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Jena ARQ issue 2331 describes these symptoms, although it was fixed in Jena 4.6.0. We are currently using 4.6.1.
In looking at the dependencies, we're pulling in a later version of Jackson Databind to resolve possible security vulnerabilities which is overriding the version of Databind used in Jena. The error is related to Woodstox which is pulled in by Databind.
When reading or writing RDF files, the following error is logged:
Note: This issue is split out from issue #88
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