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Are you using the built-in CoNLL-U converter?

If so, have you validated your CoNLL-U input with the UD tools? You can validate the format with the UD validation tools (https://github.com/universaldependencies/tools) with validate.py --level 2 for the CoNLL-U + basic UD validation only. The output might include errors related to non-UD deprels if you have any of those, but you can ignore those errors and focus on errors related to ID/HEAD values.

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@toufiglu
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Answer selected by polm
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feat / training Feature: Training utils, Example, Corpus and converters
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