Closed langse62171 closed 4 years ago
Hi, I found a similar issue here. Apparently someone solved it by adding line allow_softlinks: False
to .condarc file with something like:
echo "allow_softlinks: False" | cat - /home/sysadmin/.condarc > /tmp/out && mv /tmp/out /home/sysadmin/.condarc
.
I tried to reproduce your issue removing entrez_qiime_env environment and repeating the installation from scratch. It installed exactly the same versions you listed, but it worked successfully, so I was not able to reproduce it. My guess is that you may have some environmental variables set that don't allow gcc to work correctly.
First of all I would try this: open file Import_database.sh and replace gcc with gcc_linux-64. Then try rerunning the script and let me know.
Simone
Hi Simon. Thanks a lot for your quick response, the change in Import_database.sh to gcc_linux-64 worked. Setting up entrez_qiime_env and creating the files sequence_sequnze.qza and sequence_taxonomy.qza now worked without errors.
Now I have one more question. In the meantime I have run the pipeline with the enclosed test file "Test_BC04_xxx.zip" and the SILVA database. According to logfile.txt the pipeline is finished. All files in the folders "analysis, basecalling, preprocessing and qc" seem to have been created. Only the files taxa-bar-plots.qzv and taxa-bar-plots-no-Unassigned.qzv in the analysis folder are missing. Therefore I ask for help here, too. What could be the reason for this?
In the nohup.out file is several times deposited that no metadata file is present. I did not specify this file in the config_MinION_mobile_lab.R. Could that possibly be the reason?
Best regards, Sebastian
Yes, you must specify the path to a file. In the config_MinION_mobile_lab.R file you may set:
SAMPLE_METADATA <- "/home/sysadmin/sample-metadata.tsv"
Let me know if it works!
Simone
Hi and many thanks again! It works now after just adding a path :-) Best Sebastian
Good! I am going to close the issue. Feel free to open another one if you need any other clarifications. Best, Simone
Hello, first of all thank you for the MetONTIIME pipeline. The script "install.sh" ran without any error message. The import of SILVA_132 with "qiime tools import" also worked wll. If I run the script "Importing_database.sh" now, I get the following error message: # ./Import_database.sh /home/sysadmin/NCBI33175/sequence.fasta # Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: done
Package Plan ##
environment location: /home/sysadmin/miniconda3/envs/entrez_qiime_env
added / updated specs:
The following NEW packages will be INSTALLED:
ca-certificates anaconda/linux-64::ca-certificates-2020.1.1-0 certifi anaconda/linux-64::certifi-2019.11.28-py27_0 cloog anaconda/linux-64::cloog-0.18.0-0 gcc anaconda/linux-64::gcc-4.8.5-7 gmp anaconda/linux-64::gmp-6.1.2-hb3b607b_0 isl anaconda/linux-64::isl-0.12.2-0 libedit anaconda/linux-64::libedit-3.1.20181209-hc058e9b_0 libffi anaconda/linux-64::libffi-3.2.1-h4deb6c0_3 libgcc-ng anaconda/linux-64::libgcc-ng-9.1.0-hdf63c60_0 libstdcxx-ng anaconda/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0 mpc anaconda/linux-64::mpc-1.1.0-h10f8cd9_1 mpfr anaconda/linux-64::mpfr-4.0.1-hdf1c602_3 ncurses anaconda/linux-64::ncurses-6.2-he6710b0_0 openssl anaconda/linux-64::openssl-1.1.1-h7b6447c_0 pip anaconda/linux-64::pip-19.3.1-py27_0 python anaconda/linux-64::python-2.7.17-h9bab390_0 readline anaconda/linux-64::readline-7.0-h7b6447c_5 setuptools anaconda/linux-64::setuptools-44.0.0-py27_0 sqlite anaconda/linux-64::sqlite-3.31.1-h7b6447c_0 tk anaconda/linux-64::tk-8.6.8-hbc83047_0 wheel anaconda/linux-64::wheel-0.33.6-py27_0 zlib anaconda/linux-64::zlib-1.2.11-h7b6447c_3
Proceed ([y]/n)? y
Preparing transaction: done Verifying transaction: done Executing transaction: done ERROR conda.core.link:_execute(700): An error occurred while installing package 'anaconda::gcc-4.8.5-7'. Rolling back transaction: done
LinkError: post-link script failed for package anaconda::gcc-4.8.5-7 location of failed script: /home/sysadmin/miniconda3/envs/entrez_qiime_env/bin/.gcc-post-link.sh ==> script messages <==