Open 2061574124 opened 1 month ago
Hi,
it seems the 'database' folder is not exist under our PhaBOX path.
Can you check whether the zip files are unzipped correctly? try
unzip phagesuite_database.zip
unzip phagesuite_parameters.zip
You can also attach a screenshot for all the files within your PhaBOX
Best, Jiayu
Hi,
it seems the 'database' folder is not exist under our PhaBOX path.
Can you check whether the zip files are unzipped correctly? try
unzip phagesuite_database.zip unzip phagesuite_parameters.zip
You can also attach a screenshot for all the files within your PhaBOX
Best, Jiayu
Thanks so much!ABOVE IS THE SCREENSHOT FOR ALL FILES WITHIN PhaBOX
I suddenly found your error message is SyntaxError: invalid syntax
which means there should be a problem with your environment. Can you show the terminal you run the codes?
Best, Jiayu
And this error usually occurs when your python is 2, but the phabox env should be 3
And this error usually occurs when your python is 2, but the phabox env should be 3
Thank you very much for your patient. It is true that python2 was used before. I directly conda install python=3.8 in phabox environment. However, the following error occurs when i run following code:
And this error usually occurs when your python is 2, but the phabox env should be 3
Thank you very much for your patient. It is true that python2 was used before. I directly conda install python=3.8 in phabox environment. However, the following error occurs when i run following code:
This should be a problem caused by your personal computer, because when running conda env create -f webserver.yml -n phabox
, it will only install the python3.
There are several steps maybe you can try:
conda env create -f webserver.yml -n phabox
Hope this will help.
If you still cannot solve the problem, please try our webserver PhaBOX
Best, Jiayu
firstly, i run: git clone https://github.com/KennthShang/PhaBOX.git and then, cd PhaBOX/ conda env create -f webserver.yml -n phabox conda activate phabox
download the database.zip and parameters.zip to the PhaBOX folder with baidu cloud.
and run: unzip phagesuite_database.zip > /dev/null unzip phagesuite_parameters.zip > /dev/null
after that i make a test; python PhaMer_single.py --contigs test_contigs.fa --threads 8 --len 3000 --rootpth simple_test --out out/ --dbdir database/ --parampth parameters/ --scriptpth scripts/ File "PhaMer_single.py", line 65 print(f'Database directory {db_dir} missing or unreadable') ^ SyntaxError: invalid syntax
I don't know that it was caused by my operation error in that step. I am looking forward to your reply very much