Thanks so much!
And I would have another try. I want to reinstall Qiime2 on Linux. Though I have obtained some solutions in this forum, I cannot deal with it and I cannot install this bioconda::bioconductor-genomeinfodbdata-1.2.9
, by ---conda install
. So I tried to remove it from yml and install independently.
That's really help and I will check and compare the raw sequences obtained by --fasterq-dump
and --fastq-dump
on linux.
Appreciate for all of you for your time and help.
The Error shows here:
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(945): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0'.
Rolling back transaction: done
class: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0
location of failed script: /home/YangJingyi/anaconda3/envs/qiime2-amplicon-2024.2/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/YangJingyi/anaconda3/envs/qiime2-amplicon-2024.2/bin/installBiocDataPackage.sh
- SCRIPT_DIR=/home/YangJingyi/anaconda3/envs/qiime2-amplicon-2024.2/bin/../share/bioconductor-data-packages
- json=/home/YangJingyi/anaconda3/envs/qiime2-amplicon-2024.2/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."genomeinfodbdata-1.2.9".fn' /home/YangJingyi/anaconda3/envs/qiime2-amplicon-2024.2/bin/../share/bioconductor-data-packages/dataURLs.json
- FN='"GenomeInfoDbData_1.2.9.tar.gz"'
- IFS=
- read -r value
++ yq '."genomeinfodbdata-1.2.9".urls' /home/YangJingyi/anaconda3/envs/qiime2-amplicon-2024.2/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-1.2.9".md5' /home/YangJingyi/anaconda3/envs/qiime2-amplicon-2024.2/bin/../share/bioconductor-data-packages/dataURLs.json
- MD5='"7cc138cfb74665fdfa8d1c244eac4879"'
- STAGING=/home/YangJingyi/anaconda3/envs/qiime2-amplicon-2024.2/share/genomeinfodbdata-1.2.9
- mkdir -p /home/YangJingyi/anaconda3/envs/qiime2-amplicon-2024.2/share/genomeinfodbdata-1.2.9
- TARBALL='/home/YangJingyi/anaconda3/envs/qiime2-amplicon-2024.2/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
- SUCCESS=0
- for URL in ${URLS[@]}
++ echo '"https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz"'
++ tr -d '"'
- URL=https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
++ tr -d '"'
++ echo '"7cc138cfb74665fdfa8d1c244eac4879"'
- MD5=7cc138cfb74665fdfa8d1c244eac4879
- curl -L https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 415 100 415 0 0 375 0 0:00:01 0:00:01 --:--:-- 375
40 11.1M 40 4657k 0 0 11872 0 0:16:27 0:06:41 0:09:46 11701
curl: (18) transfer closed with 6955914 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/YangJingyi/anaconda3/bin/conda", line 13, in
sys.exit(main())
^^^^^^
File "/home/YangJingyi/anaconda3/lib/python3.11/site-packages/conda/cli/main.py", line 128, in main
return conda_exception_handler(main, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/YangJingyi/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 388, in conda_exception_handler
return_value = exception_handler(func, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/YangJingyi/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 20, in call
return self.handle_exception(exc_val, exc_tb)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/YangJingyi/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 62, in handle_exception
return self.handle_application_exception(exc_val, exc_tb)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/YangJingyi/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 78, in handle_application_exception
self._print_conda_exception(exc_val, exc_tb)
File "/home/YangJingyi/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 84, in _print_conda_exception
print_conda_exception(exc_val, exc_tb)
File "/home/YangJingyi/anaconda3/lib/python3.11/site-packages/conda/exceptions.py", line 1258, in print_conda_exception
stderrlog.error("\n%r\n", exc_val)
File "/home/YangJingyi/anaconda3/lib/python3.11/logging/init.py", line 1518, in error
self._log(ERROR, msg, args, **kwargs)
File "/home/YangJingyi/anaconda3/lib/python3.11/logging/init.py", line 1634, in _log
self.handle(record)
File "/home/YangJingyi/anaconda3/lib/python3.11/logging/init.py", line 1643, in handle
if (not self.disabled) and self.filter(record):
^^^^^^^^^^^^^^^^^^^
File "/home/YangJingyi/anaconda3/lib/python3.11/logging/init.py", line 830, in filter
result = f.filter(record)
^^^^^^^^^^^^^^^^
File "/home/YangJingyi/anaconda3/lib/python3.11/site-packages/conda/gateways/logging.py", line 65, in filter
record.msg = record.msg % new_args
~~~^~
File "/home/YangJingyi/anaconda3/lib/python3.11/site-packages/conda/init.py", line 104, in repr
errs.append(e.repr())
^^^^^^^^^^^^
File "/home/YangJingyi/anaconda3/lib/python3.11/site-packages/conda/init.py", line 58, in repr
return f"{self.class.name}: {self}"
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/YangJingyi/anaconda3/lib/python3.11/site-packages/conda/init.py", line 62, in str
return str(self.message % self._kwargs)
~^~
ValueError: unsupported format character 'T' (0x54) at index 2212