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Troubleshooting

This page collects a few issues that users have asked about more than once.

CSV_XS separator error

If you see an error like:

CSV_XS ERROR: 2023 - EIQ - QUO character not allowed @ rec 1 pos 21 field 1

the most common cause is a mismatch between the file separator and what Convert-Pheno expects from the file extension.

What to check

  • If the input is REDCap, make sure the data export and dictionary use the same separator.
  • If the file is not using the default separator, pass it explicitly with --sep.

Example for a tab-separated file:

--sep $'\t'

REDCap export mode

For REDCap input, the recommended export is:

  • CSV / Microsoft Excel (raw data)

and the matching REDCap dictionary file should be included.

If your export uses labels instead of raw data, you can still work through the CSV route instead of the -iredcap route.

PyPerler / Python binding installation

If you are installing the non-containerized version from source and run into problems around the legacy Python binding, check whether the system is missing:

  • cython3
  • libperl-dev

On Debian or Ubuntu systems, that usually means:

sudo apt-get install cython3 libperl-dev

This only applies if you need the old Python binding layer.