Troubleshooting Steps
Error 1. Issues with PASTA
Solution
When running the pipeline, if you encounter that the pipeline fails by the failure of PASTA, please install PASTA from source by executing the following commands. Please run the following steps from the main ROADIES repository directory (after doing cd ROADIES) - within the activated Conda environment:
git clone https://github.com/smirarab/pasta.git
git clone https://github.com/smirarab/sate-tools-linux.git
cd pasta
python3 setup.py develop --user
Also, in the align.smk file (inside the workflow/rules directory of the ROADIES repository), please replace any instance of pasta.py with python pasta/run_pasta.py, AND
run_seqtools.py with python pasta/run_seqtools.py.
After doing this change, please re-run the ROADIES pipeline.
Error 2. Environment conflict
Solution
If you encounter the following error message - "ls: relocation error: /lib64/libacl.so.1: symbol getxattr, version ATTR_1.0 not defined in file libattr.so.1 with link time reference", please run the following command to resolve it:
Error 3. Mamba not found in the shell
When running the following command:
You may encounter this error:rm: cannot remove 'output_files': No such file or directory
Unlocking working directory.
snakemake --cores 1 --config mode=accurate config_path=config/config.yaml num_threads=0 --use-conda --rerun-incomplete
Config file config/config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
CreateCondaEnvironmentException:
The 'mamba' command is not available in the shell /usr/bin/bash that will be used by Snakemake. You have to ensure that it is in your PATH, e.g., first activating the conda base environment with `conda activate base`.The mamba package manager (https://github.com/mamba-org/mamba) is a fast and robust conda replacement. It is the recommended way of using Snakemake's conda integration. It can be installed with `conda install -n base -c conda-forge mamba`. If you still prefer to use conda, you can enforce that by setting `--conda-frontend conda`.
mamba package manager is missing or not available in the environment.
Solution
Install mamba:
If you prefer using conda, you can enforce it by adding the --conda-frontend conda argument.
Step 1: In the downloaded ROADIES repository, open the file noconverge.py inside the workflow folder (ROADIES/workflow/noconverge.py).
Step 2: At line 31, add the argument --conda-frontend conda to the cmd command, as shown below:
cmd = [
"snakemake",
"--cores",
str(cores),
"--config",
"mode=" + str(mode),
"config_path=" + str(config_path),
"num_threads=" + str(num_threads),
"--use-conda",
"--rerun-incomplete",
"--conda-frontend", "conda"
]
Error 4. Conda not recognized
This can happen if conda is not added to your system's PATH.
Solution
To resolve this, please ensure conda is added to the PATH by running the following commands:
Error 5. Handling dependencies (glibc)
Solution
Ensure that the glibc version on your system is updated to 2.29 or higher. Update your system libraries if necessary. Otherwise you may encounter this error:
Error 6. PASTA fails with insufficient core count
Pasta fails when the number of cores is insufficient for the number of instances.
The pipeline provides NUM_INSTANCES as a configuration parameter in config.yaml to run multiple instances in parallel. Each instance can also be parallelized using threads. The number of threads per instance is calculated as:
num_instances > number_of_cores, then num_threads will be 0 and the process (e.g., pasta) will fail.
Solution
Ensure that the number of cores is greater than or equal to the number of instances. By default, NUM_INSTANCES is set to 4, so the number of cores (--cores in command line argument) must be at least 4. To run the pipeline with fewer cores, modify the NUM_INSTANCES parameter in the config file: