Troubleshooting Documentation

This document describes some issues that may arise in the course of using the workflows, and steps to take to diagnose and correct these issues.

Files not found

ERROR: No Files Found in Path: <PATH_TO_SAMPLES> Matching Pattern: _R{1,2}. and file extension: .fastq.gz

This error occurs when the workflow is unable to find input files in the specified --sample_folder location matching the expected pattern and file extension. The parameters that handle these settings are --pattern, which has a default value of _R{1,2} and --extension, which has a default value of .fastq.gz, and so if the input data do not match that pattern these parameters should be modified in the run script to match the structure of the data.

Cannot find script file

Cannot find script file: ../main.nf

The run scripts provided in run_scripts/ directory of the workflow repository are written such that they can be run directly from that subdirectory, and so they reference the file main.nf in the next directory up with the path ../main.nf. If you are running a script in a different directory, the command should be modified to nextflow run <PATH_TO_WORKFLOWS>/main.nf

Error Code 140

Error code: 140 for task: ${task.name}. Likely caused by the task wall clock: ${task.time} or memory: ${task.mem} being exceeded.Attempting orderly shutdown. See .command.log in: ${task.workDir} for more info."

We have benchmarked the workflows for a range of inputs, but it is possible that some inputs that are very large or extremely heterogeneous may exceed the default resource allocations we have set. In this case, the module resource allocations would need to be increased. Please contact [email protected] for guidance if necessary.