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Tips and guidelines for troubleshooting

Here we describe how debug errors during the execution of ete-build workflows.


General guidelines

ete-build may fail due to different reasons. Most typically:

  • A Job fails during execution When this occurs, the associated tasks will raise a TaskError providing the Task and Job IDs. If other workflows are running in parallel, they will continue working. You can stop the whole process or wait until the valid workflows are done.

    If the error message raised is not informing about an obvious problem, you may want to inspect the exact command line and output files associated to the error job. All those data are contained in the tasks/ folder, under the subdirectory whose name corresponds to the relevant JobID. If the error is not caused by incorrect input data, bad symbols in sequences or sequence names, please consider reporting it as a bug.

  • A Task without Job fails This may occur when a post-processing step produces an error. If the error message is not informative, please consider reporting it as bug.

  • A Job is never ending In rare situation, a job could die without notifying ete-build. This will make ete-build to continue monitoring forever (there is no timeout for jobs). In this case, interrupt the main program with Ctrl-C and proceeds as follows:

    • restart the analysis from scratch using the --clearall option
    • or, to avoid re-computing data generated by other jobs, delete the error job subdirectory from the tasks/ folder and restart the analysis