Troubleshooting Steps

1. Mamba not found in the shell

When running the following command:

$ python ROADIES-main/run_roadies.py --cores 1

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`.

Cause

The mamba package manager is missing or not available in the environment.

Solution

Install mamba:

conda install -n base -c conda-forge 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"
]

Step 3: Rerun the pipeline as follows:

python run_roadies.py --cores 16

2. Conda not recognized

Cause

Conda is not added to your system's PATH.

Solution

Ensure conda is added to the PATH by running the following commands:

export PATH="$HOME/miniconda3/bin:$PATH"
source ~/.bashrc

3. Singularity issues

Cause

Problems arise when trying to run the pipeline with Singularity.

Solution

We recommend using Docker instead of Singularity. Ensure Docker is installed and running on your system. We have also provided Bioconda support for users who face issues with Singularity.

4. Handling dependencies (glibc)

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:

workflow/scripts/lastz_32: /lib64/libm.so.6: version 'GLIBC_2.29' not found

5. PASTA fails with insufficient core count

Cause

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_threads = number_of_cores / num_instances

If 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:

python run_roadies.py --cores <available_cores> --config_path config/config.yaml