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Susana Posada-Cespedes edited this page May 21, 2020 · 2 revisions

TROUBLESHOOTING

  1. What does the following error mean MissingInputException in the gunzip rule?

This can happen if the sample identifiers, which are parsed from the samples.tsv file do not coincide with the folder names. You can delete the samples.tsvfile, and let V-pipe parse the values from the` directory

  1. How can I resolve configuration file issues?

You can pass the environment variable VPIPE_CONFIG_OPTS in the execution command:

VPIPE_CONFIG_OPTS =True ./vpipe
  1. The preprocessing rule fails with an error, what can I do?

Oftentime this happens because all reads are filtered out. I suggest to run

./vpipe alltrimmed

to trigger the run of the pipeline until the preprocessing rule and adjust the configuration, e.g., to relax the filtering options. Then, samples that depict low quality should be dropped from the analysis.

  1. What can I do when mafft is not found?

If you are not running V-pipe with option --use-conda, and ngshmmalign is not in your path, you can use the enviroment variable MAFFT_BIN to indicate the location of the binary files

  1. What can I do about the following message: Error: you need to specify the maximum number of CPU cores to be used at the same time with --cores.?

Starting Snakemake 5.11.0 the --cores option is mandatory. Depending on the Snakemake version you are using, you might have to specify the number of cores.

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