https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 416 100 416 0 0 2161 0 --:--:-- --:--:-- --:--:-- 2166

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
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curl: (18) transfer closed with 4418943 bytes remaining to read

return code: 18

kwargs:
{}

: <exception str() failed>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/alla/mambaforge/bin/conda", line 13, in
sys.exit(main())
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/cli/main.py", line 128, in main
return conda_exception_handler(main, *args, **kwargs)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/exception_handler.py", line 388, in conda_exception_handler
return_value = exception_handler(func, *args, **kwargs)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/exception_handler.py", line 21, in call
return self.handle_exception(exc_val, exc_tb)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/exception_handler.py", line 62, in handle_exception
return self.handle_application_exception(exc_val, exc_tb)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/exception_handler.py", line 78, in handle_application_exception
self._print_conda_exception(exc_val, exc_tb)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/exception_handler.py", line 84, in _print_conda_exception
print_conda_exception(exc_val, exc_tb)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/exceptions.py", line 1260, in print_conda_exception
stderrlog.error("\n%r\n", exc_val)
File "/home/alla/mambaforge/lib/python3.10/logging/init.py", line 1506, in error
self._log(ERROR, msg, args, **kwargs)
File "/home/alla/mambaforge/lib/python3.10/logging/init.py", line 1624, in _log
self.handle(record)
File "/home/alla/mambaforge/lib/python3.10/logging/init.py", line 1633, in handle
if (not self.disabled) and self.filter(record):
File "/home/alla/mambaforge/lib/python3.10/logging/init.py", line 821, in filter
result = f.filter(record)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/gateways/logging.py", line 66, in filter
record.msg = record.msg % record.args
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/init.py", line 125, in repr
errs.append(e.repr())
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/init.py", line 79, in repr
return f"{self.class.name}: {self}"
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/init.py", line 83, in str
return str(self.message % self._kwargs)
ValueError: unsupported format character 'T' (0x54) at index 2174

lizgehret · September 17, 2024, 8:12pm

Hey @ShevchenkoAlla,

Hmm, there might be something that's been corrupted with an existing environment on your machine that's causing this error. Can you please try the following?

conda remove -n qiime2-amplicon-2024.5 --all
conda install conda=24.5.0
conda clean --all
wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml
conda env create -n qiime2-amplicon-2024.5 --file qiime2-amplicon-2024.5-py39-linux-conda.yml

ShevchenkoAlla · September 17, 2024, 10:37pm

Thank you so much
It worked.