EDTA
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oushujun
Error in test
Hello Dr. Ou, Thank you for the tool and tutorials! However, I have the following problems when using and testing:
Because I don't have root, I use CONDA to install.
Using git clone https://github.com/oushujun/EDTA.git``conda env create -f EDTA.yml , following problems:
nohup.out.txt
so I changed a new method to install, I try to use mamba install -c conda-forge -c bioconda edta python=3.6 tensorflow=1.14 'h5py<3' to intall, but following error when I test:
nohup.out2.txt
Run command：
1、perl ../EDTA.pl --genome genome.fa --cds genome.cds.fa --curatedlib ../database/rice6.9.5.liban --exclude genome.exclude.bed --overwrite 1 --sensitive 1 --anno 1 --evaluate 1 --threads 10 （Tutorials on GitHub）
Next，I used another command：
2、nohup /usr/bin/time -v perl ../EDTA.pl --genome genome.fa --cds genome.cds.fa --curatedlib ../database/rice6.9.5.liban --exclude genome.exclude.bed --overwrite 1 --sensitive 1 --anno 1 --evaluate 1 --threads 10 > EDTA.test & （in /test/README.txt）
conda env create -f EDTA.yml‘s error is：
EDTA.test.txt
mamba install -c conda-forge -c bioconda edta python=3.6 tensorflow=1.14 'h5py<3' 's erros is :
EDTA.test1.txt
What is the problem？ Thanks.
Cheers! wang
Hi Wang,
I am not sure what caused your issues. You may want to create an clean conda env to reinstall EDTA. Let me know if this doesn't work.
Best, Shujun
On Wed, Aug 31, 2022 at 3:33 AM wangxuleiii @.***> wrote:
Hello Dr. Ou, Thank you for the tool and tutorials! However, I have the following problems when using and testing:
Because I don't have root, I use CONDA to install. Using git clone https://github.com/oushujun/EDTA.git``conda https://github.com/oushujun/EDTA.gitconda env create -f EDTA.yml , following problems: nohup.out.txt https://github.com/oushujun/EDTA/files/9459360/nohup.out.txt
so I changed a new method to install, I try to use mamba install -c conda-forge -c bioconda edta python=3.6 tensorflow=1.14 'h5py<3' to intall, but following error when I test: nohup.out2.txt https://github.com/oushujun/EDTA/files/9459376/nohup.out2.txt
Run command： 1、perl ../EDTA.pl --genome genome.fa --cds genome.cds.fa --curatedlib ../database/rice6.9.5.liban --exclude genome.exclude.bed --overwrite 1 --sensitive 1 --anno 1 --evaluate 1 --threads 10 （Tutorials on GitHub）
Next，I used another command： 2、nohup /usr/bin/time -v perl ../EDTA.pl --genome genome.fa --cds genome.cds.fa --curatedlib ../database/rice6.9.5.liban --exclude genome.exclude.bed --overwrite 1 --sensitive 1 --anno 1 --evaluate 1 --threads 10 > EDTA.test & （in /test/README.txt）
conda env create -f EDTA.yml‘s error is： EDTA.test.txt https://github.com/oushujun/EDTA/files/9459514/EDTA.test.txt
mamba install -c conda-forge -c bioconda edta python=3.6 tensorflow=1.14 'h5py<3' 's erros is : EDTA.test1.txt https://github.com/oushujun/EDTA/files/9459540/EDTA.test1.txt
What is the problem？ Thanks.
Cheers! wang
— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/296, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NDRWHW4IZGKNOL3ZHLV34DFDANCNFSM6AAAAAAQBDFS3I . You are receiving this because you are subscribed to this thread.Message ID: @.***>
These two installation methods are newly created environments, and then encounter such problems.
The first and last error is (core dumped) perl, and the second and third error is Error while loading sequence. You should check your conda installation or your system. The installation is not proper.