In an external special remote, if I set annex-readonly=true, I get

 git annex --verbose --debug checkpresentkey MD5E-s18932--663e2e38c829d7b3fff12fce3a6fdb6d.fasta 380286ac-2e8f-4285-94da-406eca323411  
...
(checking dnanexus...) Configuration does not allow accessing dx://file-BXF0vYQ0QyBF509G9J12g927/contaminants.clip_db.fasta

Removing the annex-readonly setting lets checkpresentkey work. But isn't checkpresentkey a read-only operation?