Frequently Asked Questions

Some commonly encountered questions are addressed here. For more detailed or specific questions that have not been included below, feel free to submit an issue on Github.

Installation Questions

For errors encountered during the installation process, unless installation is successful for all packages but specifically fails during the installation of the Snekmer package itself, we recommend searching the Conda troubleshooting page for the issue. If packages other than Snekmer are also failing to install, or else the environment is not created successfully, the installation issues likely involve either Conda or the user’s individual configuration.

Why is the `conda install` command is taking a long time?

Installation of snakemake via conda typically requires a fairly long compile time. To avoid this, you can install Snakemake via Mamba (see the official Snakemake installation instructions for details).

Why am I getting a `CondaEnvException: Pip failed`? Does this mean my Snekmer installation failed?

This error appears when BSF is unable to be installed on a user’s system. However, conda still installs Snekmer and its dependencies without BSF, despite the error. Since BSF is optional for Snekmer, Snekmer should still run without any issues.

To verify this, run conda activate <ENV_NAME> (i.e. conda activate snekmer), followed by conda list, to check that the environment was created successfully and that Snekmer was indeed installed.

Troubleshooting Error Messages

If you encounter an error while using Snekmer, we recommend first checking the Snakemake FAQs page for a solution. We have also listed some common error messages below. If your error message cannot be solved, feel free to let us know via Github issues.

MissingInputException

Non-Windows Systems

Generally, this error type means that Snekmer is unable to detect input files, and the input files may not follow the required directory structure. For more information, including an example of the file structure needed, see Configuration.

Windows Systems

For Windows systems specifically, there is a known issue with handling unzipping files that will raise a MissingInputException and cause Snekmer to terminate under failure. We are aware of this issue and are actively working on a resolution; in the meantime, we recommend separately unzipping any zipped files prior to evaluation via Snekmer.

FileNotFoundError

This error usually indicates that the file system latency is not sufficiently long. In order words, the system is taking longer to create the file than Snakemake is allotting to wait for the file to be created. To troubleshoot this issue, we recommend increasing the --latency parameter (see All Options). The default is set to 30 seconds, but the parameter can be adjusted to suit your individual system.

/bin/sh: line 0: cd: {PATH}: No such file or directory

This is a known issue with Snakemake v7.3.0+. Check your Snakemake version and reinstall a lower version if necessary (we recommend Snakemake v7.0).

Error: Directory cannot be locked.

The full error message should provide further instructions, but this error will appear when Snekmer has been unexpectedly terminated. Run snekmer {mode} --unlock (note: this command will not execute the workflow) before rerunning the workflow.

If the error persists, delete the .snakemake directory and try again.

AttributeError in _load_configfile

Typically, this error arises if the path to the config.yaml file is not specified correctly. To resolve this error, check that your config.yaml file is located in the same directory from which you are executing Snekmer. You can also specify the location of the config.yaml file, e.g. snekmer {mode} --configfile /path/to/config.yaml, to fix the issue.

General Usage Questions

My logs are very long, resulting in large log file sizes. How can I reduce this?

By default, Snekmer logs all Snakemake output, including construction of the DAG and information about individual jobs. However, the default settings will produce very big log files if several files are being evaluated at once. To reduce the verbosity of output logs, we recommend invoking the --quiet parameter (see All Options).

Snekmer model mode is not working.

If snekmer model is not building models as intended, check the following:

At least two input files are in the input directory. Note that Snekmer will not run as intended without 2+ input files.
All configuration parameters have been correctly specified. For more details and parameter descriptions, refer to Setting up User Configuration. Verify that no misspellings or invalid parameter specifications have been entered.
The snekmer model command is executed from the directory containing the input directory, and that a config.yaml file has been placed in the top-level directory. Refer to Configuration for the file structure required for Snekmer.

Snekmer cluster mode is producing an unusual number of clusters.

If Snekmer cluster results in an unexpected number of clusters, we recommend tuning the parameter set used to generate the clusters. Most likely, the parameters used to generate the clusters are too generalized, or specific, for the given dataset. For instance, if Snekmer determines only 1 cluster for a given protein sequence set of many individual sequences, the parameters guiding the clustering algorithm is likely not sensitive enough to differentiate the underlying clusters. See Parameter Selection for more details.