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luigi and ratatosk print a lot of debugging information, and it is not always easy (actually, it’s really difficult) to tell where something has gone wrong. This page summarizes some of the most common problems, and where to look for solutions. If you redirect the output to log files, a good place to start is by running grep WARNING on the log file.

Missing external dependency

WARNING:luigi-interface:Task FastqFile(target=target.fastq.gz,
label=None, suffix=.fastq.gz) is not complete and run() is not
implemented. Probably a missing external dependency.

This error means the file is missing, either because you forgot to put it there (in case it’s an external task), or because the automatically generated target names are incorrect. The latter case is by far the commonest, and to make matters worse, extremely difficult to solve. First, one should try to find the task that first generates an erroneous name. Then, make sure that task and its parent tasks have the appropriate label, add_label, and diff_label attributes. In most cases, the error lies here. See also Generating source names.