Table 7.

Sources and Solutions to Potential Errors

Problem	Possible Cause	Solution
Error “make: *** No rule to make target”	Input files are not in the current working directory, or full paths to files are used.	Make soft links to ensure that input files are available in the current working directory, and do not use absolute or relative paths to input files.
Error “zsh: no such option: pipefail”	An older version of zsh is installed, or zsh is missing.	Install zsh or update to the newest version.
“UnsatisfiableError” when installing ntLink using conda	Incompatible versions of tools were previously installed in the conda environment.	Install ntLink in a fresh conda environment.
“source file is in invalid format!” when running ntLink	Input long reads or draft assembly files are in an unexpected format.	Ensure that the input long reads are in correctly-formatted FASTA or FASTQ format (gzipped or uncompressed), and the draft assembly is in FASTA format (uncompressed).
“ModuleNotFoundError: No module named <package_name>” error	A required python module is not installed properly.	Ensure that the expected python version is being used (ex. with which python3), and install the missing package (using conda or pip).
“Error 127” in ntLink terminal output after abyss-scaffold step	ABySS is not installed, or not found in your PATH environment variable.	Install ABySS if needed, and ensure that the ABySS executables are found in your PATH.
Running ntLink -h prints the make help page instead of the ntLink help page	ntLink requires parameters to be specified in the form “variable_name=variable_value”, so using options with the form “-<letter>” will specify options to make itself, not the ntLink program.	Run ntLink help to see the full ntLink help page.
Contiguity gains post-ntLink are minimal	Incorrect selection of k/w	If ntLink makes minimal joins, it is likely that the k and w parameters specified are not optimal. See the Critical Parameters section for more details about setting k and w.
Error when running Tigmint-long: “samtools: error while loading shared libraries”	An older version of samtools is installed.	Update the samtools installation.