GRiD crashes; Cannot open check_R_libraries.R
nattzy94 opened this issue · 14 comments
Hi I am trying to run GRiD on the test files but keep running into the following error:
Fatal error: cannot open file 'check_R_libraries.R': No such file or directory
R libraries ok
rm: .checkedR: No such file or directory
usage: mkdir [-pv] [-m mode] directory ...
Output directory not Empty
Would you happen to know how to solve this error?
Hi,
First, the output directory should be empty before running GRiD. Please confirm the output folder specified with the -o flag is empty. Second, do you have write permissions to the installation folder? I usually recommend creating a conda environment for any package to be installed via conda like the example below.
conda create --name GRiD
source activate GRiD
conda install grid=1.2
Before use, always activate the environment using "source activate GRiD". You should be able to run the example test
Hi, thanks so much for the reply.
-
I performed the test code:
grid single -r . -g S_epidermidis.LRKNS118.fna -o output_singlein the /GRiD-1.2/test folder. The output folder does not exist when I input the code, am I suppose to create a "output_single" folder? -
Yes, I have write permissions, am using a personal computer.
-
I tried downloading grid=1.2 using the command you gave but I get this error
PackagesNotFoundError: The following packages are not available from current channels:
- grid=1.2
I ended up just using conda install grid and managed to download it so I'm not sure if this might be an issue with the version of grid? I have also done conda config --add for defaults, bioconda and conda-forge beforehand.
Hi,
- You do not need to create the output folder. it creates it automatically. The error "PackagesNotFoundError" may be an issue with the anaconda server. Can you confirm if version 1.2 was installed? You can check this using "grid -v".
I checked the folder and it appears to be version 1.1.
lrwxr-xr-x 1 nat staff 24 24 Mar 18:14 grid -> ../share/grid-1.1-1/grid
Oh. You need version 1.2. Simply upgrade using "conda update grid"
Hi, I am getting the same error as nattzy94.
I have installed the grid on my Mac and searched the version, and it turns out version 1.1
I have tried to run "conda update grid" on my Mac, however it did not let me to install the 1.2 (not available). Could you let me know how to solve this error?
Ok. I think I think this is what is happening. In version 1.2, mosdepth replaces samtools for genome coverage calculation since is significantly faster than samtools. Mosdepth is however, unavailable for Mac. That being said, I'll figure out why the current example test does not work with version 1.1 and get back to you soonest.
Thanks!
- Tunde
@hkoo877 @nattzy94
@gaarangoa has nicely provided an alternative way to install GRiD using docker (https://github.com/gaarangoa/GRiD). Could you give this a try?
Thanks!
- Tunde
Thank you for the reply. I have tried the docker by running:
docker run --rm -it -v /Users/hhhh/Desktop/GRID/GRiD-1.2/test:/data/ gaarangoa/grid:1.0 /bin/bash
and then got a error message below:
docker: Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?.
See 'docker run --help'.
Could you let me know what I have missed?
Run with "sudo docker" instead of "docker"
I typed with sudo command and still got the same error message below:
docker: Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?.
See 'docker run --help'.
It works fine in my machine. Could you check this post to see if it could be related? https://stackoverflow.com/questions/44084846/cannot-connect-to-the-docker-daemon-on-macos
Thank you for sharing the link. I ran the command "brew cask install docker" and ran the "docker ps". After the two command, the test set worked. Thank you so much!
You are welcome. Thanks to @gaarangoa for making GRiD installation possible via docker.